Consulta: subjectFacets:"Evolutionary Biology"
Registros recuperados: 383
Data/hora: 13/06/2024 14:45:13

Biological taxonomy and ontology development: scope and limitations
Provedor de dados: 17
Autores: Nico M. Franz; David M. Thau.
The prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are reviewed. We contrast the common usage of a static &amp;#x27;snapshot&amp;#x27; hierarchy in ontological representations of taxonomy with a more realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical semantic background from which ontological entities and relationships originate, and therefore pose special challenges to ontological representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4593/version/1

GMOD for Evolutionary Biology
Provedor de dados: 17
Autores: Robert Buels; Dave Clements.
The Generic Model Organism Database (GMOD, &amp;#x22;http://gmod.org&amp;#x22;:http://gmod.org) project provides interoperable, open source software tools for managing, visualizing and annotating biological data.  GMOD is also a community of people addressing common challenges with biological data.  Some well known software in GMOD includes GBrowse and JBrowse for genome browsing, Apollo for genome annotation, Chado for managing data, CMap for comparative map viewing, Galaxy for workflow creation and persistence, and BioMart for warehousing biological data.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This talk will focus on three areas of particular interest to iEvoBio participants.  &amp;#xd;&amp;#xa;1) GBrowse_syn comparative genomics viewer&amp;#xd;&amp;#xa;2)...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4611/version/1

Human metabolic adaptations and prolonged expensive neurodevelopment: A review
Provedor de dados: 17
Autores: John R. Skoyles.
1.&amp;#x9;After weaning, human hunter-gatherer juveniles receive substantial (&amp;#x2248;3.5-7 MJ day^-1^), extended (&amp;#x2248;15 years) and reliable (kin and nonkin food pooling) energy provision.&amp;#xd;&amp;#xa;2.&amp;#x9;The childhood (pediatric) and the adult human brain takes a very high share of both basal metabolic rate (BMR) (child: 50-70%; adult: &amp;#x2248;20%) and total energy expenditure (TEE) (child: 30-50%; adult: &amp;#x2248;10%).&amp;#xd;&amp;#xa;3.&amp;#x9;The pediatric brain for an extended period (&amp;#x2248;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; Neuroscience; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1856/version/2

The Teleost Taxonomy Ontology
Provedor de dados: 17
Autores: Peter E. Midford; James P. Balhoff; Wasila Dahdul; Cartik R. Kothari; Hilmar Lapp; John Lundberg; Paula Mabee; Todd J. Vision; Monte Westerfield.
The Teleost Taxonomy Ontology (TTO) is an ontology of taxonomic groups and associated names for fish (not just teleosts). This ontology has served as a source of names and taxonomic structure within the Phenoscape project since early 2008. Although the TTO is based on Eschmeyer&amp;#x27;s Catalog of Fishes (CoF) and incorporates all valid species and genus names, it is also extended by the curation needs of the Phenoscape project. Names of fossil taxa not included in the CoF as well as references to specimens identi&amp;#xc;ed only to genus (e.g., _Eigenmannia sp._ (Fink and Fink 1981)) are incorporated into the TTO as required by the curation needs of the Phenoscape project. As Phenoscape receives updates to the CoF, a tool called TTOUpdate merges the...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4629/version/1

Reply to &amp;#x201c;Limusaurus and bird digit identity&amp;#x201d;
Provedor de dados: 17
Autores: Xing Xu; James Clark; Jonah  Choiniere; David Hone; Corwin Sullivan.
Vargas et al. agree with us that a lateral shift in theropod dinosaur digits occurred prior to the origin of birds, but contend that it occurred as a single &amp;#x201c;frameshift&amp;#x201d; with little outward change to the three main digits involved^1^.  We consider the digital morphology of Limusaurus, other ceratosaurs, and non-avian tetanurans to provide evidence that the shift was stepwise, and that a stepwise shift better explains theropod manual morphology than a hidden frameshift.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6375/version/1

The Earliest Perfect Flower
Provedor de dados: 17
Autores: Xin Wang; Shaolin Zheng.
Despite of angiosperms in the Yixian Formation (&amp;#x3e;125 Ma, early Cretaceous), there is no perfect flower typical of angiosperms to date. Here we report _Euanthus dilaensis_ gen. et sp. nov as the earliest perfect flower known to date. The flower includes tepals, androecium and gynoecium. The anthers are globose in form, with bristles atop and in situ round-triangular pollen grains. The gynoecium is composed of probably two carpels with plumose stigmas and a carpel-enclosing receptacle. The discovery of _Euanthus_ increases the diversity of early angiosperms, and indicates that perfect flowers occurred as early as 125 Ma ago.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1320/version/1

Motif analysis of amphioxus, lamprey and invertebrate estrogen receptors and amphioxus and human estrogen-related receptors: Towards a better understanding of estrogen receptor evolution
Provedor de dados: 17
Autores: Michael E. Baker; Charlie Chandsawangbhuwana.
*Background.*  The origins of steroid-dependent regulation of the vertebrate estrogen receptor (ER) are poorly understood.  Genes with statistically significant sequence similarity to vertebrate ERs have been found in lamprey, a basal vertebrate, and amphioxus, a basal chordate.  Motif analysis of these sequences provides an opportunity to investigate early events in the evolution of the ER.&amp;#xd;&amp;#xa;*Results.*  We used artificial intelligence-based software to construct twelve motifs specific to the estrogen-binding domain of ER[alpha] and ER[beta] in land vertebrates and teleosts.  We mapped these ER-specific motifs onto the sequences of lamprey, amphioxus, invertebrate and selected vertebrate ERs and amphioxus, Ciona and human estrogen-related...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1542/version/2

Homochirality through Photon-Induced Melting of RNA/DNA: the Thermodynamic Dissipation Theory of the Origin of Life
Provedor de dados: 17
Autores: Karo Michaelian.
The homochirality of the molecules of life has been a vexing problem with no generally accepted solution to date. Since a racemic mixture of chiral nucleotides frustrates the extension and replication of RNA and DNA, understanding the origin of homochirality has important implications to the investigation of the origin of life. Theories on the origin of life have generally elected to presume an abiotic mechanism giving rise to a large prebiotic enantiomer enrichment. Although a number of such mechanism have been suggested, none has enjoyed sufficient plausibility or relevance to be generally accepted. Here we suggest a novel solution to the homochirality problem based on a recently proposed thermodynamic dissipation theory for the origin of life. The...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5177/version/1

Self-organization of intrinsically disordered proteins with folded N-termini
Provedor de dados: 17
Autores: Philip C. Simister; Fred Schaper; Nicola O&amp;#x27;Reilly; Simon McGowan; Stephan M. Feller.
Thousands of human proteins lack recognizable tertiary structure in most of their chains. Here we hypothesize that some use their structured N-terminal domains (SNTDs) to organise the remaining protein chain via intramolecular interactions, generating partially structured proteins. This model has several attractive features: as protein chains emerge, SNTDs form spontaneously and serve as nucleation points, creating more compact shapes. This reduces the risk of protein degradation or aggregation. Moreover, an interspersed pattern of SNTD-docked regions and free loops can coordinate assembly of sub-complexes in defined loop-sections and enables novel regulatory mechanisms, for example through posttranslational modifications of docked regions.
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5124/version/1

ABO and Rh Blood Group Distribution Among Kunbis (Maratha) population of Amravati District, Maharashtra
Provedor de dados: 17
Autores: NANDKISHOR E. WARGHAT; NAVIN R. SHARMA; MUMTAZ M. BAIG; A. R. Yadav; S. H. Sharma; G. S. Pachalore.
The present study reports the distribution of ABO and Rh blood groups among the Kunbis (Maratha) population of Amravati district. The phenotypic frequency of blood group B is observed highest (33.06) percent, O (31.04), A (27.02) and AB is lowest (08.33) percent. The phenotypic frequency of Rh negative is (04.26) percent. TheKunbis (Maratha) population shows close genetic relationship with the Gujratis.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4868/version/1

Words make people think, ... but pictures make people feel: The effect negative vs. positive images on charitable behavior
Provedor de dados: 17
Autores: Carolina  Perez Due&amp;#xf1;as; Maria Fernanda Rivas; Olusegun A. Oyediran; Alberto Acosta; Pablo Bra&amp;#xf1;as Garza.
We ran an experiment where the subjects initially played a four-round dictator game, after which each subject was shown either a set of positive images or a set of negative images. Finally the subjects played another four-round dictator game.&amp;#xd;&amp;#xa;The effect of the sign of images shown is clear on the players&amp;#x2019; behaviors: positive images have moderate effects on charitable behavior while negative images dramatically increase charity.&amp;#xd;&amp;#xa;We could therefore infer from our experimental results that showing negative images of the Haitian and Chilean catastrophes to the international public would have significant positive impacts on international donations to the victims and the rebuilding programs in both countries.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4287/version/1

Fossil evidence for the origin of spider spinnerets
Provedor de dados: 17
Autores: Paul A. Selden; William A. Shear.
Silk production from opisthosomal glands is a defining characteristic of spiders (Araneae). Silk emerges from spigots (modified setae) borne on spinnerets (modified appendages). Spigots from _Attercopus fimbriunguis_ (Shear, Selden &amp;#x26; Rolfe, 1987^1^), from Middle Devonian (386 Ma) strata of Gilboa, New York were described in 1989^2^ as evidence for the oldest spider and the first use of silk by animals. Slightly younger (374 Ma) material from South Mountain, New York, conspecific with _A. fimbriunguis_, includes spigots and other evidence which elucidate the evolution of early Araneae and the origin of spider silk. No known _Attercopus_ spigots, including the original specimen^2^, occur on true spinnerets but are arranged along the edges of plates....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2088/version/1

Parameter Estimation for Hidden Markov models with Intractable Likelihoods
Provedor de dados: 17
Autores: Ajay  Jasra; Thomas A. Dean; Sumeetpal  S. Simgh; Gareth W. Peters.
In this talk I consider sequential Monte Carlo (SMC) methods for hidden Markov models. In the scenario for which the conditional density of the observations given the latent state is intractable we give a simple ABC approximation of the model along with some basic SMC algorithms for sampling from the associated filtering distribution. Then, we consider the problem of smoothing, given access to a batch data set. We present a simulation technique which combines forward only smoothing (Del Moral et al, 2011) and particle Markov chain Monte Carlo (Andrieu et al 2010), for an algorithm which scales linearly in the number of particles.
Tipo: Presentation
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5957/version/1

An experimental and modelling exploration of the host-sanction hypothesis in legume-rhizobia mutualism
Provedor de dados: 17
Autores: Diana Marco; Juan Carbajal; Sergio Cannas; Rebeca Perez-Arnedo; Angeles Hidalgo-Perea; Jose Olivares; Jose  Ruiz-Sainz; Juan Sanju&amp;#xe1;n.
Despite the importance of mutualism as a key ecological process, its persistence in nature is difficult to explain since the existence of exploitative, &amp;#x27;cheating&amp;#x27; 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 &amp;#x22;cheating&amp;#x22; strains are present, using an...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1964/version/1

Lengthening of 3&amp;#x27;UTR Increases Morphological Complexity in Animal Evolution
Provedor de dados: 17
Autores: Cho-Yi Chen; Shui-Tein Chen; Hsueh-Fen Juan; Hsuan-Cheng Huang.
By analyzing the structure of mRNA transcripts in multiple metazoan species, we observed a striking exponential correlation between the length of 3&amp;#x27; untranslated regions (3&amp;#x27;UTR) and morphological complexity as measured by the number of cell types in each organism. Cellular diversity was similarly associated with the accumulation of microRNA genes and their putative targets. We propose that the lengthening of 3&amp;#x27;UTRs together with a commensurate expansion in post-transcriptional regulation can contribute to the emergence of new cell types during animal evolution.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4915/version/1

Third-codon transversion rate-based _Nymphaea_ basal angiosperm phylogeny -- concordance with developmental evidence
Provedor de dados: 17
Autores: Xiaohan Yang; Gerald A. Tuskan; Timothy J. Tschaplinski; (Max) Zong-Ming Cheng.
Flowering plants (angiosperms) appeared on Earth rather suddenly approximately 130 million years ago and underwent a massive expansion in the subsequent 10-12 million years. Current molecular phylogenies have predominantly identified _Amborella_, followed by _Nymphaea_ (water lilies) or _Amborella_ plus _Nymphaea_, in the ANITA clade (_Amborella_, Nymphaeales, Illiciaceae, Trimeniaceae and Austrobaileyaceae) as the earliest angiosperm. However, developmental studies suggest that the earliest angiosperm had a 4-cell/4-nucleus female gametophyte and a diploid endosperm represented by _Nymphaea_, suggesting that _Amborella_, having an 8-cell/9-nucleus female gametophyte and a triploid endosperm, cannot be representative of the basal angiosperm. This...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/320/version/1

Solubilization of M2 Transmembrane Peptide of Influenza A in Pure Water: Implications for Emergence of Proteins and Protein-embedded Primeval Membranes in Unsalted Oceans
Provedor de dados: 17
Autores: Jianxing Song; Linlin  Miao.
We demonstrated that M2 transmembrane peptide, one of the most hydrophobic sequences in nature, can be solublized to at least ~100 &amp;#xb5;M in unsalted water without any lipid molecules. Strikingly, the M2 peptide also forms a highly-helical conformation in water which remains almost unchanged even at 95 &amp;#xba;C, as characterized by CD spectroscopy. Our result has critical implications in understanding emergence of proteins and protein-embedded primeval membranes in unsalted oceans.
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6773/version/1

A Draft Sequence of the Puerto Rican Parrot Genome (Amazona vittata) &amp;#x2013; a Genome Project funded by a Local Community Effort
Provedor de dados: 17
Autores: Taras K. Oleksyk.
The genome of the Puerto Rican parrot (Amazona vittata) has been sequenced and assembled in an international collaboration supported by many individual donations from the people of Puerto Rico.  This is a critically endangered endemic bird, the only surviving native parrot species in the territory of the United States, and the first parrot belonging to the large genus Amazona to have its genome sequenced and assembled.  A genome of one A. vittata female was sequenced resulting in a total of almost 42.5 billion nucleotide bases equivalent to 26.89X average coverage depth. After filtering out the short fragments (&amp;#x3c;500bp), the assembly resulted in 259,423 short fragment library contigs, half of them (N50) of at least 6,983 bp in length, with a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6552/version/1

Identification of transcription regulation associated proteins in plants and stramenopiles
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o Pach&amp;#xf3;n; Silvia Restrepo; Bernd Mueller-Roeber; Francisco Buitrago Florez.
The generation of biodiversity is tied to the evolution and re-wiring of gene regulatory networks (GRNs). One component of these GRN are transcription factors and other transcriptional regulators. We have devised a pipeline for the identification of TFs and TRs, exploiting the domain architecture of these proteins. Currently we have a set of rules, representing 138 proteins families, that we have applied to the identification of ~20 different plant species and several species of Stramenopiles, where important plant pathogens are found. Results for plant species are available at http://plntfdb.uniandes.edu.co/; we are now developing a newer interface for Stramenopiles.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7000/version/1

Mega- change gene copies are produced by reverse transcription of precursor RNA with replaced introns.
Provedor de dados: 17
Autores: Drew Schwartz.
This report describes the presence of copy genes in plants where the sequence similarity to their parental genes is almost completely limited to limited to the exons. Evidence is presented that indicates that they arose via a novel processing of transcribed precursor RNA during which the introns are replaced rather than excised, followed by reverse transcription and incorporation into the chromosomes. Intron replacement may play an important role in evolution as it results in megagene changes.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3834/version/1

A Study on the Origin of Peroxisomes: Possibility of Actinobacteria Symbiosis
Provedor de dados: 17
Autores: Duhita Narendra; Saruhashi Satoshi; Hamada Kazuo; Miyata Daisuke; Horiike Tokumasa; Shinozawa Takao.
The origin of peroxisomes as having developed from the endoplasmic reticulum (ER) was proposed on the basis of the similarity between some peroxisomal proteins and ER proteins, and the localization of some peroxisomal proteins on the ER. To study the evolutionary distance between peroxisomes and ER and Prokaryotes, we carried out a phylogenetic analysis of CDC48 (cell division control 48) and its homologs, including ER-localized CDC48, CDC48 homologs in Prokaryotes and peroxisome-localized PEX1 and PEX6. A similarity search analysis of peroxisomal protein sequences to prokaryotic protein sequences using BLAST at several thresholds (E-values) was also done. We propose Actinobacteria symbiosis for the origin of peroxisomes based on the following evidence:...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1866/version/1

Specificity and Evolvability in Eukaryotic Protein Interaction Networks
Provedor de dados: 17
Autores: Pedro Beltrao; Luis Serrano.
Progress in uncovering the protein interaction networks of several species has led to questions of what underlying principles might govern their organization. Few studies have tried to determine the impact of protein interaction network evolution on the observed physiological differences between species. Using comparative genomics and structural information, we show here that eukaryotic species have rewired their interactomes at a fast rate of approximately 10?5 interactions changed per protein pair, per million years of divergence. For Homo sapiens this corresponds to 103 interactions changed per million years. Additionally we find that the specificity of binding strongly determines the interaction turnover and that different biological processes show...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/26/version/1

Graphs, Networks, Extinction and Paleocommunity Food Webs
Provedor de dados: 17
Autores: Peter Roopnarine.
Food webs represent the trophic interactions among species in communities. Those interactions both structure and are structured by species richness, ecological diversity, and evolutionary processes. Geological and macroevolutionary timescales are therefore important to the understanding of food web dynamics, and there is a need for proper reconstruction and analysis of paleocommunity food webs. The fossil record presents many challenges, but the problem may be approached with combinatoric analysis, and graph and network theories. This paper is a brief introduction to the aspects of those disciplines relevant to the study of paleo-food webs, and explores several probabilistic and numerical approaches.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4433/version/1

Molecular phylogenies and evolutionary behavior of AhR (aryl hydrocarbon receptor) pathway genes in aquatic animals
Provedor de dados: 17
Autores: Hailong Zhou; Ying Qu; Qinzhao Xue.
Phylogenetic analysis of AhR pathway genes and their evolutionary rate variations were studied on aquatic animals. The gene sequences for the proteins involved in this pathway were obtained from major phylogenetic groups of mollusc, amphibian, fish and aquatic mammal. These genes were distributed under four major steps of toxicology regulation: formation of cytosolic complex, translocation of AhR, heterodimerization of AhR and induction of CYP1A. The NJ, MP and ML algorithm were used on protein coding DNA sequences to deduce the evolutionary relationship for the respective AhR pathway gene among different aquatic animals. The rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d~N~) and synonymous nucleotide substitutions per synonymous...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2928/version/1

Exploiting evolution to treat drug resistance: Combination therapy and the double bind
Provedor de dados: 17
Autores: David Basanta; Robert Gatenby; Alexander R. A. Anderson.
Although many anti cancer therapies are successful in killing a large percentage of tumour cells when initially administered, the evolutionary dynamics underpinning tumour progression mean that often resistance is an inevitable outcome, allowing for new tumour phenotypes to emerge that are unhindered by the therapy. Research in the field of ecology suggests that an evolutionary double bind could  be an effective way to treat tumours. In an evolutionary double bind two therapies are used in combination such that evolving resistance to one leaves individuals more susceptible to the other. In this paper we present a general evolutionary game theory model of a double bind to study the effect that such approach would have in cancer. Furthermore we use this...
Tipo: Manuscript
Palavras-chave: Cancer; Ecology; Pharmacology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6380/version/1

On the status of the Michaelis-Menten equation and its implications for enzymology
Provedor de dados: 17
Autores: Sosale Chandrasekhar.
The Michaelis-Menten equation (MME) is considered to be the fundamental equation describing the rates of enzyme-catalysed reactions, and thus the &amp;#x27;physicochemical key&amp;#x27; to understanding all life processes. It is the basis of the current view of enzymes as generally proteinaceous macromolecules that bind the substrate reversibly at the active site, and convert it to the product in a relatively slow overall sequence of bonding changes (&amp;#x27;turnover&amp;#x27;). The manifested &amp;#x27;saturation kinetics&amp;#x27;, by which the rate of the enzymic reaction (essentially) increases linearly with the substrate concentration ([S]) at low [S] but reaches a plateau at high [S], is apparently modelled by the MME. However, it is argued herein...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1637/version/1

Phenex: Ontological Annotation of Phenotypic Diversity
Provedor de dados: 17
Autores: James P. Balhoff; Wasila M. Dahdul; Cartik R. Kothari; Hilmar Lapp; John G. Lundberg; Paula Mabee; Peter E. Midford; Monte Westerfield; Todd J. Vision.
Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. Thus, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.&amp;#xd;&amp;#xa;Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4068/version/1

Underlying Mathematics in Diversification of Human Olfactory Receptors in Different Loci
Provedor de dados: 17
Autores: Sk. Sarif  Hassan; Pabitra  Pal Choudhury; Arunava Goswami.
As per conservative estimate, approximately (51-105) Olfactory Receptors (ORs) loci are present in human genome occurring in clusters. These clusters are apparently unevenly spread as mosaics over 21 pair of human chromosomes. Olfactory Receptor (OR) gene families which are thought to have expanded for the need to provide recognition capability for huge number of pure and complex odorants. ORs form the largest known multi-gene family in the human genome. Recent studies have shown that 388 full length and 414 OR pseudo-genes are present in these OR genomic clusters. In this paper, the authors report a classification method for all human ORs based on their sequential quantitative information like presence of poly strings of nucleotides bases, long range...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5475/version/1

Enhanced display of scienti&amp;#xfb01;c articles using extended metadata
Provedor de dados: 17
Autores: Roderic D. M. Page.
Although the Web has transformed science publishing, scientific papers themselves are still essentially &amp;#x22;black boxes&amp;#x22;, with much of their content intended for human readers only.  Typically, computer-readable metadata associated with an article is limited to bibliographic details. By expanding article  metadata to include taxonomic names, identifiers for cited material (e.g., publications, sequences, specimens, and other data), and geographical  coordinates,  publishers could greatly  increase the scientific value of their digital content. At the same time this will provide  novel ways for users to discover and navigate through this content, beyond the relatively limited linkage provided by bibliographic...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3173/version/1

Dogs Never Gets Prion Diseases. The Entropic Landscape Analysis of Prion Proteins Answers Why.
Provedor de dados: 17
Autores: Kentaro Onizuka.
The Entropic Landscape Analysis was applied to the prion protein sequences of various mammals in order to detect potential sites of variants that would be responsible for the susceptibility of prion disease infection. Among familiar mammals, canines including dogs have been demonstrating strong resistance to prion diseases. Among the canine specifc substitutions the entropic landscape analysis pinpoints the substitutions Asn104Gly and Ser107Asn having the biggest impact to the conformational transition and stability. Although they must be further corroborated by experiments in vivo et vitro, the results are demonstrating that the entropic landscape analysis is useful enough to screen substitutions and polymorphisms potentially relevant to conformational...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3043/version/1

&amp;#x22;Dark Mediators&amp;#x22; of Proteins as Revealed by NMR in Water: Residue-selective Anion Bindings that are Masked by Pre-existing Buffer
Provedor de dados: 17
Autores: Jianxing Song; Linlin Miao; Haina Qin.
Ions are commonly believed to impose their effects on proteins by unspecific electrostatic screening. Here, by NMR we reveal that in water sulfate, chloride and thiocyanate are able to bind a well-folded WW domain at distinctive residues and affinities, which is surprisingly masked by the pre-existing buffer. Our study reveals that the specific anion binding is so ubiquitous and consequently no longer negligible in establishing &amp;#x22;postreductionist framework&amp;#x22; for protein biochemistry.
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6769/version/1

Is your phylogeny informative? Measuring the power of comparative methods
Provedor de dados: 17
Autores: Peter Ralph; Graham Coop; Carl Boettiger.
Phylogenetic comparative methods have become all but ubiquitous in only a few decades, forcing us to reconsider if information from a phylogenetic tree can justify the results. Existing approaches to this question have been inadequate and do not scale with tree size or the ability to resolve branches. For instance, selection between phylogenetic models typically based on information criteria fails to adequately reflect this uncertainty, and can lead to preference for arbitrarily complicated models. Common measures of phylogenetic signal tend to characterize the goodness-of-fit of a Brownian motion model to the data, rather than indicate whether the data is sufficient to confidently distinguish between different hypotheses. We present a Monte Carlo based...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6453/version/1

Treemap Versus BPA (Again): A Response to Dowling
Provedor de dados: 17
Autores: Roderic Page; Michael Charleston.
TreeMap is a computer program for analysing host-parasite cospeciation. We respond to Dowling&amp;#x2019;s (Cladistics, 18: 416-435) recent comparison of TreeMap and Brooks Parsimony Analysis (BPA) by showing that Dowling&amp;#x2019;s comparison suffers from several mistakes and flaws. We discuss the problems with both BPA and TreeMap, and show that BPA incorrectly counts the true number coevolutionary events more often than TreeMap 1. We also discuss the two main limitations of TreeMap 1 correctly identified by Dowling, namely its inability to handle widespread parasites, and its coarse optimality criterion (the number of cospeciation events). We suggest a simple fix for widespread parasites. The newly released TreeMap 2 uses a more sensitive optimality...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1030/version/1

Two &amp;#x27;protein folding codes&amp;#x27; can be inferred from empirical classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;s topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. Unlike the genetic case, two protein folding codes are found, a &amp;#x27;normal&amp;#x27; globular and a &amp;#x27;pathological&amp;#x27; amyloid version. The underlying normal &amp;#x27;protein folding code error network&amp;#x27; is found to have one major, highly dominant, &amp;#x27;spherical&amp;#x27; component, a minor attachment handle in the Morse Theory sense, and as many as three additional subminor handles. The basic amyloid folding code error network appears to be more complicated, of genus two, giving the eightfold symmetry of the steric zipper. Like many before us, we conjecture that the elaborate...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4665/version/1

The likelihood that two proteins interact might depend on the proteins&amp;#x27; age
Provedor de dados: 17
Autores: Pedro Beltrao.
It has been previously shown [1] that _S. cerevisiae_ proteins preferentially interact with proteins of the same estimated likely time of origin.  To study this observation further, the protein interaction networks of _S. cerevisiae_ and _H. sapiens_ were analyzed taking into account an estimate for the age of the proteins in these species.  These estimates were obtained by studying the presence and absence of putative orthologs in other eukaryotic species. In this work preliminary results are described that point to a dependence of the likelihood of protein interaction on the proteins&amp;#x2019; age. The probability of two proteins interactions was found to be linearly dependent on the time the proteins have co-existed in the species.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/22/version/1

Population genetic structure of the pelagic goby, Sufflogobius bibarbatus, in the Northern Benguela ecosystem, based on PCR-RFLP analysis of the mitochondrial control region and the ND 3 and 4 region (Dissertation).
Provedor de dados: 17
Autores: Pallagae M. C. S. De Silva.
Polymorphism within the mitochondrial NADH-3,4 dehydrogenase(ND-3/4) and control region (D-Loop) was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of Sufflogobius bibarbatus (Pelagic Goby) population in the Northern Benguela ecosystem. Three major geographical areas representing the north-south axis (Ludritz, Walvis Bay and North of Ambrose Bay) were selected. Polymorphism was detected using three and two restriction enzymes respectively in ND- 3 / 4 and D-Loop regions, and a total number of 25 composite haplotypes were identified. The most common haplotype accounted for 36% of 238 individuals. Recorded haplotype diversities were quite high, ranging 0.70 to 0.86.The highest haplotype diversity was found...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3007/version/1

Ecological dynamics and the basis of sympatric phenotypic diversification
Provedor de dados: 17
Autores: Mario  Pineda-Krch; Richard Svanb&amp;#xe4;ck; Michael Doebeli.
Theoretical and empirical studies are showing evidence in support of evolutionary branching and sympatric speciation due to frequency&amp;#x2010;dependent competition. However, phenotypic diversification due to underlying genetic diversification is only one possible evolutionary response to disruptive selection. Another potentially general response is phenotypic diversification in the form of phenotypic plasticity. It has been suggested that genetic variation is favored in stable environments, whereas phenotypic plasticity is favored in unstable and fluctuating environments. We investigate the &amp;#x201c;competition&amp;#x201d; between the processes of evolutionary branching and the evolution of phenotypic plasticity in a predator&amp;#x2010;prey model...
Tipo: Presentation
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3672/version/1

Discovery of the Principal Cystic Fibrosis Mutation (F508del) in Ancient DNA from Iron Age Europeans
Provedor de dados: 17
Autores: Philip Farrell; Cedric  Le Marechal; Claude Ferec; Malika  Siker; Maria Teschler-Nicola.
The most common, life-threatening autosomal recessive disease of Europeans and Euro-Americans, cystic fibrosis (CF), occurs predominately in patients with the F508del mutation.1 Although F508del is currently detectable as a single allele in 1/30-1/40 Europeans2-4 and Euro-Americans,5 it has not been determined what heterozygote selective advantage(s) might account for its relatively high prevalence. Indirect evidence6 suggests that this mutation was present in Brittany at least 3000 years ago, but no direct analyses of ancient DNA have been reported to identify F508del and clarify its frequency in prehistoric inhabitants of Europe. Here we show that F508del was present in 3 of 32 Iron Age inhabitants of Austria from whom DNA could be recovered from molar...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1276/version/1

Structural and functional validation of Microsystin synthetases
Provedor de dados: 17
Autores: Swapnil G. Sanmukh; Waman N. Paunikar.
The structure and function prediction for the Microsystin synthetases from Microsystis aerogenosa (LNSAMB) were carried out for verifying the authenticity of the sequenced genes. The genes for Microsystin synthetases (mcyA, mcyB, mcyD and mcyE,), were predicted by the application of computational methods and Bioinformatics web tools. The probable function prediction for the proteins was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching protein databases for the presence of conserved domains. While tertiary structures were constructed using PS2 Server- Protein Structure Prediction server. This study revealed structural and functional validation of sequenced genes.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6835/version/1

Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs
Provedor de dados: 17
Autores: Zeba Wunderlich; Leonid Mirny.
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6^-10^9^ decoy sites? Our analysis of 319 known TF binding motifs clearly demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations; eukaryotic TFs exhibit widespread nonfunctional binding and require clustering of sites in regulatory regions for specificity.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2688/version/2

A Unifying Scenario on the Origin and Evolution of Cellular and Viral Domains
Provedor de dados: 17
Autores: Claudiu I. Bandea.
The cellular theory on the nature of life has been one of the first major advancements in biology. Viruses, however, are the most abundant life forms, and their exclusion from mainstream biology and the Tree of Life (TOL) is a major paradox in biology. This article presents a broad, unifying scenario on the origin and evolution of cellular and viral domains that challenges the conventional views about the history of life and supports a TOL that includes viruses. Co-evolution of viruses and their host cells has led to some of the most remarkable developments and transitions in the evolution of life, including the origin of non-coding DNA as a genomic protective device against viral insertion damage. However, one of the major fundamental evolutionary...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3888/version/1

In-group/out-group bias in contagious yawning
Provedor de dados: 17
Autores: J. Ryan  Porter; Steven M. Platek.
Bias for an in-group is a social phenomenon characterized by an affinity for one&amp;#x2019;s in-group over a perceived out-group. Activation in the amygdala, which is implicated in social and emotional processes, is increased when humans view other-race faces. This increase in activation is associated with implicit racial bias as indicated by scores on an implicit attitude test. Contagious yawning is a social process that appears to subserve empathic processes enabling the inferential modeling of the mental states of others and is exhibited in few species other than humans, including chimpanzees (Pan troglodytes), stumptail macaques (Macaca arctoides), dogs (Canis familiaris), and budgerigars (Melopsittacus undulatus). Despite these comparative data,...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6875/version/1

3D models of lamprey corticoid receptor complexed with 11-deoxycortisol and deoxycorticosterone
Provedor de dados: 17
Autores: Michael E. Baker; Kayla Y. Uh; Paiyuam Asnaashari.
The serum of Atlantic sea lamprey, a basal vertebrate, contains two corticosteroids, 11-deoxycortisol and deoxycorticosterone.  Only 11-deoxycortisol has high affinity [Kd~3 nM] for the corticoid receptor [CR] in lamprey gill cytosol.  To investigate the binding of 11-deoxycortisol to the CR, we constructed 3D models of lamprey CR complexed with 11-deoxycortisol and deoxycorticosterone.  These 3D models reveal that Leu-220 and Met-299 in lamprey CR have contacts with the 17[alpha]-hydroxyl on 11-deoxycortisol.  Lamprey CR is the ancestor of the mineralocorticoid receptor [MR] and glucocorticoid receptor [GR].  Unlike human MR and human GR, the 3D model of lamprey CR finds a van der Waals contact between Cys-227 in helix 3 and Met-264 in helix 5.  Mutant...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6216/version/1

Enhancing Jatropha Productivity by Canopy Management
Provedor de dados: 17
Autores: 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 &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3700/version/1

Natural Selection of Paths in Networks
Provedor de dados: 17
Autores: Chrisantha Fernando; Vera Vasas; E&amp;#xf6;rs Szathm&amp;#xe1;ry; Philip Husbands.
We present a novel algorithm that exhibits natural selection of paths in a network. If each node and weighted directed edge has a unique identifier, a path in the network is defined as an ordered list of these unique identifiers. We take a population perspective and view each path as a genotype. If each node has a node phenotype then a path phenotype is defined as the list of node phenotypes in order of traversal. We show that given appropriate path traversal, weight change and structural plasticity rules, a path is a unit of evolution because it can exhibit multiplicative growth (i.e. change it&amp;#x2019;s probability of being traversed), and have variation and heredity. Thus, a unit of evolution need not be a spatially distinct physical individual. The...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5535/version/1

Assembling the Tree of Life in Europe (AToLE)
Provedor de dados: 17
Autores: Olaf R. P. Bininda-Emonds; Wieslaw  Bogdanowicz; Thomas Borsch; Frederic Delsuc; Alexandre  Hassanin; Ulf Jondelius; Gitte Petersen; Susanne S. Renner; Vincent Savolainen; Ole Seberg; Erik Smets; Alfried Vogler.
A network of scientists under the umbrella of &amp;#x27;Assembling the Tree of Life in Europe (AToLE)&amp;#x27; seeks funding under the FP7-Theme: Cooperation - Environment (including Climate Change and Biodiversity Conservation) programme of the European Commission.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2891/version/1

DNA^+Pro^: an Improved Progressive Multiple Sequence Alignment Algorithm for Evolutionary Analysis Using Combined DNA-Protein Sequences
Provedor de dados: 17
Autores: Xiaolong Wang; Shuang-yong  Xu; Deming  Gou.
Alignment of DNA and protein sequences is a basic tool in the study of evolutionary, structural and functional relationship among macromolecules. Present sequence alignment methods are somewhat error-prone, often producing systematic bias. Errors in sequence alignments sometimes lead to subsequent misinterpretation of evolutionary, structural and functional information in genes, proteins and genomes. In traditional sequence alignment algorithms, alignments of DNA and protein sequences are conducted separately. It has been long believed that the phylogenetic signal disappears more rapidly from DNA sequences than from encoded proteins. It is therefore generally preferable to align sequences at the amino acid level. Here we present a new...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4898/version/1

A Note On The Denisova Cave mtDNA Sequence
Provedor de dados: 17
Autores: Niccolo Caldararo.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5360/version/1

Speciation &amp;#x26; the origin of communities
Provedor de dados: 17
Autores: Philippe Desjardins-Proulx.
Patterns of biodiversity predicted by the neutral theory rely on a simple phenomenological model of speciation. To further investigate the effect of speciation on neutral biodiversity, we define the metacommunity as a system of populations exchanging migrants and use this framework to study allopatric &amp;#x26; parapatric speciation. We find that with realistic mutation rates, our metacommunity model driven by neutral processes cannot support more than a few species. Adding natural selection in the population genetics of speciation increases the number of species in the metacommunity but the level of diversity found in Barro Colorado Island is difficult to reach.
Tipo: Presentation
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6054/version/1

Lightning Talk: Biopython (bio) Geography Module
Provedor de dados: 17
Autores: Nicholas J. Matzke.
For Google Summer of Code 2009/NESCENT Phyloinformatics Summer of Code 2009, I built a Geography module for Biopython.  The purpose of the module is to search, download, and process biogeographical data from GBIF, much as Biopython currently accesses Genbank.  Application of the tool to a historical biogeography study on bivalves will be illustrated.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As required by Google Summer of Code and Biopython, the code is open access and is released under the Biopython License:&amp;#xd;&amp;#xa;&amp;#x22;http://www.biopython.org/DIST/LICENSE&amp;#x22;:http://www.biopython.org/DIST/LICENSE&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The module is described, and a tutorial is presented, on the Biopython...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4676/version/1

Over-Imitation in the Kalahari Desert and the Origins of Human Cultural Cognition
Provedor de dados: 17
Autores: Mark Nielsen; Keyan Tomaselli.
Children grow up in environments saturated with tools and objects which they must learn to use. One of the most efficient ways in which children do this is by imitating. Recent work has shown that, in contrast to non-human primates, when young children learn by imitating they focus more on reproducing the specific actions used than the actual outcomes achieved. From about 18 months of age children will routinely copy arbitrary and unnecessary actions. This puzzling behaviour is called &amp;#x27;over-imitation&amp;#x27;. By documenting similarities exhibited by children from a large, industrialised city and children from remote Bushman communities in southern Africa, we provide here the first indication that over-imitation is a universal human trait. We...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3049/version/1

Names on Nodes: Automating the Application of Taxonomic Names within a Phylogenetic Context
Provedor de dados: 17
Autores: T. Michael Keesey.
_Names on Nodes_^1^ is an open&amp;#x2011;source^2^ Flex application which utilizes a mathematical approach to automate the application of phylogenetically&amp;#x2011;defined names to phylogenetic hypotheses. Phylogenetic hypotheses are modeled as directed, acyclic graphs, and may be read from bioinformatics or graph files (NEXUS, NexML, Newick, and GraphML) or created de novo. Hypotheses may also be merged from multiple sources. _Names on Nodes_ stores hypotheses as MathML, an XML&amp;#x2011;based language for representing mathematical content and presentation. Phylogenetic definitions may be constructed using a visual editor and exported in MathML. Thus, it is possible to create a dictionary of defined names and automatically apply them to phylogenetic...
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4653/version/1

Some Computational Aspects of Essential Properties of Evolution and Life
Provedor de dados: 17
Autores: Hector Zenil; James A. R. Marshall.
While evolution has inspired algorithmic methods of heuristic optimisation, little has been done in the way of using concepts of computation to advance our understanding of salient aspects of biological evolution. We argue that under reasonable assumptions, interesting conclusions can be drawn that are of relevance to behavioural evolution. We will focus on two important features of life--robustness and fitness optimisation--which, we will argue, are related to algorithmic probability and to the thermodynamics of computation, subjects that may be capable of explaining and modelling key features of living organisms, and which can be used in understanding and formulating algorithms of evolutionary computation.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6867/version/1

Aggregation of Single Nucleotide Polymorphisms in a Human H5N1 Clade 2.2 Hemagglutinin
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Jeffery Tjaden; Kenneth C. Earhart; Marshall R. Monteville; Mona M. Aly; Moustafa M. Mansour; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Emad M. Labib; Ehab A. Ayoub; Abdelattar Arafa; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
The rapid evolution of the H5N1 serotype of avian influenza has been explained by a mechanism involving the selection of single nucleotide polymorphisms generated by copy errors.  The recent emergence of H5N1 Clade 2.2 in fifty countries, offered a unique opportunity to view the acquisition of new polymorphism in these evolving genomes.  We analyzed the H5N1 hemagglutinin gene from a fatal human case from Nigeria in 2007.  The newly emerged polymorphisms were present in diverse H5N1 isolates from the previous year.  The aggregation of these polymorphisms from clade 2.2 sub-clades was not supported by recent random mutations, and was most easily explained by recombination between closely related sequences.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/743/version/2

Signatures of spatial organizations &amp;#x2013; From the universe of proteins to the universe in general
Provedor de dados: 17
Autores: Aditya Mittal.
Pattern generation and recognition in 3-D space have been of wide interest in fields varying from atomic and molecular structures to organization of celestial objects. Our thoughts towards investigating patterns (and elucidation of geometrical rules) followed by a known number of points with specific or specified coordinates are guided by the assumption/belief that there must be some thermodynamic and/or kinetic basis leading to the organization of coordinates of the known points. In terms of biomolecular structures, the DNA double helix is one of the strongest examples of such structures with coordinates of atoms in the phosphate backbone and the side-chains provide a helical geometrical configuration. It needs to be appreciated (and emphasized) that,...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6038/version/1

Circadian Preference and Sexual Selection: A Novel Evolutionary Approach
Provedor de dados: 17
Autores: Davide Piffer.
Human sleep patterns differ across age groups and between males and females, and their association with age and gender suggest that they might have been the target of sexual selection during human evolutionary history. In this study, I will test the hypothesis that a phase-delayed circadian phase is a sexually selected trait in humans. A short version of the Horne and Ostberg questionnaire and a questionnaire on sexual behaviour were administered to 134 males and 140 females. A significant negative relationship was found between the MEQ score and the number of sexual partners among males, with evening types reporting more sexual partners than morning types. No significant relationship between females MEQ and number of sexual partners was found. Findings...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2964/version/1

Study of planktonic morphotype of the Abderaz Formation at type section, Iran
Provedor de dados: 17
Autores: Meysam Shafiee Ardestani.
Abderaz Formation at its type section with an age of Turonian-Early Campanian and a thickness of 300 m contains light grey shale and marl. The study of the planktonic foraminifera in isolated form led to differentiate three morphotype groups. The first group is characterized by trochospiral tests usually indicate shallow  waters, the second group contains forms with strong ornamentations and the primary keels representing mid waters and finally compact trochospiral tests with keels known as deep water indices are included in the third group. Studies on the morphotypes showed a regressive cycle for Abderaz Formation.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3189/version/1

Ustilago and the accidental domestication of maize
Provedor de dados: 17
Autores: Juan Pablo Martinez-Soriano; Katia Avina-Padilla.
Maize is the essential crop of the Americas. Maize appeared suddenly about 8,500 years ago as domesticated teosinte; however, there is no evidence (genetical, archaeological, linguistic or ethnobotanical) able to support a gradual transformation from the teosinte ear into the corn ear. Teosinte has never been cultivated by Americans, nor did they ever attempt to domesticate it. Its grains were not used as food, making unrealistic the assumption that prehispanics created something edible from seeds that were not so. Plant domestication is a slow process in almost every known crop but maize evolution might not be the case. Teosinte has a brittle cob, whereas maize forms solid ones that do not release their seeds 2. The latter are soft, while in teosinte they...
Tipo: Manuscript
Palavras-chave: Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3240/version/1

High Perceptual Load Makes Monocular Attention Different
Provedor de dados: 17
Autores: Dingyuan Tan.
Attention is a fundamental function of the human which is important in our daily life. Perceptual load is thought to play an important role in selective attention^1,2^. When perceptual load is high, the distracting information will be kept out of perception and will not affect us. When perceptual load is low, the distracting information will be processed deeply by us and will influence us^3^. However, most of the past research was concerned with binocular attention instead of monocular attention. In spite of the differences such as visual acuity^4^, stereopsis^5,6^ between binocular and monocular vision, there were few reports of their difference regarding to perceptual load which means more items and features in our research. Here we show their difference...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5166/version/1

Living unicellular eukaryote Tetrahymena pyriformis as a model for study of mitochondrial energetics in mammalian cells under conditions of reduced oxidative metabolism.
Provedor de dados: 17
Autores: Elena Mokhova.
Some &amp;#x201c;animal-like&amp;#x201d; protozoa are used instead of mammalian cells in diverse investigations.  _Tetrahymena pyriformis_ cells in stationary phase of growth and washed from oxidative substrates (_T.pyriformis_) function under conditions of reduced oxidative metabolism. To elucidate if _T.pyriformis_ can be applied as a model for mitochondrial energetics study in   mammalian cells during hibernation, the features of _T.pyriformis_ mitochondria were compared with that of liver mitochondria isolated from hibernating animals; the published earlier data were used. Based on the respiration recording and observation of Mito Tracker Red fluorescence in living _T.pyriformis_ we tentatively concluded that the mitochondrial electrical membrane...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4521/version/2

Phylontal: Using Phylogenies to Align Phenotype Ontologies
Provedor de dados: 17
Autores: Peter Midford.
Phylontal is a simple approach to generating alignments of ontologies or constructs based on controlled vocabularies that correspond to tips on a phylogeny.  The method requires only a downpass (tips to root) and thus constructing alternative alignments from multiple or uncertain phylogenies may be relatively inexpensive.
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4628/version/1

Human Transcript Database Search Showed Existence Of Extremely Short Introns
Provedor de dados: 17
Autores: Makoto Shimada; Noriko Haraguchi; Akila Mayeda.
Since pre-mRNA splicing is processed by a spliceosome that is a huge complex consists of RNAs and as many as 200 proteins, it is considered that minimum intron size is limited by molecular size of the spliceosome.  To understand splicing mechanism, we investigate human intron size distribution using annotated transcriptome database, H-InvDB.  Distribution of obtained intron length shows that there is a mode at 83 nt in length with 4049 transcripts and number of introns decreases drastically in shorter than 65 nt, where numbers of transcripts in each locus also decrease.  However, some introns less than 65 nt are observed, both shows high Codon Adaptation Index (CAI) and also observed orthologous transcripts in other mammals.  These suggests that there is a...
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5115/version/1

Balancing noise and plasticity in gene expression
Provedor de dados: 17
Autores: Djordje Bajic; Juan F. Poyatos.
Coupling the control of expression stochasticity (noise) with the capacity to expression change (plasticity) can constrain gene function and limit adaptation. Which factors contribute then to modulate this coupling? Transcription re-initiation is generally associated with coupling and this is commonly related to strong chromatin regulation. We alternatively show how strong regulation can however lead to plasticity uncorrelated to noise. The character of the regulation is also relevant, with plastic but noiseless genes usually subjected to broad expression activation whereas plastic and noisy genes experience targeted repression. This differential action is similarly noticed in how histones influence these genes. In contrast, we find that translational...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6729/version/1

ABC for Temporally Sampled Genetic Data
Provedor de dados: 17
Autores: Mark A. Beaumont.
ABC for Temporally Sampled Genetic Data
Tipo: Presentation
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5953/version/1

Understanding Consciousness: An Online Workshop on Contemporary Theories
Provedor de dados: 17
Autores: Alfredo Pereira Jr; Jonathan Edwards; Dietrich Lehmann; Chris Nunn; Arnold Trehub; Max Velmans.
An invited workshop on &amp;#x2018;Theories of Consciousness&amp;#x2019; was organized in the format of a Nature Network closed group during the second semester of 2009. There were presentations by each of 15 authors active in the field, followed by debate with other presenters and invitees. A week was allocated to each of the theories proposed; general discussion threads were also opened from time to time, as seemed appropriate. We (who had been participants in the workshop) offer here an account of the principal outcomes. It can be regarded as a contemporary, &amp;#x2018;state of the art&amp;#x2019; snapshot of thinking in this field.
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4348/version/1

On the origin of the mitochondrial genetic code: Towards a unified mathematical framework for the management of genetic information
Provedor de dados: 17
Autores: Diego Luis Gonzalez; Simone Giannerini; Rodolfo Rosa.
The origin of the genetic code represents one of the most challenging problems in molecular evolution. The genetic code is an important universal feature of extant organisms and indicates a common ancestry of different forms of life on earth. Known variants of the genetic code can be mainly divided in mitochondrial and nuclear classes. Here we provide a new insight on the origin of the mitochondrial genetic code: we found that its degeneracy distribution can be explained by using a mathematical approach recently developed for the description of the Euplotes nuclear variant of the genetic code. The results point to a primeval mitochondrial genetic code composed of four base codons, which we call tesserae, that, among other features, exhibit outstanding...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7136/version/1

Expanding the modern synthesis II: Formal perspectives on the inherent role of niche construction in fitness
Provedor de dados: 17
Autores: 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 &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5059/version/1

The Origin and Evolution of Viruses as Molecular Organisms
Provedor de dados: 17
Autores: Claudiu I. Bandea.
Viruses are the most abundant life forms and the repertoire of viral genes is greater than that of cellular genes. It is also evident that viruses have played a major role in driving cellular evolution, and yet, viruses are not part of mainstream biology, nor are they included in the Tree of Life. A reason for this major paradox in biology is the misleading dogma of viruses as viral particles and their enigmatic evolutionary origin. This article presents an alternative view about the nature of viruses based on their properties during the intracellular stage of their life cycle, when viruses express features comparable to those of many parasitic cellular species. Supporting this view about the nature of viruses is a novel hypothetical evolutionary model for...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3886/version/1

Networks, Extinction and Paleocommunity Food Webs
Provedor de dados: 17
Autores: Peter Roopnarine.
Food webs represent trophic interactions among species in communities. Those interactions both structure and are structured by species richness, ecological diversity, and evolutionary processes. Geological and macroevolutionary timescales are therefore important to the understanding of food web dynamics, and there is a need for the consideration of paleocommunity food webs. The fossil record presents challenges in this regard, but the problem can be approached with combinatoric analysis and network theory. This paper is an introduction to the aspects of those disciplines relevant to the study of paleo-food webs, and explores a probabilistic and numerical approach.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4433/version/2

On biological homochirality
Provedor de dados: 17
Autores: Rodrick Wallace.
Generalizing Landau&amp;#x27;s spontaneous symmetry breaking arguments using the standard groupoid approach to stereochemistry allows reconsideration of the origin of biological homochirality. On Earth, limited metabolic free energy density may have served as a low temperature analog to &amp;#x27;freeze&amp;#x27; the system into the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process licked in this initial condition. Astrobiological outcomes, in the presence of higher initial metabolic free energy densities, could well be considerably richer, perhaps of mixed chirality. One result would be a...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3902/version/1

Essay: On the close relationship between speciation, inbreeding and recessive mutations.
Provedor de dados: 17
Autores: Etienne Joly.
Whilst the principle of adaptive evolution is unanimously recognised as being caused by the process of natural selection favouring the survival and/or reproduction of individuals having acquired new advantageous traits, a consensus has proven much harder to find regarding the actual origin of species. Indeed, since speciation corresponds to the establishment of reproductive barriers, it is difficult to see how it could bring a selective advantage because it amounts to a restriction in the opportunities to breed with as many and/or as diverse partners as possible. In this regard, Darwin himself did not believe that reproductive barriers could be selected for, and today most evolutionary biologists still believe that speciation can only occur through a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5003/version/1

The Evolutionary Seesaw: Origins of biodiversity?
Provedor de dados: 17
Autores: Carl Boettiger.
I consider the problem of evolutionary branching in adaptive dynamics without applying the limits of separation of timescales between ecological and evolutionary processes.  I derive expressions for the waiting time for a branching event to occur and survive in terms of both ecological and evolutionary parameters, and show  how demographic stochasticity alone can result in the frequent failure of adaptive branching.
Tipo: Presentation
Palavras-chave: Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6852/version/1

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Provedor de dados: 17
Autores: I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn &amp;#x2013;algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata.  Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7083/version/2

Dating the cyanobacterial ancestor of the chloroplast
Provedor de dados: 17
Autores: Luisa Falcon; Susana Magallon; Amanda Castillo.
Cyanobacteria have played a pivotal role in the history of life on Earth being the first organism to carry out oxygenic photosynthesis, which changed atmospheric chemistry and allowed the evolution of Eukarya. Chloroplasts are the cellular organelles of photoautotrophic eukaryotes in which photosynthesis is conducted. Although the initial suggestion from Mereschkowsky (1905) that cyanobacteria are the ancestors of chloroplasts was greeted with skepticism, the idea is now widely accepted. Here we attempt to resolve and date the cyanobacterial ancestry of the chloroplast using phylogenetic analysis and molecular clocks, because until now, the long-standing question of, from which, among the vast diversity of cyanobacteria, did chloroplasts evolve, has not...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3696/version/1

Novel determinants describe chaperonin substrate proteins
Provedor de dados: 17
Autores: Emanuele Raineri; Paolo Ribeca; Luis Serrano; Tobias Maier.
Molecular chaperones ensure that their substrate proteins reach the functional native state and prevent their aggregation. The bacterial GroEL/ES chaperonin system is understood in great detail on a structural, mechanistic and functional level. Its substrate proteins in E. coli have been identified and characterized. However, a long standing and yet unresolved question in the field is: what makes a protein a chaperone substrate?&amp;#xd;&amp;#xa;Here we demonstrate with a bioinformatics-based approach that a simple set of criteria is sufficient to describe the GroEL substrate proteome to unprecedented accuracy. We define two novel parameters differentiating GroEL substrates from other cellular proteins: evolutionary rate and hydrophobicity. We demonstrate...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2968/version/2

Natural Biomolecules from Marine Snail Telescopium telescopium and structure of its sperm: A Phylogenetic Study
Provedor de dados: 17
Autores: Uttam Datta; Manik Lal Hembram; Subhasis Roy; Prasenjit Mukherjee.
Abstract:&amp;#xd;&amp;#xa;Biochemical analysis of the cytosol fraction isolated from the ovotestis / spermatheca glands of marine mollusc Telescopium telescopium and it&amp;#x2019;s sperm microtubular structure revealed that relatively similar biomolecules like different enzymes,  hormones, minerals and structures of the sperm  are also exist in humans. Moreover, antiserum of the cytosol fraction was found to cross-react with the human sperm antigen indicated presence of a common sperm surface antigenicity between these two diversified species. These findings might support and / or hypothesize about the origin and diversification of the vertebrate molecules from its ancestral form (s) from the invertebrates, and basic physiological functions of these...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3386/version/1

Extending the Modern Synthesis: The evolution of ecosystems
Provedor de dados: 17
Autores: Rodrick Wallace.
The Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction, and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of communication theory, that instantiates the punctuated dynamic relations of organisms with their embedding environments, including the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis, making application to both relatively rapid evolutionary punctuated equilibrium and to the conservation of ecological interactions across deep evolutionary time.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4496/version/2

DNA Sequence Evolution through Integral Value Transformations
Provedor de dados: 17
Autores: Sk Sarif Hassan; Pabitra Pal Choudhury; Ranita Guha; Shantanav Chakraborty; Arunava Goswami.
In deciphering the DNA structures, evolutions and functions, Cellular Automata (CA) do have a significant role. DNA can be thought of as a one-dimensional multi-state CA, more precisely four states of CA namely A, T, C, and G which can be taken as  numerals 0, 1, 2 and 3. Earlier, G.Ch. Sirakoulis et al reported the DNA structure, evolution and function through quaternary logic one dimensional CA and the authors have found the simulation results of DNA evolutions with the help of only four linear CA rules. The DNA sequences which are produced through the CA evolutions, however, are seen by our research team not to exist in the established databases of various genomes although the initial seed (initial global state of CA) was taken from the database. This...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5729/version/1

A general model of continuous character evolution
Provedor de dados: 17
Autores: Carl Boettiger.
I present a general model for continuous character evolution, review some of the common challenges that emerge in such complex methods and review strategies for handling them.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6080/version/1

Two cases of mother-infant cannibalism in orangutans
Provedor de dados: 17
Autores: David F. Dellatore; C. D. Waitt; Ivona Foitova.
Two unrelated female orangutans (_Pongo abelii_) were observed on different occasions cannibalizing the remains of their infants, a behavior never before reported in apes. Both orangutans are free-ranging ex-captive individuals in an area of forest which also hosts large numbers of visiting tourists. The cannibalism events appear to have been aberrant behavior, perhaps due to stress and the environmental conditions of the area.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1998/version/1

Photometric properties of microfossil shells
Provedor de dados: 17
Autores: Stergios Zarkogiannis; Ruediger Henrich.
The chromatic characteristics of fossil planktonic foraminifera were measured with the use of an opticoelectric microscope and a new aspect of their nature has been revealed.
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4037/version/1

Earth History and the Evolution of Caribbean Bats
Provedor de dados: 17
Autores: Liliana D&amp;#xe1;valos.
Although the natural history of the Caribbean is better understood now than ever before, a general biogeographic explanation for the peculiar faunal composition of the islands remains elusive. New molecular phylogenetic and divergence analyses presented here show that dispersal and diversification in Caribbean bats are synchronous with sea level drops during inter-stage transitions in the Miocene. The phylogenies indicate that several continental bat species descended from West Indian ancestors, as the exceptionally low sea level of the Miocene transitions allowed for two-way biotic exchange between the islands and the continent. These results suggest a common mechanism underlies colonization and subsequent speciation in the Caribbean, and underscore the...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3901/version/1

Modeling, Simulation and Application of Bacterial Transduction in Genetic Algorithms
Provedor de dados: 17
Autores: Carlos Perales-Gravan; Javier de Vicente Buendia; Rafael Lahoz-Beltra.
At present, all methods in Evolutionary Computation are bioinspired in the fundamental principles of neo-Darwinism as well as on a vertical gene transfer. Thus, on a mechanism in which an organism receives genetic material from its ancestor. Horizontal, lateral or cross-population gene transfer is any process in which an organism transfers a genetic segment to another one that is not its offspring. Virus transduction is one of the key mechanisms of horizontal gene propagation in microorganism (e.g. bacteria). In the present paper, we model and simulate a transduction operator, exploring a possible role and usefulness of transduction in a genetic algorithm. The genetic algorithm including transduction has been named PETRI (abbreviation of Promoting...
Tipo: Manuscript
Palavras-chave: Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3732/version/1

Molecular evolution of RRM-containing proteins and glycine-rich RNA-binding proteins in plants
Provedor de dados: 17
Autores: Judith L. Gomez-Porras; Martin Lewinski; Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Dorothee Staiger.
*Abstract*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Background:*&amp;#xd;&amp;#xa;In angiosperms, RNA-binding proteins with an RNA recognition motif (RRM)-type RNA interaction domain play an important role in developmental and environmental responses. Despite their pivotal role, a comprehensive analysis of their number and diversity has only been performed in _Arabidopsis_ so far.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Results:*&amp;#xd;&amp;#xa;Here we present a detailed phylogenetic analysis of RRM-containing proteins in plants, the red algae _Cyanidioschyzon merolae_ and cyanobacteria. We identified two major events during the diversification of the RRM in plants, one at the emergence of green plants, and the other at the water-to-land transition. We focused on...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5970/version/1

11[beta]-hydroxysteroid dehydrogenase-type 2 evolved from an ancestral 17[beta]-hydroxysteroid dehydrogenase-type 2
Provedor de dados: 17
Autores: Michael E. Baker.
11[beta]-hydroxysteroid dehydrogenase type-2 (11[beta]-HSD2) regulates the local concentration of cortisol that can activate the glucocorticoid receptor and mineralocorticoid receptor, as well as the concentration of 11-keto-testosterone, the active androgen in fish.  Similarly, 17[beta]-HSD2 regulates the levels of testosterone and estradiol that activate the androgen receptor and estrogen receptor, respectively.  Interestingly, although human 11[beta]-HSD2 and 17[beta]-HSD2 act at different positions on different steroids, these enzymes are paralogs.  Despite the physiological importance of 11[beta]-HSD2 and 17[beta]-HSD2, details of their origins and divergence from a common ancestor are not known.  An opportunity to understand their evolution is...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4649/version/1

Cortical Bone Ontogeny: Activity, Nutritional Stress and Archaeology
Provedor de dados: 17
Autores: Gwen Robbins.
This poster introduces the idea that femoral compact bone growth and development demonstrates a very different pattern among infants and children in a contemporary sample of well-nourished active children versus archaeological samples of stressed, malnourished children.
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2470/version/1

Evidence of Massive Horizontal Gene Transfer Between Humans and Plasmodium vivax
Provedor de dados: 17
Autores: Daniel Z. Bar.
The horizontal transfer of DNA between different organisms is a major force shaping the genomes of prokaryotes, but is considered to have a minor role in eukaryotes, with only a handful of known examples, mostly of limited size. The nucleotide databases of Plasmodium genomes were divided into small fragments and compared to human, as well as to other Plasmodium genomes.  This computational approach revealed that the Plasmodium vivax genome is interlaced with multiple DNA fragments that were likely acquired via horizontal transfer from humans. Contamination is a major concern in such studies; moreover, it must be determined if the identified homologies might be due to chance. These reservations are supported by the fact that the identified homologous...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5690/version/1

Crosstalk and the spectrum of biological global broadcasts: Toward generalization of the Baars consciousness model across physiological subsystems
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognitive biological phenomena are recognized as necessarily having &amp;#x27;dual&amp;#x27; information sources, it is easy to show that the information theory chain rule implies isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to dynamic global broadcasts of interacting cognitive biological processes analogous to, but slower than, consciousness, itself included within the paradigm. The argument is closely analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Immunology; Molecular Cell Biology; Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6898/version/1

NamesforLife Semantic Resolution Services for the Life Sciences
Provedor de dados: 17
Autores: Charles T. Parker; Dorothea K. Taylor; Kara Mannor; Sarah Wigley; Nicole Osier; Catherine Lyons; George M. Garrity.
A major challenge in bioinformatics, life sciences, and medicine is using correct and informative names. While this sounds simple enough, many different naming conventions exist in the life sciences and medicine that may be either complementary or competitive with other naming conventions. For a variety of reasons, proper names are not always used, leading to an accumulated semantic ambiguity that readers of the literature and end users of databases are left to resolve on their own. This ambiguity is a growing problem and the biocuration community is aware of its consequences. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To assist those confronted with ambiguous names (which not only includes researchers but clinicians, manufacturers, patent attorneys, and others...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5137/version/1

Thermal characterization of Plasmodium falciparum species specific proteins in Indian geographical area.
Provedor de dados: 17
Autores: Mohit Bhardwaj; Leena Bharadwaj; Kritika Trigunayat; Madan Mohan Trigunayat.
The paper reveals thermal characteristics of _P.falciparum_ species specific proteins. These proteins determine why _P. vivex_ species are dominant over _P.falciparum_ in Indian geographical area. Outside human host plasmodium parasite survives in poikilothermal mosquitoes. Climatic temperature conditions greatly affect native state of _P.falciparum_ species specific proteins in mosquitoes. Study of climatic temperature conditions in Indian geographical area reveals that Pfsd protein for _Plasmodium falciparum_ can remain in native state between &amp;#x2265;7 degree centigrade and &amp;#x2264;42.6 degree centigrade temperature conditions. While their best optimum functions (activity) was noted between 25.3 degree centigrade to 33degree centigrade. Pfsd...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4565/version/1

Investigating prostate cancer tumour-stroma interactions - clinical and biological insights from an evolutionary game
Provedor de dados: 17
Autores: David Basanta; Jacob G. Scott; Mayer N. Fishman; Gustavo E. Ayala; Simon W. Hayward; Alexander R. A. Anderson.
BACKGROUND: Tumours are made up of a mixed population of different types of cells that include normal structures as well as ones associated with the malignancy, and there are multiple interactions between the malignant cells and the local microenvironment. These intercellular interactions, modulated by the microenvironment, effect tumour progression and represent a largely under appreciated therapeutic target. We use observations of primary tumor biology from prostate cancer to extrapolate a mathematical model: specifically; it has been observed that in prostate cancer three disparate cellular outcomes predominate: (i) the tumour remains well differentiated and clinically indolent - in this case the local stromal cells may act to restrain the growth of the...
Tipo: Manuscript
Palavras-chave: Cancer; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6385/version/1

A logistic regression model for microalbuminuria prediction in overweight male population
Provedor de dados: 17
Autores: BaoDe Chen; WeiYi Xu; Chen Yu; ZhenYun Ni; XueFen Li; DaWei Cui.
Background: Obesity promotes progression to microalbuminuria and increases the risk of chronic kidney disease. Current protocols of screening microalbuminuria are not recommended for the overweight or obese.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Design and Methods: A cross-sectional study was conducted. The relationship between metabolic risk factors and microalbuminuria was investigated. A regression model based on metabolic risk factors was developed and evaluated for predicting microalbuminuria in the overweight or obese.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: The prevalence of MA reached up to 17.6% in Chinese overweight men. Obesity, hypertension, hyperglycemia and hyperuricemia were the important risk factors for microalbuminuria in the overweight....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5372/version/1

Assessment Of Response To Heart Failure Therapy: Ventricular Volume Changes Versus Shape Changes
Provedor de dados: 17
Autores: Srilakshmi Adhyapak; V.Rao Parachuri.
The prolate ellipsoid left ventricular geometry is crucial for its unique contraction and relaxation patterns. Perturbations in optimal cardiac function preceding overt heart failure ensue when this ellipsoid shape assumes a more spherical configuration. This stage of spherical configuration, prior to overt dilatation, is when therapy should be intensified. The dynamic shape changes during the cardiac cycle of systole and diastole in valvular regurgitations when ventricular volumes are within normal range have proved that shape changes are clearly dissociated from volume changes in the early stages. In the scenario of advanced heart failure, several therapeutic interventions have been tried with variable success. These therapies aim at decreasing the...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6707/version/1

Altruism among relatives and non-relatives
Provedor de dados: 17
Autores: Howard Rachlin; Bryan A. Jones.
The amount of their own monetary reward that undergraduate participants claimed they were willing to forgo, in order to give $75 to another person, decreased hyperbolically as social distance increased between the participant and the other person. Relatives tended to be ranked at closer social distances than were non-relatives. However, even at the same social distance, participants were willing to forgo significantly more money for the benefit of relatives than for the benefit of non-relatives. These results imply that altruism is determined by factors in addition to social distance.
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1565/version/1

Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA)
Provedor de dados: 17
Autores: Xiaolong Wang; Yu  Fu; Yue  Zhao; Qi  Wang; Chandra Sekhar  Pedamallu; Shuang-yong  Xu; Yingbo  Niu; Jingjie  Hu.
Based on molecular clock hypothesis, and neutral theory of molecular evolution, molecular phylogenies have been widely used for inferring evolutionary history of organisms and individual genes. Traditionally, alignments and phylogeny trees of proteins and their coding DNA sequences are constructed separately, thus often different conclusions were drawn. Here we present a new strategy for sequence alignment and phylogenetic tree reconstruction, codon and amino acid unified sequence alignment (CAUSA), which aligns DNA and protein sequences and draw phylogenetic trees in a unified manner. We demonstrated that CAUSA improves both the accuracy of multiple sequence alignments and phylogenetic trees by solving a variety of molecular evolutionary problems in...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6730/version/1

Molecular evidence for the hadrosaur B. canadensis as an outgroup to a clade containing the dinosaur T. rex and birds
Provedor de dados: 17
Autores: Shi Huang.
Molecular analysis of collagen sequences from an 80 million year old hadrosaur _B. canadensis_ and a 68 million year old dinosaur _T. rex_ suggest strongly that _B. canadensis_ is an outgroup to a clade containing _T. rex_ and birds, fully consistent with the well-established phylogeny based on morphological analyses of fossils.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3255/version/1

When Spandrels Become Arches: Neural crosstalk and the evolution of consciousness
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognition is recognized as having a &amp;#x27;dual&amp;#x27; information source, the information theory chain rule implies that isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to the rapid, shifting global neural broadcasts of consciousness. The argument is quite analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in neurons and neuronal subsystems. Astrobiological implications are obvious.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6115/version/2

Extending Astrobiology: Consciousness and Culture
Provedor de dados: 17
Autores: Rodrick Wallace.
The Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not likely to have followed the particular, highly contingent and path-dependent, evolutionary trajectory found on Earth. Are many alien organisms likely to be conscious in ways that we would recognize? Almost certainly. Will some develop high order technology? Less likely, but still fairly probable. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The argument is fairly direct.
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5286/version/2

Evolution as a language that speaks itself
Provedor de dados: 17
Autores: Rodrick Wallace.
The &amp;#x27;self-referential&amp;#x27; character of evolutionary process noted by Goldenfeld and Woese (2010) can be restated through a &amp;#x27;language&amp;#x27; model in which genes, gene expression, and environment are represented as interacting information sources. The larger, composite, source that characterizes the high probability evolutionary paths then becomes, in a real sense, a language that speaks itself. The approach represents a significant extension of nonequilibrium condensed matter formalism in which the asymptotic limit theorems of information theory beat back the mathematical thicket a full step, providing necessary, but not sufficient, conditions for punctuated evolutionary transitions that can themselves be expressed as highly...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5339/version/1

An insight into the kinships of the fungi
Provedor de dados: 17
Autores: Riddhi Datta; Joy Sarkar; Krishnendu  Acharya.
The evolutionary origin of fungi is important in determining the phylogenetic relationships between fungi, animals and plants. However, determining the true relationship of fungi has been somewhat difficult owing to their simple morphology and presence of convergent characters. With the advent of newer molecular techniques, analysis of conserved protein sequences, cytochrome systems, mitochondrial and nuclear genetic material and rRNAs are being employed in elucidating   phylogenetic kinships among the eukaryotes. These emerging evidences suggest that the derivation of the fungi from plants or algae would require more evolutionary changes than its derivation from protozoa, the unicellular ancestor of the animals. To gain an overview of the current state of...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7095/version/1

Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing Competences of Viruses
Provedor de dados: 17
Autores: 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

Frequency-dependent selection predicts patterns of radiations and biodiversity
Provedor de dados: 17
Autores: Carlos Melian; David Alonso; Diego Vazquez; James Regetz; Stefano Allesina.
Most empirical studies support a decline in speciation rates through time, although evidence for constant speciation rates also exists. Declining rates have been explained by invoking niche-filling processes, whereas constant rates have been attributed to non-adaptive processes such as sexual selection, mutation, and dispersal. Trends in speciation rate and the processes underlying it remain unclear, representing a critical information gap in understanding patterns of global diversity. Here we show that the speciation rate is driven by frequency dependent selection. We used a frequency-dependent and DNA sequence-based model of populations and genetic-distance-based speciation, in the absence of adaptation to ecological niches. We tested the...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3752/version/1

Evolution signatures in genome network properties
Provedor de dados: 17
Autores: Rita de Almeida; Leonardo Brunnet; Jos&amp;#xe9; Luiz Rybarczyk-Filho; Ricardo Ferreira; Jose Claudio Moreira; Mauro Castro; Rodrigo Dalmolin.
Genomes maybe organized as networks where protein-protein association plays the role of network links. The resulting networks are far from being random and their topological properties are a consequence of the underlying mechanisms for genome evolution. Considering data on protein-protein association networks from STRING database, we present experimental evidence that degree distribution is not scale free, presenting an increased probability for high degree nodes. We also show that the degree distribution approaches a scale invariant state as the number of genes in the network increases, although real genomes still present finite size effects. Based on the experimental evidence unveiled by these data analyses, we propose a simulation model for genome...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6653/version/1

Circadian Preference and Sexual Selection: A Novel Evolutionary Approach
Provedor de dados: 17
Autores: Davide Piffer.
Human sleep patterns differ across age groups and between males and females, and their association with age and gender suggest that they might have been the target of sexual selection during human evolutionary history. In this study, I will test the hypothesis that a phase-delayed circadian phase is a sexually selected trait in humans. A short version of the Horne and Ostberg questionnaire and a questionnaire on sexual behaviour were administered to 134 males and 140 females. A significant negative relationship was found between the MEQ score and the number of sexual partners among males, with evening types reporting more sexual partners than morning types. No significant relationship between females MEQ and number of sexual partners was found. Findings...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/2964/version/2

Why are women smaller than men? When anthropology meets evolutionary biology
Provedor de dados: 17
Autores: Priscille Touraille; Pierre-Henri Gouyon.
There are large variations of size among humans but in all populations, men are larger on average than women. For most biologists this fact can be easily explained by the same processes that explain the size dimorphism in large mammals in general and in apes in particular. Due to fights between males for the possession of females, sexual selection has favoured bigger males. Indeed, this factor certainly explains why males are selected for being large but lets aside the question of selection on the female side. Actually, it has been shown that larger females are also favoured by natural selection. This is particularly relevant for women because their probability of dying when giving birth is then reduced. In this paper, the common view that size dimorphism...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1832/version/1

Deciphering the genome structure and paleohistory of _Theobroma cacao_
Provedor de dados: 17
Autores: Xavier Argout; Jerome Salse; Jean Marc Aury; Gaetan Droc; Jerome Gouzy; Mathilde Allegre; Cristian Chaparro; Thierry Legavre; Mark Guiltinan; Siela Maximova; Michael Abrouk; Florent Murat; Olivier Fouet; Julie Poulain; Manuel Ruiz; Yolande Roguet; Maguy Rodier-Goud; Jose Fernandes Barbosa-Neto; Francois Sabot; Dave Kudrna; Jetty Siva S. Ammiraju; Stephan C. Schuster; John E. Carlson; Erika Sallet; Schiex T.; Anne Dievart; Melissa Kramer; Laura Gelley; Zi Sh; Aur&amp;#xe9;lie B&amp;#xe9;rard; Christopher Viot; Michel Boccara; Ange Marie Risterucci; Valentin Guignon; Xavier Sabau; Michael Axtell; Zhaorong Ma; Yufan Zhang; Spencer Brown; Mickael Bourge; Wolfgang Golser; Xiang Song; Didier Clement; Ronan Rivalan; Mathias Tahi; Joseph Moroh Akaza; Bertrand Pitollat; Karina Gramacho; Ang&amp;#xe9;lique D&amp;#x2019;Hont; Dominique Brunel; Diogenes Infante; Ismael Kebe; Pierre Costet; Rod Wing; W.  Richard McCombie; Emmanuel Guiderdoni; Francis Quetier; Olivier Panaud; Patrick Wincker; Stephanie Sidibe-Bocs; Claire Lanaud.
We sequenced and assembled the genome of _Theobroma cacao_, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 _T. cacao_ chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for _T. cacao_ disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten _T. cacao_ chromosomes were shaped from an ancestor through eleven chromosome...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Plant Biology; Evolutionary Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4908/version/1

Extreme energy lability in human children: An overlooked and central aspect of human biology
Provedor de dados: 17
Autores: John Skoyles.
A four year old child devotes half their total energy expenditure (TEE) to their brains. Even by 10 years-of-age it is still 30% (compared to an adult&amp;#x2019;s &amp;#x2248;12%). This extreme energy use results from a high brain/body size ratio &amp;#x2013; combined with a doubling of cerebral gray matter energy utilization (due to synaptic exuberance during cognitive neuromaturation). &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;With extreme energy expenditure goes extreme vulnerability to hypoglycemia: (1) children become hypoglycemic after 24-36 hours of fast (compared to 60-72 hours in adults), and (2) their brains suffer neurological impairment (shown in disrupted P300 potentials) at a lower decrease in plasma glucose: 3.6 - 4.2 mmol L-1 in children rather...
Tipo: Presentation
Palavras-chave: Developmental Biology; Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7097/version/1

The Dryad Digital Repository: Published evolutionary data as part of the greater data ecosystem
Provedor de dados: 17
Autores: Todd Vision.
Here we describe the motivation and workings of Dryad, a digital repository for data underlying published articles in the biosciences, that grew out of a grassroots effort to support a joint data archiving policy adopted by a consortium of journals in ecology and evolutionary biology.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4595/version/1

The existence of species rests on a metastable equilibrium  between inbreeding and outbreeding
Provedor de dados: 17
Autores: Etienne Joly.
Background: Speciation corresponds to the progressive establishment of reproductive barriers between groups of individuals derived from an ancestral stock. Since Darwin did not believe that reproductive barriers could be selected for, he proposed that most events of speciation would occur through a process of separation and divergence, and this point of view is still shared by most evolutionary biologists today. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: I do, however, contend that, if so much speciation occurs, it must result from a process of natural selection, whereby it is advantageous for individuals to reproduce preferentially within a group and reduce their breeding with the rest of the population, leading to a model whereby new species arise not...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5003/version/4

Positive Darwinian Selection And The Birth Of An Olfactory Receptor Clade In Teleost Fish
Provedor de dados: 17
Autores: Ashiq Hussain; Luis Saraiva; Sigrun Korsching.
Trace amine-associated receptors (TAARs) in mammals recently have been shown to function as olfactory receptors. We have delineated the taar gene family in jawless, cartilaginous and bony fish (zero, two, and more than hundred genes, respectively). We conclude that taar genes are evolutionary much younger than the related OR and ORA/V1R olfactory receptor families, which are present already in lamprey, a jawless vertebrate. The two cartilaginous fish genes appear to be ancestral for two taar classes, each with mammalian and bony fish (teleost) representatives. Unexpectedly, a whole new clade, class III, of taar genes originated even later, within the teleost lineage. Taar genes from all three classes are expressed in subsets of zebrafish olfactory receptor...
Tipo: Poster
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6448/version/1

Variety in evolutionary strategies favours biodiversity in habitats of moderate productivity
Provedor de dados: 17
Autores: Simon Pierce.
The mechanism whereby biodiversity varies between habitats differing in productivity is a missing link between ecological and evolutionary theory with vital implications for biodiversity conservation, management and the assessment of ecosystem services. A unimodal, humped-back relationship, with biodiversity greatest at intermediate productivities, is evident when plant, animal and microbial communities are compared across productivities in nature. However, the mechanistic, evolutionary basis of this observation remains enigmatic. We show, for natural and semi-natural plant communities across a range of bioclimatic zones, that biodiversity is greatest where communities include species with widely divergent values for phenotypic traits involved in resource...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6618/version/1

Can ABC be Used for Model Selection?
Provedor de dados: 17
Autores: Xavier  Didelot; Rich  Everitt; Adam  Johansen; Dan  Lawson.
Over the past ten years, Approximate Bayesian Computation (ABC) has become hugely popular to estimate the parameters of a model when the likelihood function cannot be computed in a reasonable amount of time. ABC can in principle be used also to perform Bayesian model comparison, but this raises the  question of which summary statistic should be used for such applications. Here we present a general method for constructing a summary statistic that is sufficient for the model choice problem. We apply this construction to models from the exponential family. Unfortunately, in more complex models, our construct often results in statistics with too high dimensionality to use in ABC. We therefore discuss the possibility of applying ABC with non-sufficient...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5955/version/1

Effective Phylogenetic Compression with TreeZip
Provedor de dados: 17
Autores: Suzanne J. Matthews; SeungJin Sul; Tiffani L. Williams.
Phylogenetic trees are family trees that represent the relationships between a group of organisms, or taxa. The most popular techniques for reconstructing phylogenetic trees intelligently navigate an exponentially-sized tree space by solving NP-hard optimization problems that that best hypothesize the evolutionary history for a given set of taxa. Instead of reconstructing a single tree, these heuristics often return tens to hundreds of thousands of trees that represent equally-plausible hypotheses for how the taxa of interest evolved from a common ancestor. As biologists attempt to reconstruct increasingly larger phylogenies, these tree collections only continue to grow in size. To combat the cost of storage and to facilitate the transfer of these large...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4613/version/1

Molecular Models of DNA Structures and Dynamics: Principles, Techniques and Applications
Provedor de dados: 17
Autores: I. C. Baianu.
Molecular models of DNA structures are representations of the molecular geometry and topology of Deoxyribonucleic acid (DNA) molecules using one of several means, such as: closely packed spheres (CPK models) made of plastic, metal wires for &amp;#x27;skeletal models&amp;#x27;, graphic computations and animations by computers, artistic rendering, and so on, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7075/version/1

Music can reduce cognitive dissonance
Provedor de dados: 17
Autores: Nobuo  Masataka; Leonid Perlovsky.
The fundamental cognitive functions of music in the brain have not been known and evolutionary reasons for musical abilities seem mysterious. A recent hypothesis suggested that a fundamental function of music has been to help mitigating cognitive dissonances. A cognitive dissonance is &amp;#x22;a discomfort caused by holding conflicting cognitions&amp;#x22; simultaneously; it usually leads to devaluation of conflicting knowledge. Since every concept implies some degree of contradictions to other knowledge, unmitigated cognitive dissonances could prevent evolution of cognition. Thus music might be fundamental for the evolution of cognition. Here we provide experimental confirmation of this hypothesis using a classical paradigm known to induce a cognitive...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7080/version/1

Universal Features in the Genome-level Evolution of Protein Domains
Provedor de dados: 17
Autores: Marco Cosentino Lagomarsino; Alessandro L. Sellerio; Philip D. Heijning; Bruno Bassetti.
Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity.  Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are probabilities of duplication, innovation, and loss of domains. However, no one so far has addressed the issue that these distributions follow definite trends depending on protein-coding genome size only.  We present a stochastic duplication/innovation model, falling in the class of so-called Chinese Restaurant Processes, able to explain this feature of the data.  Using only two universal parameters, related to a minimal number of domains and to the relative weight of innovation to duplication, the model reproduces two...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1376/version/2

ABC for ancestral inference
Provedor de dados: 17
Autores: Richard  Wilkinson; Simon  Tavare.
ABC for ancestral inference
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5963/version/1

Comment to &amp;#x22;Endogenous Viral Etiology of Prion Diseases&amp;#x22;
Provedor de dados: 17
Autores: Claudiu Bandea.
This note is intended as a comment to a paper in Nature Precedings entitled &amp;#x22;Endogenous viral etiology of prion diseases&amp;#x22;:http://precedings.nature.com/documents/3887/version/1 . Because it contains illustrations that could not be displayed in the comments section of that paper, I&amp;#x2019;m posting this comment here as a PDF document.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Neuroscience; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4101/version/1

Deciphering the phylogenetic history of neuroserpin orthologs  across metazoans by analysis of synteny and rare genomic characters
Provedor de dados: 17
Autores: Abhishek Kumar; Hermann Ragg.
The superfamily of serine proteinase inhibitors (serpins) is involved in wide arrays of fundamental biological processes such as blood coagulation, complement activation, fibrinolysis, angiogenesis, inflammation and tumor suppression. The average protein size of a serpin family member is 350-400 amino acids, but gene structure varies in terms of number and position of exons and introns. All known serpins can be grouped into 16 clades and 10 orphan sequences. Vertebrate serpins can be conveniently classified into six sub-groups, based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels.&amp;#xd;&amp;#xa;The objective of this study was to elucidate the phylogenetic kinships of serpins involved in...
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2496/version/1

On the close relationship between speciation, inbreeding and recessive mutations.
Provedor de dados: 17
Autores: Etienne Joly.
Whilst the principle of adaptive evolution is unanimously recognised as being caused by the process of natural selection favouring the survival and/or reproduction of individuals having acquired new advantageous traits, a consensus has proven much harder to find regarding the actual origin of species. Indeed, since speciation corresponds to the establishment of reproductive barriers, it is difficult to see how it could bring a selective advantage because it amounts to a restriction in the opportunities to breed with as many and/or as diverse partners as possible. In this regard, Darwin himself did not believe that reproductive barriers could be selected for, and today most evolutionary biologists still believe that speciation can only occur through a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5003/version/3

EvolveAGene 3: A DNA coding sequence evolution simulation program
Provedor de dados: 17
Autores: Barry G. Hall.
EvolveAGene 3 is a realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions, including variable regions of selection intensity within the sequence and variation in intensity of selection over branches.  Variation includes base substitutions, insertions and deletions.  Output includes a log file,  the true tree and both unaligned coding sequence and protein sequences and the true DNA and protein alignments.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1230/version/1

EvoIO: Community-driven standards for sustainable interoperability
Provedor de dados: 17
Autores: Arlin Stoltzfus; Karen Cranston; Hilmar Lapp; Sheldon McKay; Enrico Pontelli; Rutger Vos; Nico Cellinese.
Interoperability is the property that allows systems to work together independent of who created them, or how or for what purpose they were implemented. It is crucial for aggregating data from different online resources and for integrating different kinds of data. Interoperability is based on effective standards that become and remain broadly adopted. We argue that to develop and apply such standards for evolutionary and biodiversity data sustainably, we need a community-driven, open, and participatory approach. With the goal to build such an approach, the EvoIO collaboration emerged in 2009 from several NESCent-sponsored activities.  EvoIO aims to be a nucleating center for developing, applying and disseminating interoperability technology that connects...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4588/version/1

TreeBASE2: Rise of the Machines
Provedor de dados: 17
Autores: Rutger A. Vos; Hilmar Lapp; William H. Piel; Val Tannen.
TreeBASE is a public repository of peer-reviewed phylogenetic knowledge. Researchers submit their results to TreeBASE when they are writing a manuscript based on them for publication in a suitable journal. The submitted data are assigned permanent, unique identifiers and web addresses that authors can refer to in their article. Anyone can locate and access the data once the study has been published by TreeBASE and by the targeted journal.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A prototype of this system has served the phylogenetics community well for a number of years, accumulating the results of thousands of studies. The usage model was that of a silo where data could only be accessed through a web browser, and only be downloaded in representations that...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4600/version/1

A Note On The Denisova Cave mtDNA Sequence
Provedor de dados: 17
Autores: Niccolo Caldararo; Michael Guthrie.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5360/version/3

Delving into Vertebrate Serpins for Understanding their Evolution
Provedor de dados: 17
Autores: Abhishek Kumar.
The superfamily of serine proteinase inhibitors (serpins) is involved in an array of fundamental biological processes such as blood coagulation, cell differentiation, cell migration, complement activation, embryo implantation, fibrinolysis, angiogenesis, and inflammation, and tumor suppression. Vertebrate serpins can be conveniently classified into six sub-groups, based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels. The present vertebrate serpins are derived from an original serpin most probably by intron insertion and we are trying to reconstruct the phylogeny of vertebrate serpin and looking for the reconstruction of original vertebrate gene(s). We started with fish genomes and characterized...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3050/version/1

The unique mouse pollination in an orchid species
Provedor de dados: 17
Autores: Yong Wang; Yang Zhang; Xiao-Kai Ma; Li Dong.
The Chinese orchid, _Cymbidium serratum_, is pollinated by the wild mountain mouse _Rattus fulvescens_. The flowers use both odor and colour as attractants, and provide labellum as food reward for the pollinators. The mice pollinate the flowers during their endeavour to eat the labellums.
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1824/version/1

Using TreeBASE from R
Provedor de dados: 17
Autores: Carl Boettiger.
I introduce an R package allowing programmatic access to the phylogenetic data in the TreeBASE archive and highlight why this is important.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6851/version/1

Phylogeny of conserved adenines in linkers of Group-I introns
Provedor de dados: 17
Autores: Natarajan Ganesan; Chandrasekhar Kesavan.
We have analyzed the linkers in group-I introns, a characteristic region that is crucial to the folding and splicing process of the folded RNA, in seventy sequences spreading across r-RNA, t-RNA and organelle genes from various organisms including algae, fungi and protozoa. The study revealed a high degree of consensus of specific adenine residues in J3/4, J6/7 and J8/7 stems of the linker regions that were required to stabilize the local orientation, either as single residue or by forming unusual base pairs along with divalent metal ions. Conservation of these residues in the Group-I intron linkers suggests their significant contribution to the folded structure whose bonding and geometry recruit metal ions to interact in stabilizing the folded nature of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2909/version/1

Speciation of chilean Rhinocryptidae (Avian) based on their behaviour
Provedor de dados: 17
Autores: Alejandro Correa Rueda; Jorge Mpodozis.
The current classification of the chilean representatives of the passerine family Rhinocryptidae includes eight species. Three of them contain subspecies that don&amp;#x2019;t exhibit clear differences. Moreover, differences among two lineages of _Scytalopus_ genera and two species of _Pteroptochos_ are very scarce. We propose  a new methodology  based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds. According to our results, we postulate that there is not a cut criteria to establish differences among three sister lineages of current classification. This way the methodology developed by us does not allow to establish divergence for a given common ancestor. Our methodology allows to establish...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1597/version/2

Understanding Genomic Evolution of Olfactory Receptors through Fractal and Mathematical Morphology
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; B. S. Dayasagar; Shantanav Chakraborty; Ranita  Guha; Arunava Goswami.
Fractals and Mathematical Morphology are immensely used to study many problems in different branches of science and technology including the domain of Biology. There are many more unrevealed facts and figures of genes and genome in Computational Biology. In this paper, our objective is to explore how the evolutionary network is associated among Human, Chimpanzee and Mouse with regards to their genomic information. We are about to explore their genomic evolution through the quantitative measures of fractals and morphology. We have considered olfactory receptors for our case study. These olfactory receptors do function in different species with subtle differences in the structures of DNA sequences. Those subtle differences can be exposed through intricate...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5674/version/1

H-InvDB release 6, a comprehensive annotation resource for human genes and transcripts
Provedor de dados: 17
Autores: Chisato Yamasaki; Katsuhiko Murakami; Jun-ichi Takeda; Yoshiharu Sato; Akiko Noda; Ryuichi Sakate; Takuya Habara; Hajime Nakaoka; Fusano Todokoro; Akihiro Matsuya; Tadashi Imanishi; Takashi Gojobori.
H-Invitational Database (H-InvDB; &amp;#x22;http://www.h-invitational.jp/&amp;#x22;:http://www.h-invitational.jp/) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups.  The latest release of H-InvDB (release 6.0) provide annotation for 219,765 human transcripts in 43,159 human gene...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3251/version/1

Did nature also choose arsenic?
Provedor de dados: 17
Autores: Felisa Wolfe-Simon; Paul C. W. Davies; Ariel Anbar.
All known life requires phosphorus (P) in the form of inorganic phosphate (PO&amp;#x3c;sub&amp;#x3e;4&amp;#x3c;/sub&amp;#x3e;&amp;#x3c;sup&amp;#x3e;-&amp;#x3c;/sup&amp;#x3e; or P&amp;#x3c;sub&amp;#x3e;i&amp;#x3c;/sub&amp;#x3e;) and phosphate-containing organic molecules. P&amp;#x3c;sub&amp;#x3e;i&amp;#x3c;/sub&amp;#x3e; serves as the backbone of the nucleic acids that constitute genetic material and as the major repository of chemical energy for metabolism in polyphosphate bonds. Arsenic (As) lies directly below P on the periodic table and so the two elements share many chemical properties, although their chemistries are sufficiently dissimilar that As cannot directly replace P in modern biochemistry. Arsenic is toxic precisely because As and P are similar...
Tipo: Manuscript
Palavras-chave: Chemistry; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1482/version/1

The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases
Provedor de dados: 17
Autores: D.B.R.K. Gupta Udatha; Irene  Kouskoumvekaki; Lisbeth Olsson; Gianni  Panagiotou.
One of the most intriguing groups of enzymes, the feruloyl esterases (FAEs), is ubiquitous in both simple and complex organisms. FAEs have gained importance in biofuel, medicine and food industries due to their capability of acting on a large range of substrates for cleaving ester bonds and synthesizing high-added value molecules through esterification and transesterification reactions. During the past two decades extensive studies have been carried out on the production and partial characterization of FAEs from fungi, while much less is known about FAEs of bacterial or plant origin. Initial classification studies on FAEs were restricted on sequence similarity and substrate specificity on just four model substrates and considered only a handful of FAEs...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4762/version/1

A potential cyanobacterial ancestor of Viridiplantae chloroplasts
Provedor de dados: 17
Autores: Wriddhiman Ghosh; Prabir Haldar; Sabyasachi Bhattacharya; Jaideb Chatterjee; Prosenjit Pyne; Masrure Alam.
The theory envisaging the origin of plastids from endosymbiotic cyanobacteria is well-established but it is difficult to explain the evolution (spread) of plastids in phylogenetically diverse plant groups. It is widely believed that primordial endosymbiosis occurred in the last common ancestor of all algae^1^, which then diverged into the three primary photosynthetic eukaryotic lineages, viz. the Rhodophyta (red algae), Glaucocystophyta (cyanelle-containing algae) and Viridiplantae (green algae plus all land plants)^2^. Members of these three groups invariably have double membrane-bound plastids^3^, a property that endorses the primary endosymbiotic origin of the organelles. On the other hand, the three or four membrane-bound plastids of the evolutionary...
Tipo: Manuscript
Palavras-chave: Microbiology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6607/version/1

Robust information from phylogenetic trees?
Provedor de dados: 17
Autores: Carl Boettiger.
Traditional information criteria approaches can lead to misleading model choice in comparative phylogenetics.  I present both these weaknesses and a more robust comparison by likelihood ratio.  I then discuss a new class of models to capture the transition process between evolutionary regimes.
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4614/version/1

Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
Provedor de dados: 17
Autores: Ralph Haygood; Olivier Fedrigo; Brian Hanson; Ken-Daigoro Yokoyama; Gregory Wray.
Surveys of protein-coding sequences for evidence of positive selection in humans and chimpanzees have flagged surprisingly few genes known to be involved in neural or nutritional processes, despite the pronounced differences between humans and chimpanzees in behavior, cognition, and diet. It may be that most such differences are due to changes in gene regulation rather than protein structure. Here, we present the first survey of promoter (5&amp;#x27;-flanking) regions, which are rich in _cis_-regulatory sequences, for signatures of positive selection in humans. Our results indicate that positive selection has targeted the regulation of many genes known to be involved in neural development and function, both in the brain and elsewhere in the nervous system,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/69/version/1

&amp;#x22;Ribopepzymes&amp;#x22; are probably a link from ribozymes to protein enzymes
Provedor de dados: 17
Autores: Yongjie Sheng; Dazhi Jiang; Zhen Zeng; Feng Pan; Jin Zhang.
The evolutionary relationship between RNA- and protein-based biocatalysts was key to the evolution of living systems. This relationship is thought to have depended upon the transfer of both genetic information and catalytic function in living systems. We investigated whether ribozymes could transfer genetic information and catalytic function at the chemical level. We identified a family of peptides encoded by ribozymes: 13-residue peptide encoded by the hammerhead ribozyme, a 19-residue peptide encoded by the genomic hepatitis delta virus (HDV+) ribozyme, a 25-residue peptide encoded by the antigenomic HDV (HDV-) ribozyme, a 15-residue peptide encoded by the smallest trans-acting genomic HDV (SHDV) ribozyme, and a 22-residue peptide encoded by an open...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1708/version/1

Visualization of Minute Mechanical-Excitation/Relaxation Wave-front Propagation in Myocardial Tissue
Provedor de dados: 17
Autores: Hiroshi Kanai; Motonao Tanaka.
Unlike the case of skeletal muscle, the direction of myocardial contraction does not coincide with the direction of work necessary to eject the intraventricular blood, contributing to great complexity of the wall deformation sequence of cardiac contraction. The advent of advanced techniques (CT^1^, MRI^2,3^, SPECT^4^, echocardiology^5-9^, electrocardiography^10^, and magnetocardiography^11,12^) has enabled to the evaluation of cardiac function and disorders by the measurement of blood flow, pressure, electrical reaction process, and other factors. However, complexity of the contraction sequence is still not fully understood because the dynamic mechanical excitation process, which directly correlates with contraction, cannot be accurately measured based on...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4931/version/1

The Vaginal Microbiome: Disease, Genetics and the Environment
Provedor de dados: 17
Autores: Jennifer M. Fettweis; Joao P. Alves; Joseph F. Borzelleca; James  P. Brooks; Christopher J. Friedline; Yuan Gao; Xi Gao; Philippe Girerd; Michael  D. Harwich; Stephanie L. Hendricks; Kimberly K. Jefferson; Vladimir Lee; Huan Mo; Michael C. Neale; Federico A. Puma; Mark A. Reimers; Maria C. Rivera; Seth B. Roberts; Myrna G. Serrano; Nihar U. Sheth; Judy L. Silbert; Logan Voegtly; Elizabeth C. Prom-Wormley; Bin Xie; Timothy  P. York; Cynthia N. Cornelissen; Jerome L. Strauss; Lindon J. Eaves; Gregory A. Buck.
The vagina is an interactive interface between the host and the environment. Its surface is covered by a protective epithelium colonized by bacteria and other microorganisms. The ectocervix is nonsterile, whereas the endocervix and the upper genital tract are assumed to be sterile in healthy women. Therefore, the cervix serves a pivotal role as a gatekeeper to protect the upper genital tract from microbial invasion and subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease, and other gynecologic and reproductive disorders. Homeostasis of the microbiome in the vagina and ectocervix plays a paramount role in reproductive health. Depending on its composition, the microbiome may protect...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5150/version/1

Evolvability of Chaperonin Substrate Proteins
Provedor de dados: 17
Autores: Emanuele Raineri; Paolo Ribeca; Luis Serrano; Tobias Maier.
Molecular chaperones ensure that their substrate proteins reach the functional native state, and prevent their aggregation. Recently, an additional function was proposed for molecular chaperones: they serve as buffers (_capacitors_) for evolution by permitting their substrate proteins to mutate and at the same time still allowing them to fold productively.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Using pairwise alignments of _E. coli_ genes with genes from other gamma-proteobacteria, we showed that the described buffering effect cannot be observed among substrate proteins of GroEL, an essential chaperone in _E. coli_. Instead, we find that GroEL substrate proteins evolve less than other soluble _E. coli_ proteins. We analyzed several specific structural and...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2968/version/1

Human neuromaturation, juvenile extreme energy liability, and adult cognition/cooperation
Provedor de dados: 17
Autores: 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&amp;#x2019;s survival at risk due to the high vulnerability of their brain to energy shortage. The brain of a 4 year-old human uses &amp;#x2248;50% of its total energy expenditure (TEE) (cf. adult &amp;#x2248;12%). This brain expensiveness is due to (1) the brain making up &amp;#x2248;6% of a 4 year-old body compared to 2% in an adult, and (2) increased energy metabolism that is &amp;#x2248;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

Precise Similarity of Many Human Proteins to Proteins of Prokarya
Provedor de dados: 17
Autores: Roy Britten.
&amp;#x9; Proteins originated in early forms of life and have long survived, because they have always been required. Some recognizably similar proteins are found in all sequence comparisons between species, no matter how distant, including prokaryotes and eukaryotes. Reported  here are observations on the relationships of human  proteins to the proteins of  458 prokaryotes for which protein libraries are available. Each of these libraries includes a protein that matches a human protein with a BLAST score of 573 or more, indicating excellent conservation of  certain amino acid sequences. A majority of these proteins also match a yeast protein and other eukaryote proteins with comparable accuracy, indicating that protein conservation is responsible in most...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/800/version/1

A Quantitative Approach to Investigating the Hypothesis of Prokaryotic Intron Loss
Provedor de dados: 17
Autores: Robert M. Sinclair.
Using a novel method, we show that ordered triplets of motifs usually associated with spliceosomal intron recognition are underrepresented in the protein coding sequence of complete Thermotogae, archaeal and bacterial genomes. The underrepresentation observed does not extend to the noncoding strand, suggesting that the cause of the asymmetry is related to mRNA rather than DNA. Our data do not suggest that the underrepresentation is due to gene transfer from eukaryotes. We speculate that one possible explanation for these observations is that the protein coding sequence of Thermotogae, Archaea and Bacteria was at some time in the past subjected to selection against certain motifs appearing in an order which might initiate splicing in environments harboring...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5770/version/1

Evolution of malaria virulence in cross-generation transmission through selective immune pressure
Provedor de dados: 17
Autores: David E. Gurarie.
Theoretical arguments and some mathematical models of host-parasite coevolution (e.g. [1- 6]) suggest host immunity as the driving source for the evolution of parasite virulence. Imperfect vaccines in particular, can play the role and recent work [7] sets to test these ideas experimentally, using the mouse malaria model, Plasmodium chabaudi. To this end the authors evolve parasite lines in immunized and nonimmunized (&amp;#x201c;na&amp;#xef;ve&amp;#x201d;) mice using serial passage of infected blood samples. They find parasite lines evolved in immunized mice become more virulent than those evolved in naive mice. Furthermore, this feature persisted even when the evolved strains were transmitted through mosquitoes. &amp;#xd;&amp;#xa;Here we develop a...
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/203/version/1

Cancer and the social induction of aging
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
Age has long been known as the primary population &amp;#x27;risk factor&amp;#x27; for cancer. We suggest that the observed disparities in hormonal cancers by ethnicity, gender, and other indices of social structure and power relationships, imply a differential aging by psychosocial and environmental exposures, in the context of cross-generational epigenetic heritage. A relatively simple model of malignancy regulation illuminates the cellular root of induced aging, and explains the decline in cancer rate with extreme old age via telomere shortening. We find that the multifactorial determinants of the disorder cannot be effectively addressed by &amp;#x27;small molecule&amp;#x27; interventions at the individual level, but must involve comprehensive prevention...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Pharmacology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6146/version/1

Early Life Relict Feature in Peptide Mass Distribution
Provedor de dados: 17
Autores: Roman A. Zubarev; Konstantin Artemenko; Alexander  R. Zubarev; Corina Mayrhofer; Eva Y. M. Fung.
Molecular mass of a biomolecule is characterized in mass spectroscopy by the monoisitopic mass M~mono~ and the average isotopic mass M~av~. We found that peptide masses mapped on a plane made by two parameters derived from M~mono~ and M~av~ form a peculiar global feature in form of a band-gap 5-7 ppm wide stretching across the whole peptide galaxy, with a narrow (FWHM 0.2 ppm) line in the centre. The a priori probability of such a feature to emerge by chance is less than 1:100. Peptides contributing to the central line have elemental compositions following the rules S=0; Z = (2C - N - H)/2 =0, which nine out of 20 amino acid residues satisfy. The relative abundances of amino acids in the peptides contributing to the central line correlate with the...
Tipo: Manuscript
Palavras-chave: Chemistry; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2402/version/1

Optimizing automated preprocessing streams for brain morphometric comparisons across multiple primate species
Provedor de dados: 17
Autores: Daniel Mietchen; Robert Dahnke; Christian Gaser.
INTRODUCTION&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;MR techniques have delivered images of brains from a wide array of species, ranging from invertebrates to birds to elephants and whales. However, their potential to serve as a basis for comparative brain morphometric investigations has rarely been tapped so far (Christidis and Cox, 2006; Van Essen &amp;#x26; Dierker, 2007), which also hampers a deeper understanding of the mechanisms behind structural alterations in neurodevelopmental disorders (Kochunov et al., 2010).  One of the reasons for this is the lack of computational tools suitable for morphometrci comparisons across multiple species. In this work, we aim to characterize this gap, taking primates as an...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4511/version/2

Animal emergence during Snowball Earths by thermosynthesis in submarine hydrothermal vents
Provedor de dados: 17
Autores: 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

Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm _Elaeis guineensis_ and _E. oleifera_
Provedor de dados: 17
Autores: Aikkal Riju; Vadivel Arunachalam.
Oil palm is the second largest source of edible oil, which meets one-fifth of global demands of oils and fats. Expressed sequence tag (EST) sequencing programs have provided a wealth of information, identifying novel genes from a broad range of organisms and providing an indication of gene expression level in particular tissues. It also provides the richest source of biologically useful SNPs due to the relatively high redundancy of gene sequence, the diversity of genotypes represented within databases. EST based SNPs are potential molecular markers and aid in genetic improvement. A total of 21062 and 2053 polymorphic (SNP and Indel) sites in _E. guineensis_ species and in _E. oleifera_, 4955 SNPs and 1172 Indels were detected. SNP(17.5/kbp) and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3593/version/2

The study of the umbilical system in planktonic foraminifera in relation with depth of the Abderaz Formation at type section, IRAN
Provedor de dados: 17
Autores: Meysam Shafiee Ardestani; Ebrahim Ghasemi-Nejad.
Prospect of changes in such umbilical structures as Lip, Portici and Tegilla throughout Turonian-Campanian was also investigated. The phylogenic trend show that Lip structure in primary morphogroups turns gradually to tegilla in more developed forms in which the opening become also entirely umbilical. Statistical an analysis showed that the trends of changes are correlatable with increase in water depth while a decrease in depth result in development of lip in the planktonic foraminifera studied. The changes are considered to be in accord with Pascal law.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3206/version/1

Systema Naturae. Classification of living things.
Provedor de dados: 17
Autores: Alexey Shipunov.
Original classification of living organisms containing four kingdoms (Monera, Protista, Vegetabilia and Animalia), 60 phyla and 254 classes, is presented. The classification is based on latest available information.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/241/version/2

A Rate Distortion approach to protein symmetry
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry breaking argument is applied to the problem of protein form, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein &amp;#x27;molten globule&amp;#x27;. The Rate Distortion Function, under coding constraints, serves as a temperature analog, so that low values act to drive proteins to simple symmetries. The Rate Distortion Function itself is significantly constrained by the availability of metabolic free energy. This work extends Tlusty&amp;#x27;s (2007) elegant exploration of the evolution of the genetic code, suggesting that rate distortion considerations may play a critical role across a broad spectrum of molecular expressions of evolutionary process.
Tipo: Manuscript
Palavras-chave: Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4280/version/1

Subtyping of Dengue Viruses using Return Time Distribution based Appproach
Provedor de dados: 17
Autores: Pandurang Kolekar; Mohan Kale; Urmila Kulkarni-Kale.
Dengue virus (DENV) is the causative agent of Dengue Hemorrhagic Fever and Dengue Shock Syndrome, and continues to represent a major public health hazard. DENVs are antigenically classified in four serotypes and each serotype is further divided into respective genotypes. The association between DENV subtypes and the kind &amp;#x26; severity of disease caused by them is known. Experimental and computational approaches for subtyping are routinely used for the purpose of diagnosis and treatment of DENV, in addition to the study of phylodynamics. All virus-specific molecular subtyping tools make use of sequence alignments at backend. But as the volume of molecular data increases, alignment-dependent methods become computationally intensive. Hence, the need for...
Tipo: Poster
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5590/version/1

Evolution of Thriftiness: An analytical viewpoint
Provedor de dados: 17
Autores: Prajakta Belsare; Milind Watve.
We examine here, using a simple mathematical model, the conditions under which thrifty genes or fetal programming could evolve. Obesity and related disorders are thought to have their roots in metabolic thirftiness that evolved to combat periodic starvation. The failure to detect any thrifty genes and the association of low birth weight with type 2 diabetes, caused a shift in the concept from thrifty gene to thrifty phenotype and fetal programming. This hypothesis assumes that intra-uterine undernutrition programs the body to be thrifty, predicting and preparing for starvation in later life. However, there are reproductive costs associated with thriftiness. Results of the model suggest that under no condition thrifty and non-thrifty genes would co-exist...
Tipo: Poster
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2709/version/1

The joys and perils of recombination - The hotspot conversion paradox and the evolution of recombination
Provedor de dados: 17
Autores: Mario Pineda-Krch; Rosemary J. Redfield.
The contradiction between the long-term persistence of the chromosomal hotspots that initiate meiotic recombination and the self-destructive mechanism by which they act strongly suggests that our understanding of recombination is incomplete. To investigate the requirements for hotspot persistence, Rosemary Redfield and I developed a computer simulation model, hotspot, of their activity and its evolutionary consequences.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3636/version/1

Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers
Provedor de dados: 17
Autores: Shi Huang.
Interpretations of molecular data by the modern evolution theory are often sharply inconsistent with paleontological results.  This is to be expected since the theory is only true for microevolution and yet fossil records are mostly about macroevolution.  The maximum genetic diversity (MGD) hypothesis is a more coherent and complete account of evolution that has yet to meet a single contradiction.  Here, molecular data were analyzed based on the MGD to resolve key questions of primate phylogeny.  A new method was developed from a novel result predicted by the MGD: genetic non-equidistance to a simpler taxon only in slow but not in fast evolving sequences given non-equidistance in time.  This &amp;#x2018;slow clock&amp;#x2019; method showed that humans are...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3794/version/1

A new phylogenetic comparative method: detecting niches and transitions with continuous characters
Provedor de dados: 17
Autores: Carl Boettiger.
Traditional information criteria approaches can lead to misleading model choice in comparative phylogenetics. I present examples of these weaknesses using a classic data set on Anoles lizards.  I describe a more robust comparison by likelihood ratio. I then discuss a new class of models to capture the transition process between evolutionary regimes.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4615/version/1

Exploring The Hidden Realms Of Global Biodiversity: Interesting Endophytic Yeast Flora From Floral Ovaries
Provedor de dados: 17
Autores: Nandkumar Kamat; Shweta S. Saudagar.
Soil is considered the ultimate reservoir of all the microbiota  and specifically the yeasts. However their association with different plant organs and at different developmental stages is not fully explored. Although about 1000 yeast species have been identified, exploration of various microhabitats such as plant storage organs, flowers, nectar, and tree sap is expected to yield a large number of novel species, including interesting endophytic yeasts(Carlos &amp;#x26; Gabor, 2006). Angiosperms are considered the most diverse group of the plant kingdom comprising of about 250,000 species (Kenrick, 1999). As part of an exhaustive exploration of yeasts associated with angiosperm flowers, specific attention was paid to floral ovaries to detect the presence of...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Ecology; Genetics &amp; Genomics; Microbiology; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6268/version/1

Essay: On the close relationship between speciation, inbreeding and recessive mutations.
Provedor de dados: 17
Autores: Etienne Joly.
Whilst the principle of adaptive evolution is unanimously recognised as being caused by the process of natural selection favouring the survival and/or reproduction of individuals having acquired new advantageous traits, a consensus has proven much harder to find regarding the actual origin of species. Indeed, since speciation corresponds to the establishment of reproductive barriers, it is difficult to see how it could bring a selective advantage because it amounts to a restriction in the opportunities to breed with as many and/or as diverse partners as possible. In this regard, Darwin himself did not believe that reproductive barriers could be selected for, and today most evolutionary biologists still believe that speciation can only occur through a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5003/version/2

Copyrights and digitizing the systematic literature: the horror... the horror...
Provedor de dados: 17
Autores: N. Dean Pentcheff.
It is time for us to take full advantage of the investment that our societies have made in documenting the biodiversity of the world. It is time for us to fully, and legally, make systematic literature available worldwide. Using U.S. &amp;#x22;Fair Use&amp;#x22; guidelines, we can.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4644/version/1

Tuberculosis vaccine strain _Mycobacterium bovis_ BCG Russia is a natural _recA_ mutant
Provedor de dados: 17
Autores: Peter M. Keller; Erik C. Boettger; Peter Sander.
The current tuberculosis vaccine is a live vaccine derived from _Mycobacterium bovis_ and attenuated by serial _in vitro_ passaging. All vaccine substrains in use stem from one source, strain Bacille Calmette-Gu&amp;#xe9;rin. However, they differ in regions of genomic deletions, antigen expression levels, immunogenicity, and protective efficacy. As a RecA phenotype increases genetic stability and may contribute restricting the ongoing evolution of the various BCG substrains, we aimed to inactivate _recA_ by allelic replacement in BCG vaccine strains representing different phylogenetic lineages (Pasteur, Frappier, Denmark, Russia). Homologous gene replacement was successful in three out of four strains. However, only illegitimate recombination was observed...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1576/version/1

Mechanistic mechanisms of competition and biodiversity
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The nature of competition and biodiversity are open basic questions since Darwin. To investigate mechanisms of interspecific competition and their contribution in biodiversity as closely as possible we offer a white-box modelling method based on physically interpreted ecological axioms. These models are implemented as deterministic individual-based cellular automata and able to give a direct physico-mechanistic insight into studied phenomena. Competition of two trophically identical but fitness different species, competing for one limiting resource in one stable uniform habitat (which is closed for immigration, emigration, predation, herbivory and parasitism) has been investigated in conditions, which are the most unfavourable for their coexistence. The...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7105/version/1

A Note On The Denisova Cave mtDNA Sequence
Provedor de dados: 17
Autores: Niccolo Caldararo; Michael Guthrie.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/5360/version/4

Drone congregation areas of red dwarf honeybee, Apis florea
Provedor de dados: 17
Autores: Narayanappa Nagaraja; Axel Brockmann.
The drones of dwarf honeybees assemble at the drone congregation areas close to small trees with dense leafage at the heights between 2 to 4 meters.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3955/version/1

The Evolution of Homochirality
Provedor de dados: 17
Autores: Rodrick Wallace.
It is possible to reconsider the origin of biological homochirality in a novel way by formally invoking the standard groupoid approach to stereochemistry in a thermodynamic context that generalizes Landau&amp;#x27;s spontaneous symmetry breaking arguments. On Earth, limited metabolic free energy may have served as a low temperature analog to &amp;#x27;freeze&amp;#x27; the system in the lowest energy state, i.e., the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in a Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process locked in this initial condition, in spite of increases in available metabolic free energy. Astrobiological outcomes, given higher...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Molecular Cell Biology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/3902/version/2

Living unicellular eukaryote Tetrahymena pyriformis as a model for study of mitochondrial energetics in mammalian cells under conditions of reduced oxidative metabolism.
Provedor de dados: 17
Autores: Elena Mokhova.
Some &amp;#x201c;animal-like&amp;#x201d; protozoa are used instead of mammalian cells in diverse investigations.  _Tetrahymena pyriformis_ cells in stationary phase of growth and washed from oxidative substrates (_T.pyriformis_) function under conditions of reduced oxidative metabolism. To elucidate if _T.pyriformis_ can be applied as a model for mitochondrial energetics study in   mammalian cells during hibernation, the features of _T.pyriformis_ mitochondria were compared with that of liver mitochondria isolated from hibernating animals; the published earlier data were used. Based on the respiration recording and observation of Mito Tracker Red fluorescence in living _T.pyriformis_ we tentatively concluded that the mitochondrial electrical membrane...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4521/version/1

Nucleotide repeats in mitochondrial genome determine human lifespan
Provedor de dados: 17
Autores: Konstantin Popadin; Georgii Bazykin.
Direct nucleotide repeats can facilitate deletions of segments of mitochondrial genome1, leading to a wide range of neuromuscular disorders1,2 as well as aging2,3 in humans. We hypothesized that the number of the direct perfect repeats in human mitochondrial genomes influences longevity through the formation of harmful mtDNA deletions in the somatic cells. The analysis of the complete mitochondrial genomes of 762 unrelated Japanese individuals4-6 reveals a negative correlation between the abundance of the direct perfect repeats and the expected longevity. This association is largely due to the disruption of the common repeat (8470,13447) by a point mutation 8473C which occurred at the origin of the D4a haplogroup characterized by extreme longevity in...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2399/version/1

Family values: Maternal care in rattlesnakes is more than mere attendance
Provedor de dados: 17
Autores: Melissa Amarello; Jeffrey J. Smith; John Slone.
Parental care is important in many diverse taxa because of its positive impact on the parent&amp;#x27;s fitness.  Relatively simple forms of parental care, such as female attendance and defense, which is present in many squamate reptiles, will likely provide insight into the evolution of more complex forms observed in crocodilians, birds, and mammals. Historically, observations of adult and newborn rattlesnakes in close proximity were dismissed as mere coincidence of live-birth, and only recently acknowledged as examples of parental care. In 2010, we monitored 11 pregnant Arizona black rattlesnakes (_Crotalus cerberus_): 4 solitary individuals and 2 aggregations composed of three and four individuals.  We documented various forms of parental care,...
Tipo: Poster
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6671/version/1

2011 German Escherichia coli outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles
Provedor de dados: 17
Autores: Man Kit Cheung; Lei LI; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 9 E.coli isolates from the 2011 German outbreak against existing E. coli genomes using the alignment-free feature frequency profile method. In addition, we looked for gene elements that distinguish the outbreak group from the other E. coli strains and possibly accounted for the emergence of the outbreak isolates using the distinguishing feature analysis.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6109/version/1

Aging as a consequence of misrepair -- A novel theory of aging
Provedor de dados: 17
Autores: 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 &amp;#x2018;faults&amp;#x2019; 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 &amp;#x2018;damage&amp;#x2019; and &amp;#x2018;fault&amp;#x2019; 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/2

A unified mechanistic model of niche, neutrality and violation of the competitive exclusion principle
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The origin of species richness is one of the most widely discussed questions in ecology. The absence of unified mechanistic model of competition makes difficult our deep understanding of this subject. Here we show such a two-species competition model that unifies (i) a mechanistic niche model, (ii) a mechanistic neutral (null) model and (iii) a mechanistic violation of the competitive exclusion principle. Our model is an individual-based cellular automaton. We demonstrate how two trophically identical and aggressively propagating species can stably coexist in one stable homogeneous habitat without any trade-offs in spite of their 10% difference in fitness. Competitive exclusion occurs if the fitness difference is significant (approximately more than 30%)....
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7089/version/1

Ediacaran Macro Body Fossils
Provedor de dados: 17
Autores: Timothy D. Huang; Jei-Fu Shaw; Liang Zheng; Chun-Lan Huang; YiLung Chang; ChuanWei Yang.
This paper, Ediacaran Macro Body Fossils, reports a new discovery of well preserved three dimensional macro body fossils of the Ediacaran Period in central YunNan province in the People&amp;#x27;s Republic of China. These body fossils will enable more detailed and in-depth exploration of the evolution of multi-cellular macro organisms on this planet, whereas in the past, researches could only rely on cast or imprint fossils.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4423/version/1

The study of the umbilical system in planktonic foraminifera in relation with depth of the Ziarat-kola section at the Maastrichtian, Central Alborz, IRAN
Provedor de dados: 17
Autores: Meysam Shafiee Ardestani; Behnaz Balmaki; Massod Asgharian.
The main aim of this research is study of the planktonic foraminifera morphogroups distinction genus to perform by changing the umbilicus area in Ziarat-kola section to find novel results. Therefore, original objection at this research considers the cause of organizing umbilicus structures (Lip, Portici, Tegilla) at this protests. it seems that phylogeny trend entirely the changes of planktonic foraminifera changing from lip at primary morphogroup to tegilla at development shape which continued this phylogeny trend opening become entirely umbilicus that this trend accompanied to increasing deep. Therefore, the study of planktonic foraminifera morphotype, and recognizing, the obtained results from planktonic foraminifera analysis percent and their...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3342/version/1

Aging as a consequence of misrepair -- A novel theory of aging
Provedor de dados: 17
Autores: 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 &amp;#x2018;faults&amp;#x2019; 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 &amp;#x2018;damage&amp;#x2019; and &amp;#x2018;fault&amp;#x2019; are not specified. Therefore we introduce here a specification of the underlying mechanism 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 original...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2988/version/1

Tuning and regulating the repertoire of glycan determinants
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
We apply Tlusty&amp;#x27;s information-theoretic index theorem analysis of the genetic code to the glycome, using a cognitive paradigm by which external information sources constrain and tune the glycan code error network, in the context of available metabolic energy. The model suggests spontaneous symmetry breaking of the glycan code as a function of metabolic energy intensity, an effect that may be currently present, or embedded in evolutionary trajectory, recording large-scale ecosystem resilience shifts in energy availability such as the aerobic transition. Once focused on a subset of the glycan error code network however, the glycan production machinery must then be regulated by an elaborate cognitive process to ensure that what is produced matches...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Ecology; Molecular Cell Biology; Pharmacology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5932/version/2

Unique features of Plasmids among different Citrobacter species
Provedor de dados: 17
Autores: Swapnil G. Sanmukh; Waman N. Paunikar.
The _Citrobacter_ plasmids are supposed to represent the host genetic association within the living bacterial cell. The plasmids impart various beneficial characteristics to the host, helping it to retain suitable characteristics for adaptation as well as evolution. The study aims at understanding the role of prophage in influencing host functional characteristics by horizontal gene transfer or as whole plasmids. The  _Citrobacter_ plasmid can be understood by analyzing many hypothetical protein sequences within its genome. Our study included 82 hypothetical proteins in 5 _Citrobacter_ plasmids genomes. The function predictions in 31 hypothetical proteins and 3-D structures were predicted for 11 protein sequences using PS2 server. The probable function...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6836/version/1

The Evolution Ontology
Provedor de dados: 17
Autores: Adam M. Goldstein.
Existing ontologies model components of evolution, but none synthesize them or describe the framework of ideas used to conceptualize evolution. The Evolution Ontology (EO) aims to do just this. EO models processes (e.g. natural selection); contexts (e.g. habitats); the entities that undergo evolution; and the theories, methods, and disciplines of evolutionary science. Uses include data curation, data mining, and literature curation, EO&amp;#x2019;s developers working on the latter two for works of Darwin and the Biodiversity Heritage Library.
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3557/version/1

Assessing the Genotypic Differences for Seed Set and Seed Abortion in Tomato Genotypes
Provedor de dados: 17
Autores: Chalapathy  K. Reddy; Ganeshaiah Narayana; Uma  Shaanker.
Tomato (_Lycopersicon esculentum_ Mill.) is one of the most popular fruit vegetable around the world. Seed abortion where in only a small proportion of ovules in an ovary develops into matured seeds, is a wide spread phenomenon in multi-ovulated species. In agriculturally important crops such as chickpea, groundnut, Brassica, pigeon pea and field bean seed abortion substantially reduces their productivity. Tomato genotypes exhibited seed abortion where in only some proportion of ovules developed into matured seeds. Seed abortion in tomato cultivars would increase the cost of hybrid seed production. In this study, we have analyzed 19 genotypes for number of ovules, seed set and seed abortion. Tomato genotypes differed significantly for number of ovules per...
Tipo: Manuscript
Palavras-chave: Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3183/version/1

Population genomics of domestic and wild yeasts
Provedor de dados: 17
Autores: David M. Carter; Gianni Liti; Alan M. Moses; Leopold Parts; Stephen A. James; Robert P. Davey; Ian N. Roberts; Anders Blomberg; Jonas Warringer; Austin Burt; Vassiliki Koufopanou; Isheng J. Tsai; Casey M. Bergman; Douda Bensasson; Michael J. T. O&amp;#x27;Kelly; Alexander van Oudenaarden; David B. H. Barton; Elizabeth Bailes; Matthew Jones; Michael A. Quail; Ian Goodhead; Sarah Sims; Frances Smith; Richard Durbin; Edward Louis.
The natural genetics of an organism is determined by the distribution of sequences of its genome. Here we present one- to four-fold, with some deeper, coverage of the genome sequences of over seventy isolates of the domesticated baker&amp;#x27;s yeast, _Saccharomyces cerevisiae_, and its closest relative, the wild _S. paradoxus_, which has never been associated with human activity. These were collected from numerous geographic locations and sources (including wild, clinical, baking, wine, laboratory and food spoilage). These sequences provide an unprecedented view of the population structure, natural (and artificial) selection and genome evolution in these species. Variation in gene content, SNPs, indels, copy numbers and transposable elements provide...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1988/version/1

Wikipedia as an encyclopaedia of life
Provedor de dados: 17
Autores: Roderic Page.
In his 2003 essay E O Wilson outlined his vision for an &amp;#x201c;encyclopaedia of life&amp;#x201d; comprising &amp;#x201c;an electronic page for each species of organism on Earth&amp;#x201d;, each page containing &amp;#x201c;the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.&amp;#x201d; Although the &amp;#x201c;quiet revolution&amp;#x201d; in biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson&amp;#x27;s essay (e.g., &amp;#x22;http://ispecies.org&amp;#x22;:http://ispecies.org, &amp;#x22;http://www.eol.org&amp;#x22;:http://www.eol.org), we are still some way from the goal of having...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4242/version/1

Water Quality and Pollution Status of Lararpur Reservoir with Special Reference to Bacterial Contamination
Provedor de dados: 17
Autores: Subhash C. Pandey; Sadhna M. Singh; Subrata  Pani; Arti Malhosia.
Laharpur dam was constructed in the southwest of Bhopal city, M.P., India with an objective to store water for irrigational purpose. At the time of planning and construction of the reservoir it was in the outskirts of township but now, with the expansion of the city the reservoir has come well within the settlement. The developmental activities and occupancy in the area is exerting pressure on the water body. Surface water in urban water bodies almost always contains some degree of contamination. This is due to exposure to animals, humans, aquatic life, etc. In addition to this, variety of other human activities resulted in increasing the bacterial concentration of reservoir. Many of these bacteria are pathogenic and spread diseases like typhoid,...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3645/version/1

Does human imitate successful behaviors immediately?
Provedor de dados: 17
Autores: Zhao-Jin Xu; Lian-Zhong Zhang.
The emergence and abundance of cooperation in animal and human societies is a challenging puzzle to evolutionary biology. Over the past decades, various mechanisms have been suggested which are capable of supporting cooperation. Imitation dynamics, however, are the most representative microscopic rules of human behaviors on studying these mechanisms. Their standard procedure is to choose the agent to imitate at random from the population. In the spatial version this means a random agent from the neighborhood. Hence, imitation rules do not include the possibility to explore the available strategies, and then they have the possibility to reach a homogeneous state rapidly when the population size is small. To prevent evolution stopping, theorists allow for...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4480/version/1

An attempt to understand Barstar, Barnase and Olfactory receptor protein folding problems using mathematical biological approach
Provedor de dados: 17
Autores: Arunava Goswami; Sk Sarif Hassan; Pabitra  Pal Choudhury.
Protein folding problem as attracted structural biologists immensely (1). Till date, correlation between X-ray crystallographic and NMR data are considered to be the best methods for determining structure of intra-cellular proteins. Generating crystals and finding correct experimental conditions for NMR are largly a gamble and resultant data processing highly time consuming. Even if, a large number of laboratories around the world and India make crystals of protein but majority of them fail to generate crystallographic data less than or equal to 10A resolution with currently available instruments. This means that X-ray crystallographic data have been generated from protein crystals with non-uniform lattices. We believe that a large portion of (chain of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4891/version/1

CDAO-Store: A New Vision in Data Integration
Provedor de dados: 17
Autores: Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO) 1 is an ontology developed, as part of the EvoInfo2 and EvoIO3 groups supported by NESCent4, to provide semantics to the descriptions of data and transformations commonly found in the domain of phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic &amp;#xd;&amp;#xa;trees and associated character data matrices. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4585/version/2

Evolution of Cooperation on Playing Prisoner&amp;#x27;s Dilemma Game in the Finite-Capacity Spot
Provedor de dados: 17
Autores: Hiroshi Toyoizumi.
Explaining the evolution of cooperative behavior has been one of main challenges in evo- lutionary theory^1-6^. Cooperation may collapse a surge of defectors who enjoy the benefit without cooperation in situation called prisoner&amp;#x27;s dilemma. In the concept of evolutionary game theory, there are many proposals to explain the evolution of cooperation by adding further mechanism such as, kin selection^1^, reciprocity^7^, punishment^8,9^  and the finiteness of the population^6^. In evolutionary game theory, a pair is randomly picked from population, and play a prisoner&amp;#x27;s dilemma game. Here we also show the finiteness encourages cooperation but use different approach: in spite of random-pick, individuals join and leave a spot or territory with a...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3071/version/1

Robustness of self-organised systems to changes in individual level behaviour: an example from real and simulated self-organised snail aggregations
Provedor de dados: 17
Autores: Richard Stafford; Mark S. Davies; Gray A. Williams.
Perfect behaviours that are optimal to the environment an agent operates within rarely exist in real animals or in robotic systems. The costs (be they biological or economic) of building sensors and processing the information they capture become excessive compared to the small advantages that occur from the modifications of behaviour. Many self-organised systems are thought to change their properties as a result of changes in individual behaviour. Here, using both natural systems and computer simulations, we demonstrate that intertidal snail aggregations slightly decrease in size when individuals forage for shorter periods due to hotter and more desiccating conditions &amp;#x2013; a non-optimal behaviour for the snails since aggregation reduces desiccation...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3922/version/1

Trichoplax, the simplest known animal, contains an estrogen-related receptor: Implications for the evolution of vertebrate and invertebrate estrogen receptors
Provedor de dados: 17
Autores: Michael E. Baker.
Although, as their names imply, vertebrate and invertebrate estrogen receptors [ERs] and estrogen-related receptors [ERRs] are related transcription factors, their evolutionary relationships to each other are not fully understood.  We searched recently sequenced genome of _Trichoplax_, the simplest known animal, and genomes from three lophotrochozoans: _Capitella_, a worm, _Helobdella robusta_, a leech, and _Lottia gigantea_, a snail, to elucidate the origins and evolution of ERs and ERRs.  BLAST found an ERR in _Trichoplax_, but no ER.  BLAST searches of the lophotrochozaons found ERRs in all three and invertebrate ERs in _Capitella_ and _Lottia_, but not in _Helobdella_.  These database searches and a phylogenetic analyses indicate that invertebrate ERs...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1863/version/1

GreenPhylDB: A Gene Family Database for plant functional Genomics
Provedor de dados: 17
Autores: Matthieu G. Conte; Marie-Ang&amp;#xe9;lique Laporte; Christophe P&amp;#xe9;rin; Mathieu  Rouard.
With the increasing number of genomes being sequenced, a major objective is to transfer accurate annotation from characterised proteins to uncharacterised sequences. Consequently, comparative genomics has become a usual and efficient strategy in functional genomics. The release of various annotated genomes of plants, such as _O. sativa_ and _A. thaliana_, has allowed setting up comprehensive lists of gene families defined by automated methods. However, like for gene sequence, manual curation of gene families is an important requirement that has to be undertaken. GreenPhylDB comprises protein sequences of 12 plant species fully sequenced that were grouped into homeomorphic families using similarity-based methods. Clusters are finally processed by...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3136/version/1

Generalized Theory of Life
Provedor de dados: 17
Autores: Vyacheslav L. Kalmykov.
The paper is mathematically, physically and biologically inspired - it is a deductive attempt of the biologist to find the most appropriate language for modelling of life. Applications of mathematical structures - groupoids, groups, categories, functors and monads, which are the most effective for the description of the complex objects, are discussed. Some new conceptions and interpretations were introduced: unified classification of complex systems; the generalized conception about stationary states of any autonomous agent (&amp;#x22;Statology&amp;#x22;); the total quantitative criterions of evolutionary direction; the generalized group of symmetry. The definitions of information, entropy, organization, behavior, evolution, creation, life, culture,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7108/version/1

Hypothesis: Klotho can decouple insulin resistance from the associated pathophysiology
Provedor de dados: 17
Autores: Milind Watve; Ulfat Baig.
A very fundamental paradox of insulin resistance is that in a wide variety of animal models impairment of insulin signaling increases life span. But in humans it increases the risk of a range of fatal disorders. The Klotho protein appears to resolve this paradox. Overexpression of the Klotho gene increases longevity in mammals by inducing insulin resistance. But the Klotho protein is simultaneously anti-inflammatory, antioxidant and pro-angiogenesis. A number of other studies have indicated that systemic inflammation, angiogenesis dysfunction and oxidative stress are the main causes of pathological complications of diabetes. The Klotho protein has demonstrated that insulin resistance can be decoupled from these pathogenic mechanisms and if decoupled it...
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5420/version/1

The Olfactory Nervous System Of Terrestrial And Aquatic Vertebrates
Provedor de dados: 17
Autores: Ashiq Hussain.
Animals in their natural milieu are surrounded by odors. These odors are rich source of information, and are perceived by sophisticated olfactory systems, that have evolved over time. The sense of smell helps species to localize prey, evade predators, explore food and recognize viable mates. In humans, memoirs, thoughts, emotions, and associations are more readily reached through the sense of smell than through any other channel. This suggests that olfactory processing is imperative and may differ fundamentally from processing in other sensory modalities. The molecular age in olfaction initiated in 1991 with the significant discovery of a large, multigene family of olfactory receptors in rat by Linda Buck and Richard Axel (Buck and Axel, 1991). The first...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6642/version/1

The biological cost of consciousness
Provedor de dados: 17
Autores: Bernard J. Baars.
Some philosophers maintain that consciousness as subjective experience has no biological function. However, conscious brain events seem very different from unconscious ones. The cortex and thalamus support the reportable qualitative contents of consciousness. Subcortical structures like the cerebellum do not. Likewise, attended sensory stimuli are typically reportable as conscious, while memories of those stimuli are not so reportable until they are specifically recalled.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Reports of conscious experiences in normal humans always involve subjectivity and an implicit observing ego. Unconscious brain events are not reportable, even under optimal conditions of report. While there are claimed exceptions to these points, they...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6775/version/1

ABC Methods for Bayesian Model Choice
Provedor de dados: 17
Autores: Christian P. Robert.
Approximate Bayesian computation (ABC), also known as likelihood-free  methods, have become a standard tool for the analysis of complex models, primarily in population genetics but also for complex financial models. The development of new ABC methodology is undergoing a rapid increase in the past years, as shown by multiple publications, conferences and even software. While one valid interpretation of ABC based estimation is connected with nonparametrics, the setting is quite different for model choice issues. We examined in Grelaud et al. (2009, Bayesian Analysis) the use of ABC for Bayesian model choice in the specific of Gaussian random fields (GRF), relying on a sufficient property only enjoyed by GRFs to show that the approach was legitimate. Despite...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5961/version/1

DNA SEQUENCE PATTERNS
Provedor de dados: 17
Autores: Sriram Kannan.
There is significance in the molecular weight derived sequence patterns of adenosine, guanosine, cytosine, thymine, methyl cytosine and hydroxyl methyl cytosine if one has to consider the molecular events holistically by including single nucleotide polymorphisms, tumor suppressor gene activity like that of ten eleven translocation gene, CpG methylation, miRNA SNP patterns and SNPs neighboring CpGs. This research article focuses on observing simulation results of validated SNPs in a sequence using substitution patterns of molecular weight of A, G, C, T, 5OHC, 5MC.  The outcome helped to bring out positions in a DNA sequence where in validated bi allelic SNPs were never found to occur and SNPs neighboring methylated CpGs do show disconcordance and a...
Tipo: Presentation
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4933/version/1

Development of Incentives for Data Sharing in Ecology, Evolution, and Organismal Biology
Provedor de dados: 17
Autores: Clifford S. Duke.
Ready access to data is a key concern in both basic research and problem-solving in the biological sciences, as the scale and scope of the questions that researchers ask expand, and as global problems demand data collected from around the world. With a grant from the National Science Foundation, from 2004 through 2009, the Ecological Society of America (ESA) has led a series of five workshops on data sharing, to help the ecology, evolution, and organismal biology communities find common ground on how to make data more readily discoverable and accessible in their own disciplines. The most recent of these focused in the development of incentives for data sharing, both at the individual and organizational level. This presentation will summarize the workshop...
Tipo: Presentation
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3647/version/1

CDAO-Store: A New Vision in Data Integration
Provedor de dados: 17
Autores: Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO)  is an ontology developed, as part of the EvoInfo and EvoIO groups supported by NESCent, to provide semantics to the descriptions of data and transformations commonly found in the domain of phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic trees and associated character data matrices. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;CDAO-store is a repository providing a rich set of API&amp;#x2019;s for querying and visualizing phyloinformatics data. It is a triple-store encoding data as RDF triples constructed according to the CDAO concept vocabulary. CDAO-store provides three classes of services: a service for importing data in CDAO format, a PhyloWS interface supporting an...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4586/version/1

The largest reservoir of mitochondrial introns is a relic of an ancestral split gene
Provedor de dados: 17
Autores: Cyril Ferandon; Serge Moukha; Philippe Callac; Jean-Pierre Benedetto; Michel Castroviejo; Gerard Barroso.
In eukaryotes, introns are located in nuclear and organelle genes from several kingdoms (ref. 1-4). Large introns (0.1 to 5 kbp) are frequent in mitochondrial genomes of plant and fungi (ref. 1,5) but scarce in Metazoa, despite these organisms are grouped with fungi among Opisthokonts. Introns are classified in two main groups (I and II) according to their RNA secondary structure involved in the intron self-splicing mechanism (ref. 5,6). Most of the group I introns carry a &amp;#x22;Homing Endonuclease Gene&amp;#x22; (ref. 7-9) encoding a DNA endonuclease acting in the transfer and site specific integration &amp;#x22;homing&amp;#x22;) and allowing the intron spreading and gain after lateral transfer even between species from different kingdoms (ref....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4373/version/1

Trichoplax, the simplest known animal, contains an estrogen-related receptor but no estrogen receptor: Implications for estrogen receptor evolution
Provedor de dados: 17
Autores: Michael E. Baker.
Although, as their names imply, estrogen receptors [ERs] and estrogen-related receptors [ERRs] are related transcription factors, their evolutionary relationships to each other are not fully understood.  To elucidate the origins and evolution of ERs and ERRs, we searched for their orthologs in the recently sequenced genome of _Trichoplax_, the simplest known animal, and in the genomes of three lophotrochozoans: _Capitella_, an annelid worm, _Helobdella robusta_, a leech, and _Lottia gigantea_, a snail.  BLAST searches found an ERR in _Trichoplax_, but no ER.  BLAST searches also found ERRs in all three lophotrochozoans and invertebrate-like ERs in _Capitella_ and _Lottia_, but not in _Helobdella_.  Unexpectedly we find that the _Capitella_ ER sequence is...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2170/version/1

Assortative human pair-bonding for partner ancestry and allelic variation of the dopamine receptor D4 (DRD4) gene
Provedor de dados: 17
Autores: Dan T. A. Eisenberg; Coren L. Apicella; Benjamin C. Campbell; Anna Dreber; Justin R. Garcia; J. Koji Lum.
The 7R allele of the dopamine receptor D4 gene has been associated with attention-deficit hyperactivity disorder and risk taking. On the cross-population scale, 7R allele frequencies have been shown to be higher in populations with more of a history of long-term migrations. It has also been shown that the 7R allele is associated with individuals having multiple-ancestries. Here we conduct a replication of this latter finding with two independent samples. Measures of subjects&amp;#x2019; ancestry are used to examine past reproductive bonds. The individuals&amp;#x2019; history of inter-racial/ancestral dating and their feelings about this are also assessed. Tentative support for an association between multiple ancestries and the 7R allele were found. These...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2660/version/1

Evolution of social behaviour
Provedor de dados: 17
Autores: Vidyanand Nanjundiah.
Nowak et al.1 wish to explain why the version of kin selection theory that is summarised by the formula R&amp;#x3e;c/b (c=cost of performing &amp;#x27;altruistic&amp;#x27; act, b=benefit derived by recipient of act, R=relatedness between the two) is of little utility for understanding the evolution of eusociality. But in trying to do so they omit much that is relevant and risk misrepresenting the issue to anyone who is not familiar with the literature. A fairer account would include the following facts.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4941/version/1

A Note On The Denisova Cave mtDNA Sequence
Provedor de dados: 17
Autores: Niccolo Caldararo; Michael Guthrie.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5360/version/2

Mitochondrial Molecular Adaptations and Life History Strategies Coevolve in Plants
Provedor de dados: 17
Autores: Neeraja M. Krishnan; Basuthkar J. Rao.
Messenger RNA secondary structure prevents mutations at functionally important sites. Mutations at exposed sites would cause micro-adaptations, niche-specialization, and therefore, can be thought to promote K-strategists. Exposing, rather than protecting, conserved sites, is also potentially adaptive because they probably promote macro-adaptive changes. This presumably fits r-strategists: their population dynamics tolerate decreased survival. We found that helix-forming tendencies are greater at evolutionary conserved sites of plant mitochondrial mRNAs than at evolutionary variable sites in a majority (73%) of species&amp;#x2013;gene combinations. K-strategists preferentially protect conserved sites in short genes, r-strategists protect them most in larger...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1922/version/1

Publishing re-usable phylogenetic trees, in theory and practice
Provedor de dados: 17
Autores: Brian O&amp;#x27;Meara; Jamie Whitacre; Ross Mounce; Dan F. Rosauer; Rutger A. Vos; Arlin Stoltzfus.
Sharing and re-use of data are essential to the progressive and self-correcting nature of science. In recognition of this principle, journals and funding agencies have adopted policies to encourage sharing of information (&amp;#x27;data&amp;#x27;), including empirical data as well as computed inferences such as phylogenetic trees. &amp;#xd;&amp;#xa;Here we summarize an ongoing analysis of 1) current practices for sharing phylogenetic trees and associated data; 2) current barriers to effective sharing and reuse of such data; and 3) prospects for reducing these barriers to promote more widespread sharing and re-use. Currently, the technical infrastructure is available to support (with some limitations) rudimentary archiving in conjunction with manuscript...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6048/version/1

Hunter-gatherers in a howling wilderness: Neoliberal capitalism as a language that speaks itself
Provedor de dados: 17
Autores: Rodrick Wallace.
The &amp;#x27;self-referential&amp;#x27; character of evolutionary process noted by Goldenfeld and Woese (2010) can be restated in the context of a generalized Darwinian theory applied to economic process through a &amp;#x27;language&amp;#x27; model: The underlying inherited and learned culture of the firm, the short-time cognitive response of the firm to patterns of threat and opportunity that is sculpted by that culture, and the embedding socioeconomic environment, are represented as interacting information sources constrained by the asymptotic limit theorems of information theory. If unregulated, the larger, compound, source that characterizes high probability evolutionary paths of this composite then becomes, literally, a self-dynamic language that...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5650/version/1

Eco-evolutionary consequences of road adjacency and road salt on the wood frog, Rana sylvatica
Provedor de dados: 17
Autores: Steven P. Brady.
The network of roads on the landscape is vast, and has wide-reaching ecological influence. Recent investigations have focused on understanding impacts of contaminants from road runoff, especially deicing agents such as road salt. Despite growing research concerning ecological impacts of roads, our understanding of long-term consequences remains nascent. This stems in part from a dearth of investigations, and in part because ecological research typically ignores evolution on contemporary timescales. Yet reports of evolution influencing ecological outcomes are growing, suggesting this influence may be the rule rather than the exception. This may be especially true for species with spatially structured populations. For amphibians, such structuring coupled...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3674/version/1

It is better than you think: fluid intelligence across the lifespan
Provedor de dados: 17
Autores: Tracy Packiam Alloway; Ross Alloway.
The growth and decline of fluid intelligence is associated with brain structural changes. For example, development of fluid IQ is associated with cortex thickness during the critical period between 6 to 12 years old. On the other end of the lifespan, poor performance in cognitive functioning is attributed to a decrease of frontal gray matter density in elderly populations. In particular, there is a sharp decline in fluid IQ scores after 65 years of age. There is substantial evidence that working memory and fluid intelligence (Gf) share neural substrates, such as the prefrontal and parietal cortices. However, very little research has examined whether the pattern of growth and decline in working memory mirrors that of fluid intelligence. For example, does...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4655/version/1

A conceptual framework for the evolutionary selection of biologically &amp;#x27;essential&amp;#x27; elements
Provedor de dados: 17
Autores: Mark Conyers.
Standard texts dutifully list 16 essential elements for plant growth, yet the literature indicates that the boundary between essential and nonessential nutrients for plants is not always clear. When animals and &amp;#x27;lower&amp;#x27; organisms are considered, the team of 16 is considerably expanded and the notion of essentiality is blurred. Why are some elements more important than others to plants and to organisms in general? Here I propose three criteria by which elements might have been selected in the development of organisms: low atomic weight, at least modest abundance, and ease of assembly into complex structures. Assembly of the structural elements C, N, S, P, and O is based on valency and ionic potential. The selection of monovalent elements...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3223/version/1

On Asymmetry in Biology and Nature
Provedor de dados: 17
Autores: I. C. Baianu.
Symmetry has attracted a substantial amount of effort because considerable simplifications are possible in the mathematical and physical treatment of phenomena and natural systems that possess a certain degree of symmetry. Among physical and chemical systems the most widely known are those related to crystals and fluids. Whereas crystals have a lattice structure and a symmetry caused by &amp;#x2018;perfect&amp;#x2019; order which can be classified by mathematical symmetry groups, most fluids have an average isotropic, highly-disordered &amp;#x2018;structure&amp;#x2019; that is often considered to be random.Asymmetry is widely encountered in Biology and ecological systems- from amino acids to trees forests, and tribes, from physiological processes to...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7134/version/1

Age and origin of enigmatic megaherbs from the subantarctic islands
Provedor de dados: 17
Autores: Steven J. Wagstaff; Ilse Breitwieser; Christopher Quinn; Motomi Ito.
Biogeographic relationships in the southern hemisphere have puzzled biologists for the last two centuries. Once joined to form the supercontinent Gondwana, Africa, Antarctica, Australia, New Zealand and South America are widely separated by the Pacific and Indian oceans. Sir Joseph Hooker was the first to suggest that Antarctica served as a corridor for plant migration not unlike the land-bridges in the northern hemisphere. While the Antarctic flora was largely erased by glaciation during the Pleistocene, at least some of these Antarctic plant communities found refuge on the subantarctic islands. Here we provide support for the hypothesis that giant herbs persisted in the subantactic islands prior to the onset of Pleistocene glaciation, then dispersed...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1272/version/1

Theory of the Origin, Evolution, and Nature of Life
Provedor de dados: 17
Autores: Erik D. Andrulis.
Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations.  Thus, the advancement of scientific understanding requires new models that resolve fundamental problems.  Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life.  This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and...
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7050/version/1

The Size-Weight Illusion Is Not an Illusion When Picking the Best Objects to Throw
Provedor de dados: 17
Autores: 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&amp;#x27;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

Toward a Complete Phyloreferencing Language
Provedor de dados: 17
Autores: T. Michael Keesey.
A phyloreference is a statement indicating a taxon within a phylogenetic context. A common use for phyloreferences is in phylogenetic definitions, which tie taxonomic names to taxa via such statements. Several conventions for writing phyloreferences have been proposed, but most only cover a few &amp;#x201c;standard&amp;#x201d; forms (node&amp;#x2011;, branch&amp;#x2011;, and perhaps apomorphy&amp;#x2011;based clades) without the capacity to represent more &amp;#x201c;exotic&amp;#x201d; forms (e.g., ancestor&amp;#x2011;based clades and qualified/modified references). In order to build a complete phyloreferencing language, the mathematical underpinnings of phylogenetic contexts must be clarified. A phylogenetic context may be modeled as a directed, acyclic...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4652/version/2

Atmospheric hypoxia limits selection for large body size in insects
Provedor de dados: 17
Autores: C Jaco Klok; Jon Harrison.
Recent geological models indicate a marked increase in atmospheric oxygen partial pressure (aPO~2~) to 32 kPa in the Permo-Carboniferous (approx. 300 million years ago), subsequently falling to 13 kPa in the Triassic^1^.These aPO~2~ changes have been hypothesized to cause multiple major evolutionary events^2^ including the appearance and subsequent extinction of giant insects and other taxa^3, 4^. Patterns of increasing tracheal investment in larger insects support this hypothesis^5^, as do observations of positive relationships between aPO~2~ and body size in single- or multi-generational experiments with _Drosophila melanogaster_ and other insects^6^. Large species likely result from many generations of selection for large body size driven by predation,...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1831/version/1

Transpiration in plants: A thermodynamic imperative
Provedor de dados: 17
Autores: Carmen Noemi Hernandez Candia; Karo Michaelian.
In this article we determine the importance of transpiration in plants at three different levels of organization: the plant itself, the ecosystem, and the biosphere, all in terms of entropy production due to transpiration. We propose that transpiration is a thermodynamic imperative rather than a physiological burden for the plant. Plants have not replaced their prevalent metabolism C3 with those of less loss of water, C4 or CAM. We argue that the fact that plants retain higher rates of transpiration along evolution could be explained using thermodynamic criteria.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5463/version/1

Molecular Bio-imprinting of Biocatalysts
Provedor de dados: 17
Autores: Israr  Khan; Muhammad Waheed Akhtar.
Energy conservation is the cry of the day. Attempts are made all over the world to occupy and use energy reserves. Increased industrialization and mechanization has led to the  depletion of natural energy reserves. Its unavoidable to search for renewable sources of energy, which may be not used now but can be used by future generations. We are using the expertise of our ancestors. Thus exploiting the nature and newer techniques in this area would yield the best results. Bio-imprinting is one of those techniques whereby chemical modification is done in order to achieve highly expressed protein which can be stored in its highly active form in the specific solvent.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5665/version/1

Biodiversity is a cauliflower under the sunlight
Provedor de dados: 17
Autores: Roberto Gatti Cazzolla.
For a long time ecologists have questioned the variations of biodiversity across the latitudinal gradient. Recently it has emerged that the changes in [beta]-diversity are caused simply by changes in the sizes of species pools. I combined the species pool size and the fractal nature of ecosystems to clarify some general patterns of this gradient. Considering temperature, humidity and NPP as the main variables of an ecosystem niche and as the axis of the polygon in the Cartesian plane, it is possible to build fractal hypervolumes, whose the fractal dimension rises up to three, moving towards the equator. It follows that the best figure that graphically synthesizes the evolutionary forces that fit this ecosystem hypervolume is the fractal cauliflower.
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6917/version/1

SNP analysis reveals an evolutionary acceleration of the human-specific microRNAs
Provedor de dados: 17
Autores: Qipeng Zhang; Ming Lu; Qinghua Cui.
MicroRNAs are one class of important gene regulators at the post-transcriptional level by binding to the 3&amp;#x2019;UTRs of target mRNAs. It has been reported that human microRNAs are evolutionary conserved and show lower single nucleotide polymorphisms (SNPs) than their flanking regions. However, in this study, we report that the human-specific microRNAs show a higher SNP density than both the conserved microRNAs and other control regions, suggesting rapid evolution and positive selection has occurred in these regions. Furthermore, we observe that the human-specific microRNAs show greater SNPs minor allele frequency and the SNPs in the human-specific microRNAs show fewer effects on the stability of the microRNA secondary structure, indicating that the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2127/version/1

Independent elaboration of steroid hormone signaling pathways in Metazoans
Provedor de dados: 17
Autores: 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 &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3374/version/1

Birth Control Does Not Significantly Alter Women&amp;#x2019;s Preferences for Variants of Men&amp;#x2019;s Voices
Provedor de dados: 17
Autores: Jason W. J. W. W. Whitaker; Ryan R. S. Setten; Ulv U. A. Ankerstjerne.
Research shows that women&amp;#x2018;s preferences for masculine voices (low pitch) vary as a function of the menstrual cycle, becoming positively augmented around ovulation. The proximate cause catalyzing this effect is attributed to fluctuating estrogen levels. Thus, the introduction of hormonally based birth control has been to shown to have a dampening effect in experiments researching women&amp;#x2018;s preference of dimorphic secondary sexual characteristics. However, this dampening effect has not yet been explored in respect to women&amp;#x2018;s preferences for masculine voice types. This experiment sought, first, to investigate the effect of birth control on subjects off and on birth control; and, second, to replicate past findings:...
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5895/version/1

P-POD, The Princeton Protein Orthology Database, as a Tool for Identifying Gene Function
Provedor de dados: 17
Autores: Michael S. Livstone; Rose Oughtred; Sven Heinicke; Fan Kang; Benjamin Vernot; Aiton Goldman; Dannie Durand; David Botstein; Kara Dolinski.
P-POD, the Princeton Protein Orthology Database, classifies proteins from model organisms and medically-important organisms into families of homologs and provides curated evidence from the literature addressing these relationships.  The web page for each protein family includes a phylogenetic tree, sequence alignment, and cross-references to disease-related papers from SGD, papers describing complementation experiments, and OMIM gene and disease information.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As participants in the Gene Ontology Consortium&amp;#x2019;s Reference Genome project, we seek to provide a consistent centralized method to identify orthologous proteins.  We have expanded P-POD to include the protein complement of the twelve Reference Genomes.  In...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3119/version/1

Genome Structural-Functional Peculiarities Affecting Plant Epigenetic Variability and Evolution
Provedor de dados: 17
Autores: Evgenii  Levites.
There is an attempt to explain some evolutionary processes in plants such as saltatory changes on the base of multidimensionality of plant inherited information coding. According to the suggested hypothesis, inherited information is coded by not only a nucleotide sequence but also by chromosome differential endoreduplication. It is supposed that chromosomes compete among each other for the contact with the nuclear membrane, but a change in the endoreduplication degree of various chromosome sites can result in a change of  a competition ability for the contact with a nuclear membrane. A simultaneous increase of chromosome endoreduplication degree of many sites can lead to an increase of nuclear membrane surface and to a change in chromosome competitive...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Plant Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4405/version/1

The origin of vertebrates and their symmetry, segmentation, chord and tubular nervous system
Provedor de dados: 17
Autores: 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

Lightning talk: PyPop - a software pipeline for large-scale multilocus population genomics
Provedor de dados: 17
Autores: Alex K. Lancaster; Richard M. Single; Owen D. Solberg; Mark P. Nelson; Glenys Thomson.
PyPop (Python for Population Genomics) is an open-source framework for performing large-scale population genetic analyses on multilocus genotype and allele frequency data. It computes tests and measures of Hardy-Weinberg equilibrium (locus-level and individual genotype-level), linkage disequilibrum, and selection, and estimates multi-locus haplotypes. PyPop supplements and extends existing population genetic software incorporating them as modules, modified to accommodate highly polymorphic data, rather than reimplementing them from scratch. It facilitates evolutionary analyses by integrating population genetic statistics within and across populations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Originally developed to analyze the highly polymorphic genetic data of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4700/version/1

A database of orthologous exons in primates for comparative analysis of RNA-seq data
Provedor de dados: 17
Autores: Ran Blekhman.
RNA-seq technology facilitates the study of gene expression at the level of individual exons and transcripts. Moreover, RNA-seq enables unbiased comparative analysis of expression levels across species. Such analyses typically start by mapping sequenced reads to the appropriate reference genome before comparing expression levels across species. However, this comparison requires prior knowledge of orthology at the exon level. With this in mind, I constructed a database of orthologous exons across three primate species (human, chimpanzee, and rhesus macaque). The database facilitates cross-species comparative analysis of exon- and transcript-level regulation. A web application allowing for an easy database query: http://giladlab.uchicago.edu/orthoExon/
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7054/version/1

New species from the deep Pacific suggest that carnivorous sponges date back to the Early Jurassic
Provedor de dados: 17
Autores: Jean Vacelet; Michelle Kelly.
Some deep-sea poecilosclerid sponges (Porifera) have developed a carnivorous feeding habit that is very surprising in sponges^1^. As shown by the typical morphology of their spicules, they most probably evolved from &amp;#x22;normal sponges&amp;#x22; under the difficult conditions of a deep-sea environment. Such evolution, which implies the loss of the diagnostic character of the phylum Porifera, i.e. a filter feeding habit through a complex aquiferous system, should be of great interest in the understanding of the origin of metazoans. Some scenarios, based on the hypothesis of the paraphyly of Porifera, allege that metazoans could derive from a sponge filter-feeding body plan. A difficulty, however, is to imagine the transition from a sponge grade of...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2327/version/1

`The frozen accident&amp;#x27; as an evolutionary adaptation: A rate distortion theory perspective on the dynamics and symmetries of genetic coding mechanisms
Provedor de dados: 17
Autores: James  F. Glazebrook; Rodrick  Wallace.
We survey some interpretations and related issues concerning the frozen hypothesis due to F. Crick and how it can be explained in terms of several natural mechanisms involving error correction codes, spin glasses, symmetry breaking and the characteristic robustness of genetic networks.  The approach to most of these questions involves using elements of Shannon&amp;#x27;s rate distortion theory incorporating a semantic system which is meaningful for the relevant alphabets and vocabulary implemented in transmission of the genetic code. We apply the fundamental homology between information source uncertainty with the free energy density of a thermodynamical system with respect to transcriptional regulators and the communication channels of sequence/structure...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5717/version/1

BHL, The Biodiversity Heritage Library:  An Expanding International Collaboration
Provedor de dados: 17
Autores: Constance Rinaldo; Catherine  Norton.
*Background/Question/Methods*&amp;#xd;&amp;#xa;The Biodiversity Heritage Library (BHL; &amp;#x22;http://www.biodiversitylibrary.org/&amp;#x22;:http://www.biodiversitylibrary.org/), one of the cornerstones of the Encyclopedia of Life (eol.org), now contains nearly 13 million digitized pages of 12,000 titles comprised of 32,000 volumes of the published literature of biodiversity held in the collections of major natural history libraries. The BHL has made this literature available for open access and responsible use as a part of a global &amp;#x201c;biodiversity commons.&amp;#x201d; The BHL partnership is working with the global taxonomic community, publishers, organizations such as JSTOR and BIOONE, and the Internet Archive, to ensure that the biodiversity...
Tipo: Poster
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3620/version/1

Towards a Taxonomically Intelligent Phylogenetic Database
Provedor de dados: 17
Autores: Roderic Page.
This note outlines some of the key intellectual obstacles that stand in the way of creating a usable phylogenetic database. These challenges include the need to accommodate multiple taxonomic names and classifications, and the need for tools to query trees in biologically meaningful ways. Until these problems are addressed, and a taxonomically intelligent phylogenetic database created, much of our phylogenetic knowledge will languish in the pages of journals.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1028/version/1

A Genome-Wide Analysis Reveals Significant Overlap of Transcription and DNA Repair in Stationary Phase Yeast
Provedor de dados: 17
Autores: Aviv de Morgan; Leonid  Brodsky; Yefim Ronin; Eviatar Nevo; Abraham Korol; Yechezkel Kashi.
The association between transcription and DNA repair is acknowledged as a player in the generation of mutations in a non-random fashion in prokaryotes and eukaryotes. Previous studies demonstrated that the transcription complex is capable of directing DNA repair to sites of transcription. This process is especially important to growth-arrested cells, in which many DNA repair capacities are diminished; it may also lead to mutations preferentially in transcribed genes. Using microarray analysis of growth-arrested yeast cultures, we demonstrated on a genomic scale, the co-localization of a DNA-turnover marker, indicative of DNA-repair-associated DNA synthesis, with genes persistently transcribed during stationary phase. This may serve as a clue regarding the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1543/version/1

Gene diversity among some endogamous population of Amravati District, Maharashtra, India.
Provedor de dados: 17
Autores: Rupali P. Tekade; Nandkishor E. Warghat; M. M. Baig.
The present work deals with the distribution of ABO, Rh and sickling alleles as markers to study the genetic structure and micro-demarcation among castes and tribal populations from the Amravati district of Maharashtra. Three loci namely, ABO, Rh and sickling were selected to measure the relative frequency of respective alleles in ten (10) endogamous populations inhabiting the Amravati District. The ABO locus was found to be less polymorphic when compared with other loci. On the other hand, Rh and sickling loci were found to be more polymorphic. Construction of a dendrogram using allele frequency data reveals an interesting relationship among the caste and tribe. An analysis shows three major clades comprising A, B and C. Clade A comprises Islamic Dawoodi...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5379/version/1

Strong and weak competitors can coexist in the same niche
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The competitive exclusion principle postulates that two trophically identical but fitness different species can not stably coexist in the same niche. However, this principle contradicts the observed nature&amp;#x27;s species richness. This fact is known as the biodiversity paradox. Here, using a simple cellular automaton model, we mechanistically show how two trophically identical, but fitness different species may stably coexist in the same niche. As environment is stable and any trade-offs are absent in this model, it strongly violates the competitive exclusion principle.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7107/version/2

My experiment with open science: Why the benefits of sharing go beyond source code
Provedor de dados: 17
Autores: Carl Boettiger.
I briefly describe three themes that help maximize the benefits of an open science approach towards code, literature, discussions, and lab notebooks.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4602/version/1

Inter-Tunneling Mechanism of Colliding Population Waves
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
Here we show a new interaction mechanism of colliding population waves. It provides a stable coexistence of two similar but different species competing for the same limiting resource during their asexual propagation in a limited homogeneous environment under constant conditions. The revealed mechanism opens new opportunities in conservation biology.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6990/version/1

Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are
Provedor de dados: 17
Autores: Shi Huang.
There exists a remarkable correlation between genetic distance as measured by protein or DNA dissimilarity and time of species divergence as inferred from fossil records.  This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily accumulated in recent years from studies of extant organisms.  Here the published DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock hypothesis.  The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister species are.  Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are.  The findings...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1676/version/2

Evaluation of effective parameters on fabrication of BSA nanoparticles
Provedor de dados: 17
Autores: 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

Thermal signatures of human pheromones in sexual and reproductive behaviour
Provedor de dados: 17
Autores: Andrea Mazzatenta; Gian Luca Romani; Luca Tommasi; Arcangelo Merla.
Chemically mediated sexual communication in humans has been largely neglected due to its non-conscious and relatively concealed nature. However, menstrual cycle synchronisation, puberty onset in young pre-pubertal girls exposed to their stepfather, and consanguinity avoidance suggest a function in the physiological regulation of sexual and reproductive behaviour in humans. These phenomena are related to activation of the limbic system by pheromones. On the basis of sexually dimorphic activation of brain hypothalamic areas and the control of body temperature via the hypothalamus, our hypothesis is that human sexual pheromones can induce thermal effects that can be revealed by high-resolution thermal infrared imaging. Here we show that in women, male sexual...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4477/version/1

TreeRipper: towards a fully automated optical tree  recognition software
Provedor de dados: 17
Autores: Joseph Hughes.
Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century. &amp;#xd;&amp;#xa;TreeRipper is a command line c++ program for the fully-automated recognition of multifurcating phylogenetic trees. The program accepts a range of input image formats  (PNG, JPG/JPEG, GIF, TIFF or PDF ). Then follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4997/version/1

Efficient learning in Approximate Bayesian Computation
Provedor de dados: 17
Autores: Mohammed  Sedki; Pierre  Pudlo.
Efficient learning in Approximate Bayesian Computation
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5962/version/1

Telomeres in Evolution and Development from Biosemiotic Perspective
Provedor de dados: 17
Autores: Guenther Witzany.
Whereas telomeres protect terminal ends of linear chromosomes, telomerases identify natural chromosome ends being different from broken DNA. Although telomeres play a crucial role in the linear chromosome organisation of eukaryotic cells, their molecular syntax descended from an ancient retroviral competence. This is an indicator for the early retroviral colonization of large double stranded DNA viruses, which are putative ancestors of the eukaryotic nucleus.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This contribution will demonstrate an advantage of the biosemiotic approach towards our evolutionary understanding of telomeres: focus on the genetic/genomic structures as language-like text which follows combinatorial (syntactic), context-sensitive (pragmatic) and...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/932/version/2

To every man his own language: Are we all Darwin&amp;#x2019;s children?
Provedor de dados: 17
Autores: Shantanu Ghosh.
Although current theories of language evolution have examined both molecular evolution as well as functional connectivity of the cortex in humans as well as other primates, a description of language as pre-adaptation open to natural selection has eluded us so far. Here I review the evidence in favor of natural selection that trigger growth and plasticity of the prefrontal cortex in humans and its links to the mirror neuron system. Evolvability of recursive mechanisms as the hallmark of evolution of symbolic communication in humans is also investigated. The polymorphism of genes like ASPM, Microcephalin and FOXP2 in the evolution of language as an emergent property has also been examined.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1375/version/1

Metabolic, Replication and Genomic  Category of Systems in Biology,  Bioinformatics and Medicine
Provedor de dados: 17
Autores: I. C. Baianu.
Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life&amp;#x2019;s origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important question of the minimal living organism by defining the functional relations that would have made life possible in such a minimal system- a grandad and grandma of all living organisms on Earth. Genomic systems are also considered as molecular realizations of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7051/version/1

To be resistant or tolerant: the evolution of mixed defence strategies
Provedor de dados: 17
Autores: Etzel Garrido; Juan Fornoni.
Theory predicts that resistance and tolerance represent mutually exclusive strategies of host defence. However, empirical evidence reveals that individual hosts simultaneously allocate resources to both mechanisms. Understanding the maintenance of this defence pattern remains controversial because empirical evidence is at odds with theoretical assumptions. Here, we present a novel host-enemy dynamic that considers: the differential effect of each defence strategy upon the evolutionary response of natural enemies; the process of local adaptation of the natural enemies to their hosts and the effect of negative and positive frequency-dependent selection acting on resistance and tolerance respectively. Our analysis suggests that a mixed pattern of defence...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4791/version/1

Ant Species Richness Around Amravati City Maharashtra, India
Provedor de dados: 17
Autores: Aravind B. Chavhan; Santosh S. Pawar; Mumtaz M. Baig.
Ants deserve a special place in the study of ecology, including behavior, given their species richness, social habits, and high densities, contributing to much of the animal biomes on earth (Gadagkar et.at. 1993). As ants can be studied virtually everywhere from forest interiors below ground, right up to the kitchen, we attempted a study to assess the ant species richness in a variety of habitats in and around Amravati city. The prime objective of this study is to prepare a partial checklist of ants of Amravati and to compare species richness between selected study sites. Eight study sites with different levels and types of vegetation were selected for the study.&amp;#xd;&amp;#xa;We employed an &amp;#x201c;all out search&amp;#x201d; method for collection...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5491/version/1

Non-linear Regression Approaches in ABC
Provedor de dados: 17
Autores: Michael G. B. Blum.
In this talk, we consider different methods of parameter inference for ABC. Derivations of the asymptotic bias and variance of the standard ABC estimators indicates that ABC may achieve poor performance when the dimension of the summary statistics is large. The linear adjustment introduced by Beaumont et al. (2002) is found to achieve better performance when there is a nearly homoscedastic relationship between the summary statistics and the parameter of interest. To provide a more flexible adjustment method, we propose two innovations. The new method fits 1/a heteroscedatic rather than a homoscedastic regression model and consider 2/non linear instead of linear regression. The new algorithm is compared to the state-of-the-art approximate Bayesian methods...
Tipo: Presentation
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5954/version/1

Inverse relationship between genetic diversity and epigenetic complexity
Provedor de dados: 17
Autores: 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 &amp;#x2018;Neutral Theory&amp;#x2019;, 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: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/1751/version/2

The Shape and Dimensionality of Phylogenetic Tree-Space Based on Mitochondrial Genomes
Provedor de dados: 17
Autores: James C. Wilgenbusch; Wen Huang; Kyle A. Gallivan.
Phylogenetic analyses of large and diverse data sets generally result in large sets of competing phylogenetic trees. Consensus tree methods used to summarize sets of competing trees discard important information regarding the similarity and distribution of competing trees. A more fine grain approach is to use a dimensionality reduction method to project tree-to-tree distances in 2D or 3D space. In this study, we systematically evaluate the performance of several  nonlinear dimensionality reduction (NLDR) methods on tree-to-tree distances obtained from independent nonparametric bootstrap analyses of genes from three mid- to large-sized mitochondrial genome alignments.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4605/version/1

Unnatural Selection: A new formal approach to punctuated equilibrium in economic systems
Provedor de dados: 17
Autores: Rodrick Wallace.
Generalized Darwinian evolutionary theory has emerged as central to the description of economic process (e.g., Aldrich et. al., 2008). Here we demonstrate that, just as Darwinian principles provide necessary, but not sufficient, conditions for understanding the dynamics of social entities, in a similar manner the asymptotic limit theorems of information theory provide another set of necessary conditions that constrain the evolution of socioeconomic process. These latter constraints can, however, easily be formulated as a statistics-like analytic toolbox for the study of empirical data that is consistent with a generalized Darwinism, and this is no small thing.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5612/version/1

Phenex: Ontological Annotation of Phenotypic Diversity
Provedor de dados: 17
Autores: James P. Balhoff; Wasila M. Dahdul; Cartik R. Kothari; Hilmar Lapp; John G. Lundberg; Paula Mabee; Peter E. Midford; Monte Westerfield; Todd J. Vision.
Phenex is a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic variation using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Despite the centrality of the phenotype to so much of biology, traditions for communicating information about phenotypes are idiosyncratic to different disciplines. Phenotypes seem to elude standardized descriptions due to the variety of traits that compose them and the difficulty of capturing the complex forms and subtle differences among organisms that we can readily observe. Consequently, phenotypes are refractory to attempts at data integration that would allow computational...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4636/version/1

Range of motion in intervertebral joints: why we don&amp;#x2019;t trust DinoMorph
Provedor de dados: 17
Autores: Michael P. Taylor.
Attempts to quantitatively reconstruct the range of motion of sauropod necks are intrinsically flawed because of ubiquitous distortion in preserved cervical vertebrae.  This is true even for specimens that are usually considered particularly well preserved, such as the Carnegie Diplodocus and the Berlin Giraffatitan.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6878/version/1

Genomic Replikin Counts of Infectious Salmon Anemia Virus (ISAV) in Canada Exceed the Counts in Lethal Outbreaks in Norway, Chile, and Scotland. Real-Time Tracking of the Evolution of the ISAV Genome and the Resultant Replikins Solid Phase ISAV Vaccine Make ISAV Pandemic Prevention Possible.
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Genomic Replikin CountsTM  of Infectious Salmon Anemia Virus (ISAV) in Canada Exceed the Counts in Lethal Outbreaks in Norway, Chile, and Scotland. Real-Time Tracking of the Evolution of the ISAV Genome and the Resultant Replikins Solid Phase ISAV Vaccine Make ISAV Pandemic Prevention Possible.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6991/version/1

Hunter-Gatherers in a Howling Wilderness: Farming economic systems for human needs
Provedor de dados: 17
Autores: Rodrick Wallace.
Recent advances in evolutionary theory applied to economic structure and process may permit construction of both new economic theory and new tools for data analysis that can help in the design of more robust economic policies and practices, resulting in less frequent and less disruptive Knightian transitions, and enabling as well the design of institutions that are, in turn, less disrupted by those that do occur.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5650/version/2

Data citation in the wild
Provedor de dados: 17
Autores: Valerie Enriquez; Sarah Walker Judson; Nicholas M. Walker; Suzie Allard; Robert B. Cook; Heather A. Piwowar; Robert J. Sandusky; Todd J. Vision; Bruce E. Wilson.
Consistent attribution of research data upon reuse is necessary to reward the original data-producing investigators, reconstruct provenance, and inform data sharing policies, tool requirements, and funding decisions.  Unfortunately, norms for data attribution are varied and often weak.  As part of the DataONE 2010 summer internship program, three interns studied the policies, practice, and implications of current data attribution behavior in the environmental sciences.  We found that few policies recommend robust data citation practices: in our preliminary evaluation, only one-third of repositories (n=26), 6% of journals (n=307), and 1 of 53 funders suggested a best practice for data citation.  We manually reviewed 500 papers published between 2000 and...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5452/version/1

Strong and weak competitors can coexist in the same niche
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The competitive exclusion principle postulates that two trophically identical but fitness different species can not stably coexist in the same niche. However, this principle contradicts the observed nature&amp;#x27;s species richness. This fact is known as the biodiversity paradox. Here, using a simple cellular automaton model, we mechanistically show how two trophically identical, but fitness different species may stably coexist in the same niche. As environment is stable and any trade-offs are absent in this model, it strongly violates the competitive exclusion principle.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7107/version/1

Roots and Emergence of Cognition in Evolution
Provedor de dados: 17
Autores: Walter Riofrio.
Trying to understand when and how the cognitive phenomena arise in evolution continues being a hard problem of confronting. One important task is to find the ways in which we will be able to arrive at those explanations that will enable us to understand how living beings put together perceived sensory information as well as how they represent it. In this presentation, we address some conceptual questions involved in the relationships between sensorial information perceived by brains and its representational capacities. &amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/413/version/2

Aging as a consequence of misrepair -- A novel theory of aging
Provedor de dados: 17
Autores: 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 &amp;#x2018;faults&amp;#x2019; 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 &amp;#x2018;damage&amp;#x2019; and &amp;#x2018;fault&amp;#x2019; 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

A condition of cooperation. Games on network
Provedor de dados: 17
Autores: Tomohiko Konno.
Natural selection is often regarded as a result of severe competition. Defect seems beneficial for a single individual in many cases.However, cooperation is observed in many levels of biological systems ranging from single cells to animals, including human society. We have yet known that in unstructured populations, evolution favors defectors over cooperators. On the other hand, there have been much interest on evolutionary games^1,2^ on structured population and on graphs^3-16^. Structures of biological systems and societies of animals can be taken as networks. They discover that network structures determine results of the games. Together with the recent interest of complex networks^17,18^, many researchers investigate real network structures. Recently...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3028/version/1

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry lifting model based on Tlusty&amp;#x27;s elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4120/version/4

Exaptation and emergence as mechanisms to cross fitness valleys during evolution: an example using simulated homing behaviour
Provedor de dados: 17
Autores: Richard Stafford.
Evolution is often considered a gradual hill climbing process, slowly increasing the fitness of organisms. I investigate the evolution of homing behaviour in simulated intertidal limpets. In order to evolve path integration as a homing mechanism, a temporary reduction in an organism&amp;#x2019;s fitness is required &amp;#x2013; since high developmental costs occur before a successful homing strategy evolves. Simple hill-climbing algorithms, therefore, only rarely result in the evolution of a functional homing behaviour. The inclusion of a second behaviour (trail-following) greatly increases the frequency of success of evolution of a path integration strategy. Initially an emergent homing behaviour is formed combining path integration with trail following....
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2172/version/1

Detection of substrate binding motifs for morphine biosynthetic pathway intermediates in novel wound inducible (R,S)-reticuline 7-O-methyltransferase of Papaver somniferum
Provedor de dados: 17
Autores: Sonal Mishra; Abha Meena; Sema Singh; Dharmendra Kumar Yadav; Feroz  Khan; Rakesh K. Shukla.
The benzylisoquinoline alkaloids (BIA) comprise a large and diverse group of nitrogen-containing secondary metabolites with about 2500 compounds identified in plants. BIA biosynthesis begins with the condensation of the tyrosine derived precursors dopamine and p-hydroxyphenylacetaldehyde to (S)-norcoclaurine. Subsequent regiospecific O- and N-methylations and aromatic ring hydroxylation lead to (S)-reticuline, which is the central intermediate for almost all BIAs. For morphinan alkaloid biosynthesis, (S)-reticuline undergoes an inversion of stereochemistry to (R)-reticuline, followed by C-C phenol coupling catalyzed by a unique cytochrome P450-dependent monooxygenase to yield salutaridine. The cDNA sequence of enzymes leading to (S)-reticuline, as well as...
Tipo: Poster
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5790/version/1

Animal emergence during Snowball Earths by thermosynthesis in submarine hydrothermal vents
Provedor de dados: 17
Autores: 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

The hypothesis of basic phenotype modules
Provedor de dados: 17
Autores: 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

Using ABC for model design and inference across biological scales
Provedor de dados: 17
Autores: Oliver  Ratmann.
Using ABC for model design and inference across biological scales.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5960/version/1

Paleolinguistics brings more light on the earliest history of the traditional Eurasian pulse crops
Provedor de dados: 17
Autores: Aleksandar M. Mikic; Aleksandar P. Medovic; Branko T. Cupina; Vojislav M. Mihailovic; Aleksandra M. Ignjatovic-Cupina; Vuk B. Djordjevic; Borislav D. J. Kobiljski.
Traditional pulse crops such as pea, lentil, field bean, bitter vetch, chickpea and common vetch originate from Middle East, Mediterranean and Central Asia^1^. They were a part of human diets in hunter-gatherers communities^2^ and are one of the most ancient cultivated crops^3,4^. Europe has always been rich in languages^5^, with individual families still preserving common vocabularies related to agriculture^6,7^. The evidence on the early pulse history witnessed by the attested roots in diverse Eurasian proto-languages remains insufficiently clarified and its potential for supporting archaeobotanical findings is still non-assessed. Here we show that the paleolinguistic research may contribute to archaeobotany in understanding the role traditional Eurasian...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5837/version/1

Eco-evolutionary consequences of road adjacency and road salt on the wood frog, Rana sylvatica
Provedor de dados: 17
Autores: Steven P. Brady.
The network of roads on the landscape is vast, and has wide-reaching ecological influence. Recent investigations have focused on understanding impacts of contaminants from road runoff, especially deicing agents such as road salt. Despite growing research concerning ecological impacts of roads, our understanding of long-term consequences remains nascent. This stems in part from a dearth of investigations, and in part because ecological research typically ignores evolution on contemporary timescales. Yet reports of evolution influencing ecological outcomes are growing, suggesting this influence may be the rule rather than the exception. This may be especially true for species with spatially structured populations. For amphibians, such structuring coupled...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3674/version/2

Allelic Frequency of ABO And Rh D Blood Group Among The Banjara Caste Population of Akola District, Maharashtra , India
Provedor de dados: 17
Autores: Aravind B. Chavhan.
The distribution of ABO blood groups and Rh (D) factor has been studied among the Banjara Caste population of Akola District (Maharashtra). The O, A, B, and AB blood group percentage were recorded as 27.64%, 22.91%, 37.45% and 12% respectively. The Rh negative incidence was recorded as 02.55%. The allele frequencies of O, A, B and AB groups in the combined data were found to be 0.5196, 0.2880, and 0.1924 respectively and Rh (D) positive allelic frequency was 0.8405.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5771/version/1

A war-prone tribe migrated out of Africa to populate the world.
Provedor de dados: 17
Autores: Eduardo  Moreno.
Of the tribal hunter gatherers still in existence today, some lead lives of great violence, whereas other groups live in societies with no warfare and very little murder^1,2,3,4,5^. Here I find that hunter gatherers that belong to mitochondrial haplotypes L0, L1 and L2 do not have a culture of ritualized fights. In contrast to this, almost all L3 derived  hunter gatherers have a more belligerent culture that includes ritualized fights such as wrestling, stick fights or headhunting expeditions. This appears to be independent of their environment, because ritualized fights occur in all climates, from the tropics to the arctic. There is also a correlation between mitochondrial haplotypes and warfare propensity or the use of murder and suicide to resolve...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4303/version/1

The &amp;#x27;consciousness&amp;#x27; of the living state: Extending the Baars global broadcast model across physiological subsystems
Provedor de dados: 17
Autores: Rodrick Wallace.
For the broad spectrum of cognitive biological phenomena having &amp;#x27;dual&amp;#x27; 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

A Target Restricted Assembly Method (TRAM) for Phylogenomics
Provedor de dados: 17
Autores: Kevin P. Johnson; Kimberly K. O. Walden; Hugh M. Robertson.
While next generation sequencing technology can produce sequences covering the entire genome, assembly and annotation are still prohibitive steps for many phylogenomics applications.  Here we describe a method of Target Restricted Assembly (TRAM) of a single lane of Illumina sequences for genes of relevance to phylogeny reconstruction, i.e. single copy protein-coding genes.  This method has the potential to produce a data set of hundreds of genes using only one Illumina lane per taxon.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4612/version/1

The Gramene Genetic Diversity Module: a resource for genotype-phenotype association analysis in grass species
Provedor de dados: 17
Autores: Charles Chen; Genevieve DeClerck; Terry Casstevens; Ken Youens-Clark; Jon Zhang; Doreen Ware; Pankaj Jaiswal; Susan McCouch; Edward Buckler.
The Genetic Diversity module of the Gramene database (&amp;#x22;http://www.gramene.org/diversity&amp;#x22;:http://www.gramene.org/diversity) is specifically designed to handle data from high-throughput sequencing and array-based genotyping plateforms. Empowered by the Genomic Diversity and Phenotype Data Model, Gramene Genetic Diversity module provides live database connectivities of RFLP, SSR and SNP allele data, information about QTL, passport data for wild and cultivated germplasm from rice, maize, wheat, and _Arabidopsis_, and quantitative phenotypic data for some of these accessions. Large datasets of SNP variation are searchable via genomic positions of interest by SNP Query tool on a sequenced genome; and, trait associations, patterns of linkage...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4645/version/1

Data Management Plan for Monogram BioSciences
Provedor de dados: 17
Autores: Christos J. Petropoulos.
This is the data plan for access to data underlying published reports by Monogram BioSciences.
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Pharmacology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5668/version/1

Adaptive evolution and then what?
Provedor de dados: 17
Autores: Richard Svanb&amp;#xe4;ck; Mario Pineda-Krch; Michael Doebeli.
Traits determining ecological interactions and dynamics are generally subject to natural selection. That genetically based individual variation in ecological traits can influence population dynamics has interested population biologist from various perspectives. Population ecologists recognized the need to incorporate individual variation in models of population regulation, while evolutionary biologists wish to understand genetic and evolutionary dynamics, e.g. of life history traits, in density-regulated populations. But how does adaptation in ecological traits affect population dynamics? In this project we investigated how ecological dynamics changes as a consequence of adaptive evolution in ecological traits using an individual-based predator-prey model.
Tipo: Poster
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/57/version/1

Roman roads: The hierarchical endosymbiosis of cognitive modules
Provedor de dados: 17
Autores: Rodrick Wallace.
Serial endosymbiosis theory provides a unifying paradigm for examining the interaction of cognitive modules at vastly different scales of biological, social, and cultural organization. A trivial but not unimportant model associates a dual information source with a broad class of cognitive processes, and punctuated phenomena akin to phase transitions in physical systems, and associated coevolutionary processes, emerge as consequences of the homology between information source uncertainty and free energy density. The dynamics, including patterns of punctuation similar to ecosystem resilience transitions, are largely dominated by the availability of &amp;#x27;Roman roads&amp;#x27; constituting channels for the transmission of information between modules.
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3892/version/1

On The Dangers Of Aligning RNA Sequences Using &amp;#x201c;Conserved&amp;#x201d; Motifs
Provedor de dados: 17
Autores: Roderic Page.
Aligning RNA sequences can be a challenging task. Automatic sequence alignment programs typically align sequences only with respect to primary sequence, and as a result may yield spurious alignments. Incorporating information on RNA secondary structure can improve the alignment, but this must usually be done by hand. One approach to aligning RNA sequences uses &amp;#x22;conserved motifs&amp;#x22;, however relying on these motifs may lead to gross errors of alignment if, in fact, those motifs are not conserved.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1029/version/1

New discovery of the oldest maize weevils in the world from Jomon potteries, Japan
Provedor de dados: 17
Autores: Hiroki Obata; Aya Manabe; Naoko Nakamura; Tomokazu Onishi; Yasuko Senba.
The maize weevil (_Sitophilus zeamais_) and rice weevil (_Sitophilus oryzae_) are two of the most damaging insects for stored grains, and are characteristic species of ancient Japan. Both species and the granary weevil (_Sitophilus granarius_) are common elsewhere in the world, but the natural distribution of maize and rice weevils is restricted to the Old World^1^. Japanese archaeological records contain a few maize weevil fossils after the Middle Yayoi period (ca. 2000 aBP)^2^. However, since evidence of weevils was discovered as impressions in Jomon potsherds in 2004^3^, many weevil impressions have been found. The oldest is from the Late Jomon (ca. 4000 to 3200 aBP). These findings and other archaeological evidence suggest that the maize weevil invaded...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4407/version/1

Reassessing the Lineage Fusion Hypothesis for the Origin of Double Membrane Bacteria
Provedor de dados: 17
Autores: Kristen S. Swithers; Gregory P. Fournier; J. Peter Gogarten; Pascal Lapierre.
In 2009, James Lake introduced a new hypothesis in which reticulate phylogeny reconstruction is used to elucidate the origin of Gram-negative bacteria.  The presented data supported the Gram-negative bacteria originating from an ancient endosymbiosis between the Actinobacteria and Clostridia.  His conclusion was based on a presence-absence analysis of protein families that divided all prokaryotes into five groups: Actinobacteria, Double Membrane bacteria (DM), Clostridia, Archaea and Bacilli.  Of these five groups, the DM are by far the largest and most diverse group compared to the other groupings.  While the fusion hypothesis for the origin of double membrane bacteria is enticing, we show that the signal supporting an ancient symbiosis is lost when the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5812/version/1

Study of Echinoids of Gurpi formation, Iran
Provedor de dados: 17
Autores: Behnaz Balmaki; Masoud  Asgharian Rostami.
In order to detailed study of Echinoids, some samples are collected from Brown limestone member of Seimare from Gurpi Formation with 213 meter thickness which located in the vicinity of Ilam province; settling over Ilam Formation continuously. Paleontological results indicated Campanian - maastrichtian age at this section. Detailed analysis of the 300 samples led to recognition of Bivalve especially Bivalve of Lofa, Brachiopods and five species of Echinoids such as: _Salenia nutrix_, _Globator bleicheri_, _Orthopsis miliarisi_, _Goniopygus superbus_, and _Conulus douville_
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3839/version/1

Future Predictions of _Cyclamen_ Distribution in the Mediterranean Region
Provedor de dados: 17
Autores: Claudia Ciotir; Chris Yesson; Alastair Culham.
_Cyclamen_ (Myrsinaceae) occupy the Mediterranean region, with highest diversity in Greece and Turkey, with a few species endemic to islands. _Cyclamen_ species have a phenological preference for dry summers and wet winters. A recent study developed models of the climatic niches of _Cyclamen_. These models were projected into future climate scenarios for 2050. The area of climatic suitability for every _Cyclamen_ species is predicted to decrease. A limited dispersal capacity places them at high risk of extinction. Half of the species are threat ened with extinction due to their potential area loss, indicating that conservation and protection for these species has to be implemented by adding them to the red list.
Tipo: Poster
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3066/version/1

Fish play Minority Game as humans do
Provedor de dados: 17
Autores: Sy-Sang Liaw; Ruey-Tarng Liu; Fei Fang Chung.
Previous computer simulations of the Minority Game (MG) have shown that the average agent number in the winning group (i.e., the minority group) had a maximal value such that the global gain was also maximal when an optimal amount of information was available to all agents . This property was further examined and its connection to financial markets has also been discussed . Here we report the results of an unprecedented real MG played by university staff members who clicked one of two identical buttons (A and B) on a computer screen while clocking in or out of work. We recorded the number of people who clicked button A for 1288 games, beginning on April 21, 2008 and ending on October 31, 2010, and calculated the variance among the people who clicked A as a...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5440/version/1

Quadruple context-free L-System mathematical tools as origin of biological evolution
Provedor de dados: 17
Autores: Arunava Goswami; Pabitra Pal Choudhury; Rajneesh Singh; Sk. Sarif Hassan.
It is well known that A, T, G, C annealed together early in evolution and the long stretch of DNA was found which ultimately resulted into chromosomes of different organisms.  But it is unclear till date how exons, introns, conserved protein domains was formed. Using the DNA sequences of the largest known gene-family present in human genome, i.e., olfactory receptors and simplest possible quadruple context-free L-Systems, we show that conserved protein domains and intergenic regions which lies at the heart of the biological evolution started with a sixteen base-pairs stretch of DNA.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4851/version/1

Strong violation of the competitive exclusion principle
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
Bacteria and plants are able to form population waves as a result of their consumer behaviour and propagation. A soliton-like interpenetration of colliding population waves was assumed but not proved earlier. Here we show how and why colliding population waves of trophically identical but fitness different species can interpenetrate through each other without delay. We have hypothesized and revealed here that the last mechanism provides a stable coexistence of two, three and four species, competing for the same limiting resource in the small homogeneous habitat under constant conditions and without any fitness trade-offs. We have explained the mystery of biodiversity mechanistically because (i) our models are bottom-up mechanistic, (ii) the revealed...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Microbiology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6667/version/1

Pioneer Discovery of secondary gold deposits-unique bacterioforms andplacers in north Goa from deep coremetabiosphere
Provedor de dados: 17
Autores: Nandkumar M. Kamat.
Bacterioform secondary gold deposits were discovered in tilloid overlaying archaean base rock (metagraywacke) in Sanvordem rock formation, at the depth of 65 metres in north Goa , India and were confirmed optically as microbiogenic Gold. Multiple and unique forms were seen. This is claimed to be first report of bacterioform Gold in deep cores in Goa, India and Asia.
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Ecology; Genetics &amp; Genomics; Microbiology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5497/version/1

Development of human limbs.
Provedor de dados: 17
Autores: Alexander Ermolenko.
This work offers a new view on the developmental history of tetrapods. It proposes an original evolution model of human limbs based on metameric formation of osteogenic buds in accordance to primary segmentation and biplanar symmetry. While going through evolution, osteogenic buds initially identical to each other were changing their sizes, realigning, regressing, uniting while keeping the direction of the formation in accordance to the following formula (taking into account sesamoid bones):&amp;#xd;&amp;#xa;2; 1; 2; 3; 2; 3; 5; 5; 8; 8 (in the upper limb together with the upper limb girdle); 3; 2; 3; 2; 1; 2; 8; 8; 5; 5 (in the lower limb together with the pelvic bones).
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5539/version/1

Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico
Provedor de dados: 17
Autores: Alexander V. Spirov; David M. Holloway.
A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The effectiveness of the approach is demonstrated on a series of benchmark tests.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3913/version/1

Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions
Provedor de dados: 17
Autores: Pedro Beltrao; Luis Serrano.
Protein interaction networks are an important part of the post-genomic effort to integrate a part-list view of the cell into system-level understanding. Using a set of 11 yeast genomes we show that combining comparative genomics and secondary structure information greatly increases consensus-based prediction of SH3 targets. Benchmarking of our method against positive and negative standards gave 83% accuracy with 26% coverage. The concept of an optimal divergence time for effective comparative genomics studies was analyzed, demonstrating that genomes of species that diverged very recently from _Saccharomyces cerevisiae_ (_S. mikatae_, _S. bayanus_, and _S. paradoxus_), or a long time ago (_Neurospora crassa_ and _Schizosaccharomyces pombe_), contain less...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/16/version/1

Vermiculiphily: Larvae Pollinating Orchids!
Provedor de dados: 17
Autores: Pankaj Kumar; Gopal S. Rawat.
Orchids are truly extraordinary organisms exhibiting a wide range of pollination mechanism, many of which awaits discovery. Epipactis veratrifolia is a terrestrial orchid that has been reported to be pollinated by various species of hoverflies in Israel1,2. This orchid is known to emit the smell of aphid pheromone that attracts hoverflies, which lay eggs inside the flower and in the process pollinate them. Recently, we observed a species of hoverfly (Ischiodon scutellaris) pollinate the same orchid species in the Western Himalaya while laying eggs inside the flowers. Ischiodon scutellaris is being reported for the first time as pollinator of this orchid. However, all flowers don&amp;#x2019;t get pollinated, even though insects visit them and lay eggs...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6295/version/1

Natural Selection: A Deselection vs Proselection Analysis
Provedor de dados: 17
Autores: Raymond Hardy.
Since the dawn of Darwinian evolution theory evolutionists have assumed that evolution favors adaptive traits. In this analysis article the author explores the usefulness of assuming that natural selection works only by disfavoring deleterious traits.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1787/version/1

Anthropogenic Renourishment Feedback on Shorebirds: a Multispecies Bayesian Perspective
Provedor de dados: 17
Autores: Matteo  Convertino; Joseph Donoghue; Ma Librada Chu-Agor; Gregory Kiker; Rafael  Munoz-Carpena; Richard  Fischer; Igor Linkov.
In this paper the realized niche of the Snowy Plover (Charadrius alexandrinus), a primarily resident Florida shorebird, is described as a function of the scenopoetic and bionomic variables at the nest-, landscape-, and regional-scale. We identified some possible geomorphological controls that influence nest-site selection and survival using data collected along the Florida Gulf coast. In particular we focused on the effects of beach replenishment interventions on the Snowy Plover (SP), and on the migratory Piping Plover&amp;#x9;(PP)&amp;#x9;(Charadrius&amp;#x9;melodus )&amp;#x9;and&amp;#x9;Red&amp;#x9;Knot&amp;#x9;(RK)&amp;#x9;(Calidris&amp;#x9;canutus ).&amp;#x9;Additionally, we investigated the potential differences between the SP breeding and wintering...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5872/version/1

Ecological, phenological and biochemical significance of bimodal fruiting of Boletus alutaceus morgan
Provedor de dados: 17
Autores: Nandkumar Kamat.
Boletus alutaceus Morgan an ectomycorrhizal species was extensively studied from an ecologically fragmented microhabitt colonized by its&amp;#x27; 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 &amp; Genomics; Microbiology; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2835/version/1

3D model of amphioxus steroid receptor complexed with estradiol
Provedor de dados: 17
Autores: Michael E. Baker; David J. Chang.
The origins of signaling by vertebrate steroids are not fully understood.  An important advance was the report that an estrogen-binding steroid receptor [SR] is present in amphioxus, a basal chordate with a similar body plan as vertebrates.  To investigate the evolution of estrogen binding to steroid receptors, we constructed a 3D model of amphioxus SR complexed with estradiol.  This 3D model indicates that although the SR is activated by estradiol, some interactions between estradiol and human ER[alpha] are not conserved in the SR, which can explain the low affinity of estradiol for the SR.  These differences between the SR and ER[alpha] in the steroid-binding domain are sufficient to suggest that another steroid is the physiological regulator of the SR....
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3316/version/1

Structural Analysis of Polarizing Indels Argues the Root of the Tree of Life is Near the Chloroflexi
Provedor de dados: 17
Autores: Ruben E. Valas; Philip E. Bourne.
Determining which branches of the tree of life have derived features narrows down the possible location of the root. Currently the polarization of indels done by Lake _et al_.^1-5^ and the polarizing transitions of Cavalier-Smith^6^ arrive at contradictory positions for the root of the tree.  We have analyzed the sequence based indel arguments using protein structure wherever possible. Structure strongly supports some of the polarizations, but in other indels it argues for a different conclusion. We conclude that there is no contradiction between Lake _et al_. and Cavalier-Smith; the root of the tree of life must be near the Chloroflexi.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3290/version/1

Evolutionary descent of prion genes from a ZIP metal ion transport ancestor
Provedor de dados: 17
Autores: Gerold Schmitt-Ulms; Sepehr Ehsani; Joel C. Watts; David Westaway; Holger Wille.
In the more than 20 years since its discovery, both the phylogenetic origin and cellular function of the prion protein (PrP) have remained enigmatic. Insights into the function of PrP may be obtained through a characterization of its molecular neighborhood. Quantitative interactome data revealed the spatial proximity of a subset of metal ion transporters of the ZIP family to mammalian prion proteins. A subsequent bioinformatic analysis revealed the presence of a prion-like protein sequence within the N-terminal, extracellular domain of a phylogenetic branch of ZIPs. Additional structural threading and ortholog sequence alignment analyses consolidated the conclusion that the prion protein gene family is phylogenetically derived from a ZIP-like ancestor...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2867/version/1

Ageing as a price of cooperation and complexity: Self-organization of complex systems causes the ageing of constituent networks
Provedor de dados: 17
Autores: Huba J. M. Kiss; &amp;#xc1;goston Mihalik; Tibor N&amp;#xe1;n&amp;#xe1;si; B&amp;#xe1;lint &amp;#x150;ry; Zolt&amp;#xe1;n Spir&amp;#xf3;; Csaba S&amp;#x151;ti; Peter Csermely.
The analysis of network topology and dynamics is increasingly used for the description of the structure, function and evolution of complex systems. Here we summarize key aspects of the evolvability and robustness of the hierarchical network-set of macromolecules, cells, organisms, and ecosystems. Listing the costs and benefits of cooperation as a necessary behaviour to build this network hierarchy, we outline the major hypothesis of the paper: the emergence of hierarchical complexity needs cooperation leading to the ageing of the constituent networks. Local cooperation in a stable environment may lead to over-optimization developing an &amp;#x2018;always-old&amp;#x2019; network, which ages slowly, and dies in an apoptosis-like process. Global cooperation...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2610/version/1

Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm _Elaeis guineensis_ and _E. oleifera_
Provedor de dados: 17
Autores: Aikkal Riju; Vadivel Arunachalam.
Oil palm is the second largest source of edible oil, which meets one-fifth of global demands of oils and fats. Expressed sequence tag (EST) sequencing programs have provided a wealth of information, identifying novel genes from a broad range of organisms and providing an indication of gene expression level in particular tissues. It also provides the richest source of biologically useful SNPs due to the relatively high redundancy of gene sequence, the diversity of genotypes represented within databases. EST based SNPs are potential molecular markers and aid in genetic improvement. A total of 21062 and 2053 polymorphic (SNP and Indel) sites in _E. guineensis_ species and in _E. oleifera_, 4955 SNPs and 1172 Indels were detected. SNP(17.5/kbp) and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3593/version/1

On the reliability of Bayesian posterior clade probabilities in phylogenetic analysis
Provedor de dados: 17
Autores: Graham Jones.
This article discusses possible reasons why posterior clade probabilities obtained from Bayesian phylogenetic analyses might be inaccurate. It attempts to list all possible sources of uncertainty and error in Bayesian phylogenetic analysis. The choice of priors on trees has been suggested by several authors as a cause of inaccurate posterior clade probabilities. I argue strongly for using priors based on biological knowledge. Two possible sources of bias which do not seem to have been published before are also discussed. One is a computational problem and the other related to majority rule consensus trees.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1494/version/1

Transcriptional coupling of neighbouring genes and gene expression noise: evidence that gene orientation and non-coding transcripts are modulators of noise
Provedor de dados: 17
Autores: Guang-Zhong Wang; Martin J. Lercher; Laurence D. Hurst.
For some genes, notably essential genes, expression when expression is needed is vital hence low noise in expression is favourable. For others noise is necessary for coping with stochasticity or for providing dice-like mechanisms to control cell fate.  But how is noise in gene expression modulated?  We hypothesise that gene orientation may be crucial, as for divergently organized gene pairs expression of one gene could affect chromatin of a neighbour thereby reducing noise. Transcription of antisense non-coding RNA from a shared promoter is similarly argued to be a noise-reduction mechanism.   Stochastic simulation models confirm the expectation.  The model correctly predicts: that protein coding genes with bi-promoter architecture, including those with a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4792/version/1

Statistical analysis of network data and evolution on GPUs: High-performance statistical computing
Provedor de dados: 17
Autores: Thomas W. Thorne; Michael P. H. Stumpf.
Network analysis typically involves as set of repetitive tasks that are particularly amenable to poor-man&amp;#x27;s parallelization. This is therefore an ideal application are for GPU architectures, which help to alleviate the tedium inherent to statistically sound analysis of network data. Here we will illustrate the use of GPUs in a range of applications, which include percolation processes on networks, the evolution of protein-protein interaction networks, and the fusion of different types of biomedical and disease data in the context of molecular interaction networks. We will pay particular attention to the numerical performance of different routines that are frequently invoked in network analysis problems. We conclude with a review over recent...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6874/version/1

Comment on &amp;#x22;Embryological evidence identifies wing digits in birds as digits 1, 2, and 3.&amp;#x22;
Provedor de dados: 17
Autores: Xing Xu; Jonah  Choiniere; Corwin Sullivan; Fenglu Han.
Tamura et al. (Science, 11 Febuary 2011, p. 753) claim that the three avian wing digits should be identified as digits I-III based on new embryological data and suggest that these identifications help to remove the conflict between the paleontological data and developmental data concerning the homology of the avian digits. However, their results are not novel, and the authors fail to address the critical problems relating to this interesting issue.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6433/version/1

Thermal characterization of Plasmodium falciparum species specific proteins in Indian geographical area.
Provedor de dados: 17
Autores: Mohit Bhardwaj; Leena Bharadwaj; Kritika Trigunayat; Madan Mohan Trigunayat.
The paper reveals thermal characteristics of _P.falciparum_ species specific proteins. These proteins determine why _P. vivex_ species are dominant over _P.falciparum_ in Indian geographical area. Outside human host plasmodium parasite survives in poikilothermal mosquitoes. Climatic temperature conditions greatly affect native state of _P.falciparum_ species specific proteins in mosquitoes. Study of climatic temperature conditions in Indian geographical area reveals that Pfsd protein for _Plasmodium falciparum_ can remain in native state between &amp;#x2265;7 degree centigrade and &amp;#x2264;42.6 degree centigrade temperature conditions. While their best optimum functions (activity) was noted between 25.3 degree centigrade to 33degree centigrade. Pfsd...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4565/version/2

The Necessity of Darwin
Provedor de dados: 17
Autores: Stanley K. Sessions; Herbert C. Macgregor.
February 12th, 2009 was Charles Darwin&amp;#x27;s 200th birthday, and November 2009 represents the 150th anniversary of the publication of his transformative book, The Origin of Species. It seems a good time to look back and assess Darwin&amp;#x27;s legacy within the perspective of current knowledge of genetics, cytogenetics, and molecular biology in general. Although a comprehensive understanding of evolution would no doubt have emerged eventually, it is difficult to imagine how anyone could have matched Darwin&amp;#x2019;s prodigious and sustained efforts, as well as his talent for explaining things in simple terms.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2887/version/1

Quantum probabilities in competing lizard communities
Provedor de dados: 17
Autores: Diederik Aerts; Marek Czachor; Bart D&amp;#x27;Hooghe; Maciej Kuna; Barry Sinervo; Sandro Sozzo.
Despite predictive success, population dynamics and evolutionary game theory still pose fundamental problems. Violation of the competitive exclusion principle in plankton communities provides an example. A promising solution of this &amp;#x2018;paradox of the plankton&amp;#x2019; comes from theories involving cyclic competition, an evolutionary analogue of the classical rock-paper-scissors (RPS) game. However, modeling probabilistic RPS structures, one encounters a fundamental difficulty: the pairs rock-scissors, scissors-paper, and paper-rock possess representations in separate Kolmogorovian probability spaces, but a single global probability space for entire triplets does not exist. Populations that take part in cyclic competition should therefore...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6954/version/1

Biased amino acid composition in warm-blooded animals
Provedor de dados: 17
Autores: Guang-Zhong Wang; Martin  J. Lercher.
Among eubacteria and archeabacteria, amino acid composition is correlated with habitat temperatures. In particular, species living at high temperatures have proteins enriched in the amino acids E-R-K and depleted in D-N-Q-T-S-H-A. Here, we show that this bias is a proteome-wide effect in prokaryotes, and that the same trend is observed in fully sequenced mammals and chicken compared to cold-blooded vertebrates (Reptilia, Amphibia and fish). Thus, warm-blooded vertebrates likely experienced genome-wide weak positive selection on amino acid composition to increase protein thermostability.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2974/version/1

Phenoscape: Ontologies for Large Multi-species Phenotype Datasets
Provedor de dados: 17
Autores: Peter Midford; Paula Mabee; Todd Vision; Hilmar Lapp; Jim Balhoff; Wasila Dahdul; Cartik Kothari; John Lundberg; Monte Westerfield.
The Phenoscape project is developing ontologies and tools to integrate morphological and genomic data to address comparative questions in evolutionary biology. We are currently curating 81 publications describing ~5000 phenotypic characters in 4,000 species of Ostariophysian fishes, and will be making our database of ontology-based annotations concurrently with this meeting via a web-based interface at &amp;#x22;http://kb.phenoscape.org&amp;#x22;:http://kb.phenoscape.org.
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3594/version/1

Endogenous Viral Etiology of Prion Diseases
Provedor de dados: 17
Autores: Claudiu I. Bandea.
Transmissible spongiform encephalopathies (TSEs), or prion diseases, are a group of incurable neurodegenerative disorders, including Kuru and Creutzfeldt-Jakob disease in humans, &amp;#x201c;mad cow&amp;#x201d; disease in cattle, and scrapie in sheep. This paper presents structural, genetic, and evolutionary evidence supporting an endogenous TSE virus model that integrates the three major traditional views on the nature of TSE pathogens, the conventional virus view, the prion hypothesis, and the virino concept, into a novel conceptual and evolutionary framework. According to this model, the TSE pathogens are symbiotic endogenous viruses that inadvertently produce transmissible viral particles that lack the viral genome and are composed primarily of the...
Tipo: Manuscript
Palavras-chave: Microbiology; Neuroscience; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3887/version/1

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry lifting model based on Tlusty&amp;#x27;s elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4120/version/3

A Study on the Origin of Peroxisomes: Possibility of Actinobacteria Symbiosis
Provedor de dados: 17
Autores: Duhita Narendra; Saruhashi Satoshi; Hamada Kazuo; Miyata Daisuke; Horiike Tokumasa; Shinozawa Takao.
Withdrawn
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/1866/version/2

Codonopsis pilosula twines either to the left or to the right
Provedor de dados: 17
Autores: Gonghua Lin; Fang Zhao; Eviatar Nevo; Tongzuo Zhang; Jianping Su.
We report the twining handedness of Codonopsis pilosula, which has either a left- or right-handed helix among different plants, among different tillers within a single plant, and among different branches within a single tiller. The handedness was randomly distributed among different plants, among the tillers within the same plants, but not among the branches within the same tillers. Moreover, the handedness of the stems can be strongly influenced by external forces, i.e. the compulsory left and right forming inclined to produce more left- and right-handed twining stems, respectively, and the reversing could make a left-handed stem to be right-handed and vice versa. We also discuss the probable mechanisms these curious cases happen.
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7026/version/1

Toward a Complete Phyloreferencing Language
Provedor de dados: 17
Autores: T. Michael Keesey.
A phyloreference is a statement indicating a taxon within a phylogenetic context. A common use for phyloreferences is in phylogenetic definitions, which tie taxonomic names to taxa via such statements. Several conventions for writing phyloreferences have been proposed, but most only cover a few &amp;#x201c;standard&amp;#x201d; forms (node&amp;#x2011;, branch&amp;#x2011;, and perhaps apomorphy&amp;#x2011;based clades) without the capacity to represent more &amp;#x201c;exotic&amp;#x201d; forms (e.g., ancestor&amp;#x2011;based clades and qualified/modified references). In order to build a complete phyloreferencing language, the mathematical underpinnings of phylogenetic contexts must be clarified. A phylogenetic context may be modeled as a directed, acyclic...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4652/version/1

When Spandrels Become Arches: Neural crosstalk and the evolution of consciousness
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognition is recognized as having a &amp;#x27;dual&amp;#x27; information source, the information theory chain rule implies that isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to the rapid, shifting global neural broadcasts of consciousness. The argument is quite analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in neurons and neuronal subsystems. Astrobiological implications are obvious.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6115/version/1

Idiosyncratic evolution of conserved eukaryote proteins that are similar in sequence to archaeal or bacterial proteins
Provedor de dados: 17
Autores: Roy J. Britten.
&amp;#x9;Sequence comparisons have been made between the proteins of 571 prokaryote species including 46 archaea and 525 bacteria and the set of  human proteins. Highly conserved eukaryotic proteins are often strikingly similar in sequence to archaeal and bacterial proteins. Yet in many cases similarity to archaeal proteins is not correlated to the similarity to bacterial proteins. In these comparisons there are hundreds of eukaryote proteins that match well archeal proteins, but do not match recognizably to bacterial proteins, while thousands of proteins match well to bacterial proteins but not recognizably to archeal proteins. Forty percent of the 21,440 human proteins that significantly match prokaryote proteins are in this extreme idiosyncratic...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1752/version/1

Bio::Phylo - Phyloinformatic Analysis Using Perl
Provedor de dados: 17
Autores: Rutger Vos.
Recent years have seen the emergence of the field of phyloinformatics. In the course of a phyloinformatic analysis, data and metadata are generated, transformed, filtered, analyzed and summarized before they can be interpreted to answer meaningful biological questions. Based on first principles of good science such steps should be reproducible; and, in practice, analysis steps often need to be redone by the researcher multiple times anyway  and are too error-prone, tedious and time-consuming to do by hand. Hence, phyloinformatic analyses benefit from increased automation. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The Bio::Phylo toolkit promotes this by giving easy access to phylogenetic data objects (trees, taxa, character state matrices) read from a variety of...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4601/version/1

A snake of a different color: physiological color change in Arizona black rattlesnakes
Provedor de dados: 17
Autores: Melissa Amarello; Jeffrey J. Smith.
Coloration may serve a variety of behavioral (e.g., crypsis, communication) and physiological (e.g., thermoregulation, protection) functions for terrestrial ectotherms.  However, optimal coloration for a given function may vary over environments (spatial or temporal) or conflict with other functions.  Physiological color change (rapid change due to movement of pigment granules within chromatophores) may be an adaptation to resolve conflicting selective pressures on coloration.  The proximate factors related to physiological color change are well known in many animals, but few studies have investigated the ecological or evolutionary implications of this behavior.  Here, we present alternative hypotheses for physiological color change and discuss biotic and...
Tipo: Poster
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6711/version/1

Insular gigantism and dwarfism in a snake, adaptive response or spandrel to selection on gape size?
Provedor de dados: 17
Autores: Shawn Vincent; Matthew Brandley; Takeo Kuriyama; Akira Mori; Anthony Herrel; Masami Hasegawa.
In biology, spandrels are phenotypic traits that evolve through their underlying developmental, genetic, and/or structural links to another trait under selection^1, 2, 3^. Despite the importance of the concept of spandrels in biology, empirical examples of spandrels are exceedingly rare at the organismal level^2, 3^. Here we test whether body size evolution in insular populations of a snake (_Elaphe quadrivirgata_) is the result of an adaptive response to differences in available prey, or the result of a non-adaptive spandrel resulting from selection on gape size. In contrast to previous hypotheses, Mantel tests show that body size does not coevolve with diet. However, gape size tightly matches diet (birds vs. lizards) across populations, even after...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3360/version/1

New methods for analyzing serological data with applications to influenza surveillance
Provedor de dados: 17
Autores: Wilfred Ndifon.
Two important challenges to the use of serological assays for influenza surveillance include the substantial amount of experimental effort involved, and the inherent noisiness of serological data. Here, informed by the observation that log-transformed serological data (obtained from the hemagglutination-inhibition assay) exist in an effectively one-dimensional space, computational methods are developed for accurately and efficiently recovering unmeasured serological data from a sample of measured data, and systematically minimizing noise found in the measured data. Careful application of these methods would enable the collection of better-quality serological data on a greater number of circulating influenza viruses than is currently possible, and improve...
Tipo: Manuscript
Palavras-chave: Immunology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3820/version/1

In vitro Evolution and Engineering for Improved Ribozyme Polymerase Production
Provedor de dados: 17
Autores: Israr  Khan; Muhammad Waheed Akktar; Ayaz Ali Khan.
According to the &amp;#x22;RNA World Hypothesis&amp;#x22; the first self replicating molecule formed from the prebiotic chemicals is the ribozyme. A model compartmentalized self replicating system for ribozyme polymerases is designed and used to improve activity, fidelity and generality of the enzyme.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6064/version/1

Plasmodium falciparum has rare correlation properties
Provedor de dados: 17
Autores: Kushal Shah.
A plot of the correlation function of a given DNA sequence has certain characteristic features common to almost all organisms. One common feature is that the correlation values at distances that are multiples of three is higher than correlation values at other distances. Because of this such a correlation plot can be divided into two or three curves with different scalings. P. falciparum has a rare correlation property which is probably unique. I have analyzed genomes of many bacteria, fungi and protozoa and found that P. falciparum is the only organism whose DNA sequence correlation plot can be divided into four curves with different scalings. This property is neither shared by other species of the Plasmodium genus nor by other AT rich genomes. This could...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6817/version/1

The Opisthokonta and the Ecdysozoa may be clades: An update on Philip et al. (2005)
Provedor de dados: 17
Autores: Marko Prous.
To test the monophyly of Opisthokonta (animal-fungal clade) and Ecdysozoa (nematode-arthropod clade), Philip et al [Mol. Biol. Evol. 22: 1175&amp;#x2013;1184 (2005)] used sequence data from 10 eukaryotic genomes (an alveolate, a plant, two ascomycetous yeasts, a nematode, two dipterans, and three vertebrates). Strict criteria were used to select genes for phylogenetic analyses: single-gene families were identified and from these families, genes capable of recovering the uncontroversial parts of the phylogenetic tree (for example animal and vertebrate monophyly) were selected. Only five single-copy genes were found to be universally distributed across the analyzed taxa and capable of recovering all the uncontroversial parts of the tree. Phylogenetic...
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3306/version/1

Natural Selection _In Utero_ Contributes to the Male Longevity Deficit in Contemporary Human Populations
Provedor de dados: 17
Autores: Ralph Catalano.
Much literature invokes natural selection to explain the pervasive deficit in the average lifespan of men compared to women.^1^ The explanation assumes that mothers, not fathers, provisioned children over much of human existence, and that women who lived long enough to help their children and grand children survive to reproductive age had more grandchildren and great-grandchildren than did shorter-lived women.^2^ Although this argument implies that natural selection would conserve mutations that conferred longevity on mothers but not fathers,^3,4^ it offers no explanation of the considerable changes over historic time in the male longevity deficit thereby implying that these arise solely from culture.^5^ I show, however, that natural selection _in utero_...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3915/version/1

Constructing ABC summary statistics: semi-automatic ABC
Provedor de dados: 17
Autores: Paul Fearnhead; Dennis  Prangle.
To analyze complex datasets efficiently, ABC algorithms require well-chosen low dimensional summary statistics of the data. We present a method to construct appropriate summary statistics for ABC in a semi-automatic manner. Previous attempts at this have been based around constructing statistics that are sufficient (or approximately sufficient). However, in most real applications it is difficult to know if low-dimensional sufficient statistics exist, or how to approximate them if they do. We take an alternative approach of aiming for summary statistics which will enable inference about certain parameters of interest to be as accurate as possible. &amp;#xa0;This talk describes our method, the underpinning theory, and promising empirical results on a range...
Tipo: Presentation
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5959/version/1

Identification of the prebiotic translation apparatus within the contemporary ribosome
Provedor de dados: 17
Autores: Ilana Agmon; Chen Davidovich; Anat Bashan; Ada Yonath.
A structural element that could have existed independently in the prebiotic era was identified at the active site of the contemporary ribosome. It is suggested to have functioned as a proto-ribosome catalyzing peptide bond formation and non-coded elongation in the same manner that contemporary ribosomes exert positional catalysis, namely by accommodating the reactants in stereochemistry favourable for inline nucleophilic attack. This simple apparatus is a dimer of self-folding RNA units that could have assembled spontaneously into a symmetrical pocket-like structure, sufficiently efficient to be preserved throughout evolution as the active site of modern ribosomes, thus presenting a conceivable starting point for translation.Here we discuss the...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2921/version/1

Using Trees: Myrmecocystus Phylogeny and Character Evolution and New Methods for Investigating Trait Evolution and Species Delimitation (PhD Dissertation)
Provedor de dados: 17
Autores: Brian C. O&amp;#x27;Meara.
1) Rates of phenotypic evolution have changed throughout the history of life, producing variation in levels of morphological, functional, and ecological diversity among groups. Testing for the presence of these rate shifts is a key component of evaluating hypotheses about what causes them. General predictions regarding changes in phenotypic diversity as a function of evolutionary history and rates are developed, and tests are derived to evaluate rate changes. Simulations show that these tests are more powerful than existing tests using standardized contrasts. &amp;#xd;&amp;#xa;2) Species delimitation and species tree inference are difficult problems in the case of recent divergences, especially when different loci have different histories. I quantify the...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2261/version/1

Altered copy gene function in plants following total intron replacement in precursor RNA
Provedor de dados: 17
Autores: Drew Schwartz.
Evidence is presented for two novel genetic mechanisms: total intron replacement in transcribedprecursor RNA by multiple short sequences and reverse transcription of the precursor RNA followedby incorporation into the genome as copy genes, some of which have acquired an altered function.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4307/version/1

Sensory adaptation in the light of information and energy
Provedor de dados: 17
Autores: Nikon Rasumov; Jeremy Niven; Michael Baker; Simon Laughlin.
Signal processing in neurons is constrained by internal noise and energy consumption. Neural systems often invest energy in amplifying signals to protect them against internal noise. There is no general expression for the trade-off between energy and information, because it is strongly dependent on the properties of signal, noise and underlying mechanism. We present the first analysis of this energy-information trade-off in a specific system, the R1-6 photoreceptors of the blowfly, Calliphora vicina. These photoreceptors adapt to light level by adjusting their transduction gain (number of light-gated channels opened per photon) and potassium conductance. By combining experimental measures of photoreceptor impedances, transfer functions and signal quality...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5805/version/1

Can bacteria adapt to starvation-free environment?
Provedor de dados: 17
Autores: Kei Kitahara.
Bacteria will experience starvation-free environment if infinite nutrition is supplied continuously for a long period. In this study, an evolutionary experiment was performed for 118 days where bacteria adapted to starvation-free environment and reduced their doubling time. It is anticipated that this finding will help to select bacterial strains that can grow more rapidly in rich media.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7017/version/1

Expanding the modern synthesis II: Formal perspectives on the inherent role of niche construction in fitness
Provedor de dados: 17
Autores: 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 &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5059/version/2

Genome-scale approach proves that the lungfish-coelacanth sister group is the closest living relative of tetrapods with the BEST program
Provedor de dados: 17
Autores: Yunfeng Y. S. Shan; Robin Gras.
The origin of tetrapods has not been resolved for decades. Three principal hypotheses (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed. We used the Bayesian method under the coalescence model with the latest program (BEST) to perform a phylogenetic analysis for seven relevant taxa and 43 nuclear genes encoding amino acid residues with the jackknife method for taxon sub-sampling. The results, combined with those of other three genome-scale approaches, successfully prove the hypothesis that lungfishes and coelacanths form a monophyletic sister group and are equally related to tetrapods supported by high Bayesian posterior probabilities of the branch (a lungfish-coelacanth clade) and high taxon jackknife supports.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3865/version/1

The hotspot conversion paradox
Provedor de dados: 17
Autores: Mario Pineda-Krch; Rosemary J. Redfield.
The contradiction between the long-term persistence of the chromosomal hotspots that initiate meiotic recombination and the self-destructive mechanism by which they act strongly suggests that our understanding of recombination is incomplete. This &amp;#x22;hotspot paradox&amp;#x22; has been reinforced by the finding that biased gene conversion also removes active hotspots from human sperm. To investigate the requirements for hotspot persistence, we developed a detailed computer simulation model of their activity and its evolutionary consequences. With this model, unopposed hotspot activity could drive strong hotspots from 50% representation to extinction within 70 generations. Although the crossing over that hotspots cause can increase population fitness,...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3637/version/1

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Provedor de dados: 17
Autores: I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn &amp;#x2013;algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata.  Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7083/version/1

Herd Immunity/Herd Infection: Cultural Artifacts of Marginalization and the Dynamics of AIDS
Provedor de dados: 17
Autores: Rodrick Wallace.
We examine conditions under which high prevalence of infectious disease can become endemic within a community, in effect constituting a state of &amp;#x27;herd infection&amp;#x27; inverse to epidemiological herd immunity. For something like AIDS, under such circumstances, a single behavioral lapse or adverse accident will probably be a death sentence.
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Pharmacology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5864/version/1

Ultrasonic frogs show extraordinary sex differences in auditory frequency sensitivity
Provedor de dados: 17
Autores: Jun-Xian Shen; Zhi-Min Xu; Zu-Lin Yu; Shuai Wang; De-Zhi Zheng.
Acoustic communication plays an important role in the reproductive behavior of anurans. Males of concave-eared torrent frog (_Odorrana tormota_) have ultrasonic communication capacity 1, 2, but it is unknown whether females communicate with ultrasound. Here we show that _O. tormota_ exhibits great sex differences in the auditory frequency sensitivity. Acoustic playback experiments demonstrated that the male&amp;#x27;s advertisement calls evoke gravid females&amp;#x27; positive phonotaxis and vocal responses, whereas ultrasonic components of the male&amp;#x27;s calls (frequencies above 20 kHz) do not elicit female phonotaxis or vocalization. The behavioral study was complemented by electrophysiological recordings from the auditory midbrain and by laser...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5337/version/1

Migration potential as a new predictor of long-distance dispersal rate for plants
Provedor de dados: 17
Autores: Tianhua He; Byron B. Lamont; Neal Enright; Siegy Krauss; Laura Merwin.
How biotic and abiotic factors interact to shape the overall pattern of dispersal of propagules is critical in understanding the evolution of dispersal mechanisms as well as predicting dispersal rates between patchily-distributed habitats. But which plant traits, demographic and/or habitat factors best predict the capacity for dispersal? We introduce the concept of migration potential (v), a readily interpretable parameter that combines recruitment efficiency (recruits per adult / seeds per adult per dispersal cycle) with level of habitat occupancy for predicting effective long-distance dispersal (LDD) of seeds. Using our empirical (genotype assignment) estimates of LDD and statistics on life-history traits and demographic features for contrasting...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5890/version/1

Structural dynamics and divergence of the polygalacturonase gene family in land plants
Provedor de dados: 17
Autores: Soon-Jae Kwon; Jae-Han Son; Kyong-Cheul Park; Hae-Young Oh; Pyeung-Hyeun Kim; Woo-Hyeon Byeon; Nam-Soo Kim.
A distinct feature of eukaryotic genomes is the presence of gene families. The polygalacturonase (PG) (EC3.2.1.15) gene family is one of the largest gene families in plants. PG is a pectin-digesting enzyme with a glycoside hydrolase 28 domain. It is involved in numerous plant developmental processes. The evolutionary processes accounting for the functional divergence and the specialized functions of PGs in land plants are unclear. Here, phylogenetic and gene structure analysis of PG genes in algae and land plants revealed that land plant PG genes resulted from differential intron gain and loss, with the latter event predominating. PG genes in land plants contained 15 homologous intron blocks and 13 novel intron blocks. Intron position and phase were not...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Plant Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1608/version/1

Climate Change and Disease Simulation
Provedor de dados: 17
Autores: Somnath Jha.
Climate change has manifested differential impacts on various components of the earth system. The impact of climate change is not merely limited to the climatic variable. Climate change has resulted in complex, unforeseen consequences in the biosphere of earth. The silent but gradual changes arise out of varied responses of disease-causing organism to the combination of the disease-conducive environmental variables. The change is the same for both the target hosts plant as well as the animal kingdom. There is an urgent need to look into the changing disease dynamics and the disease pathogen genome sensitivity to the changes in climatic variables. The long memory of genetic makeup of disease pathogen to capture, inherit and evolve or mutate the changed or...
Tipo: Presentation
Palavras-chave: Ecology; Genetics &amp; Genomics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6949/version/1

Insights from the Structure of Estrogen Receptor into the Evolution of Estrogens: Implications for Endocrine Disruption
Provedor de dados: 17
Autores: Michael E. Baker.
In the last decade, there has been important progress in understanding the origins and evolution of receptors for adrenal steroids (aldosterone, cortisol) and sex steroids (estradiol, progesterone, testosterone) due to the sequencing of genomes from animals that are at key sites in vertebrate evolution.  Although the estrogen receptor [ER] appears to be the ancestral vertebrate steroid receptor and estradiol [E2] is the physiological ligand for vertebrate ERs, the identity of the ancestral ligand(s) for the ER remains unknown.  Here, using an analysis of crystal structures of human ER[alpha] with E2 and other chemicals and 3D models of human ER[alpha] with 27-hydroxycholesterol and 5-androsten-3[beta],17[beta]-diol, we propose that one or more [DELTA]5...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Ecology; Genetics &amp; Genomics; Pharmacology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5777/version/1

Hacking the JPEG/PDF tree format
Provedor de dados: 17
Autores: Joseph Hughes.
We have been illustrating the relationships between species and genes as trees for over a century. Whilst in the early years of morphological and molecular phylogenetics, embedding illustrations into manuscripts might have been the most appropriate way to disseminate knowledge, this has resulted in the locking up of phylogenetic hypotheses into the pages of journals and books without an easy way to access this information. As a result, most phylogenetic knowledge is lost upon publication. I will explain the reasons for re-using published trees, discuss ways to liberate this information and avoid these problems in the future.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6556/version/1

Intra-specific variation in plant hydraulic sectoriality along a latitudinal gradient
Provedor de dados: 17
Autores: Angela Zeng; Roberto Salguero-Gomez; Agustin Santos-Alvarez; Amy Zanne; Brenda Casper.
High temperatures and nutrient limitations in deserts challenge plant survival. Large temperature oscillations and droughts typical of cold deserts can result in cavitation, the precipitation of dissolved air within a xylem vessel. If xylem vessels are closely packed, then a cavitation event may expand to neighboring vessels, resulting in runaway embolism, and potentially paralyze the vital functions of the plant.&amp;#xd;&amp;#xa;      Hydraulic sectoriality, where the plant  is functionally composed of independent hydraulic units, has been suggested as a strategy to decrease the risk associated with cavitation. This can occur by increasing xylem vessel isolation and/or increasing the physical modularity of the plant. Furthermore, hydraulic sectoriality...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5277/version/1

Gene tree reconciliation: new developments in Bayesian concordance analysis with BUCKy
Provedor de dados: 17
Autores: C&amp;#xe9;cile An&amp;#xe9;; Colin N. Dewey; Satish K. Kotha; Bret R. Larget.
When phylogenetic trees inferred from different genes are incongruent, several methods are available to reconcile gene trees and extract the shared phylogenetic information from the sequence data. Bayesian Concordance Analysis, implemented in BUCKy, aims to extract the vertical signal and to infer clusters of genes that share the same tree topology. The new version of BUCKy includes a quartet-based estimate of the species tree with branch lengths in coalescent units.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4625/version/1

The Vaginal Microbiome: Disease, Genetics and the Environment
Provedor de dados: 17
Autores: Jennifer M. Fettweis; Joao P. Alves; Joseph F. Borzelleca; James  P. Brooks; Christopher J. Friedline; Yuan Gao; Xi Gao; Philippe Girerd; Michael  D. Harwich; Stephanie L. Hendricks; Kimberly K. Jefferson; Vladimir Lee; Huan Mo; Michael C. Neale; Federico A. Puma; Mark A. Reimers; Maria C. Rivera; Seth B. Roberts; Myrna G. Serrano; Nihar Sheth; Judy L. Silberg; Logan Voegtly; Elizabeth C. Prom-Wormley; Bin Xie; Timothy  P. York; Cynthia N. Cornelissen; Jerome F. Strauss III; Lindon J. Eaves; Gregory A. Buck.
The vagina is an interactive interface between the host and the environment. Its surface is covered by a protective epithelium colonized by bacteria and other microorganisms. The ectocervix is nonsterile, whereas the endocervix and the upper genital tract are assumed to be sterile in healthy women. Therefore, the cervix serves a pivotal role as a gatekeeper to protect the upper genital tract from microbial invasion and subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease, and other gynecologic and reproductive disorders. Homeostasis of the microbiome in the vagina and ectocervix plays a paramount role in reproductive health. Depending on its composition, the microbiome may protect...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5150/version/2

CDAO-Store: A New Vision in Data Integration
Provedor de dados: 17
Autores: Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO) 1 is an ontology developed, as part of the EvoInfo2 and EvoIO3 groups supported by NESCent4, to provide semantics to the descriptions of data and transformations commonly found in the domain of phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic &amp;#xd;&amp;#xa;trees and associated character data matrices. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4585/version/1

Internal conformation of the &amp;#x27;protein folding code&amp;#x27; inferred from empirical tertiary structural classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;s topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. The underlying &amp;#x27;protein folding code network&amp;#x27; is found to have one major, highly dominant &amp;#x27;spherical&amp;#x27; component, a minor attachment handle in the Morse Theory sense, and as many as two or three additional subminor handles.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4640/version/1

An ancient adaptive episode of convergent molecular evolution confounds phylogenetic inference
Provedor de dados: 17
Autores: Todd A. Castoe*; A.P. Jason de Koning*; Hyun-Min Kim; Wanjun Gu; Brice P. Noonan; Zhi J. Jiang; Christopher L. Parkinson; David D. Pollock.
Convergence can mislead phylogenetic inference by mimicking shared ancestry, but has been detected only rarely in molecular evolution. Here, we show that significant convergence occurred in snake and agamid lizard mitochondrial genomes. Most evidence, and most of the mitochondrial genome, supports one phylogenetic tree, but a subset of mostly amino acid-altering mitochondrial sites strongly support a radically different phylogeny. These sites are convergent, probably selected, and overwhelm the signal from other sites. This suggests that convergent molecular evolution can seriously mislead phylogenetics, even with large data sets. Radical phylogenies inconsistent with previous evidence should be treated cautiously.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2123/version/1

The phyogenetic principles of mma: A hypothetical biostratigraphic model
Provedor de dados: 17
Autores: Alfred Czarnetzki; Dirk von Rautenfeld; Madjid Samii.
Two erectoid hominids from Sarstedt prompted a detailed examination of the course of the impressions of the Arteria meningea media and their characteristics within the line of hominidae.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6993/version/1

Phyloinformatics in the age of Wikipedia
Provedor de dados: 17
Autores: Roderic Page.
This talk describes a mapping between the NCBI taxonomy database and Wikipedia. These two databases were chosen because the NCBI taxonomy contains all the taxa for which sequences are publicly available, and for many taxa Wikipedia is the first site returned in a Google search on that taxon&amp;#x27;s scientific name. The NCBI web pages for nearly 53,000 NCBI taxa now have a link to the corresponding page in Wikipedia.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4583/version/1

Origin and diversification of steroids: Co-evolution of enzymes and nuclear receptors
Provedor de dados: 17
Autores: Michael E. Baker.
Recent sequencing of amphioxus and sea urchin genomes has provided important data for understanding the origins of enzymes that synthesize adrenal and sex steroids and the receptors that mediate physiological response to these vertebrate steroids.  Phylogenetic analyses reveal that CYP11A and CYP19, which are involved in the synthesis of adrenal and sex steroids, first appear in the common ancestor of amphioxus and vertebrates.  This correlates with recent evidence for the first appearance in amphioxus of receptors with close similarity to vertebrate steroid receptors.  Other CYP450 enzymes involved in steroid synthesis can be traced back to invertebrates, in which they have at least two functions: detoxifying xenobiotics and catalyzing the synthesis of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4674/version/1

Accounting for molecular stochasticity in systematic revisions: species limits and phylogeny of Paroaria
Provedor de dados: 17
Autores: Liliana M. D&amp;#xe1;valos; Ana L. Porzecanski.
Different frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the systematic revision of Paroaria, a group of conspicuous songbirds endemic to South America. We delimited species based on examination of &amp;#x3e; 600 specimens, and developed distance-gap, and distance- and character-based coalescent simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using parsimony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits than using genetic distances....
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3357/version/1

Living unicellular eukaryote Tetrahymena pyriformis as a model for study
Provedor de dados: 17
Autores: Elena Mokhova.
Some animals are able to survive for a long time under conditions of drastically reduced oxidative metabolism, called metabolic depression. The most investigated type of metabolic depression is hibernation. Research into the basic properties of liver mitochondria energetics during hibernation is essential for fundamental biology and medicine. However, the absence of the suitable hepatocyte culture makes it impossible to study the characteristic features of mitochondrial metabolic states in living cells during hibernation. We proposed that under selected conditions, the unicellular eukaryote Tetrahymena pyriformis resembles hepatocytes under hibernation, as (i) both cell types survive under condition of restricted food supply, hypoxia, and accumulation of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4521/version/3

Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models
Provedor de dados: 17
Autores: I. C. Baianu.
Operational logic and bioinformatics models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes are proposed. &amp;#x141;ukasiewicz 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. An algebraic formulation of variable &amp;#x27;next-state functions&amp;#x27; is extended to a &amp;#x141;ukasiewicz Topos with an n-valued &amp;#x141;ukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6206/version/1

Evolution of 11[beta]-Hydroxysteroid Dehydrogenase-Type 1 and 11[beta]-Hydroxysteroid Dehydrogenase-type 3
Provedor de dados: 17
Autores: Michael E. Baker.
A key regulator of glucocorticoid action is 11[beta]-hydroxysteroid dehydrogenase type-1 (11[beta]-HSD1), which catalyzes the conversion of cortisone to cortisol, the biologically active glucocorticoid.  11[beta]-HSD1 is a paralog of 11[beta]-HSD3, whose physiological function remains unclear.  As reported here, 11[beta]-HSD3 has orthologs in sea urchin, amphioxus and Ciona, while 11[beta]-HSD1 first appears in sharks.  Thus, 11[beta]HSD3 arose before the evolution of glucocorticoid signaling, suggesting different ancestral function(s) for 11[beta]-HSD3.  Four perplexing findings arise from this evolutionary analysis: 1) 11[beta]-HSD1 is not present in a ray-finned fish genome, 2) zebrafish and fathead minnow contain two isoforms of 11[beta]-HSD3; 3)...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Genetics &amp; Genomics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4296/version/1

_Limusaurus_ and bird digit identity
Provedor de dados: 17
Autores: Alexander O. Vargas; G&amp;#xfc;nter P. Wagner; Jacques A. Gauthier.
_Limusaurus_ is a remarkable herbivorous ceratosaur unique among theropods in having digits II, III and IV, with only a small metacarpal vestige of digit I. This raises interesting questions regarding the controversial identity of avian wing digits. The early tetanuran ancestors of birds had tridactyl hands with digital morphologies corresponding to digits I, II &amp;#x26; III of other dinosaurs. In bird embryos, however, the pattern of cartilage formation indicates that their digits develop from positions that become digits II, III, &amp;#x26; IV in other amniotes. _Limusaurus_ has been argued to provide evidence that the digits of tetanurans, currently considered to be I, II and III, may actually be digits II, III, &amp;#x26; IV, thus explaining the...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3828/version/1

Recombination modulates how selection affects linked sites in Drosophila
Provedor de dados: 17
Autores: Suzanne  E. McGaugh; Caiti S. Smukowski; Brenda Manzano-Winkler; Tiffany  L. Himmel; Mohamed A. F. Noor.
One of the most influential observations in molecular evolution has been a strong association between regional recombination rate and amount of nucleotide polymorphism in those genomic regions, interpreted as evidence for ubiquitous natural selection. The alternative explanation, that recombination is mutagenic, has been rejected by the absence of a similar association between regional recombination rate and nucleotide divergence between species. However, many recent studies show that recombination rates are often very different even in closely related species, questioning whether an association between recombination rate and divergence between species has been tested satisfactorily. To circumvent this problem, we directly surveyed recombination across...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7005/version/1

Beyond the fuzzy lock-and-key: spontaneous symmetry shifts and glycan/lectin logic gates
Provedor de dados: 17
Autores: Rodrick Wallace.
Changes in the molecular topology of glycan/lectin interaction may explain observed reaction punctuation driven by experimental gradients in reactant concentration. Adoption of a &amp;#x27;biological renormalization&amp;#x27; perspective from statistical physics for the analysis of such phase transitions suggests, in marked contrast to conventional physical systems, a broad spectrum of possible universality class behaviors. This spectrum may, in typical perverse biological manner, be of central scientific interest. Generalization, via formalism abducted from coevolutionary theory, suggests that glycan/lectin molecular switches instantiate logic gates that may be as sophisticated as those characterizing basic neural process, if on a different scale.
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Microbiology; Molecular Cell Biology; Pharmacology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6849/version/1

Barlow-Hall in vitro Evolution Protocol
Provedor de dados: 17
Autores: Barry G. Hall; Miriam Barlow.
The Barlow-Hall method for in vitro evolution is a simple alternative to methods such as DNA shuffling and is particularly applicable to predicting the evolution of target genes in nature.  This detailed protocol includes the procedure itself and, as Appendices, describes particularly effective protocols for electroporation and for preparation of electrocompetent cells.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1772/version/1

Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico
Provedor de dados: 17
Autores: Alexander V. Spirov; David M. Holloway.
A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The effectiveness of the approach is demonstrated on a series of benchmark tests.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/3913/version/2

2011 German Escherichia coli O104:H4 outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles
Provedor de dados: 17
Autores: Man Kit Cheung; Lei Li; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 10 isolates from the current German E. coli outbreak against 30 existing E. coli genomes as well as that of a historical EHEC isolate using the alignment-free feature frequency profile method. Our results revealed a high similarity among E. coli isolates from the current outbreak and the historical EHEC being the most closely related isolate sequenced thus far.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6109/version/2

A Systems Biology Approach to the Evolution of Codon Use Pattern
Provedor de dados: 17
Autores: Ines Thiele; Ronan M. T. Fleming; Richard Que; Aarash Bordbar; Bernhard O. Palsson.
The genetic code is redundant as amino acids are encoded by synonymous codons that are unequally used.This codon usage bias (CUB) affects gene expression and cellular functions yet the underlying mechanisms have not been elucidated. We used a sequence-specific, stoichiometric model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655 to test the effect of randomly changed CUB on growth maximization under various environmental conditions. Amongst CUB mutant strains, we identified reduced growth phenotypes, which were caused by tRNA supply shortage. We propose, supported by computations and bibliomic data, that expansion of tRNA gene content or tRNA reading is a mechanism to respond to changes in CUB. Our systems biology modelling...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6312/version/1

Optimizing automated preprocessing streams for brain morphometric comparisons across multiple primate species
Provedor de dados: 17
Autores: Daniel Mietchen; Robert Dahnke; Christian Gaser.
Introduction: MR techniques have delivered images of a wide array of species, ranging from invertebrates to birds to elephants and whales. However, their potential to serve as a basis for comparative brain morphometric investigations has rarely been tapped so far (Christidis and Cox, 2006; Van Essen &amp;#x26; Dierker, 2007). In order to address one of the potential reasons behind this, we tested various automated segmentation streams (using CARET, FSL and lab-written code) that have been mainly designed for applications in humans, with the aim of optimizing them for comparisons across multiple species.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: T1-weighted MR images from individuals representing 11 primate species have been acquired by Rilling and Insel...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4511/version/1

Genetic similarity promotes evolution of cooperation under lethal intergroup competition
Provedor de dados: 17
Autores: Oleg Smirnov; John Orbell.
Altruism (helping others at a cost to oneself) may evolve via group selection if the cost of altruism to the individual is compensated for by growth differences among groups when (1) there is high genetic variation among members of different groups; (2) more altruistic groups grow faster and (3) between-group migration is low. Nevertheless, group selection may not fully explain the actual evolution of helping behaviour if between-group migration was sufficiently common to have reduced between-group genetic variance. Lethal intergroup competition, which amplifies such growth differences between groups, appears to have been frequent in humans&amp;#x27;; ancestral environments and could bear importantly on the evolution of altruism. Here we show that...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1710/version/1

Determination of linkage disequilibrium region suggests association of the ancient haplotype, hX with neural function
Provedor de dados: 17
Autores: Makoto Shimada; Tsutomu Kanasashi.
Modern human populations are known to contain &amp;#x22;ancient haplotypes&amp;#x22; that originated from archaic humans by hybridization.  Some of them had been reported before the development of human genomic diversity databases, such as HapMap.  Consequently, some of them have no information about linkage disequilibrium (LD) regions.  Because genetic information within LD is tightly linked, to know LD region containing ancient haplotypes will be useful to estimate basic parameters of admixture events, and to infer biological functions that linked with the ancient haplotypes.  One of these ancient haplotypes, haplotype X (_hX_) was found in a 10.1 kb-region located on Xp11.22, which diverged at 1.4 M years ago, with low diversity within the cluster in...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6737/version/1

Many in vivo  &amp;#x27;protein folding codes&amp;#x27; can be inferred from empirical classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;s topological rate distortion approach to the genetic code is applied to the problem of protein symmetries and to the analysis of protein folding rates. Unlike the genetic case, numerous &amp;#x27;protein folding codes&amp;#x27; can be identified from empirical classifications. Protein folding rates follow from a topologically-driven rate distortion argument. These results imply markedly different evolutionary trajectories for the genetic and protein folding codes, and suggest that the &amp;#x27;protein folding code&amp;#x27; is, in fact, a complicated composite, distributed across protein production and a cellular, or higher, regulatory apparatus acting as a canalizing catalyst that drives the system to converge on particular transitive...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4665/version/2

Inference of population splits and mixtures from genome-wide allele frequency data
Provedor de dados: 17
Autores: Joseph K. Pickrell; Jonathan K. Pritchard.
Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6956/version/1

Towards an Open Taxonomy
Provedor de dados: 17
Autores: Roderic Page.
Taxonomy is in many ways still predigital. Most taxonomic databases are little more than digitized index cards linking names to often-cryptic bibliographic citations, oblivious to the growing volume of scientific literature that is now online. A growing fraction of taxonomic literature is becoming freely available, either through adoption of Open Access publishing models, or through digitizing efforts such as the Biodiversity Heritage Library. Yet much of the most basic information about biodiversity, namely taxonomic description, remains either behind a pay wall, or only available in paper form. This talk sketches the goal of an &amp;#x22;Open Taxonomy.&amp;#x22; The first step towards this goal is digitally linking scientific names to the primary...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6560/version/1

Extending the Modern Synthesis: The evolution of ecosystems
Provedor de dados: 17
Autores: Rodrick Wallace.
The Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of information theory, that instantiates the punctuated dynamic relations of organisms and their embedding environments. The mathematical overhead is considerable, and we conclude that the model must itself be extended even further to allow the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4496/version/1

Identification of transcription factor genes and their correlation with the high diversity of Stramenopiles
Provedor de dados: 17
Autores: Francisco Buitrago; Silvia Restrepo; Diego Ria&amp;#xf1;o-Pach&amp;#xf3;n.
In this study we identify, and classify into families, transcription factors (TFs) and other transcriptional regulators (TRs) in genome sequences available from the Stramenopile group. For this we exploit the presence of protein domains and their combinations to build rules in the form of boolean rules, that are specific for each family of TFs and TRs. We found a correlation between the family size and some traits that has been described to be involved in the complexity of organisms. Furthermore, we found specific gains, losses and families that shows higher abundance in different lineages, which may be involved in the regulation of specific traits for some Stramenopile species.
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7002/version/1

Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations.
Provedor de dados: 17
Autores: Shimon Bershtein; Eugene Shakhnovich.
Protein stability is widely recognized as a major evolutionary constraint. However, the relation between mutation-induced perturbations of protein stability and biological fitness has remained elusive. Here we explore this relation by introducing a selected set of mostly destabilizing mutations into an essential chromosomal gene of E.coli encoding dihydrofolate reductase (DHFR) to determine how changes in protein stability, activity and abundance affect fitness. Several mutant strains showed no growth while many exhibited fitness higher than wild type. Overexpression of chaperonins (GroEL/ES) buffered the effect of mutations by rescuing the lethal phenotypes and worsening better-fit strains. Changes in stability affect fitness by mediating the abundance of...
Tipo: Manuscript
Palavras-chave: Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6219/version/1

Estimating body Mass and Nutritional Status from Subadult Hominin Skeletons
Provedor de dados: 17
Autores: 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

Design and construction of a new Drosophila species, D.synthetica, by synthetic regulatory evolution
Provedor de dados: 17
Autores: Eduardo Moreno.
Here, I merge the principles of synthetic biology^1,2^ and regulatory evolution^3-11^ to create a new species^12-15^ with a minimal set of known elements. Using preexisting transgenes and recessive mutations of Drosophila melanogaster, a transgenic population arises with small eyes and a different venation pattern that fulfills the criteria of a new species according to Mayr&amp;#x27;s &amp;#x22;Biological Species Concept&amp;#x22;^7,10^. The genetic circuit entails the loss of a non-essential transcription factor and the introduction of cryptic enhancers. Subsequent activation of those enhancers causes hybrid lethality. The transition from &amp;#x22;transgenic organisms&amp;#x22; towards &amp;#x22;synthetic species&amp;#x22;, such as Drosophila...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6511/version/1

Why plants lose their inhibitions in the Arctic: functional traits, phylogenetics and respiration in the light
Provedor de dados: 17
Autores: Nicholas Mirotchnick; Owen Atkin; Marc Cadotte; Matthew Turnbull; Kevin Griffin.
Background/Questions/Methods:&amp;#xd;&amp;#xa;Arctic vegetation represents a significant portion of the world&amp;#x2019;s&amp;#xd;&amp;#xa;global carbon stocks and is particularly sensitive to global climate&amp;#xd;&amp;#xa;change. Net plant carbon exchange depends on both photosynthesis and&amp;#xd;&amp;#xa;respiration, the latter of which is poorly understood in arctic&amp;#xd;&amp;#xa;ecosystems and yet is highly sensitive to global environmental change.&amp;#xd;&amp;#xa; Mitochondrial respiration can confound measurements of photosynthesis&amp;#xd;&amp;#xa;and thus is often isolated by measuring it in the dark.  We also know,&amp;#xd;&amp;#xa;however, that respiration can be inhibited by light, which complicates&amp;#xd;&amp;#xa;extrapolations from...
Tipo: Presentation
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5375/version/1

Community content building for evolutionary biology: Lessons learned from LepTree and Encyclopedia of Life
Provedor de dados: 17
Autores: Cynthia Parr; Dana Campbell; John Park.
Online resources to aid large-scale ecological and evolutionary biology are beginning to take root, only a decade behind fields such as genomics and molecular biology. One barrier has been a long tradition, in evolutionary biology at least, of work by individuals on the order of a few hundred of species rather than the thousands or hundreds of thousands necessary to understand the general evolutionary or ecological processes that explain species characteristics and distributions. Advances in collaborative and semantic software offer promise &amp;#x2013; it should be possible to develop high quality online species-level datasets for comparative analyses and even to integrate, via machine reasoning, across highly customized datasets. In this talk we will...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4603/version/1

Astrobiological Perspectives on Consciousness
Provedor de dados: 17
Autores: Rodrick Wallace.
The Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not likely to have followed the particular, highly contingent and path-dependent, trajectory found on Earth. Are many of these life forms likely to be conscious in ways that we would recognize? Almost certainly. Will many conscious entities develop high order technology? Less likely. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The argument is straightforward.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5286/version/1

Complex Systems Analysis of Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: I. C. Baianu.
A new approach to the modular, complex systems analysis of nonlinear dynamics in cell cycling network transformations involved in carcinogenesis is proposed. Carcinogenesis is a complex process that involves dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments that form numerous inter-related pathways referred to as networks.&amp;#xd;&amp;#xa;The variable biotopology of such dynamic networks is highly complex, and has a number of interesting properties that can be formally characterized at one level of organization by mathematical structures called &amp;#x27;biogroupoids&amp;#x27;. &amp;#xd;&amp;#xa;One such family of pathways contains the cell cyclins. Cyclins are proteins that link several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6205/version/1

Adoption of simultaneous different strategies against different  opponents enhances cooperation
Provedor de dados: 17
Autores: Lucas Wardil; Jafferson  K. L. da Silva.
The emergence of cooperation has been widely studied in the context of game theory on  structured populations. Usually the individuals adopt one strategy against all their neighbors. The structure can provide reproductive success for the cooperative strategy, at least for low values of defection tendency. Other mechanisms, such punishment, can also be responsible for  cooperation emergence. But what happens if the players adopt simultaneously different strategies against each one of their opponents, not just a single one? Here we study this question in the prisoner dilemma scenario structured on a square lattice and on a ring. We show that if an update rule is defined in which the players replace the  strategy that furnishes the smallest payoff,  a...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3035/version/1

Pachydermoperiostosis-Like Disease In Captive Red Ruffled Lemurs (Varecia Variegatus Rubra)
Provedor de dados: 17
Autores: Bruce Rothschild; Donald Neiffer; Steve Marks.
Pachydermatoperiostosis, a rare form of hypertrophic osteoarthropathy, is of unknown etiology and previously thought limited to humans. The only periosteal reaction previously reported in prosimians is related to renal disease. Notation of hypertrophic osteoarthritis in three prosimians led to recognition that this was the first non-human documentation of the disease. Three related red ruffed lemurs (Varecia variegatus rubra) had diaphyseal periosteal reaction classic for hypertrophic osteoarthropathy. Workup was negative for known underlying causes and for the secondary hyperparathyroidism which produces bone alterations in black Eulemur macao, black and white Varecia variegatatus varigatus and ringtail Lemur catta lemurs. Recognition of facial coarsening...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6374/version/1

Diffusion Approximations for Demographic Inference: DaDi
Provedor de dados: 17
Autores: Ryan N. Gutenkunst; Ryan D. Hernandez; Scott H. Williamson; Carlos D. Bustamante.
Models of demographic history (population sizes, migration rates, and divergence times) inferred from genetic data complement archeology and serve as null models in genome scans for selection. Most current inference methods are computationally limited to considering simple models or non-recombining data. We introduce a method based on a diffusion approximation to the joint frequency spectrum of genetic variation between populations. Our implementation, DaDi, can model up to three interacting populations and scales well to genome-wide data. We have applied DaDi to human data from Africa, Europe, and East Asia, building the most complex statistically well-characterized model of human migration out of Africa to date.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4594/version/1

Multifunction moonlighting and intrinsically disordered proteins: Information catalysis, nonrigid molecule symmetries, and the &amp;#x27;logic gate&amp;#x27; spectrum
Provedor de dados: 17
Autores: Rodrick Wallace.
Intrinsically disordered proteins (IDP) appear far more likely to engage in functional moonlighting than well-structured proteins. The recent use of nonrigid molecule theory to address IDP structure and dynamics produces this result directly: Mirror image subgroup or subgroupoid tiling matching of the molecular fuzzy lock-and-key can be much richer for IDPs since the number of possible group or groupoid symmetries can grow exponentially with molecule length, while tiling matching for 3D structured proteins is relatively limited. A simple information catalysis model suggests how this mechanism can produce a vast spectrum of biological &amp;#x27;logic gates&amp;#x27; having subtle properties far beyond familiar AND, OR, XOR, etc. behaviors. Inferring the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Molecular Cell Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6413/version/1

Estimation of DNA Sequence Context-dependent Mutation Rates Using Primate Genomic Sequences: Application to Estimation of Selection Bias in Protein (Human TP53) Evolution
Provedor de dados: 17
Autores: Wei Zhang.
Understanding of the mechanism of DNA mutation process is critical for studying the functional consequences of genetic variation in clinical medicine (eg. drug response) as well as other complex traits (eg. gene expression and cause of common diseases). During the last several decades, many probabilistic models of DNA nucleotide substitution have been proposed for studying this process. A common feature of these mutation models is that they assume the nucleotides evolve independently at each site. In other words, they are sequence context-independent models. However, based on various biochemical studies, it is now recognized that the DNA mutation process resulting in substitutions in both coding and non-coding regions may depend on sequence context. We...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1243/version/1

Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications
Provedor de dados: 17
Autores: Shang-Hong Zhang; Ya-Zhi Huang.
One of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth&amp;#x2019;s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist;...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2146/version/1

New Spontaneous Model of Fibrodysplasia Ossificans Progressiva
Provedor de dados: 17
Autores: Bruce Rothschild; Larry Martin; Robert Timm.
We report the first known example of spontaneous, naturally occurring fibrodysplasia ossificans progressiva (FOP) in a mammal. The Southeast Asian mouse deer of the genus _Tragulus_ (Artiodactyla: Tragulidae) have an osseous sheath covering the lower back and upper thigh region consistent with the clinical definition of FOP. This heterotophic bone deposition is sex related apparently with a genetic basis - it only occurs in males and is lacking in females; it is present in all adults males, including both wild obtained and zoo bred animals. _Tragulus_ may offer the opportunity to examine many of the disease&amp;#x27;s most significant attributes experimentally.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1541/version/1

Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies
Provedor de dados: 17
Autores: Jennifer Hoyal Cuthill; Michael Charleston.
The unpalatable and warning-patterned butterflies _Heliconius erato_ and _Heliconius melpomene_ provide the best studied example of mutualistic M&amp;#xfc;llerian mimicry, thought &amp;#x2013; but rarely demonstrated &amp;#x2013; to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and this was initially hailed as the most striking known case of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence)...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6829/version/1

BBSRC Data Sharing Policy
Provedor de dados: 17
Autores: Amanda Collis; David McAllister; Michael Ball.
BBSRC recognizes the importance of contributing to the growing international efforts in data sharing. BBSRC is committed to getting the best value for the funds we invest and believes that making research data more readily available will reinforce open scientific inquiry and stimulate new investigations and analyses. BBSRC supports the view that data sharing should be led by the scientific community and driven by scientific need. It should also be cost effective and the data shared should be of the highest quality. Members of the community are expected and encouraged to practice and promote data sharing, determine standards and best practice, and create a scientific culture in which data sharing is embedded.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Immunology; Microbiology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Plant Biology; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6015/version/1

Application of a periodic table for the genetic code to influenza A/H3N2 virus
Provedor de dados: 17
Autores: Susumu Morimoto.
If biologists can utilize a table to have access to biological phenomena in the manner analogous to the periodic table for chemical elements, they may get hold of a directing post in life science. Currently the mutational rule of influenza viruses have remained perplexed and to reveal it should be now desired when avian influenza virus has just then threatened human beings. Here I examine the applicability of a novel periodic table for the genetic code to influenza A/H3N2 virus, while presenting two rules regarding single point mutations of its virus hemagglutinin gene. One rule is that non-synonymous single point mutations are intimately associated with the first or second base replacements between four groups (5, 6, 9, and 10) in the periodic table....
Tipo: Manuscript
Palavras-chave: Chemistry; Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/428/version/1

Living unicellular eukaryote Tetrahymena pyriformis as a model for study
Provedor de dados: 17
Autores: Elena N. Mokhova.
Some animals are able to survive for a long time under conditions of drastically reduced oxidative metabolism, called metabolic depression. The most investigated type of metabolic depression is hibernation. Research into the basic properties of liver mitochondria energetics during hibernation is essential for fundamental biology and medicine. However, the absence of a suitable hepatocyte culture makes it impossible to study the characteristic features of mitochondrial metabolic states in living cells during hibernation. We proposed that under selected conditions, the unicellular eukaryote Tetrahymena pyriformis resembles hepatocytes under hibernation, as (i) both cell types survive under condition of restricted food supply, hypoxia, and accumulation of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4521/version/4

Evolution of Co-operation When the Strategies are Hidden: The Human Mating Game
Provedor de dados: 17
Autores: Milind Watve; Anuja Damle; Bratati Ganguly; Anagha Kale.
Defection is frequently seen in co-operative systems [1-3]. Game theoretical solutions to stabilize cooperation rely on reciprocity and reputation in iterated games[4-5]. One of the basic requirements for reciprocity or reputation building is that the strategies of players and the resulting payoffs should be open at the end of every interaction. For games in which the strategies and payoffs remain hidden, these stabilizing factors are unlikely to work. We examine the evolution of cooperation for hidden-strategy games using human mating game as an example.  Here faithful parenting can be considered as cooperation and extra-pair mating (EPM) or cuckoldry as defection. Cuckoldry may get exposed only occasionally and the genetic benefits of cuckoldry also...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/740/version/1

Category of Metabolic-Replication Systems in Biology and Medicine
Provedor de dados: 17
Autores: I. C. Baianu.
Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life&amp;#x27;s origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important question of the minimal living organism by defining the functional relations that would have made life possible in such a minimal system- a grandad and grandma of all living organisms on Earth.
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Neuroscience; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7045/version/1

Collaboration Networks in the Brazilian Scientific Output in Evolutionary Biology: 2000-2012
Provedor de dados: 42
Autores: Santin,Dirce M.; Vanz,Samile A.S.; Stumpf,Ida R.C.
This article analyzes the existing collaboration networks in the Brazilian scientific output in Evolutionary Biology, considering articles published during the period from 2000 to 2012 in journals indexed by Web of Science. The methodology integrates bibliometric techniques and Social Network Analysis resources to describe the growth of Brazilian scientific output and understand the levels, dynamics and structure of collaboration between authors, institutions and countries. The results unveil an enhancement and consolidation of collaborative relationships over time and suggest the existence of key institutions and authors, whose influence on research is expressed by the variety and intensity of the relationships established in the co-authorship of...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Co-authorship; Collaboration networks; Evolutionary Biology; Scientific collaboration; Scientific output; Scientometrics.
Ano: 2016
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652016000100165