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Explaining microbial population genomics through phage predation Nature Precedings
Francisco Rodriguez-Valera; Ana-Belén Martín-Cuadrado; Beltrán Rodriguez-Brito; Lejla Pasic; T. Frede Thingstad; Forest Rohwer; Alex Mira.
The remarkable diversity of genes within the pool of prokaryotic genomes belonging to the same species or pan-genome is difficult to reconcile with the widely accepted paradigm which asserts that periodic selection within bacterial populations would regularly purge genomic diversity by clonal replacement. Recent evidence from metagenomics indicates that even within a single sample a large diversity of genomes can be present for a single species. We have found that much of the differential gene content affects regions that are potential phage recognition targets. We therefore propose the operation of Constant-Diversity dynamics in which the diversity of prokaryotic populations is preserved by phage predation. We provide supporting evidence for this model...
Tipo: Manuscript Palavras-chave: Microbiology.
Ano: 2009 URL: http://precedings.nature.com/documents/3489/version/1
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Trichoscopy criteria for diagnosing female androgenic alopecia. Nature Precedings
Adriana Rakowska; Monika Slowinska; Elzbieta Kowalska-Oledzka; Malgorzata Olszewska; Lidia Rudnicka.
Differential diagnosis of chronic hair loss remains a challenge in dermatology. The aim of the study was to evaluate the value of a new scalp visualization technique, trichoscopy, in differential diagnosis of hair loss. Trichoscopy was performed in 131 females (59 with androgenic alopecia, 33 with chronic telogen effluvium, 39 healthy controls). Based study results, a standardized trichoscopy report was developed and diagnostic criteria for female androgenic alopecia were established. Major criteria: increased number of yellow dots and thin hairs, as well as decreased average hair thickness in frontal area. Minor criteria: increased frontal area to occiput ratio of single-hair units (>2:1), vellus hairs (>1.5:1) and follicles with...
Tipo: Manuscript Palavras-chave: Biotechnology.
Ano: 2008 URL: http://precedings.nature.com/documents/1913/version/1
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Inverse relationship between genetic diversity and epigenetic complexity Nature Precedings
Shi Huang.
Early studies of molecular evolution revealed a correlation between genetic distance and time of species divergence. This observation provoked the molecular clock hypothesis and in turn the ‘Neutral Theory’, which however remains an incomplete explanation since it predicts a constant mutation rate per generation whereas empirical evidence suggests a constant rate per year. Data inconsistent with the molecular clock hypothesis have steadily accumulated in recent years that show no correlation between genetic distance and time of divergence. It has therefore become a challenge to find a testable idea that can reconcile the seemingly conflicting data sets. Here, an inverse relationship between genetic diversity and epigenetic...
Tipo: Manuscript Palavras-chave: Ecology; Genetics & Genomics; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/1751/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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On the nucleotide distribution in bacterial DNA sequences Nature Precedings
Marcelo Sobottka; Andrew Glenn Hart.
It is probable that the distributional structure of DNA sequences arises from the accumulation of many successive stochastic events such as nucleotide deletions, insertions, substitutions and elongations [1, 2, 3, 4, 5, 6, 7]. Although the existence of long-range correlations in non-coding portions of DNA sequences is well established [8, 9, 10, 11], first order Markov chains might well capture aspects of their nucleotide distributions [12]. Here we propose a hidden Markov model based on a coupling of an urn process with a Markov chain to approximate the distributional structure of primitive DNA sequences. Then, by supposing that a bacterial DNA sequence can be derived from uniformly distributed mutations of some primitive DNA, we use the model to explain...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/5245/version/1
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Second-Hand Stress: Neurobiological Evidence for a Human Alarm Pheromone Nature Precedings
Lilianne R. Mujica-Parodi; Helmut H. Strey; Blaise Frederick; Robert Savoy; David D. Cox; Yevgeny Botanov; Denis Tolkunov; Denis Rubin; Jochen Weber.
Alarm pheromones are airborne chemical signals, released by an individual into the environment, which transmit warning of danger to conspecifics via olfaction. Using fMRI, we provide the first neurobiological evidence for a human alarm pheromone. Individuals showed activation of the amygdala in response to sweat produced by others during emotional stress, with exercise sweat as a control; behavioral data suggest facilitated evaluation of ambiguous threat.
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2008 URL: http://precedings.nature.com/documents/2561/version/1
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A PI3K-mediated negative feedback regulates Drosophila motor neuron excitability Nature Precedings
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
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Why Intelligent People Live Longer Nature Precedings
Robert Hauser; Alberto Palloni.
Numerous studies find a positive relationship between cognitive ability, IQ as measured in childhood or youth, and subsequent survival. Explanations range from the idea that low ability is an indicator of adverse systemic events in early life to the idea that high cognitive functioning is required continuously to maintain health and reduce threats to survival. The Wisconsin Longitudinal Study (WLS) has followed a large cohort of Wisconsin high school seniors from ages 18 to 69. As expected, in the WLS survival varies positively with adolescent IQ. However, rank in high school class accounts completely for the relationship between IQ and survival, and it has a much larger effect on survival. These findings suggest that cognitive functioning improves...
Tipo: Manuscript Palavras-chave: Developmental Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4340/version/1
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Counting absolute number of molecules using unique molecular identifiers Nature Precedings
Teemu Kivioja; Anna Vähärautio; 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 & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/5903/version/1
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Ambiguous Dependence Of Minimal Plant Generation Time On Nuclear DNA Content Nature Precedings
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
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The impact of Bt cotton on poor households in rural India Nature Precedings
Arjunan Subramanian; Matin Qaim.
The impact of genetically modified (GM) crops on the poor in developing countries is still the subject of controversy. While previous studies have examined direct productivity effects of _Bacillus thuringiensis_ (Bt) cotton and other GM crops, little is known about wider socioeconomic outcomes. We develop a microeconomic modeling approach and use comprehensive survey data from India to analyze welfare and distribution effects in a typical village economy. Bt cotton adoption increases aggregate employment with interesting gender implications. Likewise, aggregate household incomes rise, including for poor and vulnerable farmers, suggesting that Bt cotton contributes to poverty reduction and rural development.
Tipo: Manuscript Palavras-chave: Biotechnology; Ecology.
Ano: 2008 URL: http://precedings.nature.com/documents/1812/version/1
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Manual annotation of the mouse genome: HAVANA and EUCOMM Nature Precedings
Mark Thomas.
The European Conditional Mouse Mutagenesis (EUCOMM) project aims to establish a mutant resource containing up to 13,000 conditional mouse mutations in C57BL/6N embryonic stem cells. As part of this resource, up to 8,000 targeted conditional mutations will be generated for genes that can not be readily trapped by random gene trapping methods. Non-symmetrical critical exons are identified as part of the targeting approach, which when deleted produce a knockout (KO) transcript that is susceptible to nonsensemediated decay (NMD). The success of this approach is dependent on detailed and accurate genome annotation, which is provided by the Human and Vertebrate Analysis and Annotation (HAVANA) group at the Wellcome Trust Sanger Institute. Based on a combination...
Tipo: Presentation Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3181/version/1
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Surface Modified Ultrathin Polyelectrolyte Nanoreservoir for Delivery of Proteins: Evaluation in Terms of Controlled Release and Biocompatibility Nature Precedings
Girish Kumar Gupta; Vikas Jain; Prabhat Ranjan Mishra.
The proposed ultrathin polyelectrolyte nanoreservoir (UPN) was fabricated in two combinations by alternate layering of polyelectrolytes poly (allylamine hydrochloride) along with sodium poly (styrene sulfonate) (PAH/PSS)5 and sodium alginate (PAH/SA)5 using porous calcium carbonate as a template using layer-by-layer adsorption technique with the subsequent template removal at low pH. We studied the possibility whether remnant intact nanoreservoir could be suited for encapsulation as well as delivery vehicle for protein such as bovine serum albumin as a model. To tune biocompatibility with biological cells the assembled surface was modified using pluronic (F-68) by adsorption and possible hydrophobic interaction. The prepared system was characterized for...
Tipo: Poster Palavras-chave: Pharmacology.
Ano: 2008 URL: http://precedings.nature.com/documents/2548/version/1
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Metabolic Network Representation in SBGN PD: EC and Identity Gate Nature Precedings
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
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Absolute Aqueous Redox Potentials ( via a new link between aqueous and gaseous properties) Nature Precedings
Raji Heyrovska.
The new finding here, that the conventional standard potentials (based on S.H.E.) are linearly dependent on ionization potentials, has yielded the absolute values of aqueous standard potentials.
Tipo: Presentation Palavras-chave: Chemistry.
Ano: 2009 URL: http://precedings.nature.com/documents/3395/version/1
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The 2010 Scientific Strategic Plan of the Global HIV Vaccine Enterprise: A Roadmap for the Future Nature Precedings
Alan Bernstein; Peter Piot.
HIV/AIDS is arguably the most significant health challenge facing the world today. The 2008 numbers tell the story: 33.4 million were living with HIV, 2 million people died of AIDS and 2.7 million people were newly infected. Despite impressive scientific advances in developing over two dozen drugs to treat HIV infections, there is still no cure. In addition, only about one-third of those who need drugs have access to therapy.

In 2003, recognizing the enormity of the scientific and humanitarian challenge of HIV/AIDS, two-dozen leading investigators and major funding organizations formed the Global HIV Vaccine Enterprise, a voluntary alliance of independent organizations committed to working together to accelerate the...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Immunology; Microbiology.
Ano: 2010 URL: http://precedings.nature.com/documents/4803/version/2
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Computerized Protein Modeling and Molecular Docking Analysis of Human Proto Oncogene Tyrosine Protein Kinase YES for Discovery of Novel Lead Molecules Nature Precedings
Karuna J. Jaya Sai; Dibyabhaba Pradhan; Amineni Umamaheswari.
Human proto-oncogene tyrosine-protein kinase YES (YES) is a non receptor kinase belongs to Src family. This gene lies in close proximity to thymidylate synthase gene on chromosome 18, and a corresponding pseudogene has been found on chromosome 22. In hepatocellular carcinoma and colorectal carcinoma elevated human YES activity was observed. Inhibitors of human YES reported till date are in clinical trials and associated with several side effects. The present study was mainly aimed in homology modeling of human YES and discovery of novel lead molecules that inhibit YES kinase more efficiently with fewer side effects. Virtual screening and docking techniques were applied to identify novel lead molecule of YES kinase. As there was no reported human YES...
Tipo: Poster Palavras-chave: Cancer; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4902/version/1
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Review: Dystroglycan in the Nervous System Nature Precedings
Matthias Samwald.
Dystroglycan is part of a large complex of proteins, the dystrophin-glycoprotein complex, which has been implicated in the pathogenesis of muscular dystrophies for a long time. Besides muscular degeneration many patients manifest symptoms of neurological and cognitive dysfunction. Newer findings suggest that dystroglycan is implicated in brain development, synapse formation and plasticity, nerve-glia interactions and maintenance of the blood-brain barrier.
Most research so far has focused on the functions of dystroglycan in muscle and neuromuscular junctions, while its role in the brain and interneuronal synapses has been largely neglected. 
This review will give an overview of the biochemistry of dystroglycan, its...
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2007 URL: http://precedings.nature.com/documents/196/version/1
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Temperature factor analysis of outer membrane β-stranded porin crystal structures suggests the pore is not uniformly rigid Nature Precedings
S. Krishnaswamy; Abhishek Kumar.
Outer membrane beta-stranded porins form a diverse and complex set of proteins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective using atomic temperature factors or B-factors. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. Structures of six porins (four 16 stranded beta barrel porins and two 8 stranded beta barrel porins) were taken from the PDB for the analysis based on resolution (better than 3.0 Å) and R-factor (< 0.23). The residue distribution and mobility distribution was found to be characteristic of each of the porins. The mobility and residue...
Tipo: Manuscript Palavras-chave: Biotechnology.
Ano: 2008 URL: http://precedings.nature.com/documents/2495/version/1
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A Simple, Rapid Method for Extracting Large Plasmid DNA from Bacteria Nature Precedings
Spencer D. Heringa; Jonathan D. Monroe; James B. Herrick.
We are studying the lateral transfer of transmissible antibiotic resistance plasmids among stream bacteria impacted by fecal runoff from poultry and cattle. Such plasmids are typically large (ca. 40 – 100 kb) and occur in low copy numbers in the cell and have therefore typically been difficult to isolate and therefore to study. Traditional protocols, based upon variations of the standard alkaline-lysis method, are long (ca. 1 1/2 to 2 days) and difficult. Commercial kits designed for the isolation of Baterial Artificial Chromosomes (BACs) can be used and are an improvement; however, these are expensive and still require hours of sustained effort. We have adapted a method published by Rondon et al. (1999), originally designed for the isolation of...
Tipo: Poster Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology.
Ano: 2007 URL: http://precedings.nature.com/documents/1249/version/1
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