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| Registros recuperados: 383 | |
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| 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 |
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| 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.

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 |
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| 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 & Genomics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5360/version/3 |
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| 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 & Genomics; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3050/version/1 |
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| 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 |
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| 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’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 |
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| 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; "http://www.h-invitational.jp/":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 & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3251/version/1 |
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| Felisa Wolfe-Simon; Paul C. W. Davies; Ariel Anbar. |
| All known life requires phosphorus (P) in the form of inorganic phosphate (PO<sub>4</sub><sup>-</sup> or P<sub>i</sub>) and phosphate-containing organic molecules. P<sub>i</sub> 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 |
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| 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 |
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| 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'-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 & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/69/version/1 |
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| 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 |
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| 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 |
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| 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.

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 |
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| Registros recuperados: 383 | |
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