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https://www.readbyqxmd.com/read/29783941/a-transposable-element-annotation-pipeline-and-expression-analysis-reveal-potentially-active-elements-in-the-microalga-tisochrysis-lutea
#1
Jérémy Berthelier, Nathalie Casse, Nicolas Daccord, Véronique Jamilloux, Bruno Saint-Jean, Grégory Carrier
BACKGROUND: Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution. RESULTS: To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: https://doi...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29777591/bioengineering-triacetic-acid-lactone-production-in-yarrowia-lipolytica-for-pogostone-synthesis
#2
James Yu, Jenny Landberg, Farbod Shavarebi, Virginia Bilanchone, Adam Okerlund, Umayangani Wanninayake, Le Zhao, George Kraus, Suzanne Sandmeyer
Yarrowia lipolytica is an oleaginous yeast that is recognized for its ability to accumulate high levels of lipids, which can serve as precursors to biobased fuels and chemicals. Polyketides such as triacetic acid lactone (TAL) can also serve as a precursor for diverse commodity chemicals. This study used Y. lipolytica as a host organism for the production of TAL via expression of the 2-pyrone synthase gene from Gerbera hybrida. Induction of lipid biosynthesis by nitrogen-limited growth conditions increased TAL titers...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777339/characterization-of-a-cryptic-rolling-circle-replication-plasmid-pmk8-from-enterococcus-durans-1-8
#3
Penyu Zhou, Zhengyuan Zhai, Xiong Yao, Peihua Ma, Yanling Hao
A novel cryptic plasmid from Enterococcus durans 1-8, designated as pMK8, was sequenced and analyzed in this study. It consists of 3337 bp with a G + C content of 33.11%. Sequence analysis of pMK8 revealed three putative open reading frames (ORFs). Based on homology, two of them were identified as genes encoding replication initiation (RepC) and mobilization (Mob) protein, respectively. Sequence analysis revealed a pT181 family double-strand origin (dso) and a putative single-strand origin (sso) located upstream of the repC gene...
May 17, 2018: Current Microbiology
https://www.readbyqxmd.com/read/29771911/asymmetric-polar-localization-dynamics-of-the-serine-chemoreceptor-protein-tsr-in-escherichia-coli
#4
Dongmyung Oh, Yang Yu, Hochan Lee, Jae-Hyung Jeon, Barry L Wanner, Ken Ritchie
The spatial location of proteins in living cells can be critical for their function. For example, the E. coli chemotaxis machinery is localized to the cell poles. Here we describe the polar localization of the serine chemoreceptor Tsr using a strain synthesizing a fluorescent Tsr-Venus fusion at a low level from a single-copy chromosomal construct. Using photobleaching and imaging during recovery by new synthesis, we observed distinct asymmetry between a bright (old) pole and a dim (new) pole. The old pole was shown to be a more stable cluster and to recover after photobleaching faster, which is consistent with the hypothesis that newly synthesized Tsr proteins are inserted directly at or near the old pole...
2018: PloS One
https://www.readbyqxmd.com/read/29753149/exploring-abundance-diversity-and-variation-of-a-widespread-antibiotic-resistance-gene-in-wastewater-treatment-plants
#5
Ziyan Wei, Kai Feng, Shuzhen Li, Yu Zhang, Hongrui Chen, Huaqun Yin, Meiying Xu, Ye Deng
An updated sul1 gene sequence database was constructed and new degenerate primers were designed to better investigate the abundance, diversity, and variation of a ubiquitous antibiotic resistance gene, sul1, with PCR-based methods in activated sludge from wastewater treatment plants (WWTPs). The newly designed degenerate primers showed high specificity and higher coverage in both in-silico evaluations and activated sludge samples compared to previous sul1 primers. Using the new primers, the abundance and diversity of sul1 gene, together with 16S rRNA gene, in activated sludge from five WWTPs in summer and winter were determined by quantitative PCR and MiSeq sequencing...
May 9, 2018: Environment International
https://www.readbyqxmd.com/read/29739668/whole-genome-comparison-of-high-and-low-virulent-staphylococcus-aureus-isolates-inducing-implant-associated-bone-infections
#6
Gopala Krishna Mannala, Julian Koettnitz, Walid Mohamed, Ursula Sommer, Katrin Susanne Lips, Cathrin Spröer, Boyke Bunk, Jörg Overmann, Torsten Hain, Christian Heiss, Eugen Domann, Volker Alt
Staphylococcus aureus can cause wide range of infections from simple soft skin infections to severe endocarditis, bacteremia, osteomyelitis and implant associated bone infections (IABI). The focus of the present investigation was to study virulence properties of S. aureus isolates from acute and chronic IABI by means of their in vivo lethality, in vitro osteoblasts invasion, biofilm formation and subsequently whole genome comparison between high and low virulent strains. Application of insect infection model Galleria mellonella revealed high, intermediate and low virulence phenotypes of these clinical isolates, which showed good correlation with osteoblast invasion and biofilm formation assays...
April 25, 2018: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/29739320/mobilization-of-retrotransposons-as-a-cause-of-chromosomal-diversification-and-rapid-speciation-the-case-for-the-antarctic-teleost-genus-trematomus
#7
J Auvinet, P Graça, L Belkadi, L Petit, E Bonnivard, A Dettaï, W H Detrich, C Ozouf-Costaz, D Higuet
BACKGROUND: The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment to understanding the roles of TEs in genome evolution is the lack of comparative and integrative analyses on complete taxonomic groups. To help overcome this problem, we have focused on the Antarctic teleost genus Trematomus (Notothenioidei: Nototheniidae), as they experienced rapid speciation accompanied by dramatic chromosomal diversity...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29734603/effect-of-microbially-mediated-iron-mineral-transformation-on-temporal-variation-of-arsenic-in-the-pleistocene-aquifers-of-the-central-yangtze-river-basin
#8
Yamin Deng, Tianliang Zheng, Yanxin Wang, Lun Liu, Hongchen Jiang, Teng Ma
Significant seasonal variation of groundwater arsenic (As) concentrations in shallow aquifers of the Jianghan Plain, central Yangtze River Basin has been reported recently, but the underlying mechanisms remain not well understood. To elaborate biogeochemical processes responsible for the observed As concentration variation, 42-day incubation experiments were done using sediment samples collected respectively from the depth of 26, 36 and 60m of the As-affected aquifer which were labeled respectively as JH26, JH36, JH60...
April 1, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29729369/reference-intervals-for-putative-biomarkers-of-drug-induced-liver-injury-and-liver-regeneration-in-healthy-human-volunteers
#9
Ben Francis, Joanna I Clarke, Lauren E Walker, Nathalie Brillant, Andrea L Jorgensen, B Kevin Park, Munir Pirmohamed, Daniel J Antoine
BACKGROUND & AIMS: The potential of mechanistic biomarkers to improve the prediction of drug-induced liver injury (DILI) and hepatic regeneration is widely acknowledged. We sought to determine reference intervals for new biomarkers of DILI and regeneration as well as to characterize their natural variability and impact of diurnal variation. METHODS: Serum samples from 200 healthy volunteers were recruited as part of a cross sectional study; of these, 50 subjects had weekly serial sampling over 3 weeks, while 24 had intensive blood sampling over a 24h period...
May 2, 2018: Journal of Hepatology
https://www.readbyqxmd.com/read/29703854/evaluation-of-plasma-microrna-122-high-mobility-group-box-1-and-keratin-18-concentrations-to-stratify-acute-gallstone-disease-a-pilot-observational-cohort-study-in-an-emergency-general-surgery-unit
#10
Francesca Th'ng, Bastiaan Vliegenthart, Jonathan D Lea, Daniel J Antoine, James W Dear, Damian J Mole
OBJECTIVE: To obtain pilot data to evaluate the discriminatory power of biomarkers microRNA-122 (miR-122), high-mobility group box 1 (HMGB1), full-length keratin-18 (flk-18) and caspase-cleaved keratin-18 (cck-18) in plasma to identify potential biliary complications that may require acute intervention. DESIGN: An observational biomarker cohort pilot study. SETTING: In a Scottish University teaching hospital for 12 months beginning on 3 September 2014...
April 27, 2018: BMJ Open
https://www.readbyqxmd.com/read/29691340/extensive-gene-amplification-as-a-mechanism-for-piperacillin-tazobactam-resistance-in-escherichia-coli
#11
Lisa M Schechter, David P Creely, Cherilyn D Garner, Dee Shortridge, Hoan Nguyen, Lei Chen, Blake M Hanson, Erica Sodergren, George M Weinstock, W Michael Dunne, Alex van Belkum, Shana R Leopold
Although the TEM-1 β-lactamase (BlaTEM-1 ) hydrolyzes penicillins and narrow-spectrum cephalosporins, organisms expressing this enzyme are typically susceptible to β-lactam/β-lactamase inhibitor combinations such as piperacillin-tazobactam (TZP). However, our previous work led to the discovery of 28 clinical isolates of Escherichia coli resistant to TZP that contained only bla TEM-1 One of these isolates, E. coli 907355, was investigated further in this study. E. coli 907355 exhibited significantly higher β-lactamase activity and BlaTEM-1 protein levels when grown in the presence of subinhibitory concentrations of TZP...
April 24, 2018: MBio
https://www.readbyqxmd.com/read/29683387/primary-transcriptome-analysis-reveals-importance-of-is-elements-for-the-shaping-of-the-transcriptional-landscape-of-bordetella-pertussis
#12
Fabian Amman, Alexandre D'Halluin, Rudy Antoine, Ludovic Huot, Ilona Bibova, Kristina Keidel, Stéphanie Slupek, Peggy Bouquet, Loïc Coutte, Ségolène Caboche, Camille Locht, Branislav Vecerek, David Hot
Bordetella pertussis is the causative agent of whooping cough, a respiratory disease still considered as a major public health threat and for which recent re-emergence has been observed. Constant reshuffling of Bordetella pertussis genome organization was observed during evolution. These rearrangements are essentially mediated by Insertion Sequences (IS), a mobile genetic elements present in more than 230 copies in the genome, which are supposed to be one of the driving forces enabling the pathogen to escape from vaccine-induced immunity...
April 23, 2018: RNA Biology
https://www.readbyqxmd.com/read/29682879/commissioning-an-in-room-mobile-ct-for-adaptive-proton-therapy-with-a-compact-proton-system
#13
Jasmine A Oliver, Omar Zeidan, Sanford L Meeks, Amish P Shah, Jason Pukala, Patrick Kelly, Naren R Ramakrishna, Twyla R Willoughby
PURPOSE: To describe the commissioning of AIRO mobile CT system (AIRO) for adaptive proton therapy on a compact double scattering proton therapy system. METHODS: A Gammex phantom was scanned with varying plug patterns, table heights, and mAs on a CT simulator (CT Sim) and on the AIRO. AIRO-specific CT-stopping power ratio (SPR) curves were created with a commonly used stoichiometric method using the Gammex phantom. A RANDO anthropomorphic thorax, pelvis, and head phantom, and a CIRS thorax and head phantom were scanned on the CT Sim and AIRO...
April 6, 2018: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/29673993/dynamics-of-bacterial-composition-and-the-fate-of-antibiotic-resistance-genes-and-mobile-genetic-elements-during-the-co-composting-with-gentamicin-fermentation-residue-and-lovastatin-fermentation-residue
#14
Yuanwang Liu, Yao Feng, Dengmiao Cheng, Jianming Xue, Steven Wakelin, Zhaojun Li
Dynamics in bacterial community composition, along with 13 antibiotic resistance genes (ARGs) and eight mobile genetic elements (MGEs), were assessed during co-composting with gentamicin and lovastatin fermentation residue (GFR and LFR, respectively). Using next generation sequencing, the key bacterial taxa associated with the different stages of composting were identified. Most importantly, Bacillus, belonging to Phylum Firmicutes, was associated with enhanced degradation of gentamicin, decomposition of organic matter (OM) and dissolved organic carbon (DOC), and also extension of the thermophilic phase of the composting cycle...
April 5, 2018: Bioresource Technology
https://www.readbyqxmd.com/read/29669226/gene-therapy-in-patients-with-transfusion-dependent-%C3%AE-thalassemia
#15
Alexis A Thompson, Mark C Walters, Janet Kwiatkowski, John E J Rasko, Jean-Antoine Ribeil, Suradej Hongeng, Elisa Magrin, Gary J Schiller, Emmanuel Payen, Michaela Semeraro, Despina Moshous, Francois Lefrere, Hervé Puy, Philippe Bourget, Alessandra Magnani, Laure Caccavelli, Jean-Sébastien Diana, Felipe Suarez, Fabrice Monpoux, Valentine Brousse, Catherine Poirot, Chantal Brouzes, Jean-François Meritet, Corinne Pondarré, Yves Beuzard, Stany Chrétien, Thibaud Lefebvre, David T Teachey, Usanarat Anurathapan, P Joy Ho, Christof von Kalle, Morris Kletzel, Elliott Vichinsky, Sandeep Soni, Gabor Veres, Olivier Negre, Robert W Ross, David Davidson, Alexandria Petrusich, Laura Sandler, Mohammed Asmal, Olivier Hermine, Mariane De Montalembert, Salima Hacein-Bey-Abina, Stéphane Blanche, Philippe Leboulch, Marina Cavazzana
BACKGROUND: Donor availability and transplantation-related risks limit the broad use of allogeneic hematopoietic-cell transplantation in patients with transfusion-dependent β-thalassemia. After previously establishing that lentiviral transfer of a marked β-globin (βA-T87Q ) gene could substitute for long-term red-cell transfusions in a patient with β-thalassemia, we wanted to evaluate the safety and efficacy of such gene therapy in patients with transfusion-dependent β-thalassemia...
April 19, 2018: New England Journal of Medicine
https://www.readbyqxmd.com/read/29669108/genomic-context-of-resistance-genes-within-a-french-clinical-mdr-proteus-mirabilis-identification-of-the-novel-genomic-resistance-island-gipmi1
#16
Eliane Siebor, Claire de Curraize, Catherine Neuwirth
Objectives: To determine the location of the antibiotic resistance genes in the MDR Proteus mirabilis PmPHI clinical isolate. Methods: WGS and de novo assembly were performed. BLAST searches were used to identify relevant contigs. PCR and Sanger sequencing were used to link the fragments of interest and fill the gaps. Results: P. mirabilis PmPHI was resistant to six classes of antibiotics: penicillins, aminoglycosides, phenicols, tetracyclines, folate inhibitors and fluoroquinolones...
April 12, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29668013/drosophila-relics-hobo-and-hobo-mites-transposons-as-raw-material-for-new-regulatory-networks
#17
Elgion L S Loreto, Maríndia Deprá, José F Diesel, Yanina Panzera, Vera Lucia S Valente-Gaiesky
Hypermutable strains of Drosophila simulans have been studied for 20 years. Several mutants were isolated and characterized, some of which had phenotypes associated with alteration in development; for example, showing ectopic legs with eyes being expressed in place of antennae. The causal agent of this hypermutability is a non-autonomous hobo-related sequence (hoboVA). Around 100 mobilizable copies of this element are present in the D. simulans genome, and these are likely mobilized by the autonomous and canonical hobo element...
2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29666335/identification-molecular-characterization-and-analysis-of-the-expression-pattern-of-soxf-subgroup-genes-the-yellow-river-carp-cyprinus-carpio
#18
Tingting Liang, Yongfang Jia, Ruihua Zhang, Qiyan Du, Zhongjie Chang
Sox7, Sox17 and Sox18 are the members of the Sry-related high-mobility group box family (SoxF) of transcription factors. SoxF factors regulate endothelial cell fate as well as development and differentiation of blood cells and lymphatic vessels. There is very less information about the functions of these genes in fish. We obtained the full-length cDNA sequence of SoxF genes including Sox7, Sox17 and Sox18 in Cyprinus carpio, where Sox7 and Sox18 had two copies. The construction of a phylogenetic tree showed that these genes were homologous to the genes in other species...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29659815/plant-lineage-specific-amplification-of-transcription-factor-binding-motifs-by-miniature-inverted-repeat-transposable-elements-mites
#19
Jordi Morata, Fatima Marín, Jordi Payet, Josep M Casacuberta
Transposable elements are one of the main drivers of plant genome evolution. Transposon insertions can modify the gene coding capacity or the regulation of their expression, the latter being a more subtle effect, and therefore particularly useful for evolution. Transposons have been show to contain transcription factor binding sites that can be mobilized upon transposition with the potential to integrate new genes into transcriptional networks. MITEs are a type of non-coding DNA transposons that could be particularly suited as a vector to mobilize transcription factor binding sites and modify transcriptional networks during evolution...
April 5, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29651978/tracking-the-rules-of-transmission-and-introgression-with-networks
#20
Chloé Vigliotti, Cédric Bicep, Eric Bapteste, Philippe Lopez, Eduardo Corel
Understanding how an animal organism and its gut microbes form an integrated biological organization, known as a holobiont, is becoming a central issue in biological studies. Such an organization inevitably involves a complex web of transmission processes that occur on different scales in time and space, across microbes and hosts. Network-based models are introduced in this chapter to tackle aspects of this complexity and to better take into account vertical and horizontal dimensions of transmission. Two types of network-based models are presented, sequence similarity networks and bipartite graphs...
April 2018: Microbiology Spectrum
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