keyword
MENU ▼
Read by QxMD icon Read
search

HGT

keyword
https://www.readbyqxmd.com/read/28621762/the-landscape-of-the-emergence-of-life
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
James A Raymond
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
#10
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
https://www.readbyqxmd.com/read/28541467/global-epidemiology-of-ctx-m-%C3%AE-lactamases-temporal-and-geographical-shifts-in-genotype
#11
Edward R Bevan, Annie M Jones, Peter M Hawkey
Globally, rates of ESBL-producing Enterobacteriaceae are rising. We undertook a literature review, and present the temporal trends in blaCTX-M epidemiology, showing that blaCTX-M-15 and blaCTX-M-14 have displaced other genotypes in many parts of the world. Explanations for these changes can be attributed to: (i) horizontal gene transfer (HGT) of plasmids; (ii) successful Escherichia coli clones; (iii) ESBLs in food animals; (iv) the natural environment; and (v) human migration and access to basic sanitation...
May 25, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28525714/characterization-of-bitter-compounds-via-modulation-of-proton-secretion-in-human-gastric-parietal-cells-in-culture
#12
Kathrin I Liszt, Joachim Hans, Jakob P Ley, Elke Köck, Veronika Somoza
Humans perceive bitterness via around 25 different bitter receptors. Therefore, the identification of antagonists remains a complex challenge. We previously demonstrated several bitter tasting compounds such as caffeine to induce acid secretion in the stomach and in a human gastric tumor cell line (HGT-1). Here, the results of a fluorescent-based in vitro assay using HGT-1 cells and a human sensory panel testing nine selected potential bitter modulators with or without the bitter compounds caffeine or theobromine, were compared...
May 19, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28512626/anti-restriction-protein-klcahs-promotes-dissemination-of-carbapenem-resistance
#13
Wei Liang, Yingzhou Xie, Wei Xiong, Yu Tang, Gang Li, Xiaofei Jiang, Yuan Lu
Carbapenemase-producing Klebsiella pneumoniae (KPC) has emerged and spread throughout the world. A retrospective analysis was performed on carbapenem-resistant K. pneumoniae isolated at our teaching hospital during the period 2009-2010, when the initial outbreak occurred. To determine the mechanism(s) that underlies the increased infectivity exhibited by KPC, Multilocus Sequence Typing (MLST) was conducted. A series of plasmids was also extracted, sequenced and analyzed. Concurrently, the complete sequences of blaKPC-2-harboring plasmids deposited in GenBank were summarized and aligned...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28500327/metazoan-ribosome-inactivating-protein-encoding-genes-acquired-by-horizontal-gene-transfer
#14
Walter J Lapadula, Paula L Marcet, María L Mascotti, M Virginia Sanchez-Puerta, Maximiliano Juri Ayub
Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first time in silico evidence of RIP encoding genes in metazoans, in two closely related species of insects: Aedes aegypti and Culex quinquefasciatus. Here, we have experimentally confirmed the presence of these genes in mosquitoes and attempted to unveil their evolutionary history...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28482857/horizontal-gene-transfer-is-not-a-hallmark-of-the-human-genome
#15
Steven L Salzberg
Crisp et al. recently reported that 145 human genes have been horizontally transferred from distant species. Here, I re-analyze those genes listed by Crisp et al. as having the highest certainty of having been horizontally transferred, as well as 17 further genes from the 2001 human genome article, and find little or no evidence to support claims of horizontal gene transfer (HGT).Please see related Research article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0607-3.
May 8, 2017: Genome Biology
https://www.readbyqxmd.com/read/28460114/differential-retention-of-gene-functions-in-a-secondary-metabolite-cluster
#16
Hannah Reynolds, Jason C Slot, Hege H Divon, Erik Lysøe, Robert H Proctor, Daren W Brown
In fungi, distribution of secondary metabolite (SM) gene clusters is often associated with host- or environment-specific benefits provided by SMs. In the plant pathogen Alternaria brassicicola (Dothideomycetes), the DEP cluster confers an ability to synthesize the SM depudecin, a histone deacetylase inhibitor that contributes weakly to virulence. The DEP cluster includes genes encoding enzymes, a transporter, and a transcription regulator. We investigated the distribution and evolution of the DEP cluster in 585 fungal genomes and found a wide but sporadic distribution among Dothideomycetes, Sordariomycetes, and Eurotiomycetes...
April 28, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28458094/in-and-out-contribution-of-natural-transformation-to-the-shuffling-of-large-genomic-regions
#17
REVIEW
Melanie Blokesch
Naturally competent bacteria can pull free DNA from their surroundings. This incoming DNA can serve various purposes, ranging from acting as a source of nutrients or DNA stretches for repair to the acquisition of novel genetic information. The latter process defines the natural competence for transformation as a mode of horizontal gene transfer (HGT) and led to its discovery almost a century ago. However, although it is widely accepted that natural competence can contribute to the spread of genetic material among prokaryotes, the question remains whether this mode of HGT can foster the transfer of larger DNA regions or only transfers shorter fragments, given that extracellular DNA is often heavily fragmented...
April 27, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28441577/membrane-vesicles-and-horizontal-gene-transfer-in-prokaryotes
#18
REVIEW
Sara Domingues, Kaare M Nielsen
Membrane vesicles (MVs) are released from all living cells. MVs are lumen-containing spheres of lipid-bilayers derived from the cell surface. MVs are biologically active and contain various components, including genetic material. Both chromosomal and plasmid DNA, as well as different types of RNA have been detected in MVs. Vesicle-mediated transfer of genes coding for antibiotic resistance, virulence and metabolic traits has been reported in Gram-negative and Gram-positive bacteria and in Archaea. MVs can persist over time in natural environments...
April 22, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28440015/hypertriglyceridemia-during-asparaginase-treatment-in-children-with-acute-lymphoblastic-leukemia-correlates-with-antithrombin-activity-in-adolescents
#19
Lisa Persson, Arja Harila-Saari, Ida Hed Myrberg, Mats Heyman, Anna Nilsson, Susanna Ranta
BACKGROUND: Asparaginase (ASP) is a cornerstone in the treatment of acute lymphoblastic leukemia (ALL). It is also known for its ability to cause side effects, such as allergy and pancreatitis, as well as lipid and coagulation disturbances. The most important laboratory abnormalities are hypertriglyceridemia (HTG) and low antithrombin (AT). HTG is usually considered to be transient and benign in children with ALL, whereas low AT activity predisposes to thrombosis. Studies on the incidence and significance of HTG in children with ALL are scarce, and their findings have not always been congruent...
April 25, 2017: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/28432093/diversity-of-integrative-and-conjugative-elements-of-streptococcus-salivarius-and-their-intra-and-interspecies-transfer
#20
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
keyword
keyword
69168
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"