keyword
MENU ▼
Read by QxMD icon Read
search

Transposon mutagenesis

keyword
https://www.readbyqxmd.com/read/29472909/metagenomic-profiling-of-soil-microbes-to-mine-salt-stress-tolerance-genes
#1
Vasim Ahmed, Manoj K Verma, Shashank Gupta, Vibha Mandhan, Nar S Chauhan
Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanisms involved in osmoadaptation. The present study explores the saline soil microbiome for its native structure and novel genetic elements involved in osmoadaptation...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29470858/genes-affecting-progression-of-bacteriophage-p22-infection-in-salmonella-identified-by-transposon-and-single-gene-deletion-screens
#2
Kaitlynne Bohm, Steffen Porwollik, Weiping Chu, John A Dover, Eddie B Gilcrease, Sherwood R Casjens, Michael McClelland, Kristin N Parent
Bacteriophages rely on their hosts for replication, and many host genes critically determine either viral progeny production or host success via phage resistance. A random insertion transposon library of 240,000 mutants in Salmonella enterica serovar Typhimurium was used to monitor effects of individual bacterial gene disruptions on bacteriophage P22 lytic infection. These experiments revealed candidate host genes that alter the timing of phage P22 propagation. Using a False Discovery Rate of <0.1, mutations in 235 host genes either blocked or delayed progression of P22 lytic infection, including many genes for which this role was previously unknown...
February 22, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29463657/the-essential-genome-of-escherichia-coli-k-12
#3
Emily C A Goodall, Ashley Robinson, Iain G Johnston, Sara Jabbari, Keith A Turner, Adam F Cunningham, Peter A Lund, Jeffrey A Cole, Ian R Henderson
Transposon-directed insertion site sequencing (TraDIS) is a high-throughput method coupling transposon mutagenesis with short-fragment DNA sequencing. It is commonly used to identify essential genes. Single gene deletion libraries are considered the gold standard for identifying essential genes. Currently, the TraDIS method has not been benchmarked against such libraries, and therefore, it remains unclear whether the two methodologies are comparable. To address this, a high-density transposon library was constructed in Escherichia coli K-12...
February 20, 2018: MBio
https://www.readbyqxmd.com/read/29454685/genes-involved-in-tolerance-to-osmotic-stress-by-random-mutagenesis-in-cronobacter-malonaticus
#4
Maofeng Zhang, Xiyan Zhang, Liaowang Tong, Yaping Wang, Dexin Ou, Jumei Zhang, Qingping Wu, Yingwang Ye
Cronobacter malonaticus is one of the opportunistic food-borne pathogens in powdered infant formula and has unusual abilities to survive under environmental stresses such as osmotic conditions. However, the genes involved in osmotic stress have received little attention in C. malonaticus. Here, genes involved in osmotic stress were determined in C. malonaticus using a transposon mutagenesis approach. According to the growth of mutants (n = 215) under 5.0% NaCl concentration, the survival of 5 mutants under osmotic stress was significantly decreased compared with that of the wild type strain...
February 14, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29445422/sleeping-beauty-transposon-integrates-into-non-ta-dinucleotides
#5
Yabin Guo, Yin Zhang, Kaishun Hu
Background: Sleeping Beauty transposon (SB) has become an increasingly important genetic tool for generating mutations in vertebrate cells. It is widely thought that SB exclusively integrates into TA dinucleotides. However, this strict TA-preference has not been rigorously tested in large numbers of insertion sites that now can be detected with next generation sequencing. Li et al. found 71 SB insertions in non-TA dinucleotides in 2013, suggesting that TA dinucleotides are not the only sites of SB integration, yet further studies on this topic have not been carried out...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29444170/genotypic-and-phenotypic-characterization-of-the-sdccag8tn-sb-tyr-2161b-ca1c2ove-mouse-model
#6
Katie Weihbrecht, Wesley A Goar, Calvin S Carter, Val C Sheffield, Seongjin Seo
Nephronophthisis-related ciliopathies (NPHP-RC) are a group of disorders that present with end-stage renal failure in childhood/adolescence, kidney cysts, retinal degeneration, and cerebellar hypoplasia. One disorder that shares clinical features with NPHP-RC is Bardet-Biedl Syndrome (BBS). Serologically defined colon cancer antigen 8 (SDCCAG8; also known as NPHP10 and BBS16) is an NPHP gene that is also associated with BBS. To better understand the patho-mechanisms of NPHP and BBS caused by loss of SDCCAG8 function, we characterized an SDCCAG8 mouse model (Sdccag8Tn(sb-Tyr)2161B...
2018: PloS One
https://www.readbyqxmd.com/read/29435491/genomewide-identification-of-essential-genes-and-fitness-determinants-of-streptococcus-mutans-ua159
#7
Robert C Shields, Lin Zeng, David J Culp, Robert A Burne
Transposon mutagenesis coupled with next-generation DNA sequencing (Tn-seq) is a powerful tool for discovering regions of the genome that are required for the survival of bacteria in different environments. We adapted this technique to the dental caries pathogen Streptococcus mutans UA159 and identified 11% of the genome as essential, with many genes encoding products required for replication, translation, lipid metabolism, and cell wall biogenesis. Comparison of the essential genome of S. mutans UA159 with those of selected other streptococci for which such information is available revealed several metabolic pathways and genes that are required in S...
January 2018: MSphere
https://www.readbyqxmd.com/read/29386109/a-forward-genetic-screen-targeting-the-endothelium-reveals-a-regulatory-role-for-the-lipid-kinase-pi4ka-in-myelo-and-erythropoiesis
#8
Safiyyah Ziyad, Jesse D Riordan, Ann M Cavanaugh, Trent Su, Gloria E Hernandez, Georg Hilfenhaus, Marco Morselli, Kristine Huynh, Kevin Wang, Jau-Nian Chen, Adam J Dupuy, M Luisa Iruela-Arispe
Given its role as the source of definitive hematopoietic cells, we sought to determine whether mutations initiated in the hemogenic endothelium would yield hematopoietic abnormalities or malignancies. Here, we find that endothelium-specific transposon mutagenesis in mice promotes hematopoietic pathologies that are both myeloid and lymphoid in nature. Frequently mutated genes included previously recognized cancer drivers and additional candidates, such as Pi4ka, a lipid kinase whose mutation was found to promote myeloid and erythroid dysfunction...
January 30, 2018: Cell Reports
https://www.readbyqxmd.com/read/29385532/sequence-specific-dna-binding-activity-of-the-cross-brace-zinc-finger-motif-of-the-piggybac-transposase
#9
Nelly Morellet, Xianghong Li, Silke A Wieninger, Jennifer L Taylor, Julien Bischerour, Séverine Moriau, Ewen Lescop, Benjamin Bardiaux, Nathalie Mathy, Nadine Assrir, Mireille Bétermier, Michael Nilges, Alison B Hickman, Fred Dyda, Nancy L Craig, Eric Guittet
The piggyBac transposase (PB) is distinguished by its activity and utility in genome engineering, especially in humans where it has highly promising therapeutic potential. Little is known, however, about the structure-function relationships of the different domains of PB. Here, we demonstrate in vitro and in vivo that its C-terminal Cysteine-Rich Domain (CRD) is essential for DNA breakage, joining and transposition and that it binds to specific DNA sequences in the left and right transposon ends, and to an additional unexpectedly internal site at the left end...
January 27, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29378819/maize-transposable-elements-ac-ds-as-insertion-mutagenesis-tools-in-candida-albicans
#10
Kevin Mielich, Ella Shtifman-Segal, Julia C Golz, Guisheng Zeng, Yue Wang, Judith Berman, Reinhard Kunze
In non-model systems genetic research is often limited by the lack of techniques for the generation and identification of gene mutations. One approach to overcome this bottleneck is the application of transposons for gene tagging. We have established a two-element transposon tagging system, based on the transposable elements Activator (Ac)/Dissociation (Ds) from maize, for in vivo insertion mutagenesis in the fungal human pathogen Candidaalbicans A non-autonomous Ds transposon carrying a selectable marker was constructed into the ADE2 promoter on chromosome 3 and a codon usage-adapted Ac transposase gene was inserted into the neutral NEUT5L locus on chromosome 5...
January 29, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29362365/fungal-networks-shape-dynamics-of-bacterial-dispersal-and-community-assembly-in-cheese-rind-microbiomes
#11
Yuanchen Zhang, Erik K Kastman, Jeffrey S Guasto, Benjamin E Wolfe
Most studies of bacterial motility have examined small-scale (micrometer-centimeter) cell dispersal in monocultures. However, bacteria live in multispecies communities, where interactions with other microbes may inhibit or facilitate dispersal. Here, we demonstrate that motile bacteria in cheese rind microbiomes use physical networks created by filamentous fungi for dispersal, and that these interactions can shape microbial community structure. Serratia proteamaculans and other motile cheese rind bacteria disperse on fungal networks by swimming in the liquid layers formed on fungal hyphae...
January 23, 2018: Nature Communications
https://www.readbyqxmd.com/read/29359196/magic-pools-parallel-assessment-of-transposon-delivery-vectors-in-bacteria
#12
Hualan Liu, Morgan N Price, Robert Jordan Waters, Jayashree Ray, Hans K Carlson, Jacob S Lamson, Romy Chakraborty, Adam P Arkin, Adam M Deutschbauer
Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach for discovering the functions of bacterial genes. However, the development of a suitable TnSeq strategy for a given bacterium can be costly and time-consuming. To meet this challenge, we describe a part-based strategy for constructing libraries of hundreds of transposon delivery vectors, which we term "magic pools." Within a magic pool, each transposon vector has a different combination of upstream sequences (promoters and ribosome binding sites) and antibiotic resistance markers as well as a random DNA barcode sequence, which allows the tracking of each vector during mutagenesis experiments...
January 2018: MSystems
https://www.readbyqxmd.com/read/29351606/analysis-of-metal-tolerance-in-rhizobium-leguminosarum-strains-isolated-from-an-ultramafic-soil
#13
Laura Rubio-Sanz, Belén Brito, Jose Palacios
Natural habitats containing high amounts of heavy metals provide a valuable source of bacteria adapted to deal with metal toxicity. A functional analysis of the population of legume endosymbiotic bacteria in an ultramafic soil was undertaken by studying a collection of Rhizobium leguminosarum bv viciae (Rlv) isolates obtained using pea as trap plant. One of the isolates, Rlv UPM1137, was selected on the basis of its higher tolerance to nickel and cobalt and presence of inducible mechanisms for such tolerance...
January 17, 2018: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29321585/site-specific-randomization-of-the-endogenous-genome-by-a-regulatable-crispr-cas9-piggybac-system-in-human-cells
#14
Kentaro Ishida, Huaigeng Xu, Noriko Sasakawa, Mandy Siu Yu Lung, Julia Alexandra Kudryashev, Peter Gee, Akitsu Hotta
Randomized mutagenesis at an endogenous chromosomal locus is a promising approach for protein engineering, functional assessment of regulatory elements, and modeling genetic variations. In mammalian cells, however, it is challenging to perform site-specific single-nucleotide substitution with single-stranded oligodeoxynucleotide (ssODN) donor templates due to insufficient homologous recombination and the infeasibility of positive selection. Here, we developed a DNA transposon based CRISPR-Cas9 regulated transcription and nuclear shuttling (CRONUS) system that enables the stable transduction of CRISPR-Cas9/sgRNA in broad cell types, but avoids undesired genome cleavage in the absence two chemical inducing molecules...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321321/functional-analysis-of-the-dengue-virus-genome-using-an-insertional-mutagenesis-screen
#15
Jeffrey W Perry, Yanhua Chen, Elizabeth Speliotes, Andrew W Tai
In the last few decades, dengue virus, an arbovirus, has spread to over 120 countries. Although a vaccine has been approved in some countries, limitations on its effectiveness, and a lack of effective antiviral treatments reinforce the need for additional research. The functions of several viral nonstructural proteins are essentially unknown. To better understand the functions of these proteins and thus dengue virus pathogenesis, we embarked on a genome wide transposon mutagenesis screen with Next Generation Sequencing to determine sites in the viral genome that tolerate 15 nucleotide insertions...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29301589/linking-foxo3-ncoa3-and-tcf7l2-to-ras-pathway-phenotypes-through-a-genome-wide-forward-genetic-screen-in-human-colorectal-cancer-cells
#16
Snehangshu Kundu, Muhammad Akhtar Ali, Niklas Handin, Narendra Padhan, Jimmy Larsson, Maria Karoutsou, Kenneth Ban, Jacek R Wiśniewski, Per Artursson, Liqun He, Mats Hellström, Tobias Sjöblom
BACKGROUND: The Ras pathway genes KRAS, BRAF, or ERBBs have somatic mutations in ~ 60% of human colorectal carcinomas. At present, it is unknown whether the remaining cases lack mutations activating the Ras pathway or whether they have acquired mutations in genes hitherto unknown to belong to the pathway. METHODS: To address the second possibility and extend the compendium of Ras pathway genes, we used genome-wide transposon mutagenesis of two human colorectal cancer cell systems deprived of their activating KRAS or BRAF allele to identify genes enabling growth in low glucose, a Ras pathway phenotype, when targeted...
January 4, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29290613/the-antiviral-and-cancer-genomic-dna-deaminase-apobec3h-is-regulated-by-an-rna-mediated-dimerization-mechanism
#17
Nadine M Shaban, Ke Shi, Kate V Lauer, Michael A Carpenter, Christopher M Richards, Daniel Salamango, Jiayi Wang, Michael W Lopresti, Surajit Banerjee, Rena Levin-Klein, William L Brown, Hideki Aihara, Reuben S Harris
Human APOBEC3H and homologous single-stranded DNA cytosine deaminases are unique to mammals. These DNA-editing enzymes function in innate immunity by restricting the replication of viruses and transposons. APOBEC3H also contributes to cancer mutagenesis. Here, we address the fundamental nature of RNA in regulating human APOBEC3H activities. APOBEC3H co-purifies with RNA as an inactive protein, and RNase A treatment enables strong DNA deaminase activity. RNA-binding-defective mutants demonstrate clear separation of function by becoming DNA hypermutators...
January 4, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29286406/high-throughput-parallel-sequencing-to-measure-fitness-of-leptospira-interrogans-transposon-insertion-mutants-during-golden-syrian-hamster-infection
#18
Kristel Lourdault, James Matsunaga, Karen V Evangelista, David A Haake
In this manuscript, we describe a transposon sequencing (Tn-Seq) technique to identify and quantify Leptospira interrogans mutants altered in fitness during infection of Golden Syrian hamsters. Tn-Seq combines random transposon mutagenesis with the power of high-throughput sequencing technology. Animals are challenged with a pool of transposon mutants (input pool), followed by harvesting of blood and tissues a few days later to identify and quantify the number of mutants in each organ (output pools). The output pools are compared to the input pool to evaluate the in vivo fitness of each mutant...
December 18, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29281637/cell-envelope-stress-in-mycobacteria-is-regulated-by-the-novel-signal-transduction-atpase-inir-in-response-to-trehalose
#19
Maikel Boot, Vincent J C van Winden, Marion Sparrius, Robert van de Weerd, Alexander Speer, Roy Ummels, Tige Rustad, David R Sherman, Wilbert Bitter
The cell envelope of mycobacteria is a highly unique and complex structure that is functionally equivalent to that of Gram-negative bacteria to protect the bacterial cell. Defects in the integrity or assembly of this cell envelop must be sensed to allow the induction of stress response systems. The promoter that is specifically and most strongly induced upon exposure to ethambutol and isoniazid, first line drugs that affect cell envelope biogenesis, is the iniBAC promoter. In this study, we set out to identify the regulator of the iniBAC operon in Mycobacterium marinum using an unbiased transposon mutagenesis screen in a constitutively iniBAC-expressing mutant background...
December 27, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29250489/identification-of-conserved-abc-importers-necessary-for-intracellular-survival-of-legionella-pneumophila-in-multiple-hosts
#20
Amrita Lama, Samuel L Drennan, Rudd C Johnson, Grace L Rubenstein, Eric D Cambronne
It is established that the human pathogen Legionella pneumophila becomes significantly augmented for infection of macrophages after intracellular growth in amoebae when compared to like-strains cultivated in laboratory media. Based on this observation, we reasoned that the most critical virulence determinants of L.p. are expressed by responding to stimuli generated by the protozoan host specifically; a process we term "protozoan-priming." We sought to identify L.p. virulence factors that were required for replication in amoebae in order to highlight the genes necessary for production of the most infectious form of the bacterium...
2017: Frontiers in Cellular and Infection Microbiology
keyword
keyword
9262
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"