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Within host evolution

Félix LaRoche-Johnston, Caroline Monat, Benoit Cousineau
BACKGROUND: Group II introns are catalytically active RNA and mobile retroelements present in certain eukaryotic organelles, bacteria and archaea. These ribozymes self-splice from the pre-mRNA of interrupted genes and reinsert within target DNA sequences by retrohoming and retrotransposition. Evolutionary hypotheses place these retromobile elements at the origin of over half the human genome. Nevertheless, the evolution and dissemination of group II introns was found to be quite difficult to infer...
October 20, 2016: BMC Evolutionary Biology
Martha S Hunter, Peter Asiimwe, Anna G Himler, Suzanne E Kelly
Arthropods commonly carry maternally-inherited intracellular bacterial symbionts that may profoundly influence host biology and evolution. The intracellular symbiont Rickettsia sp. nr. bellii swept rapidly into populations of the sweetpotato whitefly Bemisia tabaci in the southwestern USA. Previous laboratory experiments showed female-bias and fitness benefits were associated with Rickettsia infection, potentially explaining the high frequencies of infection observed in field populations, but the effects varied with whitefly genetic line...
October 17, 2016: Journal of Evolutionary Biology
Utsav Pandey, Andrew S Bell, Daniel W Renner, David A Kennedy, Jacob T Shreve, Chris L Cairns, Matthew J Jones, Patricia A Dunn, Andrew F Read, Moriah L Szpara
The intensification of the poultry industry over the last 60 years facilitated the evolution of increased virulence and vaccine breaks in Marek's disease virus (MDV-1). Full-genome sequences are essential for understanding why and how this evolution occurred, but what is known about genome-wide variation in MDV comes from laboratory culture. To rectify this, we developed methods for obtaining high-quality genome sequences directly from field samples without the need for sequence-based enrichment strategies prior to sequencing...
September 2016: MSphere
Pankaj Trivedi, Chanda Trivedi, Jasmine Grinyer, Ian C Anderson, Brajesh K Singh
Plant health and productivity is strongly influenced by their intimate interaction with deleterious and beneficial organisms, including microbes, and insects. Of the various plant diseases, insect-vectored diseases are of particular interest, including those caused by obligate parasites affecting plant phloem such as Candidatus (Ca.) Phytoplasma species and several species of Ca. Liberibacter. Recent studies on plant-microbe and plant-insect interactions of these pathogens have demonstrated that plant-microbe-insect interactions have far reaching consequences for the functioning and evolution of the organisms involved...
2016: Frontiers in Plant Science
Theresia E B Stradal, Sonia C P Costa
A key aspect of bacterial pathogenesis is the colonization and persistence within the host and, later on, its dissemination to new niches. During evolution, bacteria developed a myriad of virulence mechanisms to usurp the host's sophisticated defense mechanisms in order to establish their colonization niche. Elucidation of the highly dynamic and complex interactions between host and pathogens remains an important field of study. Here, we highlight the conserved manipulation of the actin cytoskeleton by some Gram-negative gastrointestinal pathogens, addressing the role of type III secreted bacterial GEFs at the different steps of pathogenesis...
October 16, 2016: Current Topics in Microbiology and Immunology
Timothy L Haskett, Jason J Terpolilli, Amanuel Bekuma, Graham W O'Hara, John T Sullivan, Penghao Wang, Clive W Ronson, Joshua P Ramsay
Integrative and conjugative elements (ICEs) are ubiquitous mobile genetic elements present as "genomic islands" within bacterial chromosomes. Symbiosis islands are ICEs that convert nonsymbiotic mesorhizobia into symbionts of legumes. Here we report the discovery of symbiosis ICEs that exist as three separate chromosomal regions when integrated in their hosts, but through recombination assemble as a single circular ICE for conjugative transfer. Whole-genome comparisons revealed exconjugants derived from nonsymbiotic mesorhizobia received three separate chromosomal regions from the donor Mesorhizobium ciceri WSM1271...
October 12, 2016: Proceedings of the National Academy of Sciences of the United States of America
Azeem Mehmood Butt, Izza Nasrullah, Raheel Qamar, Yigang Tong
The codon usage patterns of viruses reflect the evolutionary changes that allow them to optimize their survival and adapt their fitness to the external environment and, most importantly, their hosts. Here we report the genotype-specific codon usage patterns of Zika virus (ZIKV) strains from the current and previous outbreaks. Several genotype-specific and common codon usage traits were noted in the ZIKV coding sequences, indicating their independent evolutionary origins from a common ancestor. The overall influence of natural selection was more profound than that of mutation pressure, acting on a specific set of viral genes in the Asian-genotype ZIKV strains from the recent outbreak...
October 12, 2016: Emerging Microbes & Infections
Björn Pietzenuk, Catarine Markus, Hervé Gaubert, Navratan Bagwan, Aldo Merotto, Etienne Bucher, Ales Pecinka
BACKGROUND: The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. However, it remains unknown whether this is a common and potentially conserved trait and how it has evolved. RESULTS: We show that ONSEN, COPIA37, TERESTRA, and ROMANIAT5 are the major families of heat-responsive TEs in A...
October 11, 2016: Genome Biology
Christopher B Rodell, Christopher B Highley, Minna H Chen, Neville N Dusaj, Chao Wang, Lin Han, Jason A Burdick
Macromolecular interactions are used to form supramolecular assemblies, including through the interaction of guest-host chemical pairs. Microstructural heterogeneity has been observed within such physical hydrogels; yet, systematic investigation of the microstructure and its determining inputs are lacking. Herein, we investigated the hierarchical self-assembly of hyaluronic acid (HA) modified by the guest-host pair adamantane (Ad-HA, guest) and β-cyclodextrin (CD-HA, host), as well as with methacrylate groups to both tether fluorescent agents and to covalently stabilize the material structure...
September 20, 2016: Soft Matter
Kirsten M Ellegaard, Philipp Engel
Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce...
2016: Frontiers in Microbiology
Kate Rockenbach, Justin C Havird, J Grey Monroe, Deborah A Triant, Douglas R Taylor, Daniel B Sloan
Rates of sequence evolution in plastid genomes are generally low, but numerous angiosperm lineages exhibit accelerated evolutionary rates in similar subsets of plastid genes. These genes include clpP1 and accD, which encode components of the caseinolytic protease (CLP) and acetyl-coA carboxylase (ACCase) complexes, respectively. Whether these extreme and repeated accelerations in rates of plastid genome evolution result from adaptive change in proteins (i.e., positive selection) or simply a loss of functional constraint (i...
October 5, 2016: Genetics
Claire L Donald, Benjamin Brennan, Stephanie L Cumberworth, Veronica V Rezelj, Jordan J Clark, Marli T Cordeiro, Rafael Freitas de Oliveira França, Lindomar J Pena, Gavin S Wilkie, Ana Da Silva Filipe, Christopher Davis, Joseph Hughes, Margus Varjak, Martin Selinger, Luíza Zuvanov, Ania M Owsianka, Arvind H Patel, John McLauchlan, Brett D Lindenbach, Gamou Fall, Amadou A Sall, Roman Biek, Jan Rehwinkel, Esther Schnettler, Alain Kohl
BACKGROUND: The outbreak of Zika virus (ZIKV) in the Americas has transformed a previously obscure mosquito-transmitted arbovirus of the Flaviviridae family into a major public health concern. Little is currently known about the evolution and biology of ZIKV and the factors that contribute to the associated pathogenesis. Determining genomic sequences of clinical viral isolates and characterization of elements within these are an important prerequisite to advance our understanding of viral replicative processes and virus-host interactions...
October 2016: PLoS Neglected Tropical Diseases
Danielle S Kelley, Christopher W Lennon, Marlene Belfort, Olga Novikova
: Inteins are self-splicing protein elements that are mobile at the DNA level and are sporadically distributed across microbial genomes. Inteins appear to be horizontally transferred, and it has been speculated that phages may play a role in intein distribution. Our attention turns to mycobacteriophages, which infect mycobacteria, where both phage and host harbor inteins. Using bioinformatics, mycobacteriophage genomes were mined for inteins. This study reveals that these mobile elements are present across multiple mycobacteriophage clusters and are pervasive in certain genes, like the large terminase subunit TerL and a RecB-like nuclease, with the majority of intein-containing genes being phage specific...
October 4, 2016: MBio
Linlin Yang, Xu Jing, Cheng He, Zhiduo Chang, Chunying Duan
The design of artificial systems that mimic highly evolved and finely tuned natural enzymes is a promising subject of intensive research. The assembly of O-symmetric cubic structures with an Fe8 L6 formula was reported through the direct combination of a C4 -symmetric tetraphenylethylene-based ligand with a C3 -symmetric tris(bipyridine)iron node. The robust metal-organic cubes are rich in π-electron density and provide favorable interactions with planar polycyclic aromatic hydrocarbons. Within the confined space of the host, the aromatic hydrocarbons molecules are forced closer to the redox active host, and the photoinduced electron transfer (PET) is modified into a pseudo-intramolecular pathway...
October 4, 2016: Chemistry: a European Journal
Eric Robert Lucien Gordon, Quinn McFrederick, Christiane Weirauch
: The insect order Hemiptera, one of the best-studied insect lineages with respect to bacterial symbioses, still contains major branches which lack comprehensive characterization of associated bacterial symbionts. The Pyrrhocoroidea (Largidae [220 species]; Pyrrhocoridae [∼300 species]) is a clade of the hemipteran infraorder Pentatomomorpha. Studies on bacterial symbionts of this group have focused on members of Pyrrhocoridae, but recent examination of species of two genera of Largidae demonstrated divergent symbiotic complexes between these putative sister families...
September 30, 2016: Applied and Environmental Microbiology
E-Bin Gao, Youhua Huang, Degang Ning
Cyanophages, a group of viruses specifically infecting cyanobacteria, are genetically diverse and extensively abundant in water environments. As a result of selective pressure, cyanophages often acquire a range of metabolic genes from host genomes. The host-derived genes make a significant contribution to the ecological success of cyanophages. In this review, we summarize the host-derived metabolic genes, as well as their origin and roles in cyanophage evolution and important host metabolic pathways, such as the light-dependent reactions of photosynthesis, the pentose phosphate pathway, nutrient acquisition and nucleotide biosynthesis...
2016: Genes
Nicola De Maio, Chieh-Hsi Wu, Daniel J Wilson
Exploiting pathogen genomes to reconstruct transmission represents a powerful tool in the fight against infectious disease. However, their interpretation rests on a number of simplifying assumptions that regularly ignore important complexities of real data, in particular within-host evolution and non-sampled patients. Here we propose a new approach to transmission inference called SCOTTI (Structured COalescent Transmission Tree Inference). This method is based on a statistical framework that models each host as a distinct population, and transmissions between hosts as migration events...
September 2016: PLoS Computational Biology
Chao Zhong, Chun You, Ping Wei, Yi-Heng Percival Zhang
We developed a simple method (simple cloning) for subcloning DNA fragments into any location of a targeted vector without the need of restriction enzyme, ligase, exonuclease, or recombinase in Escherichia coli. This technology can be applied to common E. coli hosts (e.g., DH5α, JM109, TOP10, BL21(DE3)). The protocol includes three steps: (1) generate DNA insert and linear vector backbone by regular high-fidelity PCR, where these two DNA fragments contain 3' and 5' overlapping termini; (2) generate DNA multimers based on these two DNA fragments by using prolonged overlap extension-PCR (POE-PCR) without primers added; and (3) transform POE-PCR product to competent Escherichia coli cells directly, yielding the desired plasmid...
2017: Methods in Molecular Biology
Silvia Angeletti, Alessandra Lo Presti, Marta Giovanetti, Alba Grifoni, Massimo Amicosante, Marco Ciotti, Luiz-Carlos J Alcantara, Eleonora Cella, Massimo Ciccozzi
Zika virus (ZIKV) is an emerging Flavivirus that have recently caused an outbreak in Brazil and rapid spread in several countries. In this study, the consequences of ZIKV evolution on protein recognition by the host immune system have been analyzed. Evolutionary analysis was combined with homology modeling and T-B cells epitope predictions. Two separate clades, the African one with the Uganda sequence, as the most probable ancestor, and the second one containing all the most recent sequences from the equatorial belt were identified...
September 27, 2016: Pathogens and Global Health
Alison J Scott, Bryn Flinders, Joanna Cappell, Tao Liang, Rebecca S Pelc, Bao Tran, David P A Kilgour, Ron M A Heeren, David R Goodlett, Robert K Ernst
The discovery of novel pathogenic mechanisms engaged during bacterial infections requires the evolution of advanced techniques. Here, we evaluate the dual polarity matrix norharmane (NRM) to improve detection of bacterial lipid A (endotoxin), from host and vector tissues infected with Francisella novicida (Fn). We evaluated NRM for improved detection and characterization of a wide range of lipids in both positive and negative polarities, including lipid A and phospholipids across a range of matrix assisted laser desorption-ionization (MALDI)-coupled applications...
September 19, 2016: Pathogens and Disease
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