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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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Natural Radiation Induced Developmental Disability: An Avian Model Nature Precedings
Jeni Chandar Padua; Basil Rose MR.
Radiation exposure during gestation causes mutation in the fetus leading to birth defects in the newborn. On a survey of the coastal villages of Kanyakumari District, Tamilnadu, India, high levels of background radiation were detected, which was suggestive of inducing mutations, and congenital abnormalities in the exposed population. To substantiate the dangerous impact of such natural radioactive emissions, we have established an avian model of irradiation-induced birth defect in chicks hatched from eggs exposed to natural radioactive beach sand. The hatched experimental chicks exhibited severe locomotor disability and extreme malformations. Our study proves for the first time, that natural beach sand radiation induces severe developmental abnormalities....
Tipo: Manuscript Palavras-chave: Developmental Biology; Earth & Environment.
Ano: 2011 URL: http://precedings.nature.com/documents/6191/version/1
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HBsAg-vectored DNA vaccines elicit concomitant protective responses to multiple CTL epitopes relevant in human disease. Nature Precedings
Dekun Chen; Allan Gould; Michael Mather; Oscar Haigh; Melanie Barnes; Jacqueline Kattenbelt; Scott Thomson; Robert R. Tindle.
Vaccines capable of controlling neoplastic and infectious diseases which depend on the cellular immune response for their resolution, have proven difficult to develop. We, and others, have previously demonstrated that the potent immunogenicity of hepatitis B surface antigen (HBsAg), the already- licensed human vaccine for hepatitis B infection, may be exploited to deliver foreign antigens for cytotoxic T-lymphocyte (CTL) induction. In this study we demonstrate that recombinant (r) HBsAg DNA delivering a CTL polyepitope appended at the C' terminus elicits concomitant responses to multiple epitopes restricted through a diversity of MHC class I haplotypes, which are relevant in a number of human diseases. We show that the rHBsAg DNA vaccine elicits...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Immunology.
Ano: 2008 URL: http://precedings.nature.com/documents/1910/version/1
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Early onset preeclampsia is characterized by altered placental lipid metabolism and a premature increase in circulating FABP4 Nature Precedings
Victor H. Han; Gilles Lajoie; Jennifer Ballard; Aaron Booy; Nicholas Carruthers; Delfina Siroen.
Preeclampsia is a pregnancy-associated disorder that manifests as a sudden increase in maternal blood pressure accompanied by proteinuria. Because the placenta is a key organ in preeclampsia, we used proteomic and lipidomic analyses to compare placentae from preeclamptic and gestational age matched control pregnancies. Fatty acid binding protein 4 (FABP4), enoyl-CoA dehydrogenase and delta-3,5-delta-2,4-dienoyl-CoA isomerase had altered abundance in preeclamptic placentae compared to controls. FABP4 placental protein and RNA and plasma levels were all increased in early-onset preeclampsia (prior to 28 weeks gestation) compared to controls (6-fold, 3.3-fold and 3.5-fold respectively). After 28 weeks, FABP4 protein in control placenta and plasma increased to...
Tipo: Manuscript Palavras-chave: Developmental Biology; Genetics & Genomics.
Ano: 2010 URL: http://precedings.nature.com/documents/4885/version/1
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A New General Allometric Biomass Model Nature Precedings
Wei Sheng Zeng; Shou Zheng Tang.
To implement monitoring and assessment of national forest biomass, it is becoming the trend to develop generalized single-tree biomass models suitable for large scale forest biomass estimation. Considering that the theoretical biomass allometric model developed by West et al. [1,2] was statistically different from the empirical one, the two parameters in the most commonly used biomass equation M=aDb were analyzed in this paper. Firstly, based on the knowledge of geometry, the theoretical value of parameter b was deduced, i.e., b=7/3(≈2.33), and the comparison with many empirical studies conducted throughout the globe indicated that the theoretical parameter could describe soundly the average allometric relationship between aboveground biomass M...
Tipo: Manuscript Palavras-chave: Ecology.
Ano: 2011 URL: http://precedings.nature.com/documents/6704/version/1
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Dyslexia, magnocellular integrity and rapidly presented stimuli Nature Precedings
Bernt C. Skottun; John R. Skoyles.
Conlon at al. (2011, Brain and Cognition, 76, 197-205) studied the responses of dyslexic readers and controls to rapidly presented stimuli. They found that the dyslexic readers showed poorer performance than the controls but only when the interstimulus interval (ISI) was short (150 ms), not when it was long (350 ms). This difference they attributed to a magnocellular or dorsal stream deficiency. However, they did not compute the temporal frequency spectra of the two stimuli. This is done here. It is found that it is very difficult to draw any conclusions with regard to the magnocellular system or the dorsal stream using these stimuli.
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2011 URL: http://precedings.nature.com/documents/6050/version/1
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Hydrogen sulfide: a neurotransmitter or just a cofactor of the nitrite in the NO production? Nature Precedings
Loris Grossi.
The hydrogen sulfide has been recently claimed to have an important role in the cardiovascular system, as well in the central nervous system, but its action seems directly connected to the presence of NO/NO-derivatives. We want to report here chemical evidences that suggest for the H2S a role as a cofactor, able to induce NO release from NO-donors, more than a direct neurotransmitter.
Tipo: Manuscript Palavras-chave: Chemistry; Neuroscience.
Ano: 2008 URL: http://precedings.nature.com/documents/2026/version/1
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Building Block and Building Rule: Dual Descriptor Method for Biological Sequence Analysis Nature Precedings
Bin-Guang Ma.
The emergence of “Systems Biology” in recent years highlights the systematic viewpoint of bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence analysis is proposed. From a systematic perspective, Dual Descriptor is defined as a two element set of Composition Weight Map and Position Weight Function which aim at reflecting the composition and permutation information of a sequence. An alternate training algorithm is provided to get an optimum description of the building patterns of the sequences. In this paper, dual descriptor method has been applied to the analysis of two typical problems of molecular biology: gene identification and the prediction of protein function....
Tipo: Manuscript Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/2223/version/1
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Virtual screening for NS5B inhibitors of Hepatitis C virus Nature Precedings
Amjesh R; Achuthsankar S. Nair; Sugunan V.S..
Hepatitis C Virus (HCV) infection is a serious cause of chronic liver disease worldwide with more than 170 million infected individuals at a risk of developing significant morbidity and mortality. To date there is no effective drug for the treatment or vaccine to prevent this infection. The present study aims to discover novel inhibitors which target an allosteric binding site of RNA dependent RNA polymerase enzyme of HCV. A structure based virtual screening of Zinc database by computational docking and the post docking analysis of energy calculations and interactions followed by ADMET studies were conducted. Our study revealed 10 compounds which has more potential than the existing inhibitor to be considered as lead compounds.

Tipo: Manuscript Palavras-chave: Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7055/version/1
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PocketMatch: A new algorithm to compare binding sites in protein structures Nature Precedings
Yeturu Kalidas; Nagasuma Chandra.
Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the...
Tipo: Manuscript Palavras-chave: Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/2142/version/1
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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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The Brain in Business: The Case for Organisational Cognitive Neuroscience? Nature Precedings
Nick Lee; Michael J. R. Butler; Carl Senior.
The application of cognitive neuroscientific techniques to understanding social behaviour has resulted in many discoveries. Yet advocates of the ‘social cognitive neuroscience’ approach maintain that it suffers from a number of limitations. The most notable of these is its distance from any form of real-world applicability. One solution to this limitation is ‘Organisational Cognitive Neuroscience’ – the study of the cognitive neuroscience of human behaviour in, and in response to, organizations. Given that all of us will spend most of our lives in some sort of work related organisation, organisational cognitive neuroscience allows us to examine the cognitive underpinnings of social behaviour that...
Tipo: Manuscript Palavras-chave: Ecology; Neuroscience.
Ano: 2008 URL: http://precedings.nature.com/documents/2159/version/1
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A Hypothetic Mechanism of Ordering and Shaping Cells within Discrete Regions Nature Precedings
Yaroslav Strokovskyy.
We propose a hypothetic mechanism of ordering and shaping cells during _C. elegans_ embryogenesis. The mechanism is based on the assumption that during each round of division of cells, daughter cells acquire electric charges from its mother cells (charge conservation law is taken into account). Between the acts of division, the total electric field, generated by a system of charged cells, change relative positions of the charged cells within the region. In one’s turn, the positions of the charged cells determine the pattern of the electrostatic field. A mathematical model of such self-consistent mechanism is developed. The process of developing the sixteen-cell structure starting with one cell is simulated. The results correspond to the known...
Tipo: Manuscript Palavras-chave: Developmental Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4277/version/1
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MUEGANO: A divide and conquer algorithm to overcome memory limitations when assembling shotgun projects Nature Precedings
Octavio Martinez; Araceli Fernandez-Cortes.
When assembling a large quantity of reads in a genomic shotgun project a serious limitation is the amount of random access memory (RAM) of the computers used in the project. This arises because all assembling programs must look at all the overlaps between reads at the same time, using RAM in order to construct contigs, and the memory of the computer can be filled up during this step, causing the abortion of the assembling process.
Here we propose an algorithm that is capable of overcoming any memory limitation by using redundancy of processing and thus producing an increase in computing time but overcoming the memory limitation.
The proposed algorithm consists in dividing the reads in a set of groups which size is half the...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3712/version/1
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Selective insectivory in _Nymphaea nouchali_ Burm. f. Nature Precedings
Pundarikakshudu Tetali; Shrikant Sutar; Sujata Tetali.
Carnivorous plants comprise roughly 0.24 percent of the flowering plants, or 640 species represented in 12 families. Yet they are regarded as _miracula naturae_. Over fifty percent of these taxa are represented in a single family, namely Lentibulariaceae. Carnivorous plants are generally insectivorous, and carnivory in flowering plants is generally found in taxa that are adapted to nutrient-deficient habitats. The extra nutrients such plants acquire by special ways serve merely as supplements. The origin and evolution of carnivorous plants is a mystery in the phylogenetic tree of angiosperms, they often appear without a clear linkage. Here, we report that _Nymphaea nouchali_ Burm. f. (a cultivar of var. cernua), a large aquatic member of the family...
Tipo: Manuscript Palavras-chave: Ecology; Earth & Environment; Plant Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1817/version/1
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SED-ML Script Language Nature Precedings
Frank Bergmann.
The Simulation Experiment Description Markup Language (SED-ML) is a XML format describing simulation experiments, so that they can be easily exchanged independent of software tools that created them. This document describes the SED-ML Script, a Python based shorthand that makes it easy to create / edit SED-ML documents.
Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6105/version/1
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An experimental and modelling exploration of the host-sanction hypothesis in legume-rhizobia mutualism Nature Precedings
Diana Marco; Juan Carbajal; Sergio Cannas; Rebeca Perez-Arnedo; Angeles Hidalgo-Perea; Jose Olivares; Jose Ruiz-Sainz; Juan Sanjuán.
Despite the importance of mutualism as a key ecological process, its persistence in nature is difficult to explain since the existence of exploitative, 'cheating' partners that could erode the interaction is common. By analogy with the proposed policing strategy stabilizing intraspecific cooperation, host sanctions against non N2 fixing, cheating symbionts have been proposed as a force stabilizing mutualism in legume-Rhizobium symbiosis. Following this proposal, penalizations would include decreased nodular rhizobial viability and/or early nodule senescence in nodules occupied by cheating rhizobia. In this work, we analyze the stability of Rhizobium-legume symbiosis when "cheating" strains are present, using an...
Tipo: Manuscript Palavras-chave: Ecology; Microbiology; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1964/version/1
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Breast Cancer Associated Metastasis is Significantly Increased in a Model of Autoimmune Arthritis Nature Precedings
Lopamudra Das Roy; Latha Pathangey; Teresa Tinder; Pinku Mukherjee.
Chronic inflammation is known to play a role in cancer initiation, promotion,and metastasis. However, the mechanism by which inflammation promotes metastasis is still unclear. We evaluated if chronic inflammation induced by autoimmune arthritis may contribute to increased breast cancer-associated metastasis. We report a three-fold increase in lung metastasis and a significant increase in the incidence of bone metastasis in the pro-arthritic mice compared to control mice. The metastatic breast tumors in turn augment the severity of arthritis resulting in a vicious cycle that increases both bone destruction and metastasis. Enhanced neutrophilic and granulocytic infiltration in lungs and bone of the pro-arthritic mice and subsequent increase in circulating...
Tipo: Manuscript Palavras-chave: Cancer; Immunology.
Ano: 2008 URL: http://precedings.nature.com/documents/2632/version/1
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Pegs and Ropes: Geometry at Stonehenge Nature Precedings
Anthony Johnson; Alberto Pimpinelli.
A recent computer-aided-design investigation of the Neolithic 56 Aubrey Hole circuit at Stonehenge has led to the discovery of an astonishingly simple geometrical construction for drawing an approximately regular 56-sided polygon, feasible with a compass and straightedge. In the present work, we prove analytically that the aforementioned construction yields as a byproduct, an extremely accurate method for approximating a regular heptagon, and we quantify the accuracy that prehistoric surveyors may have ideally attained using simple pegs and ropes. We compare this method with previous approximations, and argue that it is likely to be at the same time the simplest and most accurate. Implications of our findings are discussed.
Tipo: Manuscript Palavras-chave: Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/2153/version/1
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Modelling Hepatic Endoderm Development: Highly Efficient Differentiation of Human Embryonic Stem Cells to Functional Hepatic Endoderm Requires ActivinA and Wnt3a Signalling. Nature Precedings
David Hay; Judy Fletcher; Catherine Payne; John D. Terrace; Ronald C. J. Gallagher; Jan Snoeys; Jim Black; Davina Wojtacha; Kay Samuel; Zara Hannoun; Anne Pryde; Celine Filippi; Ian S. Currie; Stuart J. Forbes; James A. Ross; Philip Newsome; John Iredale.
Human embryonic stem cells (hESCs) are a valuable source of pluripotential primary cells. However, their homogeneous cellular differentiation to specific cell types _in vitro_ has proven difficult thus far. Wnt signalling has been shown to play important roles in coordinating development and we demonstrate that Wnt3a is differentially expressed at critical stages of human liver development _in vivo_. The essential role of Wnt3a in hepatocyte differentiation from hESCs is paralleled by our _in vitro_ model, demonstrating the importance of a physiological approach to cellular differentiation. Our studies provide compelling evidence that Wnt3a signaling is important for coordinated hepato-cellular function _in vitro_ and _in vivo_. In addition, we demonstrate...
Tipo: Manuscript Palavras-chave: Biotechnology; Developmental Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1454/version/1
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