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Justin Hardick, David Metzgar, Lisa Risen, Christopher Myers, Melinda Balansay, Trent Malcom, Richard Rothman, Charlotte Gaydos
Clinical samples were evaluated with the Mobile Analysis Platform (MAP) to determine platform performance for detecting respiratory viruses in samples previously characterized using clinical reverse transcriptase polymerase chain reaction assays. The percent agreement between MAP and clinical results was 97% for influenza A (73/75), 100% (21/21) for influenza B, 100% (6/6) for respiratory syncytial virus (RSV), and 80% (4/5) for negative specimens. The approximate limit of detection of the MAP was 30 copies/assay for RSV and 1500 copies/assay for Middle East respiratory syndrome coronavirus...
February 17, 2018: Diagnostic Microbiology and Infectious Disease
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
Faizule Hassan, Shuisong Ni, Tyler C Arnett, Melanie C McKell, Michael A Kennedy
High mobility group AT-hook 1 (HMGA1) protein is an oncogenic architectural transcription factor that plays an essential role in early development, but it is also implicated in many human cancers. Elevated levels of HMGA1 in cancer cells cause misregulation of gene expression and are associated with increased cancer cell proliferation and increased chemotherapy resistance. We have devised a strategy of using engineered viruses to deliver decoy hyper binding sites for HMGA1 to the nucleus of cancer cells with the goal of sequestering excess HMGA1 at the decoy hyper binding sites due to binding competition...
March 30, 2018: Molecular Therapy Oncolytics
Dong Wu, Ruoqi Ma, Huawei Wei, Kai Yang, Bing Xie
Around 350 million tons of solid waste is disposed of in landfills every year globally, with millions of cubic meters of landfill leachates released into neighboring environment. However, to date, little is known about the variations of antimicrobial resistance (AMR) in on-site leachate treatment systems and its development in leachate-receiving water environment. Here, we quantified 7 subtypes of antibiotic resistance genes (ARGs), 3 types of culturable antibiotic resistant bacteria (ARB) and 6 subtypes of mobile genetic elements (MGEs) in the effluents from a combined leachate treatment process, including biological treatment (MBR), physical separation (UF), ultraviolet (UV) disinfection and advanced oxidation process (AOP)...
March 1, 2018: Environment International
Ji Zheng, Zhenchao Zhou, Yuanyuan Wei, Tao Chen, Wanqiu Feng, Hong Chen
The rapid expansion of human activity in a region can exacerbate human health risks induced by antibiotic resistance genes (ARGs). Peri-urban ecosystems serve at the symbiotic interface between urban and rural ecosystems, and investigations into the dissemination of ARGs in peri-urban areas provide a basic framework for tracking the spread of ARGs and potential mitigations. In this study, through the use of high-throughput quantitative PCR and 16S rRNA gene high-throughput sequencing, seasonal and geographical distributions of ARGs and their host bacterial communities were characterized in a peri-urban river...
February 27, 2018: Environment International
Liming Wang, Hui Shen, Da Zhu, Bei Feng, Lan Yu, Xun Tian, Ci Ren, Chun Gao, Xiaomin Li, Ding Ma, Zheng Hu, Hui Wang
Integration of the high risk human papillomavirus (HR-HPV) genome into host chromatin is an important step in cervical carcinogenesis. We identified HR-HPV integration sites within the human genome through detection of integrated papillomavirus sequences-PCR and assessed the role of high mobility group A 2 (HMGA2) in cervical carcinogenesis in clinical samples and cell lines. HPV integration sites were analyzed in 40 cervical cancer samples, while copy number variation and protein expression were assessed in 19 normal cervixes, 49 cervical intraepithelial neoplasia (CIN), and 52 cervical cancer samples...
January 30, 2018: Oncotarget
Ashok Kumar, Satyabrata Bag, Bhabatosh Das
BACKGROUND: Genomic islands (GIs) are discrete segments of mobile DNA with defined boundaries, acquired in the bacterial genome from another organism by horizontal gene transfer during the course of evolution. GIs contribute significantly in virulence, disease development, antimicrobial resistance and metabolic process. OBJECTIVE: The present study focuses on the development of a vector based genetic tool carrying selectable and counter-selectable markers, in order to flag the GIs in the bacterial chromosome and monitor their stability in laboratory growth conditions...
February 22, 2018: Recent Patents on Biotechnology
Edina Szekeres, Cecilia Maria Chiriac, Andreea Baricz, Tiberiu Szőke-Nagy, Ildiko Lung, Maria-Loredana Soran, Knut Rudi, Nicolae Dragos, Cristian Coman
Groundwater is an essential public and drinking water supply and its protection is a goal for global policies. Here, we investigated the presence and prevalence of antibiotic residues, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial contamination in groundwater environments at various distances from urban areas. Antibiotic concentrations ranged from below detection limit to 917 ng/L, being trimethoprim, macrolide, and sulfonamide the most abundant antibiotic classes. A total of eleven ARGs (aminoglycoside, β-lactam, chloramphenicol, Macrolide-Lincosamide-Streptogramin B - MLSB, sulfonamide, and tetracycline), one antiseptic resistance gene, and two MGEs were detected by qPCR with relative abundances ranging from 6...
February 14, 2018: Environmental Pollution
Jacopo Solari, Francois Anquez, Katharina M Scherer, Thomas S Shimizu
We describe two methods for high-resolution fluorescence imaging of the positioning and mobility of E. coli chemoreceptors fused to photoconvertible fluorescent proteins. Chemoreceptors such as Tar and Tsr are transmembrane proteins expressed at high levels (thousands of copies per cell). Together with their cognate cytosolic signaling proteins, they form clusters on the plasma membrane. Theoretical models imply that the size of these clusters is an important parameter for signaling, and recent PALM imaging has revealed a broad distribution of cluster sizes...
2018: Methods in Molecular Biology
María Eloísa Poey, Magela Laviña
Class 1 integrons are genetic elements that carry a variable set of antibiotic resistance genes, being frequently found in clinical Gram-negative isolates. It is generally assumed that they easily spread horizontally among bacteria, thus contributing to the appearance of multidrug resistant clones. However, there are few experimental studies on the lateral transfer of these elements performed with bacterial collections that had been gathered following an epidemiological design. In this work, a collection with these characteristics, comprising uropathogenic Escherichia coli (UPEC) isolates bearing class 1 integrons, was employed to study the horizontal transfer of the integron to an E...
February 8, 2018: Microbial Pathogenesis
Hendrik Glauninger, Yifan Zhang, Khadine A Higgins, Alexander D Jacobs, Julia E Martin, Yue Fu, H Jerome Coyne Rd, Kevin E Bruce, Michael J Maroney, David E Clemmer, Daiana A Capdevila, David P Giedroc
Resistance to copper (Cu) toxicity in the respiratory pathogen Streptococcus pneumoniae is regulated by the Cu-specific metallosensor CopY. CopY is structurally related to the antibiotic-resistance regulatory proteins MecI and BlaI from Staphylococcus aureus, but is otherwise poorly characterized. Here we employ a multi-pronged experimental strategy to define the Spn CopY coordination chemistry and the unique mechanism of allosteric activation by Zn(ii) and allosteric inhibition by Cu(i) of cop promoter DNA binding...
January 7, 2018: Chemical Science
Elisa Orecchini, Loredana Frassinelli, Silvia Galardi, Silvia Anna Ciafrè, Alessandro Michienzi
Long interspersed element-1 (LINE-1 or L1) retrotransposons represent the only functional family of autonomous transposable elements in humans and formed 17% of our genome. Even though most of the human L1 sequences are inactive, a limited number of copies per individual retain the ability to mobilize by a process termed retrotransposition. The ongoing L1 retrotransposition may result in insertional mutagenesis that could lead to negative consequences such as genetic disease and cancer. For this reason, cells have evolved several mechanisms of defense to restrict L1 activity...
February 2, 2018: Chromosome Research
Roy N Platt, Michael W Vandewege, David A Ray
Transposable elements (TEs) are genetic elements with the ability to mobilize and replicate themselves in a genome. Mammalian genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. As a result, TEs have had significant impacts on mammalian evolution. Here we summarize the current understanding of TE content in mammal genomes and find that, with a few exceptions, most fall within a predictable range of observations. First, one third to one half of the genome is derived from TEs...
February 1, 2018: Chromosome Research
Zhugen Yang, Gaolian Xu, Julien Reboud, Syed Atif Ali, Gurpreet Kaur, John McGiven, Nongthombam Boby, Praveen Gupta, Pallab Chaudhuri, Jonathan Mark Cooper
The health and well-being of cattle is a significant concern for global agricultural output. In dairy production within low and middle income countries (LMICs), there is a significant biosensing challenge in detecting sexually transmitted infection (STI) pathogens during animal husbandry, due in part to difficulties associated with the limited infrastructure for veterinary medicine. Here we demonstrate low-cost, multiplexed and sample-to-answer paper-origami tests for the detection of three bovine infectious reproductive diseases in semen samples, collected at a test site in rural India...
January 11, 2018: ACS Sensors
Xiaoxia Zhang, Yu Feng, Weilong Zhou, Alan McNally, Zhiyong Zong
Three carbapenem-resistant Escherichia coli were recovered from rectal swabs of different patients in a tertiary hospital and were found carrying bla NDM-4, an uncommon bla NDM variant. Genome sequences of the isolates were obtained using Illumina technology and the long-read MinION sequencer. The isolates belonged to ST405 and phylogenetic group D, a globally distributed lineage associated with antimicrobial resistance. In addition to bla NDM-4, the three isolates carried 14 known resistance genes including the extended-spectrum β-lactamase gene bla CTX-M-15...
January 10, 2018: Scientific Reports
Li Yuan, Jian-Hua Liu, Xiang-Dang Du, Zhi-Yong Zong, Min Chen, Gong-Zheng Hu, Yu-Shan Pan
Eight rmtB-carrying avian Escherichia coli strains from a farm in China were characterized in our previous study, but little is known about the backbones and entire multiresistance regions (MRRs) of these plasmids. Here, three rmtB-carrying IncI1 ST136 plasmids were analyzed by whole-plasmid sequencing and compared. These plasmids were composed of an 83,470-bp IncI1 backbone carrying genes responsible for plasmid replication, transfer, maintenance, and stability functions, and a 17,330-bp MRR for pEC006 and pEC007, and a 34,626-bp MRR for pEC008...
December 22, 2017: International Journal of Antimicrobial Agents
Lili Jin, Zhou-Fang Li, Da-Kui Wang, Meina Sun, Wei Qi, Qiang Ma, Li Zhang, Chun Chu, Elaine Y M Chan, Susanna S T Lee, Helen Wise, Ka-Fai To, Ying Shi, Naiming Zhou, Wing-Tai Cheung
Previously our lab has created a mouse ovarian xenograft model of copy number variation (CNV)-mediated G protein-coupled receptor (GPCR) MAS-driven tumorigenesis, and RNA profiling identified a putative chemokine tumor-induced factor (Tif). Sequence analysis and chemotactic study suggested that Tif was likely to be a hamster homolog of human GROγ (CXCL3) [IJC 125 (2009): 1316-1327]. In the present study, we report the molecular and functional characterization of the Tif gene. Genomic study of CHO-K1 cells indicated that Tif gene consisted of 4 exons, characterized with an antisense B1 element which is embedded in the fourth exon...
December 22, 2017: Cytokine
Swetha Raghavan, Ganesh Venkatraman, Suresh K Rayala
P21-activated kinase 1 (Pak1) is known to be involved in a plethora of functions including cell growth, survival and can lead to cell transformation and tumor progression especially in breast tissue. Multiple studies have shown Pak1 dysregulation as a change in DNA copy number as well as gene expression levels, suggesting many regulatory mechanisms at transcriptional and translational level. However, very little is known about the transcriptional regulation of the human Pak1 promoter. Here, we focus on Pak1 promoter regulation by steroid hormones along with their respective receptors that are also crucial players in breast tissue function and tumorigenesis...
December 21, 2017: Gene
Stephen M Kwong, Joshua P Ramsay, Slade O Jensen, Neville Firth
The currently widespread and increasing prevalence of resistant bacterial pathogens is a significant medical problem. In clinical strains of staphylococci, the genetic determinants that confer resistance to antimicrobial agents are often located on mobile elements, such as plasmids. Many of these resistance plasmids are capable of horizontal transmission to other bacteria in their surroundings, allowing extraordinarily rapid adaptation of bacterial populations. Once the resistance plasmids have been spread, they are often perpetually maintained in the new host, even in the absence of selective pressure...
2017: Frontiers in Microbiology
Debpali Sur, Raj Kishor Kustwar, Savita Budania, Anita Mahadevan, Dustin C Hancks, Vijay Yadav, S K Shankar, Prabhat K Mandal
Background: Recent reports indicate that retrotransposons - a type of mobile DNA - can contribute to neuronal genetic diversity in mammals. Retrotransposons are genetic elements that mobilize via an RNA intermediate by a "copy-and-paste" mechanism termed retrotransposition. Long Interspersed Element-1 (LINE-1 or L1) is the only active autonomous retrotransposon in humans and its activity is responsible for ~ 30% of genomic mass. Historically, L1 retrotransposition was thought to be restricted to the germline; however, new data indicate L1 s are active in somatic tissue with certain regions of the brain being highly permissive...
2017: Mobile DNA
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