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Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics Nature Precedings
Michel Dumontier; James R. Green; Ashkan Golshani; Myron L. Smith; Nadereh Mir-Rashed; Md Alamgir; Veronika Eroukova; Frank Dehne; James J. Cheetham.
Background
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
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The Heterochromatin Protein 1 positively regulates euchromatic gene expression by RNA binding Nature Precedings
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 & Genomics; Molecular Cell Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2687/version/1
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Evidence of existence of totally different types of ribosomes in intermediate animals Nature Precedings
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 & Genomics; Microbiology; Molecular Cell Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2608/version/2
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Visualization of the Phosphoproteomic Data from AfCS with the Google Motion Chart Gadget Nature Precedings
Huilei Xu; Avi Ma'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
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Bioconversion of eugenol into food flavouring agent vanillin Nature Precedings
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
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Pancreas islets in metabolic signaling - focus on the β-cell Nature Precedings
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 flow 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
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(Corrected) Speed effects in gliding motility assays due to surface passivation, water isotope, and osmotic stress. Nature Precedings
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.

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
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Phosphatidylserine polarization is required for proper Cdc42 localization and for development of cell polarity. Nature Precedings
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
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Effect of 2-H and 18-O water isotopes in kinesin-1 gliding assay Nature Precedings
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
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Novel Techniques for Microspectroscopy and Chemical Imaging Analysis of Soybean Seeds and Embryos Nature Precedings
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 1μ^2^.
Tipo: Poster Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6591/version/2
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NIR Spectroscopy and Microspectroscopy Analysis of Intact Soybean Seeds for Food Applications through Composition Improvements. Version 2.0 Nature Precedings
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 & Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6253/version/1
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Dysbindin-1 in dorsolateral prefrontal cortex of schizophrenia cases is reduced in an isoform-specific manner unrelated to altered dysbindin-1 gene expression Nature Precedings
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 & Genomics; Molecular Cell Biology; Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/2779/version/1
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Mammalian cells in culture actively export specific microRNAs Nature Precedings
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
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A normalization technique for next generation sequencing experiments Nature Precedings
Günter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS' 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 & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4710/version/1
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Self-organization of intrinsically disordered proteins with folded N-termini Nature Precedings
Philip C. Simister; Fred Schaper; Nicola O'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
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Chronic hyperplastic anemia as an independent risk factor for atherosclerotic lesions: a lesson from thalassemia intermedia Nature Precedings
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 (β-TM) and in transfusion-independent beta thalassemia intermedia (β-TI). In β-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 β-TI; however, until now, no factor has emerged as the major one responsible for these complications....
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Molecular Cell Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4169/version/1
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Aptamer-based multiplexed proteomic technology for biomarker discovery Nature Precedings
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
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Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for Composition Improvements. (v.3) Nature Precedings
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 “wet chemistry” 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 & Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth & Environment; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6231/version/3
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Inactivation of the Retinoblastoma Protein by Mutant B-Raf in Malignant Melanoma Nature Precedings
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
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Signaling Flux Redistribution concept can switch survival to apoptosis in cancer cells Nature Precedings
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
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