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https://www.readbyqxmd.com/read/29676720/mutagenic-repair-of-double-stranded-dna-breaks-in-vaccinia-virus-genomes-requires-cellular-dna-ligase-iv-activity-in-the-cytosol
#1
Rutger David Luteijn, Ingo Drexler, Geoffrey L Smith, Robert Jan Lebbink, Emmanuel J H J Wiertz
Poxviruses comprise a group of large dsDNA viruses that include members relevant to human and animal health, such as variola virus, monkeypox virus, cowpox virus and vaccinia virus (VACV). Poxviruses are remarkable for their unique replication cycle, which is restricted to the cytoplasm of infected cells. The independence from the host nucleus requires poxviruses to encode most of the enzymes involved in DNA replication, transcription and processing. Here, we use the CRISPR/Cas9 genome engineering system to induce DNA damage to VACV (strain Western Reserve) genomes...
April 20, 2018: Journal of General Virology
https://www.readbyqxmd.com/read/29669606/phylogenetic-relationships-of-three-tribes-of-cloacinine-nematodes-strongylida-chabertiidae-from-macropodid-marsupials
#2
N B Chilton, F Huby-Chilton, A Koehler, R B Gasser, I Beveridge
The phylogenetic relationships of 42 species of cloacinine nematodes belonging to three tribes (Coronostrongylinea, Macropostrongylinea and Zoniolaiminea) were examined based on sequence data of the first and second internal transcribed spacers (ITS-1 and ITS-2) of the nuclear ribosomal DNA. All nematodes examined are parasites of Australian macropodid marsupials. None of the three nematode tribes was monophyletic. Paraphyly was also encountered in three genera: Papillostrongylus, Monilonema and Wallabinema...
April 19, 2018: Journal of Helminthology
https://www.readbyqxmd.com/read/29668677/bayesian-reconstruction-of-transmission-within-outbreaks-using-genomic-variants
#3
Nicola De Maio, Colin J Worby, Daniel J Wilson, Nicole Stoesser
Pathogen genome sequencing can reveal details of transmission histories and is a powerful tool in the fight against infectious disease. In particular, within-host pathogen genomic variants identified through heterozygous nucleotide base calls are a potential source of information to identify linked cases and infer direction and time of transmission. However, using such data effectively to model disease transmission presents a number of challenges, including differentiating genuine variants from those observed due to sequencing error, as well as the specification of a realistic model for within-host pathogen population dynamics...
April 18, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29659807/the-genome-sequence-of-candidatus-fokinia-solitaria-insights-on-reductive-evolution-in-rickettsiales
#4
Anna M Floriano, Michele Castelli, Sascha Krenek, Thomas U Berendonk, Chiara Bazzocchi, Giulio Petroni, Davide Sassera
"Candidatus Fokinia solitaria" is an obligate intracellular endosymbiont of a unicellular eukaryote, a ciliate of the genus Paramecium. Here we present the genome sequence of this bacterium and subsequent analysis. Phylogenomic analysis confirmed the previously reported positioning of the symbiont within the "Candidatus Midichloriaceae" family (order Rickettsiales), as well as its high sequence divergence from other members of the family, indicative of fast sequence evolution. Consistently with this high evolutionary rate, a comparative genomic analysis revealed that the genome of this symbiont is the smallest of the Rickettsiales to date...
April 5, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29659762/activation-of-%C3%AF-20-dependent-recombination-and-horizontal-gene-transfer-in-mycoplasma-genitalium
#5
Sergi Torres-Puig, Carlos Martínez-Torró, Ignasi Granero-Moya, Enrique Querol, Jaume Piñol, Oscar Q Pich
In the human pathogen Mycoplasma genitalium, homologous recombination is under the control of σ20, an alternative sigma factor that boosts the generation of genetic and antigenic diversity in the population. Under laboratory growth conditions, σ20 activation is rare and the factors governing its intermittent activity are unknown. Two σ20-regulated genes, rrlA and rrlB, showed to be important for recombination of homologous DNA sequences in this bacterium. Herein, we demonstrate that rrlA and rrlB code for two small proteins that participate in a feed-forward loop essential for σ20 function...
April 11, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29657963/hologenomics-systems-level-host-biology
#6
Kevin R Theis
The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations...
March 2018: MSystems
https://www.readbyqxmd.com/read/29652800/full-genome-sequencing-reveals-new-southern-african-territories-genotypes-bringing-us-closer-to-understanding-true-variability-of-foot-and-mouth-disease-virus-in-africa
#7
Lidia Lasecka-Dykes, Caroline F Wright, Antonello Di Nardo, Grace Logan, Valerie Mioulet, Terry Jackson, Tobias J Tuthill, Nick J Knowles, Donald P King
Foot-and-mouth disease virus (FMDV) causes a highly contagious disease of cloven-hooved animals that poses a constant burden on farmers in endemic regions and threatens the livestock industries in disease-free countries. Despite the increased number of publicly available whole genome sequences, FMDV data are biased by the opportunistic nature of sampling. Since whole genomic sequences of Southern African Territories (SAT) are particularly underrepresented, this study sequenced 34 isolates from eastern and southern Africa...
April 13, 2018: Viruses
https://www.readbyqxmd.com/read/29648541/horizontal-gene-transfers-in-mycoplasmas-mollicutes
#8
C Citti, E Dordet-Frisoni, L X Nouvel, C H Kuo, E Baranowski
The class Mollicutes (trivial name "mycoplasma") is composed of wall-less bacteria with reduced genomes whose evolution was long thought to be only driven by gene losses. Recent evidences of massive horizontal gene transfer (HGT) within and across species provided a new frame to understand the successful adaptation of these minimal bacteria to a broad range of hosts. Mobile genetic elements are being identified in a growing number of mycoplasma species, but integrative and conjugative elements (ICEs) are emerging as pivotal in HGT...
April 12, 2018: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/29643236/introduction-of-viral-haemorrhagic-septicaemia-virus-vhsv-to-freshwater-cultured-rainbow-trout-is-followed-by-bursts-of-adaptive-evolution
#9
Anna A Schönherz, Roald Forsberg, Bernt Guldbrandtsen, Albert J Buitenhuis, Katja Einer-Jensen
Viral haemorrhagic septicaemia virus (VHSV), a rhabdovirus infecting teleost fish, has repeatedly crossed the boundary from marine fish species to freshwater cultured rainbow trout. These naturally replicated cross-species transmission events permit the study of general and repeatable evolutionary events occurring in connection with viral emergence into a novel host species.The purpose of this study was to investigate adaptive molecular evolution of the VHSV glycoprotein, one of the key virus proteins involved in viral emergence, following emergence from marine species into freshwater cultured rainbow trout...
April 11, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29621277/horizontal-gene-transfer-of-chlamydia-novel-insights-from-tree-reconciliation
#10
Hyaekang Kim, Woori Kwak, Sook Hee Yoon, Dae-Kyung Kang, Heebal Kim
Recent comparative genomics studies have suggested that horizontal gene transfer (HGT) is one of the major processes in bacterial evolution. In this study, HGT events of 64 Chlamydia strains were investigated based on the pipeline employed in HGTree database constructed in our recent study. Tree reconciliation method was applied in order to calculate feasible HGT events. Following initial detection and an evaluation procedure, evidence of the HGT was identified in 548 gene families including 42 gene families transferred from outside of Chlamydiae phylum with high reliability...
2018: PloS One
https://www.readbyqxmd.com/read/29618650/siv-mac239-vif-and-human-apobec3b-interactions-resemble-those-between-hiv-1-vif-and-human-apobec3g
#11
Jiayi Wang, Nadine M Shaban, Allison M Land, William L Brown, Reuben S Harris
Several members of the APOBEC3 DNA cytosine deaminase family can potently inhibit Vif-deficient HIV-1 by catalyzing cytosine deamination in viral cDNA and impeding reverse transcription. HIV-1 counteracts restriction with the virally encoded Vif protein, which targets relevant APOBEC3 proteins for proteasomal degradation. HIV-1 Vif is optimized for degrading the restrictive human APOBEC3 repertoire and, in general, lentiviral Vif proteins specifically target the restricting APOBEC3 enzymes of each host species...
April 4, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29615512/-phytophthora-palmivora-establishes-tissue-specific-intracellular-infection-structures-in-the-earliest-divergent-land-plant-lineage
#12
Philip Carella, Anna Gogleva, Marta Tomaselli, Carolin Alfs, Sebastian Schornack
The expansion of plants onto land was a formative event that brought forth profound changes to the earth's geochemistry and biota. Filamentous eukaryotic microbes developed the ability to colonize plant tissues early during the evolution of land plants, as demonstrated by intimate, symbiosis-like associations in >400 million-year-old fossils. However, the degree to which filamentous microbes establish pathogenic interactions with early divergent land plants is unclear. Here, we demonstrate that the broad host-range oomycete pathogen Phytophthora palmivora colonizes liverworts, the earliest divergent land plant lineage...
April 3, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29601845/the-evolution-distribution-and-diversity-of-endogenous-circoviral-elements-in-vertebrate-genomes
#13
Tristan P W Dennis, William Marciel de Souza, Soledad Marsile-Medun, Joshua B Singer, Sam J Wilson, Robert J Gifford
Circoviruses (family Circoviridae) are small, non-enveloped viruses that have short, single-stranded DNA genomes. Circovirus sequences are frequently recovered in metagenomic investigations, indicating that these viruses are widespread, yet they remain relatively poorly understood. Endogenous circoviral elements (CVe) are DNA sequences derived from circoviruses that occur in vertebrate genomes. CVe are a useful source of information about the biology and evolution of circoviruses. In this study, we screened 362 vertebrate genome assemblies in silico to generate a catalog of CVe loci...
March 27, 2018: Virus Research
https://www.readbyqxmd.com/read/29600767/identification-and-characterization-of-positively-selected-mutations-in-nef-of-four-hiv-1-major-subtypes-from-los-alamos-national-laboratory
#14
Elnaz Shadabi, Binhua Liang, Francis A Plummer, Ma Luo
BACKGROUND: Human immunodeficiency virus-1 (HIV-1) mutates rapidly to escape host immune pressure. This results in the generation of positively selected mutations (PSM) throughout the viral genome. Escape mutations in Nef, one of the accessory proteins of HIV-1, which plays an important role in viral pathogenicity have previously been identified in several large cohort studies, but the evolution of PSMs overtime in various HIV-1 subtypes remains unknown. METHODS: 161 clade A1, 3093 clade B, 647 clade C and 115 clade D HIV-1 nef sequences were obtained from the HIV Database of Los Alamos National Laboratory and aligned using MEGA 6...
March 30, 2018: Current HIV Research
https://www.readbyqxmd.com/read/29600535/nematode-associated-microbial-taxa-do-not-correlate-with-host-phylogeny-geographic-region-or-feeding-morphology-in-marine-sediment-habitats
#15
Taruna Schuelke, Tiago José Pereira, Sarah M Hardy, Holly M Bik
Studies of host-associated microbes are critical for advancing our understanding of ecology and evolution across diverse taxa and ecosystems. Nematode worms are ubiquitous across most habitats on earth, yet little is known about host-associated microbial assemblages within the phylum. Free-living nematodes are globally abundant and diverse in marine sediments, with species exhibiting distinct buccal cavity (mouth) morphologies that are thought to play an important role in feeding ecology and life history strategies...
March 29, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29596635/tiny-architects-biogenesis-of-intracellular-replicative-niches-by-bacterial-pathogens
#16
Eric Martinez, Fernande Ayenoue Siadous, Matteo Bonazzi
Co-evolution of bacterial pathogens with their hosts led to the emergence of a stunning variety of strategies aiming at the evasion of host defences, colonisation of host cells and tissues and, ultimately, the establishment of a successful infection. Pathogenic bacteria are typically classified as extracellular and intracellular, however intracellular lifestyle comes in many different flavours: some microbes rapidly escape to the cytosol whereas, other microbes remain within vacuolar compartments and harness membrane trafficking pathways to generate their host-derived, pathogen-specific replicative niche...
March 27, 2018: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/29593686/skin-microbiomes-of-california-terrestrial-salamanders-are-influenced-by-habitat-more-than-host-phylogeny
#17
Alicia K Bird, Sofia R Prado-Irwin, Vance T Vredenburg, Andrew G Zink
A multitude of microorganisms live on and within plant and animal hosts, yet the ecology and evolution of these microbial communities remains poorly understood in many taxa. This study examined the extent to which environmental factors and host taxonomic identity explain microbiome variation within two salamander genera, Ensatina and Batrachoseps , in the family Plethodontidae. In particular, we assessed whether microbiome differentiation paralleled host genetic distance at three levels of taxonomy: genus and high and low clade levels within Ensatina eschscholtzii ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29587626/diversity-and-distribution-of-wolbachia-in-relation-to-geography-host-plant-affiliation-and-life-cycle-of-a-heterogonic-gall-wasp
#18
Hannes Schuler, Scott P Egan, Glen R Hood, Robert W Busbee, Amanda L Driscoe, James R Ott
BACKGROUND: The maternally inherited endosymbiont Wolbachia is widespread in arthropods and nematodes and can play an important role in the ecology and evolution of its host through reproductive manipulation. Here, we survey Wolbachia in Belonocnema treatae, a widely distributed North American cynipid gall forming wasp that exhibits regional host specialization on three species of oaks and alternation of sexually and asexually reproducing generations. We investigated whether patterns of Wolbachia infection and diversity in B...
March 27, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29575852/streptococcus-suis-a-re-emerging-pathogen-associated-with-occupational-exposure-to-pigs-or-pork-products-part-ii-pathogenesis
#19
Jacek Dutkiewicz, Violetta Zając, Jacek Sroka, Bernard Wasiński, Ewa Cisak, Anna Sawczyn, Anna Kloc, Angelina Wójcik-Fatla
<i>Streptococcus suis</i> is a re-emerging zoonotic pathogen that may cause severe disease, mostly meningitis, in pigs and in humans having occupational contact with pigs and pork, such as farmers, slaughterhose workers and butchers. The first stage of the pathogenic process, similar in pigs and humans, is adherence to and colonisation of mucosal and/or epithelial surface(s) of the host. The second stage is invasion into deeper tissue and extracellular translocation of bacterium in the bloodstream, either free in circulation or attached to the surface of monocytes...
March 14, 2018: Annals of Agricultural and Environmental Medicine: AAEM
https://www.readbyqxmd.com/read/29571708/high-dimensional-random-walks-can-appear-low-dimensional-application-to-influenza-h3n2-evolution
#20
James Moore, Hasan Ahmed, Rustom Antia
One important feature of the mammalian immune system is the highly specific binding of antigens to antibodies. Antibodies generated in response to one infection may also provide some level of cross immunity to other infections. One model to describe this cross immunity is the notion of antigenic space, which assigns each antibody and each virus a point in Rn . Past studies using hemagglutination data have suggested the dimensionality of antigenic space, n, is low. We propose that influenza evolution may be modeled as a Gaussian random walk...
March 20, 2018: Journal of Theoretical Biology
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