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Independent elaboration of steroid hormone signaling pathways in Metazoans Nature Precedings
Gabriel V. Markov; Raquel Tavares; Chantal Dauphin-Villemant; Barbara A. Demeneix; Michael E. Baker; Vincent Laudet.
Steroid hormones regulate many physiological processes in vertebrates, nematodes and arthropods through binding to nuclear receptors (NR), a metazoan-specific family of ligand-activated transcription factors. The main steps controlling the diversification of this family are now well understood. In contrast, the origin and evolution of steroid ligands remain mysterious although this is crucial for understanding the emergence of modern endocrine systems. Using a comparative genomic approach, we analyzed complete metazoan genomes to provide a comprehensive view of the evolution of major enzymatic players implicated in steroidogenesis at the whole Metazoan scale. Our analysis reveals that steroidogenesis has been independently elaborated in the three main...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Bioinformatics; Earth & Environment; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3374/version/1
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Extending Tlusty's method to the glycome: Tuning the repertoire of glycan determinants Nature Precedings
Rodrick Wallace; Deborah Wallace.
We apply Tlusty'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 & Environment.
Ano: 2011 URL: http://precedings.nature.com/documents/5932/version/1
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The origin of vertebrates and their symmetry, segmentation, chord and tubular nervous system Nature Precedings
Alexander Ermolenko; Elena A. Perepada.
Development of vertebrata begins with formation of a multicellular organism by ordered repeated division of a reproductive cell and nondisjunction of the new formed cells, which have kept connection by means of the extracellular matrix. Further there is a consecutive formation of organisms due to aggregation of similar structures: blastaea; segmentella, supersegmentella. Supersegmentella gave development to tunicates, hemichordates, chordates like lancelet and to predecessors of vertebrata. Segmentation of organisms is determined by aggregation of supergastraeas into one integrated. Symmetry is determined by structure-forming quality of extracellular matrix. Symmetry of primary organisms was radial; then radial-bilateral, and the first plane of symmetry...
Tipo: Manuscript Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4164/version/1
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Near Infrared Microspectroscopy, Fluorescence Microspectroscopy, Infrared Chemical Imaging and High-Resolution Nuclear Magnetic Resonance Analysis of Soybean Seeds, Embryos and Single Cells Nature Precedings
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 (1μ) 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 2μ3. 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 & Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6200/version/1
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Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment Nature Precedings
Andrey Ptitsyn; Shane Kanatous.
*_Background:_* The metabolic transformation that changes Weddell seal pups born on land into aquatic animals is not only interesting for the study of general biology, but it also provides a model for the acquired and congenital muscle disorders which are associated with oxygen metabolism in skeletal muscle. However, the analysis of gene expression in seals is hampered by the lack of specific microarrays and the very limited annotation of known Weddell seal (_Leptonychotes weddellii_) genes.

*_Results:_* Muscle samples from newborn, juvenile, and adult Weddell seals were collected during an Antarctic expedition. Extracted RNA was hybridized on Affymetrix Human Expression chips. Preliminary studies showed a detectable...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3380/version/1
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Nonlinear Models of Neural and Genetic Network Dynamics Nature Precedings
I. C. Baianu.
A categorical and Łukasiewicz-Topos framework for Łukasiewicz LM-Algebraic Logic models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes is proposed. Łukasiewicz 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 & Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7114/version/1
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Collective cell guidance by cooperative intercellular forces Nature Precedings
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.	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
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Evaluation of effective parameters on fabrication of BSA nanoparticles Nature Precedings
Mostafa Rahimnejad; Ghasem Najafpour; Mohsen Jahanshahi.
Coacervation technique was implemented in fabrication of BSA nanoparticle for the purpose of drug delivery system. Nanoparticle was purified with 48,800 g centrifuge, and then followed by dialysis, micro and ultra filtration. The fabricated nanoparticles were subjected to physical, morphological and biochemical characterization. The analyzed samples by SEM and AFM proved the semi-spherically shape of the particles whilst the size distribution was measured by photon correlation spectroscopy. Fourier transforms infra-red spectroscopy (FTIR) spectrum indicated that the fabricated nanoparticles were pure. The impact of various parameters upon the particle size was extensively investigated. The concentration of glutaraldehyde at fixed temperature had absolutely...
Tipo: Manuscript Palavras-chave: Biotechnology; Developmental Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/2966/version/1
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Translational Oncogenomics and Human Cancer Interactome Networks Nature Precedings
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 & Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6190/version/2
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Multi-scale network biology model & the model library Nature Precedings
Jianghui Xiong.
Multi-scale network biology model & the model library
Tipo: Presentation Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/5778/version/1
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Quantitative Models for Efficient Cloning of Different Vectors with Various Clone sites Nature Precedings
Gang Zhang; Anurag Tandon.
We developed an efficient "Combinatorial Strategy” 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 & Genomics; Immunology; Microbiology; Molecular Cell Biology; Neuroscience.
Ano: 2012 URL: http://precedings.nature.com/documents/6965/version/1
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Bio-communication of Plants Nature Precedings
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 – 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
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ACBD: Database for Ascidian Chemical Genomics Nature Precedings
Yuichiro Hira; Jun Terai; Masaya Imoto; Etsu Tashiro; Kohji Hotta.
Chemical biology approach enables us to understand the complex biological systems, using small molecules such as a specific activator or inhibitor of protein, a hormone-like inducer, or a neurotransmitter. When such approach is performed genome-widely, that research is especially called "chemical genomics". We are planning to make a new start of chemical genomics using one of chordate model animal, ascidian. As a first step, we constructed a database called ACBD (Ascidians Chemical Biology Database). 

 First, we reviewed and annotated past articles which describe the uses of small chemicals in the field of ascidians biology. In ACBD, chemical information and effects on ascidian are manually extracted...
Tipo: Poster Palavras-chave: Developmental Biology; Pharmacology.
Ano: 2010 URL: http://precedings.nature.com/documents/5087/version/1
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Pregnancy Obstructs Involution Stage II of the Mammary Gland in Cows: General Biological Implications Nature Precedings
Nissim Silanikove; Gabriel Leitner; Ana-Maria Anug; Uzi Merin.
*Background*
Repeated research findings over the last 4 decades show that involution of mammary glands in dairy cows did not regress to same extend as that noticed in other mammalian species.

*Methodology/Principal Findings*
We took an advantage of a rare event in the normal modern dairy farming: A cow that was false-positively identified as being pregnant was "dried up" (i.e., induced into involution) conventionally about 60 before her expected parturition. This cow was culled, and samples of her mammary gland tissue were examined for gross histology. In this study we demonstrate for the first time that modern dairy cow may undergo extensive obliteration of the...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Immunology.
Ano: 2007 URL: http://precedings.nature.com/documents/846/version/1
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Aging as a consequence of misrepair -- A novel theory of aging Nature Precedings
Jicun Wang; Thomas Michelitsch; Arne Wunderlin; Ravi Mahadeva.
It is now increasingly realized that the underlying mechanisms which govern aging is a complex interplay of genetic regulation and damage accumulation. Aging as a result of accumulation of ‘faults’ on cellular and molecular levels, has been proposed in the damage (fault)-accumulation theory by Kirkwood 2006. However, this theory fails to explain some aging phenotypes such as fibrosis and premature aging, since terms such as ‘damage’ and ‘fault’ are not specified. Therefore we introduce here a specification of the underlying mechanism of aging and arrive at a novel theory: aging of the body is a result of the accumulation of Misrepair of tissue. It emphasizes: a) it is Misrepair, not the...
Tipo: Manuscript Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/2988/version/3
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Where did Words Come from? A Linking Theory of Sound Symbolism and Natural Language Evolution Nature Precedings
Jamie Reilly; David Biun; Wind Cowles; Jonathan Peelle.
Where did words come from? The traditional view is that the relation between the sound of a word and its meaning is arbitrary. An alternative hypothesis, known as sound symbolism, holds that form-meaning correspondence is systematic. Numerous examples of sound symbolism exist across natural language phyla. Moreover, cross-linguistic similarities suggest that sound symbolism represents a language universal. For example, many unrelated languages affix an "ee" sound to words in order to emphasize size distinctions or express affection (e.g., look at the teeny weeny baby); other such phonetic universals are evident for object mass, color, brightness, and aggression. We hypothesize that sound symbolism reflects sensitivity to an ecological law...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Neuroscience.
Ano: 2008 URL: http://precedings.nature.com/documents/2369/version/1
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Animal emergence during Snowball Earths by thermosynthesis in submarine hydrothermal vents Nature Precedings
Anthonie W. J. Muller.
Darwin already commented on the lateness in the fossil record of the emergence of the animals, calling it a valid argument against his theory of evolution^1^. This emergence of the animals (metazoans: multicellular animals) has therefore attracted much attention^2-5^. Two decades ago it was reported that extensive global glaciations (Snowball Earths) preceded the emergence^6-7^. Here we causally relate the emergence and the glaciations by invoking benthic sessile^8-11^ thermosynthesizing^12-13^ protists that gained free energy as ATP while oscillating in the thermal gradient between a submarine hydrothermal vent^14^ and the ice-covered ocean. During a global glaciation their size increased from microscopic to macroscopic due to the selective advantage of a...
Tipo: Manuscript Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3333/version/1
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Transduction Pathways Regulating The Trophic effects of Saccharomyces boulardii in Rat small intestinal mucosa Nature Precedings
Jean-Paul Buts; Nadine De Keyser.
_S . boulardii_ is a probiotic yeast widely prescribed in a lyophilized form that determines in human and rat small intestine several effects including endoluminal secretion of enzymes and of polyamines, stimulation of microvillous enzymes, of sIgA ,increased production of the receptor for polymeric immunoglobulins by crypt cells, and enhanced D-glucose uptake.
Aim: The objective of this study was to determine the pathway(s) by which these effects generated by the yeast are transduced into the cell.
Methods: Litters of 6 growing Wistar rats each (30 days post partum) were treated with _S .boulardii_ (50[micro]g per g body wt) or with saline during 72 hours. For each animal, the cytosol was prepared from the whole mucosa...
Tipo: Manuscript Palavras-chave: Developmental Biology; Microbiology.
Ano: 2009 URL: http://precedings.nature.com/documents/3061/version/1
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The hypothesis of basic phenotype modules Nature Precedings
Thomas von Zelewsky.
The evolutionary events that allowed the rapid occurrence of metazoa are still enigmatic. The presumably oldest metazoan fossils are microscopic and occur just above 635 Ma, at the beginning of the Ediacaran period. Upon condition that the lack of macrofossils in the lower Ediacaran strata is real, the assumption of a sudden appearance of already complex, but still small animals that flourished during the first half of the Ediacaran is a reasonable option. Consequently, the emergence of the first macrofossils with metazoan affinity in mid Ediacaran strata would indicate a second leap in animal evolution. Here, these apparent leaps are explained in terms of a new concept of evolvability that is based on well definable developmental modules: A system based...
Tipo: Manuscript Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4189/version/1
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Human Heart Development Pathways Nature Precedings
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 & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6500/version/1
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