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https://www.readbyqxmd.com/read/27914481/conserved-3-utr-stem-loop-structure-in-l1-and-alu-transposons-in-human-genome-possible-role-in-retrotransposition
#1
Daria Grechishnikova, Maria Poptsova
BACKGROUND: In the process of retrotransposition LINEs use their own machinery for copying and inserting themselves into new genomic locations, while SINEs are parasitic and require the machinery of LINEs. The exact mechanism of how a LINE-encoded reverse transcriptase (RT) recognizes its own and SINE RNA remains unclear. However it was shown for the stringent-type LINEs that recognition of a stem-loop at the 3'UTR by RT is essential for retrotransposition. For the relaxed-type LINEs it is believed that the poly-A tail is a common recognition element between LINE and SINE RNA...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27913727/regulated-complex-assembly-safeguards-the-fidelity-of-sleeping-beauty-transposition
#2
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/27911809/unique-attributes-of-cyanobacterial-metabolism-revealed-by-improved-genome-scale-metabolic-modeling-and-essential-gene-analysis
#3
Jared T Broddrick, Benjamin E Rubin, David G Welkie, Niu Du, Nathan Mih, Spencer Diamond, Jenny J Lee, Susan S Golden, Bernhard O Palsson
The model cyanobacterium, Synechococcus elongatus PCC 7942, is a genetically tractable obligate phototroph that is being developed for the bioproduction of high-value chemicals. Genome-scale models (GEMs) have been successfully used to assess and engineer cellular metabolism; however, GEMs of phototrophic metabolism have been limited by the lack of experimental datasets for model validation and the challenges of incorporating photon uptake. Here, we develop a GEM of metabolism in S. elongatus using random barcode transposon site sequencing (RB-TnSeq) essential gene and physiological data specific to photoautotrophic metabolism...
December 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27910897/genomic-variations-leading-to-alterations-in-cell-morphology-of-campylobacter-spp
#4
Diane Esson, Alison E Mather, Eoin Scanlan, Srishti Gupta, Stefan P W de Vries, David Bailey, Simon R Harris, Trevelyan J McKinley, Guillaume Méric, Sophia K Berry, Pietro Mastroeni, Samuel K Sheppard, Graham Christie, Nicholas R Thomson, Julian Parkhill, Duncan J Maskell, Andrew J Grant
Campylobacter jejuni, the most common cause of bacterial diarrhoeal disease, is normally helical. However, it can also adopt straight rod, elongated helical and coccoid forms. Studying how helical morphology is generated, and how it switches between its different forms, is an important objective for understanding this pathogen. Here, we aimed to determine the genetic factors involved in generating the helical shape of Campylobacter. A C. jejuni transposon (Tn) mutant library was screened for non-helical mutants with inconsistent results...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910041/efficient-genome-editing-in-induced-pluripotent-stem-cells-with-engineered-nucleases-in-vitro
#5
Vittavat Termglinchan, Timon Seeger, Caressa Chen, Joseph C Wu, Ioannis Karakikes
Precision genome engineering is rapidly advancing the application of the induced pluripotent stem cells (iPSCs) technology for in vitro disease modeling of cardiovascular diseases. Targeted genome editing using engineered nucleases is a powerful tool that allows for reverse genetics, genome engineering, and targeted transgene integration experiments to be performed in a precise and predictable manner. However, nuclease-mediated homologous recombination is an inefficient process. Herein, we describe the development of an optimized method combining site-specific nucleases and the piggyBac transposon system for "seamless" genome editing in pluripotent stem cells with high efficiency and fidelity in vitro...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27909217/the-small-foxp1-isoform-predominantly-expressed-in-activated-b-cell-like-diffuse-large-b-cell-lymphoma-and-full-length-foxp1-exert-similar-oncogenic-and-transcriptional-activity-in-human-b-cells
#6
Martine van Keimpema, Leonie J Grüneberg, Esther J M Schilder-Tol, Monique E C M Oud, Esther Beuling, Paul J Hensbergen, Johann de Jong, Steven T Pals, Marcel Spaargaren
The forkhead transcription factor FOXP1 is generally regarded as an oncogene in activated B cell-like diffuse large B-cell lymphoma. Previous studies have suggested that a small isoform of FOXP1 (FOXP1-iso), rather than full-length FOXP1 (FOXP1-FL), may possess this oncogenic activity. Corroborating those studies, we here show that activated B cell-like diffuse large B-cell lymphoma cell-lines and primary activated B cell-like diffuse large B-cell lymphoma cells predominantly express FOXP1-iso and that the 5-end of the Foxp1 gene is a common insertion site in murine lymphomas in leukaemia virus- and transposon-mediated insertional mutagenesis screens...
December 1, 2016: Haematologica
https://www.readbyqxmd.com/read/27900536/t%C3%AE-4-overexpression-based-on-the-piggybac-transposon-system-in-cashmere-goats-alters-hair-fiber-characteristics
#7
Bingbo Shi, Qiang Ding, Xiaolin He, Haijing Zhu, Yiyuan Niu, Bei Cai, Jiao Cai, Anming Lei, Danju Kang, Hailong Yan, Baohua Ma, Xiaolong Wang, Lei Qu, Yulin Chen
Increasing cashmere yield is one of the vital aims of cashmere goats breeding. Compared to traditional breeding methods, transgenic technology is more efficient and the piggyBac (PB) transposon system has been widely applied to generate transgenic animals. For the present study, donor fibroblasts were stably transfected via a PB donor vector containing the coding sequence of cashmere goat thymosin beta-4 (Tβ4) and driven by a hair follicle-specific promoter, the keratin-associated protein 6.1 (KAP6.1) promoter...
November 29, 2016: Transgenic Research
https://www.readbyqxmd.com/read/27899587/temporal-self-regulation-of-transposition-through-host-independent-transposase-rodlet-formation
#8
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/27898092/transposon-mediated-generation-of-cellular-and-mouse-models-of-splicing-mutations-to-assess-the-efficacy-of-snrna-based-therapeutics
#9
Elena Barbon, Mattia Ferrarese, Laetitia van Wittenberghe, Peggy Sanatine, Giuseppe Ronzitti, Fanny Collaud, Pasqualina Colella, Mirko Pinotti, Federico Mingozzi
Disease-causing splicing mutations can be rescued by variants of the U1 small nuclear RNA (U1snRNAs). However, the evaluation of the efficacy and safety of modified U1snRNAs as therapeutic tools is limited by the availability of cellular and animal models specific for a given mutation. Hence, we exploited the hyperactive Sleeping Beauty transposon system (SB100X) to integrate human factor IX (hFIX) minigenes into genomic DNA in vitro and in vivo. We generated stable HEK293 cell lines and C57BL/6 mice harboring splicing-competent hFIX minigenes either wild type (SChFIX-wt) or mutated (SChFIXex5-2C)...
November 29, 2016: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/27898036/screening-of-a-haloferax-volcanii-transposon-library-reveals-novel-motility-and-adhesion-mutants
#10
Georgio Legerme, Evan Yang, Rianne N Esquivel, Saija Kiljunen, Harri Savilahti, Mechthild Pohlschroder
Archaea, like bacteria, use type IV pili to facilitate surface adhesion. Moreover, archaeal flagella-structures required for motility-share a common ancestry with type IV pili. While the characterization of archaeal homologs of bacterial type IV pilus biosynthesis components has revealed important aspects of flagellum and pilus biosynthesis and the mechanisms regulating motility and adhesion in archaea, many questions remain. Therefore, we screened a Haloferax volcanii transposon insertion library for motility mutants using motility plates and adhesion mutants, using an adapted air-liquid interface assay...
November 26, 2016: Life
https://www.readbyqxmd.com/read/27895128/characterization-of-the-pathogenicity-of-streptococcus-intermedius-tyg1620-isolated-from-a-human-brain-abscess-based-on-the-complete-genome-sequence-with-transcriptome-analysis-and-transposon-mutagenesis-in-a-murine-subcutaneous-abscess-model
#11
Noriko Hasegawa, Tsuyoshi Sekizuka, Yutaka Sugi, Nobuhiro Kawakami, Yumiko Ogasawara, Kengo Kato, Akifumi Yamashita, Fumihiko Takeuchi, Makoto Kuroda
Streptococcus intermedius is known to cause periodontitis and pyogenic infections in the brain and liver. Here we report the complete genome sequence of strain TYG1620 (genome size: 2,006,877 bp; GC content: 37.6%; 2,020 predicted ORFs) isolated from a brain abscess in an infant. Comparative genome analysis of S. intermedius genome sequences suggested that TYG1620 carries a notable type VII secretion system (T7SS), two long-repeat regions and 19 ORFs for cell-wall-anchored proteins (CWAPs). To elucidate genes responsible for the pathogenicity of TYG1620, transcriptome analysis was performed in a murine subcutaneous abscess model...
November 28, 2016: Infection and Immunity
https://www.readbyqxmd.com/read/27893851/expression-and-regulation-of-piwil-proteins-and-piwi-interacting-rnas-in-rheumatoid-arthritis
#12
Lenka Pleštilová, Michel Neidhart, Giancarlo Russo, Mojca Frank-Bertoncelj, Caroline Ospelt, Adrian Ciurea, Christoph Kolling, Renate E Gay, Beat A Michel, Jiří Vencovský, Steffen Gay, Astrid Jüngel
OBJECTIVE: The PIWIL (P-element induced wimpy testis like protein) subfamily of argonaute proteins is essential for Piwi-interacting RNA (piRNA) biogenesis and their function to silence transposons during germ-line development. Here we explored their presence and regulation in rheumatoid arthritis (RA). METHODS: The expression of PIWIL genes in RA and osteoarthritis (OA) synovial tissues and synovial fibroblasts (SF) was analysed by Real-time PCR, immunofluorescence and Western blot...
2016: PloS One
https://www.readbyqxmd.com/read/27893790/detection-of-a-cfr-b-variant-in-german-enterococcus-faecium-clinical-isolates-and-the-impact-on-linezolid-resistance-in-enterococcus-spp
#13
Jennifer K Bender, Carola Fleige, Ingo Klare, Stefan Fiedler, Alexander Mischnik, Nico T Mutters, Kate E Dingle, Guido Werner
The National Reference Centre for Staphylococci and Enterococci in Germany has received an increasing number of clinical linezolid-resistant E. faecium isolates in recent years. Five isolates harbored a cfr(B) variant gene locus the product of which is capable of conferring linezolid resistance. The cfr(B)-like methyltransferase gene was also detected in Clostridium difficile. Antimicrobial susceptibility was determined for cfr(B)-positive and linezolid-resistant E. faecium isolates and two isogenic C. difficile strains...
2016: PloS One
https://www.readbyqxmd.com/read/27890443/oxa-23-and-isaba1-oxa-66-class-d-%C3%AE-lactamases-in-acinetobacter-baumannii-isolates-from-companion-animals
#14
Christa Ewers, Peter Klotz, Ursula Leidner, Ivonne Stamm, Ellen Prenger-Berninghoff, Stephan Göttig, Torsten Semmler, Sandra Scheufen
Acinetobacter baumannii is recognised as a major pathogen of nosocomial infections that frequently show resistance to last-resort antimicrobials. To investigate whether A. baumannii from companion animals harbour carbapenem resistance mechanisms, 223 clinical isolates obtained from veterinary clinics between 2000 and 2013 in Germany were screened for carbapenem-non-susceptibility employing meropenem-containing Mueller-Hinton agar plates. Minimum inhibitory concentration (MIC) data were obtained using the VITEK(®)2 system...
November 16, 2016: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/27889452/an-rb-ezh2-complex-mediates-silencing-of-repetitive-dna-sequences
#15
Charles A Ishak, Aren E Marshall, Daniel T Passos, Carlee R White, Seung J Kim, Matthew J Cecchini, Sara Ferwati, William A MacDonald, Christopher J Howlett, Ian D Welch, Seth M Rubin, Mellissa R W Mann, Frederick A Dick
Repetitive genomic regions include tandem sequence repeats and interspersed repeats, such as endogenous retroviruses and LINE-1 elements. Repressive heterochromatin domains silence expression of these sequences through mechanisms that remain poorly understood. Here, we present evidence that the retinoblastoma protein (pRB) utilizes a cell-cycle-independent interaction with E2F1 to recruit enhancer of zeste homolog 2 (EZH2) to diverse repeat sequences. These include simple repeats, satellites, LINEs, and endogenous retroviruses as well as transposon fragments...
November 12, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27886654/essential-role-of-k-uptake-permease-kup-for-resistance-to-sucrose-induced-stress-in-gluconacetobacter-diazotrophicus-pal-5
#16
Marcos V V de Oliveira, Aline C Intorne, Luciano de, S Vespoli, Leandro F Andrade, Leandro de, M Pereira, Patrícia L Rangel, Gonçalo A de Souza Filho
Microorganisms are constantly challenged by stressful conditions, such as sugar-rich environments. Such environments can cause an imbalance of biochemical activities and compromise cell multiplication. Gluconacetobacter diazotrophicus PAl 5 is among the most sugar-tolerant bacteria, capable of growing in the presence of up to 876 mM sucrose. However, the molecular mechanisms involved in its response to high sucrose remain unknown. The present work aimed to identify sucrose-induced stress resistance genes in G...
November 25, 2016: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/27886494/stochastic-predator-prey-dynamics-of-transposons-in-the-human-genome
#17
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/27885613/generation-and-screening-of-an-insertion-sequencing-compatible-mutant-library-of-campylobacter-jejuni
#18
Jeremiah G Johnson, Victor J DiRita
The advent of next-generation sequencing technology has enabled experimental approaches to characterize large, complex populations of DNA molecules with high resolution. Included among these are methods to assess populations of transposon insertion libraries for the fitness cost of any particular mutant allele after applying selection to a population. These approaches have proven invaluable for identifying genetic factors that influence survival of bacterial pathogens within different environments, including animal hosts...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27884113/disrupting-ros-protection-mechanism-allows-hydrogen-peroxide-to-accumulate-and-oxidize-sb-iii-to-sb-v-in-pseudomonas-stutzeri-ts44
#19
Dan Wang, Fengqiu Zhu, Qian Wang, Christopher Rensing, Peng Yu, Jing Gong, Gejiao Wang
BACKGROUND: Microbial antimonite [Sb(III)] oxidation converts toxic Sb(III) into less toxic antimonate [Sb(V)] and plays an important role in the biogeochemical Sb cycle. Currently, little is known about the mechanisms underlying bacterial Sb(III) resistance and oxidation. RESULTS: In this study, Tn5 transposon mutagenesis was conducted in the Sb(III)-oxidizing strain Pseudomonas stutzeri TS44 to isolate the genes responsible for Sb(III) resistance and oxidation...
November 25, 2016: BMC Microbiology
https://www.readbyqxmd.com/read/27881418/environmental-pseudomonads-inhibit-cystic-fibrosis-patient-derived-pseudomonas-aeruginosa
#20
Payel Chatterjee, Elizabeth Davis, Fengan Yu, Sarah James, Julia H Wildschutte, Daniel D Wiegmann, David H Sherman, Robert M McKay, John J LiPuma, Hans Wildschutte
: Pseudomonas aeruginosa is an opportunistic pathogen which is evolving resistance to many currently used antibiotics. While much research has been devoted to the roles of pathogenic P. aeruginosa in cystic fibrosis (CF) patients, less is known of its ecological properties. P. aeruginosa dominate the lungs during chronic infection in CF patients, yet its abundance in some environments is less compared to other diverse groups of pseudomonads. Here, we sought to determine if clinical isolates of P...
November 23, 2016: Applied and Environmental Microbiology
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