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https://www.readbyqxmd.com/read/27888291/whole-genome-enrichment-provides-deep-insights-into-vibrio-cholerae-metagenome-from-an-african-river
#1
L Vezzulli, C Grande, G Tassistro, I Brettar, M G Höfle, R P A Pereira, D Mushi, A Pallavicini, P Vassallo, C Pruzzo
The detection and typing of Vibrio cholerae in natural aquatic environments encounter major methodological challenges related to the fact that the bacterium is often present in environmental matrices at very low abundance in nonculturable state. This study applied, for the first time to our knowledge, a whole-genome enrichment (WGE) and next-generation sequencing (NGS) approach for direct genotyping and metagenomic analysis of low abundant V. cholerae DNA (<50 genome unit/L) from natural water collected in the Morogoro river (Tanzania)...
November 25, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27871797/direct-pcr-a-rapid-method-for-multiplexed-detection-of-different-serotypes-of-salmonella-in-enriched-pork-meat-samples
#2
Wai Hoe Chin, Yi Sun, Jonas Høgberg, Than Linh Quyen, Pia Engelsmann, Anders Wolff, Dang Duong Bang
Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture method is time consuming. In response to the demand for rapid on line or at site detection of pathogens, in this study, we developed a multiplex Direct PCR method for rapid detection of different Salmonella serotypes directly from pork meat samples without any DNA purification steps. An inhibitor-resistant Phusion Pfu DNA polymerase was used to overcome PCR inhibition...
November 18, 2016: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/27864860/evaluation-of-a-loop-mediated-isothermal-amplification-assay-based-on-hrpz-gene-for-rapid-detection-and-identification-of-pseudomonas-syringae-pv-lachrymans-in-cucumber-leaves
#3
Xiang-Long Meng, Xue-Wen Xie, Yan-Xia Shi, A-Li Chai, Zhan-Hong Ma, Bao-Ju Li
AIMS: Cucumber angular leaf spot caused by Pseudomonas syringae pv. lachrymans (Psl) is an important and destructive disease worldwide, and no effective technique has been developed for the control of the pathogen. Detection of infection or latent in cucumber plants is critical to evaluate disease progress and strengthening management to avoid a serious epidemic in the fields. In this paper, we developed a rapid and sensitive method for detection of Psl using a isothermal method known as loop-mediated amplification (LAMP)...
November 19, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27858497/high-fat-diet-and-exercise-lead-to-a-disrupted-and-pathogenic-dna-methylome-in-mouse-liver
#4
Dan Zhou, Ryan A Hlady, Marissa J Schafer, Thomas A White, Chen Liu, Jeong-Hyeon Choi, Jordan D Miller, Lewis R Roberts, Nathan K LeBrasseur, Keith D Robertson
High-fat diet consumption and sedentary life style elevates risk for obesity, non-alcoholic fatty liver disease, and cancer. Exercise training conveys health benefits in populations with or without these chronic conditions. Diet and exercise regulate gene expression by mediating epigenetic mechanisms in many tissues; however, such effects are poorly documented in the liver, a central metabolic organ. To dissect the consequences of diet and exercise on the liver epigenome, we measured DNA methylation, using reduced representation bisulfite sequencing, and transcription, using RNA-seq, in mice maintained on a fast food diet with sedentary lifestyle or exercise, compared to control diet with and without exercise...
November 18, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27855160/transcription-factors-encoded-on-core-and-accessory-chromosomes-of-fusarium-oxysporum-induce-expression-of-effector-genes
#5
H Charlotte van der Does, Like Fokkens, Ally Yang, Sarah M Schmidt, Léon Langereis, Joanna M Lukasiewicz, Timothy R Hughes, Martijn Rep
Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called 'effectors'. In fungal plant pathogens, coordinated transcriptional up-regulation of effector genes is a key feature of pathogenesis and effectors are often encoded in genomic regions with distinct repeat content, histone code and rate of evolution. In the tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol), effector genes reside on one of four accessory chromosomes, known as the 'pathogenicity' chromosome, which can be exchanged between strains through horizontal transfer...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27852951/a-cysteine-rich-protein-kinase-associates-with-a-membrane-immune-complex-and-is-required-for-cell-death
#6
Koste Abdissa Yadeta, James Mitch Elmore, Athena Y Creer, Baomin Feng, Jessica Y Franco, Jose Sebastian Rufian, Ping He, Brett S Phinney, Gitta Laurel Coaker
Membrane localized proteins perceive and respond to biotic and abiotic stresses. We performed quantitative proteomics on plasma membrane-enriched samples from Arabidopsis treated with bacterial flagellin. We identified multiple receptor-like protein kinases (RLKs) changing in abundance, including cysteine-rich receptor-like kinases (CRKs) that are upregulated upon perception of flagellin. CRKs possess extracellular cysteine-rich domains and comprise a gene family consisting of 46 members in Arabidopsis. Single T-DNA insertion lines in CRK28 and CRK29, two CRKs induced in response to flagellin perception, did not exhibit robust alterations in immune responses...
November 16, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27852235/enrichment-dynamics-of-listeria-monocytogenes-and-the-associated-microbiome-from-naturally-contaminated-ice-cream-linked-to-a-listeriosis-outbreak
#7
Andrea Ottesen, Padmini Ramachandran, Elizabeth Reed, James R White, Nur Hasan, Poorani Subramanian, Gina Ryan, Karen Jarvis, Christopher Grim, Ninalynn Daquiqan, Darcy Hanes, Marc Allard, Rita Colwell, Eric Brown, Yi Chen
BACKGROUND: Microbiota that co-enrich during efforts to recover pathogens from foodborne outbreaks interfere with efficient detection and recovery. Here, dynamics of co-enriching microbiota during recovery of Listeria monocytogenes from naturally contaminated ice cream samples linked to an outbreak are described for three different initial enrichment formulations used by the Food and Drug Administration (FDA), the International Organization of Standardization (ISO), and the United States Department of Agriculture (USDA)...
November 16, 2016: BMC Microbiology
https://www.readbyqxmd.com/read/27835906/whole-exome-and-transcriptome-sequencing-of-refractory-diffuse-large-b-cell-lymphoma
#8
Ha Young Park, Seung-Bok Lee, Hae-Yong Yoo, Seok-Jin Kim, Won-Seog Kim, Jong-Il Kim, Young-Hyeh Ko
Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. Although rituximab therapy improves clinical outcome, some patients develop resistant DLBCL; however, the genetic alterations in these patients are not well documented. To identify the genetic background of refractory DLBCL, we conducted whole-exome sequencing and transcriptome sequencing for six patients with refractory and seven with responsive DLBCL. The average numbers of pathogenic somatic single nucleotide variants and indels in coding regions were 71 in refractory patients (range 28-120) and 38 (range 19-66) in responsive patients...
November 9, 2016: Oncotarget
https://www.readbyqxmd.com/read/27811909/fusobacterium-nucleatum-in-colorectal-carcinoma-tissue-according-to-tumor-location
#9
Kosuke Mima, Yin Cao, Andrew T Chan, Zhi Rong Qian, Jonathan A Nowak, Yohei Masugi, Yan Shi, Mingyang Song, Annacarolina da Silva, Mancang Gu, Wanwan Li, Tsuyoshi Hamada, Keisuke Kosumi, Akiko Hanyuda, Li Liu, Aleksandar D Kostic, Marios Giannakis, Susan Bullman, Caitlin A Brennan, Danny A Milner, Hideo Baba, Levi A Garraway, Jeffrey A Meyerhardt, Wendy S Garrett, Curtis Huttenhower, Matthew Meyerson, Edward L Giovannucci, Charles S Fuchs, Reiko Nishihara, Shuji Ogino
OBJECTIVES: Evidence suggests a possible role of Fusobacterium nucleatum in colorectal carcinogenesis, especially in right-sided proximal colorectum. Considering a change in bowel contents and microbiome from proximal to distal colorectal segments, we hypothesized that the proportion of colorectal carcinoma enriched with F. nucleatum might gradually increase along the bowel subsites from rectum to cecum. METHODS: A retrospective, cross-sectional analysis was conducted on 1,102 colon and rectal carcinomas in molecular pathological epidemiology databases of the Nurses' Health Study and the Health Professionals Follow-up Study...
November 3, 2016: Clinical and Translational Gastroenterology
https://www.readbyqxmd.com/read/27811324/evaluation-of-3m-molecular-detection-system-and-ansr-pathogen-detection-system-for-rapid-detection-of-salmonella-from-egg-products
#10
L Hu, L M Ma, S Zheng, X He, H Wang, E W Brown, T S Hammack, G Zhang
Isothermal amplification assay is a novel simple detection technology that amplifies DNA with high speed, efficiency, and specificity under isothermal conditions. The objective of this study was to evaluate the effectiveness of the 3M Molecular Detection System (MDS) and ANSR Pathogen Detection System (PDS) for the detection of Salmonella in egg products as compared to the Food and Drug Administration's Bacteriological Analytical Manual (BAM) culture method and a modified culture method (3M MDS and ANSR PDS preferred method)...
November 2, 2016: Poultry Science
https://www.readbyqxmd.com/read/27800428/a-culture-independent-method-for-the-detection-of-aeromonas-sp-from-water-samples
#11
Fadua Latif-Eugenín, Roxana Beaz-Hidalgo, Figueras María José
The genus Aeromonas is present in a wide variety of water environments and is recognised as potentially pathogenic to humans and animals. Members of this genus are often confused with Vibrio when using automated, commercial identification systems that are culture-dependent. This study describes a polymerase chain reaction (PCR) detection method for Aeromonas that is culture-independent and that targets the glycerophospholopid-cholesterol acyltransferase (gcat) gene, which is specific for this genus. The GCAT-PCR was 100% specific in artificially inoculated water samples, with a detection limit that ranged from 2...
January 18, 2016: Italian Journal of Food Safety
https://www.readbyqxmd.com/read/27792786/genetic-evidence-for-elevated-pathogenicity-of-mitochondrial-dna-heteroplasmy-in-autism-spectrum-disorder
#12
Yiqin Wang, Martin Picard, Zhenglong Gu
Increasing clinical and biochemical evidence implicate mitochondrial dysfunction in the pathophysiology of Autism Spectrum Disorder (ASD), but little is known about the biological basis for this connection. A possible cause of ASD is the genetic variation in the mitochondrial DNA (mtDNA) sequence, which has yet to be thoroughly investigated in large genomic studies of ASD. Here we evaluated mtDNA variation, including the mixture of different mtDNA molecules in the same individual (i.e., heteroplasmy), using whole-exome sequencing data from mother-proband-sibling trios from simplex families (n = 903) where only one child is affected by ASD...
October 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27777193/-analysis-of-causes-and-whole-microbial-structure-in-a-case-of-rampant-caries
#13
Xiao-Yu Hu, Yu-Fei Yao, Bo-Miao Cui, Jun Lv, Xin Shen, Biao Ren, Ming-Yun Li, Qiang Guo, Rui-Jie Huang, Yan Li
OBJECTIVE: To analyze the whole microbial structure in a case of rampant caries to provide evidence for its prevention and treatment. METHODS: Clinical samples including blood, supragingival plaque, plaque in the caries cavity, saliva, and mucosal swabs were collected with the patient's consent. The blood sample was sent for routine immune test, and the others samples were stained using Gram method and cultured for identifying colonies and 16S rRNA sequencing. DNA was extracted from the samples and tested for the main cariogenic bacterium (Streptococcus mutans) with qPCR, and the whole microbial structure was analyzed using DGGE...
October 20, 2016: Nan Fang Yi Ke da Xue Xue Bao, Journal of Southern Medical University
https://www.readbyqxmd.com/read/27756336/identification-of-brca1-like-triple-negative-breast-cancers-by-quantitative-multiplex-ligation-dependent-probe-amplification-mlpa-analysis-of-brca1-associated-chromosomal-regions-a-validation-study
#14
Eva Gross, Harm van Tinteren, Zhou Li, Sandra Raab, Christina Meul, Stefanie Avril, Nadja Laddach, Michaela Aubele, Corinna Propping, Apostolos Gkazepis, Manfred Schmitt, Alfons Meindl, Petra M Nederlof, Marion Kiechle, Esther H Lips
BACKGROUND: Triple-negative breast cancer (TNBC) with a BRCA1-like molecular signature has been demonstrated to remarkably respond to platinum-based chemotherapy and might be suited for a future treatment with poly(ADP-ribose)polymerase (PARP) inhibitors. In order to rapidly assess this signature we have previously developed a multiplex-ligation-dependent probe amplification (MLPA)-based assay. Here we present an independent validation of this assay to confirm its important clinical impact...
October 19, 2016: BMC Cancer
https://www.readbyqxmd.com/read/27755981/aptamers-as-a-promising-approach-for-the-control-of-parasitic-diseases
#15
Juan David Ospina-Villa, Absalom Zamorano-Carrillo, Carlos A Castañón-Sánchez, Esther Ramírez-Moreno, Laurence A Marchat
Aptamers are short single-stranded RNA or DNA oligonucleotides that are capable of binding various biological targets with high affinity and specificity. Their identification initially relies on a molecular process named SELEX (Systematic Evolution of Ligands by EXponential enrichment) that has been later modified in order to improve aptamer sensitivity, minimize duration and cost of the assay, as well as increase target types. Several biochemical modifications can help to enhance aptamer stability without affecting significantly target interaction...
October 15, 2016: Brazilian Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27747299/dna-from-dust-comparative-genomics-of-large-dna-viruses-in-field-surveillance-samples
#16
Utsav Pandey, Andrew S Bell, Daniel W Renner, David A Kennedy, Jacob T Shreve, Chris L Cairns, Matthew J Jones, Patricia A Dunn, Andrew F Read, Moriah L Szpara
The intensification of the poultry industry over the last 60 years facilitated the evolution of increased virulence and vaccine breaks in Marek's disease virus (MDV-1). Full-genome sequences are essential for understanding why and how this evolution occurred, but what is known about genome-wide variation in MDV comes from laboratory culture. To rectify this, we developed methods for obtaining high-quality genome sequences directly from field samples without the need for sequence-based enrichment strategies prior to sequencing...
September 2016: MSphere
https://www.readbyqxmd.com/read/27746189/characterization-and-comparative-analysis-of-the-genome-of-puccinia-sorghi-schwein-the-causal-agent-of-maize-common-rust
#17
Lucia Rochi, María José Diéguez, Germán Burguener, Martín Alejandro Darino, María Fernanda Pergolesi, Lorena Romina Ingala, Alba Romina Cuyeu, Adrián Turjanski, Enrique Domingo Kreff, Francisco Sacco
Rust fungi are one of the most devastating pathogens of crop plants. The biotrophic fungus Puccinia sorghi Schwein (Ps) is responsible for maize common rust, an endemic disease of maize (Zea mays L) in Argentina that causes significant yield losses in corn production. In spite of this, the Ps genomic sequence was not available. We used Illumina sequencing to rapidly produce the 99.6 Mb draft genome sequence of Ps race RO10H11247, derived from a single-uredinial isolate from infected maize leaves collected in the Argentine Corn Belt Region during 2010...
October 13, 2016: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/27726782/paleomicrobiology-of-human-tuberculosis
#18
Helen D Donoghue
Tuberculosis is a significant global disease today, so understanding its origins and history is important. It is primarily a lung infection and is transmitted by infectious aerosols from person to person, so a high population density encourages its spread. The causative organism is Mycobacterium tuberculosis, an obligate pathogen in the M. tuberculosis complex that also contains closely related species, such as Mycobacterium bovis, that primarily infect animals. Typical bone lesions occur in about 5% of untreated infections...
August 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/27703927/genome-wide-anaplasma-phagocytophilum-anka-dna-interactions-are-enriched-in-intergenic-regions-and-gene-promoters-and-correlate-with-infection-induced-differential-gene-expression
#19
J Stephen Dumler, Sara H Sinclair, Valeria Pappas-Brown, Amol C Shetty
Anaplasma phagocytophilum, an obligate intracellular prokaryote, infects neutrophils, and alters cardinal functions via reprogrammed transcription. Large contiguous regions of neutrophil chromosomes are differentially expressed during infection. Secreted A. phagocytophilum effector AnkA transits into the neutrophil or granulocyte nucleus to complex with DNA in heterochromatin across all chromosomes. AnkA binds to gene promoters to dampen cis-transcription and also has features of matrix attachment region (MAR)-binding proteins that regulate three-dimensional chromatin architecture and coordinate transcriptional programs encoded in topologically-associated chromatin domains...
2016: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/27698249/prevalence-of-shiga-toxin-producing-and-enteropathogenic-escherichia-coli-marker-genes-in-diarrhoeic-stools-in-a-new-zealand-catchment-area
#20
Rowan R Thomas, Heather J L Brooks, Rory O'Brien
BACKGROUND: Shiga toxin-producing (STEC) and enteropathogenic (EPEC) Escherichia coli are gastrointestinal pathogens causing diarrhoeal and extraintestinal disease. Due to lack of EPEC screening and use of Sorbitol-MacConkey (SMAC) agar in faecal screening, the true prevalence of EPEC and non-O157 STEC in New Zealand diarrhoeal cases is unknown. METHODS: Diarrhoeic stools sourced from Dunedin hospital were pre-enriched, DNA extracted with Chelex-100 resin and screened using a multiplex TaqMan quantitative PCR assay amplifying stx1, sxt2 and EPEC (eae) gene markers...
October 3, 2016: Journal of Clinical Pathology
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