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Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics
Provedor de dados: 17
Autores: Michel Dumontier; James R. Green; Ashkan Golshani; Myron L. Smith; Nadereh  Mir-Rashed; Md  Alamgir; Veronika  Eroukova; Frank Dehne; James  J. Cheetham.
Background&amp;#xd;&amp;#xa;High throughput yeast functional genomics experiments are revealing associations among tens to hundreds of genes using numerous experimental conditions. To fully understand how the identified genes might be involved in the observed system, it is essential to consider the widest range of biological annotation possible. Biologists often start their search by collating the annotation provided for each protein within databases such as the Saccharomyces Genome Database, manually comparing them for similar features, and empirically assessing their significance. Such tasks can be automated, and more precise calculations of the significance can be determined using established probability measures....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2311/version/1

The Heterochromatin Protein 1 positively regulates euchromatic gene expression by RNA binding
Provedor de dados: 17
Autores: Piacentini Lucia; Laura Fanti; Rodolfo Negri; Valerio Del Vescovo; Alessandro Fatica; Sergio Pimpinelli.
HP1 is a well known conserved protein involved in heterochromatin formation and gene silencing in different species including humans1-4. A general model has been proposed for heterochromatin formation and epigenetic gene silencing in different species that implies an essential role for HP1. According to the model, histone methyltransferase enzymes (HMTases) methylate the histone H3 at lysine 9 (H3-MeK9), creating selective binding sites for itself and the chromodomain of HP15. This complex is thought to form a higher order chromatin state that represses gene activity. It has also been found that HP1 plays a role in telomere capping6. Surprisingly, recent data have suggested an association of HP1 in gene activity7-10 but the nature of this interaction is...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2687/version/1

Evidence of existence of totally different types of ribosomes in intermediate animals
Provedor de dados: 17
Autores: Haoran H. Wang; Mary X. Gao; Sato Kenzo; Kazumitsu Hirai.
In all organisms, messenger-directed protein synthesis is catalyzed by ribonucleoprotein particles called ribosomes. A ribosome is typically composed of one small and one large subunit which contain one short (18S) and one long (28S) rRNAs, respectively. Surprisingly, in this study, three similar size rRNAs (18-21S) were revealed in the electrophoresis profile of the total RNAs of tapeworm _Spirometra erinaceiuropaei_. Northern blot analysis shows that one of the three bands belongs to 18S rRNA, and the other two bands are of 28S rRNAs, implying structurally distinct ribosomes in this intermediate animal. Furthermore, similar, but not identical profiles were observed in two other tapeworms _Diphyllobothrium hottai_ and _Diphyllobothrium Nipponkaiizeme_....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2608/version/2

Visualization of the Phosphoproteomic Data from AfCS with the Google Motion Chart Gadget
Provedor de dados: 17
Autores: Huilei Xu; Avi Ma&amp;#x27;ayan.
Results from multivariate molecular biological experiments become increasingly complex. Hence, the challenge of projecting high-dimensional data onto few dimensions for effective data visualization is becoming increasingly important in Systems Biology. Effective data visualization can summarize the activity of many variables over time as well as display relationships between variables. Dynamic interactive visualization tools can provide scientists with ways of visually identifying relationship and patterns, and improve communication of results on the web and in presentations. For this, interactive systems with animation have great potential since they add dimensions to static images limited to two dimensions. Interactivity and animation is particularly...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3074/version/1

Bioconversion of eugenol into food flavouring agent vanillin
Provedor de dados: 17
Autores: Suaib  Luqman; Sudeep  Tandon; Alok  Somvanshi; Suchita  Srivastava; Mahendra  P. Darokar; Suman  P. S. Khanuja.
Microorganisms have the ability to chemically modify a wide variety of organic compounds by a process referred to as biological or microbial transformation, or in general, bioconversion. The microbial cells and their catalytic machinery (enzymes) accept a wide array of complex molecules as substrates, yielding products with unparallel chiral (enantio-), positional (region-) and chemical (chemo-) selectivity through various biochemical reactions. The present study was formulated on the objective of the conversion of abundantly available phytomolecules eugenol into vanillin, a compound of industrial importance, using microorganisms Aspergillus flavus, Aspergillus niger and Pseudomonas aeruginosa. These microbes were found to be capable of converting eugenol...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6926/version/1

Pancreas islets in metabolic signaling - focus on the &amp;#x3b2;-cell
Provedor de dados: 17
Autores: Jakob Suckale; Michele Solimena.
Taken together the Islets of Langerhans form a nutrient sensing network spread throughout the pancreas. They are tightly connected to the source organ - the intestine - and the target organs - liver, muscle, and fat cells. The expression of a unique set of proteins enables [beta] cells, the most frequent islet cell type, to detect elevated blood glucose levels and secrete insulin accordingly. Neighbouring [beta]-cells achieve tighter regulation of glucose-induced insulin secretion by coordination through cell surface proteins. They also adjust their secretory pathway capacity and &amp;#xfb02;ow to avoid being damaged. The immediate reaction of the [beta] cell to nutrients is regulated by translational mechanisms, while longer term adaptations involve...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1724/version/1

(Corrected) Speed effects in gliding motility assays due to surface passivation, water isotope, and osmotic stress.
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
The molecular motor kinesin-1, an ATPase, and the substrate it walks along, microtubules, are vital components of eukaryotic cells. Kinesin converts chemical energy to linear motion as its two motor domains step along microtubules in a process similar to how we walk. Cells create systems of microtubules that direct the motion of kinesin. This directed motion allows kinesin to transport various cargoes inside cells.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;During the stepping process, the kinesin motor domains bind and unbind from their binding sites on the microtubules.  Binding and unbinding rates of biomolecules are highly dependent on hydration and exclusion of water from the binding interface. Osmotic stress will likely strongly affect the binding and...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4469/version/3

Phosphatidylserine polarization is required for proper Cdc42 localization and for development of cell polarity.
Provedor de dados: 17
Autores: Gregory Fairn; Sergio Grinstein.
We used genetically-encoded fluorescent probes to visualize the distribution of phosphatidylserine (PS) in live S. cerevisiae. The majority of the PS was found to reside in the cytosolic leaflet of the plasma membrane. Remarkably, PS was polarized, accumulating in bud necks, the bud cortex and the tips of mating projections. Polarization required vectorial delivery of PS-enriched secretory and recycling vesicles. Rapid dissipation of the PS gradient is prevented by the slow diffusion of lipids along the plasmalemmal inner leaflet, estimated by photobleaching recovery measurements to be over an order of magnitude slower than in mammalian cells. In mutants lacking PS-synthase the absence of PS was associated with, and likely responsible for impaired...
Tipo: Manuscript
Palavras-chave: Microbiology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4232/version/1

Effect of 2-H and 18-O water isotopes in kinesin-1 gliding assay
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
We show here the effects of heavy-hydrogen water (^2^H~2~O) and heavy-oxygen water (H~2~^18^O) on the gliding speed of microtubules on kinesin-1 coated surfaces. Increased fractions of isotopic waters used in the motility solution decreased the gliding speed of microtubules by a maximum of 21% for heavy-hydrogen and 5% for heavy-oxygen water. We discuss possible interpretations of these results and the importance for future studies of water effects on kinesin and microtubules. We also discuss the implication for biomolecular devices incorporating molecular motors.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7004/version/1

Novel Techniques for Microspectroscopy and Chemical Imaging Analysis of Soybean Seeds and Embryos
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng  You; Doina M. Costescu.
Novel methodologies are currently being evaluated for the Chemical Analysis of soybean seeds as well as developing mature soybean embryos by FT-IR/NIR Microspectroscopy. This is the first report of FT-NIR Chemical Images obtained with 1 micron resolution. NIR spectra of Proteins, Oil and DNA fibers are obtained for regions as small as 1&amp;#x3bc;^2^.
Tipo: Poster
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6591/version/2

NIR Spectroscopy and Microspectroscopy Analysis of Intact Soybean Seeds for Food Applications through Composition Improvements. Version 2.0
Provedor de dados: 17
Autores: Tiefeng You; I. C. Baianu.
The soybean-derived products are among the most important agricultural products in the USA and the world. Conventional analytical methods for soybean composition analysis are both time consuming and costly. Faster and less expensive methods are required for most practical applications. To improve the accuracy, reliability and sensitivity of NIR, major advancements in instrumentation, as well as, data analysis / calibration methodology are required. Novel NIR instruments, such as DA-NIR and FT-NIR spectrometers developed in recent years have the potential for improving significantly the quantification of soybean composition at a reasonable cost. We present representative calibrations and data for intact soybean composition analysis obtained at the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6253/version/1

Dysbindin-1 in dorsolateral prefrontal cortex of schizophrenia cases is reduced in an isoform-specific manner unrelated to altered dysbindin-1 gene expression
Provedor de dados: 17
Autores: Junxia Tang; Robert P. LeGros; Natalia Louneva; Lilly Yeh; Julia W. Cohen; Chang-Gyu Hahn; Derek J. Blake; Steven E. Arnold; Konrad Talbot.
DTNBP1 (dystrobrevin binding protein 1) remains one of the top candidate genes in schizophrenia. Reduced expression of this gene and the protein it encodes, dysbindin-1, has been reported in the dorsolateral prefrontal cortex (DLPFC) of schizophrenia cases. It has not been established, however, if all dysbindin-1 isoforms are reduced in the DLPFC or if the reduction is associated with reduced DTNBP1 gene expression. Using Western blotting of whole-tissue lysates of the DLPFC with antibodies differentially sensitive to the three major isoforms of this protein (dysbindin-1A, -1B, and -1C), we found no significant differences between our schizophrenia cases and matched controls in dysbindin-1A or -1B, but did find a mean 46% reduction in dysbindin-1C in 71%...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2779/version/1

Mammalian cells in culture actively export specific microRNAs
Provedor de dados: 17
Autores: Kai Wang; Shile Zhang; Jessica Weber; David Baxter; David J. Galas.
The discovery of microRNAs (miRNAs) as a new class of regulators of gene expression has triggered an explosion of research, but has left many unanswered questions about how this regulation works and how it is integrated with other regulatory mechanisms. A number of miRNAs have been found to be present in blood plasma and other body fluids of humans and mice in surprisingly high concentrations. This observation was unexpected in two respects: first, the fact that these molecules are present at all outside the cell at significant concentrations; and second, that these molecules appear to be stable outside of the cell. In light of this it has been suggested that the biological function of miRNAs may also extend outside of the cell and mediate cell-cell...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3718/version/1

A normalization technique for next generation sequencing experiments
Provedor de dados: 17
Autores: G&amp;#xfc;nter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS&amp;#x27; cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4710/version/1

Self-organization of intrinsically disordered proteins with folded N-termini
Provedor de dados: 17
Autores: Philip C. Simister; Fred Schaper; Nicola O&amp;#x27;Reilly; Simon McGowan; Stephan M. Feller.
Thousands of human proteins lack recognizable tertiary structure in most of their chains. Here we hypothesize that some use their structured N-terminal domains (SNTDs) to organise the remaining protein chain via intramolecular interactions, generating partially structured proteins. This model has several attractive features: as protein chains emerge, SNTDs form spontaneously and serve as nucleation points, creating more compact shapes. This reduces the risk of protein degradation or aggregation. Moreover, an interspersed pattern of SNTD-docked regions and free loops can coordinate assembly of sub-complexes in defined loop-sections and enables novel regulatory mechanisms, for example through posttranslational modifications of docked regions.
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5124/version/1

Chronic hyperplastic anemia as an independent risk factor for atherosclerotic lesions: a lesson from thalassemia intermedia
Provedor de dados: 17
Autores: Maria Eliana  Lai; Stefania  Vacquer; Maria Paola  Carta; Alessandra   Spiga; Pier Luigi   Cocco; Fabrizio   Angius; Antonella   Mandas; Sandra  Dessi.
Introduction. Cardiovascular involvement represents a well-known complication and the primary cause of mortality, both in transfusion-dependent beta thalassemia major (&amp;#x3b2;-TM) and in transfusion-independent beta thalassemia intermedia (&amp;#x3b2;-TI). In &amp;#x3b2;-TM, heart iron overload is considered the main cause of this complication. This is likely due to poor adherence to iron-chelating therapy, resulting in the inability of the body to efficiently remove iron excess derived from transfused red blood cell breakdown. Different clinical pictures may instead be evoked in cardiovascular involvement occurring in &amp;#x3b2;-TI; however, until now, no factor has emerged as the major one responsible for these complications....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4169/version/1

Aptamer-based multiplexed proteomic technology for biomarker discovery
Provedor de dados: 17
Autores: Larry Gold; Deborah Ayers; Jennifer Bertino; Christopher Bock; Ashley Bock; Edward N. Brody; Jeff Carter; Virginia Cunningham; Andrew Dalby; Bruce E. Eaton; Tim Fitzwater; Dylan Flather; Ashley Forbes; Trudi Foreman; Cate Fowler; Bharat Gawande; Meredith Goss; Magda Gunn; Shashi Gupta; Dennis Halladay; Jim Heil; Joe Heilig; Brian Hicke; Gregory Husar; Nebojsa Janjic; Thale Jarvis; Susan Jennings; Evaldas Katilius; Tracy R. Keeney; Nancy Kim; Terese Kaske; Tad Koch; Stephan Kraemer; Luke Kroiss; Ngan Le; Daniel Levine; Wes Lindsey; Bridget Lollo; Wes Mayfield; Mike Mehan; Robert Mehler; Michele Nelson; Sally K. Nelson; Dan Nieuwlandt; Malti Nikrad; Urs Ochsner; Rachel M. Ostroff; Matt Otis; Thomas Parker; Steve  Pietrasiewicz; Dan Resnicow; John Rohloff; Glenn Sanders; Sarah Sattin; Dan Schneider; Britta Singer; Martin Stanton; Alana Sterkel; Alex Stewart; Suzanne Stratford; Jonathan D. Vaught; Mike Vrkljan; Jeffrey J. Walker; Mike Watrobka; Sheela Waugh; Allison Weiss; Sheri Wilcox; Alexey Wolfson; Steve Wolk; Chi Zhang; Dom Zichi.
Interrogation of the human proteome in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology.  We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 [mu]L of serum or plasma).  Our current assay allows us to measure ~800 proteins with very low limits of detection (1 pM average), 7 logs of overall dynamic range, and 5% average coefficient of variation.  This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected.  Proteins in complex...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4538/version/1

Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for  Composition Improvements.  (v.3)
Provedor de dados: 17
Autores: Valentin  Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions.  Conventional &amp;#x201c;wet chemistry&amp;#x201d; analytical methods are time-consuming and costly.  As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry.  Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6231/version/3

Inactivation of the Retinoblastoma Protein by Mutant B-Raf in Malignant Melanoma
Provedor de dados: 17
Autores: Yusuke Furukawa; Yukiko Kobayashi; Takahisa Kobayashi; Jiro Kikuchi; Taeko Wada; Ken Futaki; Eiji Kusano; Satoru Murata; Mamitaro Ohtsuki.
Although activating mutations of B-Raf are the most common genetic abnormalities in human melanomas, the mechanism by which mutant B-Raf transforms melanocytes is poorly understood. Here we show that the retinoblastoma tumor suppressor protein (pRB) is a direct target of B-Raf and is inactivated by phosphorylation in melanomas carrying B-Raf mutations. In contrast, pRB is undetectable in melanomas with wild-type B-Raf. Mutant B-Raf directly interacts with pRB and induces its phosphorylation at serine-249 and threonine-252 (S249/T252). Inhibition of B-Raf activity results in dephosphorylation of pRB at S249/T252 along with other sites in melanoma cells. S249/T252 are phosphorylated earlier than other sites during cell cycle entry of normal melanocytes....
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4857/version/1

Signaling Flux Redistribution concept can switch survival to apoptosis in cancer cells
Provedor de dados: 17
Autores: Daiki Yamada; Kentaro Hayashi; Vincent Piras; Masaru  Tomita; Masa Tsuchiya; Kumar  Selvarajoo.
The tumor necrosis factor related apoptosis-inducing ligand (TRAIL) induces apoptosis in certain types of carcinoma. However, in majority of malignant tumors, it has no effect. Here we analyzed cell survival and apoptotic pathways triggered by TRAIL.  A computational model based on perturbation-response approach with mass-action equations was developed. All 48 parameter values of the model were selected by genetic algorithm that minimizes deviation between experimental and simulation data for human fibrosarcoma cells. Subsequently, we show in silico knock-down of a cell survival pathway molecule could potentially enhance the activation of apoptosis through Signaling Flux Redistribution (SFR).
Tipo: Poster
Palavras-chave: Cancer; Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4375/version/1

A PI3K-mediated negative feedback regulates Drosophila motor neuron excitability
Provedor de dados: 17
Autores: Eric Howlett; Curtis C. J. Lin; William Lavery; Michael Stern.
Negative feedback can act as a homeostatic mechanism to maintain neuronal activity at a particular specified value. At the Drosophila neuromuscular junction, a mutation in the type II metabotropic glutamate receptor gene (mGluRA) increased motor neuron excitability by disrupting an autocrine, glutamate-mediated negative feedback. We show that mGluRA mutations increase neuronal excitability by preventing PI3 kinase (PI3K) activation and consequently hyperactivating the transcription factor Foxo. Furthermore, glutamate application increases levels of phospho-Akt, a product of PI3K signaling, within motor nerve terminals in an mGluRA-dependent manner. In humans, PI3K and type II mGluRs are implicated in epilepsy, neurofibromatosis, autism, schizophrenia and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1767/version/1

Counting absolute number of molecules using unique molecular identifiers
Provedor de dados: 17
Autores: Teemu Kivioja; Anna V&amp;#xe4;h&amp;#xe4;rautio; Kasper Karlsson; Martin Bonke; Sten Linnarsson; Jussi Taipale.
Advances in molecular biology have made it easy to identify different DNA or RNA species and to copy them. Identification of nucleic acid species can be accomplished by reading the DNA sequence; currently millions of molecules can be sequenced in a single day using massively parallel sequencing. Efficient copying of DNA-molecules of arbitrary sequence was made possible by molecular cloning, and the polymerase chain reaction. Differences in the relative abundance of a large number of different sequences between two or more samples can in turn be measured using microarray hybridization and/or tag sequencing. However, determining the relative abundance of two different species and/or the absolute number of molecules present in a single sample has proven much...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5903/version/1

Ambiguous Dependence Of Minimal Plant Generation Time On Nuclear DNA Content
Provedor de dados: 17
Autores: Victor B. Ivanov.
AMBIGUOUS DEPENDENCE OF MINIMAL PLANT GENERATION TIME ON NUCLEAR DNA CONTENT Victor B. Ivanov The minimum generation time (MGT) of plant development was suggested to depend on nuclear DNA content, which varies in plants over wide limits1. In ephemeral species with the shortest MGT, the average C values were significantly lower than in annual species, whereas the average C values in annual species were lower than those in perennial plants. However, nobody has paid attention to the ratio of annual to perennial species number as a function of C values. Here I show that with increasing C the ratio of annual to perennial species increases to C values equal to 7-8 pg (monocots) and 6-7 pg (eudicots) and then decreases and that the fraction of annuals is abundant...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4943/version/1

Metabolic Network Representation in SBGN PD: EC and Identity Gate
Provedor de dados: 17
Autores: Alexander Mazein.
This presentations describes proposed changes in SBGN PD that would allow this language to be better adopted for representing metabolic network.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4974/version/1

SC1/PRDM4 recruits PRMT5 to control the timing of neural precursor differentiation in developing neural stem cells
Provedor de dados: 17
Autores: Alexandra Chittka; Ursula Grazini.
During cortical development, neural stem cells (NSCs) switch from proliferative to neuron-generating asymmetric divisions. Here we investigated the role of Schwann cell factor 1 (SC1/PRDM4), a transcriptional repressor highly expressed in the developing nervous system, during NSCs development. We found that SC1 protein levels were down-regulated in newly differentiating neurons, while remaining high in undifferentiated NSCs, suggesting an asymmetric inheritance of SC1. Knockdown of SC1 in the NSCs led to precocious differentiation of neurons and its overexpression led to an increase in Nestin-expressing precursors. We found that SC1, through its amino-terminus, recruits the chromatin modifier PRMT5, a histone arginine methyltransferase that catalyses...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4926/version/1

Solubilization of M2 Transmembrane Peptide of Influenza A in Pure Water: Implications for Emergence of Proteins and Protein-embedded Primeval Membranes in Unsalted Oceans
Provedor de dados: 17
Autores: Jianxing Song; Linlin  Miao.
We demonstrated that M2 transmembrane peptide, one of the most hydrophobic sequences in nature, can be solublized to at least ~100 &amp;#xb5;M in unsalted water without any lipid molecules. Strikingly, the M2 peptide also forms a highly-helical conformation in water which remains almost unchanged even at 95 &amp;#xba;C, as characterized by CD spectroscopy. Our result has critical implications in understanding emergence of proteins and protein-embedded primeval membranes in unsalted oceans.
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6773/version/1

Association Analysis Techniques for Discovering Functional Modules from Microarray Data
Provedor de dados: 17
Autores: Gaurav Pandey; Gowtham Atluri; Michael Steinbach; Vipin Kumar.
An application of great interest in microarray data analysis is the identification of a group of genes that show very similar patterns of expression in a data set, and are expected to represent groups of genes that perform common/similar functions, also known as functional modules. Although clustering offers a natural solution to this problem, it suffers from the limitation that it uses all the conditions to compare two genes, whereas only a subset of them may be relevant. Association analysis offers an alternative route for finding such groups of genes that may be co-expressed only over a subset of the experimental conditions used to prepare the data set. The techniques in this field attempt to find groups of data objects that contain coherent values...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2184/version/1

siRNA knockdown of SPHK1 in vivo protects mice from systemic, type-I Allergy.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Peter Natesan P. N. Pushparaj; Alirio Jose A. J. Melendez.
Systemic anaphylaxis is considered to be a typical immediate hypersensitivity response, determined by the activation of immune cells,&amp;#xd;&amp;#xa;via antigen-induced aggregation of IgE-sensitized Fc&amp;#x3b5;RI cells. Perhaps most the important cells, in the immediate hypersensitivity responses, are mast cells. We have previously shown that SPHK1 plays a key role in the intracellular signaling pathways triggered by FceRI aggregation on human&amp;#xd;&amp;#xa;mast cells. More recently, we performed a genome-wide gene expression profiling of human mast cells, sensitized with IgE alone, or stimulated by Fc&amp;#x3b5;RI aggregation. We found that sphingosine kinase 1 (SPHK1) was one&amp;#xd;&amp;#xa;of genes activated at the earlier stages of mast cell...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/1147/version/1

Dual expression recombinase based (DERB) single vector system for high throughput screening and verification of protein interactions in living cells
Provedor de dados: 17
Autores: Jian-Ping Lu; Laura Beatty; Jehonathan  Pinthus.
Identification of novel protein interactions and their mediators is fundamental in understanding cellular processes and is necessary for protein-targeted therapy. Evidently high throughput formatting of these applications in living cells would be beneficial, however no adequate system exists. We present a novel platform technology for the high throughput screening and verification of protein interactions in living cells. The platform&amp;#x2019;s series of Dual Expression Recombinase Based (DERB) destiny vectors individually encode two sets of recombinase recognizable sequences for inserting the protein open reading frame (ORF) of interest, two sets of promoters and reporter tags in frame with the ORFs for detecting interactions. Introduction into living...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1550/version/2

Hexose-6-phosphate dehydrogenase modulates the effect of inhibitors and alternative substrates of 11[beta]-hydroxysteroid dehydrogenase 1
Provedor de dados: 17
Autores: Zolt&amp;#xe1;n Bal&amp;#xe1;zs; Lyubomir G. Nashev; Charlie Chandsawangbhuwana; Michael E. Baker; Alex Odermatt.
Intracellular glucocorticoid reactivation is catalyzed by 11[beta]-hydroxysteroid dehydrogenase 1 (11[beta]-HSD1), which functions predominantly as a reductase in cells expressing hexose-6-phosphate dehydrogenase (H6PDH). We recently showed that the ratios of cortisone to cortisol and 7-keto- to 7-hydroxy-neurosteroids are regulated by 11[beta]-HSD1 and very much depend on co-expression with H6PDH, providing cosubstrate NADPH. Here, we investigated the impact of H6PDH on the modulation of 11[beta]-HSD1-dependent inter-conversion of cortisone and cortisol by inhibitors and alternative substrates. Using HEK-293 cells expressing 11[beta]-HSD1 or co-expressing 11[beta]-HSD1 and H6PDH, we observed significant differences of 11[beta]-HSD1 inhibition by natural...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2430/version/1

Gene Transfer of Calcitonin Gene-Related Peptide Inhibits Macrophages and Inflammatory Mediators in Vein Graft Disease
Provedor de dados: 17
Autores: Xiaoning Zhang; Jian Zhuang; Hongsui Wu; Zhihong Chen; Jian Su; Shiliang Chen; Jianguang Chen; Yuhui Zheng; Huanxin Yang.
Vein graft disease is a chronic inflammatory disease and limits the late results of coronary revascularization. Calcitonin gene-related peptide (CGRP) inhibits macrophages infiltrated and inflammatory mediators, we hypothesized that transfected CGRP gene inhibits macrophages infiltrated and inflammatory mediators in vein graft disease. Autologous rabbit jugular vein grafts were incubated ex vivo in a solution of mosaic adeno-associated virus vectors containing CGRP gene (AAV2/1.CGRP) &amp;#x3001;escherichia coli lac Z gene (AAV2/1.LacZ) or saline and then interposed in the carotid artery. Intima/media ratio were evaluated at postoperative 4 weeks, Macrophages were marked with CD68 antibody by immunocytochemistry. Inflammatory mediators were mensurated with...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2456/version/1

PML-RAR&amp;#x3b1; enhances autophagic activity through inhibiting Akt/mTOR pathway
Provedor de dados: 17
Autores: Guo-Qiang Chen; Ying Huang; Xu-Yun Zhao; Ting-Ting Chen; Jia-Kai Hou; Jing Zhang; Jie Yang; Scott C. Kogan.
Autophagy is a highly conserved, closely-regulated homeostatic cellular activity that allows for the bulk degradation of long-lived proteins and cytoplasmic organelles. Its roles in cancer initiation and progression and in determining the response of tumor cells to anticancer therapy are complicated, and the potential significance of autophagy in the pathogenesis and therapeutic response of acute myeloid leukemia has a little investigation. Here, we demonstrate that induction of acute promyelocytic leukemia (APL)-specific PML-RAR&amp;#x3b1; but not PLZF-RAR&amp;#x3b1;/NPM-RAR&amp;#x3b1; fusion protein up-regulates constitutive autophagic activation in leukemic and non-leukemic cells. The significant increase of autophagic activity is also found in the...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5250/version/1

The Open Practises E-Science Network (OPEN)
Provedor de dados: 17
Autores: Cameron  Neylon.
A grant proposal submitted for support to fund a research network focussed on identifying and dealing with the practical issues of enabling open practise in research. The text of the proposal was written by a large number of people and coordinated by Cameron Neylon.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1370/version/1

PID: The Pathway Interaction Database
Provedor de dados: 17
Autores: Carl F. Schaefer; Kira Anthony; Shiva Krupa; Jeffrey Buchoff; Matthew Day; Timo Hannay; Kenneth H. Buetow.
The Pathway Interaction Database (PID, &amp;#x22;http://pid.nci.nih.gov&amp;#x22;:http://pid.nci.nih.gov) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes. Created in a collaboration between the U.S. National Cancer Institute and Nature Publishing Group, the database serves as a research tool for the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists, and immunologists. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2243/version/1

The NCI-Nature Pathway Interaction Database: A cell signaling resource.
Provedor de dados: 17
Autores: Shiva Krupa; Kira Anthony; Jeffrey  R. Buchoff; Matthew Day; Timo Hannay; Carl  F. Schaefer.
The Pathway Interaction Database (*PID*, http://pid.nci.nih.gov) is a freely available&amp;#xd;&amp;#xa;collection of curated and peer-reviewed signaling pathways composed of human&amp;#xd;&amp;#xa;biomolecular interactions and cellular processes. Created in a collaboration between the&amp;#xd;&amp;#xa;U.S. National Cancer Institute and Nature Publishing Group, the database is a research&amp;#xd;&amp;#xa;tool for cell biologists, biochemists, computational biologists and bioinformaticians.&amp;#xd;&amp;#xa;The PID offers a range of tools to facilitate pathway exploration. Users can browse the&amp;#xd;&amp;#xa;pre-defi ned set of pathways and also create interaction network maps centered on&amp;#xd;&amp;#xa;a single molecule of interest or an extensive list...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1311/version/1

Reflect: Augmented Browsing for the Life Scientist
Provedor de dados: 17
Autores: Evangelos Pafilis; Se&amp;#xe1;n I. O&amp;#x27;Donoghue; Lars J. Jensen; Heiko Horn; Michael Kuhn; Nigel P. Brown; Reinhard Schneider.
Anyone who regularly reads life science literature often comes across names of genes, proteins, or small molecules that they would like to know more about. To make this process easier, we have developed a new, free service called Reflect (&amp;#x22;http://reflect.ws&amp;#x22;:http://reflect.ws) that can be installed as a plug-in to Firefox or Internet Explorer. Reflect tags gene, protein, and small molecule names in any web page, typically within a few seconds, and without affecting document layout. Clicking on a tagged gene or protein name opens a popup showing a concise summary that includes synonyms, database identifiers, sequence, domains, 3D structure, interaction partners, subcellular location, and related literature. Clicking on a tagged small...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3212/version/1

Changes in Scholarly Communication and the Potential Impact on Biocuration
Provedor de dados: 17
Autores: Philip Bourne.
Open access in particular and changes in on-line scholarship have the potential to impact biocuration which often involves translating information currently read in papers to knowledge that is found in a variety of biological resources. The implication of these changes in scholarly communication to the biocuration process will be discussed with references to our work and that of others.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3229/version/1

Is the infection/latency/reactivation cycle of viruses an oncogenic engine?
Provedor de dados: 17
Autores: Alessandro Ripalti.
Human oncogenic viruses are defined as necessary but not sufficient to initiate cancer. Experimental evidence suggests that the oncogenic potential of a virus is effective only in cells that have already accumulated a number of genetic mutations leading to cell cycle deregulation. Current models for viral driven oncogenesis cannot explain why tumor development in carriers of tumorigenic viruses is a very rare event, occurring decades after virus infection. Considering that viruses are mutagenic agents _per se_ and human oncogenic viruses additionally establish latent and persistent infections, I attempt here to provide a mechanism of tumor initiation both for RNA and DNA viruses, suggesting viruses could be both necessary and sufficient in human...
Tipo: Manuscript
Palavras-chave: Cancer; Microbiology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1285/version/1

The human genome is composed of viral DNA: Viral homologues of the protein products cause Alzheimer&amp;#x27;s disease and others via autoimmune mechanisms.
Provedor de dados: 17
Autores: Christopher J. Carter.
The human genome is composed of millions of fragmented contiguous viral DNA sequences, dating from the dawn of evolution and reflecting retroviral insertions over millions of years of coexistence. Herpes and other viral insertion points correspond to the locations of over 120 Alzheimer&amp;#x27;s disease susceptibility genes and to linkage hotspots. The greater the number of pathogen matches, the more important the gene. These DNA sequences are translated into short contiguous 5-12 amino acid stretches (vatches), identical in viruses and man, and in other pathogens implicated in Alzheimer&amp;#x27;s disease (_Borrelia_, _Chlamydia_, _Helicobacter_, _C. Neoformans_ , _P. Gingivalis_). _C. Neoformans_, which has been associated with a rare but curable form...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4765/version/1

Structure and function prediction of human homologue hABH5 of _E. coli_ ALKB5 using in silico approach
Provedor de dados: 17
Autores: Mr. Shankaracharya; Saibal Das; Ambarish Sharan Vidyarthi.
Newly discovered human homologues of ALKB protein have shown the activity of DNA damaging drugs, used for cancer therapy. Little is known about the structure and function of hABH5, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeler 9v7 to predict the 3D structure of the hABH5 protein. 3-D model of hABH5, ALKBH5.B99990005.pdb was predicted and evaluated. Validation results showed 96.8% residues in favor and an additional allowed region of the Ramachandran plot. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, conserved pattern of Pro158-X-Asp160-Xn-His266 in the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5597/version/2

Protein Regge Trajectories, Phase Coexistence and Loop Aetiology in Alzheimers Disease
Provedor de dados: 17
Autores: Antti Niemi; Andrey Krokhotin.
Alzheimer&amp;#x27;s disease has a devastating impact on its victims by causing severe neurodegeneration in the brain that leads to a certain death. Only in a small number of cases can the origin be traced to a variety of genetic mutations, for the greater part the reasons for its onset are unclear.The defining factor is the formation of extracellular senile amyloid plaques in the brain, but therapeutic approaches to remove them remain to be shown effective in humans. Here we investigate physical processes that are involved in the release of the extracellular amyloid, by scrutinizing the intracellular domain of its precursor protein. We identify a phenomenon that has never before been discussed in the context of protein research: Like ice and water...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6030/version/1

Endothelin-Induced Sarcoplasmic Reticulum Calcium Depletion Waves in Vascular Smooth Muscle Cells
Provedor de dados: 17
Autores: Mitra Esfandiarei; Yohan Choi; Arash Y. Tehrani; Jeremy G. Hoskins; Nicola Fameli; Cornelis van Breemen.
Agonist-stimulated waves of elevated cytoplasmic Ca2+ concentration ([Ca2+]i ) regulate blood vessel tone and vasomotion in vascular smooth muscle. Previous studies employing cytoplasmic Ca2+ indicators revealed that these Ca2+ waves were generated by a combination of inositol 1,4,5-trisphosphate (IP3) and Ca2+ induced Ca2+ release (CICR) from the sarcoplasmic reticulum (SR); although, some of the mechanistic details remain uncertain. However, these findings were derived indirectly from observing agonist-induced [Ca2+]i fluctuations in the cytoplasm.&amp;#xd;&amp;#xa;Here, for the first time, we have recorded Endothelin-1 (ET-1) induced waves of Ca2+ depletion from the SR lumen in vascular smooth muscle cells (VSMCs) using a calsequestrin-targeted Ca2+...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6280/version/1

Visual Molecular Dynamics Investigations of the Impact of Hydrophobic Nanoparticles on Prognosis  of Alzheimer&amp;#x2019;s Disease and Cancers
Provedor de dados: 17
Autores: I. C. Baianu; M Charles; V. I. Prisecaru.
The possible impact of hydrophobic lectin nanoparticles on the prognosis and progression of Alzheimer&amp;#x27;s disease (AD) and cancers was investigated by Visual Molecular Dynamics (VMD) computer modeling programs available from the Beckmann Advanced Research Institute at the University of Illinois at Urbana. Our results indicate the possibility of impeding pathological aggregation of certain proteins such as modified tau- or beta-amyloid that are currently being considered as possible causes of Alzheimer&amp;#x27;s disease. VMD programs serve as useful tools for investigation hydrophobic protein aggregation that may play a role in aging of human populations.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7111/version/2

Pancreas islets in metabolic signaling - focus on the &amp;#x3b2;-cell
Provedor de dados: 17
Autores: Jakob Suckale; Michele Solimena.
Taken together the Islets of Langerhans form a nutrient sensing network spread throughout the pancreas. They are tightly connected to the source organ - the intestine - and the target organs - liver, muscle, and fat cells. The expression of a unique set of proteins enables [beta] cells, the most frequent islet cell type, to detect elevated blood glucose levels and secrete insulin accordingly. Neighbouring [beta]-cells achieve tighter regulation of glucose-induced insulin secretion by coordination through cell surface proteins. They also adjust their secretory pathway capacity and &amp;#xfb02;ow to avoid being damaged. The immediate reaction of the [beta] cell to nutrients is regulated by translational mechanisms, while longer term adaptations involve...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1724/version/2

Without magic bullets: the biological basis for public health interventions against protein folding disorders
Provedor de dados: 17
Autores: Rodrick Wallace.
Protein folding disorders of aging like Alzheimer&amp;#x27;s and Parkinson&amp;#x27;s diseases currently present intractable medical challenges. &amp;#x27;Small molecule&amp;#x27; interventions - drug treatments - often have, at best, palliative impact, failing to alter disease course. The design of individual or population level interventions will likely require a deeper understanding of protein folding and its regulation than currently provided by contemporary &amp;#x27;physics&amp;#x27; or culture-bound medical magic bullet models. Here, a topological rate distortion analysis is applied to the problem of protein folding and regulation that is similar in spirit to Tlusty&amp;#x27;s (2010a) elegant exploration of the genetic code. The formalism produces...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4847/version/1

Ablation of smooth muscle myosin heavy chain SM2 increases smooth muscle contractility and results in postnatal death in mice
Provedor de dados: 17
Autores: Mei Chi; Yingbi Zhou; Srikanth Vedamoorthyrao; Gopal Babu; Muthu Periasamy.
The smooth muscle myosin heavy chains (SMHC) are motor proteins powering smooth muscle contraction. Alternate splicing of SHMC gene at the C-terminus produces SM1, and SM2 myosin isoforms; SM2 (200 kDa) contains a unique 9-amino-acid sequence at the carboxyl terminus, whereas SM1 (204 kDa) has a 43 amino acid non-helical tail region. To date the functional difference between C-terminal isoforms has not been established; therefore, we used an exon-specific gene targeting strategy and generated a mouse model specifically deficient in SM2. Deletion of exon-41 of the SMHC gene resulted in a complete loss of SM2 in homozygous (_SM2^-/-^_) mice, accompanied by a concomitant down-regulation of SM1 in bladders. While heterozygous (_SM2^+/-^_) mice appeared normal...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1643/version/1

Rabbit Muscle Actin Polymerization changes by Ultraviolet &amp;#x2013;B radiation
Provedor de dados: 17
Autores: Anita Mukherjee; Arun Kumar Attri.
Increase in Ultraviolet-B flux from the Sun has the potential to alter the protein in mammals. Rabbit muscle was processed and filtered to extract G-actin, which was tested for its protein concentration before exposing to UV-B. It was found that polymerization of actin does get affected exposure of actin monomers to UV-B radiation. Inside the cell, there are many actin binding proteins which might be playing crucial role in G-actin to F-actin formation.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2766/version/1

Suppression of TNF-&amp;#x3b1; induced NF&amp;#x3ba;B activity by gallic acid and its semi-synthetic alkyl-gallates: Possible role in cancer chemoprevention
Provedor de dados: 17
Autores: Suaib  Luqman; Mauro  C. C. Morais; Tamara  P. Kondratyuk; Maicon  S. Petronio; Luis   O. Regasini; Dulce   H. S. Silva; Vanderlan  S. Bolzani; Christiane   P. Soares; John   M. Pezzuto.
NF&amp;#x3ba;B, a transcription factor, regulates the expression of a number of genes involved in carcinogenesis. Thus, agents that can suppress NF&amp;#x3ba;B activation have the potential to suppress carcinogenesis. In the present investigation, gallic acid was isolated from Alchornea glandulosa (Euphorbiaceae) and eight semi-synthetic alkyl gallates were prepared from the reaction of the corresponding alcohols with gallic acid at 80oC for 48 h in good yields (70-97%). All the compounds were evaluated against TNF-&amp;#x3b1;-induced NF&amp;#x3ba;B activation with stable transfected 293/NF&amp;#x3ba;B-Luc human embryonic kidney cells. Treatment of cells with gallic acid and the gallate esters (20 &amp;#xb5;g/ml) significantly reduced TNF-&amp;#x3b1;...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6922/version/1

BioenergyProduction From Plant Biomass: Bioethanol From Concept To Reality
Provedor de dados: 17
Autores: Israr  Khan; Muhammad Waheed Akhtar.
Natural energy reserves like petrol and diesel etc are depleting.  As such, it is of paramount importance to find alternative fuels. Solar energy is trapped as biomass in plants. Biomass provide an excellent reserve for trapping solar energy on field. Complex enzymatic machinery comprising of hydrolytic reactions  and consolidated bioprocessing is needed to make viable bioenergy, mostly biofuels like bioethanol for locomotives, industries and general use in the future.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6286/version/1

The biotechnological perspective of Beta-Glucosidases
Provedor de dados: 17
Autores: Israr  Khan; Muhammad waheed Akhtar.
Biotechnology is the art and science of making and technology to process biological materials for the welfare of human being. This discussion includes the beta glucosidase classification, its structure, application, and recent research interests in relation to its significance and comparison with eukaryotic Beta glucosidases including plant, animal and yeast as well. The study also comprise of the various stress factors and modifications thereby the organism to cope it. The focus of the study is on the various kinetics principles and their full potential exploitation to increase the activity of the enzyme. As such making the enzyme a potent vehicle for various industrial, pharmaceutical and research purposes. It also include the various glycosylhydrolases...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4945/version/1

Activation of Ras-ERK pathway by Fgf8 and its downregulation by Sprouty2 for the isthmus organizing activity
Provedor de dados: 17
Autores: Asuka Suzuki-Hirano; Tatsuya Sato; Harukazu Nakamura.
In the previous studies, we showed that strong Fgf8 signaling activates the Ras-ERK pathway to induce cerebellum. Here, we show importance of negative regulation of this pathway. &amp;#x27;Prolonged&amp;#x27; activation of ERK by misexpression of _Fgf8b_ and dominant-negative _Sprouty2_ (_dnSprouty2_) did not change the fate of the mesencephalic alar plate. Downregulation of ERK activity using a MEK inhibitor, U0126, or by tetracycline dependent Tet-off system after co-expression of _Fgf8b_ and _dnSprouty2_, forced the mesencephalic alar plate to differentiate into cerebellum. We then paid attention to Mkp3. After misexpression of _dnMkp3_ and _Fgf8b_, slight downregulation of ERK activity occurred, which may be due to Sprouty2, and the mesencephalon...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2089/version/1

Invariant mRNA content and mitotic protein breakdown as a solution to the Russian Doll problem of the mammalian cell cycle
Provedor de dados: 17
Autores: Stephen Cooper; Kerby Shedden; Dang Vu-Phan.
It is widely accepted that numerous genes are expressed in a cell-cycle dependent manner, with cycle-specific variations in mRNA content or peaks of protein content during the cell cycle. These proposed variations raise the problem of how varying cell cycle gene expression is regulated. This is the &amp;#x22;infinite regression&amp;#x22; problem or Russian Doll problem where postulating a cell-cycle specific control element merely pushes the explanation of cell-cycle variation back one step to the problem of how that control element itself appears and disappears at particular times during the cell cycle. We present evidence that cyclin mRNA content is invariant during the cell cycle and calculations reveal that mRNA variation does not account for observed...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1218/version/1

&amp;#x22;Dark Mediators&amp;#x22; of Proteins as Revealed by NMR in Water: Residue-selective Anion Bindings that are Masked by Pre-existing Buffer
Provedor de dados: 17
Autores: Jianxing Song; Linlin Miao; Haina Qin.
Ions are commonly believed to impose their effects on proteins by unspecific electrostatic screening. Here, by NMR we reveal that in water sulfate, chloride and thiocyanate are able to bind a well-folded WW domain at distinctive residues and affinities, which is surprisingly masked by the pre-existing buffer. Our study reveals that the specific anion binding is so ubiquitous and consequently no longer negligible in establishing &amp;#x22;postreductionist framework&amp;#x22; for protein biochemistry.
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6769/version/1

Cocaine self-administration in the mouse: A low-cost, chronic catheter preparation
Provedor de dados: 17
Autores: Matthew B. Pomrenze; Michael  V. Baratta; Brian A. Cadle; Donald C. Cooper.
Intravenous drug self-administration is the most valid animal model of human addiction because it allows volitional titration of the drug in the blood based on an individual&amp;#x2019;s motivational state together with the pharmacokinetic properties of the drug. Here we describe a reliable low-cost mouse self-administration catheter assembly and protocol that that can be used to assess a variety of drugs of abuse with a variety of protocols. We describe a method for intravenous catheter fabrication that allows for efficient and long-lasting intravenous drug delivery. The intravenous catheters remained intact and patent for several weeks allowing us to establish stable maintenance of cocaine acquisition. This was followed by a dose response study in the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7040/version/1

Interaction of the TNFR-receptor associated factor TRAF1 with I-kappa B kinase 2 (IKK2, IKK-beta, IKBKB) and TRAF2 indicating a dose dependent regulatory function of TRAF1 for NF-kappa B signaling
Provedor de dados: 17
Autores: Johannes A. Schmid; Andreas Birbach.
IKK2 is one of the most crucial signaling kinases for activation of the transcription factor NF-kappa B. Since many NF-kappa B activating pathways converge at the level of IKK2, we searched for interaction partners of this kinase using the C-terminal part (aa 466-756) as bait in a yeast two-hybrid system. We identified the N-terminal part (aa 1-228) of the TNF-receptor associated factor TRAF1 as putative interaction partner, which was subsequently confirmed in mammalian cells by coimmunoprecipitation experiments. However, this interaction seemed weaker than the interaction between TRAF1 and TRAF2, an important activating adapter molecule of NF-kappa B signaling indicating that relative levels of IKK2, TRAF1 and TRAF2 might be important for the final...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4153/version/1

Valid and efficient formula for free energy difference from nonequilibrium work
Provedor de dados: 17
Autores: Liao Y. Chen.
Atomic force microscopes and optical tweezers afford direct probe into the inner working of single biomolecules by mechanically unfolding them.^1-15^ Critical to the success of this type of probe is to correctly extract the free energy differences between the various conformations of a protein/nucleic acid along its forced unfolding pathways. Current studies rely on the Jarzynski equality^16^ (JE) or its undergirding Crooks fluctuation theorem^17^ (CFT), even though questions remain on its validity^17-19^ and on its accuracy.^13,20-21^ The validity of JE relies on the assumption of microscopic reversibility.^17,18^ The dynamics of biomolecules, however, is Langevin stochastic in nature. The frictional force in the Langevin equation breaks the time reversal...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1911/version/1

The Roles of Membrane Rafts in CD32A-Mediated Phagocytosis
Provedor de dados: 17
Autores: Timothy P. Tolentino; Periasamy Selvaraj; Cheng Zhu.
Membrane rafts are highly dynamic heterogeneous sterol- and sphingolipid-rich micro-domains on cell surfaces. They are generally believed to provide residency for cell surface molecules (e.g., adhesion and signaling molecules) and scaffolding to facilitate the functions of these molecules such as membrane trafficking, receptor transport, cell signaling, and endocytosis.&amp;#xd;&amp;#xa;The governing, or overall hypothesis, for this project is that membrane rafts provide residency for Fc[gamma]RIIA (CD32A) on K562 cells, and that by doing so they provide a platform from which Fc[gamma]RIIA initiate or carry out their functions, which include migration, signaling, phagocytic synapse formation, and internalization of IgG opsonized...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1191/version/1

Two &amp;#x27;protein folding codes&amp;#x27; can be inferred from empirical classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;s topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. Unlike the genetic case, two protein folding codes are found, a &amp;#x27;normal&amp;#x27; globular and a &amp;#x27;pathological&amp;#x27; amyloid version. The underlying normal &amp;#x27;protein folding code error network&amp;#x27; is found to have one major, highly dominant, &amp;#x27;spherical&amp;#x27; component, a minor attachment handle in the Morse Theory sense, and as many as three additional subminor handles. The basic amyloid folding code error network appears to be more complicated, of genus two, giving the eightfold symmetry of the steric zipper. Like many before us, we conjecture that the elaborate...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4665/version/1

Myosin II isoforms with separate but linked functions determine the fate of lamellipodia extension during cell spreading
Provedor de dados: 17
Autores: Venkaiah Betapudi.
Non-muscle myosin II role has been implicated in the extension of lamellipodia, a critical step in the initiation of directed cell migration, invasion and other cellular processes, but the mechanistic details are limited to driving retrograde actin filaments. The present study reveals distinct localization of myosin IIA and IIB with an unexpected opposite mechanical roles in mediating lamellipodia extension during spreading. Attachment of cells to matrix is impaired in the absence of either isoforms, but differential regulation of focal contacts formation occurs in myosin IIA^-^; and IIB^-^; cells. Spreading cells expressing both isoforms display an organized actin network consisting of retrograde filaments, arcs and central filaments. Loss of actin arcs...
Tipo: Manuscript
Palavras-chave: Cancer; Microbiology; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2868/version/1

An optimized energy potential can predict SH2 domain-peptide interactions
Provedor de dados: 17
Autores: Zeba Wunderlich; Leonid Mirny.
Peptide recognition modules (PRMs) are used throughout biology to mediate protein-protein interactions, and many PRMs are members of large protein domain families.  Members of these families are often quite similar to each other, but each domain recognizes a distinct set of peptides, raising the question of how peptide recognition specificity is achieved using similar protein domains.  The analysis of individual protein complex structures often gives answers that are not easily applicable to other members of the same PRM family.  Bioinformatics-based approaches, one the other hand, may be difficult to interpret physically.  Here we integrate structural information with a large, quantitative data set of SH2-peptide interactions to study the physical origin...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1881/version/1

Diagnostic robustness of DNA microarrays in the classification of acute leukemia
Provedor de dados: 17
Autores: Marie Loh; Adrian Mondry.
Countless statistical methods have been described for the analysis of DNA microarrays, and each yields distinct results. This raises the question whether DNA microarrays are robust diagnostic tools.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In order to address this issue, we compared five formally similar statistical tests for gene selection on a single data set derived from acute leukemia patients. Inter-test agreement of gene selection, of sample classification and with standard clinical diagnosis was calculated using Cohen&amp;#x27;s &amp;#x3ba;-score.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The inter-test agreement scores were 0.15 &amp;#x3c; &amp;#x3ba; &amp;#x3c; 0.68 for gene selection, and 0.60 &amp;#x3c; &amp;#x3ba; &amp;#x3c; 0.89 for sample classification....
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1056/version/1

Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs
Provedor de dados: 17
Autores: Zeba Wunderlich; Leonid Mirny.
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6^-10^9^ decoy sites? Our analysis of 319 known TF binding motifs clearly demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations; eukaryotic TFs exhibit widespread nonfunctional binding and require clustering of sites in regulatory regions for specificity.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2688/version/2

Asynchronous Rhythm of Steroidogenic Factor 1 and Period Homolog 2 mRNA Expression in Mouse Y1 Adrenocorticol Tumor Cells
Provedor de dados: 17
Autores: Kenji Ohe; Kouichirou Sonoda; Makoto Akashi; Koichi Oba; Masatoshi Nomura; Taijiro Okabe; Koichi Node; Ryoichi Takayanagi; Hajime Nawata; Toshihiko Yanase.
The relationship between the expression of Steroidogenic factor 1 (Sf1) and the circadian-related gene, period homolog 2 (Per2), in the adrenal cortex is still unknown. We show here that in Y1 adrenocortical tumor cells, expression of steroidogenic-related genes such as P450scc mRNA and Sf1 mRNA were asynchronous with Per2 mRNA. SF1 promoter analyses showed that the E-box element functions in a rhythmic pattern. Rhythmic expression of Upstream factor 1 mRNA, correlated well with Sf1 mRNA expression. We propose that tumorigenesis of adrenocortical lesions cause disruption of synchronous expression of steroidogenic-related and circadian-related genes.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4523/version/1

Shear stress activation of nitric oxide synthase and increased NO levels in human red blood cells
Provedor de dados: 17
Autores: Pinar Ulker; Nazmi Yaras; Ciler Celik-Ozenci; Herbert Meiselman; Oguz Baskurt.
Since the discovery of nitric oxide (NO) as a vasoactive molecule, red blood cells (RBC) have been considered to participate in NO-mediated control of the circulation. The classical role attributed to RBC was scavenging of NO, thereby impacting the local bioavailability of this important regulator of vascular tone^1^. RBC have been shown to be a source of NO, primarily via its transport bound to haemoglobin^2, 3^. Under specific conditions, haemoglobin plays an active role in converting NO derivatives (e.g., nitrite) to NO^4, 5^, with this NO originating from RBC being an effective modulator of vascular smooth muscle tone^6^. Interestingly, RBC contain a NO synthase (NOS) protein^7^, can actively synthesize NO using L-arginine as a substrate^8^, and can...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4608/version/1

Protein and DNA evolution: Statistics and combinatorics are the rules of the game
Provedor de dados: 17
Autores: Arunava Goswami; Srimoyee Duttagupta; Chirantan Chakraborty; Amita Pal; Pabitra Pal Choudhury; Sk Sarif Hassan.
Let us assume AVMAYDRYVAIC or MAYDRYVAICCP, most important signature domain of&amp;#xd;&amp;#xa;olfactory receptor (OR) gene family assembled in evolution following simplest possible laws of statistics which says the addition of V after A in AVMAYDRYVAIC or addition of A after M are independent events. There are 20 amino acids present in nature so the probability of joint occurrence of such events is 1/400. Therefore for making a contiguous string of&amp;#xd;&amp;#xa;AVMAYDRYVAIC or MAYDRYVAICCP, the probability would be 1 out of 2012. Over millions of years of evolution this has certainly happened and that is why we see such a signature sequence in OR1D2, OR1D subfamily member 2 as per &amp;#x22;HORDE...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4859/version/1

Findings From an Accelerated _In Vivo_ Corrosion Model of Magnesium
Provedor de dados: 17
Autores: Chi Keung Yuen; Wing Yuk Ip.
In this article, we are presenting some findings of magnesium corrosion in an _in vivo_ model. While there is consensus that subcutaneous bubbles will occur, it was found in our corrosion-accelerated model that magnesium corrosion is more severe in areas under the gas bubbles. This finding may bring insights to novel methods in reducing the uneven corrosion.
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1833/version/1

SBGN support in BIOCHAM
Provedor de dados: 17
Autores: Dragana Jovanovska; Fran&amp;#xe7;ois Fages; Sylvain Soliman.
BIOCHAM - BioChemical Abstract Machine is an environment for modeling biological systems and formalizing experimental knowledge. Mainly, it is  composed of:&amp;#xd;&amp;#xa;* a rule-based language for modeling biochemical systems (compatible with SBML)&amp;#xd;&amp;#xa;* several simulators (boolean, differential, stochastic)&amp;#xd;&amp;#xa;* a temporal logic based language to formalize the temporal properties of a biological system and validate models with respect to such specifications,&amp;#xd;&amp;#xa;* unique features for developing/correcting/completing/reducing/coupling models, including the inference of kinetic parameters in high dimension from temporal logic constraints.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;BIOCHAM is presented with a user...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5189/version/1

Gene Expression Profiling of the Hepatic Transcriptome in Presence of TNF-alpha
Provedor de dados: 17
Autores: Amit Kumar Pandey; Neha Munjal; Malabika  Datta.
Diabetes mellitus, often simply termed Diabetes, is a syndrome characterized by disordered metabolism and high blood sugar. It is caused due to low levels of insulin hormone or from abnormal resistance to insulin in its target tissues. World Health Organization estimates that India will alone have 79.4 million diabetic patients in 2030. One of its major form Type 2 diabetes, is often associated with obesity, hypertension, elevated cholesterol and metabolic syndrome. Changes in life style, such as consumption of high-calorie diet and lack of exercise, have increased the global prevalence not only of diabetes but also of obesity. Type 2 diabetes is characterized by insulin resistance in target tissue, occurs due to several reasons and one of them being the...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2527/version/1

Connecting Seed Lists of Mammalian Proteins Using Steiner Trees
Provedor de dados: 17
Autores: Amelia G. White; Avi Ma&amp;#x27;ayan.
Multivariate experiments and genomics studies applied to mammalian cells often produce lists of genes or proteins altered under treatment/disease vs. control/normal conditions. Such lists can be identified in known protein-protein interaction networks to produce subnetworks that &amp;#x201c;connect&amp;#x201d; the genes or proteins from the lists. Such subnetworks are valuable for biologists since they can suggest regulatory mechanisms that are altered under different conditions. Often such subnetworks are overloaded with links and nodes resulting in connectivity diagrams that are illegible due to edge overlap. In this study, we attempt to address this problem by implementing an approximation to the Steiner Tree problem to connect seed lists of mammalian...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1768/version/1

Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for  Composition Improvements.  (Version 2.0)
Provedor de dados: 17
Autores: Valentin  Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions.  Conventional &amp;#x201c;wet chemistry&amp;#x201d; analytical methods are time-consuming and costly.  As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry.  Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6231/version/2

A Modular Semantic Annotation Framework: CellML Metadata Specifications 2.0
Provedor de dados: 17
Autores: Michael T. Cooling.
In the last decade or so, model encoding efforts such as CellML and SBML have greatly facilitated model availability. But, as the complexity of models increases, the utility of these models can vary. The addition of semantic information is crucial to transforming mathematical models from esoteric to informative resources. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We have developed a metadata specification framework to better enable the annotation of CellML models with metadata. The framework consists of a core specification describing, in general terms, how annotations should be attached using RDF/XML, and satellite specifications covering several domains of immediate interest, using elements from the Dublin Core, FOAF (Friend-Of-A-Friend), BIBO (Bibliographic...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6391/version/1

Soybean Composition Database from NIR, NMR and GC-MS Analyses
Provedor de dados: 17
Autores: I. C. Baianu.
This novel Soybean Composition Database from the AFC-NMR &amp;#x26; NIR Spectroscopy Facility of the College of ACES at the University of Illinois at Urbana includes more than 12,000 NIR measurements on soybeans from the International Soybean Germplasm Collection, such as those received from Peking at the National Soybean Collection.&amp;#xd;&amp;#xa;Excel files (.xls) of our novel spectroscopic data are currently available for all 80,000 + NIR and FT-NMR measurements; such data are made available from an ultra-fast and secure supercomputer server utilizing the current version of the Scientific-Linux OS-based software. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A detailed account is also presented of our high-resolution nuclear magnetic resonance (HR-NMR) and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6201/version/1

Quantification of miRNAs and Their Networks in the light of Integral Value Transformations
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; Arunava  Goswami; Vrushali Fangal.
MicroRNAs (miRNAs) which are on average only 21-25 nucleotides long are key post-transcriptional regulators of gene expression in metazoans and plants. A proper quantitative understanding of miRNAs is required to comprehend their structures, functions, evolutions etc. In this paper, the nucleotide strings of miRNAs of three organisms namely Homo sapiens (hsa), Macaca mulatta (mml) and Pan troglodytes (ptr) have been quantified and classified based on some characterizing features. A network has been built up among the miRNAs for these three organisms through a class of discrete transformations namely Integral Value Transformations (IVTs), proposed by Sk. S. Hassan et al [1, 2].  Through this study we have been able to nullify or justify one given nucleotide...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6035/version/1

Signatures of spatial organizations &amp;#x2013; From the universe of proteins to the universe in general
Provedor de dados: 17
Autores: Aditya Mittal.
Pattern generation and recognition in 3-D space have been of wide interest in fields varying from atomic and molecular structures to organization of celestial objects. Our thoughts towards investigating patterns (and elucidation of geometrical rules) followed by a known number of points with specific or specified coordinates are guided by the assumption/belief that there must be some thermodynamic and/or kinetic basis leading to the organization of coordinates of the known points. In terms of biomolecular structures, the DNA double helix is one of the strongest examples of such structures with coordinates of atoms in the phosphate backbone and the side-chains provide a helical geometrical configuration. It needs to be appreciated (and emphasized) that,...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6038/version/1

Remarks on the number of tubulin dimers per neuron and implications for Hameroff-Penrose Orch OR
Provedor de dados: 17
Autores: Danko Georgiev.
Stuart Hameroff has wrongly estimated that a typical brain neuron has 10^7^ tubulin dimers and wrongly attributed this result to Yu and Baas, J. Neurosci. 1994; 14: 2818-2829. In this letter we show that Hameroff&amp;#x2019;s estimate is based on misunderstanding of the results provided by Yu and Baas, who actually measured the total microtubule length in a single axonal projection with length of 56 &amp;#x3bc;m in a differentiating in vitro stage 3 embryonic hippocampal neuron. In order to visualize how big Hameroff&amp;#x2019;s error is, we have reconstructed two of the studied by Yu and Baas embryonic hippocampal neurons with Neuromantic v1.6.3 and compared them with previously published reconstructions of adult hippocampal neurons. Correct calculations...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3860/version/1

Formation of an SIR-Nucleosome Filament in vitro and Its Modulation by O-Acetyl-ADP-Ribose
Provedor de dados: 17
Autores: Yu-Yi Wu; Jia-Yang Hong; Sue-Ping Lee; Hsiao-Hsuian  Shen; Shu-Ping Tsai; Gunn-Guang Liou.
It is not possible to clearly visualize how chromatin condenses to heterochromatin in vivo. However, in an in vitro system for Saccharomyces cerevisiae, the requirements for heterochromatin filament formation mirror those found in vivo. Here we report that the nucleosomes and the Sir2, Sir3 and Sir4 proteins, which are required for in vitro filament assembly, are also components of these filaments, confirming that the filaments are SIR-nucleosome filaments. We show the individual localization patterns of the Sir proteins on this SIR-nucleosome filament, and demonstrate that the metabolite, AAR, plays a specific and essential role in promoting the formation of this SIR-nucleosome filament.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6063/version/1

Interruption of [beta]-Catenin Signaling Reduces Neurogenesis in Alzheimer&amp;#x27;s Disease Brains
Provedor de dados: 17
Autores: Ping He; Matthias Staufenbiel; Yong Shen.
Although studies show new neurons generated from progenitor cells in a healthy adult neocortex, neurogenic potential derived from stem/progenitor cells in the cortex of Alzheimer&amp;#x27;s patients still remains unsolved. In this study, we isolated the glial progenitor cells (GPCs) from the cortex of healthy (HC) and Alzheimer&amp;#x27;s disease (AD). The AD-GPCs displayed reduced capability to renew and decreased production of new neurons. Interestingly, we found significant reduction of [beta]-catenin in AD-GPCs compared to HC while glycogen synthase kinase 3[beta] (GSK-3[beta]) was promoted. Moreover, we found both increased phosphorylation of [beta]-catenin in AD-GPCs and their progeny cells. Amyloid [beta] peptide (A[beta]) treatment results in...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2257/version/1

Antibodies targeting Cancer stem cells, A novel pattern in Immunotherapy
Provedor de dados: 17
Autores: Sarfaraz Alam.
Antibody targeting of cancer is showing clinical and commercial success after deep research and development over the last 3 decades. They have the great potential to deliver long-term cures but a shift in thinking towards a cancer stem cell (CSC) model for tumour development is certain to have an impact on how antibodies are selected and developed, the targets they bind to and the drugs used in combination with them. CSCs have been identified from many human tumours and share many of the characteristics of normal stem cells such as the ability to renew and metabolically or physically protect themselves from xenobiotic and DNA damage. Targeting CSCs could be a strategy to improve the outcome of cancer therapy. Monoclonal antibodies are clinically and...
Tipo: Presentation
Palavras-chave: Cancer; Immunology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5428/version/1

Effect of Stimulators upon Human Hepatic Adenylate Cyclase Activity: A Tool of Nitroimidazole Cytotoxicity Assessment
Provedor de dados: 17
Autores: Rakesh Sharma; Soonjo Kwon.
Nitroimidazole is an antibiotic and radiosensitizer chemical with great potentials in imaging. The hepato-cytoxicity evaluation of nitroimidazole and possible energy status changes in liver cells due to its anti-inflammatory characteristics are crucial in tumor imaging and chemotherapy. Adenylate cyclase is key enzyme to cause energy imbalance leading to cytotoxicity. To evaluate energy status in hepatocytes and Kupffer cells, adenylate cyclase activities in isolated liver cells were compared in presence of stimulators. To evaluate the effect of effectors on adenylate cyclase in cultured hepatocyte cells, adenylate cyclase enzyme was stimulated by different GITP, GTP, progesterone and nitroimidazole effectors. In cultured Kupffer cells, prostaglandin E~2~...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2850/version/1

Synchronized Mammalian Cells in Culture: A Comparison of Normal and KB Cancer Cell Growth
Provedor de dados: 17
Autores: I. C. Baianu.
Experimentation and tests with cells in culture and cell synchronization or synchrony are important in order to be able to make both reliable and high-sensitivity measurements. This is also very important for mechanistic studies of cell division control, oncogenesis and tumor growth. A comparison is made in this article between the initially synchronized cell growth of rabbit and KB cells in synchronized cultures.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7128/version/1

A normalization technique for next generation sequencing experiments
Provedor de dados: 17
Autores: G&amp;#xfc;nter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS&amp;#x27; cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4710/version/2

Living unicellular eukaryote Tetrahymena pyriformis as a model for study of mitochondrial energetics in mammalian cells under conditions of reduced oxidative metabolism.
Provedor de dados: 17
Autores: Elena Mokhova.
Some &amp;#x201c;animal-like&amp;#x201d; protozoa are used instead of mammalian cells in diverse investigations.  _Tetrahymena pyriformis_ cells in stationary phase of growth and washed from oxidative substrates (_T.pyriformis_) function under conditions of reduced oxidative metabolism. To elucidate if _T.pyriformis_ can be applied as a model for mitochondrial energetics study in   mammalian cells during hibernation, the features of _T.pyriformis_ mitochondria were compared with that of liver mitochondria isolated from hibernating animals; the published earlier data were used. Based on the respiration recording and observation of Mito Tracker Red fluorescence in living _T.pyriformis_ we tentatively concluded that the mitochondrial electrical membrane...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4521/version/2

Protein Ontology and Community Curation
Provedor de dados: 17
Autores: Cecilia Arighi.
The Protein Ontology (PRO) is designed as a formal and well-principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from the classification of proteins, on the basis of evolutionary relationships at the homeomorphic level, to the representation of the multiple protein forms of a gene, such as those resulting from alternative splicing, cleavage and/or post-translational modifications. As an ontology, PRO differs from a database in that it provides description about the protein types and their relationships. In this way PRO can be integrated with or cross-referenced by other ontologies and/or databases. The representation of specific protein entities in PRO allows precise definition of objects in pathways,...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3169/version/1

Collagen-bound low density lipoprotein modifies endothelial cell adhesion to type V collagen: Implications for atherosclerosis
Provedor de dados: 17
Autores: Stefan Lorkowski; J&amp;#xfc;rgen Rauterberg; B&amp;#xe4;rbel Harrach-Ruprecht; David Troyer.
Low density lipoprotein (LDL) is retained in the extracellular matrix of the arterial wall where it is considered to be atherogenic, but little is known about how cell adhesion to the matrix is affected by collagen-bound LDL. We tested the effect of native, oxidized and acetylated LDL reacted with adsorbed monomeric type I, III and V collagen on endothelial cell adhesion to collagen using a colorimetric adhesion assay. We found that none of the LDL species affected adhesion to type I and III collagen, but that collagen-bound native and acetylated LDL enhanced attachment to type V collagen, whereas bound oxidized LDL inhibited adhesion to this collagen. We suggest that oxidized LDL associated with type V collagen in the arterial wall would favor...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1238/version/1

Azadirachta indica induced suppression of Mycobacterium tuberculosis secreted proteins in human monocyte
Provedor de dados: 17
Autores: Jawed Iqbal; Ajay Kumar; Najmul Islam.
The H37Rv strain of MTB was grown in modified Sauton&amp;#x2019;s medium till mid-log phase. Peripheral blood mononuclear cells (PBMC) were isolated by density gradient sedimentation on Ficoll-Paque separation medium. Adherent monocytes obtained from PBMC&amp;#x2019;s were infected with H37Rv for 90 min. in the ratio of 1:1 (1 bug: 1 cell). Thereafter, after washing, infected cells were co-cultured with varying doses of neem extract for 24 hrs, and harvested subsequently. Modulation of secreted TNF-[alpha], iNOS and MTB Ag85 complex expressions in culture supernatants was estimated by ELISA.&amp;#xd;&amp;#xa;We report the high basal expression of secreted tumor necrosis factor-[alpha] (TNF-[alpha]), inducible nitric oxide synthase (iNOS) and MTB Ag85...
Tipo: Poster
Palavras-chave: Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1562/version/1

Balancing noise and plasticity in gene expression
Provedor de dados: 17
Autores: Djordje Bajic; Juan F. Poyatos.
Coupling the control of expression stochasticity (noise) with the capacity to expression change (plasticity) can constrain gene function and limit adaptation. Which factors contribute then to modulate this coupling? Transcription re-initiation is generally associated with coupling and this is commonly related to strong chromatin regulation. We alternatively show how strong regulation can however lead to plasticity uncorrelated to noise. The character of the regulation is also relevant, with plastic but noiseless genes usually subjected to broad expression activation whereas plastic and noisy genes experience targeted repression. This differential action is similarly noticed in how histones influence these genes. In contrast, we find that translational...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6729/version/1

Early Diagnosis of Alzheimer&amp;#x27;s disease by NIRF Spectroscopy  and Nuclear Medicine-v.4.0
Provedor de dados: 17
Autores: I Baianu.
There is an urgent need for the early detection of diseases such as Alzheimer&amp;#x2019;s (AD) and Cancers in order to enable their successful treatment. Cancer is the second major cause of death after Heart Disease, and AD is the third major cause of death with major, human and financial/economics trillion dollar consequences for the society. Nuclear Medicine is concerned with applications in Medicine of Nuclear Science and Engineering techniques and knowledge. Three major Nuclear Medicine techniques that are established for diagnostic and research purposes are: Positron Emission Tomography (PET) and CAT/CT, Nuclear Magnetic Resonance Imaging (NMRI/MRI). However, these three techniques have also major limitations in terms of either cost or image...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6273/version/1

Suppression of 12-O-tetradecanoylphorbol-13-acetate-induced ornithine decarboxylase activity by resveratrol derivatives
Provedor de dados: 17
Autores: Suaib  Luqman; Tamara  P. Kondratyuk; Juma  Hosino; Mark  Cushman; John  M. Pezzuto.
As demonstrated previously, resveratrol (3,4&amp;#x27;,5-trihydroxy-trans-stilbene) inhibits 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced ornithine decarboxylase (ODC), the key rate limiting enzyme in mammalian polyamine synthesis. Using human bladder epithelial carcinoma HTB-24 cells in culture where resveratrol inhibits induction with an IC50 of 8.8 &amp;#xb5;M, we now report potential metabolites demonstrate greater activity [tetrabutylammonium (E)-4-(3,5-dihydroxystyryl)phenyl sulfate (IC50 1.2 &amp;#xb5;M),  resveratrol tripotassium 3,5,4&amp;#x27;-trisulfate (IC50 1.8  &amp;#xb5;M), resveratrol tripotassium 3,4&amp;#x27;-disulfate (IC50 1.8 &amp;#xb5;M), and resveratrol tripotassium 3,5-disulfate  (IC50 2.3 &amp;#xb5;M)]. Based on RT-PCR...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6908/version/1

Formal Systems Architectures for Biology
Provedor de dados: 17
Autores: Bradly Alicea.
When the word &amp;#x22;systems&amp;#x22; is used in systems biology, it invokes a variety of assumptions about what defines the subject under investigation, which in turn can lead to divergent research outcomes. We will take the position that systems are defined by their potential organizing and &amp;#x22;control&amp;#x22; mechanisms, which distinguishes complex, living systems from a primordial soup. This will be accomplished by defining and investigating three interesting control motifs in biological systems: dominoes and clocks, futile cycles, and complex feedforward regulation. Additional mechanisms that combine feedback and feedforward mechanisms will also be briefly elaborated upon. Throughout these examples, our focus will be on the connection...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6369/version/2

On the origin of the mitochondrial genetic code: Towards a unified mathematical framework for the management of genetic information
Provedor de dados: 17
Autores: Diego Luis Gonzalez; Simone Giannerini; Rodolfo Rosa.
The origin of the genetic code represents one of the most challenging problems in molecular evolution. The genetic code is an important universal feature of extant organisms and indicates a common ancestry of different forms of life on earth. Known variants of the genetic code can be mainly divided in mitochondrial and nuclear classes. Here we provide a new insight on the origin of the mitochondrial genetic code: we found that its degeneracy distribution can be explained by using a mathematical approach recently developed for the description of the Euplotes nuclear variant of the genetic code. The results point to a primeval mitochondrial genetic code composed of four base codons, which we call tesserae, that, among other features, exhibit outstanding...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7136/version/1

Complex Systems Biology of Organisms
Provedor de dados: 17
Autores: I. C. Baianu.
Complex Systems Biology models and theories are axiomatically defined in terms of concrete categories and organismic supercategories (OS) to include both complete self-reproduction of logically defined pi-entities founded in Quine&amp;#x27;s logic and dynamic system diagrams subject to both algebraic and topological transformations. Mathematical models of complex organisms are expressed in terms of category theory and organismic supercategories (OS). OS theories have applications in: Bioinformatics, Developmental Biology, Genomics and Molecular Cell Biology
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7044/version/1

FAIRE-seq data analysis of Chlamydomonas reinhardtii under carbon deprivation
Provedor de dados: 17
Autores: David Urbina-G&amp;#xf3;mez; Flavia  Vischi Winck; Bernd M&amp;#xfc;ller-R&amp;#xf6;ber; Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n.
For the genome-wide identification of nucleosome depleted regions under carbon deprivation, we analyze an available set of data from an assay of formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq). Mapping to the sequenced nuclear genome of C.reinhardtii, followed by the identification of the enrichment-sequenced fragments was performed. We examined the location of these fragments relative to annotated genes. The related genes were associated to the corresponding Gene-Ontology (GO), for an evaluation of over-representate GO categories. Some genes, link with functions or locations, that have been previous described, indicating the success of the method finding carbon-metabolism related fragments.
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7035/version/1

BioBrick Promoter Measurement Kit Instruction Sheets
Provedor de dados: 17
Autores: Jason Kelly.
Instructions for inserting a test promoter into the measurement kit plasmid for characterization as well as instructions for measuring the activity of the test promoter in Standard Promoter Units (SPUs).  These instructions were distributed to the teams participating in the International Genetically Engineered Machines competition (iGEM).
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2028/version/1

A three-dimensional stochastic spatio-temporal model of cell spreading
Provedor de dados: 17
Autores: Yuguang P. Xiong; Padmini Rangamani; Benjamin Dubin-Thaler; Michael  Sheetz; Ravi Iyengar.
Cell motility is important for many physiological processes and the underlying&amp;#xd;&amp;#xa;biochemical reactions motility have been well characterized. Mathematical models, using&amp;#xd;&amp;#xa;the biochemical reactions and focused on different types of spreading behavior have been&amp;#xd;&amp;#xa;constructed and analyzed. In this study, we build on these previous models to develop a&amp;#xd;&amp;#xa;three-dimensional stochastic model of isotropic spreading of mammalian fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally observed isotropic cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/62/version/2

Serine biosynthesis with one carbon catabolism represents a novel pathway for ATP generation in cells using alternative glycolysis with zero net ATP production
Provedor de dados: 17
Autores: Alexei Vazquez; Zoltan N. Oltvai.
Recent experimental evidence indicates that some cancer cells have an alternative glycolysis pathway with net zero ATP production, implying that upregulation of glycolysis in these cells may not be related to the generation of ATP. Here we use a genome-scale model of human cell metabolism to investigate the potential metabolic alterations in cells using net zero ATP glycolysis. We uncover a novel pathway for ATP generation that involves reactions from the serine biosynthesis and one-carbon metabolism pathways. This pathway has a predicted two-fold higher flux rate in cells using net zero ATP glycolysis than those using standard glycolysis and generates twice as much ATP with significantly lower rate of lactate- but higher rate of alanine secretion. Thus,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6123/version/1

Fuzzy logic as a decision-making support system for the indication of bariatric surgery based on an index (OBESINDEX) generated by the association between body fat and body mass index
Provedor de dados: 17
Autores: Joao L. M. C. Azevedo; Susana A. Miyahira; Lucas P. F. F. Leal; Glicia C. Azevedo; Otavio C. Azevedo; Joao L. C. Azevedo; Gustavo P. S. Miguel.
Background: A Fuzzy Obesity Index (OBESINDEX) for use as an alternative in bariatric surgery indication (BSI) is presented. The search for a more accurate method to evaluate obesity and to indicate a better treatment is important in the world health context. BMI (body mass index) is considered the main criteria for obesity treatment and BSI. Nevertheless, the fat excess related to the percentage of Body Fat (%BF) is actually the principal harmful factor in obesity disease that is usually neglected. This paper presents a new fuzzy mechanism for evaluating obesity by associating BMI with %BF that yields a fuzzy obesity index for obesity evaluation and treatment and allows building up a Fuzzy Decision Support System (FDSS) for...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5516/version/1

CFP and YFP photostabilities are differentially affected by common mounting fluids
Provedor de dados: 17
Autores: Johannes A. Schmid.
The use of spectrally distinct variants of green fluorescent protein (GFP) such as cyan or yellow mutants (CFP and YFP, respectively) is very common in all different fields of life sciences, e.g. for marking and tracing of specific proteins or cells or to determine protein interactions. In the later case, the quantum physical phenomenon of fluorescence resonance energy transfer (FRET) is visualized by specific microscopy techniques. When we applied a commonly used FRET microscopy technique - the increase in CFP-fluorescence after bleaching of YFP, we noticed that it worked well for live cells, but that most of the FRET-signal was lost in fixed cells mounted in commercial microscopy mounting fluids. Subsequently, we could show that CFP bleached much faster...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4517/version/1

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Provedor de dados: 17
Autores: I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn &amp;#x2013;algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata.  Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7083/version/2

Multivalent ligands of CD22 for targeting of B cells
Provedor de dados: 17
Autores: James C. Paulson.
Multivalent ligands of CD22 for active targeting of B cells. Mary O&amp;#x2019;Reilly, Wei Hsu Chen, Gladys Completo, Ying Zeng, Satoshi Futakawa and Cory Rillahan and James C. Paulson, Departments of Chemical Physiology and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The siglecs comprise 13 members of the immunoglobulin superfamily that recognize sialic acid containing glycans, and are differentially expressed on leukocytes and glial cells.   The natural ligands of siglecs typically occur on the same cell (in cis) and/or on adjacent cells (in trans).  Cis ligands mask the binding of multivalent synthetic sialoside ligands and are thought to regulate the activity of...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Chemistry; Immunology; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3549/version/1

Stomatin-like Protein 2 Links Mitochondria to T-Cell Receptor Signalosomes at the Immunological Synapse and Enhances T-Cell Activation
Provedor de dados: 17
Autores: Mark G. Kirchhof; Luan A. Chau; Caitlin D. Lemke; Santosh Vardhana; Peter J. Darlington; Maria E. Marquez; Roy Taylor; Kamilia Rizkalla; Isaac Blaca; Michael L. Dustin; Joaquin Madrenas.
T cell activation through the antigen receptor (TCR) requires sustained signalling from microclusters in the peripheral region of the immunological synapse (IS). The bioenergetics of such prolonged signaling have been linked to the redistribution of mitochondria to the IS. Here, we report that stomatin-like protein-2 (SLP-2) plays an important role in this process by bridging polarized mitochondria to these signaling TCR microclusters or signalosomes in the IS in a polymerized actin-dependent manner. In this way, SLP-2 helps to sustain TCR-dependent signalling and enhances T cell activation.
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1068/version/1

The Physiome languages: CellML and FieldML
Provedor de dados: 17
Autores: Peter J. Hunter.
Discussion of the markup languages being defined by the VPH/Physiome project for multiscale, multiphysics modeling.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4982/version/1

Regulation and feedback of cholesterol metabolism
Provedor de dados: 17
Autores: Alexander Mazein; Steven Watterson; Holly C. Gibbs; Wayne Hsieh; Mohammed Ba Abdullah; Mathieu Blanc; William J. Griffiths; Tom C. Freeman; Peter Ghazal.
Cholesterol biosynthesis serves as a central metabolic hub for numerous biological processes in health and disease. An integrative knowledge representation of how the cholesterol pathway is structured and how it interacts with other pathway systems is lacking. Here we provide using Systems Biology Graphical Notation the research synthesis of a process diagram integrating the regulatory and feedback systems for cholesterol synthesis.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6315/version/1

Complex Systems Analysis of Arrested Neural Cell Differentiation during Development and Analogous Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: V. I. Prisecaru; I C. Baianu.
A new approach to the modular, complex systems analysis of nonlinear dynamics of arrested neural cell Differentiation--induced cell proliferation during organismic development and the analogous cell cycling network transformations involved in carcinogenesis is proposed. Neural tissue arrested differentiation that induces cell proliferation during perturbed development and Carcinogenesis are complex processes that involve dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments. Such &amp;#x27;dynamically inter-connected&amp;#x27; biomolecules form numerous inter-related pathways referred to as &amp;#x27;molecular networks&amp;#x27;. One such family of signaling pathways contains the cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7101/version/2

Electron Transfer Pathways in Cell
Provedor de dados: 17
Autores: Yan Liu.
Analysis of the electron salvation process data indicates that the electron transfer between the electron donor and acceptor is hindered by the electron salvation process. It is proposed that the electron transfer in the cell environment must be assisted by intermediate messenger called the &amp;#x201c;transport protein&amp;#x201d;.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7149/version/1

In silico Genetic Network Models for &amp;#xb;Pre-clinical Drug Prioritization
Provedor de dados: 17
Autores: Jianghui Xiong; Juan Liu; Simon Rayner; Ze Tian; Yinghui Li; Shanguang Chen.
The high rates of failure in oncology drug clinical trials highlight the problems of using pre-clinical data to predict the clinical effects of drugs. Patient population heterogeneity and unpredictable physiology complicate pre-clinical cancer modeling efforts. We hypothesize that gene networks associated with cancer outcome in heterogeneous patient populations could serve as a reference for identifying drug effects. Here we propose a novel in vivo genetic interaction which we call &amp;#x2018;synergistic outcome determination&amp;#x2019; (SOD), a concept similar to &amp;#x2018;Synthetic Lethality&amp;#x2019;. SOD is defined as the synergy of a gene pair with respect to cancer patients&amp;#x27; outcome, whose correlation with outcome is due to...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5343/version/1

Sparse bayesian step-filtering for high-throughput analysis of molecular machine dynamics
Provedor de dados: 17
Autores: Max A. Little; Nick S. Jones.
Nature has evolved many molecular machines such as kinesin, myosin, and the rotary flagellar motor powered by an ion current from the mitochondria. Direct observation of the step-like motion of these machines with time series from novel experimental assays has recently become possible. These time series are corrupted by molecular and experimental noise that requires removal, but classical signal processing is of limited use for recovering such step-like dynamics. This paper reports simple, novel Bayesian filters that are robust to step-like dynamics in noise, and introduce an L1-regularized, global filter whose sparse solution can be rapidly obtained by standard convex optimization methods. We show these techniques outperforming classical filters on...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4318/version/1

Principal basis for enzyme power
Provedor de dados: 17
Autores: Alexander G. Foigel.
The reaction rate enhancement that enzymes produce had not been fully appreciated. The object of the article is to present the mechanism of the enormous catalytic power of the enzymes. I conclude that during substrate conversion to product the enzyme transfers firstly some additional small reactant group that must be initially presented in the active site of the enzyme to bound substrate (i) ; the enzyme regenerates during second substrate group transfer (ii);  the active enzyme acts as a reactant of the enzymatic reaction (iii). The detailed chemical mechanisms of enzymatic reactions, such as a the well-studied reaction of the serine proteases family, the peptide bond hydrolysis catalyzed by  &amp;#x3b1;-chymotrypsin, and the glyceraldehyde-3-phosphate...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2406/version/1

Systems Biology on Bio-Linux
Provedor de dados: 17
Autores: Mesude Bicak.
This presentation introduces the Bio-Linux Operating System which is a popular Computational Biology workstation with 500+ bioinformatics software. It then provides an overview of popular modelling approaches in systems biology, covering top-down, bottom-up and hybrid modelling. Finally it highlights the challenges being faced by systems biology modellers, agent-based modellers in particular, regarding standardisation efforts.
Tipo: Presentation
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6348/version/1

The novel adiponectin-resistin (AR) and insulin resistance (IR~AR~) indexes
Provedor de dados: 17
Autores: Cia-Hin Lau; Sekaran Muniandy.
Serum hypoadiponectinemia and hyperrestinemia independently links insulin resistance to type 2 diabetes (T2DM) and metabolic syndrome (MS). Thus, the aim of this study was propose a novel adiponectin-resistin (AR) index by unifying the effect of adiponectin and resistin. Then, a novel insulin resistance (IR~AR~) index was proposed by taking into account the AR index. Serum adiponectin and resistin levels as well as other insulin resistance, T2DM and MS risk factors were tested. Experimental results showed the AR index was more stronger correlated with insulin resistance risk factors and had stronger association (df=5; F=51.154; P&amp;#x3c;0.001) with T2DM and MS susceptibility rather than the serum adiponectin (df=5; F=15.680; P&amp;#x3c;0.001) and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4191/version/1

Structural basis of the allosteric trigger of the Hsp70 chaperone proteins.
Provedor de dados: 17
Autores: Akash Bhattacharya; Alexander Kurochkin; Grover Yip; Eric Bertelsen; Erik Zuiderweg.
This work solves a decades-old dilemma that stood in the way of understanding the allosteric mechanism of Hsp70 (heat shock 70 kDa) chaperone proteins. Hsp70s are central to protein folding, refolding, and trafficking in organisms ranging from Archae to Homo Sapiens, both at normal and at stressed cellular conditions. Hsp70s are comprised of two main domains: a 44 kDa N-terminal nucleotide-binding domain (NBD), and a 25 kDa substrate-binding domain (SBD) that harbors the substrate binding site. The nucleotide binding site in the NBD and the substrate binding site in the SBD are allosterically linked: ADP binding promotes substrate binding, while ATP binding promotes substrate release. It has long been a goal of structural biology to characterize the nature...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1978/version/1

Impact of polyplex micelles installed with cyclic RGD peptide as ligand on gene delivery to vascular lesions
Provedor de dados: 17
Autores: Hiroyuki Koyama; Hideo Kagaya; Makoto Oba; Yutaka Miura; Takehiko Ishii; Tsuyoshi Takato; Kazunori Kataoka; Tetsuro Miyata.
Gene therapy is expected to open a new strategy for the treatment of refractory vascular diseases, so the development of appropriate gene vectors for vascular lesions is needed. To realize this requirement with a non-viral approach, cyclo(RGDfK) peptide (cRGD) was introduced to block copolymer, poly(ethylene glycol)-block-polycation carrying ethylenediamine units (PEG-PAsp(DET)). cRGD recognizes &amp;#x3b1;v&amp;#x3b2;3 and &amp;#x3b1;v&amp;#x3b2;5 integrins, which are abundantly expressed in vascular lesions. cRGD-conjugated PEG-PAsp(DET) (cRGD-PEG-PAsp(DET)) formed polyplex micelles through complexation with plasmid DNA (pDNA), and the cRGD-PEG-PAsp(DET) micelles achieved significantly more efficient gene expression and cellular uptake as compared with...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5020/version/1

Nano-enabled Biological Materials
Provedor de dados: 17
Autores: Bradly J. Alicea.
This talk is an attempt to define a new field called &amp;#x201c;Nano-enabled Biological Tissues&amp;#x201d;. As such, this talk serves as a review of both the theoretical underpinnings and relevant recent results. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The presentation is divided into several parts: &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;* in the first section (slides 3-4), the concept of nano-enabled tissues are introduced as a complex system that can be engineered at multiple scales.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;* the second section (slides 5-12) contains three essential ingredients to achieve the technological vision. Current examples of each ingredient are introduced separately.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;* in the third section (slides 13-17),...
Tipo: Presentation
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5448/version/1

Angiogenesis and Vasculogenesis at 7-Day of Reperfused Acute Myocardial Infarction
Provedor de dados: 17
Autores: Sheng  Kang; Yue-jin Yang; Qing-zhi Wang; Yue L. I. Li; Yi Tian; Yu-tong Cheng; Wei-feng Shen.
Objectives &amp;#xd;&amp;#xa;This study is to investigate the angiogenesis and vasculogenesis at the first week of reperfused acute myocardial infarction (AMI).&amp;#xd;&amp;#xa;Methods &amp;#xd;&amp;#xa;16 of mini-swines (20 to 30 Kg) were randomly assigned to the sham-operated group and the AMI group. The acute myocardial infarction and reperfusion model was created and the pig tail catheter was performed to monitor hemodynamics before left anterior descending coronary artery (LAD) occlusion, 90 min of LAD occlusion and 120 min of LAD reperfusion. Pathologic myocardial tissue was collected at 7-day of LAD reperfusion and further assessed by immunochemistry, dual immunochemistry, in-situ hybridization, real-time quantitative polymerase chain reaction and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2066/version/1

Neuronal plasticity: cell-based strategy for target identification and validation
Provedor de dados: 17
Autores: Ana Mingorance-Le Meur; Timothy P. O&amp;#x27;Connor.
While growing neurites are relatively plastic during development, their plasticity levels drop rapidly as neurons mature and become integrated into neuronal networks. As a consequence, the central nervous system ability to reorganize itself in response to injury or disease is insufficient. One of the main limitations for the design of therapeutic strategies to enhance neurite sprouting following neurological diseases is our poor understanding of the mechanisms underlying neurite structural plasticity. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To overcome this limitation, we have implemented a strategy to identify, characterize and validate the most therapeutically relevant drug targets to modulate neuronal plasticity. This strategy is based on the hypothesis...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2780/version/1

Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts
Provedor de dados: 17
Autores: Oliver Stegle; Philipp Drewe; Regina Bohnert; Karsten Borgwardt; Gunnar R&amp;#xe4;tsch.
As a fruit of the current revolution in sequencing technology, transcriptomes can now be analyzed at an unprecedented level of detail. These advances have been exploited for detecting differential expressed genes across biological samples and for quantifying the abundances of various RNA transcripts within one gene. However, explicit strategies for detecting the hidden differential abundances of RNA transcripts in biological samples have not been defined. In this work, we present two novel statistical tests to address this issue: a &amp;#x27;gene structure sensitive&amp;#x27; Poisson test for detecting differential expression when the transcript structure of the gene is known, and a kernel-based test called Maximum Mean Discrepancy when it is unknown. We...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4437/version/1

Frizzled Proteins are bona fide G Protein-Coupled Receptors
Provedor de dados: 17
Autores: Vladimir L. Katanaev; Silke Buestorf.
Receptors of the Frizzled family initiate Wnt ligand-dependent signaling controlling&amp;#xd;&amp;#xa;multiple steps in organism development and highly conserved in evolution.&amp;#xd;&amp;#xa;Misactivation of the Wnt/Frizzled signaling is cancerogenic. Frizzled receptors&amp;#xd;&amp;#xa;launch several signaling cascades: the canonical pathway regulating beta-catenin-dependent transcription; the planar cell polarity pathway polarizing the&amp;#xd;&amp;#xa;cytoskeleton within the epithelial plane; and the calcium pathway. Frizzled&amp;#xd;&amp;#xa;receptors possess seven transmembrane domains and their signaling depends on&amp;#xd;&amp;#xa;trimeric G proteins in various organisms. However, Frizzleds constitute a&amp;#xd;&amp;#xa;distinct group within the G...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Molecular Cell Biology; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2765/version/1

Crosstalk and the spectrum of biological global broadcasts: Toward generalization of the Baars consciousness model across physiological subsystems
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognitive biological phenomena are recognized as necessarily having &amp;#x27;dual&amp;#x27; information sources, it is easy to show that the information theory chain rule implies isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to dynamic global broadcasts of interacting cognitive biological processes analogous to, but slower than, consciousness, itself included within the paradigm. The argument is closely analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Immunology; Molecular Cell Biology; Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6898/version/1

Thermal characterization of Plasmodium falciparum species specific proteins in Indian geographical area.
Provedor de dados: 17
Autores: Mohit Bhardwaj; Leena Bharadwaj; Kritika Trigunayat; Madan Mohan Trigunayat.
The paper reveals thermal characteristics of _P.falciparum_ species specific proteins. These proteins determine why _P. vivex_ species are dominant over _P.falciparum_ in Indian geographical area. Outside human host plasmodium parasite survives in poikilothermal mosquitoes. Climatic temperature conditions greatly affect native state of _P.falciparum_ species specific proteins in mosquitoes. Study of climatic temperature conditions in Indian geographical area reveals that Pfsd protein for _Plasmodium falciparum_ can remain in native state between &amp;#x2265;7 degree centigrade and &amp;#x2264;42.6 degree centigrade temperature conditions. While their best optimum functions (activity) was noted between 25.3 degree centigrade to 33degree centigrade. Pfsd...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4565/version/1

A logistic regression model for microalbuminuria prediction in overweight male population
Provedor de dados: 17
Autores: BaoDe Chen; WeiYi Xu; Chen Yu; ZhenYun Ni; XueFen Li; DaWei Cui.
Background: Obesity promotes progression to microalbuminuria and increases the risk of chronic kidney disease. Current protocols of screening microalbuminuria are not recommended for the overweight or obese.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Design and Methods: A cross-sectional study was conducted. The relationship between metabolic risk factors and microalbuminuria was investigated. A regression model based on metabolic risk factors was developed and evaluated for predicting microalbuminuria in the overweight or obese.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: The prevalence of MA reached up to 17.6% in Chinese overweight men. Obesity, hypertension, hyperglycemia and hyperuricemia were the important risk factors for microalbuminuria in the overweight....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5372/version/1

On ARS-interacting multifunctional protein p18
Provedor de dados: 17
Autores: Viktor Deineko.
Nine aminoacyl-tRNA synthetases with three auxiliary components are forming a multisynthetase complex which is essential component of protein biosynthesis machinery. The smallest auxiliary component p18 takes part in biosynthesis channeling. It is also a regulator of p53 and has tumor suppressing function. Particular structure of this protein is still unknown. Here methods of structural bioinformatics were applied to generate a model of p18 spatial structure suitable for further research. The structure was created using homology modeling. DNA-binding residues of p18 were also derived both from raw sequence and from three-dimensional structure model.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1593/version/1

Bioinformatics Approach for Functional Glycomics
Provedor de dados: 17
Autores: James C. Paulson.
Presentation in the Human Glycomics Proteomics Disease Initiative (HGPI) session.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/15/version/1

Novel Techniques for Microspectroscopy and Chemical Imaging Analysis of Soybean Seeds and Embryos
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng  You; Doina M. Costescu.
Novel methodologies are currently being&amp;#xd;&amp;#xa;evaluated for the Chemical Analysis of&amp;#xd;&amp;#xa;soybean seeds as well as developing &amp;#xd;&amp;#xa;mature soybean embryos by FT-IR/NIR Microspectroscopy. This is the first report of FT-NIR Chemical Images obtained with 1 micron resolution. NIR spectra of Proteins, Oil and DNA fibers are obtained for regions as small as 1&amp;#x3bc;^2^.
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6591/version/1

Cholesterol Esterification During Differentiation by Hexamethylene Bisacetamide of Friend Virus-Induced Erythrokeukemia
Provedor de dados: 17
Autores: Maria  F. Mulas; Antonella Mandas; Claudia Abete; Sandra Dessi; Mario Pani; Rosa Manconi; Alessandra Mocali; Francesco Paoletti.
Cholesterol is an essential constituent of all mammalian cell membranes, and its availability is therefore a prerequisite for cellular growth and other functions. Several lines of evidence are now indicating an association between alterations of cholesterol homeostasis and cell cycle progression in cancer cells. However, the role of cholesterol in cell differentiation is still largely unknown. To begin to address this issue, in this study we examined changes in cholesterol metabolism and in the mRNA levels of proteins involved in cholesterol import and esterification (multi-drug resistance, MDR-3) and acylCoA:cholesterol acyltransferase (ACAT) and cholesterol export (caveolin-1) in Friend virus-induced erythroleukemia cells (MELC), in the absence or in the...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5155/version/1

Water and the Biology of Prions and Plaques
Provedor de dados: 17
Autores: Graham K. Steel; Phillippa M. Wiggins.
This  is  an  attempt  to  account  for  the  insolubility  and/or  aggregation  of  prions  and plaques  in  terms  of  a  model  of  water  consisting  of  an  equilibrium  between  high &amp;#xd;&amp;#xa;density  and  low  density microdomains. Hydrophobic molecules,  including proteins, &amp;#xd;&amp;#xa;accumulate  selectively  into  stable  populations,  enriched  in  high  density  water,  at &amp;#xd;&amp;#xa;charged  sites on  biopolymers.  In enriched  high density water, proteins are probably &amp;#xd;&amp;#xa;partially unfolded and may precipitate  out when  released. All extracellular matrices &amp;#xd;&amp;#xa;contain such charged polymers. Prions, which have been shown to accumulate in soils &amp;#xd;&amp;#xa;and  clays  containing...
Tipo: Manuscript
Palavras-chave: Microbiology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1381/version/1

Protein folding disorders: Toward a basic biological paradigm
Provedor de dados: 17
Autores: Rodrick Wallace.
Mechanistic &amp;#x27;physics&amp;#x27; models of protein folding fail to account for the observed spectrum of protein folding and aggregation disorders, suggesting that a more appropriately biological paradigm will be needed for understanding the etiology, prevention, and treatment of these diseases.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4344/version/1

Why not &amp;#x22;do simple things in a simple way&amp;#x22;: Use of the Pap test as the first step in screening genetic stability for human cultured stem cell therapy?
Provedor de dados: 17
Autores: Katherine Athayde Teixeira de Carvalho; Ana Carolina Irioda; Larissa Zocche; Carolina Maria Costa de Oliveira Souza; Reginaldo J. Ferreira; Eduardo Aliprandini; Ricardo C Cunha; Julio C Francisco; Luiz Cesar Guarita-Souza; Mariester Malvezzi; Miriam Beltrame; Lismary Mesquita; Diogo Kuczera; Rafael Vargas.
The aim of this study was to analyze adipose tissue-derived mesenchymal stem cells (AT-MSCs) using the Pap test as a first screening step to evaluate genetic stability. Human adipose tissue from six healthy female donors was obtained from elective liposuction procedures. The cells were isolated, cultivated at P2/P3, characterized by flow cytometric analysis, and differentiation induced. The AT-MSCs were stained by Papanicolaou staining and analyzed according to the Bethesda classification, and viability-apoptosis relationships were evaluated. The results of the Pap test for Sample I indicated high-grade alterations consistent with genetic instability; for Samples II-V, atypical cells of undetermined significance; and for Sample VI, normal cells. These...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5676/version/1

Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing Competences of Viruses
Provedor de dados: 17
Autores: Guenther Witzany.
Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial competences derive from the aptitude of viruses for natural genome editing....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1738/version/2

THE EFFECT OF HEPARIN ON THE CELL CYCLE IN HUMAN B-LYMPHOBLASTS: AN IN VITRO STUDY
Provedor de dados: 17
Autores: Ayse Aksoy; Erol Erduran; Yusuf Gedik.
Heparin has an apoptotic effect in addition to its anticoagulant, anti-inflammatory, antihypertensive, and antiproliferative effects. In this study, we detected the effect of heparin on the cell cycle of lymphoblasts by flow cytometry (FCM) and tried to determine which phase in the cell cycle of lymphoblasts contains heparin-sensitive points. Twelve children with newly diagnosed acute lymphoblastic leukemia (ALL) were included in the study. Lymphoblasts were incubated in different levels of heparin concentrations (0, 10, and 20 U/mL) and the percentages of lymphoblasts at each phase of the cell cycle were simultaneously measured by FCM at 0, 1, and 2 hours (h). The percentages of lymphoblasts at the G2/M and S phases were significantly increased in 20 U/mL...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1989/version/1

What are the ethical and social responsibilities of scientists?
Provedor de dados: 17
Autores: Philip Campbell.
Presented as part of the session titled &amp;#x22;Sharing scientific data: who benefits?&amp;#x22; at ESOF (The Euroscience Open Forum) 2008.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Session abstract: Digital datasets&amp;#x2014;text-based, numeric, audio, video or image-based&amp;#x2014;form the output of all scientific disciplines. How are these data being made available for sharing? What quality control mechanisms are in place? What kinds of naming conventions, tags, and metadata are in use and how effective are they at helping to manage open data? Who is storing, archiving and curating open data and at which levels? And how is the production and sharing of open data assessed: what processes are in place for crediting scientists for making their raw data...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2176/version/1

Intact mitochondria migrate in membrane tubular network connections formed between human stem cells
Provedor de dados: 17
Autores: Attila Csordas; Attila Cseleny&amp;#xe1;k; Ferenc Uher; Marianna Mur&amp;#xe1;nyi; Simone Hennerbichler; Heinz Redl; M&amp;#xe1;rk Kollai; Zsombor Lacza.
The hypothesis of mitochondrial transfer between eukaryotic animal cells is intriguing, although its route of action and physiological role is unknown. Our goal was to examine intercellular connections among several types of stem cells and to observe whether intact functional mitochondria may travel via these connections. Time-lapse laser scanning confocal microscopy has shown that human amnion-derived stem cells as well as bone marrow derived mouse and human mesenchymal stem cells form cell-to-cell connections via a tubular membrane network. The maximal length of these micrometer-thick tubes is around 180 ?m. Interestingly, freshly isolated amniotic epithelial stem cells did not form these connections, only after several passages when the morphology of...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/44/version/1

Cell Adhesion: A surprising cohesive force
Provedor de dados: 17
Autores: Hugues H. Vasseur.
When an experimentalist or a biological mechanism applies an external force onto a cell chemically sticking to its substrate, a reacting &amp;#x22;suction&amp;#x22; force, due to the slow penetration of the surrounding fluid between the cell and the substrate, opposes to the dissociation. This force can overcome other known adhesive forces when the process is sufficiently violent (typically 10^5^ pN). Its maximal contribution to the total adhesive energy of the cell can then be estimated to 2 10^-3^ J/m2. The physical origin of this effect is quite simple, and it may be compared with that leaning a &amp;#x22;suction-cup&amp;#x22; against a bathroom wall. We address the consequences of this effect on (i) the separation energy, (ii) the motion of the fluid...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1416/version/1

On the social induction of Alzheimer&amp;#x27;s disease: An index theorem aging model for amyloid formation
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
The central &amp;#x27;risk factor&amp;#x27; for Alzheimer&amp;#x27;s disease (AD) is age. From first principles, we construct a mathematical model of protein folding and its in vivo regulation that gives this result in a natural manner. We extend the basic approach using topological information theory methods, and examine a case history of socially-induced premature aging in the United States.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6012/version/1

A multiple-instance scoring method to predict tissue-specific cis-regulatory motifs and regions
Provedor de dados: 17
Autores: Jin Gu.
Transcription is the central process of gene regulation. In higher eukaryotes, the transcription of a gene is usually regulated by multiple cis-regulatory regions (CRRs). In different tissues, different transcription factors bind to their cis-regulatory motifs in these CRRs to drive tissue-specific expression patterns of their target genes. By combining the genome-wide gene expression data with the genomic sequence data, we proposed multiple-instance scoring (MIS) method to predict the tissue-specific motifs and the corresponding CRRs. The method is mainly based on the assumption that only a subset of CRRs of the expressed gene should function in the studied tissue. By testing on the simulated datasets and the fly muscle dataset, MIS can identify true...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4038/version/1

Chloroplast and Cell Imaging at Submicron Resolution by Two-Photon Excitation
Provedor de dados: 17
Autores: I C. Baianu.
Novel, two-photon NIR excitation fluorescence correlation microspectroscopy tests and preliminary results were presented in this article with submicron resolution for concentrated suspensions of functional cells and chloroplast membranes. Related developments of these technique involve applications of Fluorescence Cross-Correlation Spectroscopy (FCCS) detection to monitoring: &amp;#xd;&amp;#xa;DNA- telomerase interactions, DNA hybridization kinetics, ligand-receptor interactions, and HIV-HBV testing. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7116/version/1

Cancer Clinical Trials Optimization and Pharmacogenomics
Provedor de dados: 17
Autores: I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7046/version/1

Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome
Provedor de dados: 17
Autores: Michael D. Barton; Balazs Papp; Daniel Delneri; Stephen G. Oliver; Magnus Rattray; Casey M. Bergman.
Proteins vary in their cost to the cell and natural selection may favour the use of proteins that are cheaper to produce. We develop a novel approach to estimate the amino acid biosynthetic cost based on genome-scale metabolic models, and directly investigate the effects of biosynthetic cost on transcriptomic, proteomic and metabolomic data in _Saccharomyces cerevisiae_. We find that our systems approach to formulating biosynthetic cost produces a novel measure that explains similar levels of variation in gene expression compared with previously reported cost measures. Regardless of the measure used, the cost of amino acid synthesis is weakly associated with transcript and protein levels, independent of codon usage bias. In contrast, energetic costs...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1841/version/1

Nitric oxide synthase in skeletal muscle fibres of patients with type 2 diabetes
Provedor de dados: 17
Autores: Karla Punkt; Katharina Kandt; Andreas Oberbach; Volker Adams; Igor Buchwalow; Matthias Blueher.
Muscle-derived nitric oxide (NO) mediates fundamental physiological actions on skeletal muscle including glucose uptake into muscle cells. Recently, we have shown that the altered glucose metabolism in skeletal muscle of patients with type 2 diabetes (T2D) is associated with changes in the metabolic profile of individual muscle fibres, but fibre-type specific changes in NO synthase (NOS) expression in skeletal muscle of T2D patients remain to be elucidated. Here we investigated fibre-type related NOS expression in vastus lateralis muscle of T2D patients compared with healthy individuals with normal glucose tolerance (NGT). Cytophotometrical assay and Western blotting did not reveal any quantitative differences between NOS expression in muscles from NGT and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7049/version/1

Analysis of acceptance of bacillus to various heavy metals and antibiotics
Provedor de dados: 17
Autores: Yamini Singh  Sisodia; Vivek  Bajpai; Deeksha  Gaur; Pankaj Kumar  Jain.
The present study was carried out to systematically examine the pathogenic microorganisms in sewage samples isolated from the Shekhawati region of Rajasthan. In this survey, 26 bacterial strains were isolated and identified using biochemical and molecular methods. Molecular identification of isolates was done by DNA isolation, PCR amplification using 16S rDNA primer and partial sequencing of purified product after sequencing, out of 26, 10 sequences were submitted to NCBI. Out of these 10 isolates Bacillus pumilis, Bacillus subtilis and Bacillus licheniformis were taken for further studies. There is growing awareness of the need for development of new antimicrobial agents for the treatment of human, animal and plant diseases. Keeping this fact in mind, we...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7073/version/1

Opposite effects of two zinc(II) dithiocarbamates on NF-kB pathway
Provedor de dados: 17
Autores: Boris Cvek; Zdenek Dvorak; Jan Taraba; Lukas Muller; Radim Vrzal; Jitka Ulrichova.
Inhibiting nuclear factor-kappaB (NF-kB) activation in anticancer and antiinflammatory therapy is of topical interest. Current research in molecular biology has dramatically advanced in the understanding of the cellular events involved in NF-kB induction. Dithiocarbamates, in particular diethyldithiocarbamate and pyrrolidinedithiocarbamate, have been known and widely used as strong inhibitors of NF-kB signaling pathway for more than ten years. Their activity is frequently thought to be due to chelating of zinc or copper present in serum supplemented in the culture medium. Zinc(II) diethyldithiocarbamate (Et2Zn) and zinc(II) dibenzyldithiocarbamate (Bz2Zn) were prepared by direct synthesis in aqueous millieu. They were structurally characterized by X-ray...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/735/version/1

HMGA1a induces aberrant splicing of estrogen receptor &amp;#x3b1; in MCF-7 breast cancer cells
Provedor de dados: 17
Autores: Kenji Ohe; Toshiaki Utsumi; Akila Mayeda.
The well known transcription factor, HMGA1a, also known as an oncogene, causes aberrant splicing of Presenilin-2 found in sporadic Alzheimer&amp;#x27;s disease, through sequence specific RNA binding. Since HMGA1 protein levels correlate with tumorigenic malignancy, we are interested in the potential of HMGA1a as an aberrant splicing factor in cancer. The N-terminal truncated isoform of Estrogen Receptor alpha, ER&amp;#x3b1;46, is known to increase expression when breast cancer cells (MCF-7) become hyperconfluent. Transiently expressed HMGA1a induced ER&amp;#x3b1;46 mRNA expression. Plasmid driven micro RNA containing the presenilin-2 HMGA1a RNA binding site and a micro RNA nuclear localization signal (miR_HMGBS_NLS), inhibited ER&amp;#x3b1;46 mRNA...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4104/version/2

Smoking-induced long-lasting modifications of human platelet serotonin catabolism through a MAO epigenetic regulation
Provedor de dados: 17
Autores: Jean-Marie Launay; Muriel  Del Pino; Gilles Chironi; Jacques Callebert; Katell Peoc&amp;#x27;h; Jean-Louis M&amp;#xe9;gnien; Jacques Mallet; Alain  Simon; Francine Rendu.
Postulating that serotonin, secreted from smoking-activated platelets, could be involved in smoking-induced vascular modifications, we studied 115 men distributed in smokers (S), former smokers (FS) and never smokers (NS). The platelet serotonin content was similar in S and NS but lower in FS. This was unexpected because the monoamine oxidase (MAO) activity, which catabolizes serotonin, was inhibited during smoking. However, the amount of platelet MAO was higher in S and FS than in NS. The persistent elevated MAO amount in FS prompted us to study the methylation of its gene promoter in an additional series of patients: it was markedly lower for S and FS vs. NS due to cigarette smoke-induced increase of nucleic acid demethylase activity. This...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2113/version/1

Eukaryotic translation initiation machinery can operate in a prokaryotic-like mode without eIF2
Provedor de dados: 17
Autores: Ivan N. Shatsky; Ilya Terenin; Sergey Dmitriev; Dmitri Andreev.
Unlike prokaryotes, a specialized eukaryotic initiation factor 2 (eIF2), in the form of the ternary complex eIF2*GTP*Met-tRNAiMet is utilized to deliver the initiator tRNA to the ribosome within all eukaryotic cells1. Phosphorylation of eIF2 is known to be central to the global regulation of protein synthesis under stress conditions and infection2. Another distinctive feature of eukaryotic translation is scanning of mRNA 5&amp;#x27;-leaders, whose origin in evolution may be relevant to the appearance of eIF2 in eukaryotes. Translation initiation on the hepatitis C virus (HCV) internal ribosome entry site (IRES) occurs without scanning3,4. Whether these unique features of the HCV IRES account for the formation of the final 80S initiation complex is unknown....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1518/version/1

Myosin VI Lever Arm Rotation: Fixed or Variable?
Provedor de dados: 17
Autores: Yujie Sun; Harry  W. Schroeder III; John  F. Beausang; Kazuaki Homma; Mitsuo Ikebe; Yale  E. Goldman.
Two recent articles addressed the power-stroke of myosin VI molecules during stepping. Although both groups measured the angles of fluorescent probes attached on the myosin VI molecule lever arm using polarized fluorescence techniques, they differ about whether the myosin VI lever arm rotation is fixed1 or variable2. Here we discuss the causes of the discrepancy between the two studies and the implications for myosin VI processive motility.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4182/version/1

Comparison of Cholesterol Lowering Diets: Apple, Casein Cytochrom P450 protein and Cholesterol 7&amp;#x3b1; Hydroxylase Activities in Hamsters
Provedor de dados: 17
Autores: Rakesh  Sharma; Rakesh K. Tandon.
Lithogenic diet, casein and apple fiber diets were fed to hamsters for 3-5 weeks. For control group, animals were fed on normal Purina chow without any supplement. The cholesterol lowering effect of lithogenic diet, casein and apple diets were compared. After dietary regimen, animals were screened for any gall stone formation. The isolated liver microsomes were separated from animals and tested for the cholesterol-7&amp;#x3b1; Hydroxylase (CH) enzyme activity measurement in all three groups. The control animals did not show any gall stone formation and their CH enzyme activities were normal. The lithogenic diet showed significantly enhanced CH enzyme activities while animals fed on casein and apple diet regimen showed moderate increase in microsomal CH...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4205/version/1

Molecular Models of DNA Structures and Dynamics: Principles, Techniques and Applications
Provedor de dados: 17
Autores: I. C. Baianu.
Molecular models of DNA structures are representations of the molecular geometry and topology of Deoxyribonucleic acid (DNA) molecules using one of several means, such as: closely packed spheres (CPK models) made of plastic, metal wires for &amp;#x27;skeletal models&amp;#x27;, graphic computations and animations by computers, artistic rendering, and so on, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7075/version/1

Quantification of miRNAs and Their Networks in the light of Integral Value Transformations
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; Arunava  Goswami; Navonil De Sarkar; Vrushali Fangal.
MicroRNAs (miRNAs) which are on average only 21-25 nucleotides long are key post-transcriptional regulators of gene expression in metazoans and plants. A proper quantitative understanding of miRNAs is required to comprehend their structures, functions, evolutions etc. In this paper, the nucleotide strings of miRNAs of three organisms namely Homo sapiens (hsa), Macaca mulatta (mml) and Pan troglodytes (ptr) have been quantified and classified based on some characterizing features. A network has been built up among the miRNAs for these three organisms through a class of discrete transformations namely Integral Value Transformations (IVTs), proposed by Sk. S. Hassan et al [1, 2].  Through this study we have been able to nullify or justify one given nucleotide...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6035/version/2

Food Physical Chemistry and Biophysical Chemistry
Provedor de dados: 17
Autores: I.C. Baianu.
Food Physical Chemistry is considered to be a branch of Food Chemistry^1,2^ concerned with the study of both physical and chemical interactions in foods in terms of physical and chemical principles applied to food systems, as well as the applications of physical/chemical techniques and instrumentation for the study of foods^3,4,5,6^.  This field encompasses the &amp;#x22;physiochemical principles of the reactions and conversions that occur during the manufacture, handling, and storage of foods&amp;#x22;^7^. Two rapidly growing, related areas are Food Biotechnology and Food Biophysical Chemistry.  &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6573/version/1

Induction of Stress Granule Assembly is Essential for the Orchestration of DNA Damage Response
Provedor de dados: 17
Autores: Nicole S. Verkaik; Stephan Persengiev.
DNA damage provokes several responses including DNA repair, cell cycle regulation and apoptosis that collectively represent the DNA damage response (DDR). Here, we demonstrate that the DDR incorporates the activation of stress granule (SG) formation pathway as a mechanism to process destabilized RNAs. UV irradiation induced the assembly of SGs during the G2 phase and newly formed SGs appeared exclusively in the early G1 phase. SG assembly pathway was activated within the first hours after DNA damage, suggesting that the processing of destabilized RNAs is activated at an early stage. The induction of SGs and RNAi effector protein Argonaute 2 recruitment after UV exposure was independent of ATM and ATR signaling cascades. Apoptosis occurred only in...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1591/version/1

Phylogeny of conserved adenines in linkers of Group-I introns
Provedor de dados: 17
Autores: Natarajan Ganesan; Chandrasekhar Kesavan.
We have analyzed the linkers in group-I introns, a characteristic region that is crucial to the folding and splicing process of the folded RNA, in seventy sequences spreading across r-RNA, t-RNA and organelle genes from various organisms including algae, fungi and protozoa. The study revealed a high degree of consensus of specific adenine residues in J3/4, J6/7 and J8/7 stems of the linker regions that were required to stabilize the local orientation, either as single residue or by forming unusual base pairs along with divalent metal ions. Conservation of these residues in the Group-I intron linkers suggests their significant contribution to the folded structure whose bonding and geometry recruit metal ions to interact in stabilizing the folded nature of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2909/version/1

Endothelial Massive Calcium Accumulation Death (MCAD): Mechanism, Target, and Predictive Biomarker for Anti-Angiogenic Therapy
Provedor de dados: 17
Autores: Larry  Weisenthal.
We cultured human umbilical vein endothelial cells with bevacizumab, with tyrosine kinase inhibitors known to be AA, and with traditional cytotoxic drugs. The images below show that, in the presence of physiological saline and non-favorable culture conditions, the vast majority of the endothelial cells undergo a &amp;#x22;non-specific&amp;#x22; type of cell death (NSCD), not associated with calcium accumulation, but with loss of cell membrane integrity, allowing uptake of the Fast Green dye, staining these dead dells a pale blue green. In the presence of known AA agents (e.g. bevacizumab, some TK inhibitors) a large percentage of the endothelial cells undergo death associated with massive calcium accumulation (MCAD), with these cells staining...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6647/version/1

Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway
Provedor de dados: 17
Autores: Andrey Ptitsyn; Jeffrey Gimble.
*Background*&amp;#xd;&amp;#xa;It has been previously reported that most mammalian genes display a circadian oscillation in their baseline expression. Consequently, the phase and amplitude of each component of a signal transduction cascade has downstream consequences. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Results*&amp;#xd;&amp;#xa;We report our analysis of alternative transcripts in the leptin signaling pathway which is responsible for the systemic regulation of macronutrient storage and energy balance. We focused on the circadian expression pattern of a critical component of the leptin signaling system, suppressor of cytokine signaling 3 (SOCS3). On an Affymetrix GeneChip 430A2 microarray, this gene is represented by three probe sets targeting different...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/858/version/1

Circadian rhythmic kinase CK2&amp;#x3b1; phosphorylates BMAL1 to regulate the mammalian clock
Provedor de dados: 17
Autores: Teruya Tamaru; Jun Hirayama; Yasushi Isojima; Katsuya Nagai; Shigemi Norioka; Ken Takamatsu; Paolo Sassone-Corsi.
Clock proteins govern circadian physiology and their function is regulated by a variety of signaling pathways. Here, we show that p45^PFK^, a previously reported circadian rhythmic kinase, corresponds to CK2[alpha]. Rhythmic phosphorylation of the core clock protein BMAL1 by CK2[alpha] occurs in the suprachiasmatic nuclei (SCN), the mammalian central pacemaker. Circadian BMAL1 phosphorylation controls its nucleocytoplasmic localization. Gene silencing for CK2[alpha] and BMAL1 mutagenesis of a highly conserved CK2 phosphorylation site (Ser 90) result in impaired BMAL1 accumulation in the nucleus and subsequent disruption of clock function. These findings reveal that circadian rhythmic kinase CK2 is an essential regulator of the mammalian circadian system.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1702/version/1

Solvent Induced Disulfide Bond Formation in 2,5-dimercapto-1,3,4-thiadiazole
Provedor de dados: 17
Autores: Palanisamy Kalimuthu; Palraj Kalimuthu; S. Abraham John.
Disulfide bond formation is the decisive event in the protein folding to determine the conformation and stability of protein. To achieve this disulfide bond formation in vitro, we took 2,5-dimercapto-1,3,4-thiadiazole (DMcT) as a model compound. We found that disulfide bond formation takes place between two sulfhydryl groups of DMcT molecules in methanol. UV-Vis, FT-IR and mass spectroscopic as well as cyclic voltammetry were used to monitor the course of reaction. We proposed a mechanism for the solvent induced disulfide bond formation on the basis of the results we obtained.
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/734/version/1

Huntington&amp;#x2019;s disease is a TH17 related autoimmune disorder against mutant Huntingtin coded by multiple CAG triplets
Provedor de dados: 17
Autores: Wanchung(Wanjiung) Hu.
Huntington&amp;#x2019;s disease is an inherited neurodegenerative disorder. It belongs to the polyQ accumulation disease with mutant Huntington protein. The mutant Huntington has expanded CAG triplet repeats which make it easy to accumulate. However, the exact mechanism causing Huntington&amp;#x2019;s disease pathophysiology is unknown. Here, I propose that Huntington&amp;#x2019;s disease is an autoimmune disease. During childhood, there are Treg cells from the thymus to prevent autoimmune reaction against mutant Huntington. When the patient grows older with thymus atrophy, the accumulated mutant Huntington triggers TH17 related inflammatory reaction via heat shock proteins and toll-like receptor activation. Then, TH17 related cytokines such as...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6129/version/1

&amp;#x22;Ribopepzymes&amp;#x22; are probably a link from ribozymes to protein enzymes
Provedor de dados: 17
Autores: Yongjie Sheng; Dazhi Jiang; Zhen Zeng; Feng Pan; Jin Zhang.
The evolutionary relationship between RNA- and protein-based biocatalysts was key to the evolution of living systems. This relationship is thought to have depended upon the transfer of both genetic information and catalytic function in living systems. We investigated whether ribozymes could transfer genetic information and catalytic function at the chemical level. We identified a family of peptides encoded by ribozymes: 13-residue peptide encoded by the hammerhead ribozyme, a 19-residue peptide encoded by the genomic hepatitis delta virus (HDV+) ribozyme, a 25-residue peptide encoded by the antigenomic HDV (HDV-) ribozyme, a 15-residue peptide encoded by the smallest trans-acting genomic HDV (SHDV) ribozyme, and a 22-residue peptide encoded by an open...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1708/version/1

Osmotic stress and water isotope effects in kinesin-1 gliding motility assays
Provedor de dados: 17
Autores: Steven J. Koch; Andy Maloney; Lawrence J. Herskowitz.
The osmotic pressure and kinetic properties of water play important roles in biomolecular interactions.  As pointed out by Parsegian, Rand, and Rau, these crucial roles are often overlooked[1].  In some fields, osmotic stress and isotope effects have been exploited for probing the role water plays in binding interactions of biomolecules.  To our knowledge, there have been no studies of osmotic stress and water isotope effects for kinesin, and only a handful for myosin.  We&amp;#x27;re currently using the gliding motility assay to see whether we can extract new information about kinesin-1 / microtubule interactions by changing osmotic stress and water isotopes.  We will describe our open-source, automated analysis platform for extracting microtubule gliding...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4479/version/1

Fuzzy logic as a decision-making support system for the indication of bariatric surgery based on an index (MAFOI) generated by the association between body fat and body mass index.
Provedor de dados: 17
Autores: Susana A. Miyahira; Joao L. M. C. Azevedo; Jos&amp;#xe9;  E. Araujo Filho.
Background: A fuzzy obesity index (MAFOI) for use as an alternative to bariatric surgery indication (BSI) is presented. The search for a more accurate method to evaluate obesity and to indicate a better treatment is important in the world health context. BMI (body mass index) is considered the main criteria for obesity treatment and BSI. Nevertheless, the fat excess related to the percentage of Body Fat (%BF) is actually the principal harmful factor in obesity disease that is usually neglected. This paper presents a new fuzzy mechanism for evaluating obesity by associating BMI with %BF that yields a fuzzy obesity index for obesity evaluation and treatment and allows building up a Fuzzy Decision Support System (FDSS) for BSI. Methods: Seventy-two patients...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5516/version/2

A Rate Distortion approach to protein symmetry
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry breaking argument is applied to the problem of protein folding, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein molten globule. In the &amp;#x27;energy&amp;#x27; picture, the average distortion between codon message and protein structure, under constraints driven by evolutionary selection, serves as a temperature analog, so that low values limit the possible distribution of protein forms, producing the canonical folding funnel. A dual &amp;#x27;developmental&amp;#x27; perspective sees the rate distortion function itself as the temperature analog, and permits incorporation of chaperons or toxic exposures as catalysts, driving the system to different possible outcomes or...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4280/version/2

TATA binding protein binds to single stranded DNA: A new model for eukaryotic transcription
Provedor de dados: 17
Autores: Rostem J. Irani.
Although the players mediating the initiation of eukaryotic transcription appear to be known, the mechanism is not. In this paper we report findings on the interaction between the TATA box binding protein (TBP) and DNA, using a novel optical technology, that point to a potential plausible physical mechanism, and at the same time tie together a number of otherwise disparate observations. TBP plays a central and ubiquitous role in initiating eukaryotic transcription, binding to promoters with and without the canonical 5&amp;#x2019; TATA(A/T)A(A/T)(G/A) 3&amp;#x2019; motif1. It also tends to bind to double-stranded DNA promiscuously, and though affinity is lower, the number of binding opportunities is greater. TBP-DNA complexes have been characterized...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4139/version/1

Speed effects in gliding motility assays due to surface passivation, water isotope, and osmotic stress.
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
The molecular motor kinesin-1, an ATPase, and the substrate it walks along, microtubules, are vital components of eukaryotic cells. Kinesin converts chemical energy to linear motion as its two motor domains step along microtubules in a process similar to how we walk. Cells create systems of microtubules that direct the motion of kinesin. This directed motion allows kinesin to transport various cargos inside cells.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;During the stepping process, the kinesin motor domains bind and unbind from their binding sites on the microtubules.  Binding and unbinding rates of biomolecules are highly dependent on hydration and exclusion of water from the binding interface. Osmotic stress will likely strongly affect the binding and...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4469/version/1

Genetic vehicle comprising majority of lowly expressed genes guides cell fate decision
Provedor de dados: 17
Autores: Masa Tsuchiya; Vincent Piras; Masaru Tomita; Alessandro Giuliani; Kumar Selvarajoo.
Cells remarkably take a specific differentiation path among the multiple possibilities that can arise through the multi-dimensional regulation of genome activities. Such deterministic processes suggest the existence of cellular attractors.  However, the origins and drivers of the attractors still remain elusive. Here we analyzed the temporal neutrophil differentiation microarray data for two different stimuli, dimethyl sulfoxide (DMSO) and all-trans-retinoic acid (atRA), and expressed their collective dynamics by temporal Pearson correlation and mutual information coordinates. We constructed ensemble of the genes which showed reduction of correlation fluctuations following the inverse square root law. Evaluating their temporal probability density...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4401/version/1

Creatine kinase in energy metabolic signaling in muscle
Provedor de dados: 17
Autores: Olav Kongas; Johannes H. G. M. van Beek.
There has been much debate on the mechanism of regulation of mitochondrial ATP synthesis to balance ATP consumption during changing cardiac workloads. A key role of creatine kinase (CK) isoenzymes in this regulation of oxidative phosphorylation and in intracellular energy transport had been proposed, but has in the mean time been disputed for many years. It was hypothesized that high-energy phosphoryl groups are obligatorily transferred via CK; this is termed the phosphocreatine shuttle. The other important role ascribed to the CK system is its ability to buffer ADP concentration in cytosol near sites of ATP hydrolysis. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Almost all of the experiments to determine the role of CK had been done in the steady state, but...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1317/version/1

Allicin from garlic suppresses TNF-&amp;#x3b1; and augments IFN-&amp;#x3b3; expressions in monocyte cultures from patients with Vaginitis
Provedor de dados: 17
Autores: Najmul Islam; Jawed Iqbal; Nazarul Hasan; Zeeshan Fatima; Hamida Thakur; Nazia Hasan; Abbas Ali Mahdi; Tamkin Khan; Farzana Bano; Irfan Ahmad Ansari.
Objective: We tried to explore beneficial effects of allicin- a natural antioxidant from garlic in the possible management of vaginitis. &amp;#xd;&amp;#xa;Methods: Peripheral blood mononuclear cells (PBMC&amp;#x2019;s) were isolated from blood of patients having vaginal infections as well as normal healthy subjects as per our published protocol. Monocytes (MN&amp;#x2019;s) from above PBMC&amp;#x2019;s were adhered, rested overnight and cultured without or with varying doses of allicin (0-500 ng/ml). Some cultures received SN50 and SN50M (100 ug/ml). After 24 hrs cultures, the cells were harvested and the supernatants subjected to secreted TNF-&amp;#x3b1; and sIFN-&amp;#x3b3; assays by ELISA. Treated/untreated harvested cells were subjected to glutathione...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1560/version/1

Structure and function prediction of human homologue hABH5 of _E. coli_ ALKB5 using in silico approach
Provedor de dados: 17
Autores: shankaracharya shankaracharya; Saibal Das; Ambarish Sharan Vidyarthi.
Newly discovered human homologues of ALKB protein have shown the activity of DNA damaging drugs, used for cancer therapy. Little is known about the structure and function of hABH5, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeler 9v7 to predict the 3D structure of the hABH5 protein. 3-D model of hABH5, ALKBH5.B99990005.pdb was predicted and evaluated. Validation results showed 96.8% residues in favor and an additional allowed region of the Ramachandran plot. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, conserved pattern of Pro158-X-Asp160-Xn-His266 in the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5597/version/1

A novel alveolar Krebs cycle-triggered CO2 sensing mechanism regulates regional pulmonary ventilation.
Provedor de dados: 17
Autores: Rainer Kiefmann; Paula Keller; Oliver Tritt; Kai Heckel; Sascha Tank; Martina Kiefmann; Leoni Schulte-Uentrop; Alwin Goetz.
Pulmonary perfusion disorders provoke atelectasis in order to minimize ventilation/perfusion mismatch. However, the underlying mechanisms remain unknown. Because intraalveolar CO2 concentration ([CO2]iA) declines as a consequence of poor pulmonary perfusion we postulated the existence a novel alveolar CO2-sensing mechanism which adapts the ventilation to perfusion. Real-time fluorescence imaging of rat lungs revealed that low [CO2]iA decreased cytosolic and increased mitochondrial Ca2+ in alveolar epithelial cells (AEC), leading to reduction of surfactant secretion and alveolar ventilation. Mitochondrial inhibition by ruthenium red or rotenone blocked the hypocapnia-induced responses. In cultured Type 2 AEC hypocapnia decreased cytosolic Ca2+ independently...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6185/version/1

Some Secrets of Fluorescent Proteins: Distinct Bleaching in Various Mounting Fluids and Photoactivation of cyan fluorescent proteins at YFP-Excitation
Provedor de dados: 17
Autores: Johannes Schmid; Naila Malkani.
Background&amp;#xd;&amp;#xa;The use of spectrally distinct variants of green fluorescent protein (GFP) such as cyan or yellow mutants (CFP and YFP, respectively) is very common in all different fields of life sciences, e.g. for marking specific proteins or cells or to determine protein interactions. In the latter case, the quantum physical phenomenon of fluorescence resonance energy transfer (FRET) is exploited by specific microscopy techniques to visualize proximity of proteins.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methodology/Principal Findings&amp;#xd;&amp;#xa;When we applied a commonly used FRET microscopy technique - the increase in donor (CFP)-fluorescence after bleaching of acceptor fluorophores (YFP), we obtained good signals in live cells, but very...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4517/version/2

Inhibition of Acid Phosphatase Enzyme Activity in the Presence of Noncrystalline Calcium Phosphate and Nanocrystalline Calcium Apatite: a Preliminary Study
Provedor de dados: 17
Autores: Yassen Pekounov.
_Background_&amp;#xd;&amp;#xa;Our bones are remodelled repeatedly throughout life. New and &amp;#x201c;healthy&amp;#x201d; bone tissue replaces the old one. It has been shown that the bone degrading cells, the osteoclasts, prefer old and fatigued bone. The young bone mineral, i.e. calcium apatite, is less crystalline than the mature one. Is it possible that the osteoclasts distinguish between relatively old and new bone via its mineral crystallinity?&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;_Methodology/Principal Findings_&amp;#xd;&amp;#xa;Acid phosphatase is an enzyme abundantly expressed by the osteoclasts during resorption and therefore used as a marker of the cells&amp;#x2019; activity. This study explores whether its enzymatic activity would be decreased in...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/3658/version/2

Adenovirus-mediated transfer of siRNA against survivin enhances the radiosensitivity of human non-small cell lung cancer cells
Provedor de dados: 17
Autores: Cheng-Ta Yang; Jhy-Ming Li; Hsu-Huei Weng; Ya-Chin Li; Miao-Fen Chen.
Expression of survivin has been reported to be correlated with shorter survival in patients with non-small cell lung cancer (NSCLC), and overexpression of survivin may lead to radioresistance in various human cancers. In this study, we inhibited survivin expression by using an adenoviral vector (AdsiSurvivin)-mediated RNAi to elucidate the combined effect of survivin-targeting gene therapy and radiotherapy on the NSCLC cells. Our data revealed that AdsiSurvivin exerted survivin gene silencing, induced apoptosis, and significantly attenuated the growth potential in NSCLC cells within 72 hours after infection. The combined treatment modalities with AdsiSurvivin infection and radiation were significantly more potent on cell-growth inhibition than monotherapy....
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2589/version/1

An RNA _cis_-element upstream of the HMGA1a binding site affects exon exclusion caused by HMGA1a
Provedor de dados: 17
Autores: Kenji Ohe; Takayuki Manabe; Taiichi  Katayama; Masaya Tohyama; Akila Mayeda.
In addition to its characteristics as a DNA binding transcription factor, HMGA1a is known to bind RNA, sequence specifically and regulate aberrant splicing of the _Presenilin-2_ gene in sporadic Alzheimer&amp;#x2019;s disease^1,2^. We show here that an RNA _cis_-element, immediately upstream the HMGA1a binding site, induces exon inclusion upon mutating a GU sequence to CA. Psoralen mediated UV crosslinking showed U1 snRNP did not bind this sequence but oligonucleotide-mediated RNase H digestion showed it important for U1 snRNP to recognize the authentic 5&amp;#x2019; splice site. This sequence (5&amp;#x2019;-AAGUAC-3&amp;#x2019;) was tested for hnRNPA1 binding and function. Coimmunoprecipitation of endogenous HMGA1a and hnRNPA1 in HeLa nuclear extract,...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4119/version/1

(Corrected) Osmotic stress and water isotope effects in kinesin-1 gliding motility assays
Provedor de dados: 17
Autores: Steven J. Koch; Andy Maloney; Lawrence J. Herskowitz.
The osmotic pressure and kinetic properties of water play important roles in biomolecular interactions.  As pointed out by Parsegian, Rand, and Rau, these crucial roles are often overlooked[1].  In some fields, osmotic stress and isotope effects have been exploited for probing the role water plays in binding interactions of biomolecules.  To our knowledge, there have been no studies of osmotic stress and water isotope effects for kinesin, and only a handful for myosin.  We&amp;#x27;re currently using the gliding motility assay to see whether we can extract new information about kinesin-1 / microtubule interactions by changing osmotic stress and water isotopes.  We will describe our open-source, automated analysis platform for extracting microtubule gliding...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4479/version/2

Modeling miRNA regulation in signaling networks: miR-34a regulation of the p53/Sirt1 module
Provedor de dados: 17
Autores: Xin Lai.
Micro RNAs are a family of small regulatory RNAs whose function is to regulate the activity and stability of specific messenger RNA targets through post-translational regulatory mechanisms. We studied a signaling module composed by p53, Sirt1 and the small regulatory miRNA, miR-34a, based on the integration of experimental evidence and quantitative data, with mathematical modeling. We further used the model to investigate different possible designs of the silencing mechanisms exerted by miR-34a on Sirt1, and to simulate the dynamics of the system under pathological conditions of deregulation of its components. &amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5123/version/1

Upstream Stimulatory Factor (USF) and CCAAT/Enhancer Binding Protein &amp;#x3b4; (C/EBP&amp;#x3b4;) Compete for overlapping Sites in the Negative Regulatory Region of the HIV-1 LTR
Provedor de dados: 17
Autores: Torik T. A. Ayoubi; Sandra M. P. Meulemans; Wim W. J. M. Van de Ven.
Human immunodeficiency virus type 1 (HIV-1) is a human retrovirus and the causative agent of the acquired immunodeficiency syndrome. Genetic analysis has revealed that the HIV-1 LTR contains a potential negative regulatory element (NRE) with an E box, the recognition sequence for the helix-loop-helix (HLH) family of transcription factors. Furthermore, the upstream stimulatory factor (USF) has been implicated as a negative regulator of HIV-1 expression. Here, we report that the NRE is a composite element and that both C/EBP&amp;#x3b4; and USF can specifically bind to the NRE. The recognition sequence for C/EBP&amp;#x3b4; overlaps with the E box in the NRE of HIV-1. Competition experiments showed that either USF or C/EBP&amp;#x3b4; binds to this NRE but not...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1212/version/1

Soybean Composition Database from NIR, NMR and GC-MS Analyses- (v.3)
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Jun Guo; Doina M. Costescu; V. I. Prisecaru.
This novel Soybean Composition Database from the AFC-NMR &amp;#x26; NIR Spectroscopy Facility of the College of ACES at the University of Illinois at Urbana includes more than 12,000 NIR measurements on soybeans from the International Soybean Germplasm Collection, such as those received from Peking at the National Soybean Collection.&amp;#xd;&amp;#xa;Excel files (.xls) of our novel spectroscopic data are currently available for all 80,000 + NIR and FT-NMR measurements; such data are made available from an ultra-fast and secure supercomputer server utilizing the current version of the Scientific-Linux OS-based software. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A detailed account is also presented of our high-resolution nuclear magnetic resonance (HR-NMR) and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6201/version/3

Determination of Soybean Oil, Protein and Amino Acid Residues in Soybean Seeds by High Resolution Nuclear Magnetic Resonance (NMRS) and Near Infrared (NIRS)
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng  You; Doina Costescu; P R. Lozano; Valentin Prisecaru; Randall   L. Nelson.
A detailed account is presented of our high resolution nuclear magnetic resonance (HR-NMR) and near infrared (NIR) calibration models, methodologies and validation procedures, together with a large number of composition analyses for soybean seeds. NIR calibrations were developed based on both HR-NMR and analytical chemistry reference data for oil and twelve amino acid residues in mature soybeans and soybean embryos. This is our first report of HR-NMR determinations of amino acid profiles of proteins from whole soybean seeds, without protein extraction from the seed.  It was found that the best results for both oil and protein calibrations were obtained with a Partial Least Squares Regression (PLS-1) analysis of our extensive NIR spectral data, acquired...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7053/version/1

Specification of spatial relationships in directed graphs of cell signaling networks
Provedor de dados: 17
Autores: Azi Lipshtat; Susana R. Neves; Ravi Iyengar.
Graph theory provides a useful and powerful tool for the analysis of cellular signaling networks. Intracellular components such as cytoplasmic signaling proteins, transcription factors and genes are connected by links, representing various types of chemical interactions that result in functional consequences. However, these graphs lack important information regarding the spatial distribution of cellular components. The ability of two cellular components to interact depends not only on their mutual chemical affinity but also on co-localization to the same subcellular region.  Localization of components is often used as a regulatory mechanism to achieve specific effects in response to different receptor signals.  Here we describe an approach for...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2038/version/1

A Rate Distortion approach to protein symmetry
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry breaking argument is applied to the problem of protein form, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein &amp;#x27;molten globule&amp;#x27;. The Rate Distortion Function, under coding constraints, serves as a temperature analog, so that low values act to drive proteins to simple symmetries. The Rate Distortion Function itself is significantly constrained by the availability of metabolic free energy. This work extends Tlusty&amp;#x27;s (2007) elegant exploration of the evolution of the genetic code, suggesting that rate distortion considerations may play a critical role across a broad spectrum of molecular expressions of evolutionary process.
Tipo: Manuscript
Palavras-chave: Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4280/version/1

Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation
Provedor de dados: 17
Autores: Benjamin Bouvier; Raik Gr&amp;#xfc;nberg; Michael Nilges; Frederic Cazals.
The accurate description of protein-protein interfaces remains a challenging task. Traditional criteria, based on atomic contacts or changes in solvent accessibility, tend to over or underpredict the interface itself and cannot discriminate active from less relevant parts. A recent simulation study by Mihalek and co-authors (2007, JMB 369, 584-95) concluded that active residues tend to be `dry&amp;#x27;, that is, insulated from water fluctuations. We show that patterns of `dry&amp;#x27; residues can, to a large extent, be predicted by a fast, parameter-free and purely geometric analysis of protein interfaces. We introduce the shelling order of Voronoi facets as a straightforward quantitative measure of an atom&amp;#x27;s depth inside an interface. We...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1522/version/1

Homeoprotein Hbx4 represses adhesion molecule governing cytokinesis and development
Provedor de dados: 17
Autores: Ji-Sun Kim; Ji-Hui Seo; Hyung-Soon Yim; Sa-Ouk Kang.
Homeobox genes encode proteins with a highly conserved DNA-binding motif and provoke morphological diversification of body segments by differentially controlling the expression of downstream targets. Here, we have identified _hbx4_, one of many homeobox genes in _Dictyostelium discoideum_ and investigated its role during growth and development. In suspension, Hbx4-overexpressing cells, Hbx4^OE^, showed defects in cytokinesis and growth rate. During development, Hbx4^OE^ and _hbx4_-disrupting cells, _hbx4&amp;#xaf;_ made differences in shape of mound and slug, cell-type proportioning from wild type KAx3 cells. These phenotypes were similar to those of mutant defective in _cadA_ encoding Ca^2+^-dependent cell adhesion molecule so that we investigated the...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4194/version/1

Creating a Translational Medicine Ontology
Provedor de dados: 17
Autores: Christine Denney; Colin Batchelor; Olivier Bodenreider; Sam Cheng; John Hart; John Hill; John Madden; Mark Musen; Elgar Pichler; Matthias Samwald; Sa&amp;#x301;ndor Szalma; Lynn Schriml; David Sedlock; Larisa Soldatova; Koji Sonoda; David Statham; Holger Stenzhorn; Patricia L. Whetzel; Elizabeth Wu; Susie Stephens.
*Abstract*&amp;#xd;&amp;#xa;We, participants in the Translational Medicine Ontology activity of the World Wide Web Consortium&amp;#x2019;s Health Care and Life Sciences Interest Group (&amp;#x22;http://esw.w3.org/topic/HCLSIG&amp;#x22;:http://esw.w3.org/topic/HCLSIG) and members of the National Center for Biomedical Ontology (&amp;#x22;http://bioontology.org/&amp;#x22;:http://bioontology.org/), are developing a high-level, patient-centric ontology for translational medicine which will draw on existing domain ontologies and allow the integration of data throughout the drug development process.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Introduction*&amp;#xd;&amp;#xa;The pharmaceutical industry has historically focused on the development of novel blockbuster drugs....
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3686/version/1

Check Your Data Freedom: A Taxonomy to Assess Life Science Database Openness
Provedor de dados: 17
Autores: Melanie Dulong de Rosnay.
Molecular biology data are subject to terms of use that vary widely between databases and curating institutions. This research presents a taxonomy of contractual and technical restrictions applicable to databases in life science. It builds upon research led by Science Commons demonstrating why open data and the freedom to integrate facilitates innovation and how this openness can be achieved. The taxonomy describes technical and legal restrictions applicable to life science databases, and its metadata have been used to assess terms of use of databases hosted by Life Science Resource Name (LSRN) Schema. While a few public domain policies are standardized, most terms of use are not harmonized, difficult to understand and impose controls that prevent others...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/2083/version/1

Novel role of substance-p as a systemic wound messenger to mobilize mesenchymal stem cell from bone marrow and be engaged in the wound healing epithelial layer
Provedor de dados: 17
Autores: Hyun Sook Hong; Jung Sun Lee; Young Sam Kwon; Eun Kyung Lee; Woosung Ahn; Jae Chan Kim; Youngsook Son.
Tissue injury may bring up the systemic participation of bone marrow stem cells in the repair. In this study, we report that substance-p is a systemically acting messenger to mobilize mesenchymal stem cell (MSC) probably from the bone marrow and be engaged in the wound healing process. This was supported by the injury-inducible substance-p detection in the tissue and the peripheral blood and subsequent MSC mobilization in the alkali-burn rabbit eye model, whose kinetics were dependent on the wound size. Furthermore, i.v. injection of exogenous substance-p stimulated MSC mobilization in the uninjured rabbits and those mobilized cells showed multipotent differentiation capacity. We demonstrated that earlier substance-p elevation in the circulation by...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1309/version/1

Evidence of mature adipocyte proliferation regulated by proliferin
Provedor de dados: 17
Autores: Kazuo Kajita; Ichiro Mori; Takayuki Hanamoto; Wu Zhiliang; Takahide Ikeda; Kei Fujioka; Masahiro Yamauchi; Hideyuki Okada; Aki Minami; Toshiko Kajita; Yoshihiro Uno; Hiroyuki Morita; Isao Nagano; Masao Takemura; Mitsuru Seishima; Yuzo Takahashi; Tatsuo Ishizuka.
Despite much research, whether mature adipocytes proliferate remains controversial. Here, we examined 5-bromo-2&amp;#x2032;-deoxyuridine (BrdU)-labelling of mature adipocytes. Although BrdU incorporation into subcutaneous adipocytes was less than that in visceral adipocytes, pioglitazone (Pio) treatment increased BrdU incorporation in subcutaneous, but not visceral, adipocytes in rats. Fully differentiated 3T3-L1 adipocytes exhibited an increase in cell number and BrdU incorporation with time, with this increase enhanced by Pio treatment. We therefore screened for genes that encode growth factors regulated by Pio, and selected proliferin (PLF). Both gene silencing of PLF by small interfering RNA and treatment with anti-PLF antibody suppressed proliferation...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4714/version/1

GabiPD: The GABI Primary Database - a plant integrative &amp;#x2018;omics&amp;#x2019; database
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Axel Nagel; Jost Neigenfind; Robert Wagner; Rico Basekow; Elke Weber; Bernd  Mueller-Roeber; Svenja Diehl; Birgit Kersten.
The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyse and visualise primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different &amp;#x2018;omics&amp;#x2019; fronts are incorporated (i.e., genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text based retrieval of all data types in GabiPD (e.g., clones, genes, mutant lines). All data...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2210/version/1

A coordinated phosphorylation cascade initiated by MSK1 directs RAR alpha recruitment to target gene promoters
Provedor de dados: 17
Autores: Nathalie Bruck; Dominique Vitoux; Christine Ferry; Vanessa Duong; Annie Bauer; Hughes de The; Cecile Rochette-Egly.
The nuclear retinoic acid (RA) receptor alpha (RAR&amp;#x3b1;) is a transcriptional transregulator that controls the expression of specific gene subsets through binding at response elements and dynamic interactions with coregulators, which are coordinated by the ligand. Here, we highlighted a novel paradigm in which the transcription of RAR&amp;#x3b1;-target genes is controlled by phosphorylation cascades initiated by the rapid RA activation of the p38MAPK/MSK1 pathway. We demonstrate that MSK1 phosphorylates RAR&amp;#x3b1; at S369 located in the Ligand Binding Domain, allowing the binding of TFIIH and thereby phosphorylation of the N-terminal domain at S77 by cdk7/cyclin H. MSK1 also phosphorylates Histone H3 at S10. Finally, the phosphorylation cascade...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2107/version/1

Mining Co-expression Graphs: Applications to MicroRNA Regulation and Disease Analysis
Provedor de dados: 17
Autores: Malay Bhattacharyya.
MicroRNAs (miRNAs) are known to translationally repress or post-transcriptionally regulate mRNAs and are responsible for many diseases. We are preparing a comprehensive framework of co-expression analysis to figure out co-expression, differential co-expression and co-expression dynamics within multiple phenotypes in expression profiles. The purpose is to elucidate the disease association of miRNAs via co-regulatory pattern analysis.
Tipo: Presentation
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7119/version/1

Organic consequences of ileal transposition in rats with diet-induced obesity
Provedor de dados: 17
Autores: Lucas P. F. F. Leal; Joao Luiz  M. C. Azevedo; Gilmara  S. Aguiar-Yamaguchi; Wellington  Cardia; Bianca  Marigliani; Karina  F. Neves; Paolo  H. B. Louren&amp;#xe7;o; Marcelo  C. Carlini; Joao  L. C. Azevedo; Ot&amp;#xe1;vio  C. Azevedo; Gui  M. Ko; Gustavo  P. S.  Miguel; Valderez  B. V.  Lapchick.
INTRODUCTION: The clinical management of metabolic syndrome - especially diabetes mellitus type 2 - is notoriously complex due to the progressive nature of this disease. At present, there is a need for a surgical procedure that is effective for the treatment of diabetes mellitus type 2, even in non-obese individuals. The isolated ileal transposition theory could lead to an effective alternative therapy. This intervention has not yet been performed in humans, and there are no reports of its use in an experimental model of diet-induced metabolic syndrome.&amp;#xd;&amp;#xa; OBJECTIVES: The objective of this study is to evaluate the physiological effects of ileal transposition in rats with diet-induced metabolic syndrome. The effects of this procedure on...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6122/version/1

LibSBGN: current status and future plans
Provedor de dados: 17
Autores: Alice C. Villeger.
LibSBGN is a community project started in 2009: it aims at facilitating the development of SBGN-compliant tools, and improving interoperability between these tools.&amp;#xd;&amp;#xa;These goals will be achieved by defining a standardized electronic implementation of the Systems Biology Graphical Notation: an XML-based file format (SBGN-ML), complemented by a software library (LibSBGN).&amp;#xd;&amp;#xa;The project is organized around a number of online tools, which allow the community to discuss problems, share ideas, and formalize solutions.&amp;#xd;&amp;#xa;Current versions of SBGN-ML and LibSBGN have already been adopted by three different SBGN-compliant tools. The first official release of SBGN-ML is imminent.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;For...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5304/version/1

The Evolution of Homochirality
Provedor de dados: 17
Autores: Rodrick Wallace.
It is possible to reconsider the origin of biological homochirality in a novel way by formally invoking the standard groupoid approach to stereochemistry in a thermodynamic context that generalizes Landau&amp;#x27;s spontaneous symmetry breaking arguments. On Earth, limited metabolic free energy may have served as a low temperature analog to &amp;#x27;freeze&amp;#x27; the system in the lowest energy state, i.e., the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in a Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process locked in this initial condition, in spite of increases in available metabolic free energy. Astrobiological outcomes, given higher...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Molecular Cell Biology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/3902/version/2

Living unicellular eukaryote Tetrahymena pyriformis as a model for study of mitochondrial energetics in mammalian cells under conditions of reduced oxidative metabolism.
Provedor de dados: 17
Autores: Elena Mokhova.
Some &amp;#x201c;animal-like&amp;#x201d; protozoa are used instead of mammalian cells in diverse investigations.  _Tetrahymena pyriformis_ cells in stationary phase of growth and washed from oxidative substrates (_T.pyriformis_) function under conditions of reduced oxidative metabolism. To elucidate if _T.pyriformis_ can be applied as a model for mitochondrial energetics study in   mammalian cells during hibernation, the features of _T.pyriformis_ mitochondria were compared with that of liver mitochondria isolated from hibernating animals; the published earlier data were used. Based on the respiration recording and observation of Mito Tracker Red fluorescence in living _T.pyriformis_ we tentatively concluded that the mitochondrial electrical membrane...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4521/version/1

(Corrected) Speed effects in gliding motility assays due to surface passivation, water isotope, and osmotic stress.
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
The molecular motor kinesin-1, an ATPase, and the substrate it walks along, microtubules, are vital components of eukaryotic cells. Kinesin converts chemical energy to linear motion as its two motor domains step along microtubules in a process similar to how we walk. Cells create systems of microtubules that direct the motion of kinesin. This directed motion allows kinesin to transport various cargos inside cells.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;During the stepping process, the kinesin motor domains bind and unbind from their binding sites on the microtubules.  Binding and unbinding rates of biomolecules are highly dependent on hydration and exclusion of water from the binding interface. Osmotic stress will likely strongly affect the binding and...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4469/version/2

Deficiency of interleukin-1 receptor antagonist causes spontaneous femoral artery aneurysms
Provedor de dados: 17
Autores: Kikuo Isoda; Tomiharu Niida; Harumi Kondo; Fumikaka Ohsuzu.
Interleukin (IL) -1, a proinflammatory cytokine, increases in aneurysm, and the IL-1 receptor antagonist (IL-1Ra) modulates IL-1 activity endogenously. We show here that IL-1Ra-deficiency in hematopoietic cells disrupts immune system homeostasis and causes spontaneous femoral artery aneurysms in mice lacking interventions such as drugs or surgery. Thus, IL-1Ra-deficient mice provide easy observations with age and diminish mortality that typically follows surgical procedures. Furthermore, since IL-1Ra-deficient mice contain the entire spectrum of lesions observed during inflammatory aneurysm, this mouse model likely will provide numerous opportunities to study the pathogenesis and therapy of inflammatory aneurysm.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2826/version/1

Multidrug resistance of non-adherent cancer cells
Provedor de dados: 17
Autores: Navneet  Singh; Subhas Chakrabarty; Guangming Liu.
Metastases are the cause of 90% of human cancer deaths. Cancer in _situ_ can usually be effectively removed by surgery. Once cancer cells disseminate from the original site and start to circulate in blood, lymph, or other body fluids, the disease becomes almost incurable. Here we show that cancer cells in a non-adherent, 3-dimentional growth pattern are highly drug resistant compared to their adherent counterparts that grow in monolayer, attaching to the wall of tissue culture plates. The non-adherent cancer cells retain the adhering potential and can attach to an appropriate surface to reacquire adherent phenotype. Once the non-adherent cancer cells become attached, they regain drug response, similar to the original adherent cells. A significant increase...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4488/version/1

Investigations on biological activity of Vetiveria zizanioides L. Nash, a palingenesis of some important findings in miracle grass
Provedor de dados: 17
Autores: Suaib Luqman.
Vetiveria zizanioides L. Nash synonymously known as Chrysopogon zizanioides L. Roberty (Family: Poaceae/Graminae), widely cultivated in the tropical regions of the world, is a miraculous grass native to India first developed for soil and water conservation by the World Bank during mid 1980s. Popularly known as &amp;#x2018;KHUS&amp;#x2019;, it is the major source of the well-known oil of vetiver, which is used in medicine, cosmetics and in perfumery making agarbattis, soaps, soft drinks, pan masala. Being a major constituent of &amp;#x2018;Rasayana&amp;#x2019; in Ayurveda, different parts of the vetiver plant have traditionally been used by the Indian tribes for treating various ailments, diseases and disorders including boils, burns, epilepsy, fever,...
Tipo: Poster
Palavras-chave: Cancer; Microbiology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6904/version/1

Isolated ileal interposition in enteroendocrine L cells differentiation
Provedor de dados: 17
Autores: Bianca Marigliani; Joao-Luiz  M. C. Azevedo; Lucas P. F. F. Leal; Ismael D. C. G. Silva; Valderez B. V. Lapchick; Sang W. Han; Karina F. Neves; Linda O. A. Bernardes; Gilmara S. A. Yamaguchi; Wellington Cardia; Jose F. Borborema; Joao L. C. Azevedo; Otavio C. Azevedo; Gustavo P. S. Miguel.
INTRODUCTION: &amp;#xd;&amp;#xa;Due to the progressive nature of type 2 diabetes, its complexity and drug treatment perpetuity, there is currently a search for surgical procedures that can promote euglycemia also in non-obese patients. Diabetic patients glycemic control can be achieved by increasing the blood concentration of GLP-1, a hormone produced by L cells that are more densely concentrated in the terminal ileum. Early and extended improvement of diabetes in patients submitted to bariatric surgeries awakened the necessity of investigating the isolated ileal interposition as surgical alternative for the treatment of diabetes. The interposition of this ileal segment to a more anterior region (proximal jejunum) can promote a greater stimulation of the L...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6614/version/2

Stop-and-go kinetics in amyloid fibrillation
Provedor de dados: 17
Autores: Jesper Ferkinghoff-Borg; Jesper Fonslet; Christian B. Andersen; Sandeep Krishna; Simone Pigolotti; Hisashi Yagi; Yuji Goto; Daniel Erik Otzen; Mogens H. Jensen.
Many human diseases are associated with protein aggregation and fibrillation. Using glucagon as a model system for protein fibrillation we show that fibrils grow in an intermittent fashion, with periods of growth followed by long pauses. Remarkably, even if the intrinsic transition rates vary considerably in each experiment, the probability of being in the growing (stopping) state is very close to 1/4 (3/4), suggesting the presence of 4 independent conformations of the fibril tip. We discuss this possibility in terms of existing structural knowledge.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4279/version/1

NIR Calibrations for Soybean Seeds and Soy Food Composition Analysis: Total Carbohydrates, Oil, Proteins and Water Contents
Provedor de dados: 17
Autores: I. C. Baianu; Jun Guo.
Conventional chemical analysis techniques are expensive, time consuming, and often destructive. The non-invasive Near Infrared (NIR) technology was introduced over the last decades for wide-scale, inexpensive chemical analysis of food and crop seed composition (see Williams and Norris, 1987; Wilcox and Cavins, 1995; Buning and Diller, 2000 for reviews of the NIR technique development stage prior to 1998, when Diode Arrays were introduced to NIR). NIR spectroscopic measurements obey Lambert and Beer&amp;#x2019;s law, and quantitative measurements can be successfully made with high speed and ease of operation. NIR has been used in a great variety of food applications. General applications of products analyzed come from all sectors of the food industry...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6611/version/1

Isolated ileal interposition in enteroendocrine L cells differentiation
Provedor de dados: 17
Autores: Bianca Marigliani; Joao-Luiz M. C. Azevedo; Lucas P. F. F. Leal; Karina F. Neves; Linda O. A. Bernardes; Gilmara S. Aguiar-Yamaguchi; Wellington  Cardia; Jo&amp;#xe3;o  L. C. Azevedo; Otavio  C. Azevedo; Jose F. Borborema; Gustavo P. S. Miguel.
INTRODUCTION: &amp;#xd;&amp;#xa;Due to the progressive nature of type 2 diabetes, its complexity and drug treatment perpetuity, there is currently a search for surgical procedures that can promote euglycemia also in non-obese patients. Diabetic patients glycemic control can be achieved by increasing the blood concentration of GLP-1, a hormone produced by L cells that are more densely concentrated in the terminal ileum. Early and extended improvement of diabetes in patients submitted to bariatric surgeries awakened the necessity of investigating the isolated ileal interposition as a surgical alternative for the treatment of diabetes. The interposition of this ileal segment to a more anterior region (proximal jejunum) can promote a greater stimulation of the...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6614/version/1

p53 independent epigenetic-differentiation treatment in xenotransplant models of acute myeloid leukemia
Provedor de dados: 17
Autores: Yogen Saunthararajah; Quteba Ebrahem; Soledad Negrotto; Reda Mahfouz; Kevin Link; Zhenbo Hu; Xiaorong Gu; Anjali Advani; Matt Kalaycio; Ronald Sobecks; Mikkael Sekeres; Edward Copelan; Tomas Radivoyevitch; Jaroslaw Maciejewski; James C. Mulloy, PhD; Kwok-Peng Ng.
Suppression of apoptosis by TP53 mutation contributes to resistance of acute myeloid leukemia (AML) to conventional cytotoxic treatment. Using differentiation to induce irreversible cell cycle exit in AML cells could be a p53-independent treatment alternative, however, this possibility requires evaluation. In vitro and in vivo regimens of the cytosine analogue decitabine that deplete the chromatin modifying enzyme DNA methyl-transferase 1 (DNMT1) without phosphorylating p53 or inducing early apoptosis were determined. These decitabine regimens but not equimolar DNA-damaging cytarabine up regulated the key late differentiation factors CEBP&amp;#x3b5; and p27/CDKN1B, induced cellular differentiation, and terminated AML cell-cycle, even in...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5780/version/1

Successful use of axonal transport for drug delivery by synthetic molecular vehicles
Provedor de dados: 17
Autores: Aaron G. Filler; Garth Whiteside; Mark Bacon; Martyn Frederickson; Franklyn A. Howe; Miri K. Rabinowitz; Alan J. Sokoloff; Terrence Deacon; Chris Abell; Raj Munglani; John R. Griffiths; B. Anthony Bell; Andrew Lever.
We report the use of axonal transport to achieve intraneural drug delivery. We constructed a novel tripartite complex of an axonal transport facilitator conjugated to a linker molecule bearing up to a hundred reversibly attached drug molecules. The complex efficiently enters nerve terminals after intramuscular or intradermal administration and travels within axonal processes to neuron cell bodies. The tripartite agent provided 100-fold amplification of saturable neural uptake events, delivering multiple drug molecules per complex. _In vivo_, analgesic drug delivery to systemic and to non-targeted neural tissues was greatly reduced compared to existing routes of administration, thus exemplifying the possibility of specific nerve root targeting and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2164/version/1

High efficiency transfection of thymic epithelial cell lines and primary thymic epithelial cells by Nucleofection
Provedor de dados: 17
Autores: Richard T. O&amp;#x27;Neil; Qiaozhi Wei; Brian G. Condie.
Thymic epithelial cells (TECs) are required for the development and differentiation of T cells and are sufficient for the positive and negative selection of developing T cells. Although TECs play a critical role in T cell biology, simple, efficient and readily scalable methods for the transfection of TEC lines and primary TECs have not been described. We tested the efficiency of Nucleofection for the transfection of 4 different mouse thymic epithelial cell lines that had been derived from cortical or medullary epithelium. We also tested primary mouse thymic epithelial cells isolated from fetal and postnatal stages. We found that Nucleofection was highly efficient for the transfection of thymic epithelial cells, with transfection efficiencies of 30-70% for...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6283/version/1

Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome
Provedor de dados: 17
Autores: Michael D. Barton; Balazs Papp; Daniela Delneri; Stephen G. Oliver; Magnus Rattray; Casey M. Bergman.
Background: Every protein has a variable atomic and energetic cost to the cell based on the synthesis of its constituent amino acids. Quantifying the cost of amino acid synthesis is challenging, however natural selection is expected to favour the use of proteins whose constituents are cheaper to produce in terms of energetic and atomic cost.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: We develop a systems biology approach to estimate the cost of amino acid synthesis based on genome-scale metabolic models, and directly investigate the effects of the cost of amino acid synthesis on transcriptomic, proteomic and metabolomic data in Saccharomyces cerevisiae. We used our two new and six previously reported measures of amino acid cost in conjunction with codon...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1841/version/2

Tuning and regulating the repertoire of glycan determinants
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
We apply Tlusty&amp;#x27;s information-theoretic index theorem analysis of the genetic code to the glycome, using a cognitive paradigm by which external information sources constrain and tune the glycan code error network, in the context of available metabolic energy. The model suggests spontaneous symmetry breaking of the glycan code as a function of metabolic energy intensity, an effect that may be currently present, or embedded in evolutionary trajectory, recording large-scale ecosystem resilience shifts in energy availability such as the aerobic transition. Once focused on a subset of the glycan error code network however, the glycan production machinery must then be regulated by an elaborate cognitive process to ensure that what is produced matches...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Ecology; Molecular Cell Biology; Pharmacology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5932/version/2

Internal ribosomal entry site lacks secondary structure
Provedor de dados: 17
Autores: Xuhua Xia.
The search for mechanisms of translational regulation has yielded many experimentally identified internal ribosome entry sites (IRES). Because of the lack of sequence similarity among the experimentally IRESs, it is widely assumed that IRESs posses stable secondary structure allowing them to interact with the components of the translation machinery. Contrary to this view, here we show that IRES activity in nine yeast IRESs, mapped to 60 nt immediately upstream of the initiation AUG, is strongly associated with the lack of secondary structure of IRESs. Furthermore, the reverse complements of these IRESs, with their secondary structure more stable than those of the IRESs, exhibit little IRES activity. The generality of this association is exemplified by the...
Tipo: Manuscript
Palavras-chave: Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1248/version/1

Myth about neuronal nitric oxide synthase in the sarcolemma of skeletal muscles
Provedor de dados: 17
Autores: Igor Buchwalow; Werner Boecker.
In skeletal muscles, neuronal NO synthase (nNOS, designated also as NOS1) was reported to be restricted to the sarcolemma. With the advent of modern powerful immunocytochemical techniques this commonly accepted view appears to be a delusion and has to be re-evaluated.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1718/version/1

Potential pathways of indole acetic acid (IAA) biosynthesis in Euphorbia abyssinica
Provedor de dados: 17
Autores: Raf Aerts; Els Prinsen; Bart Muys.
Desert candle (_Euphorbia abyssinica_ J.F. Gmel.) (further referred to as EAG) is a succulent tree of dry deciduous and evergreen montane forest, woodland and shrub savanna.  It occurs widely throughout dryland Africa, where it is appreciated as a live fence because it is easily propagated from untreated mature branch cuttings.&amp;#xd;&amp;#xa;Earlier we argued that the ability of large EAG branches to regenerate with ease in dry soil may be related to the natural plant growth regulator hormone indole acetic acid (IAA) contained in the latex of the plant.  EAG latex samples from northern Ethiopia (n = 3) that were chemically analyzed contained on average 0.06 mg/l latex, as well as the IAA metabolites indole lactate (ILA) and indole ethanol (IEt).  One...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2212/version/1

Topological network alignment uncovers biological function and phylogeny
Provedor de dados: 17
Autores: Oleksii Kuchaiev; Tijana Milenkovic; Vesna Memisevic; Wayne Hayes; Natasa Przulj.
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for purely topological alignment has yet been devised. In this paper, we present a novel algorithm based solely on network topology, that can be used to align any two networks. We apply it to biological networks to produce by far the most complete topological alignments of biological networks to date. We demonstrate that both species phylogeny and detailed biological function of individual proteins can be extracted from our alignments....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4089/version/1

A Micropropagation, Molecular and Physiochemical Analysis of Canola Brassica napus L. From Seeds
Provedor de dados: 17
Autores: Israr  Khan; Muhammad Shuaib; Sikandar Khan; Muhammad Amir Zia; Haji Akbar.
Canola is important for its oil, anticarcinogenic phytochemicals and low saturated fat content and has wide scope for further improvement through genetic transformations. Micropropagation is the practice of rapidly multiplying stock plant material to produce a large number of disease free progeny plants, using modern asceptic plant tissue culture methods and also to conserve germ plasm. A combination of auxin and cytikinin and a shock on growth regulator free medium is used for micropropagation. Molecular and physiochemical analysis done to know variation in seeds protein content and electric conductivity.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4781/version/2

Aging-associated Alteration in the Cardiac MIF-AMPK Cascade in Response to Ischemic Stress
Provedor de dados: 17
Autores: Heng Ma; Jingying Wang; Erin Lane; Lin Leng; Wenkui Wang; Jun Ren; Richard Bucala; Ji Li.
An important role for a macrophage migration inhibitory factor (MIF)-AMP-activated protein kinase (AMPK) signaling pathway in ameliorating myocardial damage following ischemia/reperfusion has been described. An aging-associated reduction in AMPK activity may be associated with a decline in the ability of cardiac cells to activate the MIF-AMPK cascade, thereby resulting in reduced tolerance to ischemic insults. To test this hypothesis, _in vivo_ regional ischemia was induced by occlusion of the left anterior descending (LAD) coronary artery in young (4-6 months) and aged (24-26 months) mice. The ischemic AMPK activation response was impaired in aged hearts compared to young ones (p&amp;#x3c;0.01). Notably, cardiac MIF expression in aged hearts was lower...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2466/version/1

Spiral Tissue Microarrays as Next Evolutionary Step in the High-density Tissue Microarray Technology
Provedor de dados: 17
Autores: Junya Fukuoka; Matthias Hofer; Takashi Hori; Tomonori Tanaka; Sayaka Tominaga; Ryo Ohsawa; Takeshi Uemura; Lucian Chirieac.
Tissue microarray (TMA) is a well-established technique that connects basic research with clinical applications that allow the validation of many pathobiologic events from gene expression dysregulation to genomic aberrations. However, conventional TMAs have several limitations such as limited representation of tissue heterogeneity, destruction of donor tissue blocks due to coring and usage of particular specimens that have limited evaluable material (tissue from thin specimens or needle biopsies). We have developed a novel method, which we termed &amp;#x22;Spiral TMA&amp;#x22; that generates TMAs that allow for improved representation of the donor tissue while keeping the architectural details of the donor block intact. This technology is ideal for...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4831/version/1

EAG K+ channel joins the p53&amp;#x2212;miR-34&amp;#x2212;E2F1 signaling pathway as a terminal effecter component for its oncogenic overexpression and action
Provedor de dados: 17
Autores: Zhiguo Wang; Chang Chen; Zhe Li; Xiaobin Luo; Jiening Xiao; Huixian Lin; Jianchun Zhang; Deli Dong; Yanjie Lu; Baofeng Yang.
The human ether-&amp;#xe0;-go-go-1 (h-eag1) voltage-dependent K+ channel is necessary for cell cycle progression and its overexpression stimulates tumorigenesis; specific inhibition of h-eag1 expression leads to a reduction in tumor cell proliferation in vitro and in vivo. On the other hand, the tumor-suppressor gene p53 and its downstream genes consist of a complex molecular signaling network and p53 is at the center of this network regulating diverse physiological responses to cancer-related stresses. We report here that h-eag1 expression is controlled by the p53&amp;#x2212;miR-34&amp;#x2212;E2F1 pathway through a negative feed-forward mechanism. We first established E2F1 as a transactivator of h-eag1 gene. We then revealed that miR-34, a known...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4507/version/1

Genomic Replikin Count Predicts Increased Lethality of Malaria
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Genomic Replikin Counts predict both the increase and the decrease of lethality of malaria
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Immunology; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7142/version/1

Rethinking Leucine Zipper &amp;#x2013; a ubiquitous signal transduction motif
Provedor de dados: 17
Autores: Yaroslav Nikolaev; Konstantin Pervushin.
In this essay we attempt to reconsider the concept of the &amp;#x201c;Leucine Zipper&amp;#x201d; (LZ) protein oligomerization motif. Reasoning on the wealth of existing data, we suggest that despite of the structural similarity with highly stable extended &amp;#x201c;Coiled Coil&amp;#x201d; motifs, on the functional level short and moderately stable &amp;#x201c;Leucine Zippers&amp;#x201d; might stand out as a distinct group. Namely, this family of oligomerization motifs facilitates combinatorial protein-protein recognition in the course of signal transduction events, thus going beyond the structural role of the extended &amp;#x201c;Coiled Coils&amp;#x201d;. Summarizing the existing knowledge on stability, specificity and folding of Leucine Zippers we...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3271/version/1

Dynamic Topology of Biological Networks
Provedor de dados: 17
Autores: Ravi Iyengar.
The mammalian cell can be represented as a large modular network that consists of a central signal network that interacts with and regulates multiple cellular machines that are responsible for phenotypic behavior.  We have used graph-theory approaches to analyze signal flow through a network representing the hippocampal neuron and find that signal-induced connectivity results in the formation of many regulatory motifs. Information flow through the central signaling network is initiated by extra-cellular signals such as hormones binding to their receptors. The flow of information through the signaling network results in the appearance of regulatory motifs such as feedback loops, feedforward and bifan motifs. Within the large cellular networks, these...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/24/version/1

Differences in the gene expression profile of human monocytic cells activated by high and low affinity Fc-gamma-receptors.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Renji Reghunathan; Alirio Jose Melendez; Peter Natesan Pushparaj.
Receptors for the constant (Fc) region of immunoglobulin G, play an important role in linking the humoral and cellular arms of immune response. Three different classes of receptors have been defined, Fc&amp;#x3b3;RI (CD64), Fc&amp;#x3b3;RII (CD 32), and Fc&amp;#x3b3;RIII (CD16). We have previously shown that in a human monocyte model (IFN&amp;#x3b3;-primed U937 cells), Fc&amp;#x3b3;RI and Fc&amp;#x3b3;RII stimulation trigger two very distinct intracellular signalling pathways. Here we show for the first time, the use of oligonucleotide microarrays to investigate the overall gene-expression profile of human monocytes triggered with Fc&amp;#x3b3;RI or Fc&amp;#x3b3;RII. Our data indicate that several interesting genes are differentially expressed in response...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1149/version/1

Molecular implications of prolonged aggression experience: Th, Dat1, Snca and Bdnf gene expression in the ventral tegmental area of the victorious male mice
Provedor de dados: 17
Autores: Natalia P. Bondar; Ul&amp;#x27;yana A.  Boyarskikh; Irina L. Kovalenko; Maxim L. Filipenko; Natalia  N. Kudryavtseva.
Th, Dat1, Snca and Bdnf were the genes whose mRNA levels in the ventral tegmental area of the midbrain were measured in male mice that were victorious in 20 daily agonistic interactions and in a group of such victorious mice that had later not been allowed to fight for 14 days. This experiment demonstrated increased Th, Dat1 and Snca but not Bdnf mRNA levels in the former group as compared to the controls. In the latter group, the expression of the Th and Dat1 genes was still enhanced, while the level of Snca mRNA did not differ from that in the controls. These findings suggest that positive fighting experience enhances the expression of the genes concerned with dopaminergic systems and this enhanced expression is preserved for a long time afterwards....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2042/version/1

Genetic incorporation of D-Lysine into diketoreductase in Escherichia coli cells
Provedor de dados: 17
Autores: Zhi Zhi Liu; Xin Yang; Denghuan Yi; Shuzhen Wang; Yijun Chen.
D-Lysine has been genetically introduced into diketoreductase in E. coli cells by utilization of an orthogonal Ph tRNA /Lysyl-tRNA synthetase pair. This is the first report on the genetic incoporation of D-amino acids into proteins, which may be generally applicable to a wide variety of applications.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Microbiology; Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6777/version/1

Computational Prediction and Analysis of the NAPP - DR6 Interaction: Implications for Alzheimer&amp;#x27;s Research
Provedor de dados: 17
Autores: Josheph Audie; Sergei Ponomarev.
Alzheimer&amp;#x27;s disease (AD) is a progressive neurodegenerative disorder that involves a devastating clinical course and lacks an effective treatment. A biochemical model for neuronal development that might have implications for AD, recently proposed by Nikolaev and co-workers, hinges on a novel protein-protein interaction between the death cell receptor six (DR6) ectodomain and an N-terminal fragment of amyloid precursor protein (NAPP). The model provides a coherent and satisfying framework for better understanding AD pathophysiology. Moreover, the DR6-NAPP interaction offers a tempting target for novel pharmacological intervention. Given all of this, we constructed a structural model of the DR6-NAPP interaction using the neurotrophin p75 receptor as...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4545/version/1

Heat shock transcription factor 1 preserves cardiac angiogenesis and adaptation during pressure overload
Provedor de dados: 17
Autores: Jiming Li; Junbo Ge; Jie Yuan; Hong Jiang; Hong Ma; Yanyan Liang; Yuhong Niu; Hui Gong; Ning Zhou; Aili Guan; Zhen Ma; Lingyan Yuan; Aijun Sun; Yuqi Wang; Akira Nakai; Issei Komuro; Yunzeng Zou.
To examine how heat shock transcription factor 1 (HSF1) protects against maladaptive hypertrophy during pressure overload, we subjected HSF1 transgenic (TG), knockout (KO) and wild type (WT) mice to a constriction of transverse aorta (TAC), and found that cardiac hypertrophy, functions and angiogenesis were well preserved in TG mice but were decreased in KO mice compared to WT ones at 4 weeks, which was related to HIF-1 and p53 expression. Inhibition of angiogenesis suppressed cardiac adaptation in TG mice while overexpression of angiogenesis factors improved maladaptive hypertrophy in KO mice. In vitro formation of vasculatures by microvascular endothelial cells was higher in TG mice but lower in KO mice than in WT ones. A siRNA of p53 but not a HIF-1...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2716/version/1

p63, p73, &amp;#x26; p53 are Negative Regulators of Epithelial to Mesenchymal Transition (EMT), Invasion &amp;#x26; Metastasis
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
It has recently been shown that microRNAs, such as miRs-145,192, and 215, are regulated by the tumor suppressor p53 through their p53REs.  Considering miRs-145, 192, and 215 promoters contain p53REs suggests that they could be transcriptional targets of p63 and p73 as well.  Remarkably, bioinformatics analysis of miRs-145, 192, and 215 targets suggests that they target ZEB2, suggesting that p53, p63, and p73 by increasing the expression of miRs-192, 215, &amp;#x26; 145, they could inhibit the expression of ZEB2.  ZEB2 has been shown to function as a repressor of the tumor suppressor E-cadherin, suggesting that p53, p73, and p63 by suppressing the expression of ZEB2 through their transcriptional target miRs, they could increase the expression of E-cadherin....
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4109/version/1

Kinetic control of eukaryotic chromatin structure by recursive topological restraints
Provedor de dados: 17
Autores: Dominika Borek; Zbyszek Otwinowski.
Chromatin structure undergoes many changes during the cell cycle and in response to regulatory events. A basic unit of chromatin organization is the nucleosome core particle. However, very little is known about how nucleosomes are arranged into higher-order structures in vivo, even though the efficiency and precision of cell division imply high levels of structural organization. We propose abandoning the current paradigm of chromatin organization based on thermodynamics of the lowest energy state and replace it with the idea of a topologically restrained, high-energy structure. We propose that DNA is subject to a recursive topological restraint, and is anchored by hemicatenates that are part of the chromosomal scaffold. Long-distance _cis_-regulation of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2672/version/1

CDK2 and CKI targeting can significantly lower the cellular senescence bar - reveals a mathematical model of G1/S checkpoint pathway
Provedor de dados: 17
Autores: Hong  Ling; Sandhya Samarasinghe; Don  Kulasiri.
Cellular senescence, a mechanism employed by cells for thwarting proliferation, has shown to play an important role in protecting cells against cancer development in recent experimental observations, indicating that a deeper understanding of the cellular senescence pathway can help exploit its capacity for more effective cancer treatment. Furthermore, some experimental evidence points out that inhibition of CDK2 or Skp2 can be the critical trigger for cellular senescence. However, no mathematical model has been developed to highlight cellular senescence until now. In this study, we first implement a mathematical model of G1/S transition involving the DNA-damage pathway to highlight cellular senescence by lowering the critical trigger- CDK2. For this, we...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4950/version/1

Interaction of the TNFR-Receptor Associated Factor TRAF1 with I-kappa B Kinase-2 and TRAF2 Indicates a Regulatory Function for NF-kappa B Signaling
Provedor de dados: 17
Autores: Kalsoom A. Sughra; Andreas Birbach; Rainer de Martin; Johannes A. Schmid.
*Background*&amp;#xd;&amp;#xa;I-kappa B kinase 2 (IKK2 or IKK-beta) is one of the most crucial signaling kinases for activation of NF-kappa B, a transcription factor that is important for inflammation, cell survival and differentiation. Since many NF-kappa B activating pathways converge at the level of IKK2, molecular interactions of this kinase are pivotal for regulation of NF-kappa B signaling.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Methodology/Principal Findings*&amp;#xd;&amp;#xa;We searched for proteins interacting with IKK2 using the C-terminal part (amino acids 466-756) as bait in a yeast two-hybrid system and identified the N-terminal part (amino acids 1-228) of the TNF-receptor associated factor TRAF1 as putative interaction partner. The interaction...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4153/version/2

ACAT1, Cav-1, and PrP expression in brains and skin fibroblasts from Sarda breed sheep with scrapie-resistant and scrapie-susceptible genotype.
Provedor de dados: 17
Autores: Alessandra Pani; Marirosa Putzolu; Claudia Mulas; Cristina D. Orr&amp;#xf9;; Claudia Abete; Claudia Norfo; M. Dolores Cannas; Sergio Laconi; Paolo La Colla; Sandra Dess&amp;#xec;.
Scrapie is an infective ovine neurodegenerative disease; the only identified component of the infectious agent being an aberrant isoform (PrPSc) of the cellular prion protein (PrPC). So far, no means for ante-mortem diagnosis are available for Scrapie as well as for any other mammal Transmissible Spongiform Encephalopaties. We recently found a strong relationship between cell susceptibility to scrapie-infection and intracellular cholesterol homeostasis alterations. In brain tissues as well as in ex vivo cultures of skin fibroblasts and PBMCs from healthy and scrapie-affected sheep carrying a scrapie-susceptible (ARQ/ARQ) genotype, the levels of cholesterol esters were consistently higher than in tissues and cultures derived from animals with a...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1211/version/1

Stress responsive miR-23a attenuates skeletal muscle atrophy by targeting MAFbx /atrogin-1
Provedor de dados: 17
Autores: Shogo Wada; Yoshio Kato; Mitsuharu Okutsu; Shigeru Miyaki; Katsuhiko Suzuki; Zhen Yan; Hiroshi Asahara; Takashi Ushida; Takayuki Akimoto.
Muscle atrophy occurs in many pathological states and results primarily from accelerated protein degradation by the ubiquitin-proteasome pathway. We used dexamethasone to induce muscle wasting and investigated the role of a microRNA (miRNA) in the control of muscle-specific E3 ubiquitin ligase MAFbx/atrogin-1. Here we show that miR-23a suppresses MAFbx/atrogin-1 translation by binding to 3&amp;#x27;UTR of the mRNA. Furthermore, ectopic expression of miR-23a is sufficient to protect myocytes from atrophy in vitro and in vivo in response to dexamethasone treatment, and heat stress-induced miR-23a protects muscle from dexamethasone-induced muscle atrophy. Our surprising discovery of the physiological role of miR-23a in preventing the atrophy program should...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2175/version/1

Oncogenic Product HMGA1a Might Function as an Aberrant Splicing Inducer of Estrogen Receptor [alpha] in Breast Cancer
Provedor de dados: 17
Autores: Kenji Ohe; Toshiaki Utsumi; Akila Mayeda.
Estrogen receptor (ER)-[alpha]46 is known as an important isoform for ER[alpha]. It inhibits the function of full length ER[alpha] in MCF-7 mammary carcinoma cells and associated with cell cycle arrest. On the other hand, the oncogene _HMGA1_ (formally _HMG I/Y_) is known to have increased expression in mammary carcinoma correlating with the degree of malignancy. We present here that HMGA1a (HMG I) induces the exon skipped product, ER[alpha]46 mRNA, by tethering U1 snRNP to an upstream pseudo 5&amp;#x27; splice site, which is quite analogous to the PSI-mediated splicing regulation of _Drosophila_ P-element.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4104/version/1

Detection of BCR-ABL kinase domain mutations in CD34+ cells from newly diagnosed chronic phase CML patients and their association with imatinib resistance
Provedor de dados: 17
Autores: Zafar Iqbal; Ijaz Shah; Aamer Aleem; Mubashar Naqvi; Ammara Tahir; Tariq Gill; Abid Taj; Abdul Qayyum; Najeeb ur-Rehman; Muhammad Ferhan; Mudassar Iqbal; Muhammad Khalid; Weng Qin; Ahmad Khalid; Mahwish Khan; Shahid Baig; Abid Jamil; Tanveer Akhtar; Muhammad Abbad; Riaz ul-Haq.
BCR-ABL kinase domain (KD) mutations, the most common cause of imatinib resistance, are infrequently detected in newly diagnosed chronic-phase chronic myeloid leukemia (CP-CML) patients. Recent studies indicate pre-existing mutations (PEMs) can be detected in a higher percentage of CML patients using CD34+ stem/progenitor cells, and these mutations may correlate with imatinib resistance. We investigated KD mutations in CD34+ stem cells from 100 CP-CML patients by multiplex ASO-PCR and sequencing ASO-PCR products at the time of diagnosis. PEMs were detected in 32/100 patients and included F311L, M351T, and T315I. After a median follow-up of 30 months (range 8-48), all patients with PEMs exhibited imatinib resistance. Of 68 patients without PEMs, 24...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6645/version/1

Constraints of FL Motif on the Targeting and Function of Sodium-Bicarbonate Cotransporter 1
Provedor de dados: 17
Autores: Hong C. Li; Ali Shawki; YoonKyung Park; Emily Y Li; Kyung-Soo Hahm; Joel H.  Collier; Bryan  Mackenzie; Manoocher  Soleimani.
A C-terminal dihydrophobic FL motif plays a vital role in the basolateral targeting of sodium bicarbonate cotransporter 1. To further characterize the role of dihydrophobic FL motif, 1). the FL motif in wild type (PFLS) was reversed to LF (PLFS), 2). the FL motif (PFLS) was shifted upstream (FLPS), and 3). the FL motif (PFLS) was shifted downstream (PSFL). The wild type (PFLS) and its mutant (PLFS) were exclusively expressed on the basolateral membrane by con-focal microscopy, however, the mutant (FLPS) and (PSFL) were predominantly mistargeted to the apical membrane and the cytoplasm, respectively. Functional studies showed that the mutant (PSFL) displayed a remarkably reduced current (p value&amp;#x3c;0.05 vs wild type). The mutant (PSFL) displayed a...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1638/version/1

Integrin-mediated membrane blebbing is dependent on the NHE1 and NCX1 activities.
Provedor de dados: 17
Autores: Yung-Hsiang Yi; Yu-Sun Chang; Chi-Hung Lin; Tien-Shen Lew; Chih-Yung Tang; Tsung-Yu Chen; Wei-Lien Tseng; Ching-Ping Tseng; Szecheng J. Lo.
Integrin-mediated signal transduction and membrane blebbing have been well studied to modulate cell adhesion, spreading and migration^1-6^. However, the relationship between membrane blebbing and integrin signaling has not been explored. Here we show that integrin-ligand interaction induces membrane blebbing and membrane permeability change. We found that sodium-proton exchanger 1 (NHE1) and sodium-calcium exchanger 1 (NCX1) are located in the membrane blebbing sites and inhibition of NHE1 disrupts membrane blebbing and decreases membrane permeability change. However, inhibition of NCX1 enhances cell blebbing to cause cell swelling which is correlated with an intracellular sodium accumulation induced by NHE17. These data suggest that sodium influx induced...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5723/version/1

Logical implications for regulatory relations represented by verbs in biomedical texts
Provedor de dados: 17
Autores: Sine Zambach.
Relations used in biomedical ontologies can be very general or very specific in respect to the domain. However some relations are used widely in for example regulatory networks. This work focuses on positive and negative regulatory relations, in particular their usage expressed as verbs in different biomedical genres and the properties of the relations.
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3560/version/1

ABC SMC for parameter estimation and model selection with applications in systems biology
Provedor de dados: 17
Autores: Tina Toni.
Approximate Bayesian Computation (ABC) methods can be used in situations where the evaluation of the likelihood is computationally prohibitive. They are thus ideally suited for analyzing the complex dynamical models encountered in systems biology, where knowledge of the full (approximate) posterior is often essential.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This talk gives an overview of an ABC algorithm based on Sequential Monte Carlo (ABC SMC). Different uses of the algorithm will be presented, depending on the application question of interest. The first is the general parameter estimation framework, where the interest lies in estimating the posterior parameter distribution from available experimental data. In the second context we ask whether the model can...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5964/version/1

Lost in translation: Toward a formal model of multilevel, multiscale medicine
Provedor de dados: 17
Autores: Rodrick Wallace.
For a broad spectrum of low level cognitive regulatory and other biological phenomena, isolation from signal crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts of interacting physiological processes at multiple scales. The argument is similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological subsystems. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative larger scale broadcasts that link selected subsets of functional modules to address problems. This multilevel dynamical viewpoint has implications...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Immunology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6973/version/1

The guardians of the genome dependent tumor suppressor miRNAs network
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
The tumor suppressor p53 homologues, TA-p73, and p63 have been shown to function as tumor suppressors.  However, how they function as tumor suppressors remains elusive.  Here I present a number of models that illustrates how the TA-p73/p63 could function as tumor suppressors.  Remarkably, the guardians&amp;#x2014;p53, p63, and p73&amp;#x2014;of the genome are in control of most of the known tumor suppressor miRNAs.  &amp;#xd;&amp;#xa;TA-p73/p63 and p53, by suppressing the expression of c-Myc through TRIM32 and miR-145, they could up regulate the expression of tumor suppressor microRNAs, such as miR-15/16a, miR-29, miR-34, miR-26, let-7a/d/g, miR-30b/c/d/e, miR-146a, and a number of tumor suppressor genes.  It appears that p53/TA-p73/p63-mediated repression...
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4112/version/1

Networks of intergenic long-range enhancers and snpRNAs drive castration-resistant phenotype of prostate cancer and contribute to pathogenesis of multiple common human disorders
Provedor de dados: 17
Autores: Anna Glinskii; Shuang Ma; Jun Ma; Denise Grant; Chang-Uk  Lim; Ian Guest; Stewart Sell; Ralph Buttyan; Gennadi Glinsky.
Biological and mechanistic relevance of intergenic disease-associated genetic loci (IDAGL) containing highly statistically significant disease-linked SNPs remains unknown. Here we present the experimental and clinical evidence revealing important role of IDAGL in human diseases. Targeted RT-PCR screen coupled with sequencing of purified PCR products detects widespread transcription at multiple intergenic disease-associated genomic loci (IDAGL) and identifies 96 small non-coding trans-regulatory RNAs of ~ 100-300 nt in length containing SNPs associated with 21 common human disorders (snpRNAs). Functionality of snpRNAs is supported by multiple independent lines of experimental evidence demonstrating their cell-type-specific expression and evolutionary...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6069/version/1

On Asymmetry in Biology and Nature
Provedor de dados: 17
Autores: I. C. Baianu.
Symmetry has attracted a substantial amount of effort because considerable simplifications are possible in the mathematical and physical treatment of phenomena and natural systems that possess a certain degree of symmetry. Among physical and chemical systems the most widely known are those related to crystals and fluids. Whereas crystals have a lattice structure and a symmetry caused by &amp;#x2018;perfect&amp;#x2019; order which can be classified by mathematical symmetry groups, most fluids have an average isotropic, highly-disordered &amp;#x2018;structure&amp;#x2019; that is often considered to be random.Asymmetry is widely encountered in Biology and ecological systems- from amino acids to trees forests, and tribes, from physiological processes to...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7134/version/1

Structure Prediction and Functional Characterization of ERG Proteins Involved in Ergosterol Biosynthetic Pathway of Candida albicans
Provedor de dados: 17
Autores: Sudeep  Roy; Suaib  Luqman; Ashok  Sharma.
The ERG proteins and enzymes of the ergosterol biosynthetic pathway has been the subject of intensive investigation as a target for several classes of antifungal agents used to treat C. albicans infection. Over the past few decades, a number of drugs and inhibitors with wide spectrum of activity, low toxicity and defined targets have been introduced. Several lines of evidence suggest that allylamines targets squalene epoxidase (ERG1), morpholines affects sterol C8-C7 isomerase (ERG2) and sterol reductase (ERG24), azoles inhibits a cytochrome P450 (ERG11) responsible for the 14 &amp;#x3b1;-demethylation of lanosterol and C-5 sterol desaturase (ERG3) and polyenes binds to ergosterol that leads to the damage of cell plasma membrane, ensuing in leakage of...
Tipo: Poster
Palavras-chave: Microbiology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6709/version/1

MicroDNAs and Transcriptional Regulation
Provedor de dados: 17
Autores: Reza sheikhnejad.
Synthetic &amp;#x22;microDNAs (MIDs)&amp;#x22;is a new class of ~ 20-25 nucleotide-long DNAs capable of repressing the activity of the target gene at the level of transcription by mechanisms that have not been clarified yet. However they are designed to target non-coding regions of the cancer causing genes, thus interfering with transcription. The inhibition might be possible through the direct binding of MIDs to cis-regulatory sites and/or to some Transcription Factors (TF) that normally activate transcription. Synthetic MIDs in some ways are similar to the newly discovered microRNAs a mechanism by which cell regulates its genetic activities at post-transcriptional level. Synthetic MIDs can provide a powerful tool to prevent massive production of mRNA by...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3931/version/1

A novel mathematical tool for generating highly conserved protein domain via different organismal genomic landscapes
Provedor de dados: 17
Autores: Arunava Goswami; Pabitra Pal Choudhury; Rajneesh Singh; Sk. Sarif Hassan.
Darwinian evolution hypothesizes that a short stretch of DNA was first constructed and then it expanded to give rise to a long strand. This long strand then produced a mix of exons, introns and repetitive DNA sequence. The order of production of above three kinds of DNA sequence is unknown. Reshuffling of stretches of DNA like above within organisms has given rise to different chromosomes. Till date it is not known how this process is governed. In this paper we show that starting with a sixteen base-pair human olfactory DNA sequence one can form a highly conserved protein domain. Once this domain is formed repetitive DNA sequences of a particular kind starts generating which signifies that this particular conserved protein domain will be unique in nature....
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4850/version/1

Beyond Structure: KiSAO and TEDDY -- Two Ontologies Addressing Pragmatical and Dynamical Aspects of Computational Models in Systems Biology
Provedor de dados: 17
Autores: Dagmar K&amp;#xf6;hn; Nicolas Le Nov&amp;#xe8;re; Christian Kn&amp;#xfc;pfer.
Computational models are becoming more and more the central scientific paradigm for understanding the complexity of living systems. With the increasing number and size of these models there is a growing need for model reuse and exchange. Furthermore, detailed models are not manageable without computer support. There are efforts to formalise the mathematical structure of models (e.g. SBML) and to standardise the kinetic and biological meaning of model components (e.g. SBO, GO, UniProt). However, formalising only the structure of computational models is not sufficient to easily exchange and reuse models and to achieve full computer support for modelling. We also need to formalise the pragmatical and dynamical aspects of...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3137/version/1

Activation of TRF3 Transcription Factor by Small Interfering RNAs
Provedor de dados: 17
Autores: Stephan Persengiev.
RNA interference (RNAi) is a conserved biological response to double-stranded RNAs that results in posttranscriptional silencing of target gene expression. Double-stranded processed RNAs of 21-23 nt were found to affect in a non-specific manner a number of signaling and transcription pathways, including interferon and PKR cascades. We report here that siRNAs induce the expression of general transcription factor TRF3, which can trigger an interferon response in mammalian cells.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1206/version/1

Nucleosome-mediated cooperativity between transcription factors
Provedor de dados: 17
Autores: Leonid A. Mirny.
Cooperative binding of transcription factors (TFs) to cis-regulatory regions (CRRs) is essential for precision of gene expression in development and other processes. The classical model of cooperativity requires direct interactions between TFs, thus constraining the arrangement of TFs sites in a CRR. On the contrary, genomic and functional studies demonstrate a great deal of flexibility in such arrangements with variable distances, numbers of sites, and identities of the involved TFs. Such flexibility is inconsistent with the cooperativity by direct interactions between TFs. Here we demonstrate that strong cooperativity among non-interacting TFs can be achieved by their competition with nucleosomes. We find that the mechanism of nucleosome-mediated...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2796/version/1

Molecular Bio-imprinting of Biocatalysts
Provedor de dados: 17
Autores: Israr  Khan; Muhammad Waheed Akhtar.
Energy conservation is the cry of the day. Attempts are made all over the world to occupy and use energy reserves. Increased industrialization and mechanization has led to the  depletion of natural energy reserves. Its unavoidable to search for renewable sources of energy, which may be not used now but can be used by future generations. We are using the expertise of our ancestors. Thus exploiting the nature and newer techniques in this area would yield the best results. Bio-imprinting is one of those techniques whereby chemical modification is done in order to achieve highly expressed protein which can be stored in its highly active form in the specific solvent.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5665/version/1

Without magic bullets: the biological basis for public health interventions against protein folding disorders
Provedor de dados: 17
Autores: Rodrick Wallace.
Protein folding disorders of aging like Alzheimer&amp;#x27;s and Parkinson&amp;#x27;s diseases currently present intractable medical challenges. &amp;#x27;Small molecule&amp;#x27; interventions - drug treatments - often have, at best, palliative impact, failing to alter disease course. The design of individual or population level interventions will likely require a deeper understanding of protein folding and its regulation than currently provided by contemporary &amp;#x27;physics&amp;#x27; or culture-bound medical magic bullet models. Here, a topological rate distortion analysis is applied to the problem of protein folding and regulation that is similar in spirit to Tlusty&amp;#x27;s (2010a) elegant exploration of the genetic code. The formalism produces...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4847/version/2

The E3 ubiquitin ligase c-IAP1 regulates PCSK9-mediated LDLR degradation: Linking the TNF-&amp;#x3b1; pathway to cholesterol uptake
Provedor de dados: 17
Autores: Weiming Xu; Lizhi Liu.
Proprotein convertase subtilisin/kexin type 9 (PCSK9), in addition to LDLR (low-density lipoprotein receptor) and APOB (apolipoprotein B), is one of three loci implicated in autosomal dominant hypercholesterolaemia (ADH)^1^. A number of PCSK9 gain-of-function mutations and loss-of-function mutations have been identified from families afflicted with ADH with hypercholesterolaemia or hypocholesterolaemia, respectively^1-4^. In humans, the main function of PCSK9 appears to be the post-transcriptional regulation of the number of cell-surface LDL receptors^5-7^. To date, only LDLR and its closest family members VLDLR and ApoER2 have been shown to bind with PCSK9^8,9^. To find new binding partners for PCSK9, we used a shotgun proteomic method to analyse the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4554/version/1

Cooperative effect of ribosomal protein s19 and Pim-1 kinase on murine c-Myc expression and myeloid/erythroid cellularity
Provedor de dados: 17
Autores: Anne-Sophie Frojmark; Jitendra Badhai; Joakim  Klar; Maria  Thuveson; Jens Schuster; Niklas Dahl.
Diamond Blackfan anemia (DBA) is a bone marrow failure syndrome associated with heterozygous mutations in the ribosomal protein S19 (RPS19) gene in a subgroup of patients. One of the interacting partners with RPS19 is the oncoprotein PIM-1 kinase. We intercrossed Rps19+/- and Pim-1-/- mice strains to study the effect from the disruption of both genes. The double mutant (Rps19+/-Pim-1-/-) mice display normal growth with increased peripheral white- and red blood cell counts when compared to the w.t. mice (Rps19+/+Pim-1+/+). Molecular analysis of bone marrow cells in Rps19+/-Pim-1-/- mice revealed up-regulated levels of c-Myc and the anti-apoptotic factors Bcl2, BclXL and Mcl-1. This is associated with a reduction of the apoptotic factors Bak and Caspase 3 as...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2882/version/1

PIM1-dependent phosphorylation of Histone H3 at Serine 10 is required for MYC-dependent transcriptional activation and oncogenic transformation.
Provedor de dados: 17
Autores: Salvatore Oliviero; Alessio Zippo; Alessandra De Robertis; Riccardo Serafini.
The serine/threonine kinase PIM1, cooperates with MYC in cell cycle progression and tumorigenesis. However, the nature of this cooperation remains elusive. Here we show that PIM1 contributes to the transcriptional activation of MYC-target genes by phosphorylating the histone H3 nucleosome at Serine 10 (H3S10). Recombinant PIM1 directly phosphorylates H3S10 on the nucleosome _in vitro_. Following growth factor stimulation, PIM1 accumulates in the nucleus where it forms a complex with the MYC/MAX dimer via the MYC BoxII domain (MBII). Immunofluorescence analysis coupled with _in vivo_ run-on shows a high degree of PIM1 and MYC co-localization in the nucleus at sites of active transcription. Expression profile analysis revealed that PIM1 contributes to the...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/100/version/1

NMR and Electron Microscopy Studies of Soybean Seeds, Soybean Proteins, and Oil for Improved Utilization in Foods and Feeds
Provedor de dados: 17
Autores: Doina M. Costescu; I. C. Baianu.
NMR, NIR and EM techniques are suitable methods of measuring protein and oil content in soybeans. After completion of a measurement with NMR or NIR, a soybean sample could be either replanted or consummated. NMR techniques involved in the present work are based on the response of nuclei, as nuclear spin flips, when set in a 7.05T magnetic field and excited with rf pulses of 300 MHz. NIR spectroscopy is based on outer electron molecular vibrations, when excited with radiation of frequency 1012 -4&amp;#xd7;1014Hz, and &amp;#xf06c;=2.5Om-750 nm. &amp;#xd;&amp;#xa;TEM and ESEM techniques are bulk and surface analysis techniques, respectively, working with electron beams of 15KV, and image resolution in the range of nm&amp;#x2019;s. ESEM is based on the...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6192/version/1

Membrane repair against H. pylori promotes cancer cell proliferation
Provedor de dados: 17
Autores: Li-Ling  Lin; Hsuan-Cheng Huang; Satoshi  Ogihara; Jin-Town Wang; Chiung-Nien Chen; Hsueh-Fen Juan.
Membrane repair is a universal response against physical and biological insults and enables cell survival. Helicobacter pylori is one of the most common human pathogens and the first formally recognized bacterial carcinogen associated with gastric cancer. However, little is known about host membrane repair in the context of H. pylori infection. Here we show that H. pylori disrupts the host plasma membrane and induces Ca2+ influx, which triggers the translocation of annexin family members A1 and A4 to the plasma membrane. This in turn activates a membrane repair response through the recruitment of lysosomal membranes and the induction of downstream signaling transduction pathways that promote cell survival and proliferation. Based on our data, we propose a...
Tipo: Manuscript
Palavras-chave: Cancer; Microbiology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4887/version/1

Integrative concept of homeostasis: translating physiology into medicine
Provedor de dados: 17
Autores: Ivan Spasojevic.
To truly understand living systems they must be viewed as a whole. In order to achieve this and to come to some law to which living systems obey, data obtained on cells, tissues and organs should be integrated. Because there are no such laws yet, there is usually a long path for physiological findings obtained by reductionist approaches to be translated into medical practice. The concept and accompanying equations of homeostasis presented here are aimed to develop biological laws and to bridge this gap between physiology and medicine. The concept of homeostasis takes into account energy input and output, enlisting all relevant contributors. In homeostasis, input should equal the output. What I suggest here is that if the system is out of homeostasis, the...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6741/version/1

Reactome - a knowledgebase of human biological pathways
Provedor de dados: 17
Autores: Bijay Jassal; Esther E. Schmidt; Guanming Wu; Imre Vastrik; David Croft; Bernard de Bono; Gopal Gopinath; Marc Gillespie; Steven Jupe; Gavin O&amp;#x27;Kelly; Lisa Matthews; Phani V. Garapati; Michael Caudy; Alexander Kanapin; Bruce May; Shahana Mahajan; Ewan Birney; Peter  D&amp;#x27;Eustachio; Lincoln Stein.
Reactome (&amp;#x22;http://www.reactome.org&amp;#x22;:http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2921 human proteins, 2871 reactions and 4167 literature citations. This curated dataset is integrated with a functional interaction network assembled computationally from non-curated sources of information including protein-protein interactions, gene co-expression, and gene ontology annotations, providing access. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data...
Tipo: Poster
Palavras-chave: Chemistry; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3200/version/1

Extending Tlusty&amp;#x27;s method to the glycome: Tuning the repertoire of glycan determinants
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
We apply Tlusty&amp;#x27;s information-theoretic analysis of the genetic code to the glycome, using a cognitive paradigm in which external information sources constrain and tune the glycan code error network, in the context of available metabolic energy. The resulting dynamic model suggests the possibility of observing spontaneous symmetry breaking of the glycan code as a function of metabolic energy intensity. These effects may be currently present, or embedded in evolutionary trajectory, recording large-scale ecosystem resilience shifts in energy availability such as the aerobic transition.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology; Pharmacology; Bioinformatics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5932/version/1

In Vitro Bactericidal Activities of Extracts From Ripe and Unripe Fruit of &amp;#x27;Noni&amp;#x27;
Provedor de dados: 17
Autores: Rajarajan Swaminathan; Shanthi Sabari; Nisha K John.
In an era of nutraceuticular research, &amp;#x2018;Noni&amp;#x2019; fruit is considered as a panacea because of the profound claim on its medicinal uses in treating many diseases inclusive of infections of microbial origin. Hence, the present study was done to know the antibacterial activity of aqueous extracts from ripe and unripe fruits of &amp;#x2018;Noni&amp;#x2019; Morinda citrifolia L on gastroenteritic and pyogenic bacteria. The study was done for eight gastroenteritic bacteria and six pyogenic bacteria.  The estimation of antibacterial activity of the ripe fruit &amp;#x26; unripe fruit extract were carried out by serial two fold tube dilution techniques.  Minimum Bactericidal Concentration of the ripe as well as unripe fruit extracts for the...
Tipo: Manuscript
Palavras-chave: Microbiology; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3954/version/1

Glucose-6-phosphate-dehydrogenase deficiency as a risk factor in proliferative disorder development
Provedor de dados: 17
Autores: Antonella Mandas; Enrico Peiretti; Pierluigi Cocco; Claudia Norfo; Claudia Abete; Fabrizio Angius; Alessandra Pani; Giacomo Diaz; Sandra Dess&amp;#xec;; Maurizio Fossarello.
Glucose-6-phosphate dehydrogenase (G6PD) is an important site of metabolic control in the pentose phosphate pathway (PPP) which provides reducing power (NADPH) and pentose phosphates. The former is mainly involved in the detoxification of chemical reactive species; the latter in the regulation of cell proliferation. G6PD deficiency is the most common enzymopathy in the human population, characterized by decreased G6PD activity, mainly in red blood cells, but actually also in nucleated cells. This decreased activity is not due to enzyme synthesis impairment, but rather to reduced enzyme stability, which leads to a shortening of its half-life. Therefore, a major problem is to understand the underlying mechanisms linking G6PD deficiency to oxidative stress...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3001/version/1

Formal Systems Architectures for Biology
Provedor de dados: 17
Autores: Bradly Alicea.
When the word &amp;#x22;systems&amp;#x22; is used in systems biology, it invokes a variety of assumptions about what defines the subject under investigation, which in turn can lead to divergent research outcomes. We will take the position that systems are defined by their potential organizing and &amp;#x22;control&amp;#x22; mechanisms, &amp;#xd;&amp;#xa;which distinguishes complex, living systems from a primordial soup. This will be accomplished by defining and investigating three interesting control motifs in biological systems: dominoes and clocks, futile cycles, and complex feedforward regulation. Additional mechanisms that combine feedback and feedforward mechanisms will also be briefly elaborated upon. Throughout these examples, our focus will be on...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6369/version/1

Reversal of an immunity associated plant cell death program by the growth regulator auxin
Provedor de dados: 17
Autores: Suresh Gopalan.
One form of plant immunity against pathogens involves a rapid host programmed cell death at the site of infection accompanied by resistance, termed the hypersensitive response (HR). Here it is shown that the HR programmed cell death program initiated by the bacterial type III secretion system dependent proteinaceous elicitor harpin from Erwinia amylovora can be reversed till very late in the process by the plant growth regulator auxin. Early inhibition or late reversal of this cell death program does not affect marker genes tightly correlated with local and systemic resistance. Cross-regulation between cell death programs and growth regulators is prevalent in different kingdoms. Thus, the concept that cell death program can be reversed till late provides a...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1347/version/1

Stem Cell Antigen CD34 In Native And Engineered Form Alter Its Binding Ability To Stromal Cells And Ligands: A Classical Example Of Clinical Benefits Of Therapeutic Genetic Engineering Of Stem Cells In Transplantation
Provedor de dados: 17
Autores: Gurudutta Gangenahalli; Vimal Kumar  Singh; Rajendra Prasad  Tripathi; Yogesh Kumar Verma; Pallavi  Gupta; Neeraj Kumar Satija.
CD34 is a highly glycosylated surface-expressed sialomucin and, because it is present on hematopoietic stem cells (HSCs), has demonstrated immense clinical utility in their enumeration in aphaeresis products, immunoaffinity purification for transplantation, and disease monitoring.  The success of CD34 based reagents in identifying hematopoietic progenitors led to the assumption that CD34 is expressed on cells with regenerative potential and is sufficient for hematopoietic reconstitution in marrow-ablated recipients. However, its role has not been identified in substantial detail. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;With the advent of the fact that CD34 binds adapter protein like CRK-L in cytosol and CD34 knock out studies identified a a signaling role,...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5454/version/1

Near Infrared Microspectroscopy, Fluorescence Microspectroscopy, Infrared Chemical Imaging and  High-Resolution Nuclear Magnetic Resonance Analysis of Soybean Seeds, Embryos and Single Cells
Provedor de dados: 17
Autores: I. C. Baianu; Schyler S.  Korban; Tiefeng You.
Chemical analysis of soybean seeds, somatic embryos and single cells were carried out by Fourier Transform Infrared (FT-IR), Fourier Transform Near Infrared (FT-NIR) Microspectroscopy, Fluorescence and High-Resolution NMR (HR-NMR). The first FT-NIR chemical images of biological systems approaching 1 micron (1&amp;#x3bc;) resolution are presented here. Chemical images obtained by FT-NIR and FT-IR Microspectroscopy are presented for oil in soybean seeds and somatic embryos under physiological conditions. FT-NIR spectra of oil and proteins were obtained for volumes as small as 2&amp;#x3bc;3. Related, HR-NMR analyses of oil contents in somatic embryos are also presented here with nanoliter precision. Such 400 MHz 1H NMR analyses allowed the selection of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6200/version/1

Data Curation in Biology - Past, Present and Future
Provedor de dados: 17
Autores: Janet Thornton.
Data curation has been critical in the development of biology from Darwin and Linnaeus to UniProt, the careful collection and organisation of data has been the spring from which new hypotheses and understanding have emerged. In this presentation, I will describe how we have used data curation in my own research group - and also present an overview of curation at the EBI. With new technical developments and the move towards the semantic web, the role of curation in the future needs to develop to take advantage of these new opportunities. This will be discussed.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3225/version/1

Inhibition of Acid Phosphatase Enzyme Activity in the Presence of Noncrystalline Calcium Phosphate and Nanocrystalline Calcium Apatite: a Preliminary Study
Provedor de dados: 17
Autores: Yassen Pekounov.
*Background*&amp;#xd;&amp;#xa;Our bones are remodelled repeatedly during life. A new and &amp;#x201c;healthy&amp;#x201d; bone tissue replaces the old one. Accordingly, the bone degrading cells, the osteoclasts, prefer old and fatigued bone. The young bone mineral, i.e. calcium apatite, is less crystalline than the mature one. Is it possible that the osteoclasts distinguish between relatively old and new bone via its crystallinity?&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Methodology/Principal Findings*&amp;#xd;&amp;#xa;Acid phosphatase is an enzyme largely expressed by the osteoclasts during resorption and therefore used as a marker of the cells activity. This study explores whether its enzymatic activity would be decreased in the presence of biomimitetically...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3658/version/1

Molecular implications of prolonged aggression experience: Th, Dat1, Snca and Bdnf gene expression in the ventral tegmental area of the victorious male mice
Provedor de dados: 17
Autores: N.  P. Bondar; U.  A. Boyarskikh; I. L. Kovalenko; M. L. Filipenko; N.  N. Kudryavtseva.
Th, Dat1, Snca and Bdnf were the genes whose mRNA levels in the ventral tegmental area of the midbrain were measured in male mice that were victorious in 20 daily agonistic interactions and in a group of such victorious mice that had later not been allowed to fight for 14 days. This experiment demonstrated increased Th, Dat1 and Snca but not Bdnf mRNA levels in the former group as compared to the controls. In the latter group, the expression of the Th and Dat1 genes was still enhanced, while the level of Snca mRNA did not differ from that in the controls. These findings suggest that positive fighting experience enhances the expression of the genes concerned with dopaminergic systems and this enhanced expression is preserved for a long time afterwards....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2043/version/1

Increasing Access To Bioinformatics Resources: Increase Community Curation by Increasing Your Community
Provedor de dados: 17
Autores: Jennifer M. Williams.
The amount of biological data has risen exponentially over the last decade. Along with this rise, the number and types of bioinformatics resources has risen such that the sheer number of bioinformatics resources is overwhelming. For these resources to attain their full potential, they must be efficiently and extensively utilized. But in such a plethora of resources, how does a researcher new to a field find the resources that will meet their needs. Once a resource is found, how does the researcher quickly learn to utilize that resource fully? There are resource lists such as those provided by the journal Nucleic Acid Research (NAR), BioMed Central and the Univ. of Pittsburgh Health Sciences Library, and most resources include their own documentation. But...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3163/version/1

Nonlinear Models of Neural and Genetic Network Dynamics
Provedor de dados: 17
Autores: I. C. Baianu.
A categorical and &amp;#x141;ukasiewicz-Topos framework for &amp;#x141;ukasiewicz LM-Algebraic Logic models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes is proposed. &amp;#x141;ukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7114/version/1

Collective cell guidance by cooperative intercellular forces
Provedor de dados: 17
Autores: Dhananjay T. Tambe; Charles C. Hardin; Jeffrey J. Fredberg; Xavier Trepat.
Cells comprising a tissue migrate as part of a collective. In order to coordinate collective multi- cellular migration, each constituent cell integrates local information including chemical signals and mechanical stresses.&amp;#x9;The boundary between a constituent cell and its immediate neighbors comprises cell-cell junctions and cryptic lamellipodia, but the state of local mechanical stress exerted at that boundary has not been accessible experimentally. As such it is not clear how collective mechanical processes could be coordinated over length scales spanning large multi-cellular assemblies. We report here maps of the stresses exerted within and between cells comprising a monolayer. Within the cell sheet there arise unanticipated fluctuations of...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5405/version/1

Open Data in Science
Provedor de dados: 17
Autores: Peter Murray-Rust.
Open Data (OD) is an emerging term in the process of defining how scientific data may be published and re-used without price or permission barriers. Scientists generally see published data as belonging to the scientific community, but many publishers claim copyright over data and will not allow its re-use without permission. This is a major impediment to the progress of scholarship in the digital age. This article reviews the need for Open Data, shows examples of why Open Data are valuable and summarizes some early initiatives in formalizing the right of access to and re-use of scientific data.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1526/version/1

KaPPA-View4: A Pathway Database for Gene Co-expression and Metabolite Co-accumulation Analysis
Provedor de dados: 17
Autores: Nozomu Sakurai.
Correlations of gene-to-gene co-expression and metabolite-to-metabolite co-accumulation are considered to be useful for uncovering unknown functions of genes and regulatory systems of the metabolic pathways. Although many databases and tools are available to interpret quantitative data of transcriptome and metabolome, there are only limited ones that connect correlation data to biological knowledge and can be utilized to find biological significance of it. We developed a new metabolic pathway database, KaPPA-View4 (&amp;#x22;http://kpv.kazusa.or.jp/kpv4/&amp;#x22;:http://kpv.kazusa.or.jp/kpv4/), that enables to overlay gene-to-gene and/or metabolite-to-metabolite relationships as quadratic Bez&amp;#xed;er curves on metabolic pathway maps. For up to 4 maps...
Tipo: Presentation
Palavras-chave: Microbiology; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5065/version/1

Extragenic Suppression analysis of TS mutations using Sec61p
Provedor de dados: 17
Autores: Sterling Smith.
During synthesis, secretory and membrane proteins are cotranslationally translocated into the lumen of the endoplasmic reticulum through an aqueous gated channel. Proper folding, degradation, and transport of many polypeptides depend on a diverse set of helper proteins termed chaperone. I hypothesize that&amp;#xd;&amp;#xa;Sec 61p is a membrane chaperone, which actively directs membrane protein folding.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/651/version/1

Tumor suppressors p53, p63, and p73 inhibit migrating cancer stem cells by increasing the expression of stem cell suppressing miRNAs
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
ZEB1/2 has been shown to suppress the expression of the tumor suppressors E-cadherin, TA-p73, INK4b, CDKN1a, and thereby promotes epithelial to mesenchymal transition, invasion, and metastasis.  I have recently shown that p53-dependent miRs, such as miR-192, 215, 145, 203, 200b/c, 183, suppress the expression of ZEB1/2.  Another recent study showed that ZEB1/2 suppresses the expression of miR-200b/c, miR-203, &amp;#x26; miR-183, which in turn, inhibit the expression of stem cell factors, such as Sox-2, Klf-4, and BMI.  ZEB1/2, by inhibiting the expression of stem cell factors suppressing miRs, it up regulates the expression of stem cell factors.  By up regulating the stem cell factors and down regulating metastasis suppressors, ZEB1/2 promotes both...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4385/version/1

Translational Oncogenomics and Human Cancer Interactome Networks
Provedor de dados: 17
Autores: I. C. Baianu.
An overview of translational, human oncogenomics, transcriptomics and cancer interactomic networks is presented together with basic concepts and potential, new applications to Oncology and Integrative Cancer Biology. Novel translational oncogenomics research is rapidly expanding through the application of advanced technology, research findings and computational tools/models to both pharmaceutical and clinical problems. A self-contained presentation is adopted that covers both fundamental concepts and the most recent biomedical, as well as clinical, applications. Sample analyses in recent clinical studies have shown that gene expression data can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6190/version/2

Multi-scale network biology model &amp;#x26; the model library
Provedor de dados: 17
Autores: Jianghui Xiong.
Multi-scale network biology model &amp;#x26; the model library
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5778/version/1

p53 Response to DNA Damage in S-phase
Provedor de dados: 17
Autores: David Reisman; Paula Takahashi; Amanda Polson.
p53 induces the transcription of genes that negatively regulate progression of the cell cycle in response to DNA damage or other cellular stressors, and thus participates in maintaining genome stability. Under stress conditions, p53 must be activated to prohibit the replication of cells containing damaged DNA. However, in normal, non-stressed cells, p53 activity must be inhibited. Previous studies have demonstrated that p53 transcription is activated before or during early S-phase in cells progressing from G0/G1 into S-phase. In that this is not what would be predicted from a gene involved in growth arrest and apoptosis, in this study, we provide evidence that this induction occurs to provide available p53 mRNA in order to prepare the cell for DNA damage...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4403/version/1

Metabolic, Replication and Genomic  Category of Systems in Biology,  Bioinformatics and Medicine
Provedor de dados: 17
Autores: I. C. Baianu.
Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life&amp;#x2019;s origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important question of the minimal living organism by defining the functional relations that would have made life possible in such a minimal system- a grandad and grandma of all living organisms on Earth. Genomic systems are also considered as molecular realizations of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7051/version/1

Capturing Protein Sequence Data: UniProt Knowledgebase (UniProtKB) submissions and Journal Scanning
Provedor de dados: 17
Autores: Paul Browne; Ruth Eberhardt.
Most sequences in UniprotKB are derived from the translation of nucleotide sequence, but we also add sequences obtained through direct sequencing of peptides by Edman degradation and tandem mass spectrometry. This allows us to capture protein sequences for which no nucleotide sequence is available, and can also confirm that a predicted protein exists and elucidate the post-translational processing it undergoes. Scientists submit protein sequences to UniProtKB via the web-based submission tool &amp;#x22;SPIN&amp;#x22;:http://www.ebi.ac.uk/swissprot/Submissions/spin. Curators use a range of sequence analysis tools to check the submission and frequently discuss the sequence and supporting evidence with the submitter. Submitted entries can be kept confidential...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3120/version/1

Probing the connectivity of neural circuits at single-neuron resolution using high-throughput DNA sequencing
Provedor de dados: 17
Autores: Hassana Oyibo; Gang  Cao; Huiqing Zhan; Alex Koulakov; Lynn Enquist; Joshua Dubnau; Anthony  Zador.
There is growing excitement in determining the complete connectivity diagram of the brain&amp;#x2014;the &amp;#x22;connectome&amp;#x22;. So far, the complete connectome has been established for only one organism, C. elegans, with 302 neurons connected by about 7000 synapses&amp;#x2014;and even this was a heroic task, requiring over 50 person-years of labor. Like all current approaches, this reconstruction was based on microscopy. Unfortunately, microscopy is poorly suited to the study of neural connectivity because brains are macroscopic structures, whereas synapses are microscopic. Nevertheless, there are several large-scale projects underway to scale up high-throughput microscopic approaches to the connectome.&amp;#xd;&amp;#xa;Here we present a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6452/version/1

Chemopreventive potential of natural products isolated from a alchornea glandulosa, pterogyne nitens and its semisynthetic analogs
Provedor de dados: 17
Autores: Mauro  C. C. Morais; Laura  E. Marler; Suaib  Luqman; Tamara  P. Kondratyuk; Maicon  S. Petronio; Luis  O. Regasini; Dulce  H. S. Silva; Vanderlan  S. Bolzani; Christiane  P. Soares; John  M. Pezzuto.
INTRODUCTION: Chemoprevention involves the use of natural or synthetic substances to reduce the risk of developing cancer. Gallic acid was found to possess several pharmacological activities, such as anti-oxidant and anti-inflammatory. Guanidine alkaloids display a broad spectrum of biological activities and its cytotoxic effect were well investigated.&amp;#xd;&amp;#xa;OBJECTIVES: The present study evaluated the chemopreventive potential of natural products and its semi-synthetic analogs using quinone reductase (QR) induction, aromatase inhibition and the suppression of NF&amp;#x3ba;B activity, which are well established strategies for screening compounds to cancer chemoprevention. &amp;#xd;&amp;#xa;METHODS: Gallic acid was isolated from Alchornea...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6923/version/1

Oxidative Stress and Mitochondrial Injury in Chronic Multisymptom Conditions:  From Gulf War Illness to Autism Spectrum Disorder
Provedor de dados: 17
Autores: Beatrice A. Golomb.
Background: Overlapping chronic multisymptom illnesses (CMI) include Chronic Fatigue Syndrome (CFS), fibromyalgia, irritable bowel syndrome, multiple chemical sensitivity, and Gulf War illness (GWI), and subsets of autism spectrum disorder (ASD). GWI entails a more circumscribed set of experiences that may provide insights of relevance to overlapping conditions.&amp;#xd;&amp;#xa;Objectives: To consolidate evidence regarding a role for oxidative stress and mitochondrial dysfunction (OSMD), as primary mediators in CMI, using GWI as a departure point.&amp;#xd;&amp;#xa;Methods: Exposure relations, character, timecourse and multiplicity of symptoms, and objective correlates of GWI are compared to expectation for OSMD. Objective correlates of OSMD in GWI and...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6847/version/1

Detection of MicroRNAs in Dried Serum Blots
Provedor de dados: 17
Autores: Santosh K. Patnaik; Reema Mallick; Sai Yendamuri.
MicroRNAs are short RNAs which can be utilized as biomarkers for a variety of conditions. They are detectable in serum, and changes in the levels of circulating microRNAs have been associated with different diseases. We tested for the presence of microRNAs in serum that is dried on paper and stored unrefrigerated instead of being kept frozen. MicroRNAs were readily detectable in such blots, and their detectability was improved by using paper made of cellulose instead of glass fiber, and by re-hydrating dried blots with Trizol&amp;#x2122; instead of water, phosphate-buffered saline, or guanidine hydrochloride before RNA extraction. MicroRNA preservation was not diminished by drying of blots at 37, 45 or 60 &amp;#xba;C instead of room temperature or by...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4785/version/1

Quantitative Models for Efficient Cloning of Different Vectors with Various Clone sites
Provedor de dados: 17
Autores: Gang Zhang; Anurag Tandon.
We developed an efficient &amp;#x22;Combinatorial Strategy&amp;#x201d; for cloning different vectors with various clone sites. 1) Using originally existed clone sites from circular vectors to prepare the inserts, and if no appropriate sites are available, performing SDM to create compatible sites, to achieve maximal correct digestion of the inserts. 2) Different vectors were digested with various restriction endonucleases, and then dephosphorylated with CIP. 3) Top10 competent cells were used for transformation to increase the transformant colonies. Our results showed that, when blunt sites, or a Xba I site was adopted for ligation, the percentages of positive clones were about 50%. Whereas, when different sites, including one blunt and another Pst I...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Immunology; Microbiology; Molecular Cell Biology; Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6965/version/1

Archaebacterial Whole-Genome Duplication and Origin of Eukaryots
Provedor de dados: 17
Autores: Milanko Stupar.
Division of the ancestral prokaryotic pragenome into two circular double-stranded DNA molecules by genetic recombination, is a base for the future separate evolution of the nuclear and mitochondrial gene compartment. This suggests monophyletic origin of both mitochondrion and nucleus. Presumed organism which genome undergoes genetic recombination has to be searched among an aerobic, oxygen non-producing archaeon with no rigid cell wall, but a plasma membrane. Plastids evolve from an aerobic, oxygen producing proto-eukaryot, after mitoplastide genome duplication and subsequent functional segregation.In this proposal origin of eukaryots occur by a three-step mechanism. First, replication fork pauses and collapses generating a breakage in the genome of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2302/version/1

Manual Curation of Vertebrate Proteins  in the UniProt Knowledgebase.
Provedor de dados: 17
Autores: Michael  J. Gardner; Lionel  Breuza; The UniProt  Consortium.
The UniProt Knowledgebase (UniProtKB) aims to provide the scientific community with a comprehensive, consistent and authoritative resource for protein sequence and functional information. Given the importance of human and vertebrate model data in biomedical research, a major focus is the high-quality manual curation of human proteins and their vertebrate orthologues. Manual curation involves (1) the extraction of experimental results from scientific literature to enrich protein records with a wide range of information including function, structure, interactions and subcellular location, (2) the manual verification of each sequence and clarification of discrepancies between sequence reports, and (3) the assessment of the output of a range of analysis...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5165/version/1

Design of RNAi reagents for invertebrate model organisms and human disease vectors
Provedor de dados: 17
Autores: Thomas Horn; Michael Boutros.
RNAi has become an important tool to silence gene expression in a variety of organisms, in particular when classical genetic methods are missing. However, application of this method in functional studies has raised new challenges in the design of RNAi reagents in order to minimize false positive and false negative results. Since the performance of reagents can be rarely validated on a genome-wide scale, improved computational methods are required that consider experimentally derived design parameters. Here, we describe computational methods for the design of RNAi reagents for invertebrate model organisms and human disease vectors, such as Anopheles. We describe procedures on how to design short and long double-stranded RNAs for single genes, and evaluate...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6665/version/1

EGFP-FMRP Granules Are Proto-Granules That Can Be Shunted to Stress Granules During a Stress Response
Provedor de dados: 17
Autores: Robert Denman.
Overexpressed EGFP-FMRP has been used as a substitute for endogenous fragile X mental retardation protein (FMRP) in protein-protein interaction studies, and in studies concerning the composition, the formation and the localization of neuronal granules. However, the question of whether this tool truly recapitulates the properties of the endogenous protein has not been addressed. Here we demonstrate that overexpressed EGFP-FMRP forms three distinct granule types based on colocalization with various marker proteins. The majority of EGFP-FMRP-containing granules are larger and more amorphous than known granule types. Consistent with this, there is only partial colocalization with stress granule or P-body markers and no colocalization with a putative Drosophila...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5442/version/1

Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs
Provedor de dados: 17
Autores: Leonid Mirny; Zeba Wunderlich.
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6-10^9 decoy sites? Our analysis of 319 known TF binding motifs clearly demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations; eukaryotic TFs exhibit widespread nonfunctional binding and require clustering of sites in regulatory regions for specificity.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2688/version/1

The Immune Response in Patients with SARS: differential gene expression profiling.
Provedor de dados: 17
Autores: Peter Natesan Pushparaj; Jayapal J. Manikandan; Alirio Jose A. J. Melendez.
Severe acute respiratory syndrome (SARS) emerged in 2003, as a new epidemic form of life-threatening infection. As of 26th September 2003, there were 8422 cases of SARS from 29 countries with 908 deaths (WHO). However, the pathogenesis of SARS is poorly understood. To understand the host response to this pathogen, we profiled the gene expression patterns of peripheral blood mononuclear cells (PBMC) from SARS patients compared to healthy controls using one of the latest techniques, high density oligonucleotide expression probe array (HG-Focus array, Gene Chip, Affymetrix, Santa Clara, CA). High-density oligonucleotide microarray is a promising approach for high throughput analysis. It has been extensively&amp;#xd;&amp;#xa;used in many areas of biomedical...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1145/version/1

Bio-communication of Plants
Provedor de dados: 17
Autores: Guenther Witzany.
Plants communicate with a great variety of symbiotic partners, above and below ground. Constant monitoring of signals of biotic origin as well as abiotic environmental influences allows plants to generate appropriate response behavior. These communication processes are primarily sign-mediated interactions and not simply an exchange of information. They involve active coordination and active organization of a great variety of different behavioural patterns &amp;#x2013; mediated by signs.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Molecular Cell Biology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1429/version/1

Protein folding disorders: Toward a basic biological paradigm
Provedor de dados: 17
Autores: Rodrick Wallace.
Mechanistic &amp;#x27;physics&amp;#x27; models of protein folding fail to account for the observed spectrum of protein folding and aggregation disorders, suggesting that a cognitive paradigm for protein folding regulation will be needed for understanding the etiology, prevention, and treatment of these diseases.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4344/version/2

A dynamical model of genetic networks describes cell differentiation
Provedor de dados: 17
Autores: Roberto Serra; Villani Marco; Alessia Barbieri.
Cell differentiation is a complex phenomenon whereby a stem cell becomes progressively more specialized and eventually gives rise to a specific cell type. Differentiation can be either stochastic or, when appropriate signals are present, it can be driven to take a specific route. Induced pluripotency has also been recently obtained by overexpressing some genes in a differentiated cell. Here we show that a stochastic dynamical model of genetic networks can satisfactorily describe all these important features of differentiation, and others. The model is based on the emergent properties of generic genetic networks, it does not refer to specific control circuits and it can therefore hold for a wide class of lineages. The model points to a peculiar role of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4741/version/1

Reputation, authority and incentives. Or: How to get rid of the Impact Factor
Provedor de dados: 17
Autores: Bj&amp;#xf6;rn Brembs; Peter Binfield.
A short intro into the impact factor and its limitations and potential successors.
Tipo: Presentation
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2801/version/1

Effect of a single Dialysis session on plasma Lp(a) levels in patients on Maintenance haemodialysis
Provedor de dados: 17
Autores: Varikasuvu Seshadri Reddy; MM Suchitra; Prabhakar E. Reddy; Aparna R. Bitla; Siva V. Kumar; PVLN Srinivasa Rao.
Background: &amp;#xd;&amp;#xa;Cardiovascular disease (CVD) is a major cause of mortality in End stage renal disease (ESRD) patients on Maintenance haemodialysis (MHD). Lp (a), is a specialized form of glycoprotein-LDL-cholesterol complex and is an independent risk factor for myocardial infarction. The risk is related to its atherogenic and thrombogenic properties. The present study was taken up to evaluate changes in Lp(a) and Lipid profile in patients undergoing hemodialysis session. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methodology: &amp;#xd;&amp;#xa;Twenty seven patients with end stage renal disease who were on maintenance hemodialysis were included. Plasma samples were collected hourly during a dialysis session with polysulfone membrane using bicarbonate...
Tipo: Poster
Palavras-chave: Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6473/version/1

A schistosome [beta] subunit remodels inactivation of a calcium channel _via_ an N-terminal polyacidic motif
Provedor de dados: 17
Autores: Vicenta Salvador-Recatala; Robert M. Greenberg.
The beta subunit of high voltage-activated Ca (Cav) channels targets the pore forming [alpha]~1~ subunit to the plasma membrane and defines the biophysical phenotype of the Cav channel complex. Cav channel inactivation following activation and opening is tightly regulated and is an essential property that not only prevents excessive entry of Ca^2+^ into the cell but may also have functions in signal transduction. The [beta] subunit modulates Ca^2+^-dependent and voltage-dependent components of Cav channel inactivation via its interaction with the I-II linker of the [alpha]~1~ subunit. Here, using Cav2.3 and whole-cell patch-clamp, we show that a [beta] subunit from the human parasite _Schistosoma mansoni_ ([beta]~Sm~) accelerates inactivation via a unique,...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4230/version/1

Keratinocytes from human skin respond as typical immune cells after the stimulation with _Trichophyton rubrum_
Provedor de dados: 17
Autores: Alfonso E. Islas-Rodr&amp;#xed;guez; Luz A. Garc&amp;#xed;a-Madrid.
_Trichophyton rubrum_ is the main agent causing dermatophytosis (1). Keratinocytes are&amp;#xd;&amp;#xa;considered to be the first physical barrier of defense against pathogens (2). But not&amp;#xd;&amp;#xa;only a physical barrier. They recognize antigens through Toll like receptors (TLR) (3).&amp;#xd;&amp;#xa;The activation of this TLR, present on the surface of the keratinocytes, induce the&amp;#xd;&amp;#xa;expression of different pro-inflammatory cytokines, co-stimulatory molecules and&amp;#xd;&amp;#xa;antimicrobial peptides such as [beta]-defensins (4).&amp;#xd;&amp;#xa;The main objective of this work is to determine if lipopolysaccharides of G &amp;#x2013; bacteria&amp;#xd;&amp;#xa;(LPS), lipotheichoic acid from G+ bacteria (LTA), and conidias,...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/930/version/1

SED-ML Web Tools
Provedor de dados: 17
Autores: Frank T. Bergmann.
This presentation gives a brief update of the current state of the libSedML library and its new capabilities (like the simulation of CellML models) and the SED-ML Script Editor.  &amp;#xd;&amp;#xa;Following I introduce the SED-ML Web Tools, an online application for creating, editing, simulating and validating SED-ML documents. The web application also provides a W3C Web Service, exposing all functionality.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6328/version/1

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry lifting model based on Tlusty&amp;#x27;s elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4120/version/4

DNA expression microarrays may be the wrong tool to identify biological pathways
Provedor de dados: 17
Autores: Adrian Mondry; Marie Loh; Alessandro Giuliani.
DNA microarray expression signatures are expected to provide new insights into patho- physiological pathways. Numerous variant statistical methods have been described for each step of the signal analysis. We employed five similar statistical tests on the same data set at the level of gene selection. Inter-test agreement for the identification of biological pathways in BioCarta, KEGG and Reactome was calculated using Cohen&amp;#x2019;s k- score. The identification of specific biological pathways showed only moderate agreement (0.30 &amp;#x3c; k &amp;#x3c; 0.79) between the analysis methods used.  Pathways identified by microarrays must be treated cautiously as they vary according to the statistical method used.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1036/version/1

Detection of substrate binding motifs for morphine biosynthetic pathway intermediates in novel wound inducible (R,S)-reticuline 7-O-methyltransferase of Papaver somniferum
Provedor de dados: 17
Autores: Sonal Mishra; Abha Meena; Sema Singh; Dharmendra Kumar Yadav; Feroz  Khan; Rakesh K. Shukla.
The benzylisoquinoline alkaloids (BIA) comprise a large and diverse group of nitrogen-containing secondary metabolites with about 2500 compounds identified in plants. BIA biosynthesis begins with the condensation of the tyrosine derived precursors dopamine and p-hydroxyphenylacetaldehyde to (S)-norcoclaurine. Subsequent regiospecific O- and N-methylations and aromatic ring hydroxylation lead to (S)-reticuline, which is the central intermediate for almost all BIAs. For morphinan alkaloid biosynthesis, (S)-reticuline undergoes an inversion of stereochemistry to (R)-reticuline, followed by C-C phenol coupling catalyzed by a unique cytochrome P450-dependent monooxygenase to yield salutaridine. The cDNA sequence of enzymes leading to (S)-reticuline, as well as...
Tipo: Poster
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5790/version/1

WikiPathways: Community Curation of Biological Pathways
Provedor de dados: 17
Autores: Alexander Pico.
Assembling biological pathways from information in scientific literature and biological databases is a challenging task. Building a pathway requires domain knowledge from specialists in various biological research areas. Furthermore, research is generating new biological knowledge continuously, making pathway curation an ongoing and dynamic process. To facilitate this process we developed &amp;#x22;WikiPathways&amp;#x22;:http://www.wikipathways.org ^1^, a wiki where users can curate pathways, using an easy to use pathway drawing tool. WikiPathways currently has over 1200 registered users and contains more than 1300 pathways for various organisms, spanning human, mouse, zebrafish, fruit fly, worm, yeast, plants and bacteria. WikiPathways is entering a phase...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5361/version/1

Implementation of computational methods for designing potential inhibitors against human p38&amp;#x3b1; protein
Provedor de dados: 17
Autores: Durga Devi M; Dibyabhaba  Pradhan; Manne Munikumar; Amineni Umamaheswari.
p38&amp;#x3b1;, a non-receptor serine/threonine kinase, plays an essential role in cell proliferation, cell differentiation, apoptosis, production of cytokines such as IL1&amp;#x3b2; and TNF&amp;#x3b1;, senescence and tumorigenesis. Over expression of p38&amp;#x3b1; enhances the production of cytokines, leading to inflammation causing cancers. Therefore, the protein p38&amp;#x3b1; is selected as a target for the inhibition of progression of inflammatory cancers. SB203580, BIRB796, 2H-quinolizine-2-one, 7-alkyl-1,5-bis&amp;#x2013;aryl-pyrazolo pyridinones, aML3403, N-pyrimidyl amides, Fused pyrazoles, SD0006, 4-3-(4-fluoro phenyl )-1H-pyrazol-4-yl)pyridine are the nine published inhibitors for the p38&amp;#x3b1;, but they show side effects like liver...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5456/version/1

Human Heart Development Pathways
Provedor de dados: 17
Autores: Samuel Sklar; Alexander Pico.
This pathway has been largely adapted from an article by Deepak Srivastava, Cell. 2006 Sep 22;126(6):1037-48. In this pathway are known transcription factors, miRNAs and regulatory proteins that impact the regional specificity of the human heart. Activating signals are indicated by arrows while inhibitory signals are indicated by T-bars. Special thanks to Kim Cordes for her assistance in revising this pathway, based on recent heart development research. A live version of the pathway can be found at http://www.wikipathways.org/index.php/Pathway:WP1591
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6500/version/1

Single Cancer Cell Detection by Near Infrared Microspectroscopy, Infrared Chemical Imaging and Fluorescence Microspectroscopy
Provedor de dados: 17
Autores: I. C. Baianu; Schuyler S. Korban; Doina M. Costescu.
Novel techniques are currently being developed and established for the accurate chemical analysis and detection of single cancer cells, single embryos and single seeds by Fourier Transform Near Infrared (FT-NIR) Microspectroscopy, Fourier Transform Infrared (FT-IR), Fluorescence and High-Resolution NMR (HR-NMR). The first FT-NIR chemical images of biological systems approaching 1micron resolution are here reported. 400 and 500 MHz, H-1 NMR analyses were carried out that allowed the selection of mutagenized embryos. Detailed chemical analyses are being demonstrated to be also possible by FT-NIR Chemical Imaging/ Microspectroscopy of single cancer cells. FT-NIR Microspectroscopy and Chemical Imaging are also shown to be potentially important in Functional...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6207/version/1

The effects of anti-sense interleukin-5 gene transferred by recombinant adeno-associated virus in allergic rats
Provedor de dados: 17
Autores: Daxiong Zeng; Yong Cao; Qingfeng Song; Chao Cao; Xiansheng Liu; Yongjian Xu; Weining Xiong.
The accumulation and infiltration of eosinophils in airways is one of the most important characteristics of asthma, and is mediated partly by secretion of IL-5 from Th2 lymphocytes. It is well known that interleukin-5 (IL-5) played an important role in the regulation of eosinophils. In this study, an anti-sense IL-5 gene transferred by recombinant adeno-associated virus (rAAV-ASIL-5) was prepared to transfect allergic rats. It was found that the expression of IL-5 protein in plasma and BALF were inhibited significantly. The rAAV-ASIL-5-mediated suppression of total cell counts in peripheral blood and BALF were also observed. Moreover, rAAV-ASIL-5 remarkably reduced the eosinophil counts in peripheral blood and BALF, as well as the expression of ECP protein...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2036/version/1

Accelerated Macromolecular Solution Structure Recovery
Provedor de dados: 17
Autores: Petrus Zwart; Haiguang Liu.
Small Angle X-ray Scattering (SAXS) is a standard technique for the determination of low-resolution shapes of macromolecules and their complexes, adding important insights in understanding biological function. We present a novel and computationally efficient method for shape reconstruction from SAXS data. High-quality molecular shapes are calculated in less than two minutes, providing real-time feedback during SAXS experiments.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6521/version/1

The monoclonal antibody nBT062 conjugated to maytansinoids has potent and selective cytotoxicity against CD138 positive multiple myeloma cells _in vitro_ and _in vivo_
Provedor de dados: 17
Autores: Hiroshi Ikeda; Teru Hideshima; Robert J. Lutz; Hiroshi Yasui; Yutaka Okawa; Tanyel Kiziltepe; Sonia Vallet; Samantha Pozzi; Loredana Santo; Giulia Perrone; Mariateresa Fulciniti; Yu-Tzu Tai; Diana Cristea; Noopur S. Raje; Christoph Uherek; Benjamin D&amp;#xe4;lken; Silkie Aigner; Frank Osterroth; Nikhil C. Munshi; Paul Richardson; Kenneth C. Anderson.
CD138 (Syndecan1) is highly expressed on multiple myeloma (MM) cells. In this study, we examined the anti-MM effect of murine/human chimeric CD138-specific monoclonal antibody (mAb) nBT062 conjugated with highly cytotoxic maytansinoid derivatives _in vitro_ and _in vivo_. These agents significantly inhibited growth of CD138-positive MM cell lines and primary tumor cells from MM patients, without cytotoxicity against peripheral blood mononuclear cells from healthy volunteers. In MM cells, they induced G2/M cell cycle arrest followed by apoptosis associated with cleavage of PARP and caspase-3, -8 and -9. Non-conjugated nBT062 completely blocked cytotoxicity induced by nBT062-maytansinoid conjugate, confirming that binding is required for inducing...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2374/version/1

Open Source Kinesin-1 Stochastic Simulation and Gliding Assay Tracking Software
Provedor de dados: 17
Autores: Lawrence J. Herskowitz; Anthony L. Salvagno; Brian P. Josey; Andy Maloney; Steven J. Koch.
Kinesin-1 (conventional kinesin) is a homodimeric motor protein important for axonal transport. It has been well studied through ensemble and single-molecule assays. However, the enzymatic stepping cycle is complex, with many rate constants that are modulated by interaction of the two motor domains. This makes it difficult to predict how changes in a given rate constant may affect observable properties such as processivity, velocity, or stall force. We have written a simulation of kinesin walking using a Stochastic Simulation Algorithm. The model allows for interactions between the heads, and includes states that are not considered part of the normal cycle. This adds to the complexity of the model but also allows for probing rare events, such as those that...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4468/version/1

The &amp;#x27;consciousness&amp;#x27; of the living state: Extending the Baars global broadcast model across physiological subsystems
Provedor de dados: 17
Autores: Rodrick Wallace.
For the broad spectrum of cognitive biological phenomena having &amp;#x27;dual&amp;#x27; information sources, isolation from crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts at multiple scales, similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems. Entropy gradient models adapted from nonequilibrium thermodynamics lead to an index theorem in which analytic solutions of empirical equations describe different possible topological modes. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Ecology; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6898/version/2

Effect Of A Dialysis Session On Plasma Branched Chain Aminio Acids In Hemodialysis Patients
Provedor de dados: 17
Autores: Varikasuvu Seshadri Reddy; PVLN Srinivasa Rao; Aparna R. Bitla; Siva V. Kumar; MM Suchitra; Prabhakar E. Reddy.
Protein and amino acid (AA) metabolism is abnormal in End stage renal disease (ESRD). Hemodialysis (HD) procedure is a strong catabolic stimulus. Branched chain amino acids (BCAAs) can affect other AA levels by reducing AA efflux from muscle due to inhibition of muscle protein degradation. Essential amino acids and keto acid supplements including BCAA and branched-chain keto acid (BCKA) are proposed to decrease protein intake while maintaining protein status. This study was taken up to evaluate the effect of a dialysis session on plasma BCAA&amp;#x2019;s for which fifteen patients of ESRD on Maintenance HD, thrice a week were recruited into the study. Analysis was done on samples drawn at the beginning (pre-HD) and after the end of each dialysis session...
Tipo: Presentation
Palavras-chave: Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6475/version/1

Transient-mediated fate determination in a transcriptional circuit of HIV
Provedor de dados: 17
Autores: Leor Weinberger; Roy D. Dar; Michael Simpson.
Steady-state behavior and bistability have been proposed as mechanisms for decision-making in gene circuits. However, transient gene expression has also been proposed to control cell fate with the decision arbitrated by the lifetime of the expression transient. Here, we report that transcriptional positive-feedback plays a critical role in determining HIV infected cell-fate by extending the duration of Tat expression transients far beyond what protein half-life modulation can achieve. To directly quantify feedback strength and its effects on the duration of Tat transcriptional pulses, we exploit the noise inherent to gene-expression and measure shifts in the autocorrelation of expression noise. The results indicate that transcriptional positive-feedback...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1198/version/1

Modeling Three-Dimensional Spatial Regulation of Bacterial Cell Division (Dissertation)
Provedor de dados: 17
Autores: Satya N. V. Arjunan.
Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4201/version/1

ARHI (DIRAS 3), an Imprinted Tumor Suppressor Gene, Binds to Importins, and Blocks Nuclear Translocation of Stat3
Provedor de dados: 17
Autores: Shaoyi Huang; In Soon Chang; Wenbo Lin; Robert Luo; Zhen Lu; Yiling Lu; Ke Zhang; Warren Liao; Tao Tao; Robert Bast, Jr.; Xiaomin Chen; Yinhua Yu.
ARHI (DIRAS3) is an imprinted tumor suppressor gene whose expression is lost in the majority of breast and ovarian cancers. Unlike its homologs Ras and Rap, ARHI functions as a tumor suppressor. Our previous study showed that ARHI can interact with transcription activator Stat3 and inhibit its nuclear translocation in human breast and ovarian cancer cells. To identify proteins that interact with ARHI in nuclear translocation, we have performed proteomic analysis and identified several importins that can associate with ARHI. To further explore this novel finding, we have purified 10 GST-importin fusion proteins (importin 7, 8, 13, b1, a1, a3, a5, a6, a7 as well as mutant a1). Using a GST-pull down assay, we found that ARHI can bind strongly to most...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2392/version/1

A novel regulator of the p53-mediated mitochondrial apoptotic pathway
Provedor de dados: 17
Autores: Bo Young Ahn; Diane Trinh; Laura Zajchowski; Sung-Woo Kim.
The p53 tumor suppressor protein induces apoptosis in response to genotoxic and environmental stress. Recent studies have revealed the existence of a transcription-independent mitochondrial p53 apoptosis pathway, however the mechanism regulating p53 translocation to mitochondria and subsequent initiation of apoptosis was not known. Here, we show that Tid1, also known as mtHsp40 or Dnaja3, interacts with p53 and directs its translocation to mitochondria in cells exposed to hypoxia. Overexpression of Tid1 in tumor cells promoted mitochondrial localization of both wildtype and mutant forms of p53 and was able to restore the pro-apoptotic activity of mutant p53 proteins that were otherwise unable to induce apoptosis. Tid1&amp;#x27;s mitochondrial signal...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1892/version/1

Inherited mutations impair responses to environmental carcinogens:  Cancer prevention in mutation carriers
Provedor de dados: 17
Autores: Bernard Friedenson.
Some environmental carcinogens may be responsible for a modest increase in the numbers of cancers after years of exposure.  Economic or political factors weigh against widespread bans of carcinogens.  However, lists of chemicals and agents that cause cancer assume that everyone is equally susceptible to their carcinogenic effects. &amp;#xd;&amp;#xa;Hereditary cancer gene mutations can target specific tissues if they are exposed to a carcinogen and the hereditary deficit impairs normal protective responses.  Mutation carriers should then have higher risks for specific cancers caused by specific carcinogens.&amp;#xd;&amp;#xa;  &amp;#xd;&amp;#xa;For example, it can be predicted that BRCA1 or BRCA2 mutation carriers should be highly susceptible to the...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6024/version/1

Proapoptotic Bid Association with Mre11-Rad50-Nbs1 Complex is Indispensable for Checkpoint Activation after DNA Damage
Provedor de dados: 17
Autores: Van B. T. Ta; Karel Bezstarosti; Jeroen A. A. Demmers; Timurs Maculins; Karlyn Schellekens; Dik C. C. van Gent; Stephan P. Persengiev.
The proapoptotic protein Bid is phosphorylated by ATM after double strand breaks (DSBs) induction and induces S-phase arrest by a mechanism that remains to be elucidated. Here we show that in mammalian cells, Bid is associated with Mre11, a subunit of the Mre11-Rad50-Nbs1 (MRN) complex. We demonstrate that Bid activation is abrogated in Mre11 and Nbs1 deficient primary mouse fibroblasts and cells from patients with ataxia talangiectasia-like disorder. Bid depletion by RNA interference inhibited the S-phase checkpoint activation and G2/M arrest after genotoxic insult, but had no effect on MRN complex formation. Our results explain the mechanism of Bid phosphorylation by ATM in response to DNA damage and suggest that Bid functions as a link between the MRN...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1203/version/1

Computational system biology
Provedor de dados: 17
Autores: Ankit Geete.
Systems biology is a multi-disciplinary &amp;#xfb01;eld that deals with mechanisms involved in complex biological processes by considering them as integrated systems of multiple interacting components. The huge amount of data involved in this study necessitates the use of computational tools.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7104/version/1

Endothelin-Induced Sarcoplasmic Reticulum Calcium Depletion Waves in Vascular Smooth Muscle Cells
Provedor de dados: 17
Autores: Mitra Esfandiarei; Yohan Choi; Arash Y. Tehrani; Jeremy G. Hoskins; Nicola Fameli; Cornelis van Breemen.
Agonist-stimulated waves of elevated cytoplasmic Ca2+ concentration ([Ca2+]i ) regulate blood vessel tone and vasomotion in vascular smooth muscle. Previous studies employing cytoplasmic Ca2+ indicators revealed that these Ca2+ waves were generated by a combination of inositol 1,4,5-trisphosphate (IP3) and Ca2+ induced Ca2+ release (CICR) from the sarcoplasmic reticulum (SR); although, some of the mechanistic details remain uncertain. However, these findings were derived indirectly from observing agonist-induced [Ca2+]i fluctuations in the cytoplasm.&amp;#xd;&amp;#xa;Here, for the first time, we have recorded Endothelin-1 (ET-1) induced waves of Ca2+ depletion from the SR lumen in vascular smooth muscle cells (VSMCs) using a calsequestrin-targeted Ca2+...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6280/version/2

Designing L-Systems for making three and six open reading frames from the leading strand of a single DNA molecule
Provedor de dados: 17
Autores: Arunava Goswami; Rajneesh Singh; Pabitra Choudhury; Sk. Sarif Hassan Hassan.
Current molecular biology dogma (except alternative splicing) suggests that leading strand of DNA produces mRNA and usually the leading strand gives one ORF (ORF) among the available six ORFs. We attempted to break this rule where three and six ORFs from the leading strand will be formed by designing L-Systems, originally proposed to study symmetry of biological world. We thought this would revolutionize the world of synthetic biology. While doing so, we found L-System containing A&amp;#x2192;T, T&amp;#x2192;G, C&amp;#x2192;A, and G&amp;#x2192;C, i.e., single nucleotide production rule will stop growing after one nucleotide. L-System containing either (a) A&amp;#x2192;TG, T&amp;#x2192;GC, C&amp;#x2192;GA, G&amp;#x2192;TC or (b) A&amp;#x2192;CTG,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4844/version/1

Preventing hereditary cancers caused by opportunistic carcinogens
Provedor de dados: 17
Autores: Bernard Friedenson.
Objectives&amp;#xd;&amp;#xa;Previous studies reported inherited BRCA1/2 deficits appear to cause cancer by impairing normal protective responses to some carcinogens. Opportunistic carcinogens can exploit these deficits by causing chronic inflammation, constant cell death and replacement in a mutagenic environment, DNA crosslinking or double strand breaks. Some of the resulting cancers may be prevented if BRCA1/2 specific carcinogens are identified.&amp;#xd;&amp;#xa;Methods&amp;#xd;&amp;#xa;The literature was systematically searched for carcinogens capable of exploiting deficits in BRCA1/2 pathways. Search criteria were common exposure, available information, required BRCA1/2 pathway repairs, increased risks for any cancer, and effects on stem...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6636/version/1

The Differences Between Products Of Gene Expression In Male, Female And Hermaphrodite Cucumber Floral Buds (Cucumis Sativus L.)
Provedor de dados: 17
Autores: Magdalena Pawelkowicz; Ewa Siedlecka; Zbigniew Przybecki.
Cucumber is a species in which sex expression has been extensively studied. Sexual differentiation is controlled by genotypic and environmental factors. The main genes responsible for sex determination have been described but the mechanism of their action remains unexplained. In this study we attempted to find cDNA clones which can be connected with sex differentiation and flower development  in cucumber. &amp;#xd;&amp;#xa;Two pairs of nearly isogenic lines: GY-3 (gynoecious &amp;#x2013; FFMMGG) and HGY-3 (hermaphrodite - FFmmGG), B10 (monoecious - ffMMGG) and 2gg (gynoecious - FFMMgg) were used to search for differences in gene expression in young (1 &amp;#x2013; 2mm) cucumber floral buds.&amp;#xd;&amp;#xa;In order to obtain differentially expressed cDNA...
Tipo: Poster
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5605/version/1

Preincision Processing of Cyclobutane Pyrimidine Dimers in Escherichia coli
Provedor de dados: 17
Autores: Sunirmal Paul; Mitsumasa Hashimoto; Opinder Bhanot; Yoke Kow; Moon-shong Tang.
In both prokaryotes and eukaryotes cyclobutane pyrimidine dimers (CPD) formed by UV-irradiation are repaired mainly by the nucleotide excision repair (NER) pathway. Evidence has been presented that CPDs are repaired more rapidly and efficiently in vivo than when using purified NER components in vitro, and raises the possibility that CPD can be processed at the preincision stage before being removed by NER pathway. We investigated this hypothesis in E. coli cells and found that the phosphodiester bonds in CPDs are indeed incised (for the sake of simplicity we term this result as CPD*) in a time-dependent fashion in NER-proficient cells. This CPD preincision processing also occurs in NER-deficient uvrB- and uvrC-, but not in uvrA-mutant cells, and in...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1709/version/1

Control of cell division in the adult brain by heparan sulfates in fractones and vascular basement membranes
Provedor de dados: 17
Autores: Frederic Mercier; Vanessa Douet.
Regulation of cell division in adult tissues and organs requires the coordination of growth factors at the surface of potentially-dividing cells in specific anatomic loci named germinal niches. However, the biological components and physiological system that control growth factors in the germinal niches are unknown. In the adult brain, no function has been attributed to fractones, the fractal-shaped extracellular matrix structures located in the subventricular zone (SVZ) next to neural stem and progenitor cells. Here, we show that BMP-7 (bone morphogenetic protein-7) and FGF-2 (fibroblast growth factor-2) modulate cell division in the SVZ only if the growth factors bind to heparan sulfates localized in fractones and adjoined vascular basement membranes....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5444/version/1

Novel protein antigen (JHP940) from the genomic plasticity region of Helicobacter pylori induces TNF-alpha and Interleukin- 8 secretion by human macrophages
Provedor de dados: 17
Autores: Niyaz Ahmed; Ayesha Alvi; Mohammed Rizwan.
Plasticity region of the H. pylori genome comprises strain specific gene loci. We performed genotyping and functional biology of one such locus (jhp940) that was previously found to be functionally unknown but present in gastric cancer associated strains from many different countries. We found its geographic prevalence to be independent of cagA presence and disease status. Cloning, expression and purification of the JHP940 revealed a novel, ~36kDa protein in biologically active form. The same induced strong and significant levels of TNF-alpha and Interleukin-8 in human macrophages. Induction of these cytokines by JHP940 points to its putative role in chronic gastric inflammation and various other outcomes of H. pylori infection including gastric cancer.
Tipo: Poster
Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/864/version/1

NIR Calibrations for Soybean Seeds and Soy Food Composition Analysis: Total Carbohydrates, Oil, Proteins and Water Contents [v.2]
Provedor de dados: 17
Autores: I. C. Baianu; Jun Guo; Randall L. Nelson; Tiefeng You; Doina M. Costescu.
Conventional chemical analysis techniques are expensive, time consuming, and often destructive. The non-invasive Near Infrared (NIR) technology was introduced over the last decades for wide-scale, inexpensive chemical analysis of food and crop seed composition (see Williams and Norris, 1987; Wilcox and Cavins, 1995; Buning and Diller, 2000 for reviews of the NIR technique development stage prior to 1998, when Diode Arrays were introduced to NIR). NIR spectroscopic measurements obey Lambert and Beer&amp;#x2019;s law, and quantitative measurements can be successfully made with high speed and ease of operation. NIR has been used in a great variety of food applications. General applications of products analyzed come from all sectors of the food industry...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6611/version/2

Regrowing the adult brain: NF-&amp;#x3ba;B controls functional circuit formation and tissue homeostasis in the dentate gyrus
Provedor de dados: 17
Autores: Yvonne Imielski; Jens C. Schwamborn; Patrick L&amp;#xfc;ningschr&amp;#xf6;r; Peter Heimann; Magdalena Holzberg; Hendrikje Werner; Oliver Leske; Andreas W. P&amp;#xfc;schel; Sylvie Memet; Rolf Heumann; Alain Israel; Christian Kaltschmidt; Barbara Kaltschmidt.
Cognitive decline during aging is correlated with a continuous loss of cells within the brain and especially within the hippocampus, which could be regenerated by adult neurogenesis. Here we show that genetic ablation of NF-&amp;#x3ba;B resulted in severe defects in the neurogenic region (dentate gyrus) of the hippocampus. Despite increased stem cell proliferation, axogenesis, synaptogenesis and neuroprotection were hampered, leading to disruption of the mossy fiber pathway and to atrophy of the dentate gyrus during aging. Here, NF-&amp;#x3ba;B controls the transcription of FOXO1 and PKA, regulating axogenesis. Structural defects culminated in behavioral impairments in pattern separation. Re-activation of NF-&amp;#x3ba;B resulted in integration of newborn...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6096/version/1

Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks
Provedor de dados: 17
Autores: Avi Ma&amp;#x27;ayan.
In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.&amp;#xd;&amp;#xa;Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/35/version/1

Differential Gene Expression of Human Mast cell Activation Reveals Gene profiles of Innate and Adaptive Immunity.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Reghunathan Renji; Peter Natesan Pushparaj; Alirio Jose Melendez.
High-density oligonucleotide microarray is a promising approach for high throughput analysis. It has been extensively used in many areas of biomedical research. Immunoglobulin E (IgE) mediated allergic response (type-1 hypersensitivity) is one of the most powerful reactions of the immune system. Tissue Mast Cells (MCs) and circulating basophils are the major effector cells in these reactions. By dissecting the regulatory circuitry of mast cells by analyzing the genome wide effects of antigen stimulation triggered by Fc&amp;#x3b5;RI, offers a potential for finding novel genes as &amp;#x2018;targets&amp;#x2019; for therapeutic intervention. In this work, we tried to study the gene expression pattern in IgE sensitized and Fc&amp;#x3b5;RI cross linked cord...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1148/version/1

Signaling via Alk5 Controls Ontogeny of Lung Clara Cells
Provedor de dados: 17
Autores: Yiming Xing; Changgong Li; Aimin Li; Somyoth Sridurongrit; Caterina Tiozzo; Saverio Bellusci; Zea Borok; Vesa Kaartinen; Parviz Minoo.
Clara cells, together with ciliated and pulmonary neuroendocrine cells, make up the epithelium of the bronchioles along the conducting airways. Clara cells are also known as Progenitor/Stem cells during lung regeneration after injury. The mechanisms of Clara cell differentiation are largely unknown. Transforming growth factor-beta is a multifunctional molecule with roles in normal development and disease pathogenesis. In this study, we deleted the TGF-&amp;#x3b2; type I receptor, Alk5 in the embryonic lung epithelium using Gata5-Cre mice. Absence of Alk5 blocked Clara cell differentiation but had no effect on ciliated or pulmonary neuroendocrine cells. Hairy/Enhancer of Split-1, which is expressed in Clara cell putative &amp;#x22;progenitors&amp;#x22; was...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3036/version/1

Can Vision Exist Without Somatosensation?
Provedor de dados: 17
Autores: Manivannan Muniyandi; Pawan Kumar Suresh.
The interconnection between vision and somatosensation is already well-established and is further supplemented by the evolutionary link between eyes and photoreceptors, and the functional connection between photosensation and thermoreception. However, our analysis hypothesizes a possibility that vision is not just linked to somatosensation, but may not exist without somatosensation. Surprisingly, our photoreceptor itself needs somatosensory proteins for its functioning, and our entire visual pathway depends on somatosensory cues for its functioning.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3436/version/1

Looking at the Beginnings: Enquiries about Emergence of Cognition in Evolution
Provedor de dados: 17
Autores: Walter Riofrio.
Trying to understand when and how the cognitive phenomena arise in evolution continues being a hard problem of confronting. &amp;#xd;&amp;#xa;One important task is to find the ways in which we will be able to arrive at those explanations that will enable us to understand how living beings put together perceived sensory information as well as how they represent it. &amp;#xd;&amp;#xa;In this presentation, we address some conceptual questions involved in the relationships between sensorial information perceived by brains and its representational capacities. &amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Ecology; Molecular Cell Biology; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/413/version/1

Control in technological systems and physical intelligence: an emerging theory
Provedor de dados: 17
Autores: Bradly Alicea.
The transduction and processing of physical information is becoming important in a range of research fields, from the design of materials and virtual environments to the dynamics of cellular microenvironments. Previous approaches such as morphological computation/soft robotics, neuromechanics, and embodiment have provided valuable insight. This work approaches haptic, proprioception, and physical sensing as all part of the same subject. In this presentation, three design criteria for applying physical intelligence to engineering applications will be presented. These criteria have several properties in common, which inspires two types of end-effector model: stochastic (based on a spring) and deterministic (based on a piezomechanical array). The generalized...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5910/version/1

Dynamic hydration valve controlled ion permeability and stability of NaK channel
Provedor de dados: 17
Autores: Rong Shen; Wanlin Guo; Wenyu Zhong.
The K^+^, Na^+^, Ca^2+^ channels are essential to neural signalling, but our current knowledge at atomic level is mainly limited to that of K^+^ channels. Unlike a K^+^ channel having four equivalent K^+^-binding sites in its selectivity filter, a NaK channel conducting both Na^+^ and K^+^ ions has a vestibule in the middle part of its selectivity filter, in which ions can diffuse but not bind specifically. However, how the NaK channel conducts ions remains elusive. Here we find four water grottos connecting with the vestibule of the NaK selectivity filter. Molecular dynamics and free energy calculations show that water molecules moving in the vestibule-grotto complex hydrate and stabilize ions in the filter and serve as a valve in conveying ions through...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2045/version/1

Concentration-dependent free radical scavenging and ferric reducing ability of Vetiveria zizanioides (L.) Nash: Protective effect of vetiver root extract during oxidative stress
Provedor de dados: 17
Autores: Suaib  Luqman; Ritesh  Kumar; Shubhangi  Kaushik; Suchita  Srivastava; Mahendra  P. Darokar; Suman  P. S. Khanuja.
Vetiveria zizanioides, popularly known as &amp;#x2018;KHUS&amp;#x2019; grass, has been known to India since ancient times. It is the major source of well-known oil of vetiver, which is used in medicine and in perfumery. A concentration-dependent ferric reducing, free radical scavenging and antioxidant activity of two genotypes, namely KS 1 and gulabi of vetiver (Vetiveria zizanioides L. Nash) root, were evaluated by using in vitro assays: the ferric reducing antioxidant power (FRAP), 1, 1-Diphenyl-2-picrylhydrazyl (DPPH), total phenolic content (TPC), total antioxidant capacity (TAC) and reducing power (RP) assay. A positive co-relation was observed between FRAP, DPPH and TPC of cv KS 1, whereas TAC and RP showed a negative co-relation. A significant...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6920/version/1

The Entropic Landscape of proteins revealing protein folding mechanism
Provedor de dados: 17
Autores: Kentaro Onizuka.
It has long since been a mystery why most proteins fold within a flash of time into particular structures out of astronomically large numbers of possible conformations. Even more confusing is that protein folding in vivo is played out in rich solution containing various organic and non-organic, big and small molecules and ions which would potentially bind the protein molecules and prevent them folding. A possible answer to these mysteries might be, &amp;#x22;Nature have favoured such proteins that quickly fold in rich solution through natural selection&amp;#x22;. Then what mechanism of folding has been favoured? Here I show how to decipher protein sequences to reveal the folding mechanism. The entropic landscape of a protein sequence tells which region of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2719/version/1

Transcriptional complex assembly represented in SBGN PD
Provedor de dados: 17
Autores: Alexander Mazein; Steven Watterson; Peter Ghazal.
This poster shows how transcriptional complex assembly can be represented in SBGN Process Description language. Example: LPS-induced TNF-alpha enhancer complex formation.
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4984/version/1

Inherited mutations impair responses to environmental carcinogens:  Cancer prevention in mutation carriers
Provedor de dados: 17
Autores: Bernard  Friedenson.
Some environmental carcinogens may be responsible for an increase in the numbers of cancers but economic or political factors weigh against widespread bans.  However, lists of chemicals and agents that cause cancer assume that everyone is equally susceptible to their carcinogenic effects. &amp;#xd;&amp;#xa;In carriers of cancer gene mutations, carcinogens can target specific tissues especially during periods of stem cell activity if the hereditary deficit impairs normal protective responses.  Mutation carriers should then have higher risks for specific cancers caused by specific environmental carcinogens.  &amp;#xd;&amp;#xa;For example, it can be predicted that BRCA1 or BRCA2 mutation carriers should be highly susceptible to the carcinogen formaldehyde....
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6024/version/2

A Three dimesional stochastic spatio-temporal model of cell spreading
Provedor de dados: 17
Autores: Yuguang P. Xiong; Padmini Rangamani; Benjamin Dubin-Thaler; Michael  Sheetz; Ravi Iyengar.
Cell motility is important for many physiological processes and the underlying&amp;#xd;&amp;#xa;biochemical reactions motility have been well-characterized. Mathematical models, using&amp;#xd;&amp;#xa;the biochemical reactions and focused on different types of spreading behavior have been&amp;#xd;&amp;#xa;constructed and analyzed. In this study, we build on these previous models to develop a&amp;#xd;&amp;#xa;three-dimensional stochastic model of isotropic spreading of mammalian fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally observed isotropic cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/62/version/1

Evolutionary descent of prion genes from a ZIP metal ion transport ancestor
Provedor de dados: 17
Autores: Gerold Schmitt-Ulms; Sepehr Ehsani; Joel C. Watts; David Westaway; Holger Wille.
In the more than 20 years since its discovery, both the phylogenetic origin and cellular function of the prion protein (PrP) have remained enigmatic. Insights into the function of PrP may be obtained through a characterization of its molecular neighborhood. Quantitative interactome data revealed the spatial proximity of a subset of metal ion transporters of the ZIP family to mammalian prion proteins. A subsequent bioinformatic analysis revealed the presence of a prion-like protein sequence within the N-terminal, extracellular domain of a phylogenetic branch of ZIPs. Additional structural threading and ortholog sequence alignment analyses consolidated the conclusion that the prion protein gene family is phylogenetically derived from a ZIP-like ancestor...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2867/version/1

Consortium for Functional Glycomics Overview
Provedor de dados: 17
Autores: James C. Paulson.
This presentation provides an overview of the Consortium for Functional Glycomics.
Tipo: Presentation
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/11/version/1

WikiPathways: Community Curation of Biological Pathways
Provedor de dados: 17
Autores: Alexander Pico.
Assembling biological pathways from information in scientific literature and biological databases is a challenging task. Building a pathway requires domain knowledge from specialists in various biological research areas. Furthermore, research is generating new biological knowledge continuously, making pathway curation an ongoing and dynamic process. To facilitate this process we developed &amp;#x22;WikiPathways&amp;#x22;:http://www.wikipathways.org/index.php/WikiPathways ^1^, a wiki where users can curate pathways, using an easy to use pathway drawing tool. WikiPathways currently has over 1200 registered users and contains more than 1300 pathways for various organisms, spanning human, mouse, zebrafish, fruit fly, worm, yeast, plants and bacteria....
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5359/version/1

Molecular mechanisms of the regulation of ATPase cycle in striated muscle
Provedor de dados: 17
Autores: Yuri S. Borovikov; Olga E. Karpicheva; Charles S. Redwood.
New data on the molecular mechanism of the regulation of ATPase cycle by troponin-tropomyosin system have been obtained in reconstructed muscle fibers by using the polarized fluorescence technique, which allowed us following the azimuthal movements of tropomyosin, actin subdomain-1 and myosin SH1 helix motor domain during the sequential steps of ATPase cycle. We found that tropomyosin strands &amp;#x22;rolling&amp;#x22; on thin filament surface from periphery to center at ATPase cycle increases the amplitudes of multistep changes in special arrangement of SH1 helix and subdomain-1 at force generation states. These changes seem to convey to actin monomers and to myosin &amp;#x22;lever arm&amp;#x22;, resulting in enhance of the effectiveness of each...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1391/version/1

Precocious activation of APC/C-Cdh1 at pre-anaphase causes genome instability
Provedor de dados: 17
Autores: Ayumu Yamamoto; Takashi Ushimaru; Takanori Ohyoshi; Asuka Suzuki; Kazuhiro Toda; Masaru Ueno; Masahiro Uritani.
Faithful chromosome segregation and thereby accurate gene transmission are crucial for all organisms. Until proper attachment of the mitotic spindle to the kinetochore is established, the ubiquitin ligase (E3) Cdc20-activated APC/C (anaphase promoting complex/cyclosome) is repressed by the spindle assembly checkpoint (SAC) and sister chromatin cohesion is protected. Mutants defective in SAC fail to arrest at metaphase even in the presence of damaged microtubules. Interestingly, a similar phenomenon occurs in yeast cells defective in Bub2, a negative factor of the mitotic exit network (MEN), which is required for telophase onset, although its precise molecular mechanism is unknown. Here, we show that chromosome missegregation occurs frequently in...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1603/version/1

Ferric reducing antioxidant power and free radical scavenging activity of  Moringa oleifera: Relevance in oxidative stress
Provedor de dados: 17
Autores: Suaib  Luqman.
Moringa oleifera of family Moringaceae, commonly known as Horseradish-tree or the Ben-oil tree is an exceptionally nutritious vegetable tree with a variety of medicinal uses, distributed in tropical and subtropical regions of the world. The tree&amp;#x27;s bark, roots, fruit (pod), flowers, leaves, seeds and gum are used as an antiseptic, anticancer, anti-inflammatory, hepatoprotective and in treating rheumatism, venomous bites and other conditions. The immature green pods, called &amp;#x2018;drumsticks&amp;#x2019; are probably the most valued and widely used part of the tree for water purification (e.g. desalination of ocean salt water). The leaves are highly nutritious, being a significant source of beta-carotene, vitamin C, protein, iron and potassium...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6924/version/1

Snca and Bdnf gene expression in the VTA and raphe nuclei of midbrain in chronically victorious and defeated male mice
Provedor de dados: 17
Autores: Natalia N. Kudryavtseva; Natalia P. Bondar; Ul&amp;#x27;yana A. Boyarskikh; Maxim L. Filipenko.
The study aimed to analyze the mRNA levels of Snca and Bdnf genes in the ventral tegmental area (VTA) and raphe nuclei of the midbrain in male mice that had each won or defeated 20 encounters in daily agonistic interactions. Groups of animals that had the same winning and losing track record followed by a no-fight period for 14 days were also studied. Snca mRNA levels were increased in the raphe nuclei in the losers and in the VTA of the winners. After fighting deprivation Snca mRNA levels were decreased to the control level in both groups. Snca mRNA levels were similar to the control level in the VTA of the losers and in the raphe nuclei of the winners. However Snca gene expression was increased in these areas after no-fight period in the winners and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4327/version/1

Thermal characterization of Plasmodium falciparum species specific proteins in Indian geographical area.
Provedor de dados: 17
Autores: Mohit Bhardwaj; Leena Bharadwaj; Kritika Trigunayat; Madan Mohan Trigunayat.
The paper reveals thermal characteristics of _P.falciparum_ species specific proteins. These proteins determine why _P. vivex_ species are dominant over _P.falciparum_ in Indian geographical area. Outside human host plasmodium parasite survives in poikilothermal mosquitoes. Climatic temperature conditions greatly affect native state of _P.falciparum_ species specific proteins in mosquitoes. Study of climatic temperature conditions in Indian geographical area reveals that Pfsd protein for _Plasmodium falciparum_ can remain in native state between &amp;#x2265;7 degree centigrade and &amp;#x2264;42.6 degree centigrade temperature conditions. While their best optimum functions (activity) was noted between 25.3 degree centigrade to 33degree centigrade. Pfsd...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4565/version/2

The Necessity of Darwin
Provedor de dados: 17
Autores: Stanley K. Sessions; Herbert C. Macgregor.
February 12th, 2009 was Charles Darwin&amp;#x27;s 200th birthday, and November 2009 represents the 150th anniversary of the publication of his transformative book, The Origin of Species. It seems a good time to look back and assess Darwin&amp;#x27;s legacy within the perspective of current knowledge of genetics, cytogenetics, and molecular biology in general. Although a comprehensive understanding of evolution would no doubt have emerged eventually, it is difficult to imagine how anyone could have matched Darwin&amp;#x2019;s prodigious and sustained efforts, as well as his talent for explaining things in simple terms.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2887/version/1

Genetic Normalization of Differentiating Aneuploid Human Embryos
Provedor de dados: 17
Autores: Paul Brezina; Andrew Barker; Andrew Benner; Ric Ross; Khanh-Ha Nguyen; Raymond Anchan; Kevin Richter; Garry Cutting; William Kearns.
Early embryogenesis involves a series of dynamic processes, many of which are currently not well described or understood. Aneuploidy and aneuploid mosaicism, a mixture of aneuploid and euploid cells within one embryo, in early embryonic development are principal causes of developmental failure.^1,2^ Here we show that human embryos demonstrate a significant rate of genetic correction of aneuploidy, or &amp;#x22;genetic normalization&amp;#x22; when cultured from the cleavage stage on day 3 (Cleavage) to the blastocyst stage on day 5 (Blastocyst) using routine in vitro fertilization (IVF) laboratory conditions. One hundred and twenty-six human Cleavage stage embryos were evaluated for clinically indicated preimplantation genetic screening (PGS). Sixty-four of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6045/version/1

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry lifting model based on Tlusty&amp;#x27;s elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4120/version/3

Literature Triage and Indexing in the Mouse Genome Informatics (MGI) Group
Provedor de dados: 17
Autores: Randal P. Babiuk; Dale A. Begley; Susan M. Bello; Dirck W. Bradt; Donna L. Burkart; Howard Dene; Alexander D. Diehl; Harold J. Drabkin; Jacqueline H. Finger; Terry F. Hayamizu; David P. Hill; Michelle Knowlton; Debra M. Krupke; Ira Lu; Lois J. Maltais; Monica McAndrews-Hill; Terrence F. Meehan; Li Ni; Hiroaki Onda; Dmitry Sitnikov; Constance M. Smith; Cynthia L. Smith; Monika Tomczuk.
The Mouse Genome Informatics (MGI; &amp;#x22;http://www.informatics.jax.org&amp;#x22;:http://www.informatics.jax.org) group is comprised of several collaborating projects including the Mouse Genome Database (MGD) Project, the Gene Expression Database (GXD) Project, the Mouse Tumor Biology (MTB) Database Project, and the Gene Ontology (GO) Project. Literature identification and collection is performed cooperatively amongst the groups.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In recent years many institutional libraries have transitioned from a focus largely on print holdings to one of electronic access to journals. This change has necessitated adaptation on the part of the MGI curatorial group. Whereas the majority of journals covered by the group used to be...
Tipo: Poster
Palavras-chave: Cancer; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3246/version/1

Global Network Alignment
Provedor de dados: 17
Autores: Oleksii Kuchaiev; Natasa Przulj.
Motivation: High-throughput methods for detecting molecular interactions have lead to a plethora of biological network data with much more yet to come, stimulating the development of techniques for biological network alignment. Analogous to sequence alignment, efficient and reliable network alignment methods will improve our understanding of biological systems. Network alignment is computationally hard. Hence, devising efficient network alignment heuristics is currently one of the foremost challenges in computational biology. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: We present a superior heuristic network alignment algorithm, called Matching-based GRAph ALigner (M-GRAAL), which can process and integrate any number and type of similarity measures...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4505/version/1

Empirical predictions of an intrinsically disordered protein theory approach to glycan/lectin reaction kinetics
Provedor de dados: 17
Autores: Rodrick Wallace.
Newly-developed methods from the theory of intrinsically disordered proteins can be applied to the flexible glycan structures that coat cellular surfaces and provide rich channels for biological information transmission. Extension of a mechanistic &amp;#x27;arm-in-sleeve&amp;#x27; model via a nonrigid molecule symmetry analysis leads to expectation of empirical observation of punctuated &amp;#x27;spectral&amp;#x27; classifications in glycan/lectin interaction, parameterized by an appropriate index of glycan frond length or other index of topological complexity, possibly requiring groupoid classifications analogous to quasicrystals.
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6752/version/1

Biomimetic assemblage of nucleobase 5-fluorouracil into nano-size three-dimensional particles
Provedor de dados: 17
Autores: Arun Chauhan; Swaleha Zubair; Qamar Zia; Saba Tufail; Asif Sherwani; Mohammad Sajid; Mohammad Owais.
Biomimetic nano-assembly formation offers a convenient and bio friendly approach to fabricate complex structures from simple components with sub-nanometer precision. Recently, extract from cells of microorganism/plant origin have emerged as a simple and viable route for the synthesis of metal and inorganic material nano-particles. In the present study, we have extended biological synthesis of nano-particles to organic molecules, namely the anticancer agent, 5-fluorouracil (5-FU) using Aloe vera leaf extract. The formation of 5-FU nano- particles was assessed by UV, FT-IR and fluorescence spectroscopic techniques. Transmission electron microscopy and atomic force microscopic techniques confirmed nano-size of the synthesized particles. Importantly, the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6182/version/1

The Starving Cell: Metabolic Syndrome as an Adaptive Process
Provedor de dados: 17
Autores: Beatrice A. Golomb.
Metabolic syndrome (MetS) is commonly presumed to stem from obesity, with both propelled by energy surfeit: positive balance of calories consumed to energy expended. A complementary thesis is proposed: that episodes of cell energy deficit (not expressly calorie deficit) drive MetS &amp;#x2013; the &amp;#x201c;Starving Cell.&amp;#x201d; &amp;#xd;&amp;#xa;Risk factors for MetS include hypoxemia from sleep apnea, severe calorie debt, mitochondrial dysfunction, oxidative stress; and sleep restriction, illness, surgery, trauma, cold. Each fosters inadequate cell energy, hampering production or boosting demand. MetS factors support energy: glucose, triglycerides, abdominal/visceral fat &amp;#x2013; and blood pressure, sustaining perfusion. Additional...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6535/version/1

OpenCOR
Provedor de dados: 17
Autores: Alan Garny.
A description of the OpenCOR project. What has been done so far, the choices that were made, etc., as well as the direction in which we are heading.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5898/version/1

Genome-wide association study identifies _FUT8_ and _ESR2_ as co-regulators of a bi-antennary N-linked glycan A2 (GlcNAc~2~Man~3~GlcNAc~2~) in human plasma proteins
Provedor de dados: 17
Autores: Gordan Lauc; Jennifer Huffman; Caroline Hayward; Ana Knezevic; Ozren Polasek; Olga Gornik; Veronique Vitart; Ivana Kolcic; Zrinka Biloglav; Lina Zgaga; Nicholas D. Hastie; Alan F. Wright; Harry Campbell; Pauline M. Rudd; Igor Rudan.
HPLC analysis of N-glycans quantified levels of the biantennary glycan (A2) in plasma proteins of 924 individuals. Subsequent genome-wide association study (GWAS) using 317,503 single nucleotide polymorphysms (SNP) identified two genetic loci influencing variation in A2: FUT 8 and ESR2. We demonstrate that human glycans are amenable to GWAS and their genetic regulation shows sex-specific effects with _FUT 8_ variants explaining 17.3% of the variance in pre-menopausal women, while _ESR2_ variants explained 6.0% of the variance in post-menopausal women.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2864/version/1

Kinase independent inhibition of NF&amp;#x3ba;B transcriptional activity by GRK5 through I&amp;#x3ba;B&amp;#x3b1; stabilization.
Provedor de dados: 17
Autores: Daniela  Sorriento; Michele  Ciccarelli; Gaetano  Santulli; Alfonso  Campanile; Giovanna Giuseppina  Altobelli; Vincenzo  Cimini; Gennaro Galasso; Dalila  Astone; Federico Piscione; Lucio Pastore; Bruno Trimarco; Guido  Iaccarino.
Members of the G protein receptor kinase (GRK) family that regulates receptor desensitization and members of the nuclear transcription factors family NF[kappa]B have been recently and convincingly demonstrated to interact, although the effects on transcription and gene expression have not yet been described. Using overexpression, knockdown (small interfering RNA) and mutagenesis experiments, we demonstrate that GRK5 couples to and stabilizes the NF[kappa]B inhibitor I[kappa]B[alpha], and inhibits NF[kappa]B activity. Studies with minigenes suggest that the N-terminal Regulation of G protein Signaling (RGS) homology (RH) domain confers GRK5 such ability. GRK5-RH domain overexpression affects NF[kappa]B dependent phenotypes, such as apoptosis protection,...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1196/version/1

The non-obligatory role of endothelial cells in the relaxation of arterial smooth muscle by acetylcholine
Provedor de dados: 17
Autores: Igor Buchwalow; Sona Cacanyiova; Joachim Neumann; Vera Samoilova; Werner Boecker; Frantisek Kristek.
The concept of Endothelium Derived Relaxing Factor (EDRF), put forward by Furchgott in the earlier 80s of the past century, implies that nitric oxide (NO) produced by NO synthase (NOS) in the endothelium in response to acetylcholine (ACh) passively diffuses to the underlying vascular smooth muscle cells (VSMC) thereby reducing vascular tension. It was thought that VSMC do not express NOS by themselves, but to the time of those studies immunohistochemical techniques were not what they are now. State-of-the-art immunohistochemistry permits nowadays to localize NOS both to the endothelium and to VSMC. However, the principal question remained unanswered, is the NO generation by VSMC physiologically relevant? We hypothesized that the destruction of the vascular...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1884/version/1

Protective effect of (-) &amp;#x3b1;-bisabolol on markers of oxidative stress in erythrocytes subjected to oxidative insult
Provedor de dados: 17
Autores: Suaib  Luqman; Suchita  Srivastava.
(-)-&amp;#x3b1;-bisabolol is a sesquiterpene alcohol found as a major component of essential oil of chamomile (Matricaria recutita L., Chamomilla recutita L., Matricaria chamomilla L.; Family Asteraceae). Chamomile, one of the most ancient and widely recognized herbs to mankind, has been used traditionally for centuries as an anti-inflammatory, antispasmodic, carminative, mild astringent and healing medicine. It is also known to be very helpful as an external agent for encouraging the rapid healing of ulcers and burns without infection, as well as persistent skin problems such as eczema and psoriasis. Since clinical trials and human studies are limited, we have investigated the effect of (-)-&amp;#x3b1;-bisabolol on markers of oxidative stress in human...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6903/version/1

Just-in-time assembly of cell-cycle protein complexes
Provedor de dados: 17
Autores: Lars J. Jensen; Ulrik de Lichtenberg; Thomas S. Jensen; S&amp;#xf8;ren Brunak; Peer Bork.
Our comparative analysis of eukaryotic cell-cycle complexes reveals that the identity of the periodically expressed subunits differs significantly between organisms and is often mirrored by changes in cell-cycle-dependent phosphorylation of the protein products. This indicates that many different solutions have evolved for just-in-time assembly of the same molecular machines.
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2273/version/1

Applications Of Microspectroscopy, Hyperspectral Chemical Imaging And Fluorescence Microscopy In Chemistry, Biochemistry, Biotechnology, Molecular And Cell Biology
Provedor de dados: 17
Autores: I. C. Baianu.
Chemical imaging is a technique for the simultaneous measurement of spectra (chemical information) and images or pictures (spatial information)^1,2^. The technique is most often applied to either solid or gel samples, and has applications in chemistry, biology^3-8^, medicine^9,10^, pharmacy^11^ (see also for example: Chemical Imaging Without Dyeing), food science, Food Physical Chemistry, Biotechnology^12,13^, Agriculture and industry. NIR, IR and Raman chemical imaging is also referred to as hyperspectral, spectroscopic, spectral or multi-spectral imaging (also see micro-spectroscopy). However, other ultra-sensitive and selective, chemical imaging techniques are also in use that involve either UV-visible or fluorescence microspectroscopy.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6593/version/1

Idiosyncratic evolution of conserved eukaryote proteins that are similar in sequence to archaeal or bacterial proteins
Provedor de dados: 17
Autores: Roy J. Britten.
&amp;#x9;Sequence comparisons have been made between the proteins of 571 prokaryote species including 46 archaea and 525 bacteria and the set of  human proteins. Highly conserved eukaryotic proteins are often strikingly similar in sequence to archaeal and bacterial proteins. Yet in many cases similarity to archaeal proteins is not correlated to the similarity to bacterial proteins. In these comparisons there are hundreds of eukaryote proteins that match well archeal proteins, but do not match recognizably to bacterial proteins, while thousands of proteins match well to bacterial proteins but not recognizably to archeal proteins. Forty percent of the 21,440 human proteins that significantly match prokaryote proteins are in this extreme idiosyncratic...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1752/version/1

A probabilistic model of plasmid replication regulation by a combination of handcuffing, iteron number and dimerization of RepA protein.
Provedor de dados: 17
Autores: Milind Watve; Gauri Tendulkar; Ketaki Ghate.
Plasmids are small circular DNA molecules in bacteria which replicate sharing the replication machinery with the bacterial chromosome. Since plasmids are much smaller than the chromosome, unless their replication is tightly regulated, their copy numbers can escalate quickly. A number of mechanisms of plasmid replication regulation are known in P1 plasmid of E. coli. Mechanisms such as autorepression of the replication initiator protein (RepA) and its dimerization are unable to explain copy number regulation by themselves. The number of RepA binding sites (iterons) is inversely related to copy numbers. Handcuffing of plasmids by RepA dimer is believed to be the main mechanism of arresting replication. We show here with a probabilistic model that for the...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5421/version/1

Off-target response to decoy oligodeoxynucleotide treatment
Provedor de dados: 17
Autores: Ewan J. D. Robson; Aaron R. Jeffs; Michael R. Eccles.
*Background:* The transcription factor PAX2 regulates key developmental processes, including mediation of resistance to apoptosis. Inappropriate PAX2 expression has been implicated in facilitating tumour survival, and we have previously shown that siRNA-mediated blockade of PAX2 signalling at the transcript level in EJ bladder carcinoma cells promotes cell death. In this study, we attempted to disrupt PAX2 transcriptional activity in EJ cells by using a decoy oligodeoxynucleotide (ODN). &amp;#xd;&amp;#xa;*Results:* We could not show an interaction between PAX2 and our PAX2 decoy ODN, and in both &amp;#xd;&amp;#xa;PAX2-positive EJ and PAX2-negative HEK293 control cells, decoy and control ODN transfection resulted in a marked retardation of cell growth,...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2281/version/1

A Targeted Therapeutic Rescues Botulinum Toxin-A Poisoned Neurons
Provedor de dados: 17
Autores: Prabhati Ray; Bal Ram Singh; Radharaman Ray; Peng Zhang; Dan Li; James Keller; Michael Adler.
Botulinum neurotoxin (BoNT), a Category A biothreat agent, is the most potent poison known to mankind. Currently no antidote is available to rescue poisoned synapses. BoNT acts specifically by blocking neurotransmission primarily at peripheral nerve-muscle junctions causing severe flaccid muscle paralysis, which is fatal if proper medical care is not provided. The neurotoxin acts by specifically entering the presynaptic nerve endings where it interferes with the biochemical machinery involved in the process of neurotransmitter release, i.e., neuroexocytosis. Most serotypes of BoNT are known to remain active for weeks to months after entering the nerves, but BoNT/A is the most potent and long lasting in causing muscle paralysis. An effective medical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2149/version/1

Folding pathway of the B1 domain of protein G explored by a multiscale modeling
Provedor de dados: 17
Autores: Andrzej Kolinski; Sebastian Kmiecik.
The understanding of the folding mechanisms of single domain proteins is an essential step in the understanding of protein folding in general. Recently, we developed a mesoscopic CABS protein model which was successfully applied in protein structure prediction, studies of protein thermodynamics and modeling of protein complexes. In the present research this model is employed in a detailed characterization of the folding process of a simple globular protein, the B1 domain of IgG-binding protein G (GB1). There is a vast body of experimental facts and theoretical findings for this protein. Performing unbiased, _ab initio_ simulations, we demonstrated that the GB1 folding proceeds via the successive formation of an extended folding nucleus, followed by slow...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/129/version/1

In vitro Evolution and Engineering for Improved Ribozyme Polymerase Production
Provedor de dados: 17
Autores: Israr  Khan; Muhammad Waheed Akktar; Ayaz Ali Khan.
According to the &amp;#x22;RNA World Hypothesis&amp;#x22; the first self replicating molecule formed from the prebiotic chemicals is the ribozyme. A model compartmentalized self replicating system for ribozyme polymerases is designed and used to improve activity, fidelity and generality of the enzyme.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6064/version/1

Overexpression of an isoform of AML1 in acute leukemia and its potential role in leukemogenesis
Provedor de dados: 17
Autores: Xiangrong Liu; Qing Zhang; Dong-er Zhang; Chunlin Zhou; Haiyan Xing; Zhen Tian; Qing Rao; Min Wang; Jianxiang Wang.
AML1/RUNX1 is a critical transcription factor in hematopoietic cell differentiation and proliferation. From the _AML1_ gene, at least three isoforms, _AML1a_, _AML1b_ and _AML1c_, are produced through alternative splicing. AML1a interferes with the function of AML1b/1c, which are often called AML1. In the current study, we found a higher expression level of _AML1a_ in ALL patients in comparison to the controls. Additionally, AML1a represses transcription from promotor of macrophage-colony simulating factor receptor (M-CSFR) mediated by AML1b, indicating that AML1a antagonized the effect of AML1b. In order to investigate the role of _AML1a_ in hematopoiesis and leukemogenesis _in vivo_, bone marrow mononuclear cells (BMMNCs) from mice were transduced with...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1795/version/1

Pathogenetic role of tissue factor in graft-versus-host disease
Provedor de dados: 17
Autores: Li Quan; Li Weiming; Zhang Jian; Zou Ping.
Graft-versus-host disease (GVHD) is a serious complication after allogeneic stem cell transplantation, the mechanism of it is still not elucidated. Recent findings suggest that host endothelial cells are a target of alloreactive donor cytotoxic T lymphocytes in GVHD and tissue factor (TF) plays an important role not only in coagulation-inflammation cycle, but also in transplant immunology. We postulate TF expression in vascular endothelial cells(VEC) may play an pivotal role in the pathogenesis of GVHD. TF gene andprotein expression in target organs of GVHD in aGVHD mice was significantly elevated compared to that of controls as determined by real-time PCR and Western blotting. Allogeneic CD4^+^T cell and CD8^+^T cells enhanced TF, VCAM-1, TNF-[alpha],...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2248/version/1

Genome activity profiling of monomeric-IgE and Fc-epsilon-RI-aggregation on human mast cells reveals a complex network of genes involved in inflammatory responses.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Alirio Jose P. N. Melendez; Peter Natesan A. J. Pushparaj.
Mast cell activation, mediates type-1 allergic responses, one of the most powerful reactions of the immune system. However, mast cells activation is becoming increasingly linked to inflammatory, autoimmunity, and to adaptive immunity by regulating T-cell activation.&amp;#xd;&amp;#xa;Here we analyzed the gene expression pattern in IgE-sensitized and Fc&amp;#x3b5;RI aggregation on human mast cells. Our data revealed coordinated changes in gene expression. We observed increased expression of gene-transcripts involved in allergic, innate and adaptive&amp;#xd;&amp;#xa;immune responses. Among the most prominent findings is the increased expression of transcripts encoding for MIP3a, SPARCL1, AREG, IL18, CCL1, TNFRSF9, IL1b, CX3CR1, PTGER3, MIF, MMP12, ADORA3,...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1150/version/1

Developments in CFG glycan and pathogen polysaccharide arrays
Provedor de dados: 17
Autores: Ola Blixt.
This presentation summarizes developments in glycan and pathogen polysaccharide arrays at the Consortium for Functional Glycomics (CFG).
Tipo: Presentation
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/12/version/1

ER localized bestrophin1 activates Ca2+ dependent ion channels TMEM16A and SK4
Provedor de dados: 17
Autores: Ren&amp;#xe9; Barro-Soria; Fadi AlDehni; Joana Alma&amp;#xe7;a; Jiraporn Ousingsawat; Ralph Witzgall; Rainer Schreiber; Karl Kunzelmann.
Bestrophins form Ca2+ activated Cl- channels and regulate intercellular Ca2+ signaling1. We demonstrate that bestrophin 1 is localized in the endoplasmic reticulum (ER), where it physically interacts with stromal interacting molecule 1 (Stim1), the ER-Ca2+ sensor2,3. Intracellular Ca2+ transients in HEK293 cells elicited by stimulation of purinergic P2Y2-receptors were augmented but more transient after expression of hBest1, in contrast to dominant negative hBest1-R218C, which attenuated Ca2+ increase. The p21-activated protein kinase Pak2 was found to phosphorylate hBest1, thereby enhancing Ca2+ signaling and activation of Ca2+ dependent Cl- (TMEM16A)4 and K+ (SK4)5 channels. Lack of bestrophin 1 expression in respiratory epithelial cells of mBest1...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2881/version/1

A Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for  Composition Improvements-  (v.4)
Provedor de dados: 17
Autores: Valentin  Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions.  Conventional &amp;#x201c;wet chemistry&amp;#x201d; analytical methods are time-consuming and costly.  As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry.  Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6231/version/4

Identification of the prebiotic translation apparatus within the contemporary ribosome
Provedor de dados: 17
Autores: Ilana Agmon; Chen Davidovich; Anat Bashan; Ada Yonath.
A structural element that could have existed independently in the prebiotic era was identified at the active site of the contemporary ribosome. It is suggested to have functioned as a proto-ribosome catalyzing peptide bond formation and non-coded elongation in the same manner that contemporary ribosomes exert positional catalysis, namely by accommodating the reactants in stereochemistry favourable for inline nucleophilic attack. This simple apparatus is a dimer of self-folding RNA units that could have assembled spontaneously into a symmetrical pocket-like structure, sufficiently efficient to be preserved throughout evolution as the active site of modern ribosomes, thus presenting a conceivable starting point for translation.Here we discuss the...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2921/version/1

Enhancing RNAi efficiency by inserting Nuclear factor-&amp;#x3ba;B binding sequence into SiRNA expression cassette
Provedor de dados: 17
Autores: Jianzhong Yi; Chenqian Liu.
RNAi based applications have been widely used to manipulate cellular phenotypes, analyze gene function and as a promising molecular therapy, however, there are rare reports in how to target the SiRNA expression constructs from the cytoplasm to nucleus. In this study, we inserted NF-&amp;#x3ba;B binding sequence into the SiRNA expression cassette to enhance RNAi efficiency, tested this propose by use of tRNAval and human H1 promoters, and eGFP and luciferase as reporter protein. The results showed that inserting NF-&amp;#x3ba;B binding sequence at the 3&amp;#x2019;-terminal of the SiRNA expression construct could enhance RNAi efficiency.
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4283/version/1

Altered copy gene function in plants following total intron replacement in precursor RNA
Provedor de dados: 17
Autores: Drew Schwartz.
Evidence is presented for two novel genetic mechanisms: total intron replacement in transcribedprecursor RNA by multiple short sequences and reverse transcription of the precursor RNA followedby incorporation into the genome as copy genes, some of which have acquired an altered function.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4307/version/1

Near Infrared Reflectance Spectroscopy (NIRS) Determination of Isoflavone Contents for Selected Soybean Accessions
Provedor de dados: 17
Autores: I. C. Baianu; Jun  Guo; Tiefeng  You; Randall   L. Nelson.
Soybean isoflavones are of considerable interest in relation to their possible health effects in human diets. The rapid and economical determination of soybean isoflavone concentrations is essential for the investigation and development of soybean health foods as well as the selection of soybean seeds with optimal isoflavone levels for such foods. Fourier transforms near infrared reflectance spectroscopy (FT-NIRS) calibrations were developed for the rapid and cost-effective analysis of isoflavones in soybean seeds. FT-NIRS measurements were carried out in quadruplicate for 50 soybean lines selected from the USDA Soybean Germplasm Collection. The selected soybean seeds provided a wide range of isoflavone concentrations (from 0.3 to 6.0 mg/g) that is...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7048/version/1

Memristive model of amoeba&amp;#x27;s learning
Provedor de dados: 17
Autores: Yuriy V. Pershin; Steven La Fontaine; Massimiliano  Di Ventra.
Recently, behavioural intelligence of the plasmodia of the true slime mold has been demonstrated. It was shown that a large amoeba-like cell Physarum polycephalum subject to a pattern of periodic environmental changes learns and changes its behaviour in anticipation of the next stimulus to come. Currently, it is not known what specific mechanisms are responsible for such behaviour. Here, we show that such behaviour can be mapped into the response of a simple electronic circuit consisting of an LC contour and a memory-resistor (a memristor) to a train of voltage pulses that mimic environment changes. We identify a possible microscopic origin of the memristive behaviour in the Physarum polycephalum, which together with the naturally occurring biological...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2431/version/1

New insight into DNA damage by cisplatin at the atomic scale
Provedor de dados: 17
Autores: Raji Heyrovska.
Cisplatin is cis-diamminedichloroplatinum (II) of chemical formula, Pt(NH3)Cl2, abbreviated as cis-DDP and known commercially as platinol. It is used widely as an anticancer drug for various types of cancer, ever since its discovery two centuries ago and has become a target of extensive researches. Transplatin, trans-DDP on the other hand, is found to be less or ineffective to treat cancers. Cisplatin is known to interact mainly with the N(7) nitrogen of guanine in nucleic acids, after a water molecule takes away one of the chlorines by hydrolysis. This initiates the damage of nucleic acids and eventually leads to apoptosis. However the way how this happens and why transplatin is less effective is not completely clear. Here the author brings some new...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6891/version/1

USP4 is regulated by Akt phosphorylation and deubiquitylates TGF-beta type I receptor
Provedor de dados: 17
Autores: Long Zhang; Fangfang Zhou; Yvette Drabsch; Ewa  Snaar-Jagalska; Craig Mickanin; Huizhe Huang; Kelly-Ann Sheppard; Chris Lu; Peter ten Dijke.
Stability and membrane localization of Transforming growth factor-&amp;#x3b2; (TGF-&amp;#x3b2;) type I receptor (T&amp;#x3b2;RI) is essential for controlling TGF-&amp;#x3b2; signaling. T&amp;#x3b2;RI is targeted for ubiquitination-mediated degradation by Smad7/Smurf2 complex. However, it is unclear whether polyubiquitin modified T&amp;#x3b2;RI can be reversed. Here we performed a genome-wide gain of function screen and identified ubiquitin-specific protease (USP) 4 as a strong inducer of TGF-&amp;#x3b2; signaling. Putative oncogenic USP4 was found to interact with T&amp;#x3b2;RI as deubiquitinating enzyme thus maintains T&amp;#x3b2;R1 levels at the plasma membrane. Depletion of USP4 mitigates TGF-&amp;#x3b2;-induced breast cancer cell migration, epithelial...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6804/version/1

Characterization of Fut10 and Fut11, Putative Alpha-1-3/4 Fucosyltransferase Genes Important for Vertebrate Development
Provedor de dados: 17
Autores: Santosh K. Patnaik.
Two new, putative alpha-1-3/4 fucosyltransferases ([alpha]1-3/4 Fuc-Ts), Fuc-TX and Fuc-TXI, were identified in the vertebrate genome and transcriptome sequence databases through sequence homology-based queries. These proteins have a significant sequence similarity to only [alpha]1-3/4 Fuc-Ts, and possess peptide motifs that are evolutionarily conserved among the known vertebrate [alpha]1-3/4 Fuc-Ts. However, Fuc-TX and Fuc-TXI lack the HH[R/W][D/E] sequence that determines the specificity for type 1 or 2 substrates among the known vertebrate enzymes, and Fuc-TXI proteins do not possess a transmembrane domain. The Fut10 and Fut11 genes that encode these proteins are expressed ubiquitously in the adult mouse and in the mouse embryo throughout development....
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/141/version/1

Synergistic Induction of NR4A Orphan Nuclear Receptors by LPS and cAMP in Murine Macrophage Cells
Provedor de dados: 17
Autores: Harish Shandilya; Sidney M. Morris.
Although NR4A orphan nuclear receptors have been implicated in inflammatory gene expression and atherosclerosis, there is little information regarding their regulation by combinations of stimuli likely to be found in vivo, such as LPS and inducers of cAMP. LPS rapidly induced Nur77 and NOR1 mRNAs but had little effect on expression of Nurr1 mRNA. All three NR4As were rapidly induced by 8-bromo-cAMP and remained elevated for at least 8 h. Maximum induction of NOR1 by 8-bromo-cAMP was much greater than with LPS, but maximum induction of Nur77 was similar with both agents. Whereas Nurr1 mRNA had very little response to LPS, it was strongly induced by 8-bromo-cAMP, and Nurr1 mRNA levels remained elevated for at least 20 h. The combination of 8-bromo-cAMP and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/663/version/1

The use of coral as a graft in a large cortical bone defect
Provedor de dados: 17
Autores: Hassan Z. Eskandar; Wan Zulmi; Abdul Hamid Suzina; Abd Rani Samsudin.
The use of coral as space filler in a large cortical bone defect was studied. Twelve Australian White Rabbit were divided into 8 and 12 week group. All rabbits were operated to create a 2.5cm defect in right tibia and replaced with coral; partially covered with the free autologous non-vascularized periosteum harvested from contralateral tibia. The coral was transfixed and the leg was immobilized with Plaster of Paris. At the end of 8th and 12th week, all the rabbits were assessed clinically, radiologically and sacrified for histology evaluation. Bony union achieved in 3 out of 5 rabbits at 8th week while 3 out of 4 at 12th supported by radiological studies. Histological examination showed healing at coral-cortical junction by callus formation with...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2264/version/1

Integrative Network-based Association Studies: Leveraging cell regulatory models in the post-GWAS era
Provedor de dados: 17
Autores: Andrea Califano; Atul Butte; Stephen Friend; Trey Ideker; Eric E. Schadt.
After completion of a number of large scale Genome-Wide Association Studies (GWAS), there is still a significant amount of trait and disease variance that cannot be explained by existing genetic variability. This review introduces new, Integrative Network-based Association Study (INAS) approaches that aim to minimize the impact from multiple hypothesis testing statistics, thus allowing the identification of rare variants/alterations and epistatic interactions. In particular we discuss methods that rely on the de novo computational, experimental, and integrative dissection of context specific molecular interaction networks (or interactomes, for short). We provide several examples of how these approaches may be used to tackle discovery of genetic variants...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5732/version/1

A Discrete State Model for Kinesin-1 with Rate Constants Modulated by Neck Linker Tension
Provedor de dados: 17
Autores: Steven J. Koch; Lawrence J. Herskowitz.
Kinesin-1 is a homodimeric molecular motor protein that uses ATP and a hand-over-hand motion to transport cargo along microtubules. How kinesin converts chemical energy into directed motion is a question that has been actively studied since its discovery. Even at the most coarse-grained level of chemical kinetics, understanding is still lacking. Minimal kinetic models are often developed to both explain kinesin&amp;#x2019;s hand-over-hand forward-stepping behavior and to infer important kinetic rate constants from experimental data. These minimal models are often limited to a handful of two-headed states on a core cycle and have been essential for the current level of understanding. However, it is not always clear how to evolve these core-cycle models to...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5038/version/1

Altered cholesterol ester cycle in _ex vivo_ skin fibroblasts from Alzheimer patients
Provedor de dados: 17
Autores: Alessandra Pani; Sandra Dessi; Giacomo Diaz; Claudia Abete; Claudia Mulas; Claudia Norfo; Marirosa Putzolu; Maria Dolores Cannas; Christina Doriana Orru; Alessandra Mocali; Pier Luigi Cocco; Paolo La Colla; Francesco Paoletti.
Recent studies in both animal and cell models of Alzheimer&amp;#x27;s disease (AD) indicated that sub-cellular cholesterol distribution seems to regulate amyloid-beta (A[beta]) generation in the brain. In particular, cholesterol-esters (CE), rather than total cholesterol levels, appear directly correlated with A[beta] production. Here we observed that, similarly to brain cells, skin fibroblasts obtained from AD patients produce and accumulate more CE than skin fibroblasts from age-matched healthy controls do. AD fibroblasts also exhibited a 2 fold increase in the expression of ACAT1, in addition to lower levels of SREBP2, nCEH, Caveolin-1 and ABCA1 mRNA levels, all of which are involved in the CE cycle. HMGCoA-reductase and LDL-receptor mRNAs levels did...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1602/version/1

Reactome - a knowledgebase of human biological pathways
Provedor de dados: 17
Autores: Peter D&amp;#x27;Eustachio; David Croft; Bernard de Bono; Gopal Gopinath; Marc Gillespie; Bijay Jassal; Lisa Matthews; Esther Schmidt; Imre Vastrik; Guanming Wu; Suzanna Lewis; Ewan Birney; Lincoln Stein.
Pathway curation is a powerful tool for systematically associating gene products with functions. Reactome (www.reactome.org) is a manually curated human pathway knowledgebase describing a wide range of biological processes in a computationally accessible manner. The core unit of the Reactome data model is the Reaction, whose instances form a network of biological interactions through entities that are consumed, produced, or act as catalysts. Entities are distinguished by their molecular identities and cellular locations. Set objects allow grouping of related entities. Curation is based on communication between expert authors and staff curators, facilitated by freely available data entry tools. Manually curated data are subjected to quality control and peer...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1281/version/1

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Provedor de dados: 17
Autores: I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn &amp;#x2013;algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata.  Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7083/version/1

Screening for the optimal siRNA targeting a novel gene (HA117) and construction and evaluation of a derivative recombinant adenovirus
Provedor de dados: 17
Autores: Youhua Xu; Gaihuan Zheng; Yuxia Guo; Xianqing Jin; Qing Luo.
We found a novel gene named as HA117 in our previous research. At this study, we screened for an optimal siRNA targeting the novel gene HA117 using the pSOS-HUS method, verified the results of pSOS-HUS siRNA screening for optimal affinity for the target gene, and constructed and evaluated a recombinant adenovirus carrying the DNA template for transcription of the optimal HA117 siRNA. The pSOS-HUS vector method was successfully utilized as a rapid and effective screen for an optimal siRNA for a target gene. Among five pairs of DNA templates, siRNA transcribed from HAi5 gave the strongest interference with the novel gene HA117; a HAi5-carrying recombinant adenovirus (Ad-HAi5) was successfully constructed and evaluated, laying a foundation for the further...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5301/version/1

Serine biosynthesis with one carbon catabolism represents a novel pathway for ATP generation in cells using alternative glycolysis with zero net ATP production
Provedor de dados: 17
Autores: Alexei Vazquez; Elke K. Markert; Zoltan N. Oltvai.
Recent experimental evidence indicates that some cancer cells have an alternative glycolysis pathway with net zero ATP production, implying that upregulation of glycolysis in these cells may not be related to the generation of ATP. Here we use a genome-scale model of human cell metabolism to investigate the potential metabolic alterations in cells using net zero ATP glycolysis. We uncover a novel pathway for ATP generation that involves reactions from the serine biosynthesis and one-carbon metabolism pathways. This pathway has a predicted two-fold higher flux rate in cells using net zero ATP glycolysis than those using standard glycolysis and generates twice as much ATP with significantly lower rate of lactate- but higher rate of alanine secretion. Thus,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6123/version/2

Modeling of ARS-interacting multifunctional proteins p18 and p38.
Provedor de dados: 17
Autores: Viktor V. Deineko.
ARS-interacting multifunctional proteins (auxiliary components) &amp;#x2013; are nonezymatic proteins, associated with aminoacyl-tRNA synthetases &amp;#x2013; enzymes that catalyse the joining of amino acids with their corresponding tRNAs. All these proteins are complexed into large macromolecular multisynthetase complex in eukaryotes. It includes nine different ARSs and three auxiliary components. Their spatial structures precisely defined by X-ray analysis are still not known. Nevertheless, it very useful to have this structure while making biochemical studies. Bioinformatical tools were used to create structural models of two auxiliary components of multisynthetase complex &amp;#x2013; p18 and p38.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1047/version/1

Hematopoietic Stem Cell Transcription Factor PU.1 with Mutated &amp;#x3b2;3/&amp;#x3b2;4 Domain Selectively Elicits Myeloid Differentiation
Provedor de dados: 17
Autores: Pallavi Gupta; Gurudutta U. Gangenahalli; Daman Saluja; Yogesh K. Verma; Jyoti Zack; Vimal K. Singh; Neeraj K. Satija; Rajendra P. Tripathi.
In many hematopoietic malignancies such as lymphomas &amp;#x26; leukemias, aberrant differentiation is the major feature of malignant phenotype that often results from a single genetic alteration and provides a site-specific target for therapy. Therefore, targeting of protein-protein interactions that have been identified as mediators of transcriptional repression that blocks normal hematopoietic differentiation holds great promise for therapeutic applications. An example is GATA-1, a critical erythroid transcription factor that is capable of suppressing the myeloid phenotype by down-regulating PU.1 in a dose-dependent manner. PU.1 is the most crucial transcription factor known to be required for myeloid differentiation of hematopoietic stem cells or...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5453/version/1

Direct fluorophore conjugation to genomic DNA for microarray-based epigenomic profiling
Provedor de dados: 17
Autores: Vineet Gupta.
A methodology for microarray based epigenomic profiling is presented. The method relies on platinum-based fluorescence labeling reagents for direct (non-enzymatic) labeling of DNA and RNA. This is a work in progress and only preliminary data is presented here.
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Chemistry; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/444/version/1

Reduction of circulating histone toxicity is a major function of C-reactive protein after extensive tissue damage
Provedor de dados: 17
Autores: Cheng-Hock Toh; Florence Baluwa; Nan Zhang; Joanna Manson; Caroline Dar; Susan Siyu Wang; Tingting Liu; Simon Abrams; Karim Brohi; Anja Kipar; Weiping Yu; Jecko Thachil; Yasir Alhamdi; guozheng Wang.
C-reactive protein (CRP) is a major acute phase protein. Although known to interact with chromatin, nucleosomes and histones, its functional roles are not clearly understood. Using both in vitro and in vivo models and samples from patients, this study demonstrates for the first time that CRP plays important roles in reducing the toxic effects of histones released into the circulation after extensive cell death. CRP protects endothelial cells by preventing histone integration into the cell membrane and thus reducing Ca2+ influx. In vivo, circulating histones cause endothelial damage, increased microvascular permeability, coagulation activation and IL-6 secretion. The latter induces CRP production in hepatocytes to form a negative feedback loop, a possible...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6264/version/1

Changes in Cholesterol Metabolism in Peripheral Cells of Alzheimer Disease Patients and Their Relatives
Provedor de dados: 17
Autores: Alessandra Pani; Paolo La Colla; Claudia Abete; Claudia Mulas; Marirosa Putzolu; Claudia Norfo; Sergio Laconi; Anna Borgia; Christina Zaru; Manuela Palmas; Paolo  F. Putzu; Alessandra Mocali; Francesco Paoletti; Sandra Dessi.
Background. Previous epidemiological and experimental studies indicated cholesterol as a central player  in Alzheimer disease (AD). Here, we utilized skin fibroblasts and PBMC as possible ex vivo models for the study of dysfunctions of cholesterol homeostasis which may be related to AD development. &amp;#xd;&amp;#xa;Methods. We analyzed cholesterol homeostasis using colorimetric, thin layer chromatography (TLC), and histologic technique in ex vivo cultures of skin fibroblasts and PBMCs from patients with probable AD and their first-degree relatives. Additionally, healthy age-matched individuals served as controls. &amp;#xd;&amp;#xa;Findings. As compared to controls, skin fibroblasts and PBMCs from AD patients, displayed an evident alteration of cholesterol...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1246/version/1

Effects of surface passivation on gliding motility assays
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
In this study, we report differences in the observed gliding speed of microtubules dependent on the choice of bovine casein used as a surface passivator. We observed differences in both speed and support of microtubules in each of the assays. Whole casein, comprised of [alpha]~s1~, [alpha]~s2~, [beta], and [kappa] casein, supported motility and averaged speeds of 966 &amp;#xb1; 7 nm/s. Alpha casein can be purchased as a combination of s1 and s2 and supported gliding motility and average speeds of 949 &amp;#xb1; 4 nm/s. Beta casein did not support motility very well and averaged speeds of 870 &amp;#xb1; 30 nm/s. Kappa casein supported motility very poorly and we were unable to obtain an average speed. Finally, we observed that mixing alpha, beta, and kappa...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5278/version/2

Technical Note: The Use of RNA-interference as a Tool to Find Proteins Involved in Melanosome Formation or Transport
Provedor de dados: 17
Autores: Eva M. Amsen; Daniela Rotin.
Melanosomes are lysosome-related organelles that produce and transport the pigment melanin within melanocytes. Mutations in proteins required for melanosome transport and formation lead to a range of pigmentation defects, manifested at the cellular level as perinuclear clustering of melanosomes, or reduced sorting of melanosomal cargo such as tyrosinase-related protein 1 (TYRP1). A pilot screen was carried out to investigate whether a combination of cellular imaging and RNA interference could be used to identify new proteins involved in pigmentation pathways. In this study, eleven genes known to play a role in melanosome transport/formation or other pigmentation properties were knocked down in mouse melanocytes with shRNAmir constructs. The investigated...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3419/version/1

Intracellular Regulatory Networks are close to Monotone Systems
Provedor de dados: 17
Autores: Avi Ma&amp;#x27;ayan; Ravi Iyengar; Eduardo D. Sontag.
Several meso-scale biological intracellular regulatory networks that have specified directionality of interactions have been recently assembled from experimental literature. Directed networks where links are characterized as positive or negative can be converted to systems of differential equations and analyzed as dynamical systems. Such analyses have shown that networks containing only sign-consistent loops, such as positive feed-forward and feedback loops function as monotone systems that display well-ordered behavior. Perturbations to monotone systems have unambiguous global effects and a predictability characteristic that confers advantages for robustness and adaptability. We find that three intracellular regulatory networks: bacterial and yeast...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/25/version/1

Preen Gland-Secreted Alkanols Enhance Male Attractiveness in Parrots
Provedor de dados: 17
Autores: Jian-Xu Zhang; Wei Wei; Jin-Hua Zhang.
The skin glands are widely used in pheromone production throughout the vertebrate worlds. Growing evidences show that birds also have chemical communication, but the uropygial (also called preen or oil) glands, serving as only specialized skin glands of birds, have no sex pheromones characterized. Here, by combining GC-MS analysis and bioassay, we show with the budgerigar, Melopsittacus undulatus, that birds can used the preen gland-secreted volatiles (a blend of octadecanol, nonadecanol and eicosanol for male budgerigars) spread over body plumage when preening to convey sex information. Here, we first report the avian pheromones derived from the uropyginal gland and suggests that the gland has broader implications than previously known (e.g. plumage...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2305/version/1

Beneficial role of allicin from garlic in cervical cancer
Provedor de dados: 17
Autores: Irfan Ahmad Ansari; Najmul  Islam.
Introduction: Cervical cancer remains a global health concern for females. Thus, in order to control cervical cancer, attempts are being made by researchers globally to somehow induce programmed cell death in the said cancerous cells. Wide spectrums of molecules are being probed for its ability to induce apoptosis in cervical cancer cells. Focus has now shifted in exploring natural compounds having antioxidant and anti-inflammatory molecules that may induce apoptosis in cancerous cells. Thus, we have employed allicin from garlic- a natural antioxidant, to probe the above in the present study.&amp;#xd;&amp;#xa;Objective: To probe whether or not allicin from garlic, a natural antioxidant, induces apoptosis in monocytes from patients with cervical...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1561/version/1

Molecular evidence for Toxoplasma gondii in the brain of striped dolphins (Stenella coeruleoalba) stranded along the Ligurian Sea coast of Italy
Provedor de dados: 17
Autores: Donato  Traversa; Angela Di Cesare; Cristina Casalone; Barbara Iulini; Walter Mignone; Cristiana Tittarelli; Umberto Proietto; Silvana Meloni; Giulia Buffatello; Fiona Forster; Seamus Kennedy; Giovanni Di Guardo.
Toxoplasma gondii is a protozoan agent of increasing concern for both free-ranging and captive cetaceans. Nonetheless, information on epidemiology, biology, genetics and pathogenic potential of T. gondii for aquatic mammals is incomplete. This work provides molecular evidence for T. gondii in the brain tissue from five striped dolphins (Stenella coeruleoalba) found stranded in 2007-2008 along the Ligurian Sea coast of Italy. These animals showed a more or less severe, subacute to chronic, non purulent, multifocal meningo-encephalitis. Additionally, the cerebral parenchyma of 3 animals harboured protozoan cysts and zoites which were immunohistochemically linked to T. gondii. Consequently, a preliminary molecular investigation was undertaken to confirm the...
Tipo: Poster
Palavras-chave: Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4930/version/1

Inhibiton of NF&amp;#x3ba;B activation and aromatase activity by vanilloids: An in vitro and in silico study
Provedor de dados: 17
Autores: Suaib  Luqman; Abha  Meena; Laura  E. Marler; Tamara  P. Kondratyuk; John  M. Pezzuto.
Target-specific drugs, including natural products, offer promise for the amelioration of cancer and other human ailments with reduced side-effects. Capsaicin, the pungent ingredient present in chillies (Capsicum annuum L.), and capsazepine, a synthetic analogue of capsaicin (collectively referred to as vanilloids), are known to possess a variety of pharmacological and physiological properties. In our continuous effort to discover cancer chemopreventive agents from natural products, we investigated the effect of vanilloids on NF&amp;#x3ba;B activation with stably transfected 293/NF&amp;#x3ba;B-Luc human embryonic kidney cells induced by treatment with tumor necrosis factor (TNF&amp;#x3b1;), and aromatase activity. Capsaicin and capsazepine blocked...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6913/version/1

The Effect of a Reduced-Calorie Diet on alpha-2 Adrenergic Receptor Responsiveness in Abdominal Adipose Tissue in Obese Men During Exercise
Provedor de dados: 17
Autores: Roy R. Estrada; Joseph O. Schmelz; David Turbow; Edith Neumann.
There is at present an imperfect understanding of the effect of diet on availability of inhibitory receptors in fat cells during exercise among obese men. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Objective:* The purpose of this study was to determine whether diet results in downregulation of alpha-2 adrenergic receptor ([alpha]~2-AR~) messenger RNA (mRNA), improving metabolism in exercise in obese men. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Design:* One group, pre-test, post-test design.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Measurements:* Subcutaneous abdominal adipose tissue was tested for physiologic response, such as changes in catecholamines and other markers of lipolysis measured during periods of exercise, before and after a 12-week diet. Plasma markers of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1838/version/1

A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics
Provedor de dados: 17
Autores: I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7052/version/1

Developing Predictive Molecular Maps of Human Disease through Community-based Modeling
Provedor de dados: 17
Autores: Jonathan M. J. Derry; Lara M. Mangravite; Christine Suver; Matt Furia; David  Henderson; Xavier  Schildwachter; Jonathan Izant; Solveig K. Sieberts; Michael R. Kellen; Stephen H. Friend.
The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics.
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5883/version/1

Tumor-associated EGFR over-expression specifically activates Stat3 and Smad7 resulting in desensitization of TGF-&amp;#x3b2; signaling
Provedor de dados: 17
Autores: Rodney Luwor; Lauren Taylor; Bo Wang; Hong-Jian  Zhu.
Transforming Growth Factor-[beta] (TGF-[beta]) and Epidermal Growth Factor (EGF) signaling pathways are both independently implicated as key regulators in tumor formation and progression. Here, we demonstrate that activation of the tumor-associated and over-expressed EGFR desensitizes TGF-[beta] signaling and its cytostatic regulation through specific Stat3 activation and Smad7 induction. In normal and tumor human cell lines, reduction of TGF-[beta]-mediated Smad2 phosphorylation, nuclear translocation and Smad3 target gene activation were observed where EGFR is over-expressed, but not in cells which expressed EGFR at normal levels. The EGFR downstream signaling molecules phosphatidyinositol-3 Kinase (PI3K) or mitogen-activated protein kinase/ERK kinase...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1535/version/1

Living unicellular eukaryote Tetrahymena pyriformis as a model for study
Provedor de dados: 17
Autores: Elena Mokhova.
Some animals are able to survive for a long time under conditions of drastically reduced oxidative metabolism, called metabolic depression. The most investigated type of metabolic depression is hibernation. Research into the basic properties of liver mitochondria energetics during hibernation is essential for fundamental biology and medicine. However, the absence of the suitable hepatocyte culture makes it impossible to study the characteristic features of mitochondrial metabolic states in living cells during hibernation. We proposed that under selected conditions, the unicellular eukaryote Tetrahymena pyriformis resembles hepatocytes under hibernation, as (i) both cell types survive under condition of restricted food supply, hypoxia, and accumulation of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4521/version/3

Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models
Provedor de dados: 17
Autores: I. C. Baianu.
Operational logic and bioinformatics models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes are proposed. &amp;#x141;ukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable &amp;#x27;next-state functions&amp;#x27; is extended to a &amp;#x141;ukasiewicz Topos with an n-valued &amp;#x141;ukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6206/version/1

_Limusaurus_ and bird digit identity
Provedor de dados: 17
Autores: Alexander O. Vargas; G&amp;#xfc;nter P. Wagner; Jacques A. Gauthier.
_Limusaurus_ is a remarkable herbivorous ceratosaur unique among theropods in having digits II, III and IV, with only a small metacarpal vestige of digit I. This raises interesting questions regarding the controversial identity of avian wing digits. The early tetanuran ancestors of birds had tridactyl hands with digital morphologies corresponding to digits I, II &amp;#x26; III of other dinosaurs. In bird embryos, however, the pattern of cartilage formation indicates that their digits develop from positions that become digits II, III, &amp;#x26; IV in other amniotes. _Limusaurus_ has been argued to provide evidence that the digits of tetanurans, currently considered to be I, II and III, may actually be digits II, III, &amp;#x26; IV, thus explaining the...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3828/version/1

Unlocking biomarker discovery: Large scale application of aptamer proteomic technology for early detection of lung cancer
Provedor de dados: 17
Autores: Rachel M. Ostroff; William L. Bigbee; Wilbur Franklin; Larry Gold; Mike Mehan; York E. Miller; Harvey I. Pass; William N. Rom; Jill M. Siegfried; Alex Stewart; Jeffrey J. Walker; Joel L. Weissfeld; Stephen Williams; Dom Zichi; Edward N. Brody.
Lung cancer is the leading cause of cancer deaths, because ~84% of cases are diagnosed at an advanced stage. Worldwide in 2008, ~1.5 million people were diagnosed and ~1.3 million died &amp;#x2013; a survival rate unchanged since 1960. However, patients diagnosed at an early stage and have surgery experience an 86% overall 5-year survival. New diagnostics are therefore needed to identify lung cancer at this stage. Here we present the first large scale clinical use of aptamers to discover blood protein biomarkers in disease with our breakthrough proteomic technology. This multi-center case-control study was conducted in archived samples from 1,326 subjects from four independent studies of non-small cell lung cancer (NSCLC) in long-term tobacco-exposed...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4537/version/1

Beyond the fuzzy lock-and-key: spontaneous symmetry shifts and glycan/lectin logic gates
Provedor de dados: 17
Autores: Rodrick Wallace.
Changes in the molecular topology of glycan/lectin interaction may explain observed reaction punctuation driven by experimental gradients in reactant concentration. Adoption of a &amp;#x27;biological renormalization&amp;#x27; perspective from statistical physics for the analysis of such phase transitions suggests, in marked contrast to conventional physical systems, a broad spectrum of possible universality class behaviors. This spectrum may, in typical perverse biological manner, be of central scientific interest. Generalization, via formalism abducted from coevolutionary theory, suggests that glycan/lectin molecular switches instantiate logic gates that may be as sophisticated as those characterizing basic neural process, if on a different scale.
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Microbiology; Molecular Cell Biology; Pharmacology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6849/version/1

Barlow-Hall in vitro Evolution Protocol
Provedor de dados: 17
Autores: Barry G. Hall; Miriam Barlow.
The Barlow-Hall method for in vitro evolution is a simple alternative to methods such as DNA shuffling and is particularly applicable to predicting the evolution of target genes in nature.  This detailed protocol includes the procedure itself and, as Appendices, describes particularly effective protocols for electroporation and for preparation of electrocompetent cells.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1772/version/1

Structural changes in intestinal enteroendocrine cells after ileal interposition in normal rats
Provedor de dados: 17
Autores: Gilmara S. Aguiar-Yamaguchi; Jo&amp;#xe3;o-Luiz M. C. Azevedo; Marcelo C. Carlini; Paolo H. B. Lourenco; Wellington Cardia; Maria T. S. Alves; Aparecida E. Hirata; Lucas P. F. F. Leal; Bianca Marigliani; Linda O. A. Bernardes; Karina F. Neves; Rudy N. Rocha; Jos&amp;#xe9;-Francisco Borborema; Jo&amp;#xe3;o-Luiz C. Azevedo; Otavio C. Azevedo; Gustavo P. S. Miguel.
INTRODUCTION: No therapeutic approach has significantly impacted the progression of diabetes. As early improvement of glicaemic control is observed after bariatric surgeries, there is currently a search for surgical procedures that can promote euglycemia also in non-obese patients. Glicaemic control can be achieved by increasing the blood concentration of GLP-1, a hormone produced by L cells that are more densely concentrated in the terminal ileum. The interposition of ileal segment to a more anterior region (proximal jejunum) can promote a greater stimulation of the L cells by poorly digested food, increasing the production of GLP-1 and reflecting on glicaemic control.&amp;#xd;&amp;#xa;AIMS: To investigate long-term histological modifications of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6683/version/1

Food Physical Chemistry and Biophysical Chemistry (v2)
Provedor de dados: 17
Autores: I. C. Baianu.
Food Physical Chemistry is considered to be a branch of Food Chemistry^1,2^ concerned with the study of both physical and chemical interactions in foods in terms of physical and chemical principles applied to food systems, as well as the applications of physical/chemical techniques and instrumentation for the study of foods^3,4,5,6^.  This field encompasses the &amp;#x22;physiochemical principles of the reactions and conversions that occur during the manufacture, handling, and storage of foods&amp;#x22;^7^. Two rapidly growing, related areas are Food Biotechnology and Food Biophysical Chemistry.  &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6573/version/2

Quantification of Cell Movement Reveals Distinct Edge Motility Types During Cell Spreading
Provedor de dados: 17
Autores: Benjamin J. Dubin-Thaler; Jake M. Hofman; Harry V. Xenias; Ingrid A. Spielman; Anna H. Shneidman; Lawrence David; Hans-Guenther Dobereiner; Chris Wiggins; Michael  P. Sheetz.
Actin-based motility is central to cellular processes such as migration, bacterial engulfment, and cancer metastasis, and requires precise spatial and temporal regulation of the cytoskeleton. We studied one such process, fibroblast spreading, which involves three temporal phases: early, middle, and late spreading, distinguished by differences in cell area growth. In these studies, aided by improved algorithms for analyzing edge movement, we observed that each phase was dominated by a single, kinematically and biochemically distinct cytoskeletal organization, or motility type. Specifically, early spreading was dominated by periodic blebbing; continuous protrusion occurred predominantly during middle spreading; and periodic contractions were prevalent in...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/391/version/1

Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation
Provedor de dados: 17
Autores: Benjamin Bouvier; Raik Gr&amp;#xfc;nberg; Michael Nilges; Frederic Cazals.
The accurate description and analysis of protein-protein interfaces remains a challenging task. Traditional definitions, based on atomic contacts or changes in solvent accessibility, tend to over- or underpredict the interface itself and cannot discriminate active from less relevant parts.&amp;#xd;&amp;#xa;We here extend a fast, parameter-free and purely geometric definition of protein interfaces and introduce the shelling order of Voronoi facets as a novel measure for an atom&amp;#x27;s depth inside the nterface. Our analysis of 54 protein-protein complexes reveals a strong correlation between Voronoi Shelling Order (VSO) and water dynamics. High Voronoi Shelling Order coincides with residues that were found shielded from bulk water fluctuations in a...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1522/version/2

Transcriptional memory emerges from cooperative histone modifications
Provedor de dados: 17
Autores: Hans Binder; Lydia Steiner; Thimo Rohlf; Sonja Prohaska; Joerg Galle.
Background&amp;#xd;&amp;#xa;Transcriptional regulation in cells makes use of diverse mechanisms to ensure that functional states can be maintained and adapted to variable environments; among them are chromatin-related mechanisms. While mathematical models of transcription factor networks controlling development are well established, models of transcriptional regulation by chromatin states are rather rare despite they appear to be a powerful regulatory mechanism.&amp;#xd;&amp;#xa;Results&amp;#xd;&amp;#xa;We here introduce a mathematical model of transcriptional regulation governed by histone modifications. This model describes binding of protein complexes to chromatin which are capable of reading and writing histone marks. Molecular interactions between...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6507/version/1

A Systems Biology Approach to the Evolution of Codon Use Pattern
Provedor de dados: 17
Autores: Ines Thiele; Ronan M. T. Fleming; Richard Que; Aarash Bordbar; Bernhard O. Palsson.
The genetic code is redundant as amino acids are encoded by synonymous codons that are unequally used.This codon usage bias (CUB) affects gene expression and cellular functions yet the underlying mechanisms have not been elucidated. We used a sequence-specific, stoichiometric model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655 to test the effect of randomly changed CUB on growth maximization under various environmental conditions. Amongst CUB mutant strains, we identified reduced growth phenotypes, which were caused by tRNA supply shortage. We propose, supported by computations and bibliomic data, that expansion of tRNA gene content or tRNA reading is a mechanism to respond to changes in CUB. Our systems biology modelling...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6312/version/1

Processing of insect retrotransposons by self-cleaving ribozymes
Provedor de dados: 17
Autores: Dana J. Ruminski; Chiu-Ho T. Webb; Nathan J. Riccitelli; Andrej Luptak.
We show that several classes of insect non-LTR retrotransposons harbor self-cleaving ribozymes of the HDV family at their 5&amp;#x2032; termini. In Drosophila the R2 ribozymes exhibit highly differential in vivo expression and robust in vitro activity, modulated by an upstream sequence originating from the insertion site. Our data suggest a role for self-cleaving ribozymes in co-transcriptional processing of retrotransposons with implications for downstream events, including translation and retrotransposition.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4333/version/1

Rsp5 promotes Gene Activation mediated by 9aaTAD Transcription Factors Oaf1 and Gal4
Provedor de dados: 17
Autores: Joachim Lipp; Manfred Koranda; Martin Piskacek.
Nine-amino-acid transactivation domain, 9aaTAD, defines a large superfamily of yeast and mammals transcription factors. The transactivation of the 9aaTAD has been addressed to multiple general co-activators TAF9, MED15, CBP and p300. We demonstrate for the 9aaTAD transcription factors Oaf1 and Gal4 functional and physical interaction with E3-Ubiquitin Ligase Rsp5. The Rsp5-associations with RNA polymerase II and TFIID were reported previously.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3968/version/1

Effects of surface passivation on gliding motility assays
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
In this study, we report differences in the observed gliding speed of microtubules&amp;#xd;&amp;#xa;dependent on the choice of bovine casein used as a surface passivator. We observed&amp;#xd;&amp;#xa;differences in both speed and support of microtubules in each of the assays. Whole&amp;#xd;&amp;#xa;casein, comprised of [alpha]~s1~, [alpha]~s2~, [beta], and [kappa] casein, supported motility and averaged speeds of&amp;#xd;&amp;#xa;966 &amp;#xb1; 7 nm/s. Alpha casein can be purchased as a combination of s1 and s2 and&amp;#xd;&amp;#xa;supported gliding motility and average speeds of 949 &amp;#xb1; 4 nm/s. Beta casein did not&amp;#xd;&amp;#xa;support motility very well and averaged speeds of 870 &amp;#xb1; 30 nm/s. Kappa casein&amp;#xd;&amp;#xa;supported...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5278/version/1

Many in vivo  &amp;#x27;protein folding codes&amp;#x27; can be inferred from empirical classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;s topological rate distortion approach to the genetic code is applied to the problem of protein symmetries and to the analysis of protein folding rates. Unlike the genetic case, numerous &amp;#x27;protein folding codes&amp;#x27; can be identified from empirical classifications. Protein folding rates follow from a topologically-driven rate distortion argument. These results imply markedly different evolutionary trajectories for the genetic and protein folding codes, and suggest that the &amp;#x27;protein folding code&amp;#x27; is, in fact, a complicated composite, distributed across protein production and a cellular, or higher, regulatory apparatus acting as a canalizing catalyst that drives the system to converge on particular transitive...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4665/version/2

Novel Cell type-specific aptamer-siRNA delivery system for HIV-1 therapy
Provedor de dados: 17
Autores: Jiehua Zhou; Haitang Li; Shirley Li; John Zaia; John Rossi.
The successful use of small interfering RNAs (siRNAs) for therapeutic purposes requires safe and efficient delivery to specific cells and tissues. Here we demonstrate cell type-specific delivery of anti-HIV siRNAs via fusion to an anti-gp120 aptamer. The envelope glycoprotein is  expressed on the surface of HIV-1 infected cells, allowing binding and interalization of the aptamer-siRNA chimeric molecules. We demonstrate that the anti-gp120 aptamer-siRNA chimera is specifically taken up by cells expressing HIV-1 gp120, and the appended siRNA is processed by Dicer, releasing an anti-tat/rev siRNA which in turn inhibits HIV replication. We show for the first time a dual functioning aptamer-siRNA chimera in which both the aptamer and the siRNA portions have...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1299/version/1

Density alteration in non-physiological cells
Provedor de dados: 17
Autores: Yu Liu; Yuan-Chang Zhu; Bin-Bin Wu; Xiao-Hua Wu; Fei-Fei Lan; Jian-Ge Wei; Ming Wang; Hai-Cheng Li; Lin-Na Li; Ju-Xiang Li; Jia Fei.
In the present study an important phenomenon of cells was discovered: the change of intracellular density in cell&amp;#x27;s response to drug and environmental factors. For convenience, this phenomenon is named as &amp;#x22;density alteration in non-physiological cells&amp;#x22; ( DANCE). DANCE was determined by discontinuous sucrose gradient centrifugation (DSGC), in which cells were separated into several bands. The number and position of the bands in DSGC varied with the change of cell culture conditions, drugs, and physical process, indicating that cell&amp;#x27;s response to these factors was associated with alteration of intracellular density. Our results showed that the bands of cells were molecularly different from each other, such as the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6541/version/1

Marked Rise in Replikin Counts in H5N1 Influenza Virus Localized to Lethality Gene p B1.
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Abstract: Virus outbreaks have been found to be related to the concentration of a new class of genomic peptides, Replikins^1^. The eight genes of H5N1 influenza virus were analyzed for the distribution of Replikin Counts (number Replikins /100 amino acids) in 2,441 sequences from birds and humans. An increase (p&amp;#x3c;0.001) occurred from 2004 to August 2011 in one gene, pB1.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Immunology; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6420/version/1

In silico Protein Structural Modeling and Active binding site Evaluation of Streptococcus pneumoniae
Provedor de dados: 17
Autores: M. Balakrishnan; R.C. Srivastava; M. Ramachandran.
Structure function relation of glucose kinese in Streptococcus pneumoniae. However, a solved structure for _Streptococcus pneumoniae_ glucose kinese is not available at the protein data bank. Glucose kinase is a regulatory enzyme capable of adding phosphate group to glucose in the first step of streptomycin biosynthesis. The activity of glucose kinase was regulated by the Carbon Catabolite Repression system. So, we created a model of glucose kinese from _Streptococcus pnemoniae_ using the X-ray crystallography structure of glucose kinese enzymes from _Enterobacteria faecalis_ as template with Molsoft ICM v3.5 software. The model was validated using protein structure checking tools such as PROCHECK, WHAT IF: for reliability. The active site amino acid...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3207/version/1

Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations.
Provedor de dados: 17
Autores: Shimon Bershtein; Eugene Shakhnovich.
Protein stability is widely recognized as a major evolutionary constraint. However, the relation between mutation-induced perturbations of protein stability and biological fitness has remained elusive. Here we explore this relation by introducing a selected set of mostly destabilizing mutations into an essential chromosomal gene of E.coli encoding dihydrofolate reductase (DHFR) to determine how changes in protein stability, activity and abundance affect fitness. Several mutant strains showed no growth while many exhibited fitness higher than wild type. Overexpression of chaperonins (GroEL/ES) buffered the effect of mutations by rescuing the lethal phenotypes and worsening better-fit strains. Changes in stability affect fitness by mediating the abundance of...
Tipo: Manuscript
Palavras-chave: Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6219/version/1

Fundamentals of Molecular Biology
Provedor de dados: 17
Autores: Malay Bhattacharyya.
We present some basic concepts of molecular biology and the related open problems.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7121/version/1

(Corrected) Osmotic stress and water isotope effects in kinesin-1 gliding motility assays
Provedor de dados: 17
Autores: Steven J. Koch; Andy Maloney; Lawrence J. Herskowitz.
The osmotic pressure and kinetic properties of water play important roles in biomolecular interactions.  As pointed out by Parsegian, Rand, and Rau, these crucial roles are often overlooked[1].  In some fields, osmotic stress and isotope effects have been exploited for probing the role water plays in binding interactions of biomolecules.  To our knowledge, there have been no studies of osmotic stress and water isotope effects for kinesin, and only a handful for myosin.  We&amp;#x27;re currently using the gliding motility assay to see whether we can extract new information about kinesin-1 / microtubule interactions by changing osmotic stress and water isotopes.  We will describe our open-source, automated analysis platform for extracting microtubule gliding...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4479/version/3

A novel predicted calcium-regulated kinase family  implicated in neurological disorders
Provedor de dados: 17
Autores: Ma&amp;#x142;gorzata Dudkiewicz; Anna Lenart; Krzysztof Paw&amp;#x142;owski.
Protein kinases are essential effectors of cellular signaling. Surprisingly, using bioinformatics tools, we predicted protein kinase structure and function for proteins of unknown function (FAM69 family) coded by five related human genes and their Metazoan homologues. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases in four of human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. The FAM69 genes, FAM69A, FAM69B, FAM69C, C3ORF58 and CXORF36, are by large uncharacterized molecularly, yet linked to several neurological disorders in genetics studies. An EF-hand Ca2+-binding domain in FAM69A and FAM69B proteins, inserted within the structure of the kinase...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7015/version/1

A Database for TSSs of Human MicroRNAs
Provedor de dados: 17
Autores: Malay Bhattacharyya; Sanghamitra Bandyopadhyay.
MicroRNAs (miRNAs) are small endogeneous non-coding RNAs of about 22nt length. These short RNAs regulate the expression of mRNAs by hybridizing with their 3&amp;#x27;-UTRs or by translational repression. They have been shown to take crucial roles in many biological processes. Many of the current studies are focused over how mature miRNAs regulate mRNAs, even though there is very limited knowledge about their transcriptional loci. Primary miRNAs (pri-miRs) are first transcribed from the DNA, followed by the formation of precursor miRNA (pre-miR) by endonucleases activity, which finally produces mature miRNAs. Unfortunately, the identification of the loci of pri-miRs, and the associated information about transcription start sites (TSSs) and promoters is...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6832/version/1

An open source LABVIEW platform for simulating image series of   fluorescent microtubules in gliding assays
Provedor de dados: 17
Autores: Lawrence J. Herskowitz; Steven J. Koch.
We describe an open-source LabVIEW software platform for generating simulated images of microtubules in gliding motility assays.  We describe how the software works and how to obtain the software.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4374/version/1

Versatile Control System for Automated Single-Molecule Optical Tweezers Investigations
Provedor de dados: 17
Autores: Steven J. Koch; Richard C. Yeh.
We present a versatile control system to automate single-molecule biophysics experiments. This method combines low-level controls into various functional, user-configurable modules, which can be scripted in a domain-specific instruction language. The ease with which the high-level parameters can be changed accelerates the development of a durable experiment for the perishable single-molecule samples. Once the experimental parameters are tuned, the control system can be used to repeatedly manipulate other single molecules in the same way, which is necessary to accumulate the statistics needed to report results from single-molecule studies. This system has been implemented for an optical tweezers instrument for single-molecule manipulations, with real-time...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4284/version/1

Three mutations in SASH1 cause the pathogenesis of dyschromatosis universalis hereditaria (DUH)
Provedor de dados: 17
Autores: Qinghe Xing; Dingan Zhou; Zhiyun Wei.
Dyschromatosis universalis hereditaria (DUH) is a rare genodermatosis characterized by hyper- and hypopigmented macules which form a reticulate or mottled pattern. The causal gene and the precise pathogenesis of DUH have been unclear since the disease was initially reported in 1933. However, we found three heterozygous mutations encoding amino acid substitutions in SASH1 in each of three nonconsanguineous DUH families. Immunohistochemistry and melanin staining showed distribution heterogenicity of melanocytes, predominantly melanized melanocytes in the epidermal tissues of a DUH patient. Specifically, we identified that mutations of SASH1 can up-regulate resident melanogenic proteins, transport proteins of melanosome, and induce increased mobility of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5629/version/1

Soybean Composition Database from NIR, NMR and GC-MS Analyses
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Jun Guo; Doina M. Costescu; V. I. Prisecaru.
This novel Soybean Composition Database from the AFC-NMR &amp;#x26; NIR Spectroscopy Facility of the College of ACES at the University of Illinois at Urbana includes more than 12,000 NIR measurements on soybeans from the International Soybean Germplasm Collection, such as those received from Peking at the National Soybean Collection.&amp;#xd;&amp;#xa;Excel files (.xls) of our novel spectroscopic data are currently available for all 80,000 + NIR and FT-NMR measurements; such data are made available from an ultra-fast and secure supercomputer server utilizing the current version of the Scientific-Linux OS-based software. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A detailed account is also presented of our high-resolution nuclear magnetic resonance (HR-NMR) and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6201/version/2

Integrative concept of homeostasis: translating physiology into medicine
Provedor de dados: 17
Autores: Ivan Spasojevic.
To truly understand living systems they must be viewed as a whole. In order to achieve this and to come to some law to which living systems obey, data obtained on cells, tissues and organs should be integrated. Because there are no such laws yet, there is usually a long path for physiological findings obtained by reductionist approaches to be translated into medical practice. The concept and accompanying equations of homeostasis presented here are aimed to develop biological laws and to bridge this gap between physiology and medicine. The concept of homeostasis takes into account energy input and output, enlisting all relevant contributors. In homeostasis, changes in the input should equal changes in the output within any specific period of time. What I...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6741/version/2

Hierarchical coexistence of universality and diversity controls robustness and multi-functionality in intermediate filament protein networks
Provedor de dados: 17
Autores: Theodor Ackbarow; Markus  J. Buehler.
Proteins constitute the elementary building blocks of a vast variety of biological materials such as cellular protein networks, spider silk or bone, where they create extremely robust, multi-functional materials by self-organization of structures over many length- and time scales, from nano to macro.  Some of the structural features are commonly found in a many different tissues, that is, they are highly conserved.  Examples of such universal building blocks include alpha-helices, beta-sheets or tropocollagen molecules.  In contrast, other features are highly specific to tissue types, such as particular filament assemblies, beta-sheet nanocrystals in spider silk or tendon fascicles. These examples illustrate that the coexistence of universality and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Ecology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/826/version/1

Complex Systems Analysis of Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: I. C. Baianu.
A new approach to the modular, complex systems analysis of nonlinear dynamics in cell cycling network transformations involved in carcinogenesis is proposed. Carcinogenesis is a complex process that involves dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments that form numerous inter-related pathways referred to as networks.&amp;#xd;&amp;#xa;The variable biotopology of such dynamic networks is highly complex, and has a number of interesting properties that can be formally characterized at one level of organization by mathematical structures called &amp;#x27;biogroupoids&amp;#x27;. &amp;#xd;&amp;#xa;One such family of pathways contains the cell cyclins. Cyclins are proteins that link several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6205/version/1

Early Diagnosis of Alzheimer&amp;#x27;s disease by NIRF Spectroscopy  and Nuclear Medicine
Provedor de dados: 17
Autores: I. C. Baianu.
There is an urgent need for the early detection of diseases such as Alzheimer&amp;#x2019;s (AD) and Cancers in order to enable their successful treatment. Cancer is the second major cause of death after Heart Disease, and AD is the third major cause of death with major, human and financial/economics trillion dollar consequences for the society. Nuclear Medicine is concerned with applications in Medicine of Nuclear Science and Engineering techniques and knowledge. Three major Nuclear Medicine techniques that are established for diagnostic and research purposes are: Positron Emission Tomography (PET) and CAT/CT, Nuclear Magnetic Resonance Imaging (NMRI/MRI). However, these three techniques have also major limitations in terms of either cost or image...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6271/version/1

Angiogenesis in Chronic Obstructive Pulmonary Disease
Provedor de dados: 17
Autores: Alessandro Matarese; Gaetano Santulli.
Angiogenesis is a crucial component of lung pathophysiology, not only in cancer but also in other disorders, such as chronic obstructive pulmonary disease (COPD). In COPD angiogenesis is definitely able to control and orchestrate the progression of airway remodeling. Herein, we provide several remarkable translational aspects of angiogenesis in COPD, exploring both basic and clinical research in this field. Indeed, we present a number of pro- and anti-angiogenic factors, which can be also used as potential biomarkers to monitor disease progression. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This pre-print has subsequently been published at http://www.unisa.it/uploads/7100/06.pdf
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7112/version/1

Multifunction moonlighting and intrinsically disordered proteins: Information catalysis, nonrigid molecule symmetries, and the &amp;#x27;logic gate&amp;#x27; spectrum
Provedor de dados: 17
Autores: Rodrick Wallace.
Intrinsically disordered proteins (IDP) appear far more likely to engage in functional moonlighting than well-structured proteins. The recent use of nonrigid molecule theory to address IDP structure and dynamics produces this result directly: Mirror image subgroup or subgroupoid tiling matching of the molecular fuzzy lock-and-key can be much richer for IDPs since the number of possible group or groupoid symmetries can grow exponentially with molecule length, while tiling matching for 3D structured proteins is relatively limited. A simple information catalysis model suggests how this mechanism can produce a vast spectrum of biological &amp;#x27;logic gates&amp;#x27; having subtle properties far beyond familiar AND, OR, XOR, etc. behaviors. Inferring the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Molecular Cell Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6413/version/1

High-Throughput Transcriptome Profiling Of Human Mesenchymal Stem  Cells Reveals A Role For Wnt/GSK-3 Signaling In Their Hypoimmunomodulation
Provedor de dados: 17
Autores: Gurudutta Gangenahalli; Neeraj Satija; Farhat Afrin; Rajender Prasad Tripathi.
Mesenchymal stem cells (MSCs) are gaining importance among clinicians following recent demonstration of safe allogeneic transplantation due to their ability to modulate the immune response. However,the molecular machinery regulating the expression of immunomodulatory factors in MSCs is unknown. We, therefore, inhibited glycogen synthase kinase-3 (GSK-3),a Wnt signaling inhibitor, to elucidate the role of Wnt signaling in mediating immunoregulatory effects of human MSCs using gene expression profiling. Our results highlight enhanced ability of GSK-3 inhibitor (lithium) treated MSCs to evade immune response as a result of decreased expression of immune stimulatory cytokines and chemokines.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Immunology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5512/version/1

Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing Competences of Viruses
Provedor de dados: 17
Autores: Guenther Witzany.
Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial competences derive from the aptitude of viruses for natural genome editing....
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1738/version/1

Evidence of novel type of ribosome in eukaryotic intermediate flatworm
Provedor de dados: 17
Autores: Haoran  H. Wang; Mary X. Gao; Sato Kenzo; Kazumitsu Hirai.
In all organisms, messenger-directed protein synthesis is catalyzed by ribonucleoprotein particles called ribosomes. A ribosome is typically composed of one small and one large subunit which contain one short (18S) and one long (28S) rRNAs, respectively. Surprisingly, in this study, three similar size rRNAs (18-21S) were revealed in the electrophoresis profile of the total RNAs of tapeworm _Spirometra erinaceiuropaei_. Northern blot analysis shows that one of the three bands belongs to 18S rRNA, and the other two bands are of 28S rRNAs, implying structurally distinct ribosomes in this intermediate animal. Furthermore, similar, but not identical profiles were observed in two other tapeworms _Diphyllobothrium hottai_ and _Diphyllobothrium Nipponkaiizeme_....
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2608/version/1

Green Fluorescent Protein (GFP) in Vector Systems Played Sense Role of Epigenetic in Plants
Provedor de dados: 17
Autores: Hany A. El-Shemy; Mutasim M. Khalafalla; Masao Ishimoto.
The green fluorescent protein (GFP) of jellyfish (_Aequorea victoria_) has significant advantages over other reporter genes, because expression can be detected in living cells without any substrates. Recently, epigenetic phenomena are important to consider in plant biotechnology experiments for elucidate unknown mechanism. Therefore, soybean immature cotyledons were generated embryogenesis cells and engineered with two different gene constructs (pHV and pHVS) using gene gun method. Both constructs contain a gene conferring resistance to hygromycin (_hpt_) as a selective marker and a modified glycinin (11S globulin) gene (_V3-1_) as a target. However, sGFP(_S65T_) as a reporter gene was used only in pHVS as a reporter gene for study the relation between...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1845/version/1

Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks
Provedor de dados: 17
Autores: Jeremy I. Posner; Seth Berger; Avi M. Ma&amp;#x27;ayan.
In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.&amp;#xd;&amp;#xa;Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/35/version/2

Gain-of-function oncogenic mutations in TP53 enhance defined factor-mediated cellular reprogramming
Provedor de dados: 17
Autores: Jeong Ho Moon; Hideshi Ishii; Dyah Laksmi Dewi; Yoshihiro Kano; Kazuyoshi Yamamoto; Shinpei Nishikawa; Yoshiyuki Fujiwara; Yuichiro Doki; Masaki Mori.
Cancer is a disorder with various genetic and epigenetic alterations. Genetic alterations such as mutations, i.e., substitutions, amplifications, and deletions of nucleotide sequences, are largely irreversible, whereas epigenetic alterations can be modified by pharmacological agents that target components of the epigenetic machinery. Recent studies have showed that introduction of defined factors such as those encoded by c-MYC, SOX2, OCT3/4, and KLF4 in normal somatic cells results in their dedifferentiation into induced pluripotent stem (iPS) cells. In addition, we have reported that these iPS factors induce the development of induced multipotent cancer (iPC) cells from gastrointestinal cancer cells by reducing tumor aggressiveness. The efficiency of iPS...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5681/version/1

Novel network pharmacology methods for drug mechanism of action identification, pre-clinical drug screening and drug repositioning
Provedor de dados: 17
Autores: Jianghui Xiong.
The high rates of failure in oncology drug clinical trials highlight the problems of using pre-clinical data to predict the clinical effects of drugs. Here we present two methodology innovations on network pharmacology modeling. (1) We hypothesize that the gene network associated with cancer outcome in heterogeneous patient populations could serve as a reference for identifying drug effects. We proposed a novel in vivo genetic interaction between genes as &amp;#x2018;synergistic outcome determination&amp;#x2019;, in a similar way to &amp;#x2018;synthetic lethality&amp;#x2019;. We scanned above genetic interactions based on microarray profiling for cancer prognosis, and identified a cluster of important yet epigenetically regulated gene modules. By...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6455/version/1

The disease mutation A77V in Ryanodine receptor RyR2 induces changes in energy conduction pathways in the protein
Provedor de dados: 17
Autores: Burak Erman; Nazan Walpoth.
Energetically responsive residues of the 217 amino acid N-terminal domain of the cardiac Ryanodine receptor RyR2 are identified by a simple elastic net model. These residues lie along a hydrogen bonded path through the protein. The evolutionarily conserved residues of the protein are all located on this path or in its close proximity. All of the residues of the path are either located on the two Mir domains of the protein or are hydrogen bonded to them. Two calcium binding residues, E171 and E173, are proposed as potential binding residues, based on insights gained from the elastic net analysis of another calcium channel receptor, the inositol 1,4,5-triphosphate receptor, IP3R. Analysis of the disease causing A77V mutated RyR2 showed that the path is...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6678/version/1

Dual Diode Array and Fourier Transform Near Infrared Reflectance Spectrometer Calibrations for Composition Analysis of Single Soybean Seeds for Genetic Selection, Cross-Breeding Experiments
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Randall  L. Nelson.
Experimental results of extensive evaluations of Diode-Array and FT-NIRS instruments are presented that aim at developing reliable and robust NIR calibrations for single soybean seed composition analysis on both Dual Diode Array and Fourier Transform NIR reflectance instruments. Single soybean seed, bulk, and powder calibrations were developed on four different NIRS spectrometer models that are commercially available.
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6195/version/1

RNA Vaccine: novel approach for cancer treatment
Provedor de dados: 17
Autores: L K Dwivedi; Prateeksha Goswami; Kanika Bhalla.
Cancer is still an unsolved puzzle and a major cause of mortality and morbidity in the world. Today, about one in every thousand people is dying due to cancer. No effective agent has yet been found which can cure cancer in its metastatic stage. However, attempts in the shape of chemotherapy, immunotherapy and vaccines are made worldwide to find a remedy through a proper regimen. In continuation, tumor specific mRNA has been introduced as part of vaccines in recent days. It is mostly used in transfection with Dendritic Cells (DCs) for better effectiveness and safety. The DCs are selected for transfection because they are highly potent Antigen Presenting Cells (APCs) with the ability to take up &amp;#x26; process tumor antigen in peripheral blood &amp;#x26;...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5949/version/1

Biotransformation of artemisinin mediated through fungal strains for obtaining derivatives with novel activities
Provedor de dados: 17
Autores: Suchita  Srivastava; Suaib  Luqman; Atiya  Fatima; Mahendra  P. Darokar; Arvind  S. Negi; J K. Kumar; Karuna  Shanker; Chandan  S. Chanotiya; Sudeep  Tandon; Suman  P. S. Khanuja.
Artemisinin, a sesquiterpene lactone, is the active antimalarial constituent of Artemisia annua. Several fungal strains Saccharomyces cerevisiae, Aspergillus flavus, Aspergillus niger and Picchia pastoris were used to biotransform artemisinin. Among these strains, A. flavus was the only microorganism capable of transforming artemisinin to deoxyartemisinin in higher yields than the previous reports. The structure of deoxyartemisinin was elucidated by spectroscopy. Deoxyartemisinin showed antibacterial activity against Staphylococcus aureus, S. epidermidis and S. mutans at a minimum inhibitory concentration (MIC) of 1 mg/mL compared to artemisinin whose MIC was &amp;#x3e;2 mg/mL.
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Microbiology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6925/version/1

Biophysical Effects Of Ion Concenteration On The Affinity Between Nanopore, OmpF Lumen and Passing Nucleotide
Provedor de dados: 17
Autores: Saeid Hadi; Hamid Mobasheri.
OmpF an outer-membrane porin channel of _E. Coli_ posses beta-barrel structure, whose conductivity and gating phenomena are affected by changes in pH, salt concentration and so on. The distribution of amino acids in OmpF induces a non homologous electric potential in channel lumen. The intrinsic charge distribution caused be amino acid may be affected by lipid bilayer, extra and intra cellular ion concentration, and other physico-chemical condition of environment including, pH, temperature, polyelectrolytes etc. Nucleotides are considered as one of  most important metabolite in the cell that have pass through membrane whenever necessary. The experimental study of translocation of such a molecules through channels have provided invaluable information...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5101/version/1

Tracing blastomere fate choices of early embryos in single cell culture
Provedor de dados: 17
Autores: Yunhan Hong; Haobin Zhao; Ni Hong; Zhendong Li; Meisheng Yi; Rong Liu; Mingyou Li; Yan Yan; Yongming Yuan; Chang Ming Li; Ruowen Ge; Jianxin Song.
Blastomeres of early vertebrate embryos undergo numerous fate choices for division, motility, pluripotency maintenance and restriction culminating in various cell lineages. Tracing blastomere fate choices at the single cell level in vitro has not been possible because of the inability to isolate and cultivate early blastomeres as single cells. Here we report the establishment of single cell culture system in the fish medaka, enabling the isolation and cultivation of individual blastomeres from 16- to 64-cell embryos for fate tracing at the single cell level in vitro. Interestingly, these blastomeres immediately upon isolation exhibit motility, lose synchronous divisions and even stop dividing in &amp;#x2265;50% cases, suggesting that the widely accepted...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4907/version/1

Unique for human centromeric regions of interphase chromatin homing (CENTRICH) govern dynamic features of chromatin fractal globules
Provedor de dados: 17
Autores: Gennadi Glinsky.
We report the results of the genome-wide alignment of inter- and intra-chromosomal chromatin interactions within the context of interphase chromatin binding to nuclear lamina and nucleolus. For all human chromosomes, a significant correlation exists between binding of chromosomal loci to nuclear lamina and segregation into spatially-defined distinct compartments of genome-wide chromatin interactions identified by Hi-C method. We report identification of near-centromeric intergenic regions on human chromosomes (chr2; chr10; chr17; chr1), which are highly enriched for interphase chromatin homing sites and function as attractors of long-range physical interactions (Centromeric Regions of Interphase Chromatin Homing, CENTRICH). CENTRICH are engaged in 397-1526...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6756/version/1

BBSRC Data Sharing Policy
Provedor de dados: 17
Autores: Amanda Collis; David McAllister; Michael Ball.
BBSRC recognizes the importance of contributing to the growing international efforts in data sharing. BBSRC is committed to getting the best value for the funds we invest and believes that making research data more readily available will reinforce open scientific inquiry and stimulate new investigations and analyses. BBSRC supports the view that data sharing should be led by the scientific community and driven by scientific need. It should also be cost effective and the data shared should be of the highest quality. Members of the community are expected and encouraged to practice and promote data sharing, determine standards and best practice, and create a scientific culture in which data sharing is embedded.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Immunology; Microbiology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Plant Biology; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6015/version/1

MIF-AMPK cascades
Provedor de dados: 17
Autores: Heng Ma; Jingying Wang; Erin Lane; Lin Leng; Wenkui Wang; Jun Ren; Richard Bucala; Ji Li.
Withdrawn for publication
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2466/version/2

TMEPAI, a transmembrane TGF-&amp;#x3b2;-inducible protein, sequesters Smad proteins in TGF-&amp;#x3b2; signaling
Provedor de dados: 17
Autores: Susumu Itoh; Yukihide Watanabe; Kiyotoshi Satoh; Masako Inamitsu; Liang Shi; Naoko Nakano; Aya Tanaka; Eliza Wiercinska; Hiroshi Shibuya; Peter ten Dijke; Mitsuyasu Kato.
Transforming growth factor-[beta] (TGF-[beta]) is a multifunctional cytokine of key importance for controlling embryogenesis and tissue homeostasis. How TGF-[beta] signals are attenuated and terminated is not well understood. Here, we show that TMEPAI, a direct target gene of TGF-[beta] signaling, antagonizes TGF-[beta] signaling by interfering with TGF-[beta] type I receptor (T[beta]RI)-induced R-Smad phosphorylation. TMEPAI can directly interact with R-Smads via a Smad interaction motif (SIM). TMEPAI competes with Smad anchor for receptor activation (SARA) for R-Smad binding, thereby sequestering R-Smads from T[beta]RI kinase activation. In mammalian cells, ectopic expression of TMEPAI inhibited TGF-[beta]-induced PAI-1 production, whereas specific...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1403/version/1

Structural and Dynamic Studies of Amino Acids, Proteins and Nucleic Acids By Chemical-Hyperspectral Imaging, FT-IR/NIR, Vibro-Rotational Spectroscopy, Plasma, Microwave and Neutron Spectroscopy
Provedor de dados: 17
Autores: I. C. Baianu.
A detailed review of structural and dynamic studies of amino acids, proteins and nucleic acids by spectroscopic techniques: microwaves,  near infrared, UV, X-rays and neutrons, including also EXAFS, chemical-hyperspectral imaging and fluorescence correlation spectroscopy and FLIM, FRAP imaging with references, instrumentation diagrams and  application examples for several related areas.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7079/version/1

Molecular crowding defines a common origin for the Warburg effect in proliferating cells and the lactate threshold in muscle physiology
Provedor de dados: 17
Autores: Alexei Vazquez.
Aerobic glycolysis is a seemingly wasteful mode of ATP production that is seen both in rapidly proliferating mammalian cells and highly active contracting muscles, but whether there is a common origin for its presence in these widely different systems is unknown. To study this issue, here we develop a model of human central metabolism that incorporates a solvent capacity constraint of metabolic enzymes and mitochondria, accounting for their occupied volume densities, while assuming glucose and/or fatty acid utilization. The model demonstrates that activation of aerobic glycolysis is favored above a threshold metabolic rate in both rapidly proliferating cells and heavily contracting muscles, because it provides higher ATP yield per volume density than...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5784/version/1

Complex Systems Analysis of Arrested Neural Cell Differentiation during Development and Analogous Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: I C. Baianu; V. I. Prisecaru.
A new approach to the modular, complex systems analysis of nonlinear dynamics of arrested neural cell Differentiation--induced cell proliferation during organismic development and the analogous cell cycling network transformations involved in carcinogenesis is proposed. Neural tissue arrested differentiation that induces cell proliferation during perturbed development and Carcinogenesis are complex processes that involve dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments. Such &amp;#x27;dynamically inter-connected&amp;#x27; biomolecules form numerous inter-related pathways referred to as &amp;#x27;molecular networks&amp;#x27;. One such family of signaling pathways contains the cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7101/version/1

Weight matrix based identification of terpene synthases conserved motifs in Arabidopsis thaliana proteome
Provedor de dados: 17
Autores: Suchita  Srivastava; Suaib  Luqman; Feroz  Khan.
Terpenes comprise the most diverse collection of natural products. Out of more than 30,000 individual terpenoids identified, at least half are synthesized by plants. A relatively small, but quantitatively significant, number of terpenoids are involved in primary plant metabolism. However, the vast majorities are classified as secondary metabolites; compounds not required for plant growth and development but presumed to have an ecological function in communication or defense and are widely used in industrial applications. Terpene hydrocarbon scaffolds are generated by the action of the mechanistically intriguing family of mono-, sesqui-, and diterpene synthases collectively termed as terpene synthases, that catalyze multistep reactions with diphosphorylated...
Tipo: Poster
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6909/version/1

Living unicellular eukaryote Tetrahymena pyriformis as a model for study
Provedor de dados: 17
Autores: Elena N. Mokhova.
Some animals are able to survive for a long time under conditions of drastically reduced oxidative metabolism, called metabolic depression. The most investigated type of metabolic depression is hibernation. Research into the basic properties of liver mitochondria energetics during hibernation is essential for fundamental biology and medicine. However, the absence of a suitable hepatocyte culture makes it impossible to study the characteristic features of mitochondrial metabolic states in living cells during hibernation. We proposed that under selected conditions, the unicellular eukaryote Tetrahymena pyriformis resembles hepatocytes under hibernation, as (i) both cell types survive under condition of restricted food supply, hypoxia, and accumulation of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4521/version/4

Preventing hereditary cancers caused by opportunistic carcinogens
Provedor de dados: 17
Autores: Bernard Friedenson.
Objectives&amp;#xd;&amp;#xa;Previous studies reported inherited BRCA1/2 deficits can cause cancer by impairing normal protective responses.   Opportunistic carcinogens can exploit these deficits by causing chronic inflammation, constant cell death and replacement in a mutagenic environment, DNA crosslinking or double strand breaks.  Some of the resulting cancers may be prevented if opportunistic carcinogens are identified.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods&amp;#xd;&amp;#xa;The literature was systematically searched for carcinogens capable of exploiting deficits in BRCA1/2 pathways.   Search criteria were common exposure, available information, required BRCA1/2 pathway repairs, increased risks for any cancer, and effects on stem...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6668/version/1