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https://www.readbyqxmd.com/read/28212410/a-high-throughput-genetic-screen-identifies-previously-uncharacterized-borrelia-burgdorferi-genes-important-for-resistance-against-reactive-oxygen-and-nitrogen-species
#1
Meghan E Ramsey, Jenny A Hyde, Diana N Medina-Perez, Tao Lin, Lihui Gao, Maureen E Lundt, Xin Li, Steven J Norris, Jon T Skare, Linden T Hu
Borrelia burgdorferi, the causative agent of Lyme disease in humans, is exposed to reactive oxygen and nitrogen species (ROS and RNS) in both the tick vector and vertebrate reservoir hosts. B. burgdorferi contains a limited repertoire of canonical oxidative stress response genes, suggesting that novel gene functions may be important for protection of B. burgdorferi against ROS or RNS exposure. Here, we use transposon insertion sequencing (Tn-seq) to conduct an unbiased search for genes involved in resistance to nitric oxide, hydrogen peroxide, and tertiary-butyl hydroperoxide in vitro...
February 17, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28207953/sgs1-a-neomorphic-nac52-allele-impairing-ptgs-through-sgs3-down-regulation
#2
Nicolas Butel, Ivan Le Masson, Nathalie Bouteiller, Hervé Vaucheret, Taline Elmayan
Post-transcriptional gene silencing (PTGS) is a defense mechanism that targets invading nucleic acids from endogenous (transposons) or exogenous (pathogens, transgenes) origins. Genetic screens based on the reactivation of silenced transgenes have long been used to identify cellular PTGS components and regulators. Here we show that the first isolated PTGS-deficient mutant, sgs1, is impaired in the transcription factor NAC52. This mutant exhibits striking similarities with a mutant impaired in the H3K4me3 demethylase JMJ14 isolated from the same genetic screen...
February 16, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28207789/carbapenem-resistance-and-pathogenicity-of-bovine-acinetobacter-indicus-like-isolates
#3
Peter Klotz, Stephan Göttig, Ursula Leidner, Torsten Semmler, Sandra Scheufen, Christa Ewers
The objective of this study was to characterize blaOXA-23 harbouring Acinetobacter indicus-like strains from cattle including genomic and phylogenetic analyses, antimicrobial susceptibility testing and evaluation of pathogenicity in vitro and in vivo. Nasal and rectal swabs (n = 45) from cattle in Germany were screened for carbapenem-non-susceptible Acinetobacter spp. Thereby, two carbapenem resistant Acinetobacter spp. from the nasal cavities of two calves could be isolated. MALDI-TOF mass spectrometry and 16S rDNA sequencing identified these isolates as A...
2017: PloS One
https://www.readbyqxmd.com/read/28204924/genome-wide-analysis-of-transposable-elements-in-the-coffee-berry-borer-hypothenemus-hampei-coleoptera-curculionidae-description-of-novel-families
#4
Eric M Hernandez-Hernandez, Rita Daniela Fernández-Medina, Lucio Navarro-Escalante, Jonathan Nuñez, Pablo Benavides-Machado, Claudia M A Carareto
The coffee berry borer (CBB) Hypothenemus hampei is the most limiting pest of coffee production worldwide. The CBB genome has been recently sequenced; however, information regarding the presence and characteristics of transposable elements (TEs) was not provided. Using systematic searching strategies based on both de novo and homology-based approaches, we present a library of TEs from the draft genome of CBB sequenced by the Colombian Coffee Growers Federation. The library consists of 880 sequences classified as 66% Class I (LTRs: 46%, non-LTRs: 20%) and 34% Class II (DNA transposons: 8%, Helitrons: 16% and MITEs: 10%) elements, including families of the three main LTR (Gypsy, Bel-Pao and Copia) and non-LTR (CR1, Daphne, I/Nimb, Jockey, Kiri, R1, R2 and R4) clades and DNA superfamilies (Tc1-mariner, hAT, Merlin, P, PIF-Harbinger, PiggyBac and Helitron)...
February 15, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28199335/ecological-networks-to-unravel-the-routes-to-horizontal-transposon-transfers
#5
Samuel Venner, Vincent Miele, Christophe Terzian, Christian Biémont, Vincent Daubin, Cédric Feschotte, Dominique Pontier
Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs...
February 2017: PLoS Biology
https://www.readbyqxmd.com/read/28199212/transposon-mediated-directed-mutation-in-bacteria-and-eukaryotes
#6
Milton H Saier, Chika Kukita, Zhongge Zhang
Transposon-mediated "directed" mutations occur at higher frequencies when beneficial than when detrimental and relieve the stress that causes them. The first and best-studied example involves regulation of Insertion Sequence-5 (IS5) insertion into a specific activating site upstream of the glycerol utilization operon in Escherichia coli, glpFK. This event promotes high level expression of the glpFK operon, allowing glycerol utilization in wild type cells under inhibitory conditions. The phosphoenolpyruvate-dependent, sugar transporting, phosphotransferase system (PTS) influences this process by regulating cytoplasmic glycerol-3-phosphate and cyclic AMP concentrations...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28198411/the-secondary-resistome-of-multidrug-resistant-klebsiella-pneumoniae
#7
Bimal Jana, Amy K Cain, William T Doerrler, Christine J Boinett, Maria C Fookes, Julian Parkhill, Luca Guardabassi
Klebsiella pneumoniae causes severe lung and bloodstream infections that are difficult to treat due to multidrug resistance. We hypothesized that antimicrobial resistance can be reversed by targeting chromosomal non-essential genes that are not responsible for acquired resistance but essential for resistant bacteria under therapeutic concentrations of antimicrobials. Conditional essentiality of individual genes to antimicrobial resistance was evaluated in an epidemic multidrug-resistant clone of K. pneumoniae (ST258)...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28193840/co-chaperone-hsp70-hsp90-organizing-protein-hop-is-required-for-transposon-silencing-and-pirna-biogenesis
#8
Joseph A Karam, Rasesh Y Parikh, Dhananjaya Nayak, David Rosenkranz, Vamsi K Gangaraju
piRNAs are 26-30nt germ-line specific small non-coding RNAs that have evolutionarily conserved function in mobile genetic element (transposons) silencing and maintenance of genome integrity. Drosophila Hsp70/90 Organizing Protein Homolog (Hop), a co-chaperone, interacts with piRNA binding protein Piwi and mediates silencing of phenotypic variations. However, it is not known if Hop has a direct role in piRNA biogenesis and transposon silencing. Here, we show that knockdown of Hop in the germ-line nurse cells (GLKD) of Drosophila ovaries leads to activation of transposons...
February 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28193652/characterization-of-the-plasmid-pjb12-from-pseudomonas-aeruginosa-reveals-tn6352-a-novel-putative-transposon-associated-with-mobilization-of-blavim-2-harboring-in58-integron
#9
João Botelho, Filipa Grosso, Luísa Peixe
blaVIM-2-carrying In58 integron has been linked to a chromosomal location in different bacterial species, including Pseudomonas aeruginosa This work reports the first fully sequenced In58-harboring plasmid, significantly different from the two previously identified blaVIM-2-carrying plasmids in P. aeruginosablaVIM-2 was possibly acquired by transposition of Tn6352, a novel transposon composed by In58 and ISPa17 element. The recognition of similar IR sites by ISPa17 demonstrates a common mobilization process associated with blaVIM-2 and blaVIM-1 genes acquisition...
February 13, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28188692/bioreactor-scale-up-and-protein-product-quality-characterization-of-piggybac-transposon-derived-cho-pools
#10
Yashas Rajendra, Sowmya Balasubramanian, Robert B Peery, James R Swartling, Neil A McCracken, Dawn L Norris, Christopher C Frye, Gavin C Barnard
Chinese hamster ovary (CHO) cells remain the most popular host for the production of biopharmaceutical drugs, particularly monoclonal antibodies (mAbs), bispecific antibodies and Fc-fusion proteins. Creating and characterizing the stable CHO clonally-derived cell lines (CDCLs) needed to manufacture these therapeutic proteins is a lengthy and laborious process. Therefore, CHO pools have increasingly been used to rapidly produce protein to support and enable preclinical drug development. We recently described the generation of CHO pools yielding mAb titers as high as 7...
February 11, 2017: Biotechnology Progress
https://www.readbyqxmd.com/read/28188204/siderophore-product-ornibactin-is-required-for-the-bactericidal-activity-of-burkholderia-contaminans-ms14
#11
Peng Deng, Adam Foxfire, Jianhong Xu, Sonya M Baird, Jiayuan Jia, Keren H Delgado, Ronald Shin, Leif Smith, Shi-En Lu
Burkholderia contaminans MS14 was isolated from soil in Mississippi. When cultivated on nutrient broth-yeast extract (NBY) agar medium, the colonies exhibit bactericidal activity against a wide range of plant pathogenic bacteria. Only a bacteriostatic compound with siderophore activity was successfully purified, which was determined by nuclear magnetic resonance (NMR) to be ornibactin. The isolation of the bactericidal compound has not yet been achieved, thus, the exact nature of the bactericidal compound is still unknown...
February 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28174020/necessity-is-the-mother-of-invention-ciliates-transposons-and-transgenerational-inheritance
#12
REVIEW
Sarah E Allen, Mariusz Nowacki
Ciliates are a fascinating model system for the study of the interaction between eukaryotic germlines and somatic lines, especially with regard to the invasion and defence against transposable elements. They separate their germline and somatic line into two nuclei within the same cell, and they silence transposons and repetitive elements by way of deleting them from their somatic genome. This large-scale deletion event uses a series of intricate sequence targeting pathways involving small RNAs and transposases, part of which consists of a transnuclear comparison between maternal soma and daughter germline...
February 4, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28170428/comparative-study-on-the-in-vitro-effects-of-pseudomonas-aeruginosa-and-seaweed-alginates-on-human-gut-microbiota
#13
Shaofeng Bai, Huahai Chen, Liying Zhu, Wei Liu, Hongwei D Yu, Xin Wang, Yeshi Yin
Alginates pertain to organic polysaccharides that have been extensively used in food- and medicine-related industries. The present study obtained alginates from an alginate overproducing Pseudomonas aeruginosa PAO1 mutant by screening transposon mutagenesis libraries. The interaction between bacterial and seaweed alginates and gut microbiota were further studied by using an in vitro batch fermentation system. Thin-layer chromatography (TLC) analysis indicated that both bacterial and seaweed alginates can be completely degraded by fecal bacteria isolated from study volunteers, indicating that a minor structural difference between bacterial and seaweed alginates (O-acetylation and lack of G-G blocks) didn't affect the digestion of alginates by human microbiota...
2017: PloS One
https://www.readbyqxmd.com/read/28169338/shrimp-ahpnd-causing-plasmids-encoding-the-pirab-toxins-as-mediated-by-pirab-tn903-are-prevalent-in-various-vibrio-species
#14
Jinzhou Xiao, Liyuan Liu, Yiyun Ke, Xiefei Li, Yunfei Liu, Yingjie Pan, Shuling Yan, Yongjie Wang
Acute hepatopancreatic necrosis disease (AHPND) is a newly emerging shrimp disease caused by pirAB toxins encoded by a plasmid found in Vibrio parahaemolyticus. The pirAB toxins are the homologs of the Photorhabdus insect-related (Pir) toxins. Here, we report the complete sequences of the AHPND-causing plasmid isolated from V. owensii, as well as those of its 11 siblings (pVH family). In addition, we also included 13 related plasmids (pVH-r family) without the pirAB genes isolated from a variety of species within the Vibrio Harveyi clade...
February 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28167551/genomic-characterization-of-two-kpc-producing-klebsiella-isolates-collected-in-1997-from-new-york-city
#15
Brandon Eilertson, Liang Chen, Kalyan D Chavda, Barry N Kreiswirth
Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae have now become a global public health threat. However, the origin of this pandemic and characterization of pre-2003 blaKPC-harboring plasmids remain unknown. Here we used next generation sequencing to characterize two KPC-2-producing K. pneumoniae and K. michiganensis isolates, collected from a New York City hospital in 1997. Although identified in two different Klebsiella species, the blaKPC-2 gene is harbored by Tn4401b transposon on two highly similar IncN plasmids...
February 6, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28166822/disruption-of-the-m949_rs01915-gene-changed-the-bacterial-lipopolysaccharide-pattern-pathogenicity-and-gene-expression-of-riemerella-anatipestifer
#16
Yafeng Dou, Xiaolan Wang, Guijing Yu, Shaohui Wang, Mingxing Tian, Jingjing Qi, Tao Li, Chan Ding, Shengqing Yu
Riemerella anatipestifer is an important pathogen that causes septicemia anserum exsudativa in ducks. Lipopolysaccharide (LPS) is considered to be a major virulence factor of R. anatipestifer. To identify genes involved in LPS biosynthesis, we screened a library of random Tn4351 transposon mutants using a monoclonal antibody against R. anatipestifer serotype 1 LPS (anti-LPS MAb). A mutant strain RA1067 which lost the reactivity in an indirect ELISA was obtained. Southern blot and sequencing analyses indicated a single Tn4351 was inserted at 116 bp in the M949_RS01915 gene in the RA1067 chromosomal DNA...
February 6, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28166723/prophages-and-adaptation-of-staphylococcus-aureus-st398-to-the-human-clinic
#17
Seydina M Diene, Anna Rita Corvaglia, Patrice François, Nathalie van der Mee-Marquet
BACKGROUND: It has been suggested that prophages in the ST398 S. aureus clone are responsible for expanding ST398's spectrum of action and increasing its ability to cause human infections. We carried out the first characterization of the various prophages carried by 76 ST398 bloodstream infection (BSI) isolates obtained over 9 years of observation. RESULTS: Whole-genome sequencing of 22 representative isolates showed (1) the presence of the φ3-prophage and diverse genetic features typical of animal-associated isolates (i...
February 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28165493/a-noise-trimming-and-positional-significance-of-transposon-insertion-system-to-identify-essential-genes-in-yersinia-pestis
#18
Zheng Rong Yang, Helen L Bullifent, Karen Moore, Konrad Paszkiewicz, Richard J Saint, Stephanie J Southern, Olivia L Champion, Nicola J Senior, Mitali Sarkar-Tyson, Petra C F Oyston, Timothy P Atkins, Richard W Titball
Massively parallel sequencing technology coupled with saturation mutagenesis has provided new and global insights into gene functions and roles. At a simplistic level, the frequency of mutations within genes can indicate the degree of essentiality. However, this approach neglects to take account of the positional significance of mutations - the function of a gene is less likely to be disrupted by a mutation close to the distal ends. Therefore, a systematic bioinformatics approach to improve the reliability of essential gene identification is desirable...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28159794/rifz-amed_0655-is-a-pathway-specific-regulator-for-rifamycin-biosynthesis-in-amycolatopsis-mediterranei
#19
Chen Li, Xinqiang Liu, Chao Lei, Han Yan, Zhihui Shao, Ying Wang, Guoping Zhao, Jin Wang, Xiaoming Ding
: Rifamycin and its derivatives are particularly effective against the pathogenic mycobacteria Mycobacterium tuberculosis and Mycobacterium leprae Although the biosynthetic pathway of rifamycin has been extensively studied in Amycolatopsis mediterranei, little is known about the regulation in rifamycin biosynthesis. Here, an in vivo transposon system was employed to identify genes involved in the regulation of rifamycin production in A. mediterranei U32. Totally, nine rifamycin-defecient mutants were isolated, among which three mutants had the transposon inserted in AMED_0655 (namely rifZ, encoding a LuxR_family regulator)...
February 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28159756/structure-and-origin-of-the-white-cap-locus-and-its-role-in-evolution-of-grain-color-in-maize
#20
Bao-Cai Tan, Jiahn-Chou Guan, Shou Ding, Shan Wu, Jonathan W Saunders, Karen E Koch, Donald R McCarty
Selection for yellow and white grain types has been central to post-domestication improvement of maize. While genetic control of carotenoid biosynthesis in endosperm is attributed primarily to the Yellow1 (Y1) phytoene synthase gene, less is known about the role of the dominant white endosperm factor White Cap (Wc). We show that the Wc locus contains multiple, tandem copies of a Carotenoid cleavage dioxygenase 1 (Ccd1) gene that encodes a carotenoid-degrading enzyme. A survey of 111 maize inbreds and landraces, together with 22 teosinte accessions, reveals that Wc is exclusive to maize, where it is prevalent in white-grain (y1) varieties...
February 3, 2017: Genetics
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