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pathogen dna enrichment

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https://www.readbyqxmd.com/read/28932211/strain-level-streptococcus-colonization-patterns-during-the-first-year-of-life
#1
Meredith S Wright, Jamison McCorrison, Andres M Gomez, Erin Beck, Derek Harkins, Jyoti Shankar, Stephanie Mounaud, Edelwisa Segubre-Mercado, Aileen May R Mojica, Brian Bacay, Susan A Nzenze, Sheila Z M Kimaro, Peter Adrian, Keith P Klugman, Marilla G Lucero, Karen E Nelson, Shabir Madhi, Granger G Sutton, William C Nierman, Liliana Losada
Pneumococcal pneumonia has decreased significantly since the implementation of the pneumococcal conjugate vaccine (PCV), nevertheless, in many developing countries pneumonia mortality in infants remains high. We have undertaken a study of the nasopharyngeal (NP) microbiome during the first year of life in infants from The Philippines and South Africa. The study entailed the determination of the Streptococcus sp. carriage using a lytA qPCR assay, whole metagenomic sequencing, and in silico serotyping of Streptococcus pneumoniae, as well as 16S rRNA amplicon based community profiling...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28924154/a-dna-aptamer-efficiently-inhibits-the-infectivity-of-bovine-herpesvirus-1-by-blocking-viral-entry
#2
Jian Xu, Xixi Zhang, Shuanghai Zhou, Junjun Shen, Dawei Yang, Jing Wu, Xiaoyang Li, Meiling Li, Xiufen Huang, Joshua E Sealy, Munir Iqbal, Yongqing Li
Bovine herpesvirus 1 (BoHV-1) is an important pathogen of domestic and wild cattle responsible for major economic losses in dairy and beef industries throughout the world. Inhibition of viral entry plays a crucial role in the control of BoHV-1 infection and aptamers have been reported to inhibit viral replication. In this study, nine DNA aptamers that target BoHV-1 were generated using systemic evolution of ligands by exponential enrichment. Of the nine candidates, aptamer IBRV-A4 exhibited the highest affinity and specificity for BoHV-1, which bound to BoHV-1 with a Kd value of 3...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28919685/prevalence-of-listeria-monocytogenes-yersinia-enterocolitica-staphylococcusaureus-and-salmonella-enterica-typhimurium-in-meat-and-meat-products-using-multiplex-polymerase-chain-reaction
#3
C Latha, C J Anu, V J Ajaykumar, B Sunil
AIM: The objective of the study was to investigate the occurrence of Listeria monocytogenes, Yersinia enterocolitica, Staphylococcusaureus, and Salmonella enterica Typhimurium in meat and meat products using the multiplex polymerase chain reaction (PCR) method. MATERIALS AND METHODS: The assay combined an enrichment step in tryptic soy broth with yeast extract formulated for the simultaneous growth of target pathogens, DNA isolation and multiplex PCR. A total of 1134 samples including beef (n=349), chicken (n=325), pork (n=310), chevon (n=50), and meat products (n=100) were collected from different parts of Kerala, India...
August 2017: Veterinary World
https://www.readbyqxmd.com/read/28901631/equine-behavioral-enrichment-toys-as-tools-for-non-invasive-recovery-of-viral-and-host-dna
#4
Peter A Seeber, Sanatana E Soilemetzidou, Marion L East, Chris Walzer, Alex D Greenwood
Direct collection of samples from wildlife can be difficult and sometimes impossible. Non-invasive remote sampling for the purpose of DNA extraction is a potential tool for monitoring the presence of wildlife at the individual level, and for identifying the pathogens shed by wildlife. Equine herpesviruses (EHV) are common pathogens of equids that can be fatal if transmitted to other mammals. Transmission usually occurs by nasal aerosol discharge from virus-shedding individuals. The aim of this study was to validate a simple, non-invasive method to track EHV shedding in zebras and to establish an efficient protocol for genotyping individual zebras from environmental DNA (eDNA)...
September 12, 2017: Zoo Biology
https://www.readbyqxmd.com/read/28899689/enhanced-expression-of-genes-related-to-xenobiotic-metabolism-in-the-skin-of-patients-with-atopic-dermatitis-but-not-with-ichthyosis-vulgaris
#5
Stefan Blunder, Sulev Kõks, Gea Kõks, Ene Reimann, Hubert Hackl, Robert Gruber, Verena Moosbrugger-Martinz, Matthias Schmuth, Sandrine Dubrac
Previous transcriptome analyses underscored the importance of immunological and skin barrier abnormalities in atopic dermatitis (AD). We sought to identify novel pathogenic pathways involved in AD by comparing the transcriptomes of AD patients stratified for filaggrin (FLG) null mutations to those of both healthy donors and patients with ichthyosis vulgaris (IV). We applied RNA-sequencing to analyze the whole transcriptome of nonlesional skin. Six-hundred and seven genes (476 up-regulated and 131 down-regulated by greater than 2-fold) and one-hundred and ninety-three genes (172 up-regulated and 21 down-regulated by greater than 2-fold) were differentially expressed when all AD or IV patients were compared to healthy donors, respectively...
September 9, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28882568/identification-of-pathogenic-genes-related-to-rheumatoid-arthritis-through-integrated-analysis-of-dna-methylation-and-gene-expression-profiling
#6
Lei Zhang, Shiyun Ma, Huailiang Wang, Hang Su, Ke Su, Longjie Li
The purpose of our study was to identify new pathogenic genes used for exploring the pathogenesis of rheumatoid arthritis (RA). To screen pathogenic genes of RA, an integrated analysis was performed by using the microarray datasets in RA derived from the Gene Expression Omnibus (GEO) database. The functional annotation and potential pathways of differentially expressed genes (DEGs) were further discovered by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Afterwards, the integrated analysis of DNA methylation and gene expression profiling was used to screen crucial genes...
September 4, 2017: Gene
https://www.readbyqxmd.com/read/28866698/isolation-by-culture-and-pcr-identification-of-lipl32-gene-of-pathogenic-leptospira-spp-in-wild-rats-of-kuala-lumpur
#7
I Latifah, A Abdul Halim, M S Rahmat, M F Nadia, Z E Ubil, H Asmah, I Shafariatul Akmar, M Picardeau, O Siti Haslina, M A Nasir
BACKGROUND: A study was conducted to confirm the status of rats as the carrier of pathogenic leptospira in Kuala Lumpur, Malaysia. METHOD: A total of 140 urine samples were collected from trapped rats. These samples were cultured in EMJH enriched media and 18 of these samples (12.9%) were found to be positive when observed under x40 by dark field microscope. Genomic DNA was extracted from all the 18 native isolates for PCR. RESULT: All the 18 isolates generated the expected 786 base pair band when the set of primers known to amplify LipL32 gene were utilized...
August 2017: Malaysian Journal of Pathology
https://www.readbyqxmd.com/read/28861920/higher-than-expected-population-prevalence-of-potentially-pathogenic-germline-tp53-variants-in-individuals-unselected-for-cancer-history
#8
Kelvin C de Andrade, Lisa Mirabello, Douglas R Stewart, Eric Karlins, Roelof Koster, Mingyi Wang, Susan M Gapstur, Mia M Gaudet, Neal D Freedman, Maria T Landi, Nathanaël Lemonnier, Pierre Hainaut, Sharon A Savage, Maria I Achatz
Li-Fraumeni syndrome (LFS) is an autosomal dominant cancer disorder associated with pathogenic germline variants in TP53, with a high penetrance over an individual's lifetime. The actual population prevalence of pathogenic germline TP53 mutations is still unclear. The aim of this study was to estimate the prevalence of potentially pathogenic TP53 exonic variants in three data sources, totaling 63,983 unrelated individuals from three sequencing databases. Potential pathogenicity was defined using an original algorithm combining bioinformatic prediction tools, clinical significance evidences, and functional data...
September 1, 2017: Human Mutation
https://www.readbyqxmd.com/read/28854187/decoding-the-similarities-and-differences-among-mycobacterial-species
#9
COMPARATIVE STUDY
Sony Malhotra, Sundeep Chaitanya Vedithi, Tom L Blundell
Mycobacteriaceae comprises pathogenic species such as Mycobacterium tuberculosis, M. leprae and M. abscessus, as well as non-pathogenic species, for example, M. smegmatis and M. thermoresistibile. Genome comparison and annotation studies provide insights into genome evolutionary relatedness, identify unique and pathogenicity-related genes in each species, and explore new targets that could be used for developing new diagnostics and therapeutics. Here, we present a comparative analysis of ten-mycobacterial genomes with the objective of identifying similarities and differences between pathogenic and non-pathogenic species...
August 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28851275/gapless-genome-assembly-of-colletotrichum-higginsianum-reveals-chromosome-structure-and-association-of-transposable-elements-with-secondary-metabolite-gene-clusters
#10
Jean-Félix Dallery, Nicolas Lapalu, Antonios Zampounis, Sandrine Pigné, Isabelle Luyten, Joëlle Amselem, Alexander H J Wittenberg, Shiguo Zhou, Marisa V de Queiroz, Guillaume P Robin, Annie Auger, Matthieu Hainaut, Bernard Henrissat, Ki-Tae Kim, Yong-Hwan Lee, Olivier Lespinet, David C Schwartz, Michael R Thon, Richard J O'Connell
BACKGROUND: The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. RESULTS: Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7...
August 29, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28822752/comprehensive-analysis-of-tissue-wide-gene-expression-and-phenotype-data-reveals-tissues-affected-in-rare-genetic-disorders
#11
Ariel Feiglin, Bryce K Allen, Isaac S Kohane, Sek Won Kong
Linking putatively pathogenic variants to the tissues they affect is necessary for determining the correct diagnostic workup and therapeutic regime in undiagnosed patients. Here, we explored how gene expression across healthy tissues can be used to infer this link. We integrated 6,665 tissue-wide transcriptomes with genetic disorder knowledge bases covering 3,397 diseases. Receiver-operating characteristics (ROC) analysis using expression levels in each tissue and across tissues indicated significant but modest associations between elevated expression and phenotype for most tissues (maximum area under ROC curve = 0...
August 23, 2017: Cell Systems
https://www.readbyqxmd.com/read/28822547/bacterial-diversity-in-goat-milk-from-the-guanzhong-area-of-china
#12
Fuxin Zhang, Zhaoxia Wang, Feiyan Lei, Bini Wang, Shuaiming Jiang, Qiannan Peng, Jiachao Zhang, Yuyu Shao
In this study, the V3 and V4 regions of the 16S rRNA gene from metagenomic DNA were sequenced to identify differences in microbial diversity in raw milk of Saanen and Guanzhong goats from the Guanzhong area of China. The results showed that Proteobacteria was the predominant phylum, accounting for 71.31% of all phyla identified in milk from the 2 breeds, and Enterobacter was the predominant genus (24.69%) within the microbial community. Microbial alpha diversity from Saanen goat milk was significantly higher than that of Guanzhong goat milk based on bioinformatic analysis of indices of Chao1, Shannon, Simpson, observed species, and the abundance-based coverage estimator...
August 16, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28819267/decoding-disease-causing-mechanisms-of-missense-mutations-from-supramolecular-structures
#13
Atsushi Hijikata, Toshiyuki Tsuji, Masafumi Shionyu, Tsuyoshi Shirai
The inheritance modes of pathogenic missense mutations are known to be highly associated with protein structures; recessive mutations are mainly observed in the buried region of protein structures, whereas dominant mutations are significantly enriched in the interfaces of molecular interactions. However, the differences in phenotypic impacts among various dominant mutations observed in individuals are not fully understood. In the present study, the functional effects of pathogenic missense mutations on three-dimensional macromolecular complex structures were explored in terms of dominant mutation types, namely, haploinsufficiency, dominant-negative, or toxic gain-of-function...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818557/dna-aptamer-identification-and-characterization-for-e-%C3%A2-coli-o157-detection-using-cell-based-selex-method
#14
Masoum Amraee, Mana Oloomi, Afsaneh Yavari, Saeid Bouzari
Escherichia coli (E. coli) O157:H7 is a foodborne pathogen that causes symptoms in humans. Its rapid identification should be considered to avoid toxic effects of the pathogen. In this study, systematic evolution of ligands by exponential enrichment using whole cells (Cell-SELEX) method was used for recognizing E. coli strain, O157 by single-stranded DNA library of aptamer. Nine rounds of cell-selex procedure were applied using O157, as a whole-cell target, with O42, K12, Top10, DH5α E. coli cells, Shigella flexneri and Salmonella typhi as counterparts...
August 14, 2017: Analytical Biochemistry
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
#15
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
#16
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
#17
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
#18
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 annual infections globally. 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 2017: PLoS Biology
https://www.readbyqxmd.com/read/28789678/optimization-and-validation-of-sample-preparation-for-metagenomic-sequencing-of-viruses-in-clinical-samples
#19
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
#20
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
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