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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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Enhancing Jatropha Productivity by Canopy Management Nature Precedings
Chalapathy K. Reddy; Vishal V. Naole.
Jatropha seed and oil yield is function of planting material used, growing conditions, plant architecture development and maintenance. Jatropha is hardy plant; thrives well in arid and semi arid regions with an average rainfall ranging from 500 to 1200 mm. It has been planted in varied soil types, marginal and waste lands; where in utilization of in situ resources by agronomic practices and development and management of canopy by pruning are very crucial for harvesting higher seed for biodiesel production. Building ideal canopy by pruning during first growing season is very important. Pruning is done during winter season when plants are in dormant condition.
Tipo: Manuscript Palavras-chave: Developmental Biology; Earth & Environment; Plant Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3700/version/1
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Adverse Effects of Trichothiodystrophy DNA Repair and Transcription Gene Abnormalities on Human Fetal Development Nature Precedings
Roxana Moslehi; Caroline Signore; James Troendle; Amiran Dzutsev; James L. Mills.
The effects of DNA repair and transcription genes in human prenatal life have never been studied. Trichothiodystrophy (TTD) is a rare (affected frequency of 10^-6^) recessive disorder caused by mutations in genes involved in the nucleotide excision repair (NER) pathway and in transcription. Based on our clinical observations, we conducted a genetic epidemiologic study to investigate gestational outcomes associated with TTD. We compared pregnancies resulting in TTD-affected offspring (N=24) with respect to abnormalities in their antenatal and neonatal periods to pregnancies resulting in their unaffected siblings (N=18), accounting for correlation, and to population reference values. Significantly higher incidence of several severe gestational complications...
Tipo: Poster Palavras-chave: Developmental Biology; Genetics & Genomics.
Ano: 2009 URL: http://precedings.nature.com/documents/3582/version/1
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Numbers, not value, motivate cooperation in humans and orangutans Nature Precedings
Ellen E. Furlong; John E. Opfer.
Cooperation among competitors-whether sharing the burden of wind resistance in the Tour de France, forming price-fixing cartels in economic markets, or adhering to arms-control agreements in international treaties-seldom spreads in proportion to the potential benefits. To gain insight into the minds of uncooperative agents, economists and social psychologists have used the prisoner's dilemma task to examine factors leading to cooperation among competitors. Two types of factors have emerged in these studies: the relative rewards of defecting versus cooperating and breakdowns in trust, forgiveness and communication. The generalizability of economic and social psychological factors, however, relies on the assumption that agents' comparisons...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology.
Ano: 2007 URL: http://precedings.nature.com/documents/1392/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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Ecological, phenological and biochemical significance of bimodal fruiting of Boletus alutaceus morgan Nature Precedings
Nandkumar Kamat.
Boletus alutaceus Morgan an ectomycorrhizal species was extensively studied from an ecologically fragmented microhabitt colonized by its' host plant Ficus benghalensis L. in the Goa University campus, Taleigao, Goa, India. Qualitatively the fruiting cycles were monitored for three years and thereafter detail ecological and morphological investigations were carried out in May and November 2004. A bimodal temporal fruting pattern emerged which may have significant ecological, phenological and biochemical role in EM dynamics.
Tipo: Presentation Palavras-chave: Biotechnology; Developmental Biology; Ecology; Genetics & Genomics; Microbiology; Plant Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/2835/version/1
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Estimating body Mass and Nutritional Status from Subadult Hominin Skeletons Nature Precedings
Gwendolyn Robbins.
Hominin body size and shape are key components to reconstructing phylogeny, life history, adaptation, and behavior in ancestral populations^1^. For adults, geometric properties of the femoral midshaft cross-section are used to infer locomotor behavior^2-5^, subsistence practices^6-7^, and functional adaptations^8-10^. Recently research has focused on patterns of compact bone ontogeny, particularly in regard to changes in bone strength with the acquisition of bipedal locomotion^11-13^ and examining population differences in ontogenetic trajectories for subadult humans^14-16^ and Neandertals^16^. Because femoral midshaft geometry is primarily shaped by biomechanical strains-weight bearing, locomotion, and muscle action-ontogenetic research requires estimates...
Tipo: Manuscript Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2468/version/1
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Human metabolic adaptations and prolonged expensive neurodevelopment: A review Nature Precedings
John R. Skoyles.
1.	After weaning, human hunter-gatherer juveniles receive substantial (≈3.5-7 MJ day^-1^), extended (≈15 years) and reliable (kin and nonkin food pooling) energy provision.
2.	The childhood (pediatric) and the adult human brain takes a very high share of both basal metabolic rate (BMR) (child: 50-70%; adult: ≈20%) and total energy expenditure (TEE) (child: 30-50%; adult: ≈10%).
3.	The pediatric brain for an extended period (≈4-9 years-of-age) consumes roughly 50% more energy than the adult one, and after this, continues during adolescence, at a high but declining rate. Within the brain, childhood cerebral gray matter has an even higher 1.9 to...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Neuroscience.
Ano: 2008 URL: http://precedings.nature.com/documents/1856/version/1
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Regulated peristalsis into the acidic region of the _Drosophila_ larval midgut is controlled by a novel component of the Autonomic Nervous System Nature Precedings
Dennis Richard LaJeunesse; Brooke Ann Johnson; Jason Presnell; Kathleen K. Catignas; Grzegorz Zapotoczny.
The underlying cellular and molecular mechanisms that regulate and coordinate critical physiological processes such as peristalsis are complex, often cryptic, and involve the integration of multiple tissues and organ systems within the organism. We have identified a completely novel component of the larval autonomic nervous system in the _Drosophila_ larval midgut that is essential for the peristaltic movement of food from the anterior midgut into the acidic region of the midgut. We have named this region the Superior Cupric Autonomic Nervous System or SCANS. Located at the junction of the anterior and the acidic portions of the midgut, the SCANS is characterized by a cluster of a novel neuro-enteroendocrine cells that we call Lettuce Head Cells, a valve,...
Tipo: Manuscript Palavras-chave: Developmental Biology; Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/3873/version/1
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The Size-Weight Illusion Is Not an Illusion When Picking the Best Objects to Throw Nature Precedings
Qin Zhu; Geoffrey Bingham.
Heaviness perception involves a misperception of weight known, since the 19th century, as the Size-Weight Illusion ^1^. The larger of two objects of equal mass is reported to be lighter than the smaller when they are lifted. The illusion has been found to be reliable and robust. It persists even when people know that the masses are equal and handle objects properly ^2^. It has been exhibited by children of only 2 years of age ^3,4^. All this suggests that the effect might be intrinsic to humans. Although different hypotheses have been advanced to account for the illusion over the 100+ years it has been studied ^5-11^, its origin remains unknown. More recently, people's perception of optimal objects for long distance throwing was found to exhibit a...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4584/version/1
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ChemTextMiner: An open source tool kit for mining medical literature abstracts Nature Precedings
Muthukumarasamy Karthikeyan; Yogesh Pandit; Deepak Pandit; Ganesh Nainaru; Sunil Nalwade; Renu Vyas; Esha Jain.
Text mining involves recognizing patterns from a wealth of information hidden latent in unstructured text and deducing explicit relationships among data entities by using data mining tools. Text mining of Biomedical literature is essential for building biological network connecting genes, proteins, drugs, therapeutic categories, side effects etc. related to diseases of interest. We present an approach for textmining biomedical literature mostly in terms of not so obvious hidden relationships and build biological network applied for the textmining of important human diseases like MTB, Malaria, Alzheimer and Diabetes. The methods, tools and data used for building biological networks using a distributed computing environment previously used for ChemXtreme[1]...
Tipo: Poster Palavras-chave: Chemistry; Developmental Biology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6435/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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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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Comparative Enumeration Gene Expression Nature Precedings
Leonardo Varuzza; Carlos A. D. E. B. Pereira.
This paper is about differential gene expression measured by transcript counting methods such as SAGE or MPSS. It introduces two significance tests for detection of differential expressed tags: frequentist and Bayesian. Under the frequentist view, it is proposed a test that computes the critical level as a function of each tag total frequency. Under the Bayesian view the Full Bayesian Significance Test is used considering the logistic normal distribution. The two proposed significance levels, the frequentist and the Bayesian, are compared for a data set with four libraries. The linking function between them is a Beta distribution function with mean 0.39 and standard deviation 0.30.
Tipo: Manuscript Palavras-chave: Developmental Biology; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/2002/version/1
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The 'consciousness' of the living state: Extending the Baars global broadcast model across physiological subsystems Nature Precedings
Rodrick Wallace.
For the broad spectrum of cognitive biological phenomena having 'dual' information sources, isolation from crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts at multiple scales, similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems. Entropy gradient models adapted from nonequilibrium thermodynamics lead to an index theorem in which analytic solutions of empirical equations describe different possible topological modes. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative...
Tipo: Manuscript Palavras-chave: Biotechnology; Developmental Biology; Ecology; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/6898/version/2
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Human neuromaturation, juvenile extreme energy liability, and adult cognition/cooperation Nature Precedings
John Skoyles.
Human childhood and adolescence is the period in which adult cognitive competences (including those that create the unique cooperativeness of humans) are acquired. It is also a period when neural development puts a juvenile’s survival at risk due to the high vulnerability of their brain to energy shortage. The brain of a 4 year-old human uses ≈50% of its total energy expenditure (TEE) (cf. adult ≈12%). This brain expensiveness is due to (1) the brain making up ≈6% of a 4 year-old body compared to 2% in an adult, and (2) increased energy metabolism that is ≈100% greater in the gray matter of a child than in an adult (a result of the extra costs of synaptic neuromaturation). The high absolute number of...
Tipo: Manuscript Palavras-chave: Developmental Biology; Neuroscience; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7096/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/2
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Expanding the modern synthesis II: Formal perspectives on the inherent role of niche construction in fitness Nature Precedings
Rodrick Wallace.
Expanding the modern synthesis requires elevating the role of interaction within and across various biological scales to the status of an evolutionary principle. One way to do this is to characterize genes, gene expression, and embedding environment as information sources linked by crosstalk, constrained by the asymptotic limit theorems of information theory (Wallace, 2010a). This produces an inherently interactive structure that escapes the straightjacket of mathematical population genetics or other replicator dynamics. Here, we examine fitness from that larger perspective, finding it intimately intertwined with niche construction. Two complementary models are explored: niche construction as mediating the connection between environmental signals and gene...
Tipo: Manuscript Palavras-chave: Developmental Biology; Ecology; Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5059/version/2
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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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Pregnancy Obstructs Involution Stage II of the Mammary Gland in Cows: General Biological Implications Nature Precedings
Gabriel Leitner; Ana-Maria Anug; Uzi Merin; Nissim Silanikove.
*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/2
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