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https://www.readbyqxmd.com/read/28432093/diversity-of-integrative-and-conjugative-elements-of-streptococcus-salivarius-and-their-intra-and-interspecies-transfer
#1
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/28426805/evidence-of-horizontal-gene-transfer-by-transposase-gene-analyses-in-fervidobacterium-species
#2
Alba Cuecas, Wirojne Kanoksilapatham, Juan M Gonzalez
Horizontal Gene Transfer (HGT) plays an important role in the physiology and evolution of microorganisms above all thermophilic prokaryotes. Some members of the Phylum Thermotogae (i.e., Thermotoga spp.) have been reported to present genomes constituted by a mosaic of genes from a variety of origins. This study presents a novel approach to search on the potential plasticity of Fervidobacterium genomes using putative transposase-encoding genes as the target of analysis. Transposases are key proteins involved in genomic DNA rearrangements...
2017: PloS One
https://www.readbyqxmd.com/read/28424777/influence-of-cellular-composition-and-exogenous-activation-on-growth-factor-and-cytokine-concentrations-in-canine-platelet-rich-plasmas
#3
Samuel P Franklin, Kate E Birdwhistell, Alena Strelchik, Bridget C Garner, Benjamin M Brainard
OBJECTIVE: The purposes of this study were to (1) evaluate correlations among platelet, leukocyte, growth factor, and cytokine concentrations in canine platelet-rich plasmas (PRPs) produced from five different canine PRP-concentrating systems and (2) compare the effects of different activation protocols on platelet activation and growth factor release from one of these PRPs. METHODS: PRP was made using blood from 15 dogs and each of 5 different PRP systems in a cross-over design...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/28412524/antimicrobial-resistance-and-genetic-diversity-of-the-sxt-element-in-vibrio-cholerae-from-clinical-and-environmental-water-samples-in-northeastern-thailand
#4
Wanida Mala, Kiatichai Faksri, Kittipan Samerpitak, Umaporn Yordpratum, Wanlop Kaewkes, Unchalee Tattawasart, Chariya Chomvarin
Multidrug resistance in V. cholerae has been increasing around the world including northeastern Thailand. The aquatic environment is a reservoir of V. cholerae and might be an important source of resistant strains. The aims of this study were to investigate the phylogenetic relationships of intSXT gene sequences from 31 clinical and 14 environmental V. cholerae O1 and non-O1/non-O139 isolates and 11 sequences amplified directly from environmental water samples. We also amplified class 1 integrons, the SXT elements (targeting the intSXT gene) and antimicrobial resistance genes directly from water samples...
April 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28390108/deciphering-conjugative-plasmid-permissiveness-dynamics-in-wastewater-microbiomes
#5
Samuel Jacquiod, Asker Brejnrod, Stefan M Morberg, Waleed Abu Al-Soud, Søren J Sørensen, Leise Riber
Wastewater treatment plants (WWTPs) are designed to robustly treat polluted water. They are characterized by ceaseless flows of organic, chemical and microbial matter, followed by treatment steps before environmental release. WWTPs are hotspots of horizontal gene transfer (HGT) between bacteria via conjugative plasmids, leading to dissemination of potentially hazardous genetic material such as antimicrobial resistance genes (AMRGs). While current focus is on the threat of AMRGs spreading and environmental maintenance, conjugative plasmid transfer dynamics within and between bacterial communities still remains largely uncharted...
April 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28387730/mimilook-a-phylogenetic-workflow-for-detection-of-gene-acquisition-in-major-orthologous-groups-of-megavirales
#6
Sourabh Jain, Arup Panda, Philippe Colson, Didier Raoult, Pierre Pontarotti
With the inclusion of new members, understanding about evolutionary mechanisms and processes by which members of the proposed order, Megavirales, have evolved has become a key area of interest. The central role of gene acquisition has been shown in previous studies. However, the major drawback in gene acquisition studies is the focus on few MV families or putative families with large variation in their genetic structure. Thus, here we have tried to develop a methodology by which we can detect horizontal gene transfers (HGTs), taking into consideration orthologous groups of distantly related Megavirale families...
April 7, 2017: Viruses
https://www.readbyqxmd.com/read/28377759/comparative-genomic-analysis-reveals-organization-function-and-evolution-of-ars-genes-in-pantoea-spp
#7
Liying Wang, Jin Wang, Chuanyong Jing
Numerous genes are involved in various strategies to resist toxic arsenic (As). However, the As resistance strategy in genus Pantoea is poorly understood. In this study, a comparative genome analysis of 23 Pantoea genomes was conducted. Two vertical genetic arsC-like genes without any contribution to As resistance were found to exist in the 23 Pantoea strains. Besides the two arsC-like genes, As resistance gene clusters arsRBC or arsRBCH were found in 15 Pantoea genomes. These ars clusters were found to be acquired by horizontal gene transfer (HGT) from sources related to Franconibacter helveticus, Serratia marcescens, and Citrobacter freundii...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28376762/widespread-of-horizontal-gene-transfer-in-the-human-genome
#8
Wenze Huang, Lillian Tsai, Yulong Li, Nan Hua, Chen Sun, Chaochun Wei
BACKGROUND: A fundamental concept in biology is that heritable material is passed from parents to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic materials between different species. Horizontal gene transfer has been found prevalent in prokaryotes but very rare in eukaryote. In this paper, we investigate horizontal gene transfer in the human genome. RESULTS: From the pair-wise alignments between human genome and 53 vertebrate genomes, 1,467 human genome regions (2...
April 4, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28362724/gene-mobility-promotes-the-spread-of-resistance-in-bacterial-populations
#9
Cagla Stevenson, James Pj Hall, Ellie Harrison, A Jamie Wood, Michael A Brockhurst
Theory predicts that horizontal gene transfer (HGT) expands the selective conditions under which genes spread in bacterial populations. Whereas vertically inherited genes can only spread by positively selected clonal expansion, mobile genetic elements can drive fixation of genes by infectious HGT. We tested this using populations of Pseudomonas fluorescens and the conjugative mercury resistance (Hg(R)) plasmid pQBR57. HGT expanded the selective conditions allowing the spread of Hg(R): Chromosomal Hg(R) only increased in frequency under positive selection, whereas plasmid-encoded Hg(R) reached fixation with or without positive selection...
March 31, 2017: ISME Journal
https://www.readbyqxmd.com/read/28362383/methodology-for-the-study-of-horizontal-gene-transfer-in-staphylococcus-aureus
#10
Fabio Cafini, Nguyen Thi Le Thuy, Federico Román, José Prieto, Sarah Dubrac, Tarek Msadek, Kazuya Morikawa
One important feature of the major opportunistic human pathogen Staphylococcus aureus is its extraordinary ability to rapidly acquire resistance to antibiotics. Genomic studies reveal that S. aureus carries many virulence and resistance genes located in mobile genetic elements, suggesting that horizontal gene transfer (HGT) plays a critical role in S. aureus evolution. However, a full and detailed description of the methodology used to study HGT in S. aureus is still lacking, especially regarding natural transformation, which has been recently reported in this bacterium...
March 10, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28344366/mercury-in-feathers-and-blood-of-gulls-from-the-southern-baltic-coast-poland
#11
Emilia Szumiło-Pilarska, Lucyna Falkowska, Agnieszka Grajewska, Włodzimierz Meissner
Gulls were assessed as sentinels of contamination in the coastal zone of the Southern Baltic, research material being obtained from dead birds collected on Polish beaches and near fishing ports in 2009-2012. In feathers and blood of four gull species: herring gull (Larus argentatus), common gull (Larus canus), black-headed gull (Chroicocephalus ridibundus), and great black-backed gull (Larus marinus), concentration of total mercury (HgT) was assayed, taking into account the type of feathers, sex, and age. Stable isotopes (δ(15)N, δ(13)C) were used as tracers of trophic position in the food web...
2017: Water, Air, and Soil Pollution
https://www.readbyqxmd.com/read/28320321/evolution-of-group-i-introns-in-porifera-new-evidence-for-intron-mobility-and-implications-for-dna-barcoding
#12
Astrid Schuster, Jose V Lopez, Leontine E Becking, Michelle Kelly, Shirley A Pomponi, Gert Wörheide, Dirk Erpenbeck, Paco Cárdenas
BACKGROUND: Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II)...
March 20, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28289743/molecular-modeling-and-structural-characterization-of-a-high-glycine-tyrosine-hair-keratin-associated-protein
#13
Rakesh S Singh, Jeremy C Palmer, Paul D A Pudney, Prem K C Paul, Christian Johannessen, Pablo G Debenedetti, Janhavi Raut, Ken Lee, Massimo Noro, David Tiemessen
High glycine-tyrosine (HGT) proteins are an important constituent of the keratin associated proteins (KAPs) present in human hair. The glassy state physics of hair fibres are thought to be largely regulated by KAPs, which exist in an amorphous state and are readily affected by environmental conditions. However, there are no studies characterizing the individual KAPs. In this paper, we present the first step to fill this gap by computational modeling and experimental studies on a HGT protein, KAP8.1. In particular, we have modeled the three-dimensional structure of this 63-residue protein using homology information from an anti-freeze protein in snow flea...
March 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28283023/genome-analysis-following-a-national-increase-in-scarlet-fever-in-england-2014
#14
Victoria Chalker, Aleksey Jironkin, Juliana Coelho, Ali Al-Shahib, Steve Platt, Georgia Kapatai, Roger Daniel, Chenchal Dhami, Marisa Laranjeira, Timothy Chambers, Rebecca Guy, Theresa Lamagni, Timothy Harrison, Meera Chand, Alan P Johnson, Anthony Underwood
BACKGROUND: During a substantial elevation in scarlet fever (SF) notifications in 2014 a national genomic study was undertaken of Streptococcus pyogenes (Group A Streptococci, GAS) isolates from patients with SF with comparison to isolates from patients with invasive disease (iGAS) to test the hypotheses that the increase in SF was due to either the introduction of one or more new/emerging strains in the population in England or the transmission of a known genetic element through the population of GAS by horizontal gene transfer (HGT) resulting in infections with an increased likelihood of causing SF...
March 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28262720/foreign-plastid-sequences-in-plant-mitochondria-are-frequently-acquired-via-mitochondrion-to-mitochondrion-horizontal-transfer
#15
C L Gandini, M V Sanchez-Puerta
Angiosperm mitochondrial genomes (mtDNA) exhibit variable quantities of alien sequences. Many of these sequences are acquired by intracellular gene transfer (IGT) from the plastid. In addition, frequent events of horizontal gene transfer (HGT) between mitochondria of different species also contribute to their expanded genomes. In contrast, alien sequences are rarely found in plastid genomes. Most of the plant-to-plant HGT events involve mitochondrion-to-mitochondrion transfers. Occasionally, foreign sequences in mtDNAs are plastid-derived (MTPT), raising questions about their origin, frequency, and mechanism of transfer...
March 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28217917/a-comprehensive-phylogenetic-analysis-of-copper-transporting-p1b-atpases-from-bacteria-of-the-rhizobiales-order-uncovers-multiplicity-diversity-and-novel-taxonomic-subtypes
#16
Ciro Cubillas, Fabiola Miranda-Sánchez, Antonio González-Sánchez, José Pedro Elizalde, Pablo Vinuesa, Susana Brom, Alejandro García-de Los Santos
The ubiquitous cytoplasmic membrane copper transporting P1B-1 and P1B-3 -type ATPases pump out Cu(+) and Cu(2+) , respectively, to prevent cytoplasmic accumulation and avoid toxicity. The presence of five copies of Cu-ATPases in the symbiotic nitrogen-fixing bacteria Sinorhizobium meliloti is remarkable; it is the largest number of Cu(+) -transporters in a bacterial genome reported to date. Since the prevalence of multiple Cu-ATPases in members of the Rhizobiales order is unknown, we performed an in silico analysis to understand the occurrence, diversity and evolution of Cu(+) -ATPases in members of the Rhizobiales order...
February 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28207825/discovery-of-a-new-family-of-relaxases-in-firmicutes-bacteria
#17
Gayetri Ramachandran, Andrés Miguel-Arribas, David Abia, Praveen K Singh, Isidro Crespo, César Gago-Córdoba, Jian An Hao, Juan Roman Luque-Ortega, Carlos Alfonso, Ling J Wu, D Roeland Boer, Wilfried J J Meijer
Antibiotic resistance is a serious global problem. Antibiotic resistance genes (ARG), which are widespread in environmental bacteria, can be transferred to pathogenic bacteria via horizontal gene transfer (HGT). Gut microbiomes are especially apt for the emergence and dissemination of ARG. Conjugation is the HGT route that is predominantly responsible for the spread of ARG. Little is known about conjugative elements of Gram-positive bacteria, including those of the phylum Firmicutes, which are abundantly present in gut microbiomes...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28185083/posterior-only-surgery-with-preoperative-skeletal-traction-for-management-of-severe-scoliosis
#18
Saeedreza Mehrpour, Reza Sorbi, Reza Rezaei, Keyvan Mazda
PURPOSE: The surgical treatment of severe adolescent spinal deformities is challenging and carries substantial risks of mortality and morbidity. To mitigate this risk, surgeons have employed various methods as this study designed to evaluate the safety and effectiveness of preoperative halo-femoral or halo gravity traction (HGT) followed by posterior-only surgery in the management of severe scoliosis. METHOD: A total number of 23 patients with severe scoliosis treated by preoperative skeletal traction (halo gravity or halo femoral) followed by posterior fusion and instrumentation in one stage...
February 10, 2017: Archives of Orthopaedic and Trauma Surgery
https://www.readbyqxmd.com/read/28177699/comparing-phylogenetic-trees-by-matching-nodes-using-the-transfer-distance-between-partitions
#19
Damian Bogdanowicz, Krzysztof Giaro
Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson-Foulds distance...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28137747/2b-or-not-2b-experimental-evolution-of-functional-exogenous-sequences-in-a-plant-rna-virus
#20
Anouk Willemsen, Mark P Zwart, Silvia Ambrós, José L Carrasco, Santiago F Elena
Horizontal gene transfer (HGT) is pervasive in viruses and thought to be a key mechanism in their evolution. On the other hand, strong selective constraints against increasing genome size are an impediment for HGT, rapidly purging horizontally transferred sequences and thereby potentially hindering evolutionary innovation. Here, we explore experimentally the evolutionary fate of viruses with simulated HGT events, using the plant RNA virus Tobacco etch virus (TEV), by separately introducing two functional, exogenous sequences to its genome...
February 1, 2017: Genome Biology and Evolution
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