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https://www.readbyqxmd.com/read/28732043/investigation-of-horizontal-gene-transfer-of-pathogenicity-islands-in-escherichia-coli-using-next-generation-sequencing
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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 10, 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
#7
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
#8
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
#9
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
#10
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 4,844 protein coding genes...
June 23, 2017: ELife
https://www.readbyqxmd.com/read/28621762/the-landscape-of-the-emergence-of-life
#11
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
#12
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
#13
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)...
May 27, 2017: Chemosphere
https://www.readbyqxmd.com/read/28570142/an-efficient-approach-to-explore-and-discriminate-anomalous-regions-in-bacterial-genomes-based-on-maximum-entropy
#14
Gesiele Almeida Barros-Carvalho, Marie-Anne Van Sluys, Fabricio Martins Lopes
Recently, there has been an increase in the number of whole bacterial genomes sequenced, mainly due to the advancing of next-generation sequencing technologies. In face of this, there is a need to provide new analytical alternatives that can follow this advance. Given our current knowledge about the genomic plasticity of bacteria and that those genomic regions can uncover important features about this microorganism, our goal was to develop a fast methodology based on maximum entropy (ME) to guide the researcher to regions that could be prioritized during the analysis...
June 1, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28558426/insights-into-mercury-deposition-and-spatiotemporal-variation-in-the-glacier-and-melt-water-from-the-central-tibetan-plateau
#15
Rukumesh Paudyal, Shichang Kang, Jie Huang, Lekhendra Tripathee, Qianggong Zhang, Xiaofei Li, Junming Guo, Shiwei Sun, Xiaobo He, Mika Sillanpää
Long-term monitoring of global pollutant such as Mercury (Hg) in the cryosphere is very essential for understanding its bio-geochemical cycling and impacts in the pristine environment with limited emission sources. Therefore, from May 2015 to Oct 2015, surface snow and snow-pits from Xiao Dongkemadi Glacier and glacier melt water were sampled along an elevation transect from 5410 to 5678m a.s.l. in the central Tibetan Plateau (TP). The concentration of Hg in surface snow was observed to be higher than that from other parts of the TP...
December 1, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28551392/transposable-phages-dna-reorganization-and-transfer
#16
REVIEW
Ariane Toussaint, Phoebe A Rice
Transposable bacteriophages have long been known to necessarily and randomly integrate their DNA in their host genome, where they amplify by successive rounds of replicative transposition, profoundly reorganizing that genome. As a result of such transposition, a conjugative element (plasmid or genomic island), can either become integrated in the chromosome or receive chromosome segments, which can then be transferred to new hosts by conjugation. In recent years, more and more transposable phages have been isolated or detected by sequence similarity searches in a wide range of bacteria, supporting the idea that this mode of HGT may be pervasive in natural bacterial populations...
May 25, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28548042/new-insights-into-reovirus-evolution-implications-from-a-newly-characterized-mycoreovirus
#17
Lijiang Liu, Jiasen Cheng, Yanping Fu, Huiquan Liu, Daohong Jiang, Jiatao Xie
We performed molecular cloning and complete genome sequencing of a novel mycoreovirus, Sclerotinia sclerotiorumreovirus 1 (SsReV1), isolated from an isolate of the phytopathogenic fungus Sclerotinia sclerotiorum. SsReV1 has a genome of 28 055 bp and is composed of 11 double-stranded RNA segments. With a combination of unique molecular features, virion shape and composition, and phylogenetic analysis, SsReV1 is significantly distinct from all known reoviruses and defines a novel genus in the family Reoviridae...
May 26, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28544449/metagenomic-based-impact-study-of-transgenic-grapevine-rootstock-on-its-associated-virome-and-soil-bacteriome
#18
Jean-Michel Hily, Sandrine Demanèche, Nils Poulicard, Mélanie Tannières, Samia Djennane, Monique Beuve, Emmanuelle Vigne, Gérard Demangeat, Véronique Komar, Claude Gertz, Aurélie Marmonier, Caroline Hemmer, Sophie Vigneron, Armelle Marais, Thierry Candresse, Pascal Simonet, Olivier Lemaire
For some crops, the only possible approach to gain a specific trait requires genome modification. The development of virus-resistant transgenic plants based on the pathogen-derived resistance strategy has been a success story for over three decades. However, potential risks associated with the technology, such as horizontal gene transfer (HGT) of any part of the transgene to an existing gene pool, have been raised. Here, we report no evidence of any undesirable impacts of genetically modified (GM) grapevine rootstock on its biotic environment...
May 25, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28543018/multiple-ice-binding-proteins-of-probable-prokaryotic-origin-in-an-antarctic-lake-alga-chlamydomonas-sp-ice-mdv-chlorophyceae
#19
James A Raymond, Rachael Morgan-Kiss
Ice-associated algae produce ice-binding proteins (IBPs) to prevent freezing damage. The IBPs of the three chlorophytes that have been examined so far share little similarity across species, making it likely that they were acquired by horizontal gene transfer (HGT). To clarify the importance and source of IBPs in chlorophytes, we sequenced the IBP genes of another Antarctic chlorophyte, Chlamydomonas sp. ICE-MDV (Chlamy-ICE). Genomic DNA and total RNA were sequenced and screened for known ice-associated genes...
May 19, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28541905/inferring-gene-species-assignments-in-the-presence-of-horizontal-gene-transfer
#20
Agnieszka Mykowiecka, Pawel Szczesny, Pawel Gorecki
BACKGROUND: Microbial communities from environmental samples show great diversity as bacteria quickly response to changes in their ecosystems. To assess the scenario of the actual changes, metagenomics experiments aimed at sequencing genomic DNA from such samples are performed. These new obtained sequences together with already known are used to infer phylogenetic trees assessing the taxonomic groups the species with these genes belong to. Here we propose the first approach to the gene-species assignment problem by using reconciliation with horizontal gene transfer...
May 24, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
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