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https://www.readbyqxmd.com/read/28802203/disentangling-the-origins-of-virophages-and-polintons
#1
REVIEW
Samuel Campbell, Amr Aswad, Aris Katzourakis
Virophages and polintons are part of a complex system that also involves eukaryotes, giant viruses, as well as other viruses and transposable elements. Virophages are cosmopolitan, being found in environments ranging from the Amazon River to Antarctic hypersaline lakes, while polintons are found in many single celled and multicellular eukaryotes. Virophages and polintons have a shared ancestry, but their exact origins are unknown and obscured by antiquity and extensive horizontal gene transfer (HGT). Paleovirology can help disentangle the complicated gene flow between these two, as well as their giant viral and eukaryotic hosts...
August 9, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28790994/insight-into-the-origin-and-evolution-of-the-vibrio-parahaemolyticus-pandemic-strain
#2
REVIEW
Romilio T Espejo, Katherine García, Nicolas Plaza
A strain of Vibrio parahaemolyticus that emerged in 1995 caused the first known pandemic involving this species. This strain comprises clonal autochthonous ocean-dwelling bacteria whose evolution has occurred in the ocean environment. The low sequence diversity in this population enabled the discovery of information on its origin and evolution that has been hidden in bacterial clones that have evolved over a long period. Multilocus sequencing and microarray analysis, together with phylogenetic analysis, of pandemic and pre-pandemic isolates has suggested that the founder clone was an O3:K6 non-pathogenic strain that initially acquired a toxRS/new region and subsequently acquired at least seven novel genomic islands...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28769910/plasmid-transfer-in-the-ocean-a-case-study-from-the-roseobacter-group
#3
Jörn Petersen, Irene Wagner-Döbler
Plasmid mediated horizontal gene transfer (HGT) has been speculated to be one of the prime mechanisms for the adaptation of roseobacters (Rhodobacteraceae) to their ecological niches in the marine habitat. Their plasmids contain ecologically crucial functional modules of up to ∼40-kb in size, e.g., for aerobic anoxygenic photosynthesis, flagellar formation and the biosynthesis of the antibiotic tropodithietic acid. Furthermore, the widely present type four secretion system (T4SS) of roseobacters has been shown to mediate conjugation across genus barriers, albeit in the laboratory...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28753988/evolutionary-significance-of-wolbachia-to-animal-horizontal-gene-transfer-female-sex-determination-and-the-f-element-in-the-isopod-armadillidium-vulgare
#4
REVIEW
Richard Cordaux, Clément Gilbert
An increasing number of horizontal gene transfer (HGT) events from bacteria to animals have been reported in the past years, many of which involve Wolbachia bacterial endosymbionts and their invertebrate hosts. Most transferred Wolbachia genes are neutrally-evolving fossils embedded in host genomes. A remarkable case of Wolbachia HGT for which a clear evolutionary significance has been demonstrated is the "f element", a nuclear Wolbachia insert involved in female sex determination in the terrestrial isopod Armadillidium vulgare...
July 21, 2017: Genes
https://www.readbyqxmd.com/read/28749982/comparative-genomics-of-the-tardigrades-hypsibius-dujardini-and-ramazzottius-varieornatus
#5
Yuki Yoshida, Georgios Koutsovoulos, Dominik R Laetsch, Lewis Stevens, Sujai Kumar, Daiki D Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru Tomita, Mark Blaxter, Kazuharu Arakawa
Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups...
July 2017: PLoS Biology
https://www.readbyqxmd.com/read/28743812/horizontal-gene-transfer-of-functional-type-vi-killing-genes-by-natural-transformation
#6
Jacob Thomas, Samit S Watve, William C Ratcliff, Brian K Hammer
Horizontal gene transfer (HGT) can have profound effects on bacterial evolution by allowing individuals to rapidly acquire adaptive traits that shape their strategies for competition. One strategy for intermicrobial antagonism often used by Proteobacteria is the genetically encoded contact-dependent type VI secretion system (T6SS), a weapon used to kill heteroclonal neighbors by direct injection of toxic effectors. Here, we experimentally demonstrate that Vibrio cholerae can acquire new T6SS effector genes via horizontal transfer and utilize them to kill neighboring cells...
July 25, 2017: MBio
https://www.readbyqxmd.com/read/28743462/bacteriophages-in-the-human-gut-our-fellow-travelers-throughout-life-and-potential-biomarkers-of-heath-or-disease
#7
REVIEW
Babak Bakhshinejad, Saeedeh Ghiasvand
The gastrointestinal (GI) tract is populated by a huge variety of viruses. Bacterial viruses (bacteriophages) constitute the largest and the most unrecognized part of virome. The total bacteriophage community of the human gut is called phageome. Phages colonize the gut from the earliest moments of life and become our fellow travelers throughout life. Phageome seems to be unique to each individual and shows a high degree of interpersonal variation. In the healthy gut, a vast majority of phages have a lysogenic lifestyle...
July 22, 2017: Virus Research
https://www.readbyqxmd.com/read/28732043/investigation-of-horizontal-gene-transfer-of-pathogenicity-islands-in-escherichia-coli-using-next-generation-sequencing
#8
Maxim Messerer, Wolfgang Fischer, Sören Schubert
Horizontal gene transfer (HGT) contributes to the evolution of bacteria. All extraintestinal pathogenic Escherichia coli (ExPEC) harbour pathogenicity islands (PAIs), however relatively little is known about the acquisition of these PAIs. Due to these islands, ExPEC have properties to colonize and invade its hosts efficiently. Even though these PAIs are known to be acquired by HGT, only very few PAIs do carry mobilization and transfer genes required for the transmission by HGT. In this study, we apply for the first time next-generation sequencing (NGS) and in silico analyses in combination with in vitro experiments to decipher the mechanisms of PAI acquisition in ExPEC...
2017: PloS One
https://www.readbyqxmd.com/read/28730931/a-reading-model-from-the-perspective-of-japanese-orthography-connectionist-approach-to-the-hypothesis-of-granularity-and-transparency
#9
Mutsuo Ijuin, Taeko N Wydell
This study presents a computer simulation model of reading in Japanese syllabic kana and morphographic kanji. The model was based on the simulation model developed by Harm and Seidenberg for reading in English. The purpose of building the current model was to verify the validity of the hypothesis of granularity and transparency (HGT) postulated by Wydell and Butterworth, focusing on the granularity dimension. The HGT was developed in order to explain the behavioral dissociation between excellent reading skills in Japanese and poor reading skills in English of an English-Japanese bilingual individual as well as the relatively low incidence of developmental dyslexia in Japan...
July 1, 2017: Journal of Learning Disabilities
https://www.readbyqxmd.com/read/28710833/effect-of-cellobiose-supplementation-on-in-vitro-fermentation-activity-and-bacterial-numbers-of-porcine-inocula
#10
S N Heinritz, E Weiss, J Seifert, R Mosenthin, S Kuß, A G Degenhardt, T J Koch
In this in vitro study, the modified Hohenheim gas test (HGT) was applied to determine fermentation activity and bacterial composition of pig's faecal microbial inoculum using different concentrations of cellobiose. Incubation procedures included normal buffered and osmotic stress conditions (elevated medium salinity). After 24 hr of fermentation, production of gas, ammonia and short-chain fatty acid (SCFA) was measured, and the gene copy numbers of total bacteria, Lactobacillus spp., Bifidobacterium spp., Roseburia spp...
July 15, 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/28706512/comparative-genomics-reveals-high-genomic-diversity-in-the-genus-photobacterium
#11
Henrique Machado, Lone Gram
Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28697390/exposure-and-risk-characterization-for-dietary-methylmercury-from-seafood-consumption-in-kuwait
#12
Brian Laird, Hing Man Chan, Kurunthachalam Kannan, Adnan Husain, Hanan Al-Amiri, Basma Dashti, Anwar Sultan, Amani Al-Othman, Faten Al-Mutawa
Seafood is an important source of essential nutrients; however, it can also confer health risks from methylmercury (MeHg). In this paper, we evaluate the levels of potential methylmercury exposure among Kuwaiti seafood consumers in order to support the development of dietary recommendations for fish consumption in Kuwait. Total mercury (HgT) concentration for most of the studied fish and shellfish species were on average below the 0.5μgg(-1) Codex guideline. The notable exception to this was Hamoor (Epinephelus coioides), which averaged 1...
July 8, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28696284/caffeine-induces-gastric-acid-secretion-via-bitter-taste-signaling-in-gastric-parietal-cells
#13
Kathrin Ingrid Liszt, Jakob Peter Ley, Barbara Lieder, Maik Behrens, Verena Stöger, Angelika Reiner, Christina Maria Hochkogler, Elke Köck, Alessandro Marchiori, Joachim Hans, Sabine Widder, Gerhard Krammer, Gareth John Sanger, Mark Manuel Somoza, Wolfgang Meyerhof, Veronika Somoza
Caffeine, generally known as a stimulant of gastric acid secretion (GAS), is a bitter-tasting compound that activates several taste type 2 bitter receptors (TAS2Rs). TAS2Rs are expressed in the mouth and in several extraoral sites, e.g., in the gastrointestinal tract, in which their functional role still needs to be clarified. We hypothesized that caffeine evokes effects on GAS by activation of oral and gastric TAS2Rs and demonstrate that caffeine, when administered encapsulated, stimulates GAS, whereas oral administration of a caffeine solution delays GAS in healthy human subjects...
July 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28672237/long-term-variation-in-concentrations-and-mass-loads-in-a-semi-arid-watershed-influenced-by-historic-mercury-mining-and-urban-pollutant-sources
#14
Lester J McKee, Autumn Bonnema, Nicole David, Jay A Davis, Amy Franz, Richard Grace, Ben K Greenfield, Alicia N Gilbreath, Cristina Grosso, Wesley A Heim, Jennifer A Hunt, Jon E Leatherbarrow, Sarah Lowe, Sarah A Pearce, John R M Ross, Donald Yee
Urban watersheds are significantly anthropogenically-altered landscapes. Most previous studies cover relatively short periods, without addressing concentrations, loads, and yields in relation to annual climate fluctuations, and datasets on Ag, Se, PBDEs, and PCDD/Fs are rare. Intensive storm-focused sampling and continuous turbidity monitoring were employed to quantify pollution at two locations in the Guadalupe River (California, USA). At a downstream location, we determined loads of suspended sediment (SS) for 14yrs...
June 30, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28665176/does-acinetobacter-baumannii-serve-as-a-source-for-blandm-dissemination-into-enterobacteriaceae-in-hospitalized-patients
#15
Amos Adler, Rivka Glick, Ziv Lifshitz, Yehuda Carmeli
The goal was to study the possibility that Acinetobacter baumannii serve as an epidemiologically significant source for transmission of the blaNDM gene to Enterobacteriaceae by horizontal gene transfer (HGT) in hospitalized patients. The study was done at the Tel-Aviv Sourasky Medical Center from December 2014 until August 2015. Clinical and surveillance rectal cultures were collected as per hospital policies and were analyzed for the presence of New Delhi metallo-beta-lactamase-producing Enterobacteriaceae (NDME) and A...
June 30, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28659179/coping-with-living-in-the-soil-the-genome-of-the-parthenogenetic-springtail-folsomia-candida
#16
Anna Faddeeva-Vakhrusheva, Ken Kraaijeveld, Martijn F L Derks, Seyed Yahya Anvar, Valeria Agamennone, Wouter Suring, Andries A Kampfraath, Jacintha Ellers, Giang Le Ngoc, Cornelis A M van Gestel, Janine Mariën, Sandra Smit, Nico M van Straalen, Dick Roelofs
BACKGROUND: Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of Wolbachia, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle. RESULTS: We applied Pacific Bioscience sequencing and assembly to generate a reference genome for F...
June 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28644126/extensive-horizontal-gene-transfer-in-cheese-associated-bacteria
#17
Kevin S Bonham, Benjamin E Wolfe, Rachel J Dutton
Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes...
June 23, 2017: ELife
https://www.readbyqxmd.com/read/28621762/the-landscape-of-the-emergence-of-life
#18
Sohan Jheeta
This paper reports on the various nuances of the origins of life on Earth and highlights the latest findings in that arena as reported at the Network of Researchers on Horizontal Gene Transfer and the Last Universal Common Ancestor (NoR HGT and LUCA) which was held from the 3-4th November 2016 at the Open University, UK. Although the answers to the question of the origin of life on Earth will not be fathomable anytime soon, a wide variety of subject matter was able to be covered, ranging from examining what constitutes a LUCA, looking at viral connections and "from RNA to DNA", i...
June 16, 2017: Life
https://www.readbyqxmd.com/read/28600959/beyond-the-canonical-strategies-of-horizontal-gene-transfer-in-prokaryotes
#19
REVIEW
Cristina García-Aljaro, Elisenda Ballesté, Maite Muniesa
Efforts to identify and characterize strategies for horizontal gene transfer (HGT) in prokaryotes could have overlooked some mechanisms that do not entirely fit in with the canonical ones most often described (conjugation of plasmids, phage transduction and transformation). The difficulty in distinguishing the different HGT strategies could have contributed to underestimate their real extent. Here we review non classical HGT strategies: some that require mobile genetic elements (MGEs) and others independent of MGE...
June 7, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28578196/organic-compounds-stimulate-horizontal-transfer-of-antibiotic-resistance-genes-in-mixed-wastewater-treatment-systems
#20
Ya-Nan Jiao, Hong Chen, Rui-Xia Gao, Yong-Guan Zhu, Christopher Rensing
Domestic wastewater treatment plants as a reservoir of antibiotic resistance genes (ARGs) have received much attention, but the effect of dyes on the propagation of ARGs has rarely been investigated. In this study, we investigated the differences in distributions of ARGs and microbial communities using high-throughput qPCR and 16S rRNA gene sequencing, respectively, between mixed (dyeing and domestic) wastewater and domestic sewage. The relative abundance of ARGs in inflows of mixed wastewater (IW2 and IW3) was higher than that of domestic wastewater (IW1)...
October 2017: Chemosphere
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