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https://www.readbyqxmd.com/read/29449580/botulinum-neurotoxin-encoding-plasmids-can-be-conjugatively-transferred-to-diverse-clostridial-strains
#1
Erin M Nawrocki, Marite Bradshaw, Eric A Johnson
Most Group I Clostridium botulinum strains harbor botulinum neurotoxin (bont) genes on their chromosome, while some carry these genes (including bont/a, bont/b, and bont/f) on large plasmids. Prior work in our laboratory demonstrated that Group I BoNT plasmids were mobilized to C. botulinum recipient strains containing the Tn916 transposon. Here, we show that Tn916 is nonessential for plasmid transfer. Relying on an auxotrophic donor phenotype and a plasmid-borne selectable marker, we observed the transfer of pCLJ, a 270 kb plasmid harboring two bont genes, from its host strain to various clostridia...
February 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29449116/chronic-impacts-of-oxytetracycline-on-mesophilic-anaerobic-digestion-of-excess-sludge-inhibition-of-hydrolytic-acidification-and-enrichment-of-antibiotic-resistome
#2
Zhe Tian, Yu Zhang, Min Yang
We evaluated the chronic impact of oxytetracycline (OTC) on performance and antibiotic resistance development during the mesophilic anaerobic digestion (AD) of antibiotic-containing biomass. Mesophilic AD was conducted in a completely stirred tank reactor by constantly feeding municipal excess sludge spiked with increasing concentrations of OTC (0-1000 mg L -1 ) under a solid retention time of 20 days over a period of 265 days. Results showed that methane generation of mesophilic AD was inhibited when the OTC concentration in digested sludge was increased to around 18,000 mg kg -1 (OTC dose, 1000 mg L -1 ), due to the inhibition of fermenting and acidogenic bacteria...
February 12, 2018: Environmental Pollution
https://www.readbyqxmd.com/read/29448036/molecular-characterization-of-multidrug-pneumococcal-clones-colonizing-healthy-children-in-m%C3%A3-rida-venezuela
#3
Beatríz Quintero Moreno, María Araque
We analyzed genetics mechanisms of antibiotics resistance, clonal composition and pili in forty eight MDR-pneumococci isolated from healthy children in Mérida, Venezuela. Intermediate resistance to penicillin was related to variations on pbp2b and pbp2x genes. High-level resistance to penicillin, low susceptibility to cephalosporins and carbapenems were associated with alterations on pbp1a, pbp2b and pbp2x genes. Non-beta-lactam resistance was associated with Tn3872, Tn5253, Tn6002, Tn2010 transposons. Macrolide-resistant strains carried ermB or mefE, but not the mefA gene...
February 12, 2018: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29446201/transposable-elements-shape-the-human-proteome-landscape-via-formation-of-cis-acting-upstream-open-reading-frames
#4
Shohei Kitano, Hikaru Kurasawa, Yasunori Aizawa
Transposons are major drivers of mammalian genome evolution. To obtain new insights into the contribution of transposons to the regulation of protein translation, we here examined how transposons affected the genesis and function of upstream open reading frames (uORFs), which serve as cis-acting elements to regulate translation from annotated ORFs (anORFs) located downstream of the uORFs in eukaryotic mRNAs. Among 39,786 human uORFs, 3,992 had ATG trinucleotides of a transposon origin, termed "transposon-derived upstream ATGs" or TuATGs...
February 15, 2018: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
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/29444862/targeted-dna-demethylation-of-the-arabidopsis-genome-using-the-human-tet1-catalytic-domain
#6
Javier Gallego-Bartolomé, Jason Gardiner, Wanlu Liu, Ashot Papikian, Basudev Ghoshal, Hsuan Yu Kuo, Jenny Miao-Chi Zhao, David J Segal, Steven E Jacobsen
DNA methylation is an important epigenetic modification involved in gene regulation and transposable element silencing. Changes in DNA methylation can be heritable and, thus, can lead to the formation of stable epialleles. A well-characterized example of a stable epiallele in plants is fwa , which consists of the loss of DNA cytosine methylation (5mC) in the promoter of the FLOWERING WAGENINGEN ( FWA ) gene, causing up-regulation of FWA and a heritable late-flowering phenotype. Here we demonstrate that a fusion between the catalytic domain of the human demethylase TEN-ELEVEN TRANSLOCATION1 (TET1cd) and an artificial zinc finger (ZF) designed to target the FWA promoter can cause highly efficient targeted demethylation, FWA up-regulation, and a heritable late-flowering phenotype...
February 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29444170/genotypic-and-phenotypic-characterization-of-the-sdccag8tn-sb-tyr-2161b-ca1c2ove-mouse-model
#7
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/29443066/constitutive-and-inducible-systems-for-genetic-in-vivo-modification-of-mouse-hepatocytes-using-hydrodynamic-tail-vein-injection
#8
Eric K Hubner, Christian Lechler, Thomas N Rösner, Birgit Kohnke-Ertel, Roland M Schmid, Ursula Ehmer
In research models of liver cancer, regeneration, inflammation, and fibrosis, flexible systems for in vivo gene expression and silencing are highly useful. Hydrodynamic tail vein injection of transposon-based constructs is an efficient method for genetic manipulation of hepatocytes in adult mice. In addition to constitutive transgene expression, this system can be used for more advanced applications, such as shRNA-mediated gene knock-down, implication of the CRISPR/Cas9 system to induce gene mutations, or inducible systems...
February 2, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29442195/the-changing-epidemiology-of-vanb-enterococcus-faecium-in-poland
#9
Ewa Sadowy, Iwona Gawryszewska, Alicja Kuch, Dorota Żabicka, Waleria Hryniewicz
Increasing prevalence of VanB Enterococcus faecium in Polish hospitals reported to National Reference Centre for Susceptibility Testing (NRCST) prompted us to investigate the basis of this phenomenon. Two-hundred seventy-eight E. faecium isolates of VanB phenotype from the period 1999 to 2010 obtained by NRCST were investigated by multilocus sequence typing (MLST) and multilocus VNTR analysis (MLVA). Localization, transferability, and partial structure of the vanB-carrying Tn1549 transposon were studied by hybridization, PCR mapping, sequencing, and conjugation...
February 13, 2018: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29439662/comparative-genome-analysis-of-52-fish-species-suggests-differential-associations-of-repetitive-elements-with-their-living-aquatic-environments
#10
Zihao Yuan, Shikai Liu, Tao Zhou, Changxu Tian, Lisui Bao, Rex Dunham, Zhanjiang Liu
BACKGROUND: Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. RESULTS: The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions...
February 13, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29439501/the-roles-of-mitochondrion-in-intergenomic-gene-transfer-in-plants-a-source-and-a-pool
#11
Nan Zhao, Yumei Wang, Jinping Hua
Intergenomic gene transfer (IGT) is continuous in the evolutionary history of plants. In this field, most studies concentrate on a few related species. Here, we look at IGT from a broader evolutionary perspective, using 24 plants. We discover many IGT events by assessing the data from nuclear, mitochondrial and chloroplast genomes. Thus, we summarize the two roles of the mitochondrion: a source and a pool. That is, the mitochondrion gives massive sequences and integrates nuclear transposons and chloroplast tRNA genes...
February 11, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29438479/novel-tn916-like-elements-confer-aminoglycoside-macrolide-co-resistance-in-clinical-isolates-of-streptococcus-gallolyticus-ssp-gallolyticus
#12
Stanimir Kambarev, Frédéric Pecorari, Stéphane Corvec
Background: Streptococcus gallolyticus ssp. gallolyticus (Sgg) is a commensal bacterium and an opportunistic pathogen. In humans it has been clinically associated with the incidence of colorectal cancer (CRC) and epidemiologically recognized as an emerging cause of infective endocarditis (IE). The standard therapy of Sgg includes the administration of a penicillin in combination with an aminoglycoside. Even though penicillin-resistant isolates have still not been reported, epidemiological studies have shown that this microbe is a reservoir of multiple acquired genes, conferring resistance to tetracyclines, aminoglycosides, macrolides and glycopeptides...
February 9, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29435919/the-microrna
#13
Shao-Yao Ying, Donald C Chang, Shi-Lung Lin
MicroRNAs (miRNAs), widely distributed, small regulatory RNA genes, target both messenger RNA (mRNA) degradation and suppression of protein translation based on sequence complementarity between the miRNA and its targeted mRNA. Different names have been used to describe various types of miRNA. During evolution, RNA retroviruses or transgenes invaded the eukaryotic genome and were inserted itself in the noncoding regions of DNA, conceivably acting as transposon-like jumping genes, providing defense from viral invasion and fine-tuning of gene expression as a secondary level of gene modulation in eukaryotes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29435491/genomewide-identification-of-essential-genes-and-fitness-determinants-of-streptococcus-mutans-ua159
#14
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/29434581/site-specific-recombination-at-xerc-d-sites-mediates-the-formation-and-resolution-of-plasmid-co-integrates-carrying-a-blaoxa-58-and-tnapha6-resistance-module-in-acinetobacter-baumannii
#15
María M Cameranesi, Jorgelina Morán-Barrio, Adriana S Limansky, Guillermo D Repizo, Alejandro M Viale
Members of the genus Acinetobacter possess distinct plasmid types which provide effective platforms for the acquisition, evolution, and dissemination of antimicrobial resistance structures. Many plasmid-borne resistance structures are bordered by short DNA sequences providing potential recognition sites for the host XerC and XerD site-specific tyrosine recombinases (XerC/D-like sites). However, whether these sites are active in recombination and how they assist the mobilization of associated resistance structures is still poorly understood...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29434576/candidatus-nitrosocaldus-cavascurensis-an-ammonia-oxidizing-extremely-thermophilic-archaeon-with-a-highly-mobile-genome
#16
Sophie S Abby, Michael Melcher, Melina Kerou, Mart Krupovic, Michaela Stieglmeier, Claudia Rossel, Kevin Pfeifer, Christa Schleper
Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29432776/establishment-of-cre-mediated-hbv-recombinant-cccdna-rcccdna-cell-line-for-cccdna-biology-and-antiviral-screening-assays
#17
Min Wu, Jin Li, Lei Yue, Lu Bai, Yaming Li, Jieliang Chen, Xiaonan Zhang, Zhenghong Yuan
Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA), existing in hepatocyte nuclei as a stable minichromosome, plays a central role in the life cycle of the virus and permits the persistence of infection. Despite being essential for HBV infection, little is known about the molecular mechanisms of cccDNA formation, regulation and degradation, and there is no therapeutic agents directly targeting cccDNA, fore mostly due to the lack of robust, reliable and quantifiable HBV cccDNA models. In this study, combined the Cre/loxP and sleeping beauty transposons system, we established HepG2-derived cell lines integrated with 2-60 copies of monomeric HBV genome flanked by loxP sites (HepG2-HBV/loxP)...
February 9, 2018: Antiviral Research
https://www.readbyqxmd.com/read/29425968/characterization-of-calcium-signals-in-human-induced-pluripotent-stem-cell-derived-dentate-gyrus-neuronal-progenitors-and-mature-neurons-stably-expressing-an-advanced-calcium-indicator-protein
#18
Gergő Vőfély, Tünde Berecz, Eszter Szabó, Kornélia Szebényi, Edit Hathy, Tamás I Orbán, Balázs Sarkadi, László Homolya, Maria C Marchetto, János M Réthelyi, Ágota Apáti
Pluripotent stem cell derived human neuronal progenitor cells (hPSC-NPCs) and their mature neuronal cell culture derivatives may efficiently be used for central nervous system (CNS) drug screening, including the investigation of ligand-induced calcium signalization. We have established hippocampal NPC cultures derived from human induced PSCs, which were previously generated by non-integrating Sendai virus reprogramming. Using established protocols these NPCs were differentiated into hippocampal dentate gyrus neurons...
February 6, 2018: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/29425282/presence-and-molecular-characteristics-of-oxazolidinone-resistance-in-staphylococci-from-household-animals-in-rural-china
#19
Chengtao Sun, Peng Zhang, Xing Ji, Run Fan, Baoli Chen, Yang Wang, Stefan Schwarz, Congming Wu
Objectives: To investigate the presence and molecular characteristics of oxazolidinone resistance genes cfr and optrA in staphylococci from household animals in rural China. Methods: Various samples were collected from household animals in 12 rural villages. Staphylococcal isolates showing florfenicol MICs ≥10 mg/L were identified and screened for the presence of cfr and/or optrA. PCR-positive isolates were characterized by antimicrobial susceptibility testing, S1 nuclease PFGE and Southern blotting...
February 7, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29424134/-active-miniature-inverted-repeat-transposable-elements-transposon-in-plants-a-review
#20
Bingjie Hu, Mingbing Zhou
Miniature inverted-repeat transposable elements transposon is a special transposon that could transpose by "cut-paste" mechanism, which is one of characteristics of DNA transposons. Otherwise, the copy number of MITEs is very high, which is one of characteristics of RNA transposons. Many MITE families have been reported, but little about active MITEs. We summarize recent advances in studying active MITEs. Most the MITEs belong to the Tourist-like family, such as mPing, mGing, PhTourist1, Tmi1 and PhTst-3. Additionally, DTstu1 and MITE-39 belong to Stowaway-like family, and AhMITEs1 belongs to Mutator-like family...
February 25, 2018: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
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