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Within host evolution

David Botero, Camilo Alvarado, Adriana Bernal, Giovanna Danies, Silvia Restrepo
Even in the age of big data in Biology, studying the connections between the biological processes and the molecular mechanisms behind them is a challenging task. Systems biology arose as a transversal discipline between biology, chemistry, computer science, mathematics, and physics to facilitate the elucidation of such connections. A scenario, where the application of systems biology constitutes a very powerful tool, is the study of interactions between hosts and pathogens using network approaches. Interactions between pathogenic bacteria and their hosts, both in agricultural and human health contexts are of great interest to researchers worldwide...
2018: Frontiers in Microbiology
María M Cameranesi, Jorgelina Morán-Barrio, Adriana S Limansky, Guillermo D Repizo, Alejandro M Viale
Members of the genus Acinetobacter possess distinct plasmid types which provide effective platforms for the acquisition, evolution, and dissemination of antimicrobial resistance structures. Many plasmid-borne resistance structures are bordered by short DNA sequences providing potential recognition sites for the host XerC and XerD site-specific tyrosine recombinases (XerC/D-like sites). However, whether these sites are active in recombination and how they assist the mobilization of associated resistance structures is still poorly understood...
2018: Frontiers in Microbiology
Ranjit Kumar Sahoo, David J Lohman, Niklas Wahlberg, Chris J Müller, Oskar Brattström, Steve C Collins, Djunijanti Peggie, Kwaku Aduse-Poku, Ullasa Kodandaramaiah
Hypolimnas butterflies (Nymphalidae), commonly known as eggflies, are a popular model system for studying a wide range of ecological questions including mimicry, polymorphism, wing pattern evolution, and Wolbachia-host interactions. The lack of a time-calibrated phylogeny for this group has precluded understanding its evolutionary history. We reconstruct a species-level phylogeny using a nine gene dataset and estimate species divergence times. Based on the resulting tree, we investigate the taxon's historical biogeography, examine the evolution of host plant preferences, and test the hypothesis that the endosymbiotic bacterium Wolbachia mediates gene transfer between species...
February 8, 2018: Molecular Phylogenetics and Evolution
Dominik Danso, Christel Schmeisser, Jennifer Chow, Wolfgang Zimmermann, Ren Wei, Christian Leggewie, Xiangzhen Li, Terry Hazen, Wolfgang R Streit
Polyethylene terephthalate (PET) is one of the most important synthetic polymers used nowadays. Unfortunately, the polymers accumulate in nature and until now, no highly active enzymes are known that can degrade it at high velocity. Enzymes involved in PET degradation are mainly α/β-hydrolases like cutinases and related enzymes (E.C. 3.1.-). Currently, only a small number of such enzymes are well characterized. Within this work, a search algorithm was developed that identified 504 possible PET hydrolase candidate genes from various databases...
February 2, 2018: Applied and Environmental Microbiology
Praveen Kumar Allu, Yerranna Boggula, Srinivasu Karri, Adinarayana Marada, Thanuja Krishnamoorthy, Naresh Babu V Sepuri
Cells across evolution employ reversible oxidative modification of methionine and cysteine amino acids within proteins to regulate responses to redox stress. Previously we have shown that mitochondrial localized methionine sulfoxide reductase (Mxr2) reversibly regulates oxidized yeast Mge1 (yMge1), a co-chaperone of Hsp70/Ssc1 to maintain protein homeostasis during oxidative stress. However, the specificity and the conservation of the reversible methionine oxidation mechanism in higher eukaryotes is debatable as human GrpEL1 (hGrpEL1) unlike its homolog yMge1 harbors two methionine residues and multiple cysteines besides the mammalian mitochondria hosting R and S types of Mxrs/Msrs...
February 9, 2018: Scientific Reports
Lucette Flandroy, Theofilos Poutahidis, Gabriele Berg, Gerard Clarke, Maria-Carlota Dao, Ellen Decaestecker, Eeva Furman, Tari Haahtela, Sébastien Massart, Hubert Plovier, Yolanda Sanz, Graham Rook
Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems...
February 3, 2018: Science of the Total Environment
Olivier Navaud, Adelin Barbacci, Andrew Taylor, John P Clarkson, Sylvain Raffaele
The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events, and host range variation during the evolution of this family...
February 8, 2018: Molecular Ecology
Alejandro Otero-Bravo, Shana Goffredi, Zakee L Sabree
Phytophagous stink bugs are globally-distributed and many harbor vertically-inherited bacterial symbionts that are extracellular, yet little is known about how the symbiont's genomes have evolved under this transmission strategy. Genome reduction is common in insect intracellular symbionts but limited genome sampling of the extracellular symbionts of distantly-related stink bugs has precluded inferring patterns of extracellular symbiont genome evolution. To address this knowledge gap, we completely sequenced the genomes of the uncultivable bacterial symbionts of four neotropical stink bugs of the Edessa genus...
February 6, 2018: Genome Biology and Evolution
A B F Ivens, A Gadau, E T Kiers, D J C Kronauer
Mutualistic interactions with microbes have played a crucial role in the evolution and ecology of animal hosts. However, it is unclear what factors are most important in influencing particular host-microbe associations. While closely related animal species may have more similar microbiota than distantly related species due to phylogenetic contingencies, social partnerships with other organisms, such as those in which one animal farms another, may also influence an organism's symbiotic microbiome. We studied a mutualistic network of Brachymyrmex and Lasius ants farming several honeydew-producing Prociphilus aphids and Rhizoecus mealybugs to test whether the mutualistic microbiomes of these interacting insects are primarily correlated with their phylogeny or with their shared social partnerships...
February 7, 2018: Molecular Ecology
Daniel Leduc, Zeng Qi Zhao, Valentin Verdon, Yumei Xu
The placement of the rare deep-sea nematode order Rhaptothyreida remains unclear due to the unique morphology of this group, an unknown life cycle with morphologically distinct juvenile stages which may or may not be parasitic, and lack of molecular sequences. Here, we investigate the phylogenetic placement and status of the Rhaptothyreida based on SSU and D2-D3 of LSU rDNA sequences of Rhaptothyerus typicus specimens obtained from the continental slope of New Zealand. Molecular sequences of three adults and a late stage juvenile were identical, confirming that they belong to the same species despite pronounced morphological differences...
January 30, 2018: Molecular Phylogenetics and Evolution
Shawn T Clark, David S Guttman, David M Hwang
The evolution and diversification of bacterial pathogens within human hosts represent potential barriers to the diagnosis and treatment of life-threatening infections. Tremendous genetic and phenotypic diversity is characteristic of host adaptation in strains of Pseudomonas aeruginosa that infect the airways of individuals with chronic lung diseases and prove to be extremely difficult to eradicate. In this MiniReview, we examine recent advances in understanding within-host diversity and antimicrobial resistance in P...
February 1, 2018: FEMS Microbiology Letters
Roy N Platt, Michael W Vandewege, David A Ray
Transposable elements (TEs) are genetic elements with the ability to mobilize and replicate themselves in a genome. Mammalian genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. As a result, TEs have had significant impacts on mammalian evolution. Here we summarize the current understanding of TE content in mammal genomes and find that, with a few exceptions, most fall within a predictable range of observations. First, one third to one half of the genome is derived from TEs...
February 1, 2018: Chromosome Research
Evan C Palmer-Young, Austin C Calhoun, Anastasiya Mirzayeva, Ben M Sadd
Ecological and evolutionary pressures on hosts and parasites jointly determine infection success. In pollinators, parasite exposure to floral phytochemicals may influence between-host transmission and within-host replication. In the bumble bee parasite Crithidia bombi, strains vary in phytochemical resistance, and resistance increases under in vitro selection, implying that resistance/infectivity trade-offs could maintain intraspecific variation in resistance. We assessed costs and benefits of in vitro selection for resistance to the floral phytochemical eugenol on C...
February 1, 2018: Scientific Reports
Lisbeth Ramirez-Carvajal, Steven J Pauszek, Zaheer Ahmed, Umer Farooq, Khalid Naeem, Reed S Shabman, Timothy B Stockwell, Luis L Rodriguez
Foot-and-mouth disease (FMD) is a severe infection caused by a picornavirus that affects livestock and wildlife. Persistence in ruminants is a well-documented feature of Foot-and-mouth disease virus (FMDV) pathogenesis and a major concern for disease control. Persistently infected animals harbor virus for extended periods, providing a unique opportunity to study within-host virus evolution. This study investigated the genetic dynamics of FMDV during persistent infections of naturally infected Asian buffalo...
2018: PloS One
Austin Alleman, Barbara Feldmeyer, Susanne Foitzik
The transition to parasitism is a drastic shift in lifestyle, involving rapid changes in gene structure, function, and expression. After the establishment of antagonistic relationships, parasites and hosts co-evolve through reciprocal adaptations, often resulting in evolutionary arms-races. Repeated evolution of social parasitism and slavery among Temnothorax ants allows us to examine those gene expression patterns that characterize slavemaker raiding and reciprocal host defensive phenotypes. Previous behavioural studies have established that raiding strategies between Temnothorax slavemakers diverge, while host defense portfolios shift similarly under parasite pressure...
January 31, 2018: Scientific Reports
Xue-Feng Wang, Qiang Liu, Yu-Hong Wang, Shuai Wang, Jie Chen, Yue-Zhi Lin, Jian Ma, Jian-Hua Zhou, Xiaojun Wang
The equine infectious anemia virus (EIAV) attenuated vaccine was developed by long-term passaging of a field-isolated virulent strain in cross-species hosts, followed by successive cultivation in cells in vitro To explore the molecular mechanism underlying the evolution of the EIAV attenuated vaccine, a systematic study focusing on long terminal repeat (LTR) variation in numerous virus strains ranging from virulent EIAV to attenuated EIAV was performed over time both in vitro and in vivo Two hypervariable regions were identified within the U3 region in the enhancer region (EHR) and the negative regulatory element (NRE) and within the R region in the transcription start site (TSS) and the Tat-activating region (TAR)...
January 31, 2018: Journal of Virology
Xuan Cheng, Paul A Umina, Ary A Hoffmann, Dominic Reisig
In the evolution of phytophagous arthropods, adaptation to a single type of host plant is generally assumed to lead to a reduction in fitness on other host plant types, resulting in increasing host specialization. While this process is normally considered to be genetically based, short-term effects acting within one generation (plasticity) or across two generations (cross-generation variation) could also play a role. Here, we test these effects in the redlegged earth mite, Halotydeus destructor (Tucker) (Prostigmata: Penthaleidae), a major agricultural pest of multiple crop plants...
January 29, 2018: Journal of Economic Entomology
Andrew M Sackman, Susanne P Pfeifer, Timothy F Kowalik, Jeffrey D Jensen
Human cytomegalovirus (HCMV) is a member of the β -herpesvirus subfamily within Herpesviridae that is nearly ubiquitous in human populations, and infection generally results only in mild symptoms. However, symptoms can be severe in immunonaive individuals, and transplacental congenital infection of HCMV can result in serious neurological sequelae. Recent work has revealed much about the demographic and selective forces shaping the evolution of congenitally transmitted HCMV both on the level of hosts and within host compartments, providing insight into the dynamics of congenital infection, reinfection, and evolution of HCMV with important implications for the development of effective treatments and vaccines...
January 28, 2018: Pathogens
James A Nicholls, Karsten Schönrogge, Sonja Preuss, Graham N Stone
Communities of insect herbivores and their natural enemies are rich and ecologically crucial components of terrestrial biodiversity. Understanding the processes that promote their origin and maintenance is thus of considerable interest. One major proposed mechanism is ecological speciation through host-associated differentiation (HAD), the divergence of a polyphagous species first into ecological host races and eventually into more specialized daughter species. The rich chalcid parasitoid communities attacking cynipid oak gall wasp hosts are structured by multiple host traits, including food plant taxon, host gall phenology, and gall structure...
January 2018: Ecology and Evolution
Nicolás Palopoli, Nicolás S González Foutel, Toby J Gibson, Lucía B Chemes
Pocket proteins retinoblastoma (pRb), p107 and p130 are negative regulators of cellular proliferation and multifunctional proteins regulating development, differentiation and chromatin structure. The retinoblastoma protein is a potent tumor suppressor mutated in a wide range of human cancers, and oncogenic viruses often interfere with cell cycle regulation by inactivating pRb. The LxCxE and pRb AB groove short linear motifs (SLiMs) are key to many pocket protein mediated interactions including host and viral partners...
January 23, 2018: Protein Engineering, Design & Selection: PEDS
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