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Base Composition (0):
Recent article
Base Composition
ISME Journal (5)5 2011
Abstract
We describe two complete ssDNA phage genomes that were reconstructed from a viral metagenome from 80 m depth at the Bermuda Atlantic Time-series Study (BATS) site in the northwestern Sargasso Sea and examine their spatial and temporal distributions. Both genomes (SARssφ1 and SARssφ2) exhibited s...
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PMID: 21124487
PDF is available here.
PDF is available here.
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Abstract
We report here on the existence of a high-level compositional organization of isochores in the human genome. By using a segmentation algorithm incorporating the long-range correlations existing in human DNA, we find that every chromosome is composed of a few huge segments (~ 10^{7} bp) of relatively...
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PMID: 21517526
PDF is available here.
PDF is available here.
Abstract
We report a thorough comparative study on 203 well-selected bacterial species, which strongly suggest that the previous conclusion is likely an illusion. Firstly, the previous study did not preclude species that are suffering weak or no selection pressures on their codon usages. For these species, a...
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PMID: 21829489
PDF is available here.
PDF is available here.
Abstract
Abstract
We present the complete mitochondrial DNA sequence of Eupolyphaga sinensis. This closed circular molecule is 15553 bp long and consists of 37 genes that encode for 13 inner membrane proteins, 2 ribosomal RNAs and 22 transfer RNAs. The genome shares the gene order and orientation with previously know...
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PMID: 20012368
PDF is available here.
PDF is available here.
Abstract
A Gram-negative, motile, non-spore-forming bacterial strain, designated MJ07(T), was isolated from a farm soil and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ07(T) belongs to the family Alcali...
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PMID: 19933592
PDF is available here.
PDF is available here.
Abstract
A Gram-negative, motile, non-spore-forming bacterial strain, designated HU1-GD12(T), was isolated from freshwater sediment. The strain was characterized by using a polyphasic approach in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the iso...
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PMID: 19946046
PDF is available here.
PDF is available here.
Abstract
We propose the names Mucilaginibacter gossypii sp. nov. (type strain Gh-67(T) =NCIMB 14470(T) =KCTC 22380(T)) and Mucilaginibacter gossypiicola sp. nov. (type strain Gh-48(T) =NCIMB 14471(T) =KCTC 22379(T))....
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PMID: 19946048
PDF is available here.
PDF is available here.
Abstract
I and/or anteiso-C₁₇ :₁ B), iso-C₁₅:₀ and C₁₆:₁ω5c. The fatty acid content of strain 6424S-61(T) mainly comprised iso-C₁₅ :₁ G and iso-C₁₅:₀. Comparative analysis of phenotypic and phylogenetic traits indicated that strains 6424S-25(T) and 6515J-31(T) represented t...
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PMID: 19946049
PDF is available here.
PDF is available here.
Abstract
Two strains of anaerobic, Gram-stain-negative bacilli isolated from the human oral cavity (D033B-12-2(T) and D080A-01) were subjected to a comprehensive range of phenotypic and genotypic tests and were found to be distinct from any previously described species. 16S rRNA gene sequence analysis reveal...
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PMID: 19946051
PDF is available here.
PDF is available here.
Abstract
A haloalkaliphilic archaeon, strain JX313(T), was isolated from a saline-alkaline soil from Daqing, Heilongjiang Province, China. Its morphological, physiological and biochemical features and 16S rRNA gene sequence were determined. Colonies of the strain were orange-red and cells were non-motile coc...
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PMID: 19915113
PDF is available here.
PDF is available here.
Abstract
A marine bacterial strain, designated fav-2-10-05(T), was isolated from the mucus layer of a coral of the genus Favia, collected from the coral reef in the Gulf of Eilat, Israel (29.5 ° N 34.9 ° E). On the basis of 16S rRNA gene sequence comparisons, strain fav-2-10-05(T) was affiliated with t...
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PMID: 19915103
PDF is available here.
PDF is available here.
Abstract
A Gram-positive, endospore-forming, rod-shaped bacterium, strain PD-A10(T), was isolated from salted crab (poo-khem) in Thailand and subjected to a taxonomic study. Phenotypic and chemotaxonomic characteristics, including phylogenetic analyses, showed that the novel strain was a member of the genus...
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PMID: 19933584
PDF is available here.
PDF is available here.
Abstract
A bacterial strain, SPC26(T), was isolated from a sediment sample of the Southern Ocean off Antarctica. The strain was Gram-staining- and catalase-positive and contained lysine and alanine in the cell-wall peptidoglycan. The major cellular fatty acids were anteiso-C₁₅:₀ (54.92 %), iso-C₁...
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PMID: 19783612
PDF is available here.
PDF is available here.
Abstract
A Gram-stain-positive, aerobic bacterium, designated strain BZ41(T), was isolated from hydrocarbon-contaminated soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ41(T) was related to members of the genus Agromyces and showed highest similarity with the type strain of...
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PMID: 19933590
PDF is available here.
PDF is available here.
Abstract
A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain LW7(T), was isolated from a water sample collected at a depth of 4.5 m from Lonar Lake in Buldhana district, Maharastra, India. The cell suspension was dark-reddish orange due to the presence of carotenoids. The fatty acids w...
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PMID: 19933591
PDF is available here.
PDF is available here.
Abstract
A xylanolytic bacterium, strain S1-3(T), was isolated from soil collected in Nan province, Thailand. It was characterized taxonomically based on phenotypic characteristics and 16S rRNA gene sequence comparison. The strain was a Gram-stain-positive, facultatively anaerobic, spore-forming, rod-shaped...
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PMID: 19915111
PDF is available here.
PDF is available here.
Abstract
A Gram-staining-negative, yellow-coloured, strictly aerobic, non-spore-forming, rod-shaped bacterium, designated HS39(T), isolated from a soil sample collected from a natural Populus euphratica forest in Xinjiang, China, was characterized using a polyphasic approach. The isolate grew optimally at 30...
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PMID: 19933581
PDF is available here.
PDF is available here.
Abstract
Phenotypic and phylogenetic studies were performed on three strains of an acetogenic bacterium isolated from livestock-impacted soil. The bacterium stained Gram-negative and was a non-spore-forming rod that was motile by peritrichous flagella. The novel strains had an optimum pH for growth of 8.0-8....
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PMID: 19965999
PDF is available here.
PDF is available here.
Abstract
A short coccoid- to rod-shaped, motile, mesophilic actinobacterium, strain MSL-22(T), was isolated from soil on Bigeum Island, Korea. A polyphasic study was undertaken to establish the taxonomic position of this strain. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MSL-...
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PMID: 19915109
PDF is available here.
PDF is available here.
Abstract
We propose the name Vogesella mureinivorans sp. nov. The type strain is 389(T) (=DSM 21247(T) =LMG 25302(T))....
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PMID: 19946047
PDF is available here.
PDF is available here.
Abstract
A halophilic archaeon, strain RO1-6(T), was isolated from a marine solar saltern in eastern China. Cells of strain RO1-6(T) were pleomorphic and motile and stained Gram-negative. Strain RO1-6(T) grew well on complex medium and colonies were red-pigmented. It was able to grow at 20-50°C (optimum 37...
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PMID: 19946053
PDF is available here.
PDF is available here.
Abstract
A Gram-stain-positive, neutrophilic, rod-shaped bacterium, strain A1g(T), was isolated from activated sludge of a bioreactor and was subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0-17.0 % (w/v) NaCl and at pH 6.0-9.0; optimum growth was observed in the p...
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PMID: 19946056
PDF is available here.
PDF is available here.
Abstract
We studied the physiological, biochemical properties and metabolism of Clostridium lituseburense P4-1 from soil in Namucuo.
We adopted Hungate anaerobic technique to get Strain P4-1 from soil in Namucuo. Through physiological, biochemical and phylogenetic analysis, we identified the strain P4-1.
Cel...
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PMID: 21090252
PDF is available here.
PDF is available here.
Abstract
The temperate phages PhiCD6356 and PhiCD6365 were isolated and characterised following mitomycin C induction of 43 Clostridium difficile strains. Both phages belong to the Siphoviridae family and have genome sizes of 37,664 bp for PhiCD6356 based on sequence data and approximately 50 kb for PhiCD636...
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PMID: 20438817
PDF is available here.
PDF is available here.
Epidemiology and Infection (138)8 2010
Abstract
In Uganda, limiting the extent of foot-and-mouth disease (FMD) spread during outbreaks involves short-term measures such as ring vaccination and restrictions of the movement of livestock and their products to and from the affected areas. In this study, the presence of FMD virus RNA was investigated...
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PMID: 20003615
PDF is available here.
PDF is available here.
Abstract
We developed and evaluated a broad-range Flavivirus assay designed to detect both tick- and mosquito-borne flaviviruses by using RT-PCR/electrospray ionization mass spectrometry (RT-PCR/ESI-MS) on the Ibis T5000 platform. The assay was evaluated with a panel of 13 different flaviviruses. All samples...
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PMID: 20412852
PDF is available here.
PDF is available here.
Abstract
Sequencing of plasmid pLM33 from the food isolate Listeria monocytogenes Lm1 revealed a molecule of 32,307 bp with a G+C content of 36.2%. The plasmid displays a mosaic pattern of identities common to several closely related L. monocytogenes plasmids isolated from food and clinical s...
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PMID: 20511420
PDF is available here.
PDF is available here.
Abstract
We observed that the most redundant sequences of 349 clones in a human CGI library were all generated from the human mitochondrial genome. Further analysis indicated that there was a 5,845-bp DNA transfer from mtDNA to chromosome 1, and all the clones should be the products of a 510-bp MseI fragment...
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PMID: 20691393
PDF is available here.
PDF is available here.
Abstract
We developed new scoring functions to predict nucleosome positioning. There are three principal differences between our approach and earlier studies: (i) we assume that the length of nucleosomal DNA varies from 146 to 147 bp; (ii) we consider the anisotropic flexibility of pyrimidine-purine (YR) dim...
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PMID: 20232936
PDF is available here.
PDF is available here.
Abstract
We focus on DNA conformational signals found in the growing library of known high-resolution core-particle structures and the ways in which these features may contribute to the positioning of nucleosomes on specific DNA sequences. We survey the chemical composition of the protein-DNA assemblies and...
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PMID: 20232929
PDF is available here.
PDF is available here.
Antonie Van Leeuwenhoek (98)1 2010
Abstract
A Gram-positive, moderately halophilic, facultatively alkaliphilic, catalase- and oxidase-positive, obligately aerobic, filamentous actinomycete strain, designated YIM 90022(T), was isolated from saline soil collected from the Qaidam Basin, north-west China. Phylogenetic analysis based on 16S rRNA g...
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PMID: 20232249
PDF is available here.
PDF is available here.
Antonie Van Leeuwenhoek (98)1 2010
Abstract
During the course of our research on new actinobacterial sources, a novel actinomycete strain YIM 67013(T) was isolated from rhizosphere soil of Tripterygium wilfordii Hook. f. collected from Yunnan province, south-west China. The strain formed well-differentiated aerial and substrate mycelia, grew...
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PMID: 20354787
PDF is available here.
PDF is available here.
Nucleic Acids Research (38)11 2010
Abstract
We show that the M. tuberculosis H-NS protein binds in a more structure-specific manner to DNA replication and repair intermediates, but displays lower affinity for double-stranded DNA with relatively higher GC content. Notably, M. tuberculosis H-NS was able to bind Holliday junction (HJ), the centr...
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PMID: 20176569
PDF is available here.
PDF is available here.
Archives of Virology (155)6 2010
Abstract
We characterized siRNAs derived from rice stripe virus (RSV), a member of the genus Tenuivirus with four genomic RNAs and an ambisense coding strategy. Deep sequencing of small RNAs from infected rice leaves showed that siRNAs were derived almost equally from virion and complementary RNA strands and...
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PMID: 20396917
PDF is available here.
PDF is available here.
Abstract
Establishing codon usage biases are crucial for understanding the etiology of central nervous system neurodegenerative diseases (CNSNDD) especially Alzheimer's disease (AD) as well as genetic factors. G and C ending codons are strongly biased in the coding sequences of these proteins as a result of...
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PMID: 20441557
PDF is available here.
PDF is available here.
Abstract
We explore the relationship between sequence similarity and phylogeny accuracy to test when, in terms of genetic divergence, the quality of AFLP data becomes too low to be informative for a reliable phylogenetic reconstruction. We generated DNA sequences with known phylogenies using balanced and unb...
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PMID: 20026482
PDF is available here.
PDF is available here.
Abstract
We present a benchmark consisting of two sets of simulated genomic sequences for testing the performances of segmentation algorithms. Sequences in the first set are composed of fixed-sized homogeneous domains, distinct in their between-domain guanine and cytosine (GC) content variability. The sequen...
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PMID: 20018981
PDF is available here.
PDF is available here.
Abstract
We ask 1) whether we can replicate this result in rodents, 2) whether different autosomes replicate on average at different times, and 3) whether this might explain differences in their substitution rates. Finally we ask 4) whether X, Y, and autosome replicate at different times and 5) whether any d...
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PMID: 20026481
PDF is available here.
PDF is available here.
Abstract
1) The positive relationship previously found between the percentage of homoplasy and genome size is a direct consequence of the number of observed bands and the GC content. For the same number of observed bands, the percentage of homoplasy is independent of the genome size of the species. 2) The di...
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PMID: 20056690
PDF is available here.
PDF is available here.
Genome Research (20)4 2010
Abstract
We have found that yeast promoters fall into two classes differing in NFR sharpness, and that this distinction follows a known transcriptional dichotomy in yeast genes. A class of yeast promoters having well-defined NFRs are characterized by positioned patterns of poly(dA:dT) tracts with several nov...
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PMID: 20133331
PDF is available here.
PDF is available here.
Abstract
We describe this as a new species, Thiorhodococcus modestalkaliphilus sp. nov....
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PMID: 20513956
PDF is available here.
PDF is available here.
Abstract
We analyzed the complete mitochondrial genome (mitogenome) sequence of the Eurasian otter Lutra lutra. The mitochondrial DNA sequence of the Eurasian otter is 16,505 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region (CR). The CR sequence of otters from Eur...
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PMID: 19757186
PDF is available here.
PDF is available here.
Abstract
Libraries of rumen bacterial 16S rRNA gene sequences of Gayals (Bos frontalis) and Swamp buffaloes (Bubalus bubalis) were cloned and sequenced in the present work to compare the bacterial diversity with the third published library of Holstein cow. Sequence similarity of 97% was used as the definitio...
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PMID: 19662514
PDF is available here.
PDF is available here.
Abstract
We sequenced the complete mitochondrial genome of Evania appendigaster. This genome is 17,817 bp long; with low A+T content, 77.8%, compared with other hymenopteran species. Four tRNA genes were rearranged, among which remote inversion is the dominant gene rearrangement event. Gene shuffling is caus...
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PMID: 19655273
PDF is available here.
PDF is available here.
Abstract
A novel species of ascomycetous yeast, Pichia insulana sp. nov., is described from necrotic tissue of columnar cacti on Caribbean islands. P. insulana is closely related to and phenotypically very similar to Pichia cactophila and Pichia pseudocactophila. There are few distinctions between these taxa...
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PMID: 19661524
PDF is available here.
PDF is available here.
Abstract
A novel Gram-stain-positive bacterium, designated R19-04(T), was isolated from a soil sample from Rishiri Island, Japan, and its taxonomic position was investigated by a polyphasic approach. Cells of strain R19-04( T) exhibited a rod-coccus cycle. The peptidoglycan type of the isolat...
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PMID: 19656927
PDF is available here.
PDF is available here.
Abstract
A novel, obligately anaerobic, extremely thermophilic, cellulolytic bacterium, designated OB47(T), was isolated from Obsidian Pool, Yellowstone National Park, WY. The isolate was a nonmotile, non-spore-forming, Gram-positive rod approximately 2 microm long by 0.2 microm wide and grew at temperatures...
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PMID: 20023107
PDF is available here.
PDF is available here.
Abstract
A bacterial strain, 13-25(T) with xylanolytic activity isolated from a single present soil sample, was characterized with respect to its phenetic and phylogenetic characteristics. The cells of the isolate are gram staining variable rods. The predominant fatty acids are anteiso-C(15 : 0), C(16-0), an...
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PMID: 20208449
PDF is available here.
PDF is available here.
Abstract
A Gram-negative, rod-shaped, gliding, aerobic bacterium, designated 12157(T), was isolated from the desert of Xinjiang, China and subjected to a polyphasic taxonomic study. The strain 12157(T) grew optimally at pH 7.0 and 30 degrees Celsius. MK-7 was the predominant respiratory menaquinone. The DNA...
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PMID: 20208447
PDF is available here.
PDF is available here.
Abstract
We analyzed compositional influence on genome organization in both rice and human. We demonstrated that, in GC rich rice genes, highly expressed genes are less compact than lowly expressed genes. In GC-poor class, there is no difference in gene compactness between highly and lowly expressed genes. H...
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PMID: 19916569
PDF is available here.
PDF is available here.
Abstract
We infer that genes length and the hydrophobicity of the encoded protein may play minor role in shaping codon usage bias. Additional 28 codons ending with a G or C base have been defined as "optimal codons", which may provide useful information for maize gene-transformation and gene prediction....
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PMID: 19330534
PDF is available here.
PDF is available here.
Abstract
A new strain named ZL223 was isolated from Bange Lake in Tibet, China. Cells were Gram-positive, spore-forming, motile rods. Growth pH range was from 7.0 to 10.0, optimum at pH 9.0. Growth temperature range was from 15 degrees C to 45 degrees C, optimum at 37 degrees C. The G + C content of DNA was...
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PMID: 20344941
PDF is available here.
PDF is available here.
Abstract
We propose two simple models that take into account both mutation and selection effects, which act differently at the three codon positions, and use both GC and purine contents as compositional parameters. The two models concern the theoretical composition of nucleotides, codons, and amino acids, wi...
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PMID: 21059261
PDF is available here.
PDF is available here.
Abstract
The current work extends the phenotypic and molecular characterization of the bacterial culture collection from the Rouge River to gain an understanding of the physiology of the strains and their potential for biotechnological applications. Phenotypic and molecular analyses were performed on six uni...
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PMID: 20662385
PDF is available here.
PDF is available here.
Abstract
Chordopoxviruses of the subfamily Chordopoxvirinae, family Poxviridae, infect vertebrates and consist of at least eight genera with broad host ranges. For most chordopoxviruses, the number of viral genes and their relative order are highly conserved in the central region. The GC content of chordopox...
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PMID: 19906902
PDF is available here.
PDF is available here.
Caulobacter ginsengisoli sp. nov., a novel stalked bacterium isolated from ginseng cultivating soil.
Abstract
A Gram negative, aerobic, nonspore-forming, straight or curved rod-shaped bacterium, designated Gsoil 317T, was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized using a polyphasic approach. Cells were dimorphic, with stalk (or prostheca) and nonmotile or...
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PMID: 20134228
PDF is available here.
PDF is available here.
Mikrobiologiia (79)4 2010
Abstract
In the present study the role of horizontal gene transfer events in providing the mercury resistance is depicted. merA is key gene in mer operon and has been used for this study. Phylogenetic analysis of aligned merA sequences shows broad similarities to the established 16S rRNA phylogeny. But there...
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PMID: 21058506
PDF is available here.
PDF is available here.
Abstract
Six matured male Yaks (Bos grunniens) with a mean live weight of 450 +/- 23 kg (mean +/- SD), were housed indoors in metabolism cages and fed pelleted lucerne (Medicago sativum). After an adjustment period of 24 days of feeding the diet, samples of rumen content were obtained for analysis of the bac...
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PMID: 19757178
PDF is available here.
PDF is available here.
BMC Plant Biology (10) 2010
Abstract
We report the cloning and sequencing of 10,608 putative full length cDNAs (FL-cDNAs) primarily from Moso bamboo, Phyllostachys heterocycla cv. pubescens, a large woody bamboo with the highest ecological and economic values of all bamboos. This represents the third largest FL-cDNA collection to date...
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PMID: 20565830
PDF is available here.
PDF is available here.