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https://www.readbyqxmd.com/read/28814302/ompa-protein-sequence-based-typing-and-virulence-associated-gene-profiles-of-pasteurella-multocida-isolates-associated-with-bovine-haemorrhagic-septicaemia-and-porcine-pneumonic-pasteurellosis-in-thailand
#1
Teerasak E-Kobon, Ratiporn Leeanan, Saengtian Pannoi, Pornchai Anuntasomboon, Pacharee Thongkamkoon, Arinthip Thamchaipenet
BACKGROUND: Pasteurella multocida is a Gram-negative bacterium that causes economically significant infections of a broad range of animal species. Pneumonic and septicaemic pasteurellosis caused by this bacterium remain important problems in pigs, cattle, and water buffaloes in Thailand. The aim of this study was to characterise the virulence-associated gene profiles and to develop an OmpA molecular typing scheme for classifying 191 bovine and porcine isolates of P. multocida collected between 1989 and 2012 in Thailand using polymerase chain reactions (PCRs), nucleotide sequencing, and sequence and structural bioinformatics analyses...
August 16, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28807856/low-levels-of-genetic-diversity-associated-with-evidence-of-negative-selection-on-the-babesia-bovis-apical-membrane-antigen-1-from-parasite-populations-in-thailand
#2
Amarin Rittipornlertrak, Boondarika Nambooppha, Pacharathon Simking, Veerasak Punyapornwithaya, Saruda Tiwananthagorn, Sathaporn Jittapalapong, Yang-Tsung Chung, Nattawooti Sthitmatee
Babesia bovis, a parasite infecting cattle and buffalo, continues to spread throughout the developing world. The babesial vaccine was developed to be a sustainable alternative treatment to control the parasite. However, genetic diversity is a major obstacle for designing and developing a safe and effective vaccine. The apical membrane antigen 1 (AMA-1) is considered to be a potential vaccine candidate antigen among immunogenic genes of B. bovis. To gain a more comprehensive understanding of B. bovis AMA-1 (BbAMA-1), three B...
August 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28805451/genetic-characterisation-and-analysis-of-infectious-bronchitis-virus-isolated-from-brazilian-flocks-between-2010-and-2015
#3
Claudia Carranza, Claudete S Astolfi-Ferreira, Silvana H Santander Parra, Luis F N Nuñez, Zoltan Penzes, Jorge L Chacón, Luiz Sesti, Ruy D Chacón, Antonio J Piantino Ferreira
Infectious bronchitis virus (IBV) variants in Brazil were isolated during 2010-2015 for epidemiological and molecular analysis to characterise the different variants and perform a bioinformatic analysis to compare with sequences of variants collected over the previous 40 years. Of the 453 samples examined, 61.4% were positive for IBV and 75.9% of these were considered to have the BR-I genotype and were detected in birds of all ages distributed in all five Brazilian regions. The ratio of non-synonymous substitutions per non-synonymous site (dN) to synonymous substitutions per synonymous site (dS), i...
August 14, 2017: British Poultry Science
https://www.readbyqxmd.com/read/28798740/smrt-sequencing-revealed-mitogenome-characteristics-and-mitogenome-wide-dna-modification-pattern-in-ophiocordyceps-sinensis
#4
Xincong Kang, Liqin Hu, Pengyuan Shen, Rui Li, Dongbo Liu
Single molecule, real-time (SMRT) sequencing was used to characterize mitochondrial (mt) genome of Ophiocordyceps sinensis and to analyze the mt genome-wide pattern of epigenetic DNA modification. The complete mt genome of O. sinensis, with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date. It contained 14 conserved protein-coding genes (PCGs), 1 intronic protein rps3, 27 tRNAs and 2 rRNA subunits, which are common characteristics of the known mt genomes in Hypocreales. A phylogenetic tree inferred from 14 PCGs in Pezizomycotina fungi supports O...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28797243/polymorphism-and-structure-of-style-specific-arabinogalactan-proteins-as-determinants-of-pollen-tube-growth-in-nicotiana
#5
Andrzej K Noyszewski, Yi-Cheng Liu, Koichiro Tamura, Alan G Smith
BACKGROUND: Pollen tube growth and fertilization are key processes in angiosperm sexual reproduction. The transmitting tract (TT) of Nicotiana tabacum controls pollen tube growth in part by secreting pistil extensin-like protein III (PELPIII), transmitting-tract-specific (TTS) protein and 120 kDa glycoprotein (120 K) into the stylar extracellular matrix. The three arabinogalactan proteins (AGP) are referred to as stylar AGPs and are the focus of this research. The transmitting tract regulates pollen tube growth, promoting fertilization or rejecting pollen tubes...
August 10, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28795237/the-adaptive-evolution-database-taed-a-new-release-of-a-database-of-phylogenetically-indexed-gene-families-from-chordates
#6
Russell A Hermansen, Benjamin P Oswald, Stormy Knight, Stephen D Shank, David Northover, Katharine L Korunes, Stephen N Michel, David A Liberles
With the large collections of gene and genome sequences, there is a need to generate curated comparative genomic databases that enable interpretation of results in an evolutionary context. Such resources can facilitate an understanding of the co-evolution of genes in the context of a genome mapped onto a phylogeny, of a protein structure, and of interactions within a pathway. A phylogenetically indexed gene family database, the adaptive evolution database (TAED), is presented that organizes gene families and their evolutionary histories in a species tree context...
August 9, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28759647/connectivity-in-gene-coexpression-networks-negatively-correlates-with-rates-of-molecular-evolution-in-flowering-plants
#7
Rishi R Masalia, Adam J Bewick, John M Burke
Gene coexpression networks are a useful tool for summarizing transcriptomic data and providing insight into patterns of gene regulation in a variety of species. Though there has been considerable interest in studying the evolution of network topology across species, less attention has been paid to the relationship between network position and patterns of molecular evolution. Here, we generated coexpression networks from publicly available expression data for seven flowering plant taxa (Arabidopsis thaliana, Glycine max, Oryza sativa, Populus spp...
2017: PloS One
https://www.readbyqxmd.com/read/28642787/mutational-signatures-are-critical-for-proper-estimation-of-purifying-selection-pressures-in-cancer-somatic-mutation-data-when-using-the-dn-ds-metric
#8
Jimmy Van den Eynden, Erik Larsson
Large cancer genome sequencing initiatives have led to the identification of cancer driver genes based on signals of positive selection in somatic mutation data. Additionally, the identification of purifying (negative) selection has the potential to identify essential genes that may be of therapeutic interest. The most widely used way of quantifying selection pressures in protein-coding genes is the dN/dS metric, which compares non-synonymous to synonymous substitution rates. In this study, we examine whether and how this metric is influenced by the mutational processes that have been active during tumor evolution...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28630112/rapid-evolution-of-ovarian-biased-genes-in-the-yellow-fever-mosquito-aedes-aegypti
#9
Carrie A Whittle, Cassandra G Extavour
Males and females exhibit highly dimorphic phenotypes, particularly in their gonads, which is believed to be driven largely by differential gene expression. Typically, the protein sequences of genes upregulated in males, or male-biased genes, evolve rapidly as compared to female-biased and unbiased genes. To date, the specific study of gonad-biased genes remains uncommon in metazoans. Here, we identified and studied a total of 2,927, 2,013 and 4,449 coding-sequences (CDS) with ovary-biased, testis-biased and unbiased expression respectively in the yellow-fever mosquito Aedes aegypti The results showed that ovary-biased and unbiased CDS had higher nonsynonymous to synonymous substitution rates (dN/dS) and lower optimal codon usage (those codons that promote efficient translation) than testis-biased genes...
June 19, 2017: Genetics
https://www.readbyqxmd.com/read/28585043/candidate-genes-for-migration-do-not-distinguish-migratory-and-non-migratory-birds
#10
Juan S Lugo Ramos, Kira E Delmore, Miriam Liedvogel
Migratory traits in birds have been shown to have a strong heritable component and several candidate genes have been suggested to control these migratory traits. To investigate if the genetic makeup of one or a set of these candidate genes can be used to identify a general pattern between migratory and non-migratory birds, we extracted genomic sequence data for 25 hypothesised candidate genes for migration from 70 available genomes across all orders of Aves and characterised sequence divergence between migratory and non-migratory phenotypes...
July 2017: Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology
https://www.readbyqxmd.com/read/28584717/calculating-site-specific-evolutionary-rates-at-the-amino-acid-or-codon-level-yields-similar-rate-estimates
#11
Dariya K Sydykova, Claus O Wilke
Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the dN∕dS ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it assigns a relative conservation score to each site in an alignment. How site-wise dN∕dS values relate to Rate4Site scores is not known. Here we elucidate the relationship between these two rate measurements. We simulate sequences with known dN∕dS, using either dN∕dS models or mutation-selection models for simulation...
2017: PeerJ
https://www.readbyqxmd.com/read/28578709/genetic-diversity-of-plasmodium-vivax-revealed-by-the-merozoite-surface-protein-1-icb5-6-fragment
#12
Wei Ruan, Ling-Ling Zhang, Yan Feng, Xuan Zhang, Hua-Liang Chen, Qiao-Yi Lu, Li-Nong Yao, Wei Hu
BACKGROUND: Plasmodium vivax remains a potential cause of morbidity and mortality for people living in its endemic areas. Understanding the genetic diversity of P. vivax from different regions is valuable for studying population dynamics and tracing the origins of parasites. The PvMSP-1 gene is highly polymorphic and has been used as a marker in many P. vivax population studies. The aim of this study was to investigate the genetic diversity of the PvMSP-1 gene icb5-6 fragment and to provide more genetic polymorphism data for further studies on P...
June 5, 2017: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/28578201/correlated-evolutionary-rates-across-genomic-compartments-in-annonaceae
#13
Paul H Hoekstra, Jan J Wieringa, Erik Smets, Rita D Brandão, Jenifer de Carvalho Lopes, Roy H J Erkens, Lars W Chatrou
The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models...
May 31, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28533181/comparative-genome-analysis-of-lactobacillus-plantarum-gb-lp3-provides-candidates-of-survival-related-genetic-factors
#14
Soomin Jeon, Jaehoon Jung, Kwondo Kim, DongAhn Yoo, Chanho Lee, Jungsun Kang, Kyungjin Cho, Dae-Kyung Kang, Woori Kwak, Sook Hee Yoon, Heebal Kim, Seoae Cho
Lactobacillus plantarum is found in various environmental niches such as in the gastrointestinal tract of an animal host or a fermented food. This species isolated from a certain environment is known to possess a variety of properties according to inhabited environment's adaptation. However, a causal relationship of a genetic factor and phenotype affected by a specific environment has not been systematically comprehended. L. plantarum GB-LP3 strain was isolated from Korean traditional fermented vegetable and the whole genome of GB-LP3 was sequenced...
May 19, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28529468/contrasting-patterns-of-nucleotide-polymorphism-suggest-different-selective-regimes-within-different-parts-of-the-pgic1-gene-in-festuca-ovina-l
#15
Yuan Li, Bengt Hansson, Lena Ghatnekar, Honor C Prentice
BACKGROUND: Phosphoglucose isomerase (PGI, EC 5.3.1.9) is an essential metabolic enzyme in all eukaryotes. An earlier study of the PgiC1 gene, which encodes cytosolic PGI in the grass Festuca ovina L., revealed a marked difference in the levels of nucleotide polymorphism between the 5' and 3' portions of the gene. METHODS: In the present study, we characterized the sequence polymorphism in F. ovina PgiC1 in more detail and examined possible explanations for the non-uniform pattern of nucleotide polymorphism across the gene...
2017: Hereditas
https://www.readbyqxmd.com/read/28484686/impact-of-pe_pgrs33-gene-polymorphisms-on-mycobacterium-tuberculosis-infection-and-pathogenesis
#16
Serena Camassa, Ivana Palucci, Raffaella Iantomasi, Tiziana Cubeddu, Mariachiara Minerva, Flavio De Maio, Samuel Jouny, Elisa Petruccioli, Delia Goletti, Francesco Ria, Michela Sali, Maurizio Sanguinetti, Riccardo Manganelli, Stefano Rocca, Priscille Brodin, Giovanni Delogu
PE_PGRS33 is a surface-exposed protein of Mycobacterium tuberculosis (Mtb) which exerts its role in macrophages entry and immunomodulation. In this study, we aimed to investigate the polymorphisms in the pe_pgrs33 gene of Mtb clinical isolates and evaluate their impact on protein functions. We sequenced pe_pgrs33 in a collection of 135 clinical strains, genotyped by 15-loci MIRU-VNTR and spoligotyping and belonging to the Mtb complex (MTBC). Overall, an association between pe_pgrs33 alleles and MTBC genotypes was observed and a dN/dS ratio of 0...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28466060/population-genetic-analysis-of-potato-virus-x-based-on-the-cp-gene-sequence
#17
Mohammad Hajizadeh, Nemat Sokhandan-Bashir
To investigate the genetic variation and molecular evolution of potato virus X (PVX), 87 coat protein (CP) gene sequences were retrieved from GenBank and analyzed. Of the PVX isolates studied, one recombinant isolate (X3) was detected from South America population of the virus. The other isolates belonged to two lineages, Eurasia and America, with the significant FST value (0.60). Non-synonymous nucleotide diversity to synonymous nucleotide diversity (ω = dN/dS) was less than 1 indicating that the CP gene has been under negative selection or neutral evolution...
March 2017: Virusdisease
https://www.readbyqxmd.com/read/28454644/genetic-diversity-of-immune-related-antigens-in-region-of-difference-2-of-mycobacterium-tuberculosis-strains
#18
Yi Jiang, Haican Liu, Xuezhi Wang, Shiqi Xiao, Machao Li, Guilian Li, Lili Zhao, Xiuqin Zhao, Xiangfeng Dou, Kanglin Wan
Region of Difference 2 (RD2) was lost during the ongoing propagation of BCG between 1927 and 1931, a time that coincides with reports of the ongoing attenuation of the vaccine. Some data demonstrate that RD2 plays a role in mycobacterial virulence, and that its deletion from Mycobacterium tuberculosis leads to a decrease in bacterial growth in both a macrophage and a murine model. Human T-cell epitopes of M. tuberculosis are evolutionarily hyperconserved and thus it was deduced that M. tuberculosis lacks antigenic variation and immune evasion...
May 2017: Tuberculosis
https://www.readbyqxmd.com/read/28424354/less-effective-selection-leads-to-larger-genomes
#19
Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N Pierre Charrier, David Eme, Florian Mermillod-Blondin, Laurent Duret, Cristina Vieira, Ludovic Orlando, Christophe Jean Douady
The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical data sets. Here, we tested this hypothesis using 22 de novo transcriptomes and low-coverage genomes of asellid isopods, which represent 11 independent habitat shifts from surface water to resource-poor groundwater...
June 2017: Genome Research
https://www.readbyqxmd.com/read/28423875/adaptive-selection-at-agouti-gene-inferred-breed-specific-selection-signature-within-the-indigenous-goat-populations
#20
Hafiz Ishfaq Ahmad, Guiqiong Liu, Xunping Jiang, Chenhui Liu, Xu Fangzheng, Yuqing Chong, Nabeel Ijaz, Huang Huarong
Objective: The aim of this study was to calculate selection signatures at possible loci leading to population differentiation, as well as pattern of selection of agouti gene within the local goat breeds and its correlation among other animal species to reveal molecular evolution. Methods: The high Fst outlier method corresponding to Fst distribution was used to identify the loci subject to positive selection. According to the empirical distribution of Fst estimates, we selected the SNPs having high Fst outlier corresponded to the upper 1% of the distribution as the loci under selection...
April 19, 2017: Asian-Australasian Journal of Animal Sciences
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