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Within host evolution

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https://www.readbyqxmd.com/read/28106948/genetic-differentiation-associated-with-host-plants-and-geography-among-six-widespread-species-of-south-american-blepharoneura-fruit-flies-tephritidae
#1
Kristina Ottens, Isaac S Winkler, Matthew L Lewis, Sonja J Scheffer, Géssica A Gomes-Costa, Marty A Condon, Andrew A Forbes
Tropical herbivorous insects are astonishingly diverse and many are highly host-specific. Much evidence suggests that herbivorous insect diversity is a function of host-plant diversity; yet, the diversity of some lineages exceeds the diversity of plants. Although most species of herbivorous fruit flies in the Neotropical genus Blepharoneura are strongly host-specific (they deposit their eggs in a single host plant species and flower sex), some species are collected from multiple hosts or flowers and these may represent examples of lineages that are diversifying via changes in host use...
January 20, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28103791/high-virulence-does-not-necessarily-impede-viral-adaptation-to-a-new-host-a-case-study-using-a-plant-rna-virus
#2
Anouk Willemsen, Mark P Zwart, Santiago F Elena
BACKGROUND: Theory suggests that high virulence could hinder between-host transmission of microparasites, and that virulence therefore will evolve to lower levels. Alternatively, highly virulent microparasites could also curtail host development, thereby limiting both the host resources available to them and their own within-host effective population size. In this case, high virulence might restrain the mutation supply rate and increase the strength with which genetic drift acts on microparasite populations...
January 19, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28103318/static-and-evolving-norovirus-genotypes-implications-for-epidemiology-and-immunity
#3
Gabriel I Parra, R Burke Squires, Consolee K Karangwa, Jordan A Johnson, Cara Lepore, Stanislav V Sosnovtsev, Kim Y Green
Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII...
January 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28103248/effect-of-the-latent-reservoir-on-the-evolution-of-hiv-at-the-within-and-between-host-levels
#4
Hilje M Doekes, Christophe Fraser, Katrina A Lythgoe
The existence of long-lived reservoirs of latently infected CD4+ T cells is the major barrier to curing HIV, and has been extensively studied in this light. However, the effect of these reservoirs on the evolutionary dynamics of the virus has received little attention. Here, we present a within-host quasispecies model that incorporates a long-lived reservoir, which we then nest into an epidemiological model of HIV dynamics. For biologically plausible parameter values, we find that the presence of a latent reservoir can severely delay evolutionary dynamics within a single host, with longer delays associated with larger relative reservoir sizes and/or homeostatic proliferation of cells within the reservoir...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28102347/low-level-predation-by-lytic-phage-phiipla-rodi-promotes-biofilm-formation-and-triggers-the-stringent-response-in-staphylococcus-aureus
#5
Lucía Fernández, Silvia González, Ana Belén Campelo, Beatriz Martínez, Ana Rodríguez, Pilar García
An important lesson from the war on pathogenic bacteria has been the need to understand the physiological responses and evolution of natural microbial communities. Bacterial populations in the environment are generally forming biofilms subject to some level of phage predation. These multicellular communities are notoriously resistant to antimicrobials and, consequently, very difficult to eradicate. This has sparked the search for new therapeutic alternatives, including phage therapy. This study demonstrates that S...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28099506/spatial-and-host-related-variation-in-prevalence-and-population-density-of-wheat-curl-mite-aceria-tosichella-cryptic-genotypes-in-agricultural-landscapes
#6
Anna Skoracka, Mariusz Lewandowski, Brian G Rector, Wiktoria Szydło, Lechosław Kuczyński
The wheat curl mite (WCM), Aceria tosichella Keifer, is a major pest of cereals worldwide that also comprises a complex of at least 16 genetic lineages with divergent physiological traits, including host associations and specificity. The goal of this study was to test the extent to which host-plant species and landscape spatial variation influence WCM presence and population density across the entire area of Poland (>311,000 km2). Three important findings arose from the results of the study. (1) The majority of WCM lineages analyzed exhibited variation in patterns of prevalence and/or population density on both spatial and host-associated scales...
2017: PloS One
https://www.readbyqxmd.com/read/28096484/evolutionary-dynamics-of-pandemic-methicillin-sensitive-staphylococcus-aureus-st398-and-its-international-spread-via-routes-of-human-migration
#7
Anne-Catrin Uhlemann, Paul R McAdam, Sean B Sullivan, Justin R Knox, Hossein Khiabanian, Raul Rabadan, Peter R Davies, J Ross Fitzgerald, Franklin D Lowy
: Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for the majority of S. aureus infections globally, and yet surprisingly little is known about its clonal evolution. We applied comparative whole-genome sequencing (WGS) analyses to epidemiologically and geographically diverse ST398-MSSA, a pandemic lineage affecting both humans and livestock. Bayesian phylogenetic analysis predicted divergence of human-associated ST398-MSSA ~40 years ago. Isolates from Midwestern pigs and veterinarians differed substantially from those in New York City (NYC)...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096240/coevolution-of-leukemia-and-host-immune-cells-in-chronic-lymphocytic-leukemia
#8
Noelia Purroy, C J Wu
Cumulative studies on the dissection of changes in driver genetic lesions in cancer across the course of the disease have provided powerful insights into the adaptive mechanisms of tumors in response to the selective pressures of therapy and environmental changes. In particular, the advent of next-generation-sequencing (NGS)-based technologies and its implementation for the large-scale comprehensive analyses of cancers have greatly advanced our understanding of cancer as a complex dynamic system wherein genetically distinct subclones interact and compete during tumor evolution...
January 17, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28087421/physiology-anaerobes-and-the-origin-of-mitosing-cells-50-years-on
#9
William F Martin
Endosymbiotic theory posits that some organelles or structures of eukaryotic cells stem from free-living prokaryotes that became endosymbionts within a host cell. Endosymbiosis has a long and turbulent history of controversy and debate going back over 100 years. The 1967 paper by Lynn Sagan (later Lynn Margulis) forced a reluctant field to take endosymbiotic theory seriously and to incorporate it into the fabric of evolutionary thinking. Margulis envisaged three cellular partners associating in series at eukaryotic origin: the host (an engulfing bacterium), the mitochondrion (a respiring bacterium), and the flagellum (a spirochaete), with lineages descended from that flagellated eukaryote subsequently acquiring plastids from cyanobacteria, but on multiple different occasions in her 1967 account...
January 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28081260/comparative-genome-sequencing-reveals-within-host-genetic-changes-in-neisseria-meningitidis-during-invasive-disease
#10
Johanna Klughammer, Marcus Dittrich, Jochen Blom, Vera Mitesser, Ulrich Vogel, Matthias Frosch, Alexander Goesmann, Tobias Müller, Christoph Schoen
Some members of the physiological human microbiome occasionally cause life-threatening disease even in immunocompetent individuals. A prime example of such a commensal pathogen is Neisseria meningitidis, which normally resides in the human nasopharynx but is also a leading cause of sepsis and epidemic meningitis. Using N. meningitidis as model organism, we tested the hypothesis that virulence of commensal pathogens is a consequence of within host evolution and selection of invasive variants due to mutations at contingency genes, a mechanism called phase variation...
2017: PloS One
https://www.readbyqxmd.com/read/28076891/comparative-genomics-of-mortierella-elongata-and-its-bacterial-endosymbiont-mycoavidus-cysteinexigens
#11
J Uehling, A Gryganskyi, K Hameed, T Tschaplinski, P K Misztal, S Wu, A Desirò, N Vande Pol, Z Du, A Zienkiewicz, K Zienkiewicz, E Morin, E Tisserant, R Splivallo, M Hainaut, B Henrissat, R Ohm, A Kuo, J Yan, A Lipzen, M Nolan, K LaButti, K Barry, A H Goldstein, J Labbé, C Schadt, G Tuskan, I Grigoriev, F Martin, R Vilgalys, G Bonito
Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants, and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within in a lineage of endofungal symbionts that are sister clade to Burkholderia...
January 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28073389/the-distribution-of-echinostome-parasites-in-ponds-and-implications-for-larval-anuran-survival
#12
John A Marino, Manja P Holland, Earl E Werner
Parasites can influence host population dynamics, community composition and evolution. Prediction of these effects, however, requires an understanding of the influence of ecological context on parasite distributions and the consequences of infection for host fitness. We address these issues with an amphibian - trematode (Digenea: Echinostomatidae) host-parasite system. We initially performed a field survey of trematode infection in first (snail) and second (larval green frog, Rana clamitans) intermediate hosts over 5 years across a landscape of 23 ponds in southeastern Michigan...
January 11, 2017: Parasitology
https://www.readbyqxmd.com/read/28058113/transmission-bottlenecks-and-rnai-collectively-influence-tick-borne-flavivirus-evolution
#13
Nathan D Grubaugh, Claudia Rückert, Philip M Armstrong, Angela Bransfield, John F Anderson, Gregory D Ebel, Doug E Brackney
Arthropod-borne RNA viruses exist within hosts as heterogeneous populations of viral variants and, as a result, possess great genetic plasticity. Understanding the micro-evolutionary forces shaping these viruses can provide insights into how they emerge, adapt, and persist in new and changing ecological niches. While considerable attention has been directed toward studying the population dynamics of mosquito-borne viruses, little is known about tick-borne virus populations. Therefore, using a mouse and Ixodes scapularis tick transmission model, we examined Powassan virus (POWV; Flaviviridae, Flavivirus) populations in and between both the vertebrate host and arthropod vector...
July 2016: Virus Evolution
https://www.readbyqxmd.com/read/28058112/foamy-like-endogenous-retroviruses-are-extensive-and-abundant-in-teleosts
#14
Ryan Ruboyianes, Michael Worobey
Recent discoveries indicate that the foamy virus (FV) (Spumavirus) ancestor may have been among the first retroviruses to appear during the evolution of vertebrates, demonstrated by foamy endogenous retroviruses present within deeply divergent hosts including mammals, coelacanth, and ray-finned fish. If they indeed existed in ancient marine environments hundreds of millions of years ago, significant undiscovered diversity of foamy-like endogenous retroviruses might be present in fish genomes. By screening published genomes and by applying PCR-based assays of preserved tissues, we discovered 23 novel foamy-like elements in teleost hosts...
July 2016: Virus Evolution
https://www.readbyqxmd.com/read/28052323/complex-dynamics-underlie-the-evolution-of-imperfect-wing-pattern-convergence-in-butterflies
#15
Susan D Finkbeiner, Adriana D Briscoe, Sean P Mullen
Adaptive radiation is characterized by rapid diversification that is strongly associated with ecological specialization. However, understanding the evolutionary mechanisms fueling adaptive diversification requires a detailed knowledge of how natural selection acts at multiple life-history stages. Butterflies within the genus Adelpha represent one of the largest and most diverse butterfly lineages in the Neotropics. Although Adelpha species feed on an extraordinary diversity of larval hosts, convergent evolution is widespread in this group suggesting that selection for mimicry may contribute to adaptive divergence among species...
January 4, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28049427/identification-of-candidate-infection-genes-from-the-model-entomopathogenic-nematode-heterorhabditis-bacteriophora
#16
Jonathan Vadnal, Ramesh Ratnappan, Melissa Keaney, Eric Kenney, Ioannis Eleftherianos, Damien O'Halloran, John M Hawdon
BACKGROUND: Despite important progress in the field of innate immunity, our understanding of host immune responses to parasitic nematode infections lags behind that of responses to microbes. A limiting factor has been the obligate requirement for a vertebrate host which has hindered investigation of the parasitic nematode infective process. The nematode parasite Heterorhabditis bacteriophora offers great potential as a model to genetically dissect the process of infection. With its mutualistic Photorhabdus luminescens bacteria, H...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28035894/sweet-tetra-trophic-interactions-multiple-evolution-of-nectar-secretion-a-defensive-extended-phenotype-in-cynipid-gall-wasps
#17
James A Nicholls, George Melika, Graham N Stone
Many herbivores employ reward-based mutualisms with ants to gain protection from natural enemies. We examine the evolutionary dynamics of a tetra-trophic interaction in which gall wasp herbivores induce their host oaks to produce nectar-secreting galls, which attract ants that provide protection from parasitoids. We show that, consistent with other gall defensive traits, nectar secretion has evolved repeatedly across the oak gall wasp tribe and also within a single genus (Disholcaspis) that includes many nectar-inducing species...
January 2017: American Naturalist
https://www.readbyqxmd.com/read/28033376/genome-wide-analyses-of-individual-strongyloides-stercoralis-nematoda-rhabditoidea-provide-insights-into-population-structure-and-reproductive-life-cycles
#18
Taisei Kikuchi, Akina Hino, Teruhisa Tanaka, Myo Pa Pa Thet Hnin Htwe Aung, Tanzila Afrin, Eiji Nagayasu, Ryusei Tanaka, Miwa Higashiarakawa, Kyu Kyu Win, Tetsuo Hirata, Wah Win Htike, Jiro Fujita, Haruhiko Maruyama
The helminth Strongyloides stercoralis, which is transmitted through soil, infects 30-100 million people worldwide. S. stercoralis reproduces sexually outside the host as well as asexually within the host, which causes a life-long infection. To understand the population structure and transmission patterns of this parasite, we re-sequenced the genomes of 33 individual S. stercoralis nematodes collected in Myanmar (prevalent region) and Japan (non-prevalent region). We utilised a method combining whole genome amplification and next-generation sequencing techniques to detect 298,202 variant positions (0...
December 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28032207/vector-borne-pathogen-and-host-evolution-in-a-structured-immuno-epidemiological-system
#19
Hayriye Gulbudak, Vincent L Cannataro, Necibe Tuncer, Maia Martcheva
Vector-borne disease transmission is a common dissemination mode used by many pathogens to spread in a host population. Similar to directly transmitted diseases, the within-host interaction of a vector-borne pathogen and a host's immune system influences the pathogen's transmission potential between hosts via vectors. Yet there are few theoretical studies on virulence-transmission trade-offs and evolution in vector-borne pathogen-host systems. Here, we consider an immuno-epidemiological model that links the within-host dynamics to between-host circulation of a vector-borne disease...
December 28, 2016: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28027024/whop-a-genomic-region-associated-with-woody-hosts-in-the-pseudomonas-syringae-complex-contributes-to-the-virulence-and-fitness-of-pseudomonas-savastanoi-pv-savastanoi-in-olive-plants
#20
Eloy Caballo-Ponce, Pieter van Dillewijn, Regina-Michaela Wittich, Cayo Ramos
Bacteria from the Pseudomonas syringae complex belonging to phylogroups 1 (PG1) and 3 (PG3) isolated from woody hosts share a genomic region herein referred to as WHOP (from woody host and Pseudomonas), which is absent in strains infecting herbaceous organs. In this work, we show that this region is also encoded in P. syringae pv. actinidifoliorum (PG1) and six additional members of PG3: Pseudomonas savastanoi pv. retacarpa, three P. syringae pathovars, Pseudomonas meliae and Pseudomonas amygdali. Partial conservation of the WHOP occurs in only a few PG2 strains...
December 27, 2016: Molecular Plant-microbe Interactions: MPMI
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