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https://www.readbyqxmd.com/read/29117225/genomic-comparison-between-staphylococcus-aureus-gn-strains-clinically-isolated-from-a-familial-infection-case-is1272-transposition-through-a-novel-inverted-repeat-replacing-mechanism
#1
Tsai-Wen Wan, Wataru Higuchi, Olga E Khokhlova, Wei-Chun Hung, Yasuhisa Iwao, Masataka Wakayama, Noriyoshi Inomata, Tomomi Takano, Yu-Tzu Lin, Olga V Peryanova, Kenji K Kojima, Alla B Salmina, Lee-Jene Teng, Tatsuo Yamamoto
A bacterial insertion sequence (IS) is a mobile DNA sequence carrying only the transposase gene (tnp) that acts as a mutator to disrupt genes, alter gene expressions, and cause genomic rearrangements. "Canonical" ISs have historically been characterized by their terminal inverted repeats (IRs), which may form a stem-loop structure, and duplications of a short (non-IR) target sequence at both ends, called target site duplications (TSDs). The IS distributions and virulence potentials of Staphylococcus aureus genomes in familial infection cases are unclear...
2017: PloS One
https://www.readbyqxmd.com/read/29112963/effectiveness-of-a-combination-strategy-for-linkage-and-retention-in-adult-hiv-care-in-swaziland-the-link4health-cluster-randomized-trial
#2
RANDOMIZED CONTROLLED TRIAL
Margaret L McNairy, Matthew R Lamb, Averie B Gachuhi, Harriet Nuwagaba-Biribonwoha, Sean Burke, Sikhathele Mazibuko, Velephi Okello, Peter Ehrenkranz, Ruben Sahabo, Wafaa M El-Sadr
BACKGROUND: Gaps in the HIV care continuum contribute to poor health outcomes and increase HIV transmission. A combination of interventions targeting multiple steps in the continuum is needed to achieve the full beneficial impact of HIV treatment. METHODS AND FINDINGS: Link4Health, a cluster-randomized controlled trial, evaluated the effectiveness of a combination intervention strategy (CIS) versus the standard of care (SOC) on the primary outcome of linkage to care within 1 month plus retention in care at 12 months after HIV-positive testing...
November 2017: PLoS Medicine
https://www.readbyqxmd.com/read/29109480/detection-of-subclonal-l1-transductions-in-colorectal-cancer-by-long-distance-inverse-pcr-and-nanopore-sequencing
#3
Barun Pradhan, Tatiana Cajuso, Riku Katainen, Päivi Sulo, Tomas Tanskanen, Outi Kilpivaara, Esa Pitkänen, Lauri A Aaltonen, Liisa Kauppi, Kimmo Palin
Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region by a process known as 3' transduction. L1 insertions can contribute to genome plasticity and cause potentially tumorigenic genomic instability. However, detecting the activity of a particular source L1 and identifying new insertions stemming from it is a challenging task with current methodological approaches...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29109157/an-ultra-processive-accurate-reverse-transcriptase-encoded-by-a-metazoan-group-ii-intron
#4
Chen Zhao, Fei Liu, Anna Marie Pyle
Group II introns and non-LTR retrotransposons encode a phylogenetically-related family of highly processive reverse transcriptases (RTs) that are essential for mobility and persistence of these retroelements. Recent crystallographic studies on members of this RT family have revealed that they are structurally distinct from the retroviral RTs that are typically used in biotechnology. However, quantitative, structure-guided analysis of processivity, efficiency and accuracy of this alternate RT family has been lacking...
November 6, 2017: RNA
https://www.readbyqxmd.com/read/29077766/peripheral-blood-hiv-1-dna-dynamics-in-antiretroviral-treated-hiv-hcv-co-infected-patients-receiving-directly-acting-antivirals
#5
Gabriella Rozera, Gabriele Fabbri, Patrizia Lorenzini, Ilaria Mastrorosa, Laura Timelli, Mauro Zaccarelli, Alessandra Amendola, Alessandra Vergori, Maria Maddalena Plazzi, Stefania Cicalini, Andrea Antinori, Maria Rosaria Capobianchi, Isabella Abbate, Adriana Ammassari
BACKGROUND: Aim was to determine the dynamics of peripheral blood mononuclear cells (PBMC)- associated total HIV-1 DNA in successfully ART-treated HIV/HCV co-infected patients receiving DAA treatment and to explore possible virological hypotheses underlying the phenomenon. METHODS: Longitudinal, single-centre study measuring total HIV-1 DNA before the start of DAA, at the end of treatment (EOT), and 3 months after treatment. Univariable and multivariable analyses were used to assess factors associated with HIV-1 DNA increase ≥0...
2017: PloS One
https://www.readbyqxmd.com/read/29054657/feed-additives-shift-gut-microbiota-and-enrich-antibiotic-resistance-in-swine-gut
#6
Yi Zhao, Jian-Qiang Su, Xin-Li An, Fu-Yi Huang, Christopher Rensing, Kristian Koefoed Brandt, Yong-Guan Zhu
Antibiotic resistance genes (ARGs) are emerging environmental contaminants posing a threat to public health. Antibiotics and metals are widely used as feed additives and could consequently affect ARGs in swine gut. In this study, high-throughput quantitative polymerase chain reaction (HT-qPCR) based ARG chip and next-generation 16S rRNA gene amplicon sequencing data were analyzed using multiple statistical approaches to profile the antibiotic resistome and investigate its linkages to antibiotics and metals used as feed additives and to the microbial community composition in freshly collected swine manure samples from three large-scale Chinese pig farms...
October 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29054314/bedside-chest-radiographs-in-the-intensive-care-setting-wireless-direct-radiography-compared-to-computed-radiography
#7
Craig R Audin, Shima Aran, Victorine V Muse, Gerald F Abbott, Jeanne B Ackman, Amita Sharma, Carol C Wu, Mannudeep K Kalra, Theresa C McLoud, Jo-Anne O Shepard, Florian J Fintelmann, Matthew D Gilman
OBJECTIVES: To compare image quality, visibility of anatomic landmarks, tubes and lines, and other clinically significant findings on portable (bedside) chest radiographs acquired with wireless direct radiography (DRw) and computed radiography (CR). METHODS: In a prospective IRB-approved and HIPAA-compliant study, portable DRw (DRX-1C mobile retrofit portable wireless direct radiography, CareStream Inc., Rochester, NY) and portable CR (AGFA CR (DXG) version; NIM2103, AGFA Healthcare, Ridgefield Park, NJ) images of the chest were acquired within 24-hours in 80 patients in the intensive care unit (ICU)...
September 21, 2017: Current Problems in Diagnostic Radiology
https://www.readbyqxmd.com/read/29051748/retrotransposon-domestication-and-control-in-dictyostelium-discoideum
#8
REVIEW
Marek Malicki, Maro Iliopoulou, Christian Hammann
Transposable elements, identified in all eukaryotes, are mobile genetic units that can change their genomic position. Transposons usually employ an excision and reintegration mechanism, by which they change position, but not copy number. In contrast, retrotransposons amplify via RNA intermediates, increasing their genomic copy number. Hence, they represent a particular threat to the structural and informational integrity of the invaded genome. The social amoeba Dictyostelium discoideum, model organism of the evolutionary Amoebozoa supergroup, features a haploid, gene-dense genome that offers limited space for damage-free transposition...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29046673/genome-of-ca-pandoraea-novymonadis-an-endosymbiotic-bacterium-of-the-trypanosomatid-novymonas-esmeraldas
#9
Alexei Y Kostygov, Anzhelika Butenko, Anna Nenarokova, Daria Tashyreva, Pavel Flegontov, Julius Lukeš, Vyacheslav Yurchenko
We have sequenced, annotated, and analyzed the genome of Ca. Pandoraea novymonadis, a recently described bacterial endosymbiont of the trypanosomatid Novymonas esmeraldas. When compared with genomes of its free-living relatives, it has all the hallmarks of the endosymbionts' genomes, such as significantly reduced size, extensive gene loss, low GC content, numerous gene rearrangements, and low codon usage bias. In addition, Ca. P. novymonadis lacks mobile elements, has a strikingly low number of pseudogenes, and almost all genes are single copied...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29046400/ribosome-biogenesis-modulates-ty1-copy-number-control-in-saccharomyces-cerevisiae
#10
Hyo Won Ahn, Jessica M Tucker, Joshua A Arribere, David J Garfinkel
Transposons can impact the host genome by altering gene expression and participating in chromosome rearrangements. Therefore, organisms evolved different ways to minimize the level of transposition. In Saccharomyces cerevisiae and its close relative S. paradoxus, Ty1 copy number control (CNC) is mediated by the self-encoded restriction factor p22, which is derived from the GAG capsid gene and inhibits virus-like particle (VLP) assembly and function. Based on secondary screens of Ty1 cofactors, we identified LOC1, a RNA localization/ribosome biogenesis gene that affects Ty1 mobility predominantly in strains harboring Ty1 elements...
October 18, 2017: Genetics
https://www.readbyqxmd.com/read/29045822/individual-effects-of-the-copia-and-gypsy-enhancer-and-insulator-on-chromatin-marks-erna-synthesis-and-binding-of-insulator-proteins-in-transfected-genetic-constructs
#11
Daria M Fedoseeva, Olga V Kretova, Maria A Gorbacheva, Nickolai A Tchurikov
Enhancers and insulators are involved in the regulation of gene expression, but the basic underlying mechanisms of action of these elements are unknown. We analyzed the individual effects of the enhancer and the insulator from Drosophila mobile elements copia [enh(copia)] and gypsy using transfected genetic constructs in S2 cells. This system excludes the influence of genomic cis regulatory elements. The enhancer-induced synthesis of 350-1050-nt-long enhancer RNAs (eRNAs) and H3K4me3 and H3K18ac marks, mainly in the region located about 300bp downstream of the enhancer...
October 15, 2017: Gene
https://www.readbyqxmd.com/read/29043294/integrating-networks-and-comparative-genomics-reveals-retroelement-proliferation-dynamics-in-hominid-genomes
#12
Orr Levy, Binyamin A Knisbacher, Erez Y Levanon, Shlomo Havlin
Retroelements (REs) are mobile DNA sequences that multiply and spread throughout genomes by a copy-and-paste mechanism. These parasitic elements are active in diverse genomes, from yeast to humans, where they promote diversity, cause disease, and accelerate evolution. Because of their high copy number and sequence similarity, studying their activity and tracking their proliferation dynamics is a challenge. It is particularly difficult to pinpoint the few REs in a genome that are still active in the haystack of degenerate and suppressed elements...
October 2017: Science Advances
https://www.readbyqxmd.com/read/29042801/investigating-a-rare-methicillin-resistant-staphylococcus-aureus-strain-first-description-of-genome-sequencing-and-molecular-characterization-of-cc15-mrsa
#13
Abiola C Senok, Ali M Somily, Peter Slickers, Muhabat A Raji, Ghada Garaween, Atef Shibl, Stefan Monecke, Ralf Ehricht
PURPOSE: Methicillin resistant Staphylococcus aureus CC15 strains (CC15-MRSA) have only been sporadically described in literature. This study was carried out to describe the genetic make-up for this rare MRSA strain. METHODS: Four CC15-MRSA isolates collected in Riyadh, Saudi Arabia, between 2013 and 2014 were studied. Two isolates were from clinical infection and 2 from retail meat products. Whole genome sequencing was carried out using Illumina HiSeq2500 genome analyzer...
2017: Infection and Drug Resistance
https://www.readbyqxmd.com/read/29040588/glyphosate-resistance-and-epsps-gene-duplication-convergent-evolution-in-multiple-plant-species
#14
Eric L Patterson, Dean J Pettinga, Karl Ravet, Paul Neve, Todd A Gaines
One of the increasingly widespread mechanisms of resistance to the herbicide glyphosate is copy number variation (CNV) of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene. EPSPS gene duplication has been reported in eight weed species, ranging from 3-5 extra copies to more than 150 extra copies. In the case of Palmer amaranth (Amaranthus palmeri), a section of >300 kb containing EPSPS and many other genes has been replicated and inserted at new loci throughout the genome, resulting in significant increase in total genome size...
October 10, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29023355/utility-of-mobile-communication-devices-as-a-tool-to-improve-adherence-to-antiretroviral-treatment-in-hiv-infected-children-and-young-adults-in-argentina
#15
Erica Stankievich, Adriana Malanca, Irene Foradori, Silvina Ivalo, Marcelo Losso
BACKGROUND: Optimal adherence is critical to achieve the benefits of antiretroviral treatment (ART). The aim of the study is to evaluate the use of mobile devices as a strategy to improve adherence to ART, measured by Viral Load (VL) in HIV+ patients less than 25 years of age. METHODS: A prospective study was conducted in a cohort of HIV+ patients less than 25 years of age. HIV+ patients, on ART, VL >1000 copies/mL, using mobile devices and suboptimal adherence (SOA) were included...
October 7, 2017: Pediatric Infectious Disease Journal
https://www.readbyqxmd.com/read/28978433/real-time-imaging-of-a-single-gene-reveals-transcription-initiated-local-confinement
#16
Thomas Germier, Silvia Kocanova, Nike Walther, Aurélien Bancaud, Haitham Ahmed Shaban, Hafida Sellou, Antonio Zaccaria Politi, Jan Ellenberg, Franck Gallardo, Kerstin Bystricky
Genome dynamics are intimately linked to the regulation of gene expression, the most fundamental mechanism in biology, yet we still do not know whether the very process of transcription drives spatial organization at specific gene loci. Here, we have optimized the ANCHOR/ParB DNA-labeling system for real-time imaging of a single-copy, estrogen-inducible transgene in human cells. Motion of an ANCHOR3-tagged DNA locus was recorded in the same cell before and during the appearance of nascent MS2-labeled mRNA. We found that transcription initiation by RNA polymerase 2 resulted in confinement of the mRNA-producing gene domain within minutes...
October 3, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28978128/psy153-mdr-a-p12969-dim-related-mega-plasmid-carrying-blaimp-45-and-arma-from-clinical-pseudomonas-putida
#17
Min Yuan, Hai Chen, Xiong Zhu, Jiao Feng, Zhe Zhan, Defu Zhang, Xia Chen, Xiaofei Zhao, Jinxing Lu, Jianguo Xu, Dongsheng Zhou, Juan Li
This work characterized mega plasmid pSY153-MDR, carrying blaIMP-45 and armA, from a multidrug-resistant (MDR) Pseudomonas putida isolate from the urine of a cerebral infarction patient in China. The backbone of pSY153-MDR was closely related to Pseudomonas plasmids p12969-DIM, pOZ176, pBM413, pTTS12, and pRBL16, and could not be assigned to any of the known incompatibility groups. The accessory modules of pSY153-MDR were composed of 10 individual insertion sequence elements and two different MDR regions, and differed dramatically from the above plasmids...
September 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28973983/an-energy-scaled-and-expanded-vector-based-forwarding-scheme-for-industrial-underwater-acoustic-sensor-networks-with-sink-mobility
#18
Zahid Wadud, Sajjad Hussain, Nadeem Javaid, Safdar Hussain Bouk, Nabil Alrajeh, Mohamad Souheil Alabed, Nadra Guizani
Industrial Underwater Acoustic Sensor Networks (IUASNs) come with intrinsic challenges like long propagation delay, small bandwidth, large energy consumption, three-dimensional deployment, and high deployment and battery replacement cost. Any routing strategy proposed for IUASN must take into account these constraints. The vector based forwarding schemes in literature forward data packets to sink using holding time and location information of the sender, forwarder, and sink nodes. Holding time suppresses data broadcasts; however, it fails to keep energy and delay fairness in the network...
September 30, 2017: Sensors
https://www.readbyqxmd.com/read/28962028/identification-of-a-novel-transposon-associated-phosphoethanolamine-transferase-gene-mcr-5-conferring-colistin-resistance-in-d-tartrate-fermenting-salmonella-enterica-subsp-enterica-serovar-paratyphi-b
#19
Maria Borowiak, Jennie Fischer, Jens A Hammerl, Rene S Hendriksen, Istvan Szabo, Burkhard Malorny
Objectives: Plasmid-mediated mobilized colistin resistance is currently known to be caused by phosphoethanolamine transferases termed MCR-1, MCR-2, MCR-3 and MCR-4. However, this study focuses on the dissection of a novel resistance mechanism in mcr-1 -, mcr-2 - and mcr-3 -negative d -tartrate fermenting Salmonella enterica subsp. enterica serovar Paratyphi B ( Salmonella Paratyphi B d Ta+) isolates with colistin MIC values >2 mg/L. Methods: A selected isolate from the strain collection of the German National Reference Laboratory for Salmonella was investigated by WGS and bioinformatical analysis to identify novel phosphoethanolamine transferase genes involved in colistin resistance...
September 18, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28941465/quantitative-analysis-of-l1-retrotransposons-in-alzheimer-s-disease-and-aging
#20
M S Protasova, F E Gusev, A P Grigorenko, I L Kuznetsova, E I Rogaev, T V Andreeva
LINE1 retrotransposons are members of a class of mobile genetic elements capable of retrotransposition in the genome via a process of reverse transcription. LINE1 repeats, integrating into different chromosomal loci, affect the activity of genes and cause different genomic mutations. Somatic variability of the human genome is linked to the activity of some subfamilies of LINE1, in particular, a high level of LINE1 retrotranspositions has been observed in brain tissues. However, the contribution of LINE1 to genomic variability during normal aging and in age-related neurodegenerative diseases is poorly understood...
August 2017: Biochemistry. Biokhimii︠a︡
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