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pathogen dna enrichment

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https://www.readbyqxmd.com/read/28715499/helicobacter-pylori-modulates-host-cell-responses-by-cagt4ss-dependent-translocation-of-an-intermediate-metabolite-of-lps-inner-core-heptose-biosynthesis
#1
Saskia C Stein, Eugenia Faber, Simon H Bats, Tatiana Murillo, Yvonne Speidel, Nina Coombs, Christine Josenhans
Highly virulent Helicobacter pylori cause proinflammatory signaling inducing the transcriptional activation and secretion of cytokines such as IL-8 in epithelial cells. Responsible in part for this signaling is the cag pathogenicity island (cagPAI) that codetermines the risk for pathological sequelae of an H. pylori infection such as gastric cancer. The Cag type IV secretion system (CagT4SS), encoded on the cagPAI, can translocate various molecules into cells, the effector protein CagA, peptidoglycan metabolites and DNA...
July 17, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28711269/development-of-an-isothermal-amplification-based-assay-for-the-rapid-visual-detection-of-salmonella-bacteria
#2
Hai-Bin Liu, Yu-Xuan Zang, Xin-Jun Du, Ping Li, Shuo Wang
The efficient and timely detection of pathogens is a major concern worldwide. The aim of this study was to establish a rapid detection method for Salmonella bacteria in food samples to facilitate timely treatment. Widely used detection methods currently include culture-based methods and PCR-based methods. The former are time consuming, requiring 2 to 3 d, whereas the latter have higher accuracy but are typically complicated, requiring expertise and expensive instruments. In this study, a sensitive and rapid approach for the visual and point-of-use detection of Salmonella bacteria based on recombinase polymerase amplification (RPA) and a lateral-flow (LF) nucleic acid strip was established...
July 12, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28696392/comparative-transcriptome-analysis-reveals-adaptive-evolution-of-notopterygium-incisum-and-notopterygium-franchetii-two-high-alpine-herbal-species-endemic-to-china
#3
Yun Jia, Mi-Li Liu, Ming Yue, Zhe Zhao, Gui-Fang Zhao, Zhong-Hu Li
The extreme conditions (e.g., cold, low oxygen, and strong ultraviolet radiation) of the high mountains provide an ideal natural laboratory for studies on speciation and the adaptive evolution of organisms. Up to now, few genome/transcriptome-based studies have been carried out on how plants adapt to conditions at extremely high altitudes. Notopterygium incisum and Notopterygium franchetii (Notopterygium, Apiaceae) are two endangered high-alpine herbal plants endemic to China. To explore the molecular genetic mechanisms of adaptation to high altitudes, we performed high-throughput RNA sequencing (RNA-seq) to characterize the transcriptomes of the two species...
July 11, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28687775/integrated-analysis-of-tobacco-mirna-and-mrna-expression-profiles-under-pvy-infection-provids-insight-into-tobacco-pvy-interactions
#4
Yushuang Guo, Meng-Ao Jia, Yumei Yang, Linlin Zhan, Xiaofei Cheng, Jianyu Cai, Jie Zhang, Jie Yang, Tao Liu, Qiang Fu, Jiehong Zhao, Imran Haider Shamsi
Potato virus Y (PVY) is a globally and economically important pathogen of potato, tobacco, tomato and other staple crops and caused significant yield losses and reductions in quality.To explore the molecular PVY-host interactions, we analysed changes in the miRNA and mRNA profiles of tobacco in response to PVY infection. A total of 81 differentially expressed miRNAs belonging to 29 families and 8133 mRNAs were identified. The Gene Ontology (GO) enrichment analyses showed that genes encoding the DNA/RNA binding, catalytic activity and signalling molecules were all significantly enriched...
July 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28670437/use-of-clinical-chromosomal-microarray-in-chinese-patients-with-autism-spectrum-disorder-implications-of-a-copy-number-variation-involving-dpp10
#5
Annisa Shui Lam Mak, Annie Ting Gee Chiu, Gordon Ka Chun Leung, Christopher Chun Yu Mak, Yoyo Wing Yiu Chu, Gary Tsz Kin Mok, Wing Fai Tang, Kelvin Yuen Kwong Chan, Mary Hoi Yin Tang, Elizabeth Tak-Kwong Lau Yim, Kin Wai So, Victoria Qinchen Tao, Cheuk Wing Fung, Virginia Chun Nei Wong, Mohammed Uddin, So Lun Lee, Christian R Marshall, Stephen W Scherer, Anita Sik Yau Kan, Brian Hon Yin Chung
BACKGROUND: Array comparative genomic hybridization (aCGH) is recommended as a first-tier genetic test for children with autism spectrum disorder (ASD). However, interpretation of results can often be challenging partly due to the fact that copy number variants (CNVs) in non-European ASD patients are not well studied. To address this literature gap, we report the CNV findings in a cohort of Chinese children with ASD. METHODS: DNA samples were obtained from 258 Chinese ASD patients recruited from a child assessment center between January 2011 and August 2014...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28657667/germline-genetic-variants-in-men-with-prostate-cancer-and-one-or-more-additional-cancers
#6
Patrick G Pilié, Anna M Johnson, Kristen L Hanson, Megan E Dayno, Ashley L Kapron, Elena M Stoffel, Kathleen A Cooney
BACKGROUND: Prostate cancer has a significant heritable component, and rare deleterious germline variants in certain genes can increase the risk of the disease. The aim of the current study was to describe the prevalence of pathogenic germline variants in cancer-predisposing genes in men with prostate cancer and at least 1 additional primary cancer. METHODS: Using a multigene panel, the authors sequenced germline DNA from 102 men with prostate cancer and at least 1 additional primary cancer who also met ≥1 of the following criteria: 1) age ≤55 years at the time of diagnosis of the first malignancy; 2) rare tumor type or atypical presentation of a common tumor; and/or 3) ≥3 primary malignancies...
June 28, 2017: Cancer
https://www.readbyqxmd.com/read/28646719/dna-aptamer-based-colorimetric-detection-platform-for-salmonella-enteritidis
#7
Ceren Bayraç, Füsun Eyidoğan, Hüseyin Avni Öktem
Food safety is a major issue to protect public health and a key challenge is to find detection methods for identification of hazards in food. Food borne infections affects millions of people each year and among pathogens, Salmonella Enteritidis is most widely found bacteria causing food borne diseases. Therefore, simple, rapid, and specific detection methods are needed for food safety. In this study, we demonstrated the selection of DNA aptamers with high affinity and specificity against S. Enteritidis via Cell Systematic Evolution of Ligands by Exponential Enrichment (Cell-SELEX) and development of sandwich type aptamer-based colorimetric platforms for its detection...
June 16, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28645257/relationship-between-nasopharyngeal-and-bronchoalveolar-microbial-communities-in-clinically-healthy-feedlot-cattle
#8
Mohamed M Zeineldin, James F Lowe, Elsbeth D Grimmer, Maria R C de Godoy, Mohamed M Ghanem, Yassein M Abd El-Raof, Brian M Aldridge
BACKGROUND: The importance of upper airway structure in the susceptibility of the lower respiratory tract to colonization with potential pathogens is well established. With the advent of rapid, high throughput, next generation sequencing, there is a growing appreciation of the importance of commensal microbial populations in maintaining mucosal health, and a realization that bacteria colonize anatomical locations that were previously considered to be sterile. While upper respiratory tract microbial populations have been described, there are currently no published studies describing the normal microbial populations of the bovine lower respiratory tract...
June 23, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28626092/-p53-gene-mutations-of-familial-breast-cancer-and-early-onset-breast-cancer-in-part-population-of-southern-china
#9
Xueli Hu, Huiying Ouyang, Hao Wang, Hui Li, Feiyu Chen, Xu Dai, Weibing Zhou, Yuanping Hu, Qian Xue
To investigate the site and characteristic of p53 gene mutations in familial or early-onset breast cancer patients in part population of southern China.
 Methods: A total of 150 patients with familial and early-onset breast cancer in parts population of southern China were enrolled. Genomic DNA was isolated from each peripheral blood sample, and the entire coding sequence and exon and intron splicing region of p53 gene were amplificated by PCR in the 150 patients. The mutation analysis were detected by denaturing high performance liquid chromatography (DHPLC) and confirmed by DNA sequence analysis...
May 28, 2017: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/28623657/aptamer-magnetic-bead-quantum-dot-sandwich-assays-for-foodborne-pathogen-detection-pros-cons-and-lessons-learned
#10
John G Bruno, Jeffrey C Sivils, Taylor Phillips
DNA and RNA aptamers have been extensively investigated as potential competitors for antibodies for a variety of applications including food safety testing. Ultrasensitive fluorescence detection of foodborne pathogenic bacteria as low as 1-10 cells/mL has been achieved using aptamers coupled to quantum dots in clear pristine buffers for environmental sample detection. Quantum dots offer other advantages, including single UV or blue light source multiplex (multicolored) detection. However, quantum dots can exhibit decreased fluorescence in some food matrixes and even completely fail to fluoresce in some fatty matrixes, as documented in this report...
June 16, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28618303/transcriptomic-response-of-the-insect-vector-peregrinus-maidis-to-maize-mosaic-rhabdovirus-and-identification-of-conserved-responses-to-propagative-viruses-in-hopper-vectors
#11
Kathleen M Martin, Karen Barandoc-Alviar, Derek J Schneweis, Catherine L Stewart, Dorith Rotenberg, Anna E Whitfield
Maize mosaic virus (MMV) is a plant-pathogenic rhabdovirus that is transmitted by the corn planthopper, Peregrinus maidis, in a propagative manner. P. maidis supports long-term MMV infections with no negative effects on insect performance. To elucidate whole-body transcriptome responses to virus infection, RNA-Seq was used to examine differential gene expression of virus-infected adult insects, and libraries were prepared from replicated groups of virus-exposed insects and non-exposed insects. From the 68,003 de novo-assembled transcripts, 144 were differentially-expressed (DE) during viral infection with comparable numbers up- and down-regulated...
September 2017: Virology
https://www.readbyqxmd.com/read/28611792/structural-and-functional-insights-into-wrky3-and-wrky4-transcription-factors-to-unravel-the-wrky-dna-w-box-complex-interaction-in-tomato-solanum-lycopersicum-l-a-computational-approach
#12
Mohd Aamir, Vinay K Singh, Mukesh Meena, Ram S Upadhyay, Vijai K Gupta, Surendra Singh
The WRKY transcription factors (TFs), play crucial role in plant defense response against various abiotic and biotic stresses. The role of WRKY3 and WRKY4 genes in plant defense response against necrotrophic pathogens is well-reported. However, their functional annotation in tomato is largely unknown. In the present work, we have characterized the structural and functional attributes of the two identified tomato WRKY transcription factors, WRKY3 (SlWRKY3), and WRKY4 (SlWRKY4) using computational approaches...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28604951/-analysis-of-foxl2-gene-mutations-in-5-families-affected-with-blepharophimosis-ptosis-and-epicanthus-inversus-syndrome
#13
Xiaowen Yang, Wen Li, Juan Du, Shimin Yuan, Wenbin He, Qianjun Zhang, Changgao Zhong, Guangxiu Lu, Yueqiu Tan
OBJECTIVE: To screen for FOXL2 gene mutations in 6 patients with blepharophimosis, ptosis, and epicanthus inversus syndrome (BPES), and explore their genotype-phenotype correlation. METHODS: Peripheral venous blood samples were collected from the patients for the extraction of genomic DNA. PCR and Sanger sequencing were employed to analyze the coding region and flanking sequences of the FOXL2 gene. Pathogenicity of the identified mutations was verified through literature review and bioinformatic analysis...
June 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28600759/whole-genome-enrichment-using-rna-probes-and-sequencing-of-chlamydia-trachomatis-directly-from-clinical-samples
#14
Amanda Claire Brown, Mette T Christiansen
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography, and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow-growing, or obligate intracellular pathogens, such as Chlamydia trachomatis. However clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28594148/analysis-of-selected-genes-associated-with-cardiomyopathy-by%C3%A2-next-generation-sequencing
#15
Viktoria Szabadosova, Iveta Boronova, Peter Ferenc, Iveta Tothova, Jarmila Bernasovska, Michaela Zigova, Jan Kmec, Ivan Bernasovsky
BACKGROUND: As the leading cause of congestive heart failure, cardiomyopathy represents a heterogenous group of heart muscle disorders. Despite considerable progress being made in the genetic diagnosis of cardiomyopathy by detection of the mutations in the most prevalent cardiomyopathy genes, the cause remains unsolved in many patients. High-throughput mutation screening in the disease genes for cardiomyopathy is now possible because of using target enrichment followed by next-generation sequencing...
June 8, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28578020/pathogenicity-analysis-of-novel-variations-in-chinese-han-patients-with-polycystic-kidney-disease
#16
Zishui Fang, Shiyan Xu, Yonghua Wang, Liwei Sun, Yi Feng, Yibin Guo, Hongyi Li, Weiying Jiang
OBJECTIVE: Locus and allellic heterogeneity in polycystic kidney disease (PKD) is a great challenge in precision diagnosis. We aim to establish comprehensive methods to distinguish the pathogenic mutations from the variations in PKD1, PKD2 and PKHD1 genes in a limited time and lay the foundation for precisely prenatal diagnosis, preimplantation genetic diagnosis and presymptom diagnosis of PKD. METHODS: Nested PCR combined with direct DNA sequencing were used to screen variations in PKD1, PKD2 and PKHD1 genes...
May 31, 2017: Gene
https://www.readbyqxmd.com/read/28553275/host-immune-selection-of-rumen-bacteria-through-salivary-secretory-iga
#17
Janelle M Fouhse, Luke Smiegielski, Melanie Tuplin, Le Luo Guan, Benjamin P Willing
The rumen microbiome is integral to efficient production in cattle and shows strong host specificity, yet little is known about what host factors shape rumen microbial composition. Secretory immunoglobulin A (SIgA) is produced in large amounts in the saliva, can coat both commensal and pathogenic microbes within the gut, and presents a plausible mechanism of host specificity. However, the role salivary SIgA plays in commensal bacteria selection in ruminants remains elusive. The main objectives of this study were to develop an immuno-affinity benchtop method to isolate SIgA-tagged microbiota and to determine if salivary SIgA preferentially binds selected bacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28526589/a-rapid-salmonella-detection-method-involving-thermophilic-helicase-dependent-amplification-and-a-lateral-flow-assay
#18
Xin-Jun Du, Tian-Jiao Zhou, Ping Li, Shuo Wang
Salmonella is a major foodborne pathogen that is widespread in the environment and can cause serious human and animal disease. Since conventional culture methods to detect Salmonella are time-consuming and laborious, rapid and accurate techniques to detect this pathogen are critically important for food safety and diagnosing foodborne illness. In this study, we developed a rapid, simple and portable Salmonella detection strategy that combines thermophilic helicase-dependent amplification (tHDA) with a lateral flow assay to provide a detection result based on visual signals within 90 min...
May 16, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28513808/magnetic-nanoparticle-enhanced-pcr-for-the-detection-and-identification-of-staphylococcus-aureus-and-salmonella-enteritidis
#19
Dimitra Houhoula, Joseph Papaparaskevas, Katerina Zatsou, Nikolaos Nikolaras, Hanan I Malkawi, Marie-Paule Mingenot-Leclercq, Spyros Konteles, Stamatis Koussisis, Athanassios Tsakris, Ekatherina Charvalos
This paper evaluated magnetic nanoparticle-enhanced PCR for the detection and identification of Staphylococcus aureus and Salmonella enteritidis. Two different types of magnetic nanoparticles designated MPIO (iron concentration 2.5 mg/ml, size 1 μm) and NP (iron concentration 8.7 mg/ml, size 60 nm), both conjugated with S. aureus or S. enteritidis antibodies were evaluated as an enrichment procedure for PCR-detection of the pathogens in Trypticase Soy Broth, milk, blood and meat broth. Bacterial suspensions (1...
May 17, 2017: New Microbiologica
https://www.readbyqxmd.com/read/28513534/unraveling-prion-protein-interactions-with-aptamers-and-other-prp-binding-nucleic-acids
#20
REVIEW
Bruno Macedo, Yraima Cordeiro
Transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative disorders that affect humans and other mammals. The etiologic agents common to these diseases are misfolded conformations of the prion protein (PrP). The molecular mechanisms that trigger the structural conversion of the normal cellular PrP (PrP(C)) into the pathogenic conformer (PrP(Sc)) are still poorly understood. It is proposed that a molecular cofactor would act as a catalyst, lowering the activation energy of the conversion process, therefore favoring the transition of PrP(C) to PrP(Sc)...
May 17, 2017: International Journal of Molecular Sciences
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