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| Registros recuperados: 383 | |
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| 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 & Genomics; Evolutionary Biology. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1866/version/1 |
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| 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 |
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| 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 & Environment; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4433/version/1 |
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| 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 |
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| 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 |
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| Sosale Chandrasekhar. |
| The Michaelis-Menten equation (MME) is considered to be the fundamental equation describing the rates of enzyme-catalysed reactions, and thus the 'physicochemical key' 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 ('turnover'). The manifested 'saturation kinetics', 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 |
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| 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 & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5475/version/1 |
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| Roderic D. M. Page. |
| Although the Web has transformed science publishing, scientific papers themselves are still essentially "black boxes", 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 |
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| 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 & Genomics; Neuroscience; Bioinformatics; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3043/version/1 |
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| 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 |
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| Roderic Page; Michael Charleston. |
| TreeMap is a computer program for analysing host-parasite cospeciation. We respond to Dowling’s (Cladistics, 18: 416-435) recent comparison of TreeMap and Brooks Parsimony Analysis (BPA) by showing that Dowling’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 |
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| Rodrick Wallace. |
| Tlusty'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 'normal' globular and a 'pathological' amyloid version. The underlying normal 'protein folding code error network' is found to have one major, highly dominant, 'spherical' 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 |
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| 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’ 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 |
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| 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 & Genomics; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3007/version/1 |
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| Mario Pineda-Krch; Richard Svanbäck; Michael Doebeli. |
| Theoretical and empirical studies are showing evidence in support of evolutionary branching and sympatric speciation due to frequency‐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 “competition” between the processes of evolutionary branching and the evolution of phenotypic plasticity in a predator‐prey model... |
| Tipo: Presentation |
Palavras-chave: Ecology; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3672/version/1 |
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| 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 & Genomics; Evolutionary Biology. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1276/version/1 |
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| 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 & Genomics; Microbiology; Bioinformatics; Evolutionary Biology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6835/version/1 |
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| Registros recuperados: 383 | |
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