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https://www.readbyqxmd.com/read/28221970/genomic-tools-for-customized-recovery-and-detection-of-foodborne-shiga-toxigenic-escherichia-coli
#1
Michael Knowles, Sara Stinson, Dominic Lambert, Catherine Carrillo, Adam Koziol, Martine Gauthier, Burton Blais
Genomic antimicrobial resistance (AMR) prediction tools have the potential to support foodborne illness outbreak investigations through their application in the analysis of bacterial genomes from causative strains. The AMR marker profile of a strain of interest, initially identified in outbreak-associated clinical samples, may serve as the basis for customization of selective enrichment media, facilitating its recovery from samples in a food safety investigation. Different possibilities for AMR analyses include the use of comprehensive AMR gene databases such as the Comprehensive Antibiotic Resistance Database, which can be mined with in-house bioinformatics alignment tools (e...
December 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28221883/enrichment-amplification-and-sequence-based-typing-of-salmonella-enterica-and-other-foodborne-pathogens
#2
Tom Edlind, Jeffrey D Brewster, George C Paoli
Detection of Salmonella enterica in foods typically involves microbiological enrichment, molecular-based assay, and subsequent isolation and identification of a pure culture. This is ideally followed by strain typing, which provides information critical to the investigation of outbreaks and the attribution of their sources. Pulsed-field gel electrophoresis is the "gold standard" for S. enterica strain typing, but its limitations have encouraged the search for alternative methods, including whole genome sequencing...
January 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28220432/genome-wide-analysis-of-chromatin-accessibility-in-arabidopsis-infected-with-pseudomonas-syringae
#3
Yogendra Bordiya, Hong-Gu Kang
Changes in chromatin accessibility are an important aspect of the molecular changes that occur in eukaryotic cells responding to stress, and they appear to play a critical role in stress-induced transcriptional activation/reprogramming and epigenetic changes. In plants, pathogen infection has been shown to induce rapid and drastic transcriptional reprogramming; growing evidence suggests that chromatin remodeling plays an essential role in this phenomenon. The recent development of genomic tools to assess chromatin accessibility presents a significant opportunity to investigate the relationship between chromatin dynamicity and gene expression...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28198449/recombinant-vacuolar-iron-transporter-family-homologue-pfvit-from-human-malaria-causing-plasmodium-falciparum-is-a-fe-2-h-exchanger
#4
Paola Labarbuta, Katie Duckett, Catherine H Botting, Osama Chahrour, John Malone, John P Dalton, Christopher J Law
Vacuolar iron transporters (VITs) are a poorly understood family of integral membrane proteins that can function in iron homeostasis via sequestration of labile Fe(2+) into vacuolar compartments. Here we report on the heterologous overexpression and purification of PfVIT, a vacuolar iron transporter homologue from the human malaria-causing parasite Plasmodium falciparum. Use of synthetic, codon-optimised DNA enabled overexpression of functional PfVIT in the inner membrane of Escherichia coli which, in turn, conferred iron tolerance to the bacterial cells...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28185569/a-comprehensive-collection-of-annotations-to-interpret-sequence-variation-in-human-mitochondrial-transfer-rnas
#5
Maria Angela Diroma, Paolo Lubisco, Marcella Attimonelli
BACKGROUND: The abundance of biological data characterizing the genomics era is contributing to a comprehensive understanding of human mitochondrial genetics. Nevertheless, many aspects are still unclear, specifically about the variability of the 22 human mitochondrial transfer RNA (tRNA) genes and their involvement in diseases. The complex enrichment and isolation of tRNAs in vitro leads to an incomplete knowledge of their post-transcriptional modifications and three-dimensional folding, essential for correct tRNA functioning...
November 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28174737/metagenomic-characterization-of-microbial-communities-in-situ-within-the-deeper-layers-of-the-ileum-in-crohn-s-disease
#6
Chandra Sekhar Pedamallu, Ami S Bhatt, Susan Bullman, Sharyle Fowler, Samuel S Freeman, Jacqueline Durand, Joonil Jung, Fujiko Duke, Veronica Manzo, Diana Cai, Ashwin Ananthakrishnan, Akinyemi I Ojesina, Aruna Ramachandran, Dirk Gevers, Ramnik J Xavier, Atul K Bhan, Matthew Meyerson, Vijay Yajnik
BACKGROUND & AIMS: Microbial dysbiosis and aberrant host-microbe interactions in the gut are believed to contribute to the development and progression of Crohn's disease (CD). Microbiome studies in CD typically have focused on microbiota in feces or superficial mucosal layers of the colon because accessing DNA from deeper layers of the bowel is challenging. In this study, we analyzed the deep tissue microbiome in patients who underwent surgical resection of the small intestine. METHODS: Paraffin blocks were obtained from 12 CD patients undergoing ileocecal resection, and healthy ileum samples (inflammatory bowel disease-free controls) were obtained from 12 patients undergoing surgery for right-sided colon cancer...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28174312/selective-whole-genome-amplification-is-a-robust-method-that-enables-scalable-whole-genome-sequencing-of-plasmodium-vivax-from-unprocessed-clinical-samples
#7
Annie N Cowell, Dorothy E Loy, Sesh A Sundararaman, Hugo Valdivia, Kathleen Fisch, Andres G Lescano, G Christian Baldeviano, Salomon Durand, Vince Gerbasi, Colin J Sutherland, Debbie Nolder, Joseph M Vinetz, Beatrice H Hahn, Elizabeth A Winzeler
: Whole-genome sequencing (WGS) of microbial pathogens from clinical samples is a highly sensitive tool used to gain a deeper understanding of the biology, epidemiology, and drug resistance mechanisms of many infections. However, WGS of organisms which exhibit low densities in their hosts is challenging due to high levels of host genomic DNA (gDNA), which leads to very low coverage of the microbial genome. WGS of Plasmodium vivax, the most widely distributed form of malaria, is especially difficult because of low parasite densities and the lack of an ex vivo culture system...
February 7, 2017: MBio
https://www.readbyqxmd.com/read/28167501/comprehensive-characterization-of-neutrophil-genome-topology
#8
Yina Zhu, Ke Gong, Matthew Denholtz, Vivek Chandra, Mark P Kamps, Frank Alber, Cornelis Murre
Neutrophils are responsible for the first line of defense against invading pathogens. Their nuclei are uniquely structured as multiple lobes that establish a highly constrained nuclear environment. Here we found that neutrophil differentiation was not associated with large-scale changes in the number and sizes of topologically associating domains (TADs). However, neutrophil genomes were enriched for long-range genomic interactions that spanned multiple TADs. Population-based simulation of spherical and toroid genomes revealed declining radii of gyration for neutrophil chromosomes...
February 6, 2017: Genes & Development
https://www.readbyqxmd.com/read/28129394/characterization-of-early-phase-neutrophil-extracellular-traps-in-urinary-tract-infections
#9
Yanbao Yu, Keehwan Kwon, Tamara Tsitrin, Shiferaw Bekele, Patricia Sikorski, Karen E Nelson, Rembert Pieper
Neutrophils have an important role in the antimicrobial defense and resolution of urinary tract infections (UTIs). Our research suggests that a mechanism known as neutrophil extracellular trap (NET) formation is a defense strategy to combat pathogens that have invaded the urinary tract. A set of human urine specimens with very high neutrophil counts had microscopic evidence of cellular aggregation and lysis. Deoxyribonuclease I (DNase) treatment resulted in disaggregation of such structures, release of DNA fragments and a proteome enriched in histones and azurophilic granule effectors whose quantitative composition was similar to that of previously described in vitro-formed NETs...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28127763/mutational-signature-analysis-identifies-mutyh-deficiency-in-colorectal-cancers-and-adrenocortical-carcinomas
#10
Camilla Pilati, Jayendra Shinde, Ludmil B Alexandrov, Guillaume Assié, Thierry André, Zofia Hélias-Rodzewicz, Romain Doucoudray, Delphine Le Corre, Jessica Zucman-Rossi, Jean-François Emile, Jérôme Bertherat, Eric Letouzé, Pierre Laurent-Puig
Germline alterations in DNA repair genes are implicated in cancer predisposition and can result in characteristic mutational signatures. However, specific mutational signatures associated with base excision repair (BER) defects remain to be characterized. Here, by analysing a series of colorectal cancers (CRC) using exome sequencing, we identified a particular spectrum of somatic mutations characterized by an enrichment of C > A transversions in NpCpA or NpCpT contexts, in three tumours from a MUTYH-associated polyposis (MAP) patient and in two cases harbouring pathogenic germline MUTYH mutations...
January 27, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28125078/frequent-inactivating-germline-mutations-in-dna-repair-genes-in-patients-with-ewing-sarcoma
#11
Andrew S Brohl, Rajesh Patidar, Clesson E Turner, Xinyu Wen, Young K Song, Jun S Wei, Kathleen A Calzone, Javed Khan
PURPOSE: Ewing sarcoma is a small round blue cell tumor that is highly malignant and predominantly affects the adolescent and young adult population. It has long been suspected that a genetic predisposition exists for this cancer, but the germ-line genetic underpinnings of this disease have not been well established. METHODS: We performed germline variant analysis of whole-genome or whole-exome sequencing of samples from 175 patients affected by Ewing sarcoma. RESULTS: We discovered pathogenic or likely pathogenic germline mutations in 13...
January 26, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28121468/detection-identification-and-antimicrobial-susceptibility-of-arcobacter-spp-isolated-from-shellfish-in-spain
#12
Isidro F Bayas Morejón, Ana González, María Antonia Ferrús
This work aimed to determine the presence of Arcobacter spp. in shellfish and to determine its susceptibility to quinolones. One hundred samples (41 mussels, 37 clams, and 22 cockles) were purchased from different local retail shops in Valencia, Spain, from September 2013 to June 2015. All samples were analyzed simultaneously by culture, after an enrichment step, and by polymerase chain reaction (PCR), directly and after enrichment. The susceptibility to levofloxacin and ciprofloxacin of the isolates was tested using the disk-diffusion test and E-test strips method...
January 25, 2017: Foodborne Pathogens and Disease
https://www.readbyqxmd.com/read/28121169/development-of-a-dna-aptamer-that-binds-specifically-to-group-a-streptococcus-serotype-m3
#13
Hanif Alfavian, Seyed Latif Mousavi Gargari, Samaneh Rasoulinejad, Arvin Medhat
Group A streptococcus (GAS) is an important Gram-positive pathogen that causes various human diseases ranging from peripheral lesions to invasive infections. The M protein is one of the main virulence factors present on the cell surface and is associated with invasive GAS infections. Compared with other M types, serotype M3 has a predominant role in lethal infections and demonstrates epidemic behaviors, including streptococcal toxic shock syndrome, bacteremia, and necrotizing fasciitis. Traditional methods for M typing are time-consuming, tedious, contradictory, and generally restricted to reference laboratories...
February 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28101272/isolation-and-characterization-of-agrobacterium-strains-from-soil-a-laboratory-capstone-experience
#14
Kim R Finer, Lee Fox, John J Finer
In this investigation, the students' goal was to isolate and characterize Agrobacterium strains from soil. Following selection and enrichment on 1A-t medium, putative Agrobacterium isolates were characterized by Gram stain reaction and biochemical tests. Isolates were further evaluated using polymerase chain reaction (PCR) with different primer sets designed to amplify specific regions of bacterial deoxyribonucleic acid (DNA). Primer sets included AGRH to identify isolates that were members of the Rhizobiaceae, BIOVAR1 primers to identify members of Agrobacterium biovar group I, and a third set, VIRG, to determine presence of virG (only present in pathogenic Agrobacterium strains)...
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28101126/characterisation-of-microbial-communities-within-aggressive-prostate-cancer-tissues
#15
Melissa A Yow, Sepehr N Tabrizi, Gianluca Severi, Damien M Bolton, John Pedersen, Graham G Giles, Melissa C Southey
BACKGROUND: An infectious aetiology for prostate cancer has been conjectured for decades but the evidence gained from questionnaire-based and sero-epidemiological studies is weak and inconsistent, and a causal association with any infectious agent is not established. We describe and evaluate the application of new technology to detect bacterial and viral agents in high-grade prostate cancer tissues. The potential of targeted 16S rRNA gene sequencing and total RNA sequencing was evaluated in terms of its utility to characterise microbial communities within high-grade prostate tumours...
2017: Infectious Agents and Cancer
https://www.readbyqxmd.com/read/28099491/death-of-monocytes-through-oxidative-burst-of-macrophages-and-neutrophils-killing-in-trans
#16
Viviane Ponath, Bernd Kaina
Monocytes and their descendants, macrophages, play a key role in the defence against pathogens. They also contribute to the pathogenesis of inflammatory diseases. Therefore, a mechanism maintaining a balance in the monocyte/macrophage population must be postulated. Our previous studies have shown that monocytes are impaired in DNA repair, rendering them vulnerable to genotoxic stress while monocyte-derived macrophages are DNA repair competent and genotoxic stress-resistant. Based on these findings, we hypothesized that monocytes can be selectively killed by reactive oxygen species (ROS) produced by activated macrophages...
2017: PloS One
https://www.readbyqxmd.com/read/28079684/the-cif-virulence-factor-gene-is-present-in-isolates-from-patients-with-pseudomonas-aeruginosa-keratitis
#17
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...
March 2017: Cornea
https://www.readbyqxmd.com/read/28077562/sensitive-and-inexpensive-digital-dna-analysis-by-microfluidic-enrichment-of-rolling-circle-amplified-single-molecules
#18
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
#19
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
#20
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
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