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https://www.readbyqxmd.com/read/27913727/regulated-complex-assembly-safeguards-the-fidelity-of-sleeping-beauty-transposition
#1
Yongming Wang, Diana Pryputniewicz-Dobrinska, Enikö Éva Nagy, Christopher D Kaufman, Manvendra Singh, Steve Yant, Jichang Wang, Anna Dalda, Mark A Kay, Zoltán Ivics, Zsuzsanna Izsvák
The functional relevance of the inverted repeat structure (IR/DR) in a subgroup of the Tc1/mariner superfamily of transposons has been enigmatic. In contrast to mariner transposition, where a topological filter suppresses single-ended reactions, the IR/DR orchestrates a regulatory mechanism to enforce synapsis of the transposon ends before cleavage by the transposase occurs. This ordered assembly process shepherds primary transposase binding to the inner 12DRs (where cleavage does not occur), followed by capture of the 12DR of the other transposon end...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902415/inversion-of-correia-repeat-enclosed-elements-in-neisseria-gonorrhoeae
#2
Firat Elbeyioglu, Sabrina B Roberts, Russell Spencer-Smith, Madhuri Pulijala, Marta A Zelewska, Jean-Christophe Nebel, Lori As Snyder
Neisseria gonorrhoeae is capable of causing gonorrhoea and more complex diseases in the human host. Within the gonococcal genome are over 100 copies of the IS-like Correia Repeat Enclosed Element, which has been predicted to be mobile within the neisserial genomes. Although there is evidence of ancestral movement of these elements, no previous study has provided evidence for current mobilisation. The Correia Repeat Enclosed Element has the ability to alter gene expression and regulation in many ways: by insertional mutagenesis; by introducing promoter elements; by generating mRNA processing sites, and by association with ncRNAs...
November 16, 2016: Microbiology
https://www.readbyqxmd.com/read/27886494/stochastic-predator-prey-dynamics-of-transposons-in-the-human-genome
#3
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/27845163/the-effect-of-htlv-1-virulence-factors-hbz-tax-proviral-load-hla-class-i-and-plasma-neopterin-on-manifestation-of-htlv-1-associated-myelopathy-tropical-spastic-paraparesis
#4
Hanieh Tarokhian, Mahdi Taghadosi, Hushang Rafatpanah, Taraneh Rajaei, Mahmoud Reza Azarpazhooh, Narges Valizadeh, S A Rahim Rezaee
BACKGROUND: Previous studies have suggested debatable roles of Tax and HBZ gene expression in the pathogenesis of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). In this study, HTLV-1 and host interactions in the manifestation of HAM/TSP were evaluated. METHODS: A cross-sectional study was conducted on 33 HAM/TSP patients and 38 HTLV-1 asymptomatic carriers (ACs). HTLV-1-Tax, HBZ gene expression, and proviral load (PVL) were assessed using the quantitative real-time PCR (TaqMan), host plasma neopterin level, and HLA-I, and the clinical manifestation were evaluated...
November 12, 2016: Virus Research
https://www.readbyqxmd.com/read/27814534/changes-in-antibiotic-concentrations-and-antibiotic-resistome-during-commercial-composting-of-animal-manures
#5
Wan-Ying Xie, Xin-Ping Yang, Qian Li, Long-Hua Wu, Qi-Rong Shen, Fang-Jie Zhao
The over-use of antibiotics in animal husbandry in China and the concomitant enhanced selection of antibiotic resistance genes (ARGs) in animal manures are of serious concern. Thermophilic composting is an effective way of reducing hazards in organic wastes. However, its effectiveness in antibiotic degradation and ARG reduction in commercial operations remains unclear. In the present study, we determined the concentrations of 15 common veterinary antibiotics and the abundances of 213 ARGs and 10 marker genes for mobile genetic elements (MGEs) in commercial composts made from cattle, poultry and swine manures in Eastern China...
October 27, 2016: Environmental Pollution
https://www.readbyqxmd.com/read/27809244/accumulation-of-stable-full-length-circular-group-i-intron-rnas-during-heat-shock
#6
Kasper L Andersen, Bertrand Beckert, Benoit Masquida, Steinar D Johansen, Henrik Nielsen
Group I introns in nuclear ribosomal RNA of eukaryotic microorganisms are processed by splicing or circularization. The latter results in formation of full-length circular introns without ligation of the exons and has been proposed to be active in intron mobility. We applied qRT-PCR to estimate the copy number of circular intron RNA from the myxomycete Didymium iridis. In exponentially growing amoebae, the circular introns are nuclear and found in 70 copies per cell. During heat-shock, the circular form is up-regulated to more than 500 copies per cell...
October 31, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27807467/a-map-of-mobile-dna-insertions-in-the-nci-60-human-cancer-cell-panel
#7
John G Zampella, Nemanja Rodić, Wan Rou Yang, Cheng Ran Lisa Huang, Jane Welch, Veena P Gnanakkan, Toby C Cornish, Jef D Boeke, Kathleen H Burns
BACKGROUND: The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the complete panel have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats derived from mobile DNAs are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27787520/increased-expression-of-ehf-via-gene-amplification-contributes-to-the-activation-of-her-family-signaling-and-associates-with-poor-survival-in-gastric-cancer
#8
Jing Shi, Yiping Qu, Xinru Li, Fang Sui, Demao Yao, Qi Yang, Bingyin Shi, Meiju Ji, Peng Hou
The biological function of E26 transformation-specific (ETS) transcription factor EHF/ESE-3 in human cancers remains largely unknown, particularly gastric cancer. The aim of this study was to explore the role of EHF in tumorigenesis and its potential as a therapeutic target in gastric cancer. By using quantitative RT-PCR (qRT-PCR), immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) assays, we investigated the expression and copy number of EHF in a cohort of gastric cancers and control subjects...
October 27, 2016: Cell Death & Disease
https://www.readbyqxmd.com/read/27776307/co-occurrence-of-mobile-genetic-elements-and-antibiotic-resistance-genes-in-municipal-solid-waste-landfill-leachates-a-preliminary-insight-into-the-role-of-landfill-age
#9
Zhuofeng Yu, Pinjing He, Liming Shao, Hua Zhang, Fan Lü
Since municipal solid waste (MSW) landfill harbours miscellaneous wastes, pollutants and microorganisms, it gradually becomes a huge potential reservoir for breeding antibiotic resistance genes (ARGs). The objective of this study was to determine the prevalence and diversity of ARGs associated with various mobile genetic elements (MGEs) in MSW landfill leachates. The relationship of ARGs with leachate characteristics was also studied to explore the influence of landfill age. Seven sulfonamides (sulfapyridine, sulfadiazine, sulfathiazole, sulfamethoxazole, sulfamerazine, sulfamethazine and sulfaquinoxaline), three encoded ARGs (sul-I, sul-II and sul-III) and four types of MGEs (plasmids, transposons, integrons and insertion sequences) were quantified in leachates with landfill ages ranging from 3 months-6 years...
October 18, 2016: Water Research
https://www.readbyqxmd.com/read/27742684/conjugative-transfer-system-of-incp-9-naphthalene-catabolic-plasmid-nah7-characterization-of-its-orit-region-and-relaxase-and-host-range-of-conjugative-system
#10
Kouhei Kishida, Kei Inoue, Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda
: NAH7 and pWW0 from γ-proteobacterial Pseudomonas putida strains are IncP-9 conjugative plasmids that carry the genes for degradation of naphthalene and toluene, respectively. Although such genes on these plasmids are well-characterized, experimental investigation of their conjugation systems remains at a primitive level. To clarify these conjugation systems, in this study we investigated the NAH7-encoded conjugation system by (i) analyzing the origin of its conjugative transfer (oriT)-containing region and its relaxase, which specifically nicks within the oriT region for initiation of transfer, and by (ii) comparing the conjugation systems between NAH7 and pWW0...
October 14, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27736800/generation-of-infectious-rna-complexes-in-orbiviruses-rna-rna-interactions-of-genomic-segments
#11
Teodoro Jr Fajardo, Kinda AlShaikhahmed, Polly Roy
Viruses with segmented RNA genomes must package the correct number of segments for synthesis of infectious virus particles. Recent studies suggest that the members of the Reoviridae family with segmented double-stranded RNA genomes achieve this challenging task by forming RNA networks of segments prior to their recruitment into the assembling capsid albeit direct evidence is still lacking. Here, we investigated the capability of virus recovery by preformed complexes of ten RNA segments of Epizootic Haemorrhagic Disease Virus (EHDV), a Reoviridae member, by transcribing exact T7 cDNA copies of genomic RNA segments in a single in vitro reaction followed by transfection of mammalian cells...
October 6, 2016: Oncotarget
https://www.readbyqxmd.com/read/27711162/a-de-novo-genome-sequence-assembly-of-the-arabidopsis-thaliana-accession-niederzenz-1-displays-presence-absence-variation-and-strong-synteny
#12
Boas Pucker, Daniela Holtgräwe, Thomas Rosleff Sörensen, Ralf Stracke, Prisca Viehöver, Bernd Weisshaar
Arabidopsis thaliana is the most important model organism for fundamental plant biology. The genome diversity of different accessions of this species has been intensively studied, for example in the 1001 genome project which led to the identification of many small nucleotide polymorphisms (SNPs) and small insertions and deletions (InDels). In addition, presence/absence variation (PAV), copy number variation (CNV) and mobile genetic elements contribute to genomic differences between A. thaliana accessions. To address larger genome rearrangements between the A...
2016: PloS One
https://www.readbyqxmd.com/read/27681925/correia-repeat-enclosed-elements-and-non-coding-rnas-in-the-neisseria-species
#13
Sabrina B Roberts, Russell Spencer-Smith, Mahwish Shah, Jean-Christophe Nebel, Richard T Cook, Lori A S Snyder
Neisseria gonorrhoeae is capable of causing gonorrhoea and more complex diseases in the human host. Neisseria meningitidis is a closely related pathogen that shares many of the same genomic features and virulence factors, but causes the life threatening diseases meningococcal meningitis and septicaemia. The importance of non-coding RNAs in gene regulation has become increasingly evident having been demonstrated to be involved in regulons responsible for iron acquisition, antigenic variation, and virulence. Neisseria spp...
August 25, 2016: Microorganisms
https://www.readbyqxmd.com/read/27680008/detection-of-human-fecal-contamination-by-nifh-gene-quantification-of-marine-waters-in-the-coastal-beaches-of-rio-de-janeiro-brazil
#14
Samara Sant'Anna Oliveira, Marcos Henrique Ferreira Sorgine, Kayo Bianco, Leonardo Henriques Pinto, Camila Barreto, Rodolpho Mattos Albano, Alexander Machado Cardoso, Maysa Mandetta Clementino
The identification of fecal pollution in aquatic ecosystems is one of the requirements to assess the possible risks to human health. In this report, physicochemical parameters, Escherichia coli enumeration and Methanobrevibacter smithii nifH gene quantification were conducted at 13 marine waters in the coastal beaches of Rio de Janeiro, Brazil. The pH, turbidity, dissolved oxygen, temperature, and conductivity, carried out by mobile equipment, revealed varied levels due to specific conditions of the beaches...
September 29, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27630990/the-influence-of-copy-number-of-targeted-extrachromosomal-genetic-elements-on-the-outcome-of-crispr-cas-defense
#15
Konstantin Severinov, Iaroslav Ispolatov, Ekaterina Semenova
Prokaryotic type I CRISPR-Cas systems respond to the presence of mobile genetic elements such as plasmids and phages in two different ways. CRISPR interference efficiently destroys foreign DNA harboring protospacers fully matching CRISPR RNA spacers. In contrast, even a single mismatch between a spacer and a protospacer can render CRISPR interference ineffective but causes primed adaptation-efficient and specific acquisition of additional spacers from foreign DNA into the CRISPR array of the host. It has been proposed that the interference and primed adaptation pathways are mediated by structurally different complexes formed by the effector Cascade complex on matching and mismatched protospacers...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27620479/a-model-for-transposition-of-the-colistin-resistance-gene-mcr-1-by-isapl1
#16
Erik Snesrud, Susu He, Michael Chandler, John P Dekker, Alison B Hickman, Patrick McGann, Fred Dyda
Analysis of mcr-1-containing sequences identified a common ∼2,607bp DNA segment that in many cases is flanked on one or both ends by ISApl1 We present evidence that mcr-1 is mobilized by an ISApl1 composite transposon, which has, in some cases, subsequently lost one or both copies of ISApl1 We also show that in some circumstances mcr-1 can be mobilized by a single, upstream copy of ISApl1 in conjunction with the remnants of a downstream ISApl1.
September 12, 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27619059/the-role-of-is26-in-evolution-of-a-derivative-of-the-virulence-plasmid-of-salmonella-enterica-serovar-enteritidis-which-confers-multiple-drug-resistance
#17
Vanesa García, Patricia García, Irene Rodríguez, Rosaura Rodicio, M Rosario Rodicio
pUO-SeVR1 is a resistance derivative of pSEV, the virulence plasmid specific of Salmonella enterica serovar Enteritidis. It was first detected in a Spanish isolate involved in gastroenteritis, but closely related plasmids are widespread in highly invasive isolates originating from Africa. According to its nucleotide sequence, pUO-SeVR1 consists of 110,982bp with a GC content of 53.2%. It confers resistance to multiple antimicrobial agents and contains a wealth of mobile genetic elements, including 14 copies of IS26 which have played a major role in the evolution of the plasmid...
September 9, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27600047/characterization-of-two-multidrug-resistant-inca-c-plasmids-from-the-1960s-by-using-oxford-nanopore-minion-sequencer-device
#18
Mónika Szabó, Tibor Nagy, Tímea Wilk, Tibor Farkas, Anna Hegyi, Ferenc Olasz, János Kiss
Two IncA/C family plasmids from the 1960s have been sequenced and classified into A/C2 Type 1 group. R16a and IP40a contain novel antibiotic resistance islands and a complete GIsul2 island not previously found in the family. In the 173.1 kb R16a the 29.9 kb ARI is located in a unique backbone position not utilized by ARIs. ARIR16a consists of Tn1, Tn6020, Tn6333 harboring the resistance genes blaTEM-1D, aphA1b and a mer module, respectively, a truncated Tn5393 copy and a gene cluster with unknown function. Plasmid IP40a is 170...
September 6, 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27589725/intra-peritoneal-administration-of-mitochondrial-dna-provokes-acute-lung-injury-and-systemic-inflammation-via-toll-like-receptor-9
#19
Lemeng Zhang, Songyun Deng, Shuangping Zhao, Yuhang Ai, Lina Zhang, Pinhua Pan, Xiaoli Su, Hongyi Tan, Dongdong Wu
The pathogenesis of sepsis is complex. Mitochondrial dysfunction, which is responsible for energy metabolism, intrinsic apoptotic pathway, oxidative stress, and systemic inflammatory responses, is closely related with severe sepsis induced death. Mitochondria DNA (mtDNA) contain un-methylated cytosine phosphate guanine (CpG) motifs, which exhibit immune stimulatory capacities. The aim of this study was to investigate the role and mechanism of mtDNA release on lipopolysaccharide (LPS) induced acute lung injury (ALI) and systemic inflammation...
2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27583033/convergent-evolution-of-trna-gene-targeting-preferences-in-compact-genomes
#20
Thomas Spaller, Eva Kling, Gernot Glöckner, Falk Hillmann, Thomas Winckler
BACKGROUND: In gene-dense genomes, mobile elements are confronted with highly selective pressure to amplify without causing excessive damage to the host. The targeting of tRNA genes as potentially safe integration sites has been developed by retrotransposons in various organisms such as the social amoeba Dictyostelium discoideum and the yeast Saccharomyces cerevisiae. In D. discoideum, tRNA gene-targeting retrotransposons have expanded to approximately 3 % of the genome. Recently obtained genome sequences of species representing the evolutionary history of social amoebae enabled us to determine whether the targeting of tRNA genes is a generally successful strategy for mobile elements to colonize compact genomes...
2016: Mobile DNA
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