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Mobile elements

Pragathi B Shridhar, Isha R Patel, Jayanthi Gangiredla, Lance W Noll, Xiaorong Shi, Jianfa Bai, Christopher A Elkins, Nancy A Strockbine, T G Nagaraja
Escherichia coli O104:H4, a Shiga toxin-producing hybrid pathotype that was implicated in a major foodborne outbreak in Germany in 2011, has not been detected in cattle. However, serotypes of O104, other than O104:H4, have been isolated from cattle feces, with O104:H7 being the most predominant. In this study, we investigated, based on whole genome sequence analyses, the virulence potential of E. coli O104 strains isolated from cattle feces, since cattle are asymptomatic carriers of E. coli O104. The genomes of ten bovine E...
2018: Frontiers in Microbiology
Michael W Deem, Melia Elizabeth Bonomo
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) constitute a multi-functional, constantly evolving immune system in bacteria and archaea cells. A heritable, molecular memory is generated of phage, plasmids, or other mobile genetic elements that attempt to attack the cell. This memory is used to recognize and interfere with subsequent invasions from the same genetic elements. This versatile prokaryotic tool has also been used to advance applications in biotechnology...
March 15, 2018: Physical Biology
Sophie Bischoff, Gesine Wieder, Franziska Einsle, Moritz B Petzold, Christiane Janßen, Jennifer L M Mumm, Hans-Ulrich Wittchen, Thomas Fydrich, Jens Plag, Andreas Ströhle
Exposure-based Cognitive Behavioral Therapy (eb-CBT) represents the most evidence-based psychotherapeutic approach in anxiety disorders. However, its efficacy may be limited by a delay in onset of action and a substantial number of patients does not respond sufficiently to treatment. In this context, aerobic exercise was found to be effective in reducing clinical anxiety as well as to improve (elements of) disorder-specific CBT in some mental disorders. We therefore investigated the effect of aerobic exercise supplementary to an eb-CBT in panic disorder and agoraphobia (PD/AG)...
March 5, 2018: Journal of Psychiatric Research
Lu Zeng, R Daniel Kortschak, Joy M Raison, Terry Bertozzi, David L Adelson
Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements...
2018: PloS One
Chieun Song, Jimin Lee, Taeyoon Kim, Jong Chan Hong, Chae Oh Lim
Under normal growth conditions, Arabidopsis VOZ1 interacts with DREB2C and acts as a transcriptional repressor by reducing DNA binding of DREB2C. Under heat stress conditions, VOZ1 is degraded by ubiquitination, and DREB2C, which is freed from VOZ1, functions as a transcription activator. To investigate the mechanism by which the DEHYDRATION-RESPONSIVE ELEMENT-BINDING FACTOR 2C (DREB2C)-dependent signaling cascade regulates heat stress (HS) responses, we performed a yeast two-hybrid screening using the DREB2C APETALA2 (AP2) DNA-binding domain as the bait against a cDNA library derived from Arabidopsis...
March 13, 2018: Planta
Morgan Petrovich, Binh Chu, Dorothy Wright, Jim Griffin, Maryam Elfeki, Brian T Murphy, Rachel Poretsky, George Wells
Wastewater treatment plants (WWTPs) are known to harbor antibiotic resistance genes (ARGs) that are disseminated into the environment via effluent. However, few studies have compared abundance, mobilization, and selective pressures for ARGs in WWTPs as a function of variations in secondary treatment bioprocesses. We used shotgun metagenomics to provide a comprehensive analysis of ARG composition, relationship to mobile genetic elements, and co-occurrences with antibiotic production genes (APGs) throughout two full-scale municipal WWTPs, one of which employs biofilm-based secondary treatment and another that uses a suspended growth system...
March 9, 2018: FEMS Microbiology Ecology
Sunhye Kim, Tae-Young Kim, Seung-Muk Yi, Jongbae Heo
The sources of different pollutants contributing to ambient fine particles (PM2.5 ) on Daebu Island, Korea, were estimated. Twenty four hour integrated filter samples were collected from May 21-November 1, 2016, and analyzed for organic carbon, elemental carbon, ions, and trace elements. Positive matrix factorization was conducted on the PM2.5 chemical speciation data from the samples to define the pathways and sources of PM2.5 at the sampling site. A total of 80 samples and 24 chemical species were used to run the model and a total of nine sources were identified: secondary sulfate (29...
March 10, 2018: Journal of Environmental Management
Andrew J Page, Alexander Wailan, Yan Shao, Kim Judge, Gordon Dougan, Elizabeth J Klemm, Nicholas R Thomson, Jacqueline A Keane
Increasingly rich metadata are now being linked to samples that have been whole-genome sequenced. However, much of this information is ignored. This is because linking this metadata to genes, or regions of the genome, usually relies on knowing the gene sequence(s) responsible for the particular trait being measured and looking for its presence or absence in that genome. Examples of this would be the spread of antimicrobial resistance genes carried on mobile genetic elements (MGEs). However, although it is possible to routinely identify the resistance gene, identifying the unknown MGE upon which it is carried can be much more difficult if the starting point is short-read whole-genome sequence data...
March 12, 2018: Microbial Genomics
Matteo Vecellio, Adrian Cortes, Amity R Roberts, Jonathan Ellis, Carla Jayne Cohen, Julian C Knight, Matthew A Brown, Paul Bowness, Bryan Paul Wordsworth
Objectives: To explore the functions of RUNX3 single nucleotide polymorphisms (SNPs) associated with ankylosing spondylitis (AS). Methods: Individual SNP associations were evaluated in 4230 UK cases. Their effects on transcription factor (TF) binding, transcription regulation, chromatin modifications, gene expression and gene interactions were tested by database interrogation, luciferase reporter assays, electrophoretic mobility gel shifts, chromatin immunoprecipitation and real-time PCR...
2018: RMD Open
Viktor Riklefs, Gulmira Abakassova, Aliya Bukeyeva, Sholpan Kaliyeva, Bakhtiyar Serik, Alma Muratova, Raushan Dosmagambetova
BACKGROUND: Medical education in Kazakhstan has been literally transformed in the past 10 years. Kazakhstan inherited the Soviet-time discipline-based teacher-centered system of education when no decisions could be made independently. The curriculum was mostly governed in a traditional way, with lectures being the core, little use of e-learning tools, and assessment through oral exams and multiple-choice questions. Most of the universities still preserve the subject-based curriculum with elements of integrated learning...
March 11, 2018: Medical Teacher
Inés Bado, Romina Papa Ezdra, Nicolás Cordeiro, Matilde Outeda, Leticia Caiata, Virginia García-Fulgueiras, Verónica Seija, Rafael Vignoli
OBJECTIVES: The objective of the present study was to characterise the mechanisms underlying quinolone and oxyimino-cephalosporin resistance in a Citrobacter freundii clinical isolate obtained from the ICU in Uruguay's University Hospital. METHODS: Citrobacter freundii strain CF638 was isolated from a urine culture. Identification and susceptibility testing were performed using the VITEK® 2 system, and MIC determination and disc diffusion assay, respectively. Resistance genes and mobile genetic elements were identified, by PCR and sequencing...
March 8, 2018: Journal of Global Antimicrobial Resistance
Girish Choppala, Ellen Moon, Richard Bush, Nanthi Bolan, Neil Carroll
The increased use of estuarine waters for commercial and recreational activities is one consequence of urbanisation. Western Australia's Peel-Harvey Estuary highlights the impacts of urbanisation, with a rapidly developing boating industry and periodic dredging activity. The aim of this research is to evaluate the potential mobility of nutrients and trace elements during dredging, and the influence of flocculation on iron and sulfur partitioning in iron monosulfide enriched sediments. Our findings indicate a short-term increase in nitrate, phosphate and ammonium, during dredging through the resuspension of sediments...
February 19, 2018: Chemosphere
S Mykolenko, V Liedienov, M Kharytonov, N Makieieva, T Kuliush, I Queralt, E Marguí, M Hidalgo, G Pardini, M Gispert
The work was conducted to establish contamination from improper disposal of hazardous wastes containing lead (Pb) and antimony (Sb) into nearby soils. Besides other elements in the affected area, the biological role of Sb, its behaviour in the pedosphere and uptake by plants and the food chain was considered. Wastes contained 139532 ± 9601 mg kg-1 (≈14%) Pb and 3645 ± 194 mg kg-1 (≈0.4%) Sb respectively and variability was extremely high at a decimetre scale. Dramatically high concentrations were also found for As, Cd, Cu, Mn, Ni, Sn and Zn...
March 7, 2018: Environmental Pollution
Zoé Joly-Lopez, Thomas E Bureau
Transposable elements (TEs) are mobile genetic elements that were once perceived as merely selfish, but are now recognized as potent agents of adaptation. One way TEs contribute to genome evolution is through TE exaptation, a process whereby TEs, which usually persist by replicating in the genome, transform into novel host genes, which thereafter persist by conferring phenotypic benefits. Exapted TEs are known to contribute diverse and vital functions, and may facilitate punctuated equilibrium, yet we have little understanding about the process of TE exaptation...
March 8, 2018: Current Opinion in Genetics & Development
C Blake Sullivan, Henry Hoffman
OBJECTIVE: We describe sialography as a dynamic imaging modality useful in establishing the diagnosis and planning for treatment of a parotid gland ductal foreign body. METHODS: Chart and radiographic imaging review of a 75 year-old male who had obstructive sialadenitis symptoms two years after welding slag pierced the cheek skin and identified as a 'piece of steel stuck in his cheek'. RESULTS: Sialography was used to demonstrate a foreign body adjacent to the parotid gland to indicate its presence as a mobile element within the ductal system associated with marked pre-obstructive duct dilation...
March 3, 2018: American Journal of Otolaryngology
Chao Wan, Zhixiu Hao
Graft tissues within bone tunnels remain mobile for a long time after anterior cruciate ligament (ACL) reconstruction. However, whether the graft-tunnel friction affects the finite element (FE) simulation of the ACL reconstruction is still unclear. Four friction coefficients (from 0 to 0.3) were simulated in the ACL-reconstructed joint model as well as two loading levels of anterior tibial drawer. The graft-tunnel friction did not affect joint kinematics and the maximal principal strain of the graft. By contrast, both the relative graft-tunnel motion and equivalent strain for the bone tunnels were altered, which corresponded to different processes of graft-tunnel integration and bone remodeling, respectively...
March 9, 2018: Computer Methods in Biomechanics and Biomedical Engineering
Rusen Yan, Guru Khalsa, Suresh Vishwanath, Yimo Han, John Wright, Sergei Rouvimov, D Scott Katzer, Neeraj Nepal, Brian P Downey, David A Muller, Huili G Xing, David J Meyer, Debdeep Jena
Epitaxy is a process by which a thin layer of one crystal is deposited in an ordered fashion onto a substrate crystal. The direct epitaxial growth of semiconductor heterostructures on top of crystalline superconductors has proved challenging. Here, however, we report the successful use of molecular beam epitaxy to grow and integrate niobium nitride (NbN)-based superconductors with the wide-bandgap family of semiconductors-silicon carbide, gallium nitride (GaN) and aluminium gallium nitride (AlGaN). We apply molecular beam epitaxy to grow an AlGaN/GaN quantum-well heterostructure directly on top of an ultrathin crystalline NbN superconductor...
March 7, 2018: Nature
Ying Wu, Erping Cui, Yiru Zuo, Weixiao Cheng, Hong Chen
The prevalence and persistence of antibiotic resistance genes in wastewater treatment plants (WWTPs) is of growing interest, and residual sludge is among the main sources for the release of antibiotic resistance genes (ARGs). Moreover, heavy metals concentrated in dense microbial communities of sludge could potentially favor co-selection of ARGs and metal resistance genes (MRGs). Residual sludge treatment is needed to limit the spread of resistance from WWTPs into the environment. This study aimed to explore the fate of ARGs and MRGs during thermophilic two-phase (acidogenic/methanogenic phase) anaerobic digestion by metagenomic analysis...
March 7, 2018: Environmental Science and Pollution Research International
L Q Zhang, C H Zhang, J J Li, Y C Meng, Y T Yang, Y Song, Z N Ding, T X Yan
Micro-structural characteristics and electrical properties of an n-type GaN epilayer on Al2 O3 irradiated by 290-MeV238 U32+ ions to various fluences were investigated using atomic force microscopy (AFM), scanning electron microscopy (SEM), high-resolution X-ray diffraction (HRXRD), and Raman scattering spectroscopy. AFM images show that the nano-hillocks generated, and the diameter and density of the nano-hillocks, increase obviously with increasing ion fluence, accompanied by an increase in surface roughness...
March 7, 2018: Scientific Reports
Marta Fadda, Elisa Galimberti, Maddalena Fiordelli, Peter Johannes Schulz
BACKGROUND: There is mixed evidence on the effectiveness of vaccination-related interventions. A major limitation of most intervention studies is that they do not apply randomized controlled trials (RCTs), the method that, over the last 2 decades, has increasingly been considered as the only method to provide proof of the effectiveness of an intervention and, consequently, as the most important instrument in deciding whether to adopt an intervention or not. This study, however, holds that methods other than RCTs also can produce meaningful results...
March 7, 2018: JMIR MHealth and UHealth
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