keyword
MENU ▼
Read by QxMD icon Read
search

Mariner transposon

keyword
https://www.readbyqxmd.com/read/28277948/karyotypic-evolution-and-chromosomal-organization-of-repetitive-dna-sequences-in-species-of-panaque-panaqolus-and-scobinancistrus-siluriformes-and-loricariidae-from-the-amazon-basin
#1
Thayana Ayres-Alves, Adauto Lima Cardoso, Cleusa Yoshiko Nagamachi, Leandro Melo de Sousa, Julio Cesar Pieczarka, Renata Coelho Rodrigues Noronha
Loricariidae family comprises the greatest variability of Neotropical catfish species, with more than 800 valid species. This family shows significant chromosomal diversity. Mapping of repetitive DNA sequences can be very useful in exploring such diversity, especially among groups that appear to share a preserved karyotypic macrostructure. We describe the karyotypes of Panaque armbrusteri and Panaqolus sp., as assessed using classical cytogenetic methods. Moreover, we offer a map of their repetitive sequences, including 18S and 5S ribosomal DNAs, the Rex1 and Rex3 retrotransposons, and the Tc1-mariner transposon in P...
March 9, 2017: Zebrafish
https://www.readbyqxmd.com/read/28228545/ablation-of-rnai-and-retrotransposons-accompany-acquisition-and-evolution-of-transposases-to-heterochromatin-protein-cenpb
#2
Udita Upadhyay, Suchita Srivastava, Indu Khatri, Jagpreet Singh Nanda, Srikrishna Subramanian, Amit Arora, Jagmohan Singh
Inactivation of retrotransposons is accompanied by the emergence of CENPB (centromere binding protein-B) in Schizosaccharomyces as well as in metazoans. The RNAi-induced Transcriptional Silencing (RITS) Complex, comprising Chp1 (chromodomain protein-1), Tas3 (protein with unknown function) and Ago1 (Argonaute), plays an important role in RNAi-mediated heterochromatinization. We find that while the Ago1 subunit of the RITS complex is highly conserved, Tas3 is lost and Chp1 is truncated in S. cryophilus and S...
February 22, 2017: Molecular Biology of the Cell
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
#3
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/28115300/research-progress-of-tc1-mariner-superfamily
#4
Shen Dan, Chen Cai, Wang Saisai, Chen Wei, Gao Bo, Song Chengyi
With the rapid improvement of sequencing techniques, more and more genome annotations reveal the transposons are the important components of most genomes and present on almost all organisms. Among them, the Tc1/Mariner superfamily represents the most widespread DNA transposons. Until now, fourteen active Tc1/Mariner transposons (Minos, Mos1, etc.) have been identified and some highly active artificial transposons have been created through molecular reconstruction, such as Sleeping Beauty (SB). The transposons such as SB and Mos1 have been widely used as gene transfer vectors in the fields of transgenosis, gene trapping and gene therapy...
January 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/27986731/novel-cadmium-resistance-determinant-in-listeria-monocytogenes
#5
Cameron Parsons, Sangmi Lee, Victor Jayeola, Sophia Kathariou
Listeria monocytogenes is a foodborne pathogen that can cause severe disease (listeriosis) in susceptible individuals. It is ubiquitous in the environment and often exhibits resistance to heavy metals. One of the determinants that enables Listeria to tolerate exposure to cadmium is the cadAC efflux system, with CadA being a P-type ATPase. Three different cadA genes (designated cadA1 to cadA3) were previously characterized in L. monocytogenes A novel putative cadmium resistance gene (cadA4) was recently identified through whole-genome sequencing, but experimental confirmation for its involvement in cadmium resistance is lacking...
March 1, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27933056/characterization-of-three-novel-sxt-r391-integrating-conjugative-elements-icemfuind1a-and-icemfuind1b-and-icemprchn1-identified-in-the-genomes-of-marinomonas-fungiae-jcm-18476-t-and-marinomonas-profundimaris-strain-d104
#6
Jhasketan Badhai, Subrata K Das
The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476(T) (ICEMfuInd1a and ICEMfuInd1b) and in Marinomonas profundimaris strain D104 (ICEMprChn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27929021/host-genome-integration-and-giant-virus-induced-reactivation-of-the-virophage-mavirus
#7
Matthias G Fischer, Thomas Hackl
Endogenous viral elements are increasingly found in eukaryotic genomes, yet little is known about their origins, dynamics, or function. Here we provide a compelling example of a DNA virus that readily integrates into a eukaryotic genome where it acts as an inducible antiviral defence system. We found that the virophage mavirus, a parasite of the giant Cafeteria roenbergensis virus (CroV), integrates at multiple sites within the nuclear genome of the marine protozoan Cafeteria roenbergensis. The endogenous mavirus is structurally and genetically similar to eukaryotic DNA transposons and endogenous viruses of the Maverick/Polinton family...
December 7, 2016: Nature
https://www.readbyqxmd.com/read/27913727/regulated-complex-assembly-safeguards-the-fidelity-of-sleeping-beauty-transposition
#8
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...
January 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27824140/random-mutagenesis-of-the-hyperthermophilic-archaeon-pyrococcus-furiosus-using-in-vitro-mariner-transposition-and-natural-transformation
#9
Natalia Guschinskaya, Romain Brunel, Maxime Tourte, Gina L Lipscomb, Michael W W Adams, Philippe Oger, Xavier Charpentier
Transposition mutagenesis is a powerful tool to identify the function of genes, reveal essential genes and generally to unravel the genetic basis of living organisms. However, transposon-mediated mutagenesis has only been successfully applied to a limited number of archaeal species and has never been reported in Thermococcales. Here, we report random insertion mutagenesis in the hyperthermophilic archaeon Pyrococcus furiosus. The strategy takes advantage of the natural transformability of derivatives of the P...
November 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27750255/evolutionary-dynamics-of-5s-rdna-and-recurrent-association-of-transposable-elements-in-electric-fish-of-the-family-gymnotidae-gymnotiformes-the-case-of-gymnotus-mamiraua
#10
Maelin da Silva, Patricia Barbosa, Roberto F Artoni, Eliana Feldberg
Gymnotidae is a family of electric fish endemic to the Neotropics consisting of 2 genera: Electrophorus and Gymnotus. The genus Gymnotus is widely distributed and is found in all of the major Brazilian river systems. Physical and molecular mapping data for the ribosomal DNA (rDNA) in this genus are still scarce, with its chromosomal location known in only 11 species. As other species of Gymnotus with 2n = 54 chromosomes from the Paraná-Paraguay basin, G. mamiraua was found to have a large number of 5S rDNA sites...
2016: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/27748924/a-silkworm-infection-model-to-investigate-vibrio-vulnificus-virulence-genes
#11
Mai Yamamoto, Takashige Kashimoto, Yukihiro Yoshimura, Nao Tachibana, Shiho Kuroda, Yoshiko Miki, Sou Kitabayashi, Ping Tong, Jianbo Xiao, Koichi Tanaka, Hiroshi Hamamoto, Kazuhisa Sekimizu, Koichiro Yamamoto
The halophilic marine bacterium, Vibrio vulnificus, occasionally causes fatal septicemia in immunocompromised patients. Mice are commonly used as experimental animals to investigate the virulence of V. vulnificus, however, a large number of mice are generally required for bioassays. The present study examined whether the invertebrate species, silkworms, can be used instead of mice to investigate V. vulnificus virulence. When the silkworms were inoculated with 1.2x107 colony forming units of V. vulnificus OPU1‑Rf, a virulent strain of V...
November 2016: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27729512/no-go-zones-for-mariner-transposition
#12
Brian J Akerley
The property of transposons to randomly insert into target DNA has long been exploited for generalized mutagenesis and forward genetic screens. Newer applications that monitor the relative abundance of each transposon insertion in large libraries of mutants can be used to evaluate the roles in cellular fitness of all genes of an organism, provided that transposition is in fact random across all genes. In a recent article, Kimura and colleagues identified an important exception to the latter assumption [S. Kimura, T...
October 11, 2016: MBio
https://www.readbyqxmd.com/read/27709580/a-method-for-bioinformatic-analysis-of-transposon-insertion-sequencing-inseq-results-for-identification-of-microbial-fitness-determinants
#13
Nengding Wang, Egon A Ozer
Transposon insertion sequencing is a process whereby microbial fitness determinants can be identified on a genome-wide scale. This process uses high-throughput next generation sequencing to screen for changes in the composition of a pool of transposon mutants after exposure to selective conditions. One commonly used process for generating transposon insertion sequencing libraries is called INSeq that works with mutant pools produced using a modified Mariner transposon. Libraries produced using the INSeq process are sequenced on the Illumina platform...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27695447/production-of-the-bioactive-compounds-violacein-and-indolmycin-is-conditional-in-a-maea-mutant-of-pseudoalteromonas-luteoviolacea-s4054-lacking-the-malic-enzyme
#14
Mariane S Thøgersen, Marina W Delpin, Jette Melchiorsen, Mogens Kilstrup, Maria Månsson, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Kristian F Nielsen, Lone Gram
It has previously been reported that some strains of the marine bacterium Pseudoalteromonas luteoviolacea produce the purple bioactive pigment violacein as well as the antibiotic compound indolmycin, hitherto only found in Streptomyces. The purpose of the present study was to determine the relative role of each of these two compounds as antibacterial compounds in P. luteoviolacea S4054. Using Tn10 transposon mutagenesis, a mutant strain that was significantly reduced in violacein production in mannose-containing substrates was created...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27590816/essential-genes-for-in-vitro-growth-of-the-endophyte-herbaspirillum-seropedicae-smr1-revealed-by-transposon-insertion-sequencing
#15
Federico Rosconi, Stefan P W de Vries, Abiyad Baig, Elena Fabiano, Andrew J Grant
The interior of plants contains microorganisms (referred to as endophytes) distinct to those present in the root surface or in the surrounding soil. Herbaspirillum seropedicae strain SmR1, belonging to the β-Proteobacterium, is an endophyte that colonizes crops, including rice, maize, sugarcane and sorghum. Different approaches have revealed genes and pathways regulated during the interaction of H. seropedicae with its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools...
September 2, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27578758/the-nucleoid-binding-protein-h-ns-biases-genome-wide-transposon-insertion-landscapes
#16
Satoshi Kimura, Troy P Hubbard, Brigid M Davis, Matthew K Waldor
UNLABELLED: Transposon insertion sequencing (TIS; also known as TnSeq) is a potent approach commonly used to comprehensively define the genetic loci that contribute to bacterial fitness in diverse environments. A key presumption underlying analyses of TIS datasets is that loci with a low frequency of transposon insertions contribute to fitness. However, it is not known whether factors such as nucleoid binding proteins can alter the frequency of transposon insertion and thus whether TIS output may systematically reflect factors that are independent of the role of the loci in fitness...
2016: MBio
https://www.readbyqxmd.com/read/27562083/sequence-analyses-and-chromosomal-distribution-of-the-tc1-mariner-element-in-parodontidae-fish-teleostei-characiformes
#17
Michelle Orane Schemberger, Viviane Nogaroto, Mara Cristina Almeida, Roberto Ferreira Artoni, Guilherme Targino Valente, Cesar Martins, Orlando Moreira-Filho, Marta Margarete Cestari, Marcelo Ricardo Vicari
Transposable elements are able to move along eukaryotic genomes. They are divided into two classes according to their transposition intermediate: RNA (class I or retrotransposons) or DNA (class II or DNA transposons). Most of these sequences are inactive or non-autonomous in eukaryotic genomes. Inactivate transposons can accumulate mutations at neutral rates until losing their molecular identity. They may either be eliminated from the genome or take on different molecular functions. Transposable elements may also participate in the differentiation of sex chromosomes...
November 30, 2016: Gene
https://www.readbyqxmd.com/read/27482888/phase-i-trials-using-sleeping-beauty-to-generate-cd19-specific-car-t-cells
#18
Partow Kebriaei, Harjeet Singh, M Helen Huls, Matthew J Figliola, Roland Bassett, Simon Olivares, Bipulendu Jena, Margaret J Dawson, Pappanaicken R Kumaresan, Shihuang Su, Sourindra Maiti, Jianliang Dai, Branden Moriarity, Marie-Andrée Forget, Vladimir Senyukov, Aaron Orozco, Tingting Liu, Jessica McCarty, Rineka N Jackson, Judy S Moyes, Gabriela Rondon, Muzaffar Qazilbash, Stefan Ciurea, Amin Alousi, Yago Nieto, Katy Rezvani, David Marin, Uday Popat, Chitra Hosing, Elizabeth J Shpall, Hagop Kantarjian, Michael Keating, William Wierda, Kim Anh Do, David A Largaespada, Dean A Lee, Perry B Hackett, Richard E Champlin, Laurence J N Cooper
BACKGROUND: T cells expressing antigen-specific chimeric antigen receptors (CARs) improve outcomes for CD19-expressing B cell malignancies. We evaluated a human application of T cells that were genetically modified using the Sleeping Beauty (SB) transposon/transposase system to express a CD19-specific CAR. METHODS: T cells were genetically modified using DNA plasmids from the SB platform to stably express a second-generation CD19-specific CAR and selectively propagated ex vivo with activating and propagating cells (AaPCs) and cytokines...
September 1, 2016: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/27256117/a-novel-suicide-shuttle-plasmid-for-streptococcus-suis-serotype-2-and-streptococcus-equi-ssp-zooepidemicus-gene-mutation
#19
Rui Liu, Ping Zhang, Yiqi Su, Huixing Lin, Hui Zhang, Lei Yu, Zhe Ma, Hongjie Fan
The mariner-based Himar1 system has been utilized for creating mutant libraries of many Gram-positive bacteria. Streptococcus suis serotype 2 (SS2) and Streptococcus equi ssp. zooepidemicus (SEZ) are primary pathogens of swine that threaten the swine industry in China. To provide a forward-genetics technology for finding virulent phenotype-related genes in these two pathogens, we constructed a novel temperature-sensitive suicide shuttle plasmid, pMar4s, which contains the Himar1 system transposon, TnYLB-1, and the Himar1 C9 transposase from pMarA and the repTAs temperature-sensitive fragment from pSET4s...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27234263/a-roadmap-for-gene-system-development-in-clostridium
#20
REVIEW
Nigel P Minton, Muhammad Ehsaan, Christopher M Humphreys, Gareth T Little, Jonathan Baker, Anne M Henstra, Fungmin Liew, Michelle L Kelly, Lili Sheng, Katrin Schwarz, Ying Zhang
Clostridium species are both heroes and villains. Some cause serious human and animal diseases, those present in the gut microbiota generally contribute to health and wellbeing, while others represent useful industrial chassis for the production of chemicals and fuels. To understand, counter or exploit, there is a fundamental requirement for effective systems that may be used for directed or random genome modifications. We have formulated a simple roadmap whereby the necessary gene systems maybe developed and deployed...
October 2016: Anaerobe
keyword
keyword
9264
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"