keyword
MENU ▼
Read by QxMD icon Read
search

Tn-seq

keyword
https://www.readbyqxmd.com/read/28900609/genes-contributing-to-porphyromonas-gingivalis-fitness-in-abscess-and-epithelial-cell-colonization-environments
#1
Daniel P Miller, Justin A Hutcherson, Yan Wang, Zuzanna M Nowakowska, Jan Potempa, Deborah R Yoder-Himes, David A Scott, Marvin Whiteley, Richard J Lamont
Porphyromonas gingivalis is an important cause of serious periodontal diseases, and is emerging as a pathogen in several systemic conditions including some forms of cancer. Initial colonization by P. gingivalis involves interaction with gingival epithelial cells, and the organism can also access host tissues and spread haematogenously. To better understand the mechanisms underlying these properties, we utilized a highly saturated transposon insertion library of P. gingivalis, and assessed the fitness of mutants during epithelial cell colonization and survival in a murine abscess model by high-throughput sequencing (Tn-Seq)...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28855313/complexity-of-complement-resistance-factors-expressed-by-acinetobacter-baumannii-needed-for-survival-in-human-serum
#2
Amaro F Sanchez-Larrayoz, Noha M Elhosseiny, Marc G Chevrette, Yang Fu, Peter Giunta, Raúl G Spallanzani, Keerthikka Ravi, Gerald B Pier, Stephen Lory, Tomás Maira-Litrán
Acinetobacter baumannii is a bacterial pathogen with increasing impact in healthcare settings, due in part to this organism's resistance to many antimicrobial agents, with pneumonia and bacteremia as the most common manifestations of disease. A significant proportion of clinically relevant A. baumannii strains are resistant to killing by normal human serum (NHS), an observation supported in this study by showing that 12 out of 15 genetically diverse strains of A. baumannii are resistant to NHS killing. To expand our understanding of the genetic basis of A...
August 30, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28832676/genome-wide-discovery-of-novel-m1t1-group-a-streptococcal-determinants-important-for-fitness-and-virulence-during-soft-tissue-infection
#3
Yoann Le Breton, Ashton T Belew, Jeffrey A Freiberg, Ganesh S Sundar, Emrul Islam, Joshua Lieberman, Mark E Shirtliff, Hervé Tettelin, Najib M El-Sayed, Kevin S McIver
The Group A Streptococcus remains a significant human pathogen causing a wide array of disease ranging from self-limiting to life-threatening invasive infections. Epithelium (skin or throat) colonization with progression to the subepithelial tissues is the common step in all GAS infections. Here, we used transposon-sequencing (Tn-seq) to define the GAS 5448 genetic requirements for in vivo fitness in subepithelial tissue. A near-saturation transposon library of the M1T1 GAS 5448 strain was injected subcutaneously into mice, producing suppurative inflammation at 24 h that progressed to prominent abscesses with tissue necrosis at 48 h...
August 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28806924/essential-genome-of-campylobacter-jejuni
#4
Rabindra K Mandal, Tieshan Jiang, Young Min Kwon
BACKGROUND: Campylobacter species are a leading cause of bacterial foodborne illness worldwide. Despite the global efforts to curb them, Campylobacter infections have increased continuously in both developed and developing countries. The development of effective strategies to control the infection by this pathogen is warranted. The essential genes of bacteria are the most prominent targets for this purpose. In this study, we used transposon sequencing (Tn-seq) of a genome-saturating library of Tn5 insertion mutants to define the essential genome of C...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28765224/genome-wide-sensitivity-analysis-of-the-microsymbiont-sinorhizobium-meliloti-to-symbiotically-important-defensin-like-host-peptides
#5
Markus F F Arnold, Mohammed Shabab, Jon Penterman, Kevin L Boehme, Joel S Griffitts, Graham C Walker
The model legume species Medicago truncatula expresses more than 700 nodule-specific cysteine-rich (NCR) signaling peptides that mediate the differentiation of Sinorhizobium meliloti bacteria into nitrogen-fixing bacteroids. NCR peptides are essential for a successful symbiosis in legume plants of the inverted-repeat-lacking clade (IRLC) and show similarity to mammalian defensins. In addition to signaling functions, many NCR peptides exhibit antimicrobial activity in vitro and in vivo Bacterial resistance to these antimicrobial activities is likely to be important for symbiosis...
August 1, 2017: MBio
https://www.readbyqxmd.com/read/28760848/comprehensive-arrayed-transposon-mutant-library-of-klebsiella-pneumoniae-outbreak-strain-kpnih1
#6
Beth Ramage, Roxanne Erolin, Kiara Held, Joe Gasper, Eli Weiss, Mitch Brittnacher, Larry Gallagher, Colin Manoil
Klebsiella pneumoniae and other carbapenem-resistant Enterobacteriaceae are a major cause of hospital-acquired infections, yet the basis of their success as nosocomial pathogens is poorly understood. To help provide a foundation for genetic analysis of K. pneumoniae, we created an arrayed, sequence-defined transposon mutant library of an isolate from the 2011 outbreak of infections at the U.S. National Institutes of Health Clinical Center. The library is made up of 12,000 individually arrayed mutants of a carbapenemase deletion parent strain and provides coverage of 85% of predicted genes...
July 31, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28749938/the-mecillinam-resistome-reveals-a-role-for-peptidoglycan-endopeptidases-in-stimulating-cell-wall-synthesis-in-escherichia-coli
#7
Ghee Chuan Lai, Hongbaek Cho, Thomas G Bernhardt
Bacterial cells are typically surrounded by an net-like macromolecule called the cell wall constructed from the heteropolymer peptidoglycan (PG). Biogenesis of this matrix is the target of penicillin and related beta-lactams. These drugs inhibit the transpeptidase activity of PG synthases called penicillin-binding proteins (PBPs), preventing the crosslinking of nascent wall material into the existing network. The beta-lactam mecillinam specifically targets the PBP2 enzyme in the cell elongation machinery of Escherichia coli...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28683752/tnseqdiff-identification-of-conditionally-essential-genes-in-transposon-sequencing-studies
#8
Lili Zhao, Mark T Anderson, Weisheng Wu, Harry L T Mobley, Michael A Bachman
BACKGROUND: Tn-Seq is a high throughput technique for analysis of transposon mutant libraries to determine conditional essentiality of a gene under an experimental condition. A special feature of the Tn-seq data is that multiple mutants in a gene provides independent evidence to prioritize that gene as being essential. The existing methods do not account for this feature or rely on a high-density transposon library. Moreover, these methods are unable to accommodate complex designs. RESULTS: The method proposed here is specifically designed for the analysis of Tn-Seq data...
July 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28677146/genes-essential-for-phototrophic-growth-by-a-purple-alphaproteobacterium
#9
Jianming Yang, Liang Yin, Faith H Lessner, Ernesto S Nakayasu, Samuel H Payne, Kathryn R Fixen, Larry Gallagher, Caroline S Harwood
Tn-seq was used to identify genes essential for phototrophic growth by the purple bacterium Rhodopseudomonas palustris. About 167 genes required for anaerobic growth on acetate in light were identified, 35 of which are annotated as photosynthesis genes. The essentiality of many of these genes by analysing the phenotypes of independently generated mutants that had altered pigmentation was verified. Three genes were identified, two possibly involved in biogenesis of the membrane-bound photosynthetic apparatus and one for phosphatidylcholine biosynthesis, that were not known to be essential for phototrophic growth...
July 5, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28674067/genome-scale-mutational-analysis-of-geobacter-sulfurreducens-reveals-distinct-molecular-mechanisms-for-respiration-and-sensing-of-poised-electrodes-versus-fe-iii-oxides
#10
Chi Ho Chan, Caleb E Levar, Fernanda Jiménez-Otero, Daniel R Bond
Geobacter sulfurreducens generates electrical current by coupling intracellular oxidation of organic acids to the reduction of proteins on the cell surface that are able to interface with electrodes. This ability is attributed to the bacterium's capacity to respire other extracellular electron acceptors that require contact, such as insoluble metal oxides. To directly investigate the genetic basis of electrode-based respiration, we constructed Geobacter sulfurreducens transposon-insertion sequencing (Tn-Seq) libraries for growth, with soluble fumarate or an electrode as the electron acceptor...
October 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28614382/genome-wide-transposon-mutagenesis-of-proteus-mirabilis-essential-genes-fitness-factors-for-catheter-associated-urinary-tract-infection-and-the-impact-of-polymicrobial-infection-on-fitness-requirements
#11
Chelsie E Armbruster, Valerie Forsyth-DeOrnellas, Alexandra O Johnson, Sara N Smith, Lili Zhao, Weisheng Wu, Harry L T Mobley
The Gram-negative bacterium Proteus mirabilis is a leading cause of catheter-associated urinary tract infections (CAUTIs), which are often polymicrobial. Numerous prior studies have uncovered virulence factors for P. mirabilis pathogenicity in a murine model of ascending UTI, but little is known concerning pathogenesis during CAUTI or polymicrobial infection. In this study, we utilized five pools of 10,000 transposon mutants each and transposon insertion-site sequencing (Tn-Seq) to identify the full arsenal of P...
June 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28498899/magenta-a-galaxy-implemented-tool-for-complete-tn-seq-analysis-and-data-visualization
#12
Katherine Maia McCoy, Margaret L Antonio, Tim van Opijnen
Motivation: Transposon insertion sequencing (Tn-Seq) is a microbial systems-level tool, that can determine on a genome-wide scale and in high-throughput, whether a gene, or a specific genomic region, is important for fitness under a specific experimental condition. Results: Here, we present MAGenTA, a suite of analysis tools which accurately calculate the growth rate for each disrupted gene in the genome to enable the discovery of: (i) new leads for gene function, (ii) non-coding RNAs; (iii) genes, pathways and ncRNAs that are involved in tolerating drugs or induce disease; (iv) higher order genome organization; and (v) host-factors that affect bacterial host susceptibility...
September 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28490437/high-throughput-crispri-phenotyping-identifies-new-essential-genes-in-streptococcus-pneumoniae
#13
Xue Liu, Clement Gallay, Morten Kjos, Arnau Domenech, Jelle Slager, Sebastiaan P van Kessel, Kèvin Knoops, Robin A Sorg, Jing-Ren Zhang, Jan-Willem Veening
Genome-wide screens have discovered a large set of essential genes in the opportunistic human pathogen Streptococcus pneumoniae However, the functions of many essential genes are still unknown, hampering vaccine development and drug discovery. Based on results from transposon sequencing (Tn-seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting 348 potentially essential genes by CRISPR interference (CRISPRi) and show a growth phenotype for 254 of them (73%)...
May 10, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28484050/using-tn-seq-to-identify-pigmentation-related-genes-of-porphyromonas-gingivalis-characterization-of-the-role-of-a-putative-glycosyltransferase
#14
Brian A Klein, Louis P Cornacchione, Marisha Collins, Michael H Malamy, Margaret J Duncan, Linden T Hu
Cellular pigmentation is an important virulence factor of the oral pathogen Porphyromonas gingivalis Pigmentation has been associated with many bacterial functions, including but not limited to colonization, maintaining a local anaerobic environment by binding oxygen molecules, and defense against reactive oxygen species (ROS) produced by immune cells. Pigmentation-associated loci identified to date have involved lipopolysaccharide, fimbriae, and heme acquisition and processing. We utilized a transposon mutant library of P...
July 15, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28476775/defining-genetic-fitness-determinants-and-creating-genomic-resources-for-an-oral-pathogen
#15
Ajay M Narayanan, Matthew M Ramsey, Apollo Stacy, Marvin Whiteley
Periodontitis is a microbial infection that destroys the structures that support the teeth. Although it is typically a chronic condition, rapidly progressing, aggressive forms are associated with the oral pathogen Aggregatibacter actinomycetemcomitans One of this bacterium's key virulence traits is its ability to attach to surfaces and form robust biofilms that resist killing by the host and antibiotics. Though much has been learned about A. actinomycetemcomitans since its initial discovery, we lack insight into a fundamental aspect of its basic biology, as we do not know the full set of genes that it requires for viability (the essential genome)...
July 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28455506/genome-wide-fitness-analyses-of-the-foodborne-pathogen-campylobacter-jejuni-in-in-vitro-and-in-vivo-models
#16
Stefan P W de Vries, Srishti Gupta, Abiyad Baig, Elli Wright, Amy Wedley, Annette Nygaard Jensen, Lizeth LaCharme Lora, Suzanne Humphrey, Henrik Skovgård, Kareen Macleod, Elsa Pont, Dominika P Wolanska, Joanna L'Heureux, Fredrick M Mobegi, David G E Smith, Paul Everest, Aldert Zomer, Nicola Williams, Paul Wigley, Thomas Humphrey, Duncan J Maskell, Andrew J Grant
Campylobacter is the most common cause of foodborne bacterial illness worldwide. Faecal contamination of meat, especially chicken, during processing represents a key route of transmission to humans. There is a lack of insight into the mechanisms driving C. jejuni growth and survival within hosts and the environment. Here, we report a detailed analysis of C. jejuni fitness across models reflecting stages in its life cycle. Transposon (Tn) gene-inactivation libraries were generated in three C. jejuni strains and the impact on fitness during chicken colonisation, survival in houseflies and under nutrient-rich and -poor conditions at 4 °C and infection of human gut epithelial cells was assessed by Tn-insertion site sequencing (Tn-seq)...
April 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28373355/the-rhomboid-protease-glpg-promotes-the-persistence-of-extraintestinal-pathogenic-escherichia-coli-within-the-gut
#17
Colin W Russell, Amanda C Richards, Alexander S Chang, Matthew A Mulvey
Extraintestinal pathogenic Escherichia coli (ExPEC) strains are typically benign within the mammalian gut but can disperse to extraintestinal sites to cause diseases like urinary tract infections and sepsis. As occupation of the intestinal tract is often a prerequisite for ExPEC-mediated pathogenesis, we set out to understand how ExPEC colonizes this niche. A screen using transposon sequencing (Tn-seq) was performed to search for genes within ExPEC isolate F11 that are important for growth in intestinal mucus, which is thought to be a major source of nutrients for E...
June 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28334803/statistical-analysis-of-genetic-interactions-in-tn-seq-data
#18
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...
June 20, 2017: Nucleic Acids Research
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
#19
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 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/27941863/coze-is-a-member-of-the-mrecd-complex-that-directs-cell-elongation-in-streptococcus-pneumoniae
#20
Andrew K Fenton, Lamya El Mortaji, Derek T C Lau, David Z Rudner, Thomas G Bernhardt
Most bacterial cells are surrounded by a peptidoglycan cell wall that is essential for their integrity. The major synthases of this exoskeleton are called penicillin-binding proteins (PBPs)(1,2). Surprisingly little is known about how cells control these enzymes, given their importance as drug targets. In the model Gram-negative bacterium Escherichia coli, outer membrane lipoproteins are critical activators of the class A PBPs (aPBPs)(3,4), bifunctional synthases capable of polymerizing and crosslinking peptidoglycan to build the exoskeletal matrix(1)...
December 12, 2016: Nature Microbiology
keyword
keyword
8226
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"