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https://www.readbyqxmd.com/read/28087495/comparative-analysis-of-variation-and-selection-in-the-hcv-genome
#1
Juan Ángel Patiño-Galindo, Fernando González-Candelas
Genotype 1 of the hepatitis C virus (HCV) is the most prevalent of the variants of this virus. Its two main subtypes, HCV-1a and HCV-1b, are associated to differences in epidemic features and risk groups, despite sharing similar features in most biological properties. We have analyzed the impact of positive selection on the evolution of these variants using complete genome coding regions, and compared the levels of genetic variability and the distribution of positively selected sites. We have also compared the distributions of positively selected and conserved sites considering different factors such as RNA secondary structure, the presence of different epitopes (antibody, CD4 and CD8), and secondary protein structure...
January 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28070852/functional-characterization-of-the-powdery-mildew-susceptibility-gene-smmlo1-in-eggplant-solanum-melongena-l
#2
Valentina Bracuto, Michela Appiano, Luigi Ricciardi, Deniz Göl, Richard G F Visser, Yuling Bai, Stefano Pavan
Eggplant (Solanum melongena L.) is one of the most important vegetables among the Solanaceae and can be a host to fungal species causing powdery mildew (PM) disease. Specific homologs of the plant Mildew Locus O (MLO) gene family are PM susceptibility factors, as their loss of function results in a recessive form of resistance known as mlo resistance. In a previous work, we isolated the eggplant MLO homolog SmMLO1. SmMLO1 is closely related to MLO susceptibility genes characterized in other plant species. However, it displays a peculiar non-synonymous substitution that leads to a T → M amino acid change at protein position 422, in correspondence of the MLO calmodulin-binding domain...
January 9, 2017: Transgenic Research
https://www.readbyqxmd.com/read/28062753/standard-codon-substitution-models-overestimate-purifying-selection-for-non-stationary-data
#3
Benjamin D Kaehler, Von Bing Yap, Gavin A Huttley
Estimation of natural selection on protein-coding sequences is a key comparative genomics approach for de novo prediction of lineage-specific adaptations. Selective pressure is measured on a per-gene basis by comparing the rate of non-synonymous substitutions to the rate of synonymous substitutions. All published codon substitution models have been time-reversible and thus assume that sequence composition does not change over time. We previously demonstrated that if time-reversible DNA substitution models are applied in the presence of changing sequence composition, the number of substitutions is systematically biased towards overestimation...
January 5, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28062191/tracking-hcv-protease-population-diversity-during-transmission-and-susceptibility-of-founder-populations-to-antiviral-therapy
#4
Tanvi Khera, Daniel Todt, Koen Vercauteren, C Patrick McClure, Lieven Verhoye, Ali Farhoudi, Sabin Bhuju, Robert Geffers, Thomas F Baumert, Eike Steinmann, Philip Meuleman, Thomas Pietschmann, Richard J P Brown
Due to the highly restricted species-tropism of Hepatitis C virus (HCV) a limited number of animal models exist for pre-clinical evaluation of vaccines and antiviral compounds. The human-liver chimeric mouse model allows heterologous challenge with clinically relevant strains derived from patients. However, to date, the transmission and longitudinal evolution of founder viral populations in this model have not been characterized in-depth using state-of-the-art sequencing technologies. Focusing on NS3 protease encoding region of the viral genome, mutant spectra in a donor inoculum and individual recipient mice were determined via Illumina sequencing and compared, to determine the effects of transmission on founder viral population complexity...
January 3, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28054163/genetic-variation-and-population-structure-of-cucumber-green-mottle-mosaic-virus
#5
Li-Xia Rao, Yushuang Guo, Li-Li Zhang, Xue-Ping Zhou, Jian Hong, Jian-Xiang Wu
Cucumber green mottle mosaic virus (CGMMV) is a single-stranded, positive sense RNA virus infecting cucurbitaceous plants. In recent years, CGMMV has become an important pathogen of cucurbitaceous crops including watermelon, pumpkin, cucumber and bottle gourd in China, causing serious losses to their production. In this study, we surveyed CGMMV infection in various cucurbitaceous crops grown in Zhejiang Province and in several seed lots purchased from local stores with the dot enzyme-linked immunosorbent assay (dot-ELISA), using a CGMMV specific monoclonal antibody...
January 4, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28053163/atgc-database-and-atgc-cogs-an-updated-resource-for-micro-and-macro-evolutionary-studies-of-prokaryotic-genomes-and-protein-family-annotation
#6
David M Kristensen, Yuri I Wolf, Eugene V Koonin
The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes. As such, each ATGC is suited for analysis of microevolutionary variations within a cohesive group of organisms (e...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28051058/purifying-selection-and-genetic-drift-shaped-pleistocene-evolution-of-the-mitochondrial-genome-in-an-endangered-australian-freshwater-fish
#7
A Pavlova, H M Gan, Y P Lee, C M Austin, D M Gilligan, M Lintermans, P Sunnucks
Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB)...
January 4, 2017: Heredity
https://www.readbyqxmd.com/read/28049853/genetic-stability-of-genome-scale-deoptimized-rna-virus-vaccine-candidates-under-selective-pressure
#8
Cyril Le Nouën, Thomas McCarty, Michael Brown, Melissa Laird Smith, Roberto Lleras, Michael A Dolan, Masfique Mehedi, Lijuan Yang, Cindy Luongo, Bo Liang, Shirin Munir, Joshua M DiNapoli, Steffen Mueller, Eckard Wimmer, Peter L Collins, Ursula J Buchholz
Recoding viral genomes by numerous synonymous but suboptimal substitutions provides live attenuated vaccine candidates. These vaccine candidates should have a low risk of deattenuation because of the many changes involved. However, their genetic stability under selective pressure is largely unknown. We evaluated phenotypic reversion of deoptimized human respiratory syncytial virus (RSV) vaccine candidates in the context of strong selective pressure. Codon pair deoptimized (CPD) versions of RSV were attenuated and temperature-sensitive...
January 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28039231/large-scale-comparative-analysis-reveals-the-mechanisms-driving-plastomic-compaction-reduction-and-inversions-in-conifers-ii-cupressophytes
#9
Chung-Shien Wu, Shu-Miaw Chaw
Conifers II (cupressophytes), comprising about 400 tree species in five families, are the most diverse group of living gymnosperms. Their plastid genomes (plastomes) are highly variable in size and organization, but such variation has never been systematically studied. In this study, we assessed the potential mechanisms underlying the evolution of cupressophyte plastomes. We analyzed the plastomes of 24 representative genera in all of the five cupressophyte families, focusing on their variation in size, noncoding DNA content, and nucleotide substitution rates...
December 29, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28025272/variation-in-mutational-robustness-between-different-proteins-and-the-predictability-of-fitness-effects
#10
Peter A Lind, Lars Arvidsson, Otto G Berg, Dan I Andersson
Random mutations in genes from disparate protein classes may have different distributions of fitness effects (DFEs) depending on different structural, functional, and evolutionary constraints. We measured the fitness effects of 156 single mutations in the genes encoding AraC (transcription factor), AraD (enzyme), and AraE (transporter) used for bacterial growth on l-arabinose. Despite their different molecular functions these genes all had bimodal DFEs with most mutations either being neutral or strongly deleterious, providing a general expectation for the DFE...
November 8, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28018384/allele-mining-and-selective-patterns-of-pi9-gene-in-a-set-of-rice-landraces-from-india
#11
Jahangir Imam, Nimai P Mandal, Mukund Variar, Pratyoosh Shukla
Allelic variants of the broad-spectrum blast resistance gene, Pi9 (nucleotide binding site-leucine-rich repeat region) have been analyzed in Indian rice landraces. They were selected from the list of 338 rice landraces phenotyped in the rice blast nursery at central Rainfed Upland Rice Research Station, Hazaribag. Six of them were further selected on the basis of their resistance and susceptible pattern for virulence analysis and selective pattern study of Pi9 gene. The sequence analysis and phylogenetic study illustrated that such sequences are vastly homologous and clustered into two groups...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28007887/correlated-mutations-and-homologous-recombination-within-bacterial-populations
#12
Mingzhi Lin, Edo Kussell
Inferring the rate of homologous recombination within a bacterial population remains a key challenge in quantifying the basic parameters of bacterial evolution. Due to the high sequence similarity within a clonal population, and unique aspects of bacterial DNA transfer processes, detecting recombination events based on phylogenetic reconstruction is often difficult, and estimating recombination rates using coalescent model-based methods is computationally expensive and often infeasible for large sequencing data sets...
December 22, 2016: Genetics
https://www.readbyqxmd.com/read/27999401/genetic-analysis-of-human-chymotrypsin-like-elastases-3a-and-3b-cela3a-and-cela3b-to-assess-the-role-of-complex-formation-between-proelastases-and-procarboxypeptidases-in-chronic-pancreatitis
#13
Andrea Párniczky, Eszter Hegyi, Anna Zsófia Tóth, Ákos Szücs, Andrea Szentesi, Áron Vincze, Ferenc Izbéki, Balázs Csaba Németh, Péter Hegyi, Miklós Sahin-Tóth
Human chymotrypsin-like elastases 3A and 3B (CELA3A and CELA3B) are the products of gene duplication and share 92% identity in their primary structure. CELA3B forms stable complexes with procarboxypeptidases A1 and A2 whereas CELA3A binds poorly due to the evolutionary substitution of Ala241 with Gly in exon 7. Since position 241 is polymorphic both in CELA3A (p.G241A) and CELA3B (p.A241G), genetic analysis can directly assess whether individual variability in complex formation might alter risk for chronic pancreatitis...
December 20, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27999249/genetic-structure-and-molecular-variability-analysis-of-citrus-sudden-death-associated-virus-isolates-from-infected-plants-grown-in-brazil
#14
Emilyn Emy Matsumura, Helvécio Della Coletta Filho, Silvia de Oliveira Dorta, Shahideh Nouri, Marcos Antonio Machado
Citrus sudden death-associated virus (CSDaV) is a monopartite positive-sense single-stranded RNA virus that was suggested to be associated with citrus sudden death (CSD) disease in Brazil. Here, we report the first study of the genetic structure and molecular variability among 31 CSDaV isolates collected from both symptomatic and asymptomatic trees in CSD-affected areas. Analyses of partial nucleotide sequences of five domains of the CSDaV genomic RNA, including those encoding for the methyltransferase, the multi-domain region (MDR), the helicase, the RNA-dependent RNA polymerase and the coat protein, showed that the MDR coding region was the most diverse region assessed here, and a possible association between this region and virus adaption to different host or plant tissues is considered...
December 16, 2016: Viruses
https://www.readbyqxmd.com/read/27988727/a-review-of-the-families-and-genera-of-the-superfamily-platysceloidea-bowman-amp-gruner-1973-crustacea-amphipoda-hyperiidea-together-with-keys-to-the-families-genera-and-species
#15
Wolfgang Zeidler
The systematics and phylogenetic relationships of the families and genera of the superfamily Platysceloidea are examined, following a thorough examination of the morphology of an example of the type species of each genus, or a substitute species if the true identity of the type species is in doubt. The mouthparts are described for each type species, often for the first time, providing additional characters for phylogenetic analysis. Genera are diagnosed using the taxonomic database program DELTA (Dalwitz et al...
November 13, 2016: Zootaxa
https://www.readbyqxmd.com/read/27966753/polymorphism-of-starch-pathway-genes-in-cassava
#16
L M Vasconcelos, A C Brito, C D Carmo, E J Oliveira
The distribution and frequency of single nucleotide polymorphisms (SNPs) can help to understand changes associated with characteristics of interest. We aimed to evaluate nucleotide diversity in six genes involved in starch biosynthesis in cassava using a panel of 96 unrelated accessions. The genes were sequenced, aligned, and used to obtain values for nucleotide diversity (π), segregating sites (θ), Tajima's D test, and neighbor-joining (NJ) clustering. On average, one SNP per 147 and 171 bp was identified in exon and intron regions, respectively...
December 2, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27940539/examination-of-contribution-of-pentose-catabolism-to-molecular-hydrogen-formation-by-targeted-disruption-of-arabinose-isomerase-araa-in-the-hyperthermophilic-bacterium-thermotoga-maritima
#17
Derrick White, Raghuveer Singh, Deepak Rudrappa, Jackie Mateo, Levi Kramer, Laura Freese, Paul Blum
: Thermotoga maritima ferments a broad range of sugars to form acetate, carbon dioxide, traces of lactate and near theoretic yields of molecular hydrogen (H2). In this organism, the catabolism of pentose sugars such as arabinose depends on the interaction between the pentose phosphate pathway along with the Embden Myerhoff and Entner Doudoroff pathways. While values for H2 yield have been determined using pentose supplemented complex media (CM) and predicted by metabolic pathway reconstruction, the actual effect of pathway elimination on hydrogen production has not been reported due to the lack of a genetic method for the creation of targeted mutations...
December 9, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27930647/allelic-variation-in-cxcl16-determines-cd3-t-lymphocyte-susceptibility-to-equine-arteritis-virus-infection-and-establishment-of-long-term-carrier-state-in-the-stallion
#18
Sanjay Sarkar, Ernest Bailey, Yun Young Go, R Frank Cook, Ted Kalbfleisch, John Eberth, R Lakshman Chelvarajan, Kathleen M Shuck, Sergey Artiushin, Peter J Timoney, Udeni B R Balasuriya
Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory, systemic, and reproductive disease of horses and other equid species. Following natural infection, 10-70% of the infected stallions can become persistently infected and continue to shed EAV in their semen for periods ranging from several months to life. Recently, we reported that some stallions possess a subpopulation(s) of CD3+ T lymphocytes that are susceptible to in vitro EAV infection and that this phenotypic trait is associated with long-term carrier status following exposure to the virus...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27929054/in-silico-identification-of-snp-diversity-in-cultivated-and-wild-tomato-species-insight-from-molecular-simulations
#19
Archana Bhardwaj, Yogeshwar Vikram Dhar, Mehar Hasan Asif, Sumit K Bag
Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27911958/advantages-of-an-improved-rhesus-macaque-genome-for-evolutionary-analyses
#20
Julien S Gradnigo, Abhishek Majumdar, Robert B Norgren, Etsuko N Moriyama
The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particularly to identify genes under adaptive or unique evolution in the human lineage. For such studies, it is necessary to align nucleotide sequences of homologous protein-coding genes among multiple species. The validity of these analyses is dependent on high quality genomic data. However, for most mammalian species (other than humans and mice), only draft genomes are available. There has been concern that some results obtained from evolutionary analyses using draft genomes may not be correct...
2016: PloS One
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