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Genetic evolution

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https://www.readbyqxmd.com/read/28432950/effects-of-chlortetracycline-and-copper-on-tetracyclines-and-copper-resistance-genes-and-microbial-community-during-swine-manure-anaerobic-digestion
#1
Rui Wang, Meixue Chen, Feng Feng, Junya Zhang, Qianwen Sui, Juan Tong, Yuansong Wei, Dongbin Wei
As antibiotic and heavy metals are over used in the livestock industry, animal manure is a reservoir of antibiotic resistance genes (ARGs). Anaerobic digestion has been reported to have the potential to reduce ARGs. However, few studies investigated whether reduction of ARGs would be affected by different external pressures including antibiotics and heavy metals during anaerobic digestion. The purpose of this study was thus to investigate effects of both chlortetracycline (CTC) and Cu on reduction of ARGs, heavy metal resistance genes (HMRGs) and mobile genetic elements (MGEs) during the swine manure anaerobic digestion...
March 25, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28432831/oncopeltus-fasciatus-as-an-evo-devo-research-organism
#2
REVIEW
Ariel D Chipman
The large milkweed bug Oncopeltus fasciatus was one of the main study insects for a range of biological questions throughout much of the 20(th) century. Its importance waned with the introduction of Drosophila melanogaster as a genetic model organism. The evo-devo revolution of the turn of the century re-introduced Oncopeltus into the scientific community, and it has proved increasingly useful, mostly within a comparative context for evolution driven research. The last few years have seen a number of significant contributions to our understanding of the evolution of developmental processes in insects, and in arthropods in general, arise from work on Oncopeltus...
April 22, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28432816/rhodnius-prolixus-from-classical-physiology-to-modern-developmental-biology
#3
REVIEW
Rodrigo Nunes-da-Fonseca, Mateus Berni, Vitória Tobias-Dos-Santos, Attilio Pane, Helena Marcolla Araujo
The hemiptera Rhodnius prolixus is a blood-feeding insect and a primary vector of Trypanosoma cruzi, the etiological agent of the Chagas disease. Over the past century, Rhodnius has been the subject of intense investigations, which have contributed to unveil important aspects of metabolism and physiology in insects. Recent technological innovations are helping dissect the genetic and molecular underpinnings of Rhodnius embryogenesis and organogenesis, thus fostering the use of this important species in the fields of developmental and evolutionary biology...
April 22, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28432324/optimization-of-amino-acid-replacement-costs-by-mutational-pressure-in-bacterial-genomes
#4
Paweł Błażej, Dorota Mackiewicz, Małgorzata Grabińska, Małgorzata Wnętrzak, Paweł Mackiewicz
Mutations are considered a spontaneous and random process, which is important component of evolution because it generates genetic variation. On the other hand, mutations are deleterious leading to non-functional genes and energetically costly repairs. Therefore, one can expect that the mutational pressure is optimized to simultaneously generate genetic diversity and preserve genetic information. To check if empirical mutational pressures are optimized in these ways, we compared matrices of nucleotide mutation rates derived from bacterial genomes with their best possible alternatives that minimized or maximized costs of amino acid replacements associated with differences in their physicochemical properties (e...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432093/diversity-of-integrative-and-conjugative-elements-of-streptococcus-salivarius-and-their-intra-and-interspecies-transfer
#5
Narimane Dahmane, Virginie Libante, Florence Charron-Bourgoin, Eric Guédon, Gérard Guédon, Nathalie Leblond-Bourget, Sophie Payot
Integrative and Conjugative Elements (ICEs) are widespread chromosomal mobile genetic elements, which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3' end of fda, rpsI or rpmG genes) with the conjugation module of the ICESt3 subfamily...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28431281/dengue-virus-replicates-and-accumulates-in-aedes-aegypti-salivary-glands
#6
Vincent Raquin, Louis Lambrechts
Dengue virus (DENV) is an RNA virus transmitted among humans by mosquito vectors, mainly Aedes aegypti. DENV transmission requires viral dissemination from the mosquito midgut to the salivary glands. During this process the virus undergoes several population bottlenecks, which are stochastic reductions in population size that restrict intra-host viral genetic diversity and limit the efficiency of natural selection. Despite the implications for virus transmission and evolution, DENV replication in salivary glands has not been directly demonstrated...
April 18, 2017: Virology
https://www.readbyqxmd.com/read/28431132/revealing-the-biochemical-and-genetic-basis-of-colour-variation-in-a-polymorphic-lizard
#7
Claire A McLean, Adrian Lutz, Katrina J Rankin, Devi Stuart-Fox, Adnan Moussalli
Determining the mechanistic and genetic basis of animal coloration is essential to understand the costs and constraints on colour production, and the evolution and maintenance of phenotypic variation. However, genes underlying structural colour and widespread pigment classes apart from melanin remain largely uncharacterised, in part due to restricted taxonomic focus. We combined liquid chromatography-mass spectrometry and RNA-seq gene expression analyses to characterise the pigments and genes associated with skin colour in the polymorphic lizard, Ctenophorus decresii...
April 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28431021/patterns-of-genome-wide-diversity-and-population-structure-in-the-drosophila-athabasca-species-complex
#8
Karen M Wong Miller, Ryan R Bracewell, Michael B Eisen, Doris Bachtrog
The Drosophila athabasca species complex contains three recently diverged, prezygotically isolated semispecies (Western-Northern, Eastern-A, and Eastern-B) that are distributed across North America and share zones of sympatry. Inferences based on a handful of loci suggest that this complex might be an ideal system for studying the genetics of incipient speciation and the evolution of prezygotic isolating mechanisms, but patterns of differentiation have not been characterized systematically. Here, we assembled a draft genome for D...
April 14, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28430166/-french-phage-network-second-meeting-report
#9
Clara Torres-Barceló, Oliver Kaltz, Rémy Froissart, Sylvain Gandon, Nicolas Ginet, Mireille Ansaldi
The study of bacteriophages (viruses of bacteria) includes a variety of approaches, such as structural biology, genetics, ecology, and evolution, with increasingly important implications for therapeutic and industrial uses. Researchers working with phages in France have recently established a network to facilitate the exchange on complementary approaches, but also to engage new collaborations. Here, we provide a summary of the topics presented during the second meeting of the French Phage Network that took place in Marseille in November 2016...
April 21, 2017: Viruses
https://www.readbyqxmd.com/read/28430100/discovery-of-african-bat-polyomaviruses-and-infrequent-recombination-in-the-large-t-antigen-in-the-polyomaviridae
#10
Michael Carr, Gabriel Gonzalez, Michihito Sasaki, Kimihito Ito, Akihiro Ishii, Bernard M Hang'ombe, Aaron S Mweene, Yasuko Orba, Hirofumi Sawa
Bat species represent natural reservoirs for a number of high-consequence human pathogens. The present study investigated the diversity of polyomaviruses (PyVs) in Zambian insectivorous and fruit bat species. We describe the complete genomes from four newly proposed African bat PyV species employing the recently recommended criteria provided by the Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses. A comprehensive phylogenetic and recombination analysis was performed to determine genetic relationships and the distribution of recombination events in PyV from mammalian and avian species...
April 22, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28429828/genomic-clustering-of-adaptive-loci-during-parallel-evolution-of-an-australian-wildflower
#11
Federico Roda, Greg M Walter, Rick Nipper, Daniel Ortiz-Barrientos
The buildup of the phenotypic differences that distinguish species has long intrigued biologists. These differences are often inherited as stable polymorphisms that allow the co-segregation of adaptive variation within species, and facilitate the differentiation of complex phenotypes between species. It has been suggested that the clustering of adaptive loci could facilitate this process but evidence is still scarce. Here we used QTL analysis to study the genetic basis of phenotypic differentiation between coastal populations of the Australian wildflower Senecio lautus...
April 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28429731/the-evolutionary-life-cycle-of-the-polysaccharide-biosynthetic-gene-cluster-based-on-the-sphingomonadaceae
#12
Mengmeng Wu, Haidong Huang, Guoqiang Li, Yi Ren, Zhong Shi, Xiaoyan Li, Xiaohui Dai, Ge Gao, Mengnan Ren, Ting Ma
Although clustering of genes from the same metabolic pathway is a widespread phenomenon, the evolution of the polysaccharide biosynthetic gene cluster remains poorly understood. To determine the evolution of this pathway, we identified a scattered production pathway of the polysaccharide sanxan by Sphingomonas sanxanigenens NX02, and compared the distribution of genes between sphingan-producing and other Sphingomonadaceae strains. This allowed us to determine how the scattered sanxan pathway developed, and how the polysaccharide gene cluster evolved...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429724/clonal-evolution-in-myelodysplastic-syndromes
#13
Pedro da Silva-Coelho, Leonie I Kroeze, Kenichi Yoshida, Theresia N Koorenhof-Scheele, Ruth Knops, Louis T van de Locht, Aniek O de Graaf, Marion Massop, Sarah Sandmann, Martin Dugas, Marian J Stevens-Kroef, Jaroslav Cermak, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Theo de Witte, Nicole M A Blijlevens, Petra Muus, Gerwin Huls, Bert A van der Reijden, Seishi Ogawa, Joop H Jansen
Cancer development is a dynamic process during which the successive accumulation of mutations results in cells with increasingly malignant characteristics. Here, we show the clonal evolution pattern in myelodysplastic syndrome (MDS) patients receiving supportive care, with or without lenalidomide (follow-up 2.5-11 years). Whole-exome and targeted deep sequencing at multiple time points during the disease course reveals that both linear and branched evolutionary patterns occur with and without disease-modifying treatment...
April 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28428867/adaptative-evolution-of-the-vkorc1-gene-in-mus-musculus-domesticus-is-influenced-by-the-selective-pressure-of-anticoagulant-rodenticides
#14
Joffrey Goulois, Véronique Lambert, Lionel Legros, Etienne Benoit, Virginie Lattard
Anticoagulant rodenticides are commonly used to control rodent pests worldwide. They specifically inhibit the vitamin K epoxide reductase (VKORC1), which is an enzyme encoded by the Vkorc1 gene, involved in the recycling of vitamin K. Therefore, they prevent blood clotting. Numerous mutations of Vkorc1 gene were reported in rodents, and some are involved in the resistant to rodenticides phenotype. Two hundred and sixty-six mice tails were received from 65 different locations in France. Coding sequences of Vkorc1 gene were sequenced in order to detect mutations...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28428852/stoichiometric-traits-of-stickleback-effects-of-genetic-background-rearing-environment-and-ontogeny
#15
Miguel Costa Leal, Rebecca J Best, Dan Durston, Rana W El-Sabaawi, Blake Matthews
Phenotypes can both evolve in response to, and affect, ecosystem change, but few examples of diverging ecosystem-effect traits have been investigated. Bony armor traits of fish are good candidates for this because they evolve rapidly in some freshwater fish populations, and bone is phosphorus rich and likely to affect nutrient recycling in aquatic ecosystems. Here, we explore how ontogeny, rearing environment, and bone allocation among body parts affect the stoichiometric phenotype (i.e., stoichiometric composition of bodies and excretion) of threespine stickleback...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28428851/screening-mitochondrial-dna-sequence-variation-as-an-alternative-method-for-tracking-established-and-outbreak-populations-of-queensland-fruit-fly-at-the-species-southern-range-limit
#16
Mark J Blacket, Mali B Malipatil, Linda Semeraro, Peter S Gillespie, Bernie C Dominiak
Understanding the relationship between incursions of insect pests and established populations is critical to implementing effective control. Studies of genetic variation can provide powerful tools to examine potential invasion pathways and longevity of individual pest outbreaks. The major fruit fly pest in eastern Australia, Queensland fruit fly Bactrocera tryoni (Froggatt), has been subject to significant long-term quarantine and population reduction control measures in the major horticulture production areas of southeastern Australia, at the species southern range limit...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28428842/incipient-ecological-speciation-between-successional-varieties-of-a-dominant-tree-involves-intrinsic-postzygotic-isolating-barriers
#17
Elizabeth A Stacy, Bhama Paritosh, Melissa A Johnson, Donald K Price
Whereas disruptive selection imposed by heterogeneous environments can lead to the evolution of extrinsic isolating barriers between diverging populations, the evolution of intrinsic postzygotic barriers through divergent selection is less certain. Long-lived species such as trees may be especially slow to evolve intrinsic isolating barriers. We examined postpollination reproductive isolating barriers below the species boundary, in an ephemeral hybrid zone between two successional varieties of the landscape-dominant Hawaiian tree, Metrosideros polymorpha, on volcanically active Hawai'i Island...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28428775/genomics-reveals-a-unique-clone-of-burkholderia-cenocepacia-harboring-an-actively-excising-novel-genomic-island
#18
Prashant P Patil, Swapna Mali, Samriti Midha, Vikas Gautam, Lona Dash, Sunil Kumar, Jayanthi Shastri, Lipika Singhal, Prabhu B Patil
Burkholderia cenocepacia is a clinically dominant form among the other virulent species of Burkholderia cepacia complex (Bcc). In the present study, we sequenced and analyzed the genomes of seven nosocomial Bcc isolates, five of which were isolated from the bloodstream infections and two isolates were recovered from the hospital setting during the surveillance. Genome-based species identification of the Bcc isolates using a type strain explicitly identified the species as B. cenocepacia. Moreover, single nucleotide polymorphism analysis revealed that the six isolates were clonal and phylogenetically distinct from the other B...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28427910/stochasticity-of-gene-expression-as-a-motor-of-epigenetics-in-bacteria-from-individual-to-collective-behavior
#19
REVIEW
Stéphanie Bury-Moné, Bianca Sclavi
Measuring gene expression at the single cell and single molecule level has recently made possible the quantitative measurement of stochasticity of gene expression. This enables identification of the probable sources and roles of noise. Stochastic gene expression can result in bacterial population heterogeneity, offering specific advantages for fitness and survival in various environments. This trait is therefore selected during the evolution of the species, and is consequently regulated by specific genetic network architecture...
April 18, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28427330/pan-genome-and-crispr-analyses-of-the-bacterial-fish-pathogen-moritella-viscosa
#20
Christian Karlsen, Erik Hjerde, Terje Klemetsen, Nils Peder Willassen
BACKGROUND: Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elements (MGEs) is a major driving force of bacterial diversification. To gain insight into genomic traits that could affect sublineage evolution within this bacterium we examined the genome sequences of twelve M...
April 20, 2017: BMC Genomics
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