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pathogen dna enrichment

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https://www.readbyqxmd.com/read/28079684/the-cif-virulence-factor-gene-is-present-in-isolates-from-patients-with-pseudomonas-aeruginosa-keratitis
#1
Christopher D Bahl, Jessica D St Laurent, R Siva Ganesa Karthikeyan, J Lakshmi Priya, Lalitha Prajna, Michael E Zegans, Dean R Madden
PURPOSE: To determine whether the cif gene is present in pathogenic Pseudomonas aeruginosa isolates from patients with bacterial keratitis at Aravind Eye Hospital, a referral eye care center in southern India, and from corresponding environmental isolates. METHODS: Polymerase chain reaction amplification was performed on strains of P. aeruginosa isolated from ocular infections and environmental soil samples were collected from the area surrounding Aravind Eye Hospital...
January 11, 2017: Cornea
https://www.readbyqxmd.com/read/28077562/sensitive-and-inexpensive-digital-dna-analysis-by-microfluidic-enrichment-of-rolling-circle-amplified-single-molecules
#2
Malte Kühnemund, Iván Hernández-Neuta, Mohd Istiaq Sharif, Matteo Cornaglia, Martin A M Gijs, Mats Nilsson
Single molecule quantification assays provide the ultimate sensitivity and precision for molecular analysis. However, most digital analysis techniques, i.e. droplet PCR, require sophisticated and expensive instrumentation for molecule compartmentalization, amplification and analysis. Rolling circle amplification (RCA) provides a simpler means for digital analysis. Nevertheless, the sensitivity of RCA assays has until now been limited by inefficient detection methods. We have developed a simple microfluidic strategy for enrichment of RCA products into a single field of view of a low magnification fluorescent sensor, enabling ultra-sensitive digital quantification of nucleic acids over a dynamic range from 1...
January 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28059585/initiation-of-aberrant-dna-methylation-patterns-and-heterogeneity-in-precancerous-lesions-of-human-hepatocellular-cancer
#3
Ryan A Hlady, Dan Zhou, William Puszyk, Lewis R Roberts, Chen Liu, Keith D Robertson
While intratumor heterogeneity contributes to disease progression, metastasis, and resistance to chemotherapy, it also provides a route to understanding the evolution and drivers of disease. Defects in epigenetic landscapes are intimately linked to pathogenesis of a variety of human diseases, with epigenetic deregulation promoting tumorigenesis. Understanding epigenetic heterogeneity is crucial in hepatocellular carcinoma (HCC), where epigenetic alterations are frequent, early, and pathogenic events. We determined genome-wide DNA methylation and copy number variation leveraging the Infinium 450 K in a series of regenerative nodules from within single patient livers...
January 6, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28052964/whole-genome-bisulfite-sequencing-of-human-pancreatic-islets-reveals-novel-differentially-methylated-regions-in-type-2-diabetes-pathogenesis
#4
Petr Volkov, Karl Bacos, Jones K Ofori, Jonathan Lou S Esguerra, Lena Eliasson, Tina Rönn, Charlotte Ling
Current knowledge about the role of epigenetics in type 2 diabetes (T2D) remains limited. Only a few studies have investigated DNA methylation of selected candidate genes or a very small fraction of genomic CpG sites in human pancreatic islets, the tissue of primary pathogenic importance for diabetes. Our aim was to characterize the whole-genome DNA methylation landscape in human pancreatic islets, to identify differentially methylated regions (DMRs) in diabetic islets, and to investigate the function of DMRs in islet biology...
January 4, 2017: Diabetes
https://www.readbyqxmd.com/read/28030795/aml-associated-oncofusion-proteins-pml-rara-aml1-eto-and-cbfb-myh11-target-runx-ets-factor-binding-sites-to-modulate-h3ac-levels-and-drive-leukemogenesis
#5
Abhishek A Singh, Amit Mandoli, Koen H M Prange, Marko Laakso, Joost H A Martens
Chromosomal translocations are one of the hallmarks of acute myeloid leukemia (AML), often leading to gene fusions and expression of an oncofusion protein. Over recent years it has become clear that most of the AML associated oncofusion proteins molecularly adopt distinct mechanisms for inducing leukemogenesis. Still these unique molecular properties of the chimeric proteins converge and give rise to a common pathogenic molecular mechanism. In the present study we compared genome-wide DNA binding and transcriptome data associated with AML1-ETO, CBFB-MYH11 and PML-RARA oncofusion protein expression to identify unique and common features...
December 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27998012/high-resolution-mapping-of-the-recombination-landscape-of-the-phytopathogen-fusarium-graminearum-suggests-two-speed-genome-evolution
#6
Benoit Laurent, Christos Palaiokostas, Cathy Spataro, Magalie Moinard, Enric Zehraoui, Ross D Houston, Marie Foulongne-Oriol
Recombination is a major evolutionary force, increasing genetic diversity and permitting efficient coevolution of fungal pathogen(s) with their host(s). The ascomycete Fusarium graminearum is a devastating pathogen of cereal crops, and can contaminate food and feed with harmful mycotoxins. Previous studies suggest a high-adaptive potential of this pathogen, illustrated by an increase of pathogenicity and resistance to fungicides. In this study, we provide the first detailed picture of the crossovers events occurring during meiosis and discuss the role of recombination may play for pathogen evolution...
December 20, 2016: Molecular Plant Pathology
https://www.readbyqxmd.com/read/27974384/brca-testing-by-single-molecule-molecular-inversion-probes
#7
Kornelia Neveling, Arjen R Mensenkamp, Ronny Derks, Michael Kwint, Hicham Ouchene, Marloes Steehouwer, Bart van Lier, Ermanno Bosgoed, Alwin Rikken, Marloes Tychon, Dimitra Zafeiropoulou, Steven Castelein, Jayne Hehir-Kwa, Djie Tjwan Thung, Tom Hofste, Stefan H Lelieveld, Stijn M M Bertens, Ivo B J F Adan, Astrid Eijkelenboom, Bastiaan B Tops, Helger Yntema, Tomasz Stokowy, Per M Knappskog, Hildegunn Høberg-Vetti, Vidar M Steen, Evan Boyle, Beth Martin, Marjolijn J L Ligtenberg, Jay Shendure, Marcel R Nelen, Alexander Hoischen
BACKGROUND: Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the area of clinical genetic testing. In this proof-of-concept study, we selected 2 frequently requested single gene tests, those for breast cancer 1, early onset (BRCA1) and breast cancer 2, early onset (BRCA2), and developed an automated work flow based on smMIPs...
December 14, 2016: Clinical Chemistry
https://www.readbyqxmd.com/read/27957856/high-throughput-identification-of-dna-encoded-igg-ligands-that-distinguish-active-and-latent-mycobacterium-tuberculosis-infections
#8
Kimberly R Mendes, Marie Lynne Malone, John Maina Ndungu, Irena Suponitsky-Kroyter, Valerie J Cavett, Patrick J McEnaney, Andrew B MacConnell, Todd M Doran, Katharina Ronacher, Kim Stanley, Ofelia Utset, Gerhard Walzl, Brian M Paegel, Thomas Kodadek
The circulating antibody repertoire encodes a patient's health status and pathogen exposure history, but identifying antibodies with diagnostic potential usually requires knowledge of the antigen(s). We previously circumvented this problem by screening libraries of bead-displayed small molecules against case and control serum samples to discover "epitope surrogates" (ligands of IgGs enriched in the case sample). Here, we describe an improved version of this technology that employs DNA-encoded libraries and high-throughput FACS-based screening to discover epitope surrogates that differentiate noninfectious/latent (LTB) patients from infectious/active TB (ATB) patients, which is imperative for proper treatment selection and antibiotic stewardship...
December 13, 2016: ACS Chemical Biology
https://www.readbyqxmd.com/read/27929395/deficiency-in-the-ubiquitin-conjugating-enzyme-ube2a-in-alzheimer-s-disease-ad-is-linked-to-deficits-in-a-natural-circular-mirna-7-sponge-circrna-cirs-7
#9
Yuhai Zhao, Peter N Alexandrov, Vivian Jaber, Walter J Lukiw
Our understanding of the highly specialized functions for small non-coding single-stranded RNA (ssRNA) in the transcriptome of the human central nervous system (CNS) continues to evolve. Circular RNAs (circRNAs), a recently discovered class of ssRNA enriched in the brain and retina, are extremely stable and intrinsically resilient to degradation by exonuclease. Conventional methods of ssRNA, microRNA (miRNA), or messenger RNA (mRNA) detection and quantitation requiring free ribonucleotide ends may have considerably underestimated the quantity and significance of CNS circRNA in the CNS...
December 5, 2016: Genes
https://www.readbyqxmd.com/read/27888291/whole-genome-enrichment-provides-deep-insights-into-vibrio-cholerae-metagenome-from-an-african-river
#10
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
#11
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
#12
X-L Meng, X-W Xie, Y-X Shi, A-L Chai, Z-H Ma, B-J 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 an 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
#13
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 lifestyle 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 with 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
#14
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-the-cysteine-residues-are-required-for-cell-death
#15
Koste A Yadeta, James M Elmore, Athena Y Creer, Baomin Feng, Jessica Y Franco, Jose Sebastian Rufian, Ping He, Brett Phinney, Gitta Coaker
Membrane-localized proteins perceive and respond to biotic and abiotic stresses. We performed quantitative proteomics on plasma membrane-enriched samples from Arabidopsis (Arabidopsis thaliana) treated with bacterial flagellin. We identified multiple receptor-like protein kinases changing in abundance, including cysteine (Cys)-rich receptor-like kinases (CRKs) that are up-regulated upon the perception of flagellin. CRKs possess extracellular Cys-rich domains and constitute a gene family consisting of 46 members in Arabidopsis...
January 2017: 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
#16
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
#17
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
#18
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
#19
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
#20
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
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