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https://www.readbyqxmd.com/read/29322764/rapid-veterinary-diagnosis-of-bovine-reproductive-infectious-diseases-from-semen-using-paper-origami-dna-microfluidics
#1
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
https://www.readbyqxmd.com/read/29321680/cryptic-transmission-of-st405-escherichia-coli-carrying-bla-ndm-4-in-hospital
#2
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
https://www.readbyqxmd.com/read/29277529/comparative-genomics-of-the-rmtb-carrying-inci1-st136-plasmids-in-avian-escherichia-coli-isolates-from-chickens-in-china
#3
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
https://www.readbyqxmd.com/read/29276973/molecular-and-functional-characterization-of-tumor-induced-factor-tif-hamster-homolog-of-cxcl3-gro%C3%AE-displays-tumor-suppressive-activity
#4
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
https://www.readbyqxmd.com/read/29274909/cloning-and-functional-characterization-of-human-pak1-promoter-by-steroid-hormones
#5
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
https://www.readbyqxmd.com/read/29218034/replication-of-staphylococcal-resistance-plasmids
#6
REVIEW
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
https://www.readbyqxmd.com/read/29201157/detection-of-the-line-1-retrotransposon-rna-binding-protein-orf1p-in-different-anatomical-regions-of-the-human-brain
#7
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
https://www.readbyqxmd.com/read/29197647/genetic-basis-of-chromosomally-encoded-mcr-1-gene
#8
Ruichao Li, Hua Yu, Miaomiao Xie, Kaichao Chen, Ning Dong, Dachuan Lin, Edward Wai-Chi Chan, Sheng Chen
Compared to plasmid-bearing mcr-1, the occurrence of chromosomally-encoded mcr-1 was rare although it has been reported in several cases. This study aims to investigate the genetic features of chromosomally-encoded mcr-1 among E. coli strains and potential genetic basis governing the mobilization of mcr-1 in bacterial chromosomes. The genome sequences of 16 E. coli strains containing a chromosomal mcr-1 gene were obtained and analyzed. Phylogenetic and WGS (Whole Genome Sequencing) analysis demonstrated that mcr-1 was associated with four major types of genetic arrangements, namely ISApl1-mcr1-orf, Tn6330, complex Tn6330 and ΔTn6330 in chromosomes of genetically unrelated E...
November 29, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29180282/antibiotic-resistance-genes-in-phage-particles-isolated-from-human-feces-and-induced-from-clinical-bacterial-isolates
#9
Maryury Brown-Jaque, William Calero-Cáceres, Paula Espinal, Judith Rodríguez-Navarro, Elisenda Miró, Juan José González-López, Thais Cornejo, Juan Carlos Hurtado, Ferran Navarro, Maite Muniesa
Phage particles have emerged as elements with the potential to mobilize antibiotic resistance genes (ARGs) in different environments, including the intestinal habitat. The aim of this study was to determine the occurrence of ARGs in phage particles present in fecal matter and induced from strains isolated from feces. Nine ARGs (blaTEM, blaCTX-M-1-group, blaCTX-M-9-group, blaOXA-48, qnrA, qnrS, mecA, sul1 and armA) were quantified by qPCR in the phage DNA fractions of 150 fecal samples obtained from healthy individuals...
November 24, 2017: International Journal of Antimicrobial Agents
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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