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Evolution, Molecular (0):
Recent article
Evolution, Molecular
Cancer Research (71)22 2011
Abstract
We developed a curated database of 88 nuclear receptor cistrome data sets and other associated high-throughput data sets including 121 collaborating factor cistromes, 94 epigenomes, and 319 transcriptomes. Through integrative analysis of the curated nuclear receptor ChIP-chip/seq data sets, we disco...
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PMID: 21940749
PDF is available here.
PDF is available here.
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Abstract
We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the lo...
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PMID: 21940861
PDF is available here.
PDF is available here.
Abstract
We constructed a genetic linkage map of common carp (Cyprinus carpio L.) using microsatellite and single-nucleotide polymorphism (SNP) markers in a 159 sibling family. A total of 246 microsatellites and 306 SNP polymorphic markers were genotyped in this family. Linkage analysis using JoinMap 4.0 org...
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PMID: 21870156
PDF is available here.
PDF is available here.
Endocrinology (152)10 2011
Abstract
We characterized to which GRE GR binds in the rat hippocampus. Using a position-specific scoring matrix, we identified evolutionary-conserved putative GREs from a microarray based set of hippocampal target genes. Using chromatin immunoprecipitation, we were able to confirm GR binding to 15 out of a...
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PMID: 21846803
PDF is available here.
PDF is available here.
Abstract
We review differential gene regulation focusing on evolutionary-developmental (evodevo) biology, global comparison of genomic sequences, whole-genome gene expression, and transcription factor (TF) binding profiles. We also explore the relationship between divergence rate of regulatory sequences, cod...
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PMID: 21721942
PDF is available here.
PDF is available here.
Abstract
We review evidence that the lipid-exposed surfaces of membrane proteins have generally evolved to maintain correct structure and function in the face of major changes in lipid composition. Such tolerance has allowed evolution to extensively remodel membrane lipid compositions during the emergence of...
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PMID: 21848311
PDF is available here.
PDF is available here.
Abstract
We present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end librar...
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PMID: 21832995
PDF is available here.
PDF is available here.
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] (27)5 2011
Abstract
In order to confirm the cause of the outbreak of aseptic meningitis in Zhejiang Province in 2002-2004, trace the pathogen and analyze the molecular characteristics, 271 cerebrospinal fluid (CSF) and faeces specimens were collected from suspected patients. The virus strains from the s...
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PMID: 21998959
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)8 2011
Abstract
We therefore summarise recent efforts to fundamentally improve this situation by decoupling the sampling of the energy landscape from the description of the kinetics of the process. Recent years have seen the emergence of many advanced sampling techniques, which permit efficient characterisation of...
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PMID: 20851219
PDF is available here.
PDF is available here.
Abstract
We examine the epidemiology of EV71, with three waves of increased EV71 activity since the 1970s and discuss the genotypic changes in phylogeny between the outbreaks or epidemics. Genetic changes including mutations and recombinations as well as the diversity of antigenic properties among EV71 strai...
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PMID: 21715436
PDF is available here.
PDF is available here.
Abstract
We review here the current knowledge and show that Prxs can be effectively classified by a structural/evolutionary organization into six subfamilies followed by specification of a 1-Cys or 2-Cys mechanism, and for 2-Cys Prxs, the structural location of the resolving Cys. We visualize the varied cata...
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PMID: 20969484
PDF is available here.
PDF is available here.
Abstract
We describe KIR-associated amino-acid polymorphisms in the HIV-1 sequence of chronically infected individuals, on a population level. We show that these KIR-associated HIV-1 sequence polymorphisms can enhance the binding of inhibitory KIRs to HIV-1-infected CD4(+) T cells, and reduce the antiviral a...
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PMID: 21814282
PDF is available here.
PDF is available here.
Abstract
Adenoviruses are medium-sized double stranded DNA viruses that infect vertebrates. Human adenoviruses cause an array of diseases. Currently there are 56 human adenovirus types recognized and characterized within seven species (A-G). Of those types, a majority belongs to species D. In...
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PMID: 21570490
PDF is available here.
PDF is available here.
Abstract
We have identified DNA differences between the first New Zealand isolate of S. Typhimurium DT160 and the genome-sequenced strain, S. Typhimurium LT2. All the differences could be accounted for in one cryptic phage ST64B, and one novel P22-like phage, ST160. The majority of the ST160 genome is almost...
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PMID: 20950514
PDF is available here.
PDF is available here.
Abstract
We review recent work with relatives of these species, motivated by a desire to understand the evolutionary and ecological context for morphological innovation. Unfortunately, despite a number of shining examples, progress in nonmodel systems has often been slow. The current revolution in DNA sequen...
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PMID: 21763609
PDF is available here.
PDF is available here.
Abstract
We earlier reported a network of interacting loci with large effects on body weight in an F(2) intercross between these high- and low-body weight lines. Here, most pair-wise interactions in the network are replicated in an independent eight-generation advanced intercross line (AIL). The original rep...
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PMID: 21814519
PDF is available here.
PDF is available here.
Abstract
PLoS Biology (9)6 2011
Abstract
We employ population genomics data from Escherichia coli, Saccharomyces paradoxus, and Drosophila to provide evidence suggesting that it is not the indels per se but the sequence in which indels occur that causes the accumulation of nucleotide substitutions. We found that about two-thirds of indels...
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PMID: 21697975
PDF is available here.
PDF is available here.
Trends in Genetics (27)6 2011
Abstract
Fuelled by new sequencing technologies, epigenome mapping projects are revealing epigenomic variation at all levels of biological complexity, from species to cells. Comparisons of methylation profiles among species reveal evolutionary conservation of gene body methylation patterns, pointing to the fu...
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PMID: 21507501
PDF is available here.
PDF is available here.
Abstract
Abstract
We summarized recent research progresses on avirulence genes, which are the most important effectors in M. grisea with the focus on chromosome mapping, cloning method, functional analysis, and evolution study of avirulence genes, and the possible hotspot of the research on avirulence genes in the fu...
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PMID: 21684864
PDF is available here.
PDF is available here.
Abstract
These results reconfirmed that the horizontally transferred genes are exogenous. The analysis of gene function suggested that horizontally transferred genes acquired from an ancestral host insect can increase the efficiency of baculoviruses transmission....
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PMID: 21684870
PDF is available here.
PDF is available here.
Abstract
We quantify the epidemiological, genetic and antigenic dynamics of SwIV in Hong Kong using a data set of more than 650 SwIV isolates and more than 800 swine sera from 12 years of systematic surveillance in this region, supplemented with data stretching back 34 years. Intercontinental virus movem...
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PMID: 21614079
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)9 2011
Abstract
Bacteroides fragilis and Clostridium thermocellum were recently found to synthesize diaminopimelate (DAP) by way of LL-DAP aminotransferase. Both species also contain an ortholog of meso-diaminopimelate dehydrogenase (Ddh), suggesting that they may have redundant pathways for DAP bio...
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PMID: 21616177
PDF is available here.
PDF is available here.
Abstract
The structure of ent-copalyl diphosphate synthase reveals three α-helical domains (α, β and γ), as also observed in the related diterpene cyclase taxadiene synthase. However, active sites are located at the interface of the βγ domains in ent-copalyl diphosphate synthase but exc...
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PMID: 21602811
PDF is available here.
PDF is available here.
Abstract
We have now identified three mechanisms of tetrapyrrole singlet excited state quenching by carotenoids in artificial systems: (i) Car-Pc electron transfer and recombination; (ii)(1) Pc to Car S(1) energy transfer and fast internal conversion to the Car ground state; (iii) excitonic coupling between...
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PMID: 21491907
PDF is available here.
PDF is available here.
Abstract
Root hairs are unicellular extensions of specialized epidermis cells. Under limiting conditions, they significantly increase the water and nutrient uptake capacity of plants by enlarging their root surface. Thus far, little is known about the initiation and growth of root hairs in th...
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PMID: 21417484
PDF is available here.
PDF is available here.
PLoS Genetics (7)5 2011
Abstract
We use an integrative analysis and evolutionary conservation to identify features that predict when the loss of a regulatory interaction is detrimental in the extensively mapped transcription network of budding yeast. Properties such as the strength of an interaction, location and context in a promo...
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PMID: 21637788
PDF is available here.
PDF is available here.
Genetika (Moskva) (47)5 2011
Abstract
The review surveys the development and the current state of genetic genealogy, a branch of science dealing with the history of individuals, families, and kins using molecular genetic methods. The main milestones in the development of genetic genealogy are established: the appearance of essential prer...
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PMID: 21786664
PDF is available here.
PDF is available here.
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] (27)3 2011
Abstract
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] (27)3 2011
Abstract
We performed an extensive comparative analysis of RABV N gene sequence data, representing 167 isolates sampled from 20 provinces in a 78-year period (from 1931 through 2009). The available Chinese isolates could be divided into two distinct clades:Phylogroup clades I comprised Chinese group 1-4; Phy...
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PMID: 21774248
PDF is available here.
PDF is available here.
Abstract
Coxsackievirus (CV) strains CVA2, CVA4, CVA5, and CVA10 were isolated from patients with hand, foot, and mouth disease during a 2009 outbreak in China. Full genome sequences for four representative strains, CVA2/SD/CHN/09 (A2SD09), CVA4/SZ/CHN/09 (A4SZ09), CVA5/SD/CHN/09 (A5SD09), and CVA10/SD/CHN/09...
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PMID: 21543560
PDF is available here.
PDF is available here.
Abstract
We discuss recent findings on the evolutionary process behind the gain of a resistant gene. It was shown that, for a protein to become resistant to an inhibitor, an intricate stepwise order of mutations must be followed. The projected evolutionary steps were compared with the field data, which refle...
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PMID: 21577054
PDF is available here.
PDF is available here.
Abstract
We describe the ways in which pseudogenes exert their effect on coding genes and explore the role of pseudogenes in the increasingly complex web of noncoding RNA that contributes to normal cellular regulation....
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PMID: 21398401
PDF is available here.
PDF is available here.
Abstract
Liver metastasis is a fatal step in the progression of colorectal cancer (CRC); however, the epigenetic evolution of this process is largely unknown. To decipher the epigenetic alterations during the development of liver metastasis, the DNA methylation status of 12 genes, including 5...
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PMID: 21406167
PDF is available here.
PDF is available here.
Zoological Research (32)2 2011
Abstract
We determined 592 bp D-loop sequences of 87 cape hares from Xinjiang Province. Forty-four haplotypes were defined based on 148 polymorphic sites. Both the haplotype diversity (0.977+/-0.005) and nucleotide diversity (0.064+/-0.031) are high. FST P values are significantly high and no haplotype was s...
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PMID: 21509964
PDF is available here.
PDF is available here.
Abstract
In recent developments in chemistry and genetic engineering, the humble researcher dealing with the origin of life finds her(him)self in a grey area of tackling something that even does not yet have a clear definition agreed upon. A series of chemical steps is described to be conside...
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PMID: 21641557
PDF is available here.
PDF is available here.
PLoS Genetics (7)4 2011
Abstract
We provide evidence of a rugged molecular fitness landscape arising during an evolution experiment in an asexual population of Saccharomyces cerevisiae. We identify the mutations that arose during the evolution using whole-genome sequencing and use competitive fitness assays to describe the mutation...
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PMID: 21552329
PDF is available here.
PDF is available here.
Abstract
We propose several novel algorithms to reconstruct the growth history of a present-day network. Our likelihood-based method finds a probable previous state of the graph by applying an assumed growth model backwards in time. This approach retains node identities so that the history of individual node...
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PMID: 21533211
PDF is available here.
PDF is available here.
Abstract
We compared the distribution of pathogenicity scores observed on the human phylogenetic tree to the distribution of all possible protein variations to define a measure of the effect of selection on these protein variations. The measured effect of selection increased exponentially with increasing pat...
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PMID: 21457906
PDF is available here.
PDF is available here.
A genome-wide comparison of the functional properties of rare and common genetic variants in humans.
Abstract
We address this question for humans specifically from the perspective of population allele frequency of variants across the complete genome, including both coding and noncoding regions. We establish simple criteria to assess the likelihood that variants are functional based on their genomic location...
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PMID: 21457907
PDF is available here.
PDF is available here.
Abstract
Transposable elements (TEs) are massively abundant and unstable in all plant genomes, but are mostly silent because of epigenetic suppression. Because all known epigenetic pathways act on all TEs, it is likely that the specialized epigenetic regulation of regular host genes (RHGs) was co-opted from t...
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PMID: 21444239
PDF is available here.
PDF is available here.
Abstract
We generated new sequence data of exon 2 of the Pfcrt gene and collected published information on the CQR-Pfcrt haplotype data from India, Papua New Guinea, southeast Asia and South America, and performed several population and evolutionary genetic analyses. Among several interesting findings, stati...
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PMID: 21447338
PDF is available here.
PDF is available here.
Trends in Genetics (27)5 2011
Abstract
Since the first animal genomes were completely sequenced ten years ago, evolutionary biologists have attempted to use the encoded information to reconstruct different aspects of the earliest stages of animal evolution. One of the most important uses of genome sequences is to understand relationships...
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PMID: 21414681
PDF is available here.
PDF is available here.
Abstract
We identify molecular events particularly likely to produce significant regulatory changes in humans: complete deletion of sequences otherwise highly conserved between chimpanzees and other mammals. We confirm 510 such deletions in humans, which fall almost exclusively in non-coding regions and are...
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PMID: 21390129
PDF is available here.
PDF is available here.
Abstract
These results suggest that the rotavirus VP6, NSP1 and NSP5 genes of Wa-like rotaviruses are more prone to temporal mutations. Both structural and nonstructural genes of the Western Indian rotavirus strains shared nucleotide and amino acid substitutions with the Bangladeshi strain, Dhaka16-03 (G1P[8...
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PMID: 21256248
PDF is available here.
PDF is available here.
Abstract
The efficiencies of IFN-α based therapy in chronic genotype 1b HCV patients are still unsatisfied to date. The mechanisms underlining treatment failure remain unclear and controversial. To investigate HCV sequence evolution in unsuccessfully treated genotype 1b patients before, duri...
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PMID: 21147266
PDF is available here.
PDF is available here.
Abstract
Bacterial intergenic spacers are non-coding genomic regions enriched with cis-regulatory elements for gene expression. A population genetics approach was used to investigate the evolutionary force shaping the genetic diversity of intergenic spacers among 13 genomes of group A strepto...
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PMID: 21115137
PDF is available here.
PDF is available here.
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] (27)2 2011
Abstract
In 2006, the first Chinese Tahyna virus isolate (XJ0625) was obtained in Xinjiang province and human infection were found in the same region. In this study, cell culture, animal experiments, electron microscopy, immunofluorescence assay and cross neutralization tests were performed to see the cell su...
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PMID: 21528532
PDF is available here.
PDF is available here.
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] (27)2 2011
Abstract
We compared the genome sequence of the 2 WUPyV isolates in Fuzhou, China to those documented in the GenBank database by using PHYLIP software version 3.65 and the neighbor-joining method. The 2 WUPyV strains in our study were clustered together. Strain FZTF was more closed to the reference strain B0...
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PMID: 21528542
PDF is available here.
PDF is available here.
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] (27)2 2011
Abstract
Abstract
Generation of the HLA-B*15 group of alleles has been analyzed using exon 1, intron 1, exon 2, intron 2, and exon 3 sequences from human and nonhuman primates. Results indicated that the 230 alleles analyzed could be grouped into 5 different lineages of evolution coming from nonhuman primate MHC-B* al...
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PMID: 21376098
PDF is available here.
PDF is available here.
Trends in Genetics (27)3 2011
Abstract
The past decade has seen a remarkable revision of perspectives on unisexual reproduction in vertebrates. One can no longer view it as a rare curiosity far outside the mainstream of evolution. More than 80 taxa of fish, amphibians, and reptiles are now known to reproduce by parthenogenesis (Greek for...
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PMID: 21334090
PDF is available here.
PDF is available here.
Abstract
Epidemiological studies of the naturally transformable bacterial pathogen Streptococcus pneumoniae have previously been confounded by high rates of recombination. Sequencing 240 isolates of the PMEN1 (Spain(23F)-1) multidrug-resistant lineage enabled base substitutions to be distingu...
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PMID: 21273480
PDF is available here.
PDF is available here.
Abstract
We synthesize phylogenetic data from these diverse strands, with the addition of new molecular and morphological data to examine the phylogeny of the squat lobsters and assess the status of the Galatheoidea. A total of 64 species from 16 of the 17 currently recognised anomuran families are included....
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PMID: 21095236
PDF is available here.
PDF is available here.
Mutation Research (708)1-2 2011
Abstract
We analyzed the occurrence of germline slippage mutations in the hypervariable pentanucleotide microsatellite locus HrU10 across six species of swallow (Aves: Hirundinidae). These species exhibit marked differences in the length range of the microsatellite, as well as differences in the intensity of...
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PMID: 21291898
PDF is available here.
PDF is available here.
Abstract
We amplified and cloned the ITS region from pure cultures of six Laetiporus species and one Wolfiporia species (Basidiomycota, Polyporales). An average of 66 clones were randomly selected and sequenced from 21 cultures, producing a total of 1399 interpretable sequences. Significant variation (≥ 5%...
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PMID: 21289107
PDF is available here.
PDF is available here.
Abstract
We present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceede...
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PMID: 21270892
PDF is available here.
PDF is available here.
Abstract
Abstract
We test our algorithm on a dataset of eukaryotic gene families spanning 29 taxa....
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PMID: 21431569
PDF is available here.
PDF is available here.