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within-host evolution

Ondrej Balvín, Warren Booth
For over two decades, the bed bug, Cimex lectularius L. (Hemiptera: Cimicidae) has been undergoing a dramatic global resurgence, likely in part to the evolution of mechanisms conferring resistance to insecticides. One such mechanism is knock-down resistance (kdr), resulting from nonsynonymous mutations within the voltage-gated sodium channel (VGSC) gene. To date, three mutations have been identified in C. lectularius, V419L, L925I, and I936F. Using Sanger sequencing, the frequency and distribution of these VGSC mutations across 131 populations collected from the bat-associated and human-associated lineages of C...
March 15, 2018: Journal of Medical Entomology
Andrej Steyer, Tilen Konte, Martin Sagadin, Marko Kolenc, Andrej Škoberne, Julija Germ, Tadeja Dovč-Drnovšek, Miha Arnol, Mateja Poljšak-Prijatelj
Noroviruses are the leading cause of acute gastroenteritis, and they can affect humans of all age groups. In immunocompromised patients, norovirus infections can develop into chronic diarrhea or show prolonged asymptomatic virus shedding. Chronic norovirus infections are frequently reported for solid organ transplant recipients, with rapid intrahost norovirus evolution seen. In this report, we describe a case of chronic norovirus infection in an immunocompromised patient who was followed up for over 5 years...
2018: Frontiers in Microbiology
David Williams, Joanne L Fothergill, Benjamin Evans, Jessica Caples, Sam Haldenby, Martin J Walshaw, Michael A Brockhurst, Craig Winstanley, Steve Paterson
Pseudomonas aeruginosa chronic infections of cystic fibrosis (CF) airways are a paradigm for within-host evolution with abundant evidence for rapid evolutionary adaptation and diversification. Recently emerged transmissible strains have spread globally, with the Liverpool Epidemic Strain (LES) the most common strain infecting the UK CF population. Previously we have shown that highly divergent lineages of LES can be found within a single infection, consistent with super-infection among a cross-sectional cohort of patients...
March 16, 2018: Microbial Genomics
Dilruba Sharmin, Yong Guo, Tomoyasu Nishizawa, Shoko Ohshima, Yoshinori Sato, Yusuke Takashima, Kazuhiko Narisawa, Hiroyuki Ohta
Endohyphal bacteria (EHB), dwelling within fungal hyphae, markedly affect the growth and metabolic potential of their hosts. To date, two EHB belonging to the family Burkholderiaceae have been isolated and characterized as new taxa, Burkholderia rhizoxinica (HKI 454T ) and Mycoavidus cysteinexigens (B1-EBT ), in Japan. Metagenome sequencing was recently reported for Mortierella elongata AG77 together with its endosymbiont M. cysteinexigens (Mc-AG77) from a soil/litter sample in the USA. In the present study, we elucidated the complete genome sequence of B1-EBT and compared it with those of Mc-AG77 and HKI 454T ...
March 14, 2018: Microbes and Environments
Karissa L Cross, Payal Chirania, Weili Xiong, Clifford J Beall, James G Elkins, Richard J Giannone, Ann L Griffen, Adam M Guss, Robert L Hettich, Snehal S Joshi, Elaine M Mokrzan, Roman K Martin, Igor B Zhulin, Eugene J Leys, Mircea Podar
The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously uncultured Desulfobulbus oralis , the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives, D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities...
March 13, 2018: MBio
Claudia C Paredes-Amaya, Gilberto Valdés-García, Víctor R Juárez-González, Enrique Rudiño-Piñera, Víctor H Bustamante
HilD is an AraC-like transcriptional regulator that plays a central role in Salmonella virulence. HilD controls the expression of the genes within the Salmonella pathogenicity island 1 (SPI-1) and of several genes located outside SPI-1, which are mainly required for Salmonella invasion of host cells. The expression, amount and activity of HilD are tightly controlled by the activities of several factors. The HilE protein represses the expression of the SPI-1 genes through its interaction with HilD; however, the mechanism by which HilE affects HilD is unknown...
March 13, 2018: Journal of Biological Chemistry
Katherine S Xue, Louise H Moncla, Trevor Bedford, Jesse D Bloom
The rapid global evolution of influenza virus begins with mutations that arise de novo in individual infections, but little is known about how evolution occurs within hosts. We review recent progress in understanding how and why influenza viruses evolve within human hosts. Advances in deep sequencing make it possible to measure within-host genetic diversity in both acute and chronic influenza infections. Factors like antigenic selection, antiviral treatment, tissue specificity, spatial structure, and multiplicity of infection may affect how influenza viruses evolve within human hosts...
March 10, 2018: Trends in Microbiology
Jessica L Hite, Clayton E Cressler
What drives the evolution of parasite life-history traits? Recent studies suggest that linking within- and between-host processes can provide key insight into both disease dynamics and parasite evolution. Still, it remains difficult to understand how to pinpoint the critical factors connecting these cross-scale feedbacks, particularly under non-equilibrium conditions; many natural host populations inherently fluctuate and parasites themselves can strongly alter the stability of host populations. Here, we develop a general model framework that mechanistically links resources to parasite evolution across a gradient of stable and unstable conditions...
May 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Ruth Bowness, Mark A J Chaplain, Gibin G Powathil, Stephen H Gillespie
If improvements are to be made in tuberculosis (TB) treatment, an increased understanding of disease in the lung is needed. Studies have shown that bacteria in a less metabolically active state, associated with the presence of lipid bodies, are less susceptible to antibiotics, and recent results have highlighted the disparity in concentration of different compounds into lesions. Treatment success therefore depends critically on the responses of the individual bacteria that constitute the infection. We propose a hybrid, individual-based approach that analyses spatio-temporal dynamics at the cellular level, linking the behaviour of individual bacteria and host cells with the macroscopic behaviour of the microenvironment...
March 7, 2018: Journal of Theoretical Biology
Katherine Lavelle, James Murphy, Brian Fitzgerald, Gabriele A Lugli, Aldert Zomer, Horst Neve, Marco Ventura, Charles M Franz, Christian Cambillau, Douwe van Sinderen, Jennifer Mahony
Phages of Streptococcus thermophilus present a major threat to the production of many fermented dairy products. To date, only a handful of studies have assessed the biodiversity of S. thermophilus phages in dairy fermentations. In order to develop strategies to limit phage predation in this important industrial environment, it is imperative that such studies are undertaken and that phage-host interactions of this species are better defined. The present study investigated the biodiversity and evolution of phages within an Irish dairy fermentation facility over an eleven year period...
March 9, 2018: Applied and Environmental Microbiology
Quang N Nguyen, David R Martinez, Jonathon E Himes, R Whitney Edwards, Qifeng Han, Amit Kumar, Riley Mangan, Nathan I Nicely, Guanhua Xie, Nathan Vandergrift, Xiaoying Shen, Justin Pollara, Sallie R Permar
BACKGROUND: The initial envelope (Env)-specific antibody response in acutely HIV-1-infected individuals and simian immunodeficiency virus (SIV)-infected rhesus monkeys (RMs) is dominated by non-neutralizing antibodies targeting Env gp41. In contrast, natural primate SIV hosts, such as African green monkeys (AGMs), develop a predominant Env gp120-specific antibody response to SIV infection. However, the fine-epitope specificity and function of SIV Env-specific plasma IgG, and their potential role on autologous virus co-evolution in SIV-infected AGMs and RMs remain unclear...
March 9, 2018: Retrovirology
Hugo Aguilar-Díaz, Karen E Nava-Castro, Galileo Escobedo, Lenin Domínguez-Ramírez, Martín García-Varela, Víctor H Del Río-Araiza, Margarita I Palacios-Arreola, Jorge Morales-Montor
BACKGROUND: We have previously reported that progesterone (P4 ) has a direct in vitro effect on the scolex evagination and growth of Taenia solium cysticerci. Here, we explored the hypothesis that the P4 direct effect on T. solium might be mediated by a novel steroid-binding parasite protein. METHODS: By way of using immunofluorescent confocal microscopy, flow cytometry analysis, double-dimension electrophoresis analysis, and sequencing the corresponding protein spot, we detected a novel PGRMC in T...
March 9, 2018: Parasites & Vectors
Antonino Malacrinò, Orlando Campolo, Raul F Medina, Vincenzo Palmeri
Microorganisms are acknowledged for their role in shaping insects' evolution, life history and ecology. Previous studies have shown that microbial communities harbored within insects vary through ontogenetic development and among insects feeding on different host-plant species. In this study, we characterized the bacterial microbiota of the highly polyphagous Mediterranean fruit fly, Ceratitis capitata (Diptera: Tephritidae), at different instars and when feeding on different host-plant species. Our results show that the bacterial microbiota hosted within the Mediterranean fruit fly differs among instars and host-plant species...
2018: PloS One
Jason P Andras, Peter D Fields, Dieter Ebert
Knowledge of a species' population genetic structure can provide insight into fundamental ecological and evolutionary processes including gene flow, genetic drift, and adaptive evolution. Such inference is of particular importance for parasites, as an understanding of their population structure can illuminate epidemiological and coevolutionary dynamics. Here we describe the population genetic structure of the bacterium Pasteuria ramosa, a parasite that infects planktonic crustaceans of the genus Daphnia. This system has become a model for investigations of host-parasite interactions and represents an example of coevolution via negative frequency-dependent selection (a...
March 6, 2018: Molecular Ecology
Duncan A Forbes, Nate Bastian, Mark Gieles, Robert A Crain, J M Diederik Kruijssen, Søren S Larsen, Sylvia Ploeckinger, Oscar Agertz, Michele Trenti, Annette M N Ferguson, Joel Pfeffer, Oleg Y Gnedin
We discuss some of the key open questions regarding the formation and evolution of globular clusters (GCs) during galaxy formation and assembly within a cosmological framework. The current state of the art for both observations and simulations is described, and we briefly mention directions for future research. The oldest GCs have ages greater than or equal to 12.5 Gyr and formed around the time of reionization. Resolved colour-magnitude diagrams of Milky Way GCs and direct imaging of lensed proto-GCs at z ∼6 with the James Webb Space Telescope (JWST) promise further insight...
February 2018: Proceedings. Mathematical, Physical, and Engineering Sciences
Bo Wang, Wen Li, Ji-Hua Zhou, Bei Li, Wei Zhang, Wei-Hong Yang, Hong Pan, Li-Xia Wang, C Thomas Bock, Zheng-Li Shi, Yun-Zhi Zhang, Xing-Lou Yang
Hepatitis E virus (HEV) is the prototype of the family Hepeviridae and the causative agent of common acute viral hepatitis. Genetically diverse HEV-related viruses have been detected in a variety of mammals and some of them may have zoonotic potential. In this study, we tested 278 specimens collected from seven wild small mammal species in Yunnan province, China, for the presence and prevalence of orthohepevirus by broad-spectrum reverse transcription (RT)-PCR. HEV-related sequences were detected in two rodent species, including Chevrier's field mouse (Apodemus chevrieri, family Muridae) and Père David's vole (Eothenomys melanogaster, family Cricetidae), with the infection rates of 29...
March 2, 2018: Virologica Sinica
Ulrike Böhme, Thomas D Otto, James Cotton, Sascha Steinbiss, Mandy Sanders, Samuel O Oyola, Antoine Nicot, Sylvain Gandon, Kailash P Patra, Colin Herd, Ellen Bushell, Katarzyna K Modrzynska, Oliver Billker, Joseph M Vinetz, Ana Rivero, Chris I Newbold, Matthew Berriman
Avian malaria parasites are prevalent around the world, and infect a wide diversity of bird species. Here we report the sequencing and analysis of high quality draft genome sequences for two avian malaria species, Plasmodium relictum and Plasmodium gallinaceum We identify 50 genes that are specific to avian malaria, located in an otherwise conserved core of the genome that shares gene synteny with all other sequenced malaria genomes. Phylogenetic analysis suggests that the avian malaria species form an outgroup to the mammalian Plasmodium species and using amino acid divergence between species, we estimate the avian and mammalian-infective lineages diverged in the order of 10 million years ago...
March 2, 2018: Genome Research
Sebastian Lequime, Vaea Richard, Van-Mai Cao-Lormeau, Louis Lambrechts
Like other pathogens with high mutation and replication rates, within-host dengue virus (DENV) populations evolve during infection of their main mosquito vector, Aedes aegypti . Within-host DENV evolution during transmission provides opportunities for adaptation and emergence of novel virus variants. Recent studies of DENV genetic diversity failed to detect convergent evolution of adaptive mutations in mosquito tissues such as midgut and salivary glands, suggesting that convergent positive selection is not a major driver of within-host DENV evolution in the vector...
July 2017: Virus Evolution
Jing-Wen Meng, Dun-Chun He, Wen Zhu, Li-Na Yang, E-Jiao Wu, Jia-Hui Xie, Li-Ping Shang, Jiasui Zhan
Metapopulation structure generated by recurrent extinctions and recolonizations plays an important role in the evolution of species but is rarely considered in agricultural systems. In this study, generation and mechanism of metapopulation structure were investigated by microsatellite assaying 725 isolates of Alternaria alternata sampled from potato hosts at 16 locations across China. We found a single major cluster, no isolate-geography associations and no bottlenecks in the A. alternata isolates, suggesting a metapopulation genetic structure of the pathogen...
2018: Frontiers in Plant Science
Philippe Louâpre, Cécile Le Lann, Thierry Hance
Insect parasitoids developing inside hosts face a true challenge: hosts are scattered in the field and their localization and selection require the use of complex and sometime confusing information. It was assumed for a long time that small-brained organisms like parasitoids have evolved simple and efficient behavioral mechanisms, leading them to be adapted to a given ecological situation, e.g. the spatial distribution of hosts in the habitat. However, hosts are not static and their distribution may also vary through generations and within the life of parasitoid individuals...
February 28, 2018: Insect Science
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