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https://www.readbyqxmd.com/read/28419064/the-application-of-next-generation-sequencing-for-mutation-detection-in-autosomal-dominant-hereditary-hearing-impairment
#1
Nicolas Gürtler, Benno Röthlisberger, Katja Ludin, Christoph Schlegel, Anil K Lalwani
OBJECTIVE: Identification of the causative mutation using next-generation sequencing in autosomal-dominant hereditary hearing impairment, as mutation analysis in hereditary hearing impairment by classic genetic methods, is hindered by the high heterogeneity of the disease. PATIENTS: Two Swiss families with autosomal-dominant hereditary hearing impairment. INTERVENTION: Amplified DNA libraries for next-generation sequencing were constructed from extracted genomic DNA, derived from peripheral blood, and enriched by a custom-made sequence capture library...
April 17, 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/28414467/variation-of-bacterial-communities-with-water-quality-in-an-urban-tropical-catchment
#2
Jean Pierre Nshimyimana, Adam Joshua Ehrich Freedman, Peter Shanahan, Lloyd C H Chua, Janelle Renee Thompson
A major challenge for assessment of water quality in tropical environments is the natural occurrence and potential growth of Fecal Indicator Bacteria (FIB). To gain a better understanding of the relationship between measured levels of FIB and the distribution of sewage-associated bacteria including potential pathogens in the tropics this study compared the abundance of FIB (Total coliforms and E. coli) and the Bacteroidales (HF183 marker) with bacterial community structure determined by next-generation amplicon sequencing...
April 17, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28412947/report-of-the-first-clinical-case-of-intestinal-trichomoniasis-caused-by-tritrichomonas-foetus-in-a-cat-with-chronic-diarrhoea-in-brazil
#3
Aline S Hora, Samantha I Miyashiro, Fabiana C Cassiano, Paulo E Brandão, Archivaldo Reche-Junior, Hilda F J Pena
BACKGROUND: Tritrichomonas foetus is an emergent and important enteric pathogen of cats, which causes prolonged diarrhoea in cats. CASE PRESENTATION: This study describes a T. foetus infection in a seven-month-old, entire male domestic shorthair kitten with a six-month history of persistent large intestinal diarrhoea, faecal incontinence, prostration, apathy and weight loss. Parasites were microscopically observed and confirmed by PCR and DNA sequencing. Molecular analyses were carried out comparing the sequence obtained in this study with T...
April 17, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28412515/genome-wide-determination-of-transcription-start-sites-reveals-new-insights-into-promoter-structures-in-the-actinomycete-corynebacterium-glutamicum
#4
Andreas Albersmeier, Katharina Pfeifer-Sancar, Christian Rückert, Jörn Kalinowski
The genome-wide identification of transcription start sites, enabled by high-throughput sequencing of a cDNA library enriched for native 5' transcript ends, is ideally suited for the analysis of promoters. Here, the transcriptome of Corynebacterium glutamicum, a non-pathogenic soil bacterium from the actinomycetes branch that is used in industry for the production of amino acids, was analysed by transcriptome sequencing of the 5'-ends of native transcripts. Total RNA samples were harvested from the exponential phase of growth, therefore the study mainly addressed promoters recognized by the main house-keeping sigma factor σ(A)...
April 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28397217/-study-of-two-chinese-families-affected-with-resistant-ovarian-syndrome-resulted-from-novel-mutations-of-fshr-gene
#5
Wen Li, Wenbin He, Lihua Zhou, Xiao Hu, Shuangfei Li, Fei Gong, Yueqiu Tan
OBJECTIVE: To explore the genetic etiology for two Chinese families affected with hypergonadotropic amenorrhea and normal number of antral follicles. METHODS: Peripheral venous blood samples were collected from the families for the extraction of genomic DNA. Mutations of FSHR and LHCGR genes were screened using PCR and Sanger sequencing. Suspected pathogenic mutations were verified in other members of the families. Bioinformatics software and NCBI were used to analyze the pathogenicity of the mutations...
April 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28394467/comparative-isolation-and-genetic-diversity-of-arcobacter-spp-from-fish-and-the-coastal-environment
#6
Srinu Rathlavath, Sanath Kumar, Binaya Bhusan Nayak
Arcobacter species are emerging food-borne and water-borne human pathogens associated mostly with food animals and their environment. The present study was aimed to isolate Arcobacter species from fish, shellfish and coastal water samples using two methods and to determine their genetic diversity. Of 201 samples of fish, shellfish and water samples analysed, 66 (32.8%) samples showed the presence of Arcobacter DNA from both Arcobacter enrichment broth (AEB) and Bolton broth (BB). Arcobacters were isolated from 58 (87...
April 10, 2017: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/28379065/inhibition-of-grass-carp-reovirus-infection-by-dna-aptamers-against-s10-protein
#7
Hongru Liang, Xiaozhe Fu, Lihui Liu, Qiang Lin, Huizhi Guo, Yonggang Li, JiaXu Liu, Zhibin Huang, Ningqiu Li
Grass Carp reovirus (GCRV) is one of the most pathogenic agents among aquareovirus isolates and has the ability to cause a severe epidemic outbreak of hemorrhagic disease, thus resulting in both a high mortality rate during the culture of Grass Carp Ctenopharyngodon idella and an enormous economic loss. Aptamers have been demonstrated to have strong promising applications in antiviral drug development. In the present study, a complementary DNA fragment encoding the S10 gene of GCRV was cloned. The S10 protein was expressed and purified...
June 2017: Journal of Aquatic Animal Health
https://www.readbyqxmd.com/read/28365722/ocappi-db-an-oligonucleotide-probe-database-for-pathogen-identification-through-hybridization-capture
#8
Cyrielle Gasc, Antony Constantin, Faouzi Jaziri, Pierre Peyret
The detection and identification of bacterial pathogens involved in acts of bio- and agroterrorism are essential to avoid pathogen dispersal in the environment and propagation within the population. Conventional molecular methods, such as PCR amplification, DNA microarrays or shotgun sequencing, are subject to various limitations when assessing environmental samples, which can lead to inaccurate findings. We developed a hybridization capture strategy that uses a set of oligonucleotide probes to target and enrich biomarkers of interest in environmental samples...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28361702/a-sequence-based-method-to-predict-the-impact-of-regulatory-variants-using-random-forest
#9
Qiao Liu, Mingxin Gan, Rui Jiang
BACKGROUND: Most disease-associated variants identified by genome-wide association studies (GWAS) exist in noncoding regions. In spite of the common agreement that such variants may disrupt biological functions of their hosting regulatory elements, it remains a great challenge to characterize the risk of a genetic variant within the implicated genome sequence. Therefore, it is essential to develop an effective computational model that is not only capable of predicting the potential risk of a genetic variant but also valid in interpreting how the function of the genome is affected with the occurrence of the variant...
March 14, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28361054/validation-and-utilization-of-a-clinical-next-generation-sequencing-panel-for-selected-cardiovascular-disorders
#10
Patrícia B S Celestino-Soper, Hongyu Gao, Ty C Lynnes, Hai Lin, Yunlong Liu, Katherine G Spoonamore, Peng-Sheng Chen, Matteo Vatta
The development of high-throughput technologies such as next-generation sequencing (NGS) has allowed for thousands of DNA loci to be interrogated simultaneously in a fast and economical method for the detection of clinically deleterious variants. Whenever a clinical diagnosis is known, a targeted NGS approach involving the use of disease-specific gene panels can be employed. This approach is often valuable as it allows for a more specific and clinically relevant interpretation of results. Here, we describe the customization, validation, and utilization of a commercially available targeted enrichment platform for the scalability of clinical diagnostic cardiovascular genetic tests, including the design of the gene panels, the technical parameters for the quality assurance and quality control, the customization of the bioinformatics pipeline, and the post-bioinformatics analysis procedures...
2017: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28334549/limitations-of-immunomagnetic-separation-for-detection-of-the-top-seven-serogroups-of-shiga-toxin-producing-escherichia-coli
#11
J Hallewell, T Alexander, T Reuter, K Stanford
Shiga toxin-producing Escherichia coli (STEC) strains are foodborne pathogens that negatively impact human health and compromise food safety. Serogroup O157 is the most frequently isolated and studied STEC serogroup, but six others (O26, O45, O103, O111, O121, and O145) have also been identified as significant sources of human disease and collectively have been referred to as the "top six" pathogenic serogroups. Because detection methods for non-O157 serogroups are not yet refined, the objective of this study was to compare the effectiveness of immunomagnetic separation (IMS) for recovery of serogroup O157 isolates with that for each of the top six E...
March 9, 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28330283/multiplex-pcr-for-simultaneous-identification-of-e-coli-o157-h7-salmonella-spp-and-l-monocytogenes-in-food
#12
Thuy Trang Nguyen, Vo Van Giau, Tuong Kha Vo
The rapid detection of pathogens in food is becoming increasingly critical for ensuring the safety of consumers, since the majority of food-borne illnesses and deaths are caused by pathogenic bacteria. Hence, rapid, sensitive, inexpensive and convenient approaches to detect food-borne pathogenic bacteria is essential in controlling food safety. In this study, a multiplex PCR assay for the rapid and simultaneous detection of Escherichia coli O157:H7, Salmonella spp. and Listeria monocytogenes was established...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28303131/multiplexed-single-intact-cell-droplet-digital-pcr-music-ddpcr-method-for-specific-detection-of-enterohemorrhagic-e-coli-ehec-in-food-enrichment-cultures
#13
Tanis C McMahon, Burton W Blais, Alex Wong, Catherine D Carrillo
Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin (stx) and intimin (eae)]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae-negative STEC and eae-positive E...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28300841/induction-of-intestinal-stemness-and-tumorigenicity-by-aberrant-internalization-of-commensal-non-pathogenic-e-coli
#14
Upasana Sahu, Arnab Choudhury, Suhel Parvez, Subhrajit Biswas, Sudeshna Kar
Commensal Escherichia coli has been identified as a major protagonist of microbe-induced colorectal oncogenesis. Its tumour-promoting attribute is linked to the expression of DNA-damaging genotoxins. Using a constitutively invasive variant of non-pathogenic E. coli, we demonstrate that chronic presence of internalized E. coli leads to enhanced oncogenicity in colon cancer cells. Instead of genomic damage, the tumorigenic effect is mediated through an expansion of the cancer stem cell (CSC) population, likely through dedifferentiation of lineage-committed intestinal epithelial cells...
March 16, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28298479/cyst-nematode-parasitism-induces-dynamic-changes-in-the-root-epigenome
#15
Tarek Hewezi, Thomas Lane, Sarbottam Piya, Aditi Rambani, J Hollis Rice, Meg Staton
A growing body of evidence indicates that epigenetic modifications can provide efficient, dynamic, and reversible cellular responses to a wide range of environmental stimuli. However, the significance of epigenetic modifications in plant-pathogen interactions remains largely unexplored. In this study, we provide a comprehensive analysis of epigenome changes during the compatible interaction between the beet cyst nematode Heterodera schachtii and Arabidopsis (Arabidopsis thaliana). Whole genome bisulfite sequencing was conducted to assess the dynamic changes in the methylome of Arabidopsis roots in response to H schachtii infection...
March 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28282040/impact-of-water-heater-temperature-setting-and-water-use-frequency-on-the-building-plumbing-microbiome
#16
Pan Ji, William J Rhoads, Marc A Edwards, Amy Pruden
Hot water plumbing is an important conduit of microbes into the indoor environment and can increase risk of opportunistic pathogens (for example, Legionella pneumophila). We examined the combined effects of water heater temperature (39, 42, 48, 51 and 58 °C), pipe orientation (upward/downward), and water use frequency (21, 3 and 1 flush per week) on the microbial composition at the tap using a pilot-scale pipe rig. 16S rRNA gene amplicon sequencing indicated that bulk water and corresponding biofilm typically had distinct taxonomic compositions (R(2)Adonis=0...
March 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28221970/genomic-tools-for-customized-recovery-and-detection-of-foodborne-shiga-toxigenic-escherichia-coli
#17
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
#18
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
#19
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
#20
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
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