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https://www.readbyqxmd.com/read/29787745/modeling-transposable-element-dynamics-with-fragmentation-equations
#1
Mario Banuelos, Suzanne Sindi
Transposable elements (TEs), segments of DNA capable of self-replication, are abundant in the genomes of most organisms and thus serve as a record of past mutational events. While some work suggests TEs may serve a regulatory function for the host, most empirical and theoretical studies have shown that TEs often have deleterious effects on a host. Because they are not essential, the host genome consists of both full-length (actively replicating) and partial length (inactive remnant) copies of TEs. We developed a novel mathematical formulation of TE dynamics by modeling the density of full and partial length copies resulting from mutations (insertions and deletions) and TE replication within the host genome...
May 19, 2018: Mathematical Biosciences
https://www.readbyqxmd.com/read/29785015/frequent-transmission-of-the-mycobacterium-tuberculosis-beijing-lineage-and-positive-selection-for-the-esxw-beijing-variant-in-vietnam
#2
Kathryn E Holt, Paul McAdam, Phan Vuong Khac Thai, Nguyen Thuy Thuong Thuong, Dang Thi Minh Ha, Nguyen Ngoc Lan, Nguyen Huu Lan, Nguyen Thi Quynh Nhu, Hoang Thanh Hai, Vu Thi Ngoc Ha, Guy Thwaites, David J Edwards, Artika P Nath, Kym Pham, David B Ascher, Jeremy Farrar, Chiea Chuen Khor, Yik Ying Teo, Michael Inouye, Maxine Caws, Sarah J Dunstan
To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data identify an underlying burden of disease caused by the endemic Mtb lineage 1 associated with the activation of long-term latent infection, and a threefold higher burden associated with the more recently introduced Beijing lineage and lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than the endemic lineage 1 Mtb...
May 21, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29784978/genomes-of-all-known-members-of-a-plasmodium-subgenus-reveal-paths-to-virulent-human-malaria
#3
Thomas D Otto, Aude Gilabert, Thomas Crellen, Ulrike Böhme, Céline Arnathau, Mandy Sanders, Samuel O Oyola, Alain Prince Okouga, Larson Boundenga, Eric Willaume, Barthélémy Ngoubangoye, Nancy Diamella Moukodoum, Christophe Paupy, Patrick Durand, Virginie Rougeron, Benjamin Ollomo, François Renaud, Chris Newbold, Matthew Berriman, Franck Prugnolle
Plasmodium falciparum, the most virulent agent of human malaria, shares a recent common ancestor with the gorilla parasite Plasmodium praefalciparum. Little is known about the other gorilla- and chimpanzee-infecting species in the same (Laverania) subgenus as P. falciparum, but none of them are capable of establishing repeated infection and transmission in humans. To elucidate underlying mechanisms and the evolutionary history of this subgenus, we have generated multiple genomes from all known Laverania species...
June 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29769347/avian-influenza-viruses-in-wild-birds-virus-evolution-in-a-multi-host-ecosystem
#4
Divya Venkatesh, Marjolein J Poen, Theo M Bestebroer, Rachel D Scheuer, Oanh Vuong, Mzia Chkhaidze, Anna Machablishvili, Jimsher Mamuchadze, Levan Ninua, Nadia B Fedorova, Rebecca A Halpin, Xudong Lin, Amy Ransier, Timothy B Stockwell, David E Wentworth, Divya Kriti, Jayeeta Dutta, Harm van Bakel, Anita Puranik, Marek J Slomka, Steve Essen, Ian H Brown, Ron A M Fouchier, Nicola S Lewis
Wild ducks and gulls are the major reservoirs for avian influenza A viruses (AIVs). The mechanisms that drive AIV evolution are complex at sites where various duck and gull species from multiple flyways breed, winter or stage. The Republic of Georgia is located at the intersection of three migratory flyways: Central Asian Flyway, East Asian/East African Flyway and Black Sea/Mediterranean Flyway. For six consecutive years (2010-2016), we collected AIV samples from various duck and gull species that breed, migrate and overwinter in Georgia...
May 16, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29768649/selection-for-associative-learning-of-colour-stimuli-reveals-correlated-evolution-of-this-learning-ability-across-multiple-stimuli-and-rewards
#5
Maartje Liefting, Katja M Hoedjes, Cécile Le Lann, Hans M Smid, Jacintha Ellers
We are only starting to understand how variation in cognitive ability can result from local adaptations to environmental conditions. A major question in this regard is to what extent selection on cognitive ability in a specific context affects that ability in general through correlated evolution. To address this question we performed artificial selection on visual associative learning in female Nasonia vitripennis wasps. Using appetitive conditioning in which a visual stimulus was offered in association with a host reward, the ability to learn visual associations was enhanced within 10 generations of selection...
May 16, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29765018/tracking-hiv-1-recombination-to-resolve-its-contribution-to-hiv-1-evolution-in-natural-infection
#6
Hongshuo Song, Elena E Giorgi, Vitaly V Ganusov, Fangping Cai, Gayathri Athreya, Hyejin Yoon, Oana Carja, Bhavna Hora, Peter Hraber, Ethan Romero-Severson, Chunlai Jiang, Xiaojun Li, Shuyi Wang, Hui Li, Jesus F Salazar-Gonzalez, Maria G Salazar, Nilu Goonetilleke, Brandon F Keele, David C Montefiori, Myron S Cohen, George M Shaw, Beatrice H Hahn, Andrew J McMichael, Barton F Haynes, Bette Korber, Tanmoy Bhattacharya, Feng Gao
Recombination in HIV-1 is well documented, but its importance in the low-diversity setting of within-host diversification is less understood. Here we develop a novel computational tool (RAPR (Recombination Analysis PRogram)) to enable a detailed view of in vivo viral recombination during early infection, and we apply it to near-full-length HIV-1 genome sequences from longitudinal samples. Recombinant genomes rapidly replace transmitted/founder (T/F) lineages, with a median half-time of 27 days, increasing the genetic complexity of the viral population...
May 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29764659/mechanisms-of-aphid-adaptation-to-host-plant-resistance
#7
REVIEW
Ashley D Yates, Andy Michel
Host-plant resistant (HPR) crops can play a major role in preventing insect damage, but their durability is limited due to insect adaptation. Research in basal plant resistance provides a framework to investigate adaptation against HPR. Resistance and adaptation are predicted to follow the gene-for-gene and zigzag models of plant defense. These models also highlight the importance of insect effectors, which are small molecules that modulate host plant defense signaling. We highlight research in insect adaptation to plant resistance, and then draw parallels to virulence adaptation...
April 2018: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/29764648/rapid-evolution-to-host-plant-resistance-by-an-invasive-herbivore-soybean-aphid-aphis-glycines-virulence-in-north-america-to-aphid-resistant-cultivars
#8
REVIEW
Matthew E O'Neal, Adam J Varenhorst, Matthew C Kaiser
Preventing rapid evolution of herbivores to plant traits that confer resistance is an area of active research for applied entomologists. The subfield of insect resistance management (IRM) uses elements of population genetics and ecology to prevent increases in the frequency of virulent (i.e. resistant) sub-populations of an insect pest. Efforts to delay such an increase include using highly lethal toxins (i.e., a high dose), combining multiple resistance traits in one cultivar (i.e., pyramids), and using susceptible plants (i...
April 2018: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/29763671/searching-for-signals-of-recent-natural-selection-in-genes-of-the-innate-immune-response-ancient-dna-study
#9
Magda Lewandowska, Krystyna Jędrychowska-Dańska, Tomasz Płoszaj, Piotr Witas, Alicja Zamerska, Hanna Mańkowska-Pliszka, Henryk W Witas
The last decade has seen sharp progress in the field of human evolutionary genetics and a great amount of genetic evidence of natural selection has been provided so far. Since host-pathogen co-evolution is difficult to trace due to the polygenic nature of human susceptibility to microbial diseases, of particular interest is any signal of natural selection in response to the strong selective pressure exerted by pathogens. Analysis of ancient DNA allows for the direct insight into changes of a gene pool content over time and enables monitoring allele frequency fluctuations...
May 12, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29753710/mysteries-of-host-switching-diversification-and-host-specificity-in-rodent-coccidia-associations
#10
Anna Mácová, Aneta Hoblíková, Václav Hypša, Michal Stanko, Jana Martinů, Jana Kvičerová
Recent studies show that host switching is much more frequent than originally believed and constitutes an important driver in evolution of host-parasite associations. However, its frequency and ecological mechanisms at the population level have been rarely investigated. We address this issue by analyzing phylogeny and population genetics of an extensive sample, from a broad geographic area, for commonly occurring parasites of the genus Eimeria within the abundant rodent genera Apodemus, Microtus and Myodes, using two molecular markers...
May 10, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29752940/oxidative-stress-redox-stress-or-redox-success
#11
John M C Gutteridge, Barry Halliwell
The first life forms evolved in a highly reducing environment. This reduced state is still carried by cells today, which makes the concept of "reductive stress" somewhat redundant. When oxygen became abundant on the Earth, due to the evolution of photosynthesis, life forms had to adapt or become extinct. Living organisms did adapt, proliferated and an explosion of new life forms resulted, using reactive oxygen species (ROS) to drive their evolution. Adaptation to oxygen and its reduction intermediates necessitated the simultaneous evolution of select antioxidant defences, carefully regulated to allow ROS to perform their major roles...
May 9, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29752168/mixed-mode-transmission-shapes-termite-gut-community-assemblies
#12
Rafael R da Costa, Michael Poulsen
Understanding how microbial symbiont community assemblies are shaped over evolutionary time is challenging. The current state of the art involves exploring similarities and differences in communities within and between host species, often aiming to link these to host ecology and evolution. However, this masks the evolutionary histories of individual bacterial lineages.
May 8, 2018: Trends in Microbiology
https://www.readbyqxmd.com/read/29751087/population-genetic-and-evolution-analysis-of-controversial-genus-edwardsiella-by-multilocus-sequence-typing
#13
Noemí Buján, Sabela Balboa, Jesús L Romalde, Alicia E Toranzo, Beatriz Magariños
At present, the genus Edwardsiella compiles five species: E. tarda, E. hoshinae, E. ictaluri, E. piscicida and E. anguillarum. Some species of this genus such us E. ictaluri and E. piscicida are important pathogens of numerous fish species. With the description of the two latter species, the phylogeny of Edwardsiella became more complicated. With the aim to clarify the relationships among all species in the genus, a multilocus sequence typing (MLST) approach was developed and applied to characterize 56 isolates and 6 reference strains belonging to the five Edwardsiella species...
May 8, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29743368/stat2-dependent-immune-responses-ensure-host-survival-despite-the-presence-of-a-potent-viral-antagonist
#14
Vu Thuy Khanh Le-Trilling, Kerstin Wohlgemuth, Meike U Rückborn, Andreja Jagnjic, Fabienne Maaßen, Lejla Timmer, Benjamin Katschinski, Mirko Trilling
Pathogen encounter induces interferons which signal via Janus kinases and STAT transcription factors to establish an antiviral state. However, host and pathogens are situated in a continuous arms race which shapes host evolution towards optimized immune responses and the pathogens towards enhanced immune evasive properties.Mouse cytomegalovirus (MCMV) counteracts interferon responses by pM27-mediated degradation of STAT2 which directly affects the signaling of type I as well as type III interferons. Using MCMV mutants lacking M27 and mice lacking STAT2, we studied the opposing relationship between antiviral activities and viral antagonism in a natural host-pathogen pair in vitro and in vivo In contrast to wt-MCMV, ΔM27-MCMV was efficiently cleared from all organs within a few days in BALB/c, C57BL/6, and 129 mice, highlighting the general importance of STAT2 antagonism for MCMV replication...
May 9, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29738577/widespread-plant-specialization-in-the-polyphagous-planthopper-hyalesthes-obsoletus-cixiidae-a-major-vector-of-stolbur-phytoplasma-evidence-of-cryptic-speciation
#15
Andrea Kosovac, Jes Johannesen, Oliver Krstić, Milana Mitrović, Tatjana Cvrković, Ivo Toševski, Jelena Jović
The stolbur phytoplasma vector Hyalesthes obsoletus is generally considered as a polyphagous species associated with numerous wild and cultivated plants. However, recent research in southeastern Europe, the distribution centre of H. obsoletus and the area of most stolbur-inflicted crop diseases, points toward specific host-plant associations of the vector, indicating specific vector-based transmission routes. Here, we study the specificity of populations associated with four host-plants using mitochondrial and nuclear genetic markers, and we evaluate the evolution of host-shifts in H...
2018: PloS One
https://www.readbyqxmd.com/read/29727465/biphasic-zinc-compartmentalisation-in-a-human-fungal-pathogen
#16
Aaron C Crawford, Laura E Lehtovirta-Morley, Omran Alamir, Maria J Niemiec, Bader Alawfi, Mohammad Alsarraf, Volha Skrahina, Anna C B P Costa, Andrew Anderson, Sujan Yellagunda, Elizabeth R Ballou, Bernhard Hube, Constantin F Urban, Duncan Wilson
Nutritional immunity describes the host-driven manipulation of essential micronutrients, including iron, zinc and manganese. To withstand nutritional immunity and proliferate within their hosts, pathogenic microbes must express efficient micronutrient uptake and homeostatic systems. Here we have elucidated the pathway of cellular zinc assimilation in the major human fungal pathogen Candida albicans. Bioinformatics analysis identified nine putative zinc transporters: four cytoplasmic-import Zip proteins (Zrt1, Zrt2, Zrt3 and orf19...
May 4, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29723682/intra-host-sequence-variability-in-human-papillomavirus
#17
Racheal S Dube Mandishora, Kristina S Gjøtterud, Sonja Lagström, Babill Stray-Pedersen, Kerina Duri, Nyasha Chin'ombe, Mari Nygård, Irene Kraus Christiansen, Ole Herman Ambur, Mike Z Chirenje, Trine B Rounge
Human papillomaviruses (HPVs) co-evolve slowly with the human host and each HPV genotype displays epithelial tropisms. We assessed the evolution of intra HPV genotype variants within samples, and their association to anogenital site, cervical cytology and HIV status. Variability in the L1 gene of 35 HPV genotypes was characterized phylogenetically using maximum likelihood, and portrayed by phenotype. Up to a thousand unique variants were identified within individual samples. In-depth analyses of the most prevalent genotypes, HPV16, HPV18 and HPV52, revealed that the high diversity was dominated by a few abundant variants...
April 30, 2018: Papillomavirus Research
https://www.readbyqxmd.com/read/29721287/the-effect-of-gut-microbiota-elimination-in-drosophila-melanogaster-a-how-to-guide-for-host-microbiota-studies
#18
Chloe Heys, Anne Lizé, Frances Blow, Lewis White, Alistair Darby, Zenobia J Lewis
In recent years, there has been a surge in interest in the effects of the microbiota on the host. Increasingly, we are coming to understand the importance of the gut microbiota in modulating host physiology, ecology, behavior, and evolution. One method utilized to evaluate the effect of the microbiota is to suppress or eliminate it, and compare the effect on the host with that of untreated individuals. In this study, we evaluate some of these commonly used methods in the model organism, Drosophila melanogaster ...
April 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29720997/transposable-element-genomic-fissuring-in-pyrenophora-teres-is-associated-with-genome-expansion-and-dynamics-of-host-pathogen-genetic-interactions
#19
Robert A Syme, Anke Martin, Nathan A Wyatt, Julie A Lawrence, Mariano J Muria-Gonzalez, Timothy L Friesen, Simon R Ellwood
Pyrenophora teres , P. teres f. teres (PTT) and P. teres f. maculata (PTM) cause significant diseases in barley, but little is known about the large-scale genomic differences that may distinguish the two forms. Comprehensive genome assemblies were constructed from long DNA reads, optical and genetic maps. As repeat masking in fungal genomes influences the final gene annotations, an accurate and reproducible pipeline was developed to ensure comparability between isolates. The genomes of the two forms are highly collinear, each composed of 12 chromosomes...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29720515/small-bottleneck-size-in-a-highly-multipartite-virus-during-a-complete-infectious-cycle
#20
Romain Gallet, Frédéric Fabre, Gaël Thébaud, Mircea T Sofonea, Anne Sicard, Stéphane Blanc, Yannis Michalakis
Multipartite viruses package their genomic segments independently and thus incur the risk of being unable to transmit their entire genome during host-to-host transmission if they undergo severe bottlenecks. In this paper we estimated the bottleneck size during one infection cycle of Faba bean necrotic stunt virus (FBNSV), an octopartite nanovirus whose segments have been previously shown to converge to particular and unequal relative frequencies within host plants and aphid vectors. Two methods were used to derive this estimate: one based on the probability of transmission of the virus and the other based on the temporal evolution of the relative frequency of markers for two genomic segments, one frequent and one rare (segment N and S respectively) both in plants and vectors...
May 2, 2018: Journal of Virology
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