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Genome evolution

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https://www.readbyqxmd.com/read/28525986/the-lspc3-41i-restriction-modification-system-is-the-major-determinant-for-genetic-manipulations-of-lysinibacillus-sphaericus-c3-41
#1
Pan Fu, Yong Ge, Yiming Wu, Ni Zhao, Zhiming Yuan, Xiaomin Hu
BACKGROUND: Lysinibacillus sphaericus has been widely used in integrated mosquito control program and it is one of the minority bacterial species unable to metabolize carbohydrates. In consideration of the high genetic conservation at genomic level and difficulty of genetic horizontal transfer, it is hypothesized that effective restriction-modification (R-M) systems existed in mosquitocidal L. sphaericus. RESULTS: In this study, six type II R-M systems including LspC3-41I were predicted in L...
May 19, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28525572/crosstalk-between-vertical-and-horizontal-gene-transfer-plasmid-replication-control-by-a-conjugative-relaxase
#2
Fabián Lorenzo-Díaz, Cris Fernández-López, Rudi Lurz, Alicia Bravo, Manuel Espinosa
Horizontal gene transfer is a key process in the evolution of bacteria and also represents a source of genetic variation in eukaryotes. Among elements participating in gene transfer, thousands of small (<10 kb) mobile bacterial plasmids that replicate by the rolling circle mechanism represent a driving force in the spread of antibiotic resistances. In general, these plasmids are built as genetic modules that encode a replicase, an antibiotic-resistance determinant, and a relaxase that participates in their conjugative mobilization...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28525571/one-year-genome-evolution-of-lausannevirus-in-allopatric-versus-sympatric-conditions
#3
Linda Mueller, Claire Bertelli, Trestan Pillonel, Nicolas Salamin, Gilbert Greub
Amoeba-resisting microorganisms (ARMs) raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year...
May 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28524624/pulmonary-arterial-hypertension-progress-in-understanding-the-disease-and-prioritizing-strategies-for-drug-development
#4
REVIEW
P Ghataorhe, C J Rhodes, L Harbaum, M Attard, J Wharton, M R Wilkins
Pulmonary arterial hypertension (PAH), at one time a largely overlooked disease, is now the subject of intense study in many academic and biotech groups. The availability of new treatments has increased awareness of the condition. This in turn has driven a change in the demographics of PAH, with an increase in the mean age at diagnosis. The diagnosis of PAH in more elderly patients has highlighted the need for careful phenotyping of patients and for further studies to understand how best to manage pulmonary hypertension associated with, for example, left heart disease...
May 19, 2017: Journal of Internal Medicine
https://www.readbyqxmd.com/read/28523636/informing-materials-drugs-as-tools-for-exploring-cancer-mechanisms-and-pathways
#5
Etienne Vignola-Gagné, Peter Keating, Alberto Cambrosio
This paper builds on previous work that investigated anticancer drugs as 'informed materials', i.e., substances that undergo an informational enrichment that situates them in a dense relational web of qualifications and measurements generated by clinical experiments and clinical trials. The paper analyzes the recent transformation of anticancer drugs from 'informed' to 'informing material'. Briefly put: in the post-genomic era, anti-cancer drugs have become instruments for the production of new biological, pathological, and therapeutic insights into the underlying etiology and evolution of cancer...
June 2017: History and Philosophy of the Life Sciences
https://www.readbyqxmd.com/read/28522998/genetic-polymorphism-in-wine-yeasts-mechanisms-and-methods-for-its-detection
#6
REVIEW
José M Guillamón, Eladio Barrio
The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28522611/long-terminal-repeats-power-evolution-of-genes-and-gene-expression-programs-in-mammalian-oocytes-and-zygotes
#7
Vedran Franke, Sravya Ganesh, Rosa Karlic, Radek Malik, Josef Pasulka, Filip Horvat, Maja Kuzman, Helena Fulka, Marketa Cernohorska, Jana Urbanova, Eliska Svobodova, Jun Ma, Yutaka Suzuki, Fugaku Aoki, Richard M Schultz, Kristian Vlahovicek, Petr Svoboda
Retrotransposons are 'copy-and-paste' insertional mutagens that substantially contribute to mammalian genome content. Retrotransposons often carry long terminal repeats (LTRs) for retrovirus-like reverse transcription and integration into the genome. We report an extraordinary impact of a group of LTRs from the mammalian endogenous retrovirus-related ERVL retrotransposon class on gene expression in the germline and beyond. In mouse, we identified >800 LTRs from ORR1, MT, MT2, and MLT families, which resemble mobile gene-remodeling platforms that supply promoters and first exons...
May 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28521947/ultrabithorax-and-the-evolution-of-insect-forewing-hindwing-differentiation
#8
REVIEW
Yoshinori Tomoyasu
Decades have passed since the stunning four-winged phenotype of the Drosophila Ultrabithorax (Ubx) mutant was reported, and accumulating knowledge obtained from studies on Ubx in Drosophila has provided a framework to investigate the role of Ubx during insect wing evolution. With several new insights emerging from recent studies in non-Drosophila insects, along with the outcomes of genomic studies focused on identifying Ubx targets, it appears to be an appropriate time to revisit the Drosophila paradigm regarding insect wing development and evolution...
February 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28521939/developmental-and-evolutionary-mechanisms-shaping-butterfly-eyespots
#9
REVIEW
Patrícia Beldade, Carolina M Peralta
Butterfly eyespots are visually compelling models to study the reciprocal interactions between evolutionary and developmental processes that shape phenotypic variation. They are evolutionarily diversified, ecologically relevant, and developmentally tractable, and have made key contributions to linking genotype, development, phenotype and fitness. Advances in the availability of analytical tools (e.g. gene editing and visualization techniques) and resources (e.g. genomic and transcriptomic data) are boosting the detailed dissection of the mechanisms underlying eyespot development and evolution...
February 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28521747/insights-into-the-ancestral-organisation-of-the-mammalian-mhc-class-ii-region-from-the-genome-of-the-pteropid-bat-pteropus-alecto
#10
Justin H J Ng, Mary Tachedjian, Lin-Fa Wang, Michelle L Baker
BACKGROUND: Bats are an extremely successful group of mammals and possess a variety of unique characteristics, including their ability to co-exist with a diverse range of pathogens. The major histocompatibility complex (MHC) is the most gene dense and polymorphic region of the genome and MHC class II (MHC-II) molecules play a vital role in the presentation of antigens derived from extracellular pathogens and activation of the adaptive immune response. Characterisation of the MHC-II region of bats is crucial for understanding the evolution of the MHC and of the role of pathogens in shaping the immune system...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28521727/comparative-genomic-analysis-of-innate-immunity-reveals-novel-and-conserved-components-in-crustacean-food-crop-species
#11
Alvina G Lai, A Aziz Aboobaker
BACKGROUND: Growing global demands for crustacean food crop species have driven large investments in aquaculture research worldwide. However, large-scale production is susceptible to pathogen-mediated destruction particularly in developing economies. Thus, a thorough understanding of the immune system components of food crop species is imperative for research to combat pathogens. RESULTS: Through a comparative genomics approach utilising extant data from 55 species, we describe the innate immune system of the class Malacostraca, which includes all food crop species...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28521338/klebsiella-pneumoniae-a-major-worldwide-source-and-shuttle-for-antibiotic-resistance
#12
Shiri Navon-Venezia, Kira Kondratyeva, Alessandra Carattoli
Klebsiella pneumoniae is an important multidrug-resistant (MDR) pathogen affecting humans and a major source for hospital infections associated with high morbidity and mortality due to limited treatment options. We summarize the wide resistome of this pathogen, which encompasses plentiful chromosomal and plasmid-encoded antibiotic resistance genes (ARGs). Under antibiotic selective pressure, K. pneumoniae continuously accumulates ARGs, by de novo mutations, and via acquisition of plasmids and transferable genetic elements, leading to extremely drug resistant (XDR) strains harboring a 'super resistome'...
May 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28521055/tying-the-knot-occurrence-and-possible-significance-of-gene-fusions-in-plant-metabolism-and-beyond
#13
Jillian M Hagel, Peter J Facchini
Gene fusions have recently attracted attention especially in the field of plant specialized metabolism. The occurrence of a gene fusion, in which originally separate gene products are combined into a single polypeptide, often corresponds to the functional association of individual components within a single metabolic pathway. Examples include gene fusions implicated in benzylisoquinoline alkaloid (BIA), terpenoid, and amino acid biosynthetic pathways, in which distinct domains within a fusion catalyze consecutive, yet independent reactions...
May 18, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28521046/cellular-and-population-level-processes-influence-the-rate-accumulation-and-observed-frequency-of-inherited-and-somatic-mtdna-mutations
#14
Richard G Melvin, John William O Ballard
Mitochondria are found in all animals and have the unique feature of containing multiple copies of their own small, circular DNA genome (mtDNA). The rate and pattern of mutation accumulation in the mtDNA are influenced by molecular, cellular and population level processes. We distinguish between inherited and somatic mtDNA mutations and review evidence for the often-made assumption that mutations accumulate at a higher rate in mtDNA than in nuclear DNA (nDNA). We conclude that the whole genome mutation accumulation rate is higher for mtDNA than for nDNA but include the caveat that rates overlap considerably between the individual mtDNA- and nDNA-encoded genes...
May 1, 2017: Mutagenesis
https://www.readbyqxmd.com/read/28520797/cytogenetic-studies-on-populations-of-camponotus-rufipes-fabricius-1775-and-camponotus-renggeri-emery-1894-formicidae-formicinae
#15
Hilton Jeferson Alves Cardoso de Aguiar, Luísa Antônia Campos Barros, Danúbia Rodrigues Alves, Cléa Dos Santos Ferreira Mariano, Jacques Hubert Charles Delabie, Silvia das Graças Pompolo
Two valid ant species, Camponotus rufipes and Camponotus renggeri, have recently been the subject of a broad discussion with reference to taxa synonymization. Both species are quite common among the Neotropical myrmecofauna and share some unique traits, such as the shape of the scape and the pilosity patterns of the tibiae and scapes. A single morphological trait can help distinguish these species; however, only a combination of different approaches can enlighten our view of the complex phylogenetic relationships prevailing in the different populations of these two taxa...
2017: PloS One
https://www.readbyqxmd.com/read/28517988/the-promise-and-the-hype-of-personalised-medicine
#16
Tim Maughan
Personalised medicine is widely considered as the way of the future for medicine. However, progress in cancer, with a few outstanding exceptions, has fallen below expectations because of the challenges of tumour heterogeneity and clonal evolution. In both benign and malignant disease, diseases caused by single genetic alterations are more amenable to precision medicine approaches. However, most common diseases are caused by a complex interplay of multiple genetic and environmental factors making personalised medicine far more challenging...
April 2017: New Bioethics: a Multidisciplinary Journal of Biotechnology and the Body
https://www.readbyqxmd.com/read/28517033/high-throughput-sequencing-of-transposable-element-insertions-suggests-adaptive-evolution-of-the-invasive-asian-tiger-mosquito-towards-temperate-environments
#17
Clément Goubert, Hélène Henri, Guillaume Minard, Claire Valiente Moro, Patrick Mavingui, Cristina Vieira, Matthieu Boulesteix
Invasive species represent unique opportunities to evaluate the role of local adaptation during colonization of new environments. Among these species, the Asian tiger mosquito, Aedes albopictus, is a threatening vector of several human viral diseases, including dengue and chikungunya, and raises concerns about the Zika fever. Its broad presence in both temperate and tropical environments has been considered the reflection of great "ecological plasticity". However, no study has been conducted to assess the role of adaptive evolution in the ecological success of Ae...
May 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28516864/genomic-analysis-of-salmonella-enterica-serovar-typhimurium-dt160-associated-with-a-14-year-outbreak-new-zealand-1998-2012
#18
Samuel J Bloomfield, Jackie Benschop, Patrick J Biggs, Jonathan C Marshall, David T S Hayman, Philip E Carter, Anne C Midwinter, Alison E Mather, Nigel P French
During 1998-2012, an extended outbreak of Salmonella enterica serovar Typhimurium definitive type 160 (DT160) affected >3,000 humans and killed wild birds in New Zealand. However, the relationship between DT160 within these 2 host groups and the origin of the outbreak are unknown. Whole-genome sequencing was used to compare 109 Salmonella Typhimurium DT160 isolates from sources throughout New Zealand. We provide evidence that DT160 was introduced into New Zealand around 1997 and rapidly propagated throughout the country, becoming more genetically diverse over time...
June 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28516231/molecular-evolution-of-type-ii-mage-genes-from-ancestral-maged2-gene-and-their-phylogenetic-resolution-of-basal-mammalian-clades
#19
Marcos De Donato, Sunday O Peters, Tanveer Hussain, Hectorina Rodulfo, Bolaji N Thomas, Masroor E Babar, Ikhide G Imumorin
Type II melanoma-associated antigens (MAGE) are a subgroup of about a dozen proteins found in various locations in the genome and expressed in normal tissues, thus are not related to cancer as the type I MAGE genes. This gene family exists as a single copy in non-mammals and monotremata, but found as two copies in metatherians and occur as a diverse group in all eutherians. Our studies suggest MAGED2 as the ancestor of this subfamily and the most likely evolutionary history of eutherian type II MAGE genes is hereby proposed based on synteny conservation, phylogenetic relations, genome location, homology conservation, and the protein and gene structures...
May 17, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28515781/evolutionary-restoration-potential-evaluated-through-the-use-of-a-trait-linked-genetic-marker
#20
Travis M Apgar, Devon E Pearse, Eric P Palkovacs
Human-driven evolution can impact the ecological role and conservation value of impacted populations. Most evolutionary restoration approaches focus on manipulating gene flow, but an alternative approach is to manipulate the selection regime to restore historical or desired trait values. Here we examined the potential utility of this approach to restore anadromous migratory behavior in coastal California steelhead trout (Oncorhynchus mykiss) populations. We evaluated the effects of natural and anthropogenic environmental variables on the observed frequency of alleles at a genomic marker tightly associated with migratory behavior across 39 steelhead populations from across California, USA...
June 2017: Evolutionary Applications
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