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Mobile genetic element

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https://www.readbyqxmd.com/read/27933075/a-non-specific-setaria-italica-lipid-transfer-protein-gene-plays-a-critical-role-under-abiotic-stress
#1
Yanlin Pan, Jianrui Li, Licong Jiao, Cong Li, Dengyun Zhu, Jingjuan Yu
Lipid transfer proteins (LTPs) are a class of cysteine-rich soluble proteins having small molecular weights. LTPs participate in flower and seed development, cuticular wax deposition, also play important roles in pathogen and abiotic stress responses. A non-specific LTP gene (SiLTP) was isolated from a foxtail millet (Setaria italica) suppression subtractive hybridization library enriched for differentially expressed genes after abiotic stress treatments. A semi-quantitative reverse transcriptase PCR analysis showed that SiLTP was expressed in all foxtail millet tissues...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27933056/characterization-of-three-novel-sxt-r391-integrating-conjugative-elements-icemfuind1a-and-icemfuind1b-and-icemprchn1-identified-in-the-genomes-of-marinomonas-fungiae-jcm-18476-t-and-marinomonas-profundimaris-strain-d104
#2
Jhasketan Badhai, Subrata K Das
The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476(T) (ICEMfuInd1a and ICEMfuInd1b) and in Marinomonas profundimaris strain D104 (ICEMprChn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27932039/anaerobic-digestion-of-nitrogen-rich-poultry-manure-impact-of-thermophilic-biogas-process-on-metal-release-and-microbial-resistances
#3
Reshma Anjum, Elisabeth Grohmann, Niclas Krakat
Poultry manure is a nitrogen rich fertilizer, which is usually recycled and spread on agricultural fields. Due to its high nutrient content, chicken manure is considered to be one of the most valuable animal wastes as organic fertilizer. However, when chicken litter is applied in its native form, concerns are raised as such fertilizers also include high amounts of antibiotic resistant pathogenic Bacteria and heavy metals. We studied the impact of an anaerobic thermophilic digestion process on poultry manure...
December 5, 2016: Chemosphere
https://www.readbyqxmd.com/read/27923922/mechanisms-of-evolution-in-high-consequence-drug-resistance-plasmids
#4
Susu He, Michael Chandler, Alessandro M Varani, Alison B Hickman, John P Dekker, Fred Dyda
: The dissemination of resistance among bacteria has been facilitated by the fact that resistance genes are usually located on a diverse and evolving set of transmissible plasmids. However, the mechanisms generating diversity and enabling adaptation within highly successful resistance plasmids have remained obscure, despite their profound clinical significance. To understand these mechanisms, we have performed a detailed analysis of the mobilome (the entire mobile genetic element content) of a set of previously sequenced carbapenemase-producing Enterobacteriaceae (CPE) from the National Institutes of Health Clinical Center...
December 6, 2016: MBio
https://www.readbyqxmd.com/read/27922269/genomic-study-of-the-type-ivc-secretion-system-in-clostridium-difficile-understanding-c-difficile-evolution-via-horizontal-gene-transfer
#5
Wen Zhang, Ying Cheng, Pengcheng Du, Yuanyuan Zhang, Hongbing Jia, Xianping Li, Jing Wang, Na Han, Yujun Qiang, Chen Chen, Jinxing Lu
Clostridium difficile, the etiological agent of Clostridium difficile infection (CDI), is a gram-positive, spore-forming bacillus that is responsible for ∼20% of antibiotic-related cases of diarrhea and nearly all cases of pseudomembranous colitis. Previous data have shown that a substantial proportion (11%) of the C. difficile genome consists of mobile genetic elements, including seven conjugative transposons. However, the mechanism underlying the formation of a mosaic genome in C. difficile is unknown. The type-IV secretion system (T4SS) is the only secretion system known to transfer DNA segments among bacteria...
August 30, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/27919902/genetic-environment-of-the-blakpc-2-gene-in-klebsiella-pneumoniae-isolate-which-may-have-been-imported-to-russia-from-southeast-asia
#6
Vladimir Ageevets, Julia Sopova, Irina Lazareva, Maya Malakhova, Elena Ilina, Elena Kostryukova, Vladislav Babenko, Alessandra Carattoli, Yuri Lobzin, Alexander Uskov, Sergey Sidorenko
The nucleotide sequence of a blaKPC-2-harboring plasmid (pKPCAPSS) from Klebsiella pneumoniae ST273 isolated in Saint Petersburg, Russia from a patient with history of recent travel to Vietnam is presented. This 127,970-bp plasmid possessed both IncFII and IncR replicons. blaKPC-2 was localized on a hypothetical mobile element. This element was flanked by 38bp inverted Tn3 repeats and included a Tn3-specific transposase gene, macrolide resistance operon (mphA, mrx, mphR), and a fragment of blaTEM with unique polymorphisms...
December 5, 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27917931/metagenomic-profiling-of-historic-colorado-front-range-flood-impact-on-distribution-of-riverine-antibiotic-resistance-genes
#7
Emily Garner, Joshua S Wallace, Gustavo Arango Argoty, Caitlin Wilkinson, Nicole Fahrenfeld, Lenwood S Heath, Liqing Zhang, Mazdak Arabi, Diana S Aga, Amy Pruden
Record-breaking floods in September 2013 caused massive damage to homes and infrastructure across the Colorado Front Range and heavily impacted the Cache La Poudre River watershed. Given the unique nature of this watershed as a test-bed for tracking environmental pathways of antibiotic resistance gene (ARG) dissemination, we sought to determine the impact of extreme flooding on ARG reservoirs in river water and sediment. We utilized high-throughput DNA sequencing to obtain metagenomic profiles of ARGs before and after flooding, and investigated 23 antibiotics and 14 metals as putative selective agents during post-flood recovery...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27915389/insertion-sequences-enrichment-in-extreme-red-sea-brine-pool-vent
#8
Ali H A Elbehery, Ramy K Aziz, Rania Siam
Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world's largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep...
December 3, 2016: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/27915087/genetically-unrelated-multidrug-and-carbapenem-resistant-citrobacter-freundii-detected-in-outpatients-admitted-to-a-portuguese-hospital
#9
Cátia Santos, Elmano Ramalheira, Gabriela Da Silva, Sónia Mendo
OBJECTIVES: Non-clonal, carbapenem- and multidrug-resistant Citrobacter freundii isolates were collected from unrelated outpatients admitted to a Portuguese hospital emergency department. One patient lived in a nursing home and was never hospitalised, whereas the other patient was repeatedly hospitalised in this hospital. The aim of this study was to unveil the molecular mechanisms associated with the carbapenem resistance of these isolates and to assess its potential dissemination. METHODS: Isolate identification was performed by VITEK(®)2 and was confirmed by 16S rDNA sequencing...
November 15, 2016: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/27903531/dream-plays-an-important-role-in-platelet-activation-and-thrombogenesis
#10
Kyungho Kim, Alan Tseng, Andrew Barazia, Joseph E Italiano, Jaehyung Cho
Downstream regulatory element antagonist modulator (DREAM), a transcriptional repressor, is known to modulate pain responses. However, it is unknown whether DREAM is expressed in anucleate platelets and plays a role in thrombogenesis. By using intravital microscopy with DREAM-null mice and their bone marrow chimeras, we demonstrated that both hematopoietic and non-hematopoietic cell DREAM are required for platelet thrombus formation following laser-induced arteriolar injury. In a FeCl3-induced thrombosis model, we found that compared to WT control and non-hematopoietic DREAM knockout (KO) mice, DREAM KO control and hematopoietic DREAM KO mice showed a significant delay in time to occlusion...
November 30, 2016: Blood
https://www.readbyqxmd.com/read/27899587/temporal-self-regulation-of-transposition-through-host-independent-transposase-rodlet-formation
#11
Lauren E Woodard, Laura M Downes, Yi-Chien Lee, Aparna Kaja, Eyuel S Terefe, Matthew H Wilson
Transposons are highly abundant in eukaryotic genomes, but their mobilization must be finely tuned to maintain host organism fitness and allow for transposon propagation. Forty percent of the human genome is comprised of transposable element sequences, and the most abundant cut-and-paste transposons are from the hAT superfamily. We found that the hAT transposase TcBuster from Tribolium castaneum formed filamentous structures, or rodlets, in human tissue culture cells, after gene transfer to adult mice, and ex vivo in cell-free conditions, indicating that host co-factors or cellular structures were not required for rodlet formation...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899566/asymmetric-positioning-of-cas1-2-complex-and-integration-host-factor-induced-dna-bending-guide-the-unidirectional-homing-of-protospacer-in-crispr-cas-type-i-e-system
#12
K N R Yoganand, R Sivathanu, Siddharth Nimkar, B Anand
CRISPR-Cas system epitomizes prokaryote-specific quintessential adaptive defense machinery that limits the genome invasion of mobile genetic elements. It confers adaptive immunity to bacteria by capturing a protospacer fragment from invading foreign DNA, which is later inserted into the leader proximal end of CRIPSR array and serves as immunological memory to recognize recurrent invasions. The universally conserved Cas1 and Cas2 form an integration complex that is known to mediate the protospacer invasion into the CRISPR array...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27894878/functionally-conserved-rna-binding-and-protein-protein-interaction-properties-of-line-orf1p-in-an-ancient-clade-of-non-ltr-retrotransposons-of-entamoeba-histolytica
#13
Amit Kumar Gaurav, Jitender Kumar, Mridula Agrahari, Alok Bhattacharya, Vijay Pal Yadav, Sudha Bhattacharya
Retrotransposons are mobile genetic elements found in most organisms. Their origin and evolution is not very well understood. Retrotransposons that lack long terminal repeats (non-LTR) have been classified based on their reverse transcriptase (RT) and endonuclease sequences into groups, of which R2 is the most ancient. Its members contain a single open reading frame (ORF) while there are two ORFs in the other groups, of which ORF2 contains the RT and endonuclease sequences. It is thought that ORF1 was added later to the single-ORF-containing elements, and codes for a protein with nucleic acid binding activity...
November 25, 2016: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/27892525/sxt-r391-integrative-and-conjugative-elements-in-proteus-species-reveal-abundant-genetic-diversity-and-multidrug-resistance
#14
Xinyue Li, Yu Du, Pengcheng Du, Hang Dai, Yujie Fang, Zhenpeng Li, Na Lv, Baoli Zhu, Biao Kan, Duochun Wang
SXT/R391 integrative and conjugative elements (ICEs) are self-transmissible mobile genetic elements that are found in most members of Enterobacteriaceae. Here, we determined fifteen SXT/R391 ICEs carried by Proteus isolates from food (4.2%) and diarrhoea patients (17.3%). BLASTn searches against GenBank showed that the fifteen SXT/R391 ICEs were closely related to that from different Enterobacteriaceae species, including Proteus mirabilis. Using core gene phylogenetic analysis, the fifteen SXT/R391 ICEs were grouped into six distinct clusters, including a dominant cluster and three clusters that have not been previously reported in Proteus isolates...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27886494/stochastic-predator-prey-dynamics-of-transposons-in-the-human-genome
#15
Chi Xue, Nigel Goldenfeld
Transposable elements, or transposons, are DNA sequences that can jump from site to site in the genome during the life cycle of a cell, usually encoding the very enzymes which perform their excision. However, some transposons are parasitic, relying on the enzymes produced by the regular transposons. In this case, we show that a stochastic model, which takes into account the small copy numbers of the active transposons in a cell, predicts noise-induced predator-prey oscillations with a characteristic time scale that is much longer than the cell replication time, indicating that the state of the predator-prey oscillator is stored in the genome and transmitted to successive generations...
November 11, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27880983/pantoea-ananatis-genomic-insights-into-a-versatile-pathogen
#16
Tania Weller-Stuart, Pieter De Maayer, Teresa Coutinho
Pantoea ananatis, a bacterium that is well-known for its phytopathogenic characteristics, has been isolated from a myriad of ecological niches and hosts. Infection of agronomic crops such as maize and rice can result in substantial economic losses. In the last few years, much of the research done on P. ananatis has been based on the sequencing and analysis of the genomes of strains isolated from different environments and with different lifestyles. In this review we summarise the advances made in terms of pathogenicity determinants of phytopathogenic strains of P...
November 23, 2016: Molecular Plant Pathology
https://www.readbyqxmd.com/read/27875251/the-impact-of-transposable-elements-on-mammalian-development
#17
REVIEW
Jose L Garcia-Perez, Thomas J Widmann, Ian R Adams
Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that have a significant impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues...
November 15, 2016: Development
https://www.readbyqxmd.com/read/27869745/many-activities-one-structure-functional-plasticity-of-ribozyme-folds
#18
REVIEW
Matthew W L Lau, Adrian R Ferré-D'Amaré
Catalytic RNAs, or ribozymes, are involved in a number of essential biological processes, such as replication of RNA genomes and mobile genetic elements, RNA splicing, translation, and RNA degradation. The function of ribozymes requires the formation of active sites decorated with RNA functional groups within defined three-dimensional (3D) structures. The genotype (sequence) of RNAs ultimately determines what 3D structures they adopt (as a function of their environmental conditions). These 3D structures, in turn, give rise to biochemical activity, which can further elaborate them by catalytic rearrangements or association with other molecules...
November 18, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27869532/molecular-characterization-of-methicillin-resistant-staphylococcus-aureus-from-outpatients-in-northern-japan-increasing-tendency-of-st5-st764-mrsa-iia-with-arginine-catabolic-mobile-element
#19
Meiji Soe Aung, Mitsuyo Kawaguchiya, Noriko Urushibara, Ayako Sumi, Masahiko Ito, Kenji Kudo, Shigeo Morimoto, Shino Hosoya, Nobumichi Kobayashi
Arginine catabolic mobile element (ACME) is a genomic island of staphylococcus and is considered to confer enhanced ability to survive and growth on host bacterial cells. ACME has been typically identified in Panton-Valentine Leukocidin (PVL)-positive ST8 methicillin-resistant Staphylococcus aureus (MRSA) with SCCmec type IVa (USA300 clone), and it is also found in other lineages at low frequency. Prevalence and molecular characteristics of PVL(+)and/or ACME(+) MRSA were investigated for 624 clinical isolates collected from outpatients in northern Japan from 2013 to 2014...
November 21, 2016: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/27858507/numerous-small-hammerhead-ribozyme-variants-associated-with-penelope-like-retrotransposons-cleave-rna-as-dimers
#20
Christina E Lünse, Zasha Weinberg, Ronald R Breaker
Hammerhead ribozymes represent the most common of the nine natural classes of self-cleaving RNAs. The hammerhead catalytic core includes 11 highly-conserved nucleotides located largely within the unpaired regions of a junction formed by stems I, II and III. The vast majority of previously reported examples carry an additional pseudoknot or other tertiary interactions between nucleotides that precede stem I and nucleotides in the loop of stem II. These extra contacts are critical for high-speed RNA catalysis...
November 18, 2016: RNA Biology
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