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Bioinformatics Approach for Functional Glycomics Nature Precedings
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
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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; Chemistry; Developmental Biology; Molecular Cell Biology; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6591/version/1
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Cholesterol Esterification During Differentiation by Hexamethylene Bisacetamide of Friend Virus-Induced Erythrokeukemia Nature Precedings
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
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Water and the Biology of Prions and Plaques Nature Precedings
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 
density and low density microdomains. Hydrophobic molecules, including proteins, 
accumulate selectively into stable populations, enriched in high density water, at 
charged sites on biopolymers. In enriched high density water, proteins are probably 
partially unfolded and may precipitate out when released. All extracellular matrices 
contain such charged polymers. Prions, which have been shown to accumulate in soils 
and clays containing...
Tipo: Manuscript Palavras-chave: Microbiology; Molecular Cell Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1381/version/1
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Protein folding disorders: Toward a basic biological paradigm Nature Precedings
Rodrick Wallace.
Mechanistic 'physics' 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
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Why not "do simple things in a simple way": Use of the Pap test as the first step in screening genetic stability for human cultured stem cell therapy? Nature Precedings
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
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Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing Competences of Viruses Nature Precedings
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
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THE EFFECT OF HEPARIN ON THE CELL CYCLE IN HUMAN B-LYMPHOBLASTS: AN IN VITRO STUDY Nature Precedings
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
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What are the ethical and social responsibilities of scientists? Nature Precedings
Philip Campbell.
Presented as part of the session titled "Sharing scientific data: who benefits?" at ESOF (The Euroscience Open Forum) 2008.

Session abstract: Digital datasets—text-based, numeric, audio, video or image-based—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 & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/2176/version/1
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Intact mitochondria migrate in membrane tubular network connections formed between human stem cells Nature Precedings
Attila Csordas; Attila Cselenyák; Ferenc Uher; Marianna Murányi; Simone Hennerbichler; Heinz Redl; Márk 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
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Cell Adhesion: A surprising cohesive force Nature Precedings
Hugues H. Vasseur.
When an experimentalist or a biological mechanism applies an external force onto a cell chemically sticking to its substrate, a reacting "suction" 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 "suction-cup" 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
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On the social induction of Alzheimer's disease: An index theorem aging model for amyloid formation Nature Precedings
Rodrick Wallace; Deborah Wallace.
The central 'risk factor' for Alzheimer'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
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A multiple-instance scoring method to predict tissue-specific cis-regulatory motifs and regions Nature Precedings
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 & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/4038/version/1
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Chloroplast and Cell Imaging at Submicron Resolution by Two-Photon Excitation Nature Precedings
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: 
DNA- telomerase interactions, DNA hybridization kinetics, ligand-receptor interactions, and HIV-HBV testing. 

Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics & Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Plant Biology; Data Standards.
Ano: 2012 URL: http://precedings.nature.com/documents/7116/version/1
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Cancer Clinical Trials Optimization and Pharmacogenomics Nature Precedings
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 & Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7046/version/1
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Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome Nature Precedings
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 & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/1841/version/1
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Nitric oxide synthase in skeletal muscle fibres of patients with type 2 diabetes Nature Precedings
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
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Analysis of acceptance of bacillus to various heavy metals and antibiotics Nature Precedings
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
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Opposite effects of two zinc(II) dithiocarbamates on NF-kB pathway Nature Precedings
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
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HMGA1a induces aberrant splicing of estrogen receptor α in MCF-7 breast cancer cells Nature Precedings
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'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, ERα46, is known to increase expression when breast cancer cells (MCF-7) become hyperconfluent. Transiently expressed HMGA1a induced ERα46 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 ERα46 mRNA...
Tipo: Poster Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4104/version/2
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