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https://www.readbyqxmd.com/read/29134153/hgtsim-a-simulator-for-horizontal-gene-transfer-hgt-in-microbial-communities
#1
Weizhi Song, Kerrin Steensen, Torsten Thomas
The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial community. Here, we present HgtSIM, a pipeline to simulate HGT event among microbial community members with user-defined mutation levels. It was developed for testing and benchmarking pipelines for recovering HGTs from complex microbial datasets...
2017: PeerJ
https://www.readbyqxmd.com/read/29120392/impact-of-lateral-transfers-on-the-genomes-of-lepidoptera
#2
REVIEW
Jean-Michel Drezen, Thibaut Josse, Annie Bézier, Jérémy Gauthier, Elisabeth Huguet, Elisabeth Anne Herniou
Transfer of DNA sequences between species regardless of their evolutionary distance is very common in bacteria, but evidence that horizontal gene transfer (HGT) also occurs in multicellular organisms has been accumulating in the past few years. The actual extent of this phenomenon is underestimated due to frequent sequence filtering of "alien" DNA before genome assembly. However, recent studies based on genome sequencing have revealed, and experimentally verified, the presence of foreign DNA sequences in the genetic material of several species of Lepidoptera...
November 9, 2017: Genes
https://www.readbyqxmd.com/read/29112165/poxvirus-host-range-genes-and-virus-host-spectrum-a-critical-review
#3
REVIEW
Graziele Pereira Oliveira, Rodrigo Araújo Lima Rodrigues, Maurício Teixeira Lima, Betânia Paiva Drumond, Jônatas Santos Abrahão
The Poxviridae family is comprised of double-stranded DNA viruses belonging to nucleocytoplasmic large DNA viruses (NCLDV). Among the NCLDV, poxviruses exhibit the widest known host range, which is likely observed because this viral family has been more heavily investigated. However, relative to each member of the Poxviridae family, the spectrum of the host is variable, where certain viruses can infect a large range of hosts, while others are restricted to only one host species. It has been suggested that the variability in host spectrum among poxviruses is linked with the presence or absence of some host range genes...
November 7, 2017: Viruses
https://www.readbyqxmd.com/read/29091031/inter-species-population-dynamics-enhance-microbial-horizontal-gene-transfer-and-spread-of-antibiotic-resistance
#4
Robert M Cooper, Lev Tsimring, Jeff Hasty
Horizontal gene transfer (HGT) plays a major role in the spread of antibiotic resistance. Of particular concern are Acinetobacter baumannii bacteria, which recently emerged as global pathogens, with nosocomial mortality rates reaching 19-54% (Centers for Disease Control and Prevention, 2013; Joly Guillou, 2005; Talbot et al., 2006). Acinetobacter gains antibiotic resistance remarkably rapidly (Antunes et al., 2014; Joly Guillou, 2005), with multi drug-resistance (MDR) rates exceeding 60% (Antunes et al., 2014; Centers for Disease Control and Prevention, 2013)...
November 1, 2017: ELife
https://www.readbyqxmd.com/read/29061896/sampling-the-mobile-gene-pool-innovation-via-horizontal-gene-transfer-in-bacteria
#5
REVIEW
James P J Hall, Michael A Brockhurst, Ellie Harrison
In biological systems, evolutionary innovations can spread not only from parent to offspring (i.e. vertical transmission), but also 'horizontally' between individuals, who may or may not be related. Nowhere is this more apparent than in bacteria, where novel ecological traits can spread rapidly within and between species through horizontal gene transfer (HGT). This important evolutionary process is predominantly a by-product of the infectious spread of mobile genetic elements (MGEs). We will discuss the ecological conditions that favour the spread of traits by HGT, the evolutionary and social consequences of sharing traits, and how HGT is shaped by inherent conflicts between bacteria and MGEs...
December 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29055834/long-term-industrial-metal-contamination-unexpectedly-shaped-diversity-and-activity-response-of-sediment-microbiome
#6
Samuel Jacquiod, Valentine Cyriaque, Leise Riber, Waleed Abu Al-Soud, David C Gillan, Ruddy Wattiez, Søren J Sørensen
Metal contamination poses serious biotoxicity and bioaccumulation issues, affecting both abiotic conditions and biological activity in ecosystem trophic levels, especially sediments. The MetalEurop foundry released metals directly into the French river "la Deûle" during a century, contaminating sediments with a 30-fold increase compared to upstream unpolluted areas (Férin, Sensée canal). Previous metaproteogenomic work revealed phylogenetically analogous, but functionally different microbial communities between the two locations...
September 28, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/29042105/total-mercury-flux-and-offshore-transport-via-submarine-groundwater-discharge-and-coal-fired-power-plant-in-the-jiulong-river-estuary-china
#7
Jigang Wang, Qian Liu, Jinmin Chen, Hongzhe Chen, Hui Lin, Xiuwu Sun
A mass balance of total mercury (HgT, dissolved+particulate) is constructed for China's Jiulong River estuary based on measured HgT concentrations in the surface water, sediment, porewater, and groundwater for May, August, and November 2009, combined with data from the literature. The HgT mass budget results show that the dominant source (39-55%) is desulfurized seawater discharged from the Songyu coal-fired power plant. Submarine groundwater discharge (SGD)-derived HgT flux into the estuary is equivalent to 8-58% of the HgT input from the Jiulong River, which is remarkable when compared with SGD-derived HgT fluxes reported in coastal systems worldwide...
October 14, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/29030023/on-universal-coding-events-in-protein-biogenesis
#8
REVIEW
Vladimir Kubyshkin, Carlos G Acevedo-Rocha, Nediljko Budisa
The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases (aaRS) followed by matching with the acceptor units of their cognate tRNAs ("operational RNA code") and ribosomal codon-anticodon pairing of messenger RNA ("triplet code"). However, this codon-anticodon matching is possible only when protein translation machinery (translation factors, ribosome) accepts an esterified amino acid...
October 10, 2017: Bio Systems
https://www.readbyqxmd.com/read/29018197/the-chromosomal-organization-of-horizontal-gene-transfer-in-bacteria
#9
Pedro H Oliveira, Marie Touchon, Jean Cury, Eduardo P C Rocha
Bacterial adaptation is accelerated by the acquisition of novel traits through horizontal gene transfer, but the integration of these genes affects genome organization. We found that transferred genes are concentrated in only ~1% of the chromosomal regions (hotspots) in 80 bacterial species. This concentration increases with genome size and with the rate of transfer. Hotspots diversify by rapid gene turnover; their chromosomal distribution depends on local contexts (neighboring core genes), and content in mobile genetic elements...
October 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28993333/antibiotics-promote-escherichia-coli-pseudomonas-aeruginosa-conjugation-through-inhibiting-quorum-sensing
#10
Yang Lu, Jianming Zeng, Linjing Wang, Kai Lan, E Shunmei, Lina Wang, Qian Xiao, Qiang Luo, Xianzhang Huang, Bin Huang, Cha Chen
The effect of antibiotics on horizontal gene transfer is controversial and the underlying mechanism remains poorly understood. Here, using E. coli SM10λπ which carries a chromosomally integrated RP4 plasmid as donor strain, we investigated the effect of antibiotics on conjugational transfer of a mobilizable gentamicin (Gm) resistance plasmid. The results showed that exposure to gentamicin that may restrict the survival of recipient cells significantly enhanced SM10λπ-P. aeruginosa (PAO1) conjugation, which was attenuated by deficiency of lasI/rhlI, genes associated with generation of the quorum sensing signals N-acyl homoserine lactones (AHLs) in PAO1, or deletion of the AHLs receptor SdiA in SM10λπ...
October 9, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28985292/extreme-deviations-from-expected-evolutionary-rates-in-archaeal-protein-families
#11
Celine Petitjean, Kira S Makarova, Yuri I Wolf, Eugene V Koonin
Origin of new biological functions is a complex phenomenon ranging from single-nucleotide substitutions to the gain of new genes via horizontal gene transfer or duplication. Neofunctionalization and subfunctionalization of proteins is often attributed to the emergence of paralogs that are subject to relaxed purifying selection or positive selection and thus evolve at accelerated rates. Such phenomena potentially could be detected as anomalies in the phylogenies of the respective gene families. We developed a computational pipeline to search for such anomalies in 1,834 orthologous clusters of archaeal genes, focusing on lineage-specific subfamilies that significantly deviate from the expected rate of evolution...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28983932/ecological-and-evolutionary-benefits-of-temperate-phage-what-does-or-doesn-t-kill-you-makes-you-stronger
#12
REVIEW
Ellie Harrison, Michael A Brockhurst
Infection by a temperate phage can lead to death of the bacterial cell, but sometimes these phages integrate into the bacterial chromosome, offering the potential for a more long-lasting relationship to be established. Here we define three major ecological and evolutionary benefits of temperate phage for bacteria: as agents of horizontal gene transfer (HGT), as sources of genetic variation for evolutionary innovation, and as weapons of bacterial competition. We suggest that a coevolutionary perspective is required to understand the roles of temperate phages in bacterial populations...
October 6, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28983283/the-composite-259-kb-plasmid-of-martelella-mediterranea-dsm-17316-t-a-natural-replicon-with-functional-repabc-modules-from-rhodobacteraceae-and-rhizobiaceae
#13
Pascal Bartling, Henner Brinkmann, Boyke Bunk, Jörg Overmann, Markus Göker, Jörn Petersen
A multipartite genome organization with a chromosome and many extrachromosomal replicons (ECRs) is characteristic for Alphaproteobacteria. The best investigated ECRs of terrestrial rhizobia are the symbiotic plasmids for legume root nodulation and the tumor-inducing (Ti) plasmid of Agrobacterium tumefaciens. RepABC plasmids represent the most abundant alphaproteobacterial replicon type. The currently known homologous replication modules of rhizobia and Rhodobacteraceae are phylogenetically distinct. In this study, we surveyed type-strain genomes from the One Thousand Microbial Genomes (KMG-I) project and identified a roseobacter-specific RepABC-type operon in the draft genome of the marine rhizobium Martelella mediterranea DSM 17316(T)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28961181/alienness-rapid-detection-of-candidate-horizontal-gene-transfers-across-the-tree-of-life
#14
Corinne Rancurel, Ludovic Legrand, Etienne G J Danchin
Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI) protein library...
September 29, 2017: Genes
https://www.readbyqxmd.com/read/28961177/et-tu-brute-not-even-intracellular-mutualistic-symbionts-escape-horizontal-gene-transfer
#15
REVIEW
Sergio López-Madrigal, Rosario Gil
Many insect species maintain mutualistic relationships with endosymbiotic bacteria. In contrast to their free-living relatives, horizontal gene transfer (HGT) has traditionally been considered rare in long-term endosymbionts. Nevertheless, meta-omics exploration of certain symbiotic models has unveiled an increasing number of bacteria-bacteria and bacteria-host genetic transfers. The abundance and function of transferred loci suggest that HGT might play a major role in the evolution of the corresponding consortia, enhancing their adaptive value or buffering detrimental effects derived from the reductive evolution of endosymbionts' genomes...
September 29, 2017: Genes
https://www.readbyqxmd.com/read/28952781/use-of-a-cyclooxygenase-2-inhibitor-does-not-inhibit-platelet-activation-or-growth-factor-release-from-platelet-rich-plasma
#16
Hilary C Ludwig, Kate E Birdwhistell, Benjamin M Brainard, Samuel P Franklin
BACKGROUND: It remains unestablished whether use of cyclooxygenase (COX)-2 inhibitors impairs platelet activation and anabolic growth factor release from platelets in platelet-rich plasma (PRP). PURPOSE: The purpose of this study was to assess the effects of a COX-2 inhibitor on platelet activation and anabolic growth factor release from canine PRP when using a clinically applicable PRP activator and to determine whether a 3-day washout would be sufficient to abrogate any COX-2 inhibitor-related impairment on platelet function...
September 1, 2017: American Journal of Sports Medicine
https://www.readbyqxmd.com/read/28945031/-correlation-research-of-photosynthetic-characteristics-and-medicinal-materials-production-with-4-uncariae-cum-uncis
#17
Min Luo, Zhi-Qin Song, Ping-Fei Yang, Hai Liu, Zai-Gang Yang, Ming-Kai Wu
Using four Uncariae Cum Uncis materials including Uncaria sinensis (HGT), U. hirsutea (MGT), Jianhe U. rhynchophylla (JHGT) and U. rhynchophylla(GT) as the research objects, the correlations between medicinal materials' yield and photosynthetic ecophysiology-factors in the plant exuberant growth period were studied. Results showed that the Uncaria plants net photosynthetic rate (Pn) changed by unimodal curve. There was not "midday depression" phenomenon. There was a different relationship among the photosynthetic ecophysiology-factors and between photosynthetic ecophysiology-factors and medicinal materials' yield...
January 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28920507/navigating-the-structure-function-evolutionary-relationship-of-csaa-chaperone-in-archaea
#18
Archana Sharma, Shikha Rani, Manisha Goel
CsaA is a protein involved in the post-translational translocation of proteins across the cytoplasmic membrane. It is considered to be a functional homolog of SecB which participates in the Sec-dependent translocation pathway in an analogous manner. CsaA has also been reported to act as a molecular chaperone, preventing aggregation of unfolded proteins. It is essentially a prokaryotic protein which is absent in eukaryotes, but found extensively in bacteria and earlier thought to be widely present in archaea...
September 18, 2017: Critical Reviews in Microbiology
https://www.readbyqxmd.com/read/28914880/tremblaya-phenacola-pper-an-evolutionary-beta-gammaproteobacterium-collage
#19
Rosario Gil, Carlos Vargas-Chavez, Sergio López-Madrigal, Diego Santos-García, Amparo Latorre, Andrés Moya
Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium 'Candidatus Tremblaya princeps' and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, 'Candidatus Tremblaya phenacola', has been described...
September 15, 2017: ISME Journal
https://www.readbyqxmd.com/read/28894459/a-preliminary-list-of-horizontally-transferred-genes-in-prokaryotes-determined-by-tree-reconstruction-and-reconciliation
#20
Hyeonsoo Jeong, Arshan Nasir
Genome-wide global detection of genes involved in horizontal gene transfer (HGT) remains an active area of research in medical microbiology and evolutionary genomics. Utilizing the explicit evolutionary method of comparing topologies of a total of 154,805 orthologous gene trees against corresponding 16S rRNA "reference" trees, we previously detected a total of 660,894 candidate HGT events in 2,472 completely-sequenced prokaryotic genomes. Here, we report an HGT-index for each individual gene-reference tree pair reconciliation, representing the total number of detected HGT events on the gene tree divided by the total number of genomes (taxa) member of that tree...
2017: Frontiers in Genetics
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