keyword
MENU ▼
Read by QxMD icon Read
search

Transposons

keyword
https://www.readbyqxmd.com/read/28340408/ongoing-evolution-of-pseudomonas-aeruginosa-pao1-sublines-complicates-studies-of-dna-damage-repair-and-tolerance
#1
Julia Sidorenko, Tatjana Jatsenko, Maia Kivisaar
Sublines of the major P. aeruginosa reference strain PAO1 are derivatives of the original PAO1 isolate, which are maintained in laboratories worldwide. These sublines display substantial genomic and phenotypic variation due to ongoing microevolution. Here, we examined four sublines, MPAO1, PAO1-L, PAO1-DSM and PAO1-UT, originated from different laboratories, and six DNA polymerase-deficient mutants from the P. aeruginosa MPAO1 transposon library for their employment in elucidation of DNA damage repair and tolerance mechanisms in P...
March 16, 2017: Mutation Research
https://www.readbyqxmd.com/read/28335567/cross-regulation-between-transposable-elements-and-host-dna-replication
#2
REVIEW
Mikel Zaratiegui
Transposable elements subvert host cellular functions to ensure their survival. Their interaction with the host DNA replication machinery indicates that selective pressures lead them to develop ancestral and convergent evolutionary adaptations aimed at conserved features of this fundamental process. These interactions can shape the co-evolution of the transposons and their hosts.
March 21, 2017: Viruses
https://www.readbyqxmd.com/read/28335027/a-transposon-derived-small-rna-regulates-gene-expression-in-salmonella-typhimurium
#3
Michael J Ellis, Ryan S Trussler, Onella Charles, David B Haniford
Bacterial sRNAs play an important role in regulating many cellular processes including metabolism, outer membrane homeostasis and virulence. Although sRNAs were initially found in intergenic regions, there is emerging evidence that protein coding regions of the genome are a rich reservoir of sRNAs. Here we report that the 5΄UTR of IS200 transposase mRNA (tnpA) is processed to produce regulatory RNAs that affect expression of over 70 genes in Salmonella Typhimurium. We provide evidence that the tnpA derived sRNA base-pairs with invF mRNA to repress expression...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334803/statistical-analysis-of-genetic-interactions-in-tn-seq-data
#4
Michael A DeJesus, Subhalaxmi Nambi, Clare M Smith, Richard E Baker, Christopher M Sassetti, Thomas R Ioerger
Tn-Seq is an experimental method for probing the functions of genes through construction of complex random transposon insertion libraries and quantification of each mutant's abundance using next-generation sequencing. An important emerging application of Tn-Seq is for identifying genetic interactions, which involves comparing Tn mutant libraries generated in different genetic backgrounds (e.g. wild-type strain versus knockout strain). Several analytical methods have been proposed for analyzing Tn-Seq data to identify genetic interactions, including estimating relative fitness ratios and fitting a generalized linear model...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334706/repetitive-dna-a-versatile-tool-for-karyotyping-in-festuca-pratensis-huds
#5
Anna Křivánková, David Kopecký, Štěpán Stočes, Jaroslav Doležel, Eva Hřibová
FISH is a useful method to identify individual chromosomes in a karyotype and to discover their structural changes accompanying genome evolution and speciation. DNA probes for FISH should be chromosome specific and/or exhibit specific patterns of distribution along each chromosome. Such probes are not available in many plants including meadow fescue (Festuca pratensis Huds.), an important forage grass species. In the present study, various DNA repeats identified in Illumina shotgun sequences specific to chromosome 4F of F...
March 24, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28333331/multiregional-dissemination-of-kpc-producing-klebsiella-pneumoniae-st258-st512-genotypes-in-poland-2010-14
#6
Anna Baraniak, Radoslaw Izdebski, Dorota Zabicka, Katarzyna Bojarska, Sandra Górska, Elzbieta Literacka, Janusz Fiett, Waleria Hryniewicz, Marek Gniadkowski
Objectives: In 2008-09, the KPC carbapenemase epidemiology in Poland was dominated by a Klebsiella pneumoniae ST258 KPC-2 outbreak in Warsaw and its administrative region. The aim of this study was to analyse the situation in 2010-14, with a focus on new outbreaks in other parts of the country. Methods: KPCs were detected in all suspected isolates by PCR. The detailed study was performed on 173 isolates from 2010 to 2012, and included PFGE and MLST, PCR identification of K...
March 9, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28333283/rch51-a-multiply-antibiotic-resistant-acinetobacter-baumannii-st103ip-isolate-carries-resistance-genes-in-three-plasmids-including-a-novel-potentially-conjugative-plasmid-carrying-oxa235-in-transposon-tn6252
#7
Mohammad Hamidian, Steven J Nigro, Rebecca M Hartstein, Ruth M Hall
Objectives: To determine the identity and context of genes conferring antibiotic resistance in a sporadic multiply antibiotic-resistant Acinetobacter baumannii recovered at Royal Children's Hospital, Brisbane. Methods: The antibiotic resistance phenotype for 23 antibiotics was determined using disc diffusion or MIC determination. The whole-genome sequence of RCH51 was determined using the Illumina HiSeq platform. Antibiotic resistance determinants were identified using ResFinder...
March 13, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28331161/isolation-of-cyanobacterial-mutants-exhibiting-growth-defects-under-microoxic-conditions-by-transposon-tagging-mutagenesis-of-synechocystis-sp-pcc-6803
#8
Kazuki Terauchi, Riho Sobue, Yuho Furutani, Rina Aoki, Yuichi Fujita
Cyanobacteria are photosynthetic prokaryotes that perform oxygenic photosynthesis by extracting electrons from water, with the generation of oxygen as a byproduct. Cyanobacteria use oxygen not only for respiration to produce energy in the dark but also for biosynthesis of various metabolites, such as heme and chlorophyll. Oxygen levels dynamically fluctuate in the field environments, from hyperoxic at daytime to almost anaerobic at night. Thus, adaptation to anaerobiosis should be important for cyanobacteria to survive in low-oxygen and anaerobic environments...
March 22, 2017: Journal of General and Applied Microbiology
https://www.readbyqxmd.com/read/28329687/impact-of-dietary-interventions-on-noncoding-rna-networks-and-mrnas-encoding-chromatin-related-factors
#9
Christopher D Green, Yi Huang, Xiaoyang Dou, Liu Yang, Yong Liu, Jing-Dong J Han
Dietary interventions dramatically affect metabolic disease and lifespan in various aging models. Here, we profiled liver microRNA (miRNA), coding, and long non-coding RNA (lncRNA) expression by high-throughput deep sequencing in mice across multiple energy intake and expenditure interventions. Strikingly, three dietary intervention network design patterns were uncovered: (1) lifespan-extending interventions largely repressed the expression of miRNAs, lncRNAs, and transposable elements; (2) protein-coding mRNAs with expression positively correlated with long lifespan are highly targeted by miRNAs; and (3) miRNA-targeting interactions mainly target chromatin-related functions...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28325684/monitoring-and-visualizing-microrna-dynamics-during-live-cell-differentiation-using-microrna-responsive-non-viral-reporter-vectors
#10
Hideyuki Nakanishi, Kenji Miki, Kaoru R Komatsu, Masayuki Umeda, Megumi Mochizuki, Azusa Inagaki, Yoshinori Yoshida, Hirohide Saito
MicroRNA (miRNA) activity differs with cell type, suggesting it can be used as a cell marker. In this study, we developed novel miRNA-responsive non-viral reporter vectors to continuously monitor and visualize miRNA dynamics during differentiation and to efficiently purify target living cells. Each vector codes miRNA-responsive and reference reporter genes in a single mRNA. These two genes are independent modules but transcribed by a single promoter, which enables us to distinguish miRNA-mediated post-transcriptional repression from transcriptional repression...
March 2, 2017: Biomaterials
https://www.readbyqxmd.com/read/28325297/engineering-of-pedf-expressing-primary-pigment-epithelial-cells-by-the-sb-transposon-system-delivered-by-pfar4-plasmids
#11
Gabriele Thumann, Nina Harmening, Cécile Prat-Souteyrand, Corinne Marie, Marie Pastor, Attila Sebe, Csaba Miskey, Laurence D Hurst, Sabine Diarra, Martina Kropp, Peter Walter, Daniel Scherman, Zoltán Ivics, Zsuzsanna Izsvák, Sandra Johnen
Neovascular age-related macular degeneration (nvAMD) is characterized by choroidal blood vessels growing into the subretinal space, leading to retinal pigment epithelial (RPE) cell degeneration and vision loss. Vessel growth results from an imbalance of pro-angiogenic (e.g., vascular endothelial growth factor [VEGF]) and anti-angiogenic factors (e.g., pigment epithelium-derived factor [PEDF]). Current treatment using intravitreal injections of anti-VEGF antibodies improves vision in about 30% of patients but may be accompanied by side effects and non-compliance...
March 17, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28322011/fcrav2-a-gene-with-rogdi-domain-involved-in-fusarium-head-blight-and-crown-rot-on-durum-wheat-caused-by-fusarium-culmorum
#12
Francesca Spanu, Barbara Scherm, Irene Camboni, Virgilio Balmas, Giovanna Pani, Safa Oufensou, Nicolo' Macciotta, Matias Pasquali, Quirico Migheli
Fusarium culmorum is a soil-borne fungal pathogen able to cause foot and root rot and Fusarium head blight on small grain cereals, particularly on wheat and barley. It causes significant yield and quality loss and results in the contamination of kernels with type B trichothecene mycotoxins. Knowledge on pathogenicity factors of this fungus is still limited. A transposon tagging approach based on the mimp1/impala double component system has allowed us to select a mutant altered in multiple metabolic and morphological processes, trichothecene production and virulence...
March 21, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28321208/detection-of-a-putative-tetr-like-gene-related-to-mycobacterium-bovis-bcg-growth-in-cholesterol-using-a-gfp-transposon-mutagenesis-system
#13
Isabel Otal, Esther Pérez-Herrán, Lazaro Garcia-Morales, María C Menéndez, Jorge A Gonzalez-Y-Merchand, Carlos Martín, María J García
In vitro transposition is a powerful genetic tool for identifying mycobacterial virulence genes and studying virulence factors in relation to the host. Transposon shuttle mutagenesis is a method for constructing stable insertions in the genome of different microorganisms including mycobacteria. Using an IS1096 derivative, we have constructed the Tngfp, a transposon containing a promoterless green fluorescent protein (gfp) gene. This transposon was able to transpose randomly in Mycobacterium bovis BCG. Bacteria with a single copy of the gfp gene per chromosome from an M...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28320837/the-suf-iron-sulfur-cluster-biosynthetic-system-is-essential-in-staphylococcus-aureus-and-decreased-suf-function-results-in-global-metabolic-defects-and-reduced-survival-in-human-neutrophils
#14
Christina A Roberts, Hassan M Al-Tameemi, Ameya A Mashruwala, Zuelay Rosario-Cruz, Unnati Chauhan, William E Sause, Victor J Torres, William J Belden, Jeffrey M Boyd
Staphylococcus aureus remains a causative agent for morbidity and mortality worldwide. This is, in part, a result of antimicrobial resistance highlighting the need to uncover novel antibiotic targets and discover new therapeutic agents. In the present study we explored the possibility that iron-sulfur (Fe-S) cluster synthesis is a viable antimicrobial target. RNA interference studies established that Suf (sulfur mobilization) dependent Fe-S cluster synthesis is essential in S. aureus We found that sufCDSUB were cotranscribed and suf transcription was positively influenced by sigma factor B...
March 20, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28320202/identification-and-expression-of-equine-mer-derived-mirnas
#15
Jeong-An Gim, Heui-Soo Kim
MicroRNAs (miRNAs) are single-stranded, small RNAs (21-23 nucleotides) that function in gene silencing and translational inhibition via the RNA interference mechanism. Most miRNAs originate from host genomic regions, such as intergenic regions, introns, exons, and transposable elements (TEs). Here, we focused on the palindromic structure of medium reiteration frequencies (MERs), which are similar to precursor miRNAs. Five MER consensus sequences (MER5A1, MER53, MER81, MER91C, and MER117) were matched with paralogous transcripts predicted to be precursor miRNAs in the horse genome (equCab2) and located in either intergenic regions or introns...
March 21, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28319090/a-single-copy-sleeping-beauty-transposon-mutagenesis-screen-identifies-new-pten-cooperating-tumor-suppressor-genes
#16
Jorge de la Rosa, Julia Weber, Mathias Josef Friedrich, Yilong Li, Lena Rad, Hannes Ponstingl, Qi Liang, Sandra Bernaldo de Quirós, Imran Noorani, Emmanouil Metzakopian, Alexander Strong, Meng Amy Li, Aurora Astudillo, María Teresa Fernández-García, María Soledad Fernández-García, Gary J Hoffman, Rocío Fuente, George S Vassiliou, Roland Rad, Carlos López-Otín, Allan Bradley, Juan Cadiñanos
The overwhelming number of genetic alterations identified through cancer genome sequencing requires complementary approaches to interpret their significance and interactions. Here we developed a novel whole-body insertional mutagenesis screen in mice, which was designed for the discovery of Pten-cooperating tumor suppressors. Toward this aim, we coupled mobilization of a single-copy inactivating Sleeping Beauty transposon to Pten disruption within the same genome. The analysis of 278 transposition-induced prostate, breast and skin tumors detected tissue-specific and shared data sets of known and candidate genes involved in cancer...
March 20, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28317878/kidney-specific-transposon-mediated-gene-transfer-in-vivo
#17
Lauren E Woodard, Jizhong Cheng, Richard C Welch, Felisha M Williams, Wentian Luo, Leslie S Gewin, Matthew H Wilson
Methods enabling kidney-specific gene transfer in adult mice are needed to develop new therapies for kidney disease. We attempted kidney-specific gene transfer following hydrodynamic tail vein injection using the kidney-specific podocin and gamma-glutamyl transferase promoters, but found expression primarily in the liver. In order to achieve kidney-specific transgene expression, we tested direct hydrodynamic injection of a DNA solution into the renal pelvis and found that luciferase expression was strong in the kidney and absent from extra-renal tissues...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28315830/paternal-induction-of-hybrid-dysgenesis-in-drosophila-melanogaster-is-weakly-correlated-with-both-p-element-and-hobo-element-dosage
#18
Satyam P Srivastav, Erin S Kelleher
Transposable elements (TEs) are virtually ubiquitous components of genomes, yet they often impose significant fitness consequences on their hosts. In addition to producing specific deleterious mutations by insertional inactivation, TEs also impose general fitness costs by inducing DNA damage and participating in ectopic recombination. These latter fitness costs are often assumed to be dosage-dependent, with stronger effects occurring in the presence of higher TE copy numbers. We test this assumption in Drosophila melanogaster by considering the relationship between the copy number of two active DNA transposons, P-element and hobo element, and the incidence of hybrid dysgenesis, a sterility syndrome associated with transposon activity in the germline...
March 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28315021/clinical-strains-of-streptococcus-agalactiae-carry-two-different-variants-of-pathogenicity-island-xii
#19
Eugenia Kuleshevich, Joseph Ferretti, Ilda Santos Sanches, Natesan Balasubramanian, Barbara Spellerberg, Androulla Efstratiou, Paula Kriz, Kornelia Grabovskaya, Olga Arjanova, Alevtina Savitcheva, Valentin Shevchenko, Anton Rysev, Alexander Suvorov
Streptococcus agalactiae or Group B streptococci (GBS) are a common cause of serious diseases of newborns and adults. GBS pathogenicity largely depends on genes located on the accessory genome including several pathogenicity islands (PAI). The present paper is focused on the structure and molecular epidemiological analysis of one of the GBS pathogenicity islands-the pathogenicity island PAI XII (Glaser et al. Mol Microbiol 45(6):1499-1513, 2002). This PAI was found to be composed of three different mobile genetic elements: a composite transposon (PAI-C), a genomic islet (PAI-B), and a pathogenicity island associated with gene sspB1 (PAI-A)...
March 18, 2017: Folia Microbiologica
https://www.readbyqxmd.com/read/28314934/transposon-insertion-resulted-in-the-silencing-of-wx-b1n-in-chinese-wheat-landraces
#20
Ling-Ling Zhang, Hu Chen, Mi Luo, Xiao-Wei Zhang, Mei Deng, Jian Ma, Peng-Fei Qi, Ji-Rui Wang, Guo-Yue Chen, Ya-Xi Liu, Zhi-En Pu, Wei Li, Xiu-Jin Lan, Yu-Ming Wei, You-Liang Zheng, Qian-Tao Jiang
A novel Wx-B1 allele was characterized; a transposon insertion resulted in the loss of its function, which is different from the previously reported gene silencing mechanisms at the Wx-B1 locus. The waxy protein composition of 53 Chinese wheat landraces was analyzed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional gel electrophoresis; of these, 10 did not show the expression of Wx-A1 (four accession) or Wx-B1 (six accessions) protein. The results of molecular marker detection revealed that the Wx-B1 allele (Wx-B1n) showed normal expression, inconsistent with the findings of SDS-PAGE for the Xiaobaipi accession...
March 17, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
keyword
keyword
65654
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"