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pathogen dna enrichment

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https://www.readbyqxmd.com/read/28811345/inhibitors-of-the-histone-methyltransferases-ezh2-1-induce-a-potent-antiviral-state-and-suppress-infection-by-diverse-viral-pathogens
#1
Jesse H Arbuckle, Paul J Gardina, David N Gordon, Heather D Hickman, Jonathan W Yewdell, Theodore C Pierson, Timothy G Myers, Thomas M Kristie
Epigenetic regulation is based on a network of complexes that modulate the chromatin character and structure of the genome to impact gene expression, cell fate, and development. Thus, epigenetic modulators represent novel therapeutic targets used to treat a range of diseases, including malignancies. Infectious pathogens such as herpesviruses are also regulated by cellular epigenetic machinery, and epigenetic therapeutics represent a novel approach used to control infection, persistence, and the resulting recurrent disease...
August 15, 2017: MBio
https://www.readbyqxmd.com/read/28810870/vector-borne-and-zoonotic-diseases-of-dogs-in-north-west-new-south-wales-and-the-northern-territory-australia
#2
Amanda J Shapiro, Graeme Brown, Jacqueline M Norris, Katrina L Bosward, Debbie J Marriot, Nandhakumar Balakrishnan, Edward B Breitschwerdt, Richard Malik
BACKGROUND: Vector-borne diseases of dogs in Australian Aboriginal communities are relatively unexplored. These dogs represent a unique group with variable ecto- and endo-parasitic burdens, nutritional stresses and a general lack of veterinary intervention. We investigated haemoprotozoal and bacterial pathogen prevalences in relation to erythrocyte and platelet numbers in dogs from North-West New South Wales (N-W NSW) and the Northern Territory (NT; Central Australia). METHODS: Real-time PCR (qPCR) amplification of Anaplasma platys, Babesia vogeli, Mycoplasma haemocanis, Candidatus Mycoplasma haematoparvum and Bartonella spp...
August 15, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28806924/essential-genome-of-campylobacter-jejuni
#3
Rabindra K Mandal, Tieshan Jiang, Young Min Kwon
BACKGROUND: Campylobacter species are a leading cause of bacterial foodborne illness worldwide. Despite the global efforts to curb them, Campylobacter infections have increased continuously in both developed and developing countries. The development of effective strategies to control the infection by this pathogen is warranted. The essential genes of bacteria are the most prominent targets for this purpose. In this study, we used transposon sequencing (Tn-seq) of a genome-saturating library of Tn5 insertion mutants to define the essential genome of C...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28800596/fungal-genome-and-mating-system-transitions-facilitated-by-chromosomal-translocations-involving-intercentromeric-recombination
#4
Sheng Sun, Vikas Yadav, R Blake Billmyre, Christina A Cuomo, Minou Nowrousian, Liuyang Wang, Jean-Luc Souciet, Teun Boekhout, Betina Porcel, Patrick Wincker, Joshua A Granek, Kaustuv Sanyal, Joseph Heitman
Species within the human pathogenic Cryptococcus species complex are major threats to public health, causing approximately 1 million infections globally annually. Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex, and it is non-pathogenic. Additionally, while pathogenic Cryptococcus species have bipolar mating systems with a single large mating type (MAT) locus that represents a derived state in Basidiomycetes, C. amylolentus has a tetrapolar mating system with 2 MAT loci (P/R and HD) located on different chromosomes...
August 11, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28789678/optimization-and-validation-of-sample-preparation-for-metagenomic-sequencing-of-viruses-in-clinical-samples
#5
Dagmara W Lewandowska, Osvaldo Zagordi, Fabienne-Desirée Geissberger, Verena Kufner, Stefan Schmutz, Jürg Böni, Karin J Metzner, Alexandra Trkola, Michael Huber
BACKGROUND: Sequence-specific PCR is the most common approach for virus identification in diagnostic laboratories. However, as specific PCR only detects pre-defined targets, novel virus strains or viruses not included in routine test panels will be missed. Recently, advances in high-throughput sequencing allow for virus-sequence-independent identification of entire virus populations in clinical samples, yet standardized protocols are needed to allow broad application in clinical diagnostics...
August 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28755939/multiplex-pcr-coupled-with-propidium-monoazide-for-the-detection-of-viable-cronobacter-sakazakii-bacillus-cereus-and-salmonella-spp-in-milk-and-milk-products
#6
Shuang Yu, Leina Yan, Xin Wu, Fan Li, Dong Wang, Hengyi Xu
Cronobacter sakazakii, Bacillus cereus, and Salmonella spp. are common food-borne pathogens. The aim of this study was to develop a sensitive, specific, and rapid method for the simultaneous detection of these 3 pathogens in milk and milk products. Three specific primers were designed based on ompA, invA, and cesB of C. sakazakii, Salmonella spp. and B. cereus, respectively, for use in a multiplex PCR (mPCR). To eliminate false-positive results, cells were pretreated with propidium monoazide (PMA) for the selective elimination of the genomic DNA of dead cells...
July 26, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28755293/genome-re-sequencing-analysis-uncovers-pathogenecity-related-genes-undergoing-positive-selection-in-magnaporthe-oryzae
#7
Jidong Cao, Yongqi Yu, Junkai Huang, Rui Liu, Yan Chen, Suiyan Li, Jun Liu
Rice blast caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases, which causes significant rice yield losses and affects global food security. To better understand genetic variations among different isolates of M. oryzae in nature, we re-sequenced the genomes of two field isolates, CH43 and Zhong-10-8-14, which showed distinct pathogenecity on most of the rice cultivars. Genome-wide genetic variation analysis reveals that ZHONG-10-8-14 exhibits higher sequence variations than CH43...
July 25, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28750028/clinical-impact-of-a-targeted-next-generation-sequencing-gene-panel-for-autoinflammation-and-vasculitis
#8
Ebun Omoyinmi, Ariane Standing, Annette Keylock, Fiona Price-Kuehne, Sonia Melo Gomes, Dorota Rowczenio, Sira Nanthapisal, Thomas Cullup, Rodney Nyanhete, Emma Ashton, Claire Murphy, Megan Clarke, Helena Ahlfors, Lucy Jenkins, Kimberly Gilmour, Despina Eleftheriou, Helen J Lachmann, Philip N Hawkins, Nigel Klein, Paul A Brogan
BACKGROUND: Monogenic autoinflammatory diseases (AID) are a rapidly expanding group of genetically diverse but phenotypically overlapping systemic inflammatory disorders associated with dysregulated innate immunity. They cause significant morbidity, mortality and economic burden. Here, we aimed to develop and evaluate the clinical impact of a NGS targeted gene panel, the "Vasculitis and Inflammation Panel" (VIP) for AID and vasculitis. METHODS: The Agilent SureDesign tool was used to design 2 versions of VIP; VIP1 targeting 113 genes, and a later version, VIP2, targeting 166 genes...
2017: PloS One
https://www.readbyqxmd.com/read/28749478/molecular-autopsy-in-maternal-fetal-medicine
#9
Hanan E Shamseldin, Wesam Kurdi, Fatima Almusafri, Maha Alnemer, Alya Alkaff, Zeneb Babay, Amal Alhashem, Maha Tulbah, Nada Alsahan, Rubina Khan, Bahauddin Sallout, Elham Al Mardawi, Mohamed Zain Seidahmed, Niema Meriki, Yasser Alsaber, Alya Qari, Ola Khalifa, Wafaa Eyaid, Zuhair Rahbeeni, Ahmed Kurdi, Mais Hashem, Tarfa Alshidi, Eman Al-Obeid, Firdous Abdulwahab, Niema Ibrahim, Nour Ewida, Karen El-Akouri, Mariam Al Mulla, Tawfeg Ben-Omran, Matthias Pergande, Sebahattin Cirak, Saeed Al Tala, Ranad Shaheen, Eissa Faqeih, Fowzan S Alkuraya
PurposeThe application of genomic sequencing to investigate unexplained death during early human development, a form of lethality likely enriched for severe Mendelian disorders, has been limited.MethodsIn this study, we employed exome sequencing as a molecular autopsy tool in a cohort of 44 families with at least one death or lethal fetal malformation at any stage of in utero development. Where no DNA was available from the fetus, we performed molecular autopsy by proxy, i.e., through parental testing.ResultsPathogenic or likely pathogenic variants were identified in 22 families (50%), and variants of unknown significance were identified in further 15 families (34%)...
July 27, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28742982/investigation-of-orthologous-pathogen-recognition-gene-rich-regions-in-solanaceous-species
#10
A Di Donato, Giuseppe Andolfo, A Ferrarini, M Delledonne, M R Ercolano
The genome architecture of pathogen receptor genes (PRGs) was extensively investigated in several plant species. However, we still know little about their elaborate reorganization arose during the plant speciation process. Using recently released pepper and eggplant genome sequences we were able to identify 1097 pathogen recognition genes in pepper Zunla-1 and 775 in eggplant Nakate-Shinkuro. The retrieved genes were analysed for their tendency to cluster, using different methods to infer the means of grouping...
July 25, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28740461/down-for-the-count-cryptosporidium-infection-depletes-the-gut-microbiome-in-coquerel-s-sifakas
#11
Erin A McKenney, Lydia K Greene, Christine M Drea, Anne D Yoder
Background: The gut microbiome (GMB) is the first line of defense against enteric pathogens, which are a leading cause of disease and mortality worldwide. One such pathogen, the protozoan Cryptosporidium, causes a variety of digestive disorders that can be devastating and even lethal. The Coquerel's sifaka (Propithecus coquereli) - an endangered, folivorous primate endemic to Madagascar - is precariously susceptible to cryptosporidiosis under captive conditions. If left untreated, infection can rapidly advance to morbidity and death...
2017: Microbial Ecology in Health and Disease
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
#12
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 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28711269/development-of-an-isothermal-amplification-based-assay-for-the-rapid-visual-detection-of-salmonella-bacteria
#13
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...
September 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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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