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https://www.readbyqxmd.com/read/28188180/a-population-genomics-approach-to-assessing-the-genetic-basis-of-within-host-microevolution-underlying-recurrent-cryptococcal-meningitis-infection
#1
Johanna Rhodes, Mathew A Beale, Mathieu Vanhove, Joseph N Jarvis, Shichina Kannambath, John A Simpson, Anthea Ryan, Graeme Meintjes, Thomas S Harrison, Matthew C Fisher, Tihana Bicanic
Recurrence of meningitis due to Cryptococcus neoformans after treatment causes substantial mortality in HIV/AIDS patients across sub-Saharan Africa. In order to determine whether recurrence occurred due to relapse of the original infecting isolate or reinfection with a different isolate weeks or months after initial treatment, we used whole-genome sequencing to assess the genetic basis of infection in 17 HIV-infected individuals with recurrent cryptococcal meningitis. Comparisons revealed a clonal relationship for 15 pairs of isolates recovered before and after recurrence showing relapse of the original infection...
February 10, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28185042/phylogenomic-relationship-of-feijoa-acca-sellowiana-o-berg-burret-with-other-myrtaceae-based-on-complete-chloroplast-genome-sequences
#2
Lilian Oliveira de Machado, Leila do Nascimento Vieira, Valdir Marcos Stefenon, Fábio de Oliveira Pedrosa, Emanuel Maltempi de Souza, Miguel Pedro Guerra, Rubens Onofre Nodari
Given their distribution, importance, and richness, Myrtaceae species comprise a model system for studying the evolution of tropical plant diversity. In addition, chloroplast (cp) genome sequencing is an efficient tool for phylogenetic relationship studies. Feijoa [Acca sellowiana (O. Berg) Burret; CN: pineapple-guava] is a Myrtaceae species that occurs naturally in southern Brazil and northern Uruguay. Feijoa is known for its exquisite perfume and flavorful fruits, pharmacological properties, ornamental value and increasing economic relevance...
February 9, 2017: Genetica
https://www.readbyqxmd.com/read/28163698/bacillus-amyloliquefaciens-bacillus-velezensis-and-bacillus-siamensis-form-an-operational-group-b-amyloliquefaciens-within-the-b-subtilis-species-complex
#3
Ben Fan, Jochen Blom, Hans-Peter Klenk, Rainer Borriss
The plant growth promoting model bacterium FZB42(T) was proposed as the type strain of Bacillus amyloliquefaciens subsp. plantarum (Borriss et al., 2011), but has been recently recognized as being synonymous to Bacillus velezensis due to phylogenomic analysis (Dunlap C. et al., 2016). However, until now, majority of publications consider plant-associated close relatives of FZB42 still as "B. amyloliquefaciens." Here, we reinvestigated the taxonomic status of FZB42 and related strains in its context to the free-living soil bacterium DSM7(T), the type strain of B...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28158176/plasmodium-vivax-cell-traversal-protein-for-ookinetes-and-sporozoites-pvceltos-gene-sequence-and-potential-epitopes-are-highly-conserved-among-isolates-from-different-regions-of-brazilian-amazon
#4
Lana Bitencourt Chaves, Daiana de Souza Perce-da-Silva, Rodrigo Nunes Rodrigues-da-Silva, João Hermínio Martins da Silva, Gustavo Capatti Cassiano, Ricardo Luiz Dantas Machado, Lilian Rose Pratt-Riccio, Dalma Maria Banic, Josué da Costa Lima-Junior
The Plasmodium vivax Cell-traversal protein for ookinetes and sporozoites (PvCelTOS) plays an important role in the traversal of host cells. Although essential to PvCelTOS progress as a vaccine candidate, its genetic diversity remains uncharted. Therefore, we investigated the PvCelTOS genetic polymorphism in 119 field isolates from five different regions of Brazilian Amazon (Manaus, Novo Repartimento, Porto Velho, Plácido de Castro and Oiapoque). Moreover, we also evaluated the potential impact of non-synonymous mutations found in the predicted structure and epitopes of PvCelTOS...
February 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28157073/codon-optimization-underpins-generalist-parasitism-in-fungi
#5
Thomas Badet, Remi Peyraud, Malick Mbengue, Olivier Navaud, Mark Derbyshire, Richard P Oliver, Adelin Barbacci, Sylvain Raffaele
The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom...
February 3, 2017: ELife
https://www.readbyqxmd.com/read/28146157/identification-of-circo-like-virus-brazil-genomic-sequences-in-raw-sewage-from-the-metropolitan-area-of-s%C3%A3-o-paulo-evidence-of-circulation-two-and-three-years-after-the-first-detection
#6
Silvana Beres Castrignano, Teresa Keico Nagasse-Sugahara, Patrícia Garrafa, Telma Alves Monezi, Karina Medici Barrella, Dolores Ursula Mehnert
BACKGROUND: Two novel viruses named circo-like virus-Brazil (CLV-BR) hs1 and hs2 were previously discovered in a Brazilian human fecal sample through metagenomics. CLV-BR hs1 and hs2 possess a small circular DNA genome encoding a replication initiator protein (Rep), and the two genomes exhibit 92% nucleotide identity with each other. Phylogenetic analysis based on the Rep protein showed that CLV-BRs do not cluster with circoviruses, nanoviruses, geminiviruses or cycloviruses. OBJECTIVES: The aim of this study was to search for CLV-BR genomes in sewage and reclaimed water samples from the metropolitan area of São Paulo, Brazil, to verify whether the first detection of these viruses was an isolated finding...
January 19, 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28137631/a-single-non-synonymous-ncoa5-variation-in-type-2-diabetic-patients-with-hepatocellular-carcinoma-impairs-the-function-of-ncoa5-in-cell-cycle-regulation
#7
Xinhui Liu, Feiye Liu, Shenglan Gao, Jake Reske, Aimin Li, Chin-Lee Wu, Chengfeng Yang, Fengsheng Chen, Rongcheng Luo, Hua Xiao
Type 2 Diabetes (T2D) is a risk factor for hepatocellular carcinoma (HCC). We have previously described that haploinsufficiency of nuclear receptor coactivator 5 (NCOA5) is a genetic defect linking glucose intolerance to HCC. Here we report identification and characterization of a single nucleotide variation (T445A) in NCOA5, causing an amino acid Thr to Ala substitution, in adjacent non-tumorous liver tissues derived from patients with concurrent HCC and T2D. By using Tet-On inducible expression cells, we show that ectopic expression of NCOA5wt suppressed proliferation of HCC cells via induction of G2/M arrest, while ectopic expression of NCOA5T445A had a significantly lesser effect compared to ectopic expression of NCOA5wt...
January 27, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28122952/the-impact-of-selection-at-the-amino-acid-level-on-the-usage-of-synonymous-codons
#8
Paweł Błažej, Dorota Mackiewicz, Małgorzata Wnętrzak, Paweł Mackiewicz
There are two main forces that affect usage of synonymous codons: directional mutational pressure and selection. The effectiveness of protein translation is usually considered as the main selectional factor. However, the biased codon usage can be also a by-product of a general selection at the amino acid level interacting with nucleotide replacements. To evaluate the validity and strength of such effect, we superimposed more than 3.5 billion unrestricted mutational processes on the selection of non-synonymous substitutions based on the differences in physicochemical properties of the coded amino acids...
January 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28120868/evidence-for-positive-selection-and-recombination-hotspots-in-deformed-wing-virus-dwv
#9
A Dalmon, C Desbiez, M Coulon, M Thomasson, Y Le Conte, C Alaux, J Vallon, B Moury
Deformed wing virus (DWV) is considered one of the most damaging pests in honey bees since the spread of its vector, Varroa destructor. In this study, we sequenced the whole genomes of two virus isolates and studied the evolutionary forces that act on DWV genomes. The isolate from a Varroa-tolerant bee colony was characterized by three recombination breakpoints between DWV and the closely related Varroa destructor virus-1 (VDV-1), whereas the variant from the colony using conventional Varroa management was similar to the originally described DWV...
January 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28116503/genetic-analysis-of-a-mouse-cross-implicates-an-anti-inflammatory-gene-in-control-of-atherosclerosis-susceptibility
#10
Norman E Garrett, Andrew T Grainger, Jing Li, Mei-Hua Chen, Weibin Shi
Nearly all genetic crosses generated from Apoe(-/-) or Lldlr(-/-) mice for genetic analysis of atherosclerosis have used C57BL/6 J (B6) mice as one parental strain, thus limiting their mapping power and coverage of allelic diversity. SM/J-Apoe (-/-) and BALB/cJ-Apoe (-/-) mice differ significantly in atherosclerosis susceptibility. 224 male F2 mice were generated from the two Apoe (-/-) strains to perform quantitative trait locus (QTL) analysis of atherosclerosis. F2 mice were fed 5 weeks of Western diet and analyzed for atherosclerotic lesions in the aortic root...
January 23, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28110785/genetic-diversity-of-orf-4-6-of-type-1-porcine-reproductive-and-respiratory-syndrome-virus-in-naturally-infected-pigs
#11
Dong-Uk Lee, Sung J Yoo, Taeyong Kwon, Sang H Je, Jeong Y Shin, Jeong J Byun, Myung H Kim, Young S Lyoo
Genotype 1 porcine reproductive and respiratory syndrome virus (PRRSV) has been highly prevalent throughout Korea since the virus was first detected in 2005. However, genetic analyses of genotype 1 PRRSV in Korea have been limited to ORF5 and/or ORF7. In the present study, we determined 10 representative sequence covering ORF4 to ORF6 and each individual ORFs of genotype 1 PRRSV in Korea, and performed molecular analyses. The most variable gene among the individual ORFs of field strains was ORF4, and this gene exhibited only 74...
February 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28095902/identification-of-positive-selection-in-genes-is-greatly-improved-by-using-experimentally-informed-site-specific-models
#12
Jesse D Bloom
BACKGROUND: Sites of positive selection are identified by comparing observed evolutionary patterns to those expected under a null model for evolution in the absence of such selection. For protein-coding genes, the most common null model is that nonsynonymous and synonymous mutations fix at equal rates; this unrealistic model has limited power to detect many interesting forms of selection. RESULTS: I describe a new approach that uses a null model based on experimental measurements of a gene's site-specific amino-acid preferences generated by deep mutational scanning in the lab...
January 17, 2017: Biology Direct
https://www.readbyqxmd.com/read/28093843/the-discovery-of-the-virulence-gene-toxa-in-the-wheat-and-barley-pathogen-bipolaris-sorokiniana
#13
Megan C Mcdonald, Dag Ahren, Steven Simpfendorfer, Andrew Milgate, Peter S Solomon
Bipolaris sorokiniana is the causal agent of multiple diseases on wheat and barley and is the primary constraint to cereal production throughout South Asia. Despite its significance, the molecular basis of disease is poorly understood. To address this, the genomes of three Australian isolates of B. sorokiniana were sequenced and screened for known pathogenicity genes. Sequence analysis revealed that the isolate BRIP10943 harboured the ToxA gene which was previously associated with disease in the wheat pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis...
January 17, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28092920/evolutionary-genomics-of-the-cold-adapted-diatom-fragilariopsis-cylindrus
#14
Thomas Mock, Robert P Otillar, Jan Strauss, Mark McMullan, Pirita Paajanen, Jeremy Schmutz, Asaf Salamov, Remo Sanges, Andrew Toseland, Ben J Ward, Andrew E Allen, Christopher L Dupont, Stephan Frickenhaus, Florian Maumus, Alaguraj Veluchamy, Taoyang Wu, Kerrie W Barry, Angela Falciatore, Maria I Ferrante, Antonio E Fortunato, Gernot Glöckner, Ansgar Gruber, Rachel Hipkin, Michael G Janech, Peter G Kroth, Florian Leese, Erika A Lindquist, Barbara R Lyon, Joel Martin, Christoph Mayer, Micaela Parker, Hadi Quesneville, James A Raymond, Christiane Uhlig, Ruben E Valas, Klaus U Valentin, Alexandra Z Worden, E Virginia Armbrust, Matthew D Clark, Chris Bowler, Beverley R Green, Vincent Moulton, Cock van Oosterhout, Igor V Grigoriev
The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms...
January 26, 2017: Nature
https://www.readbyqxmd.com/read/28087495/comparative-analysis-of-variation-and-selection-in-the-hcv-genome
#15
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
#16
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
#17
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
#18
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...
March 2017: Antiviral Research
https://www.readbyqxmd.com/read/28054163/genetic-variation-and-population-structure-of-cucumber-green-mottle-mosaic-virus
#19
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
#20
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
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