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pathogen dna enrichment

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https://www.readbyqxmd.com/read/29335924/brca1-and-brca2-germline-variants-in-breast-cancer-patients-from-the-republic-of-macedonia
#1
Milena Jakimovska, Ivana Maleva Kostovska, Katerina Popovska-Jankovic, Katerina Kubelka-Sabit, Mitko Karadjozov, Liljana Stojanovska, Andreja Arsovski, Snezhana Smichkoska, Emilija Lazarova, Maja Jakimovska Dimitrovska, Dijana Plaseska-Karanfilska
PURPOSE: We aimed to establish the spectrum of BRCA1/2 mutations among the breast cancer (BC) patients from the Republic of Macedonia. METHODS: We used targeted next-generation sequencing (NGS), Sanger DNA sequencing, and multiplex ligation probe amplification analysis (MLPA) to search for point mutations and deletions/duplications involving BRCA1 and BRCA2-coding regions. RESULTS: We have analyzed a total of 313 BC patients, enriched for family history of cancer, early age of onset and bilateral and/or triple negative (TN) BC...
January 15, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29321894/development-of-a-genotype-by-sequencing-immunogenetic-assay-as-exemplified-by-screening-for-variation-in-red-fox-with-and-without-endemic-rabies-exposure
#2
Michael E Donaldson, Yessica Rico, Karsten Hueffer, Halie M Rando, Anna V Kukekova, Christopher J Kyle
Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29300782/the-paradox-of-hbv-evolution-as-revealed-from-a-16th-century-mummy
#3
Zoe Patterson Ross, Jennifer Klunk, Gino Fornaciari, Valentina Giuffra, Sebastian Duchêne, Ana T Duggan, Debi Poinar, Mark W Douglas, John-Sebastian Eden, Edward C Holmes, Hendrik N Poinar
Hepatitis B virus (HBV) is a ubiquitous viral pathogen associated with large-scale morbidity and mortality in humans. However, there is considerable uncertainty over the time-scale of its origin and evolution. Initial shotgun data from a mid-16th century Italian child mummy, that was previously paleopathologically identified as having been infected with Variola virus (VARV, the agent of smallpox), showed no DNA reads for VARV yet did for hepatitis B virus (HBV). Previously, electron microscopy provided evidence for the presence of VARV in this sample, although similar analyses conducted here did not reveal any VARV particles...
January 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29289485/a-microfluidic-enrichment-platform-with-a-recombinase-polymerase-amplification-sensor-for-pathogen-diagnosis
#4
Dao Thi Thuy Nguyen, Eun Yeong Lee, Bonhan Koo, Choong Eun Jin, Tae Yoon Lee, Yong Shin
Rapid and sensitive detection of low amounts of pathogen in large samples is needed for early diagnosis and treatment of patients and surveillance of pathogen. In this study, we report a microfluidic platform for detection of low pathogen levels in a large sample volume that couples an Magainin 1 based microfluidic platform for pathogen enrichment and a recombinase polymerase amplification (RPA) sensor for simultaneous pathogenic DNA amplification and detection in a label-free and real-time manner. Magainin 1 is used as a pathogen enrichment agent with a herringbone microfluidic chip...
December 28, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/29242148/whole-bacterium-selex-of-dna-aptamers-for-rapid-detection-of-e-coli-o157-h7-using-a-qcm-sensor
#5
Xiaofan Yu, Fang Chen, Ronghui Wang, Yanbin Li
The rapid detection of foodborne pathogens is critical to ensure food safety. The objective of this study is to select aptamers specifically bound to Escherichia coli O157:H7 using the whole-bacterium SELEX (Systematic Evolution of Ligands by Exponential Enrichment) and apply the selected aptamer to a QCM (quartz crystal microbalance) sensor for rapid and sensitive detection of target bacteria. A total of 19 rounds of selection against live E. coli O157:H7 and 6 rounds of counter selection against a mixture of Staphylococcus aureus, Listeria monocytogenes, and Salmonella Typhimurium, were performed...
December 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/29234827/transcriptome-signatures-of-tomato-leaf-induced-by-phytophthora-infestans-and-functional-identification-of-transcription-factor-spwrky3
#6
Jun Cui, Pinsan Xu, Jun Meng, Jingbin Li, Ning Jiang, Yushi Luan
SpWRKY3 was identified as a resistance gene to Phytophthora infestans from Solanum pimpinellifolium L3708 and its transgenic tomato showed a significant resistance to P. infestans. This finding reveals the potential application of SpWRKY3 in future molecular breeding. Transcription factors (TFs) play crucial roles in the plant response to various pathogens. In this present study, we used comparative transcriptome analysis of tomatoes inoculated with and without Phytophthora infestans to identify 1103 differentially expressed genes...
December 12, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29228270/influenza-a-virus-subtype-h9n2-infection-disrupts-the-composition-of-intestinal-microbiota-of-chickens
#7
Alexander Yitbarek, J Scott Weese, Tamiru Negash Alkie, John Parkinson, Shayan Sharif
The impact of low pathogenic influenza viruses such as subtype H9N2, which infect the respiratory and the gastrointestinal tracts of chickens, on microbial composition are not known. Twenty day-old specific pathogen free chickens were assigned to two treatment groups, control (Uninfected) and H9N2-infected (challenged via the oral-nasal route). Fecal genomic DNA was extracted, and the V3-V4 regions of the 16S rRNA gene was sequenced using the Illumina Miseq® platform. Sequences were curated using Mothur as described in the MiSeq SOP...
December 6, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29214046/high-resolution-bacterial-16s-rrna-gene-profile-meta-analysis-and-biofilm-status-reveal-common-colorectal-cancer-consortia
#8
Julia L Drewes, James R White, Christine M Dejea, Payam Fathi, Thevambiga Iyadorai, Jamuna Vadivelu, April C Roslani, Elizabeth C Wick, Emmanuel F Mongodin, Mun Fai Loke, Kumar Thulasi, Han Ming Gan, Khean Lee Goh, Hoong Yin Chong, Sandip Kumar, Jane W Wanyiri, Cynthia L Sears
Colorectal cancer (CRC) remains the third most common cancer worldwide, with a growing incidence among young adults. Multiple studies have presented associations between the gut microbiome and CRC, suggesting a link with cancer risk. Although CRC microbiome studies continue to profile larger patient cohorts with increasingly economical and rapid DNA sequencing platforms, few common associations with CRC have been identified, in part due to limitations in taxonomic resolution and differences in analysis methodologies...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/29213059/a-comprehensive-assessment-of-the-genetic-determinants-in-salmonella-typhimurium-for-resistance-to-hydrogen-peroxide-using-proteogenomics
#9
Sardar Karash, Rohana Liyanage, Abdullah Qassab, Jackson O Lay, Young Min Kwon
Salmonella is an intracellular pathogen infecting a wide range of hosts and can survive in macrophages. An essential mechanism used by macrophages to eradicate Salmonella is production of reactive oxygen species. Here, we used proteogenomics to determine the candidate genes and proteins that have a role in resistance of S. Typhimurium to H2O2. For Tn-seq, a saturated Tn5 insertion library was grown in vitro under either 2.5 (H2O2L) or 3.5 mM H2O2 (H2O2H). We identified two sets of overlapping genes required for resistance of S...
December 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29196295/quasi-metagenomics-and-realtime-sequencing-aided-detection-and-subtyping-of-salmonella-enterica-from-food-samples
#10
Ji-Yeon Hyeon, Shaoting Li, David A Mann, Shaokang Zhang, Zhen Li, Yi Chen, Xiangyu Deng
Metagenomics analysis of food samples promises isolation-independent detection and subtyping of foodborne bacterial pathogens in a single workflow. Selective concentration of Salmonella genomic DNA through immunomagnetic separation (IMS) and multiple displacement amplification (MDA) were shown to shorten culture enrichment of Salmonella-spiked raw chicken breast samples by over 12 hours while permitting serotyping and high-fidelity single nucleotide polymorphisms (SNP) typing of the pathogen using short shotgun sequencing reads...
December 1, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29186632/integrating-sequence-and-gene-expression-information-predicts-genome-wide-dna-binding-proteins-and-suggests-a-cooperative-mechanism
#11
Shandar Ahmad, Philip Prathipati, Lokesh P Tripathi, Yi-An Chen, Ajay Arya, Yoichi Murakami, Kenji Mizuguchi
DNA-binding proteins (DBPs) perform diverse biological functions ranging from transcription to pathogen sensing. Machine learning methods can not only identify DBPs de novo but also provide insights into their DNA-recognition dynamics. However, it remains unclear whether available methods that can accurately predict DNA-binding sites in known DBPs can also identify novel DBPs. Moreover, sequence information is blind to the cellular- and disease-specific contexts of DBP activities, whereas the under-utilized knowledge from public gene expression data offers great promise...
November 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29174688/comparative-transcriptome-analysis-reveals-induction-of-apoptosis-in-chicken-kidney-cells-associated-with-the-virulence-of-nephropathogenic-infectious-bronchitis-virus
#12
Hui Liu, Xin Yang, Zhikun Zhang, Jianan Li, Wencheng Zou, Fanya Zeng, Hongning Wang
Avian infectious bronchitis virus (IBV) that causes respiratory and nephritic diseases in chicken is a major poultry pathogen leading to serious economic loss worldwide. The nephropathogenic IBV strains cause nephritis and kidney lesions intrinsically and the pathogenic mechanism is still unclear. In the present study, SPF chicks were infected with three nephropathogenic IBVs of different virulence and their gene expression profiles in chicken kidney were compared at transcriptome level. As a result, 1279 differentially expressed (DE) genes were found in very virulent SCDY2 inoculated group, 145 in virulent SCK2 group and 74 in non-virulent LDT3-A group when compared to mock infected group...
November 21, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29171901/current-advances-in-aptamer-assisted-technologies-for-detecting-bacterial-and-fungal-toxins
#13
REVIEW
Naser Alizadeh, Mohammad Yousef Memar, Bahareh Mehramuz, Saeed Shirgir Abibiglou, Fateme Hemmati, Hossein Samadi Kafil
Infectious diseases are among the common leading causes of morbidity and mortality worldwide. Associated with the emergence of new infectious diseases, the increasing number of antimicrobial resistant isolates presents a seriousthreat to public health and hospitalized patients. A microbial pathogen may elicit several host responses and use a variety of mechanisms to evade host defenses. These methods and mechanisms include capsule, LPS or cell wall components, adhesions and toxins. Toxins inhibit phagocytosis, cause septic shock and host cell damages by binding to host surface receptors and invasion...
November 24, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29166270/detection-of-yersinia-enterocolitica-species-in-pig-tonsils-and-raw-pork-meat-by-the-real-time-pcr-and-culture-methods
#14
M A Stachelska
The aim of the present study was to establish a rapid and accurate real-time PCR method to detect pathogenic Yersinia enterocolitica in pork. Yersinia enterocolitica is considered to be a crucial zoonosis, which can provoke diseases both in humans and animals. The classical culture methods designated to detect Y. enterocolitica species in food matrices are often very time-consuming. The chromosomal locus _tag CH49_3099 gene, that appears in pathogenic Y. enterocolitica strains, was applied as DNA target for the 5' nuclease PCR protocol...
September 26, 2017: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/29142257/using-a-quantitative-quadruple-immunofluorescent-assay-to-diagnose-isolated-mitochondrial-complex-i-deficiency
#15
Syeda T Ahmed, Charlotte L Alston, Sila Hopton, Langping He, Iain P Hargreaves, Gavin Falkous, Monika Oláhová, Robert McFarland, Doug M Turnbull, Mariana C Rocha, Robert W Taylor
Isolated Complex I (CI) deficiency is the most commonly observed mitochondrial respiratory chain biochemical defect, affecting the largest OXPHOS component. CI is genetically heterogeneous; pathogenic variants affect one of 38 nuclear-encoded subunits, 7 mitochondrial DNA (mtDNA)-encoded subunits or 14 known CI assembly factors. The laboratory diagnosis relies on the spectrophotometric assay of enzyme activity in mitochondrially-enriched tissue homogenates, requiring at least 50 mg skeletal muscle, as there is no reliable histochemical method for assessing CI activity directly in tissue cryosections...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138457/functional-annotation-of-structural-ncrnas-within-enhancer-rnas-in-the-human-genome-implications-for-human-disease
#16
Chao Ren, Feng Liu, Zhangyi Ouyang, Gaole An, Chenghui Zhao, Jun Shuai, Shuhong Cai, Xiaochen Bo, Wenjie Shu
Enhancer RNAs (eRNAs) are a novel class of non-coding RNA (ncRNA) molecules transcribed from the DNA sequences of enhancer regions. Despite extensive efforts devoted to revealing the potential functions and underlying mechanisms of eRNAs, it remains an open question whether eRNAs are mere transcriptional noise or relevant biologically functional species. Here, we identified a catalogue of eRNAs in a broad range of human cell/tissue types and extended our understanding of eRNAs by demonstrating their multi-omic signatures...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29137431/mitochondrial-dna-depletion-mitochondrial-mutations-and-high-tfam-expression-in-hepatocellular-carcinoma
#17
Lihua Qiao, Guoqing Ru, Zhuochao Mao, Chenghui Wang, Zhipeng Nie, Qiang Li, Yiyi Huang-Yang, Ling Zhu, Xiaoyang Liang, Jialing Yu, Pingping Jiang
We investigated the role of mitochondrial genetic alterations in hepatocellular carcinoma by directly comparing the mitochondrial genomes of 86 matched pairs of HCC and non-tumor liver samples. Substitutions in 637 mtDNA sites were detected, comprising 89.80% transitions and 6.60% transversions. Forty-six somatic variants, including 15 novel mutations, were identified in 40.70% of tumor tissues. Of those, 21 were located in the non-coding region and 25 in the protein-coding region. Twenty-two somatic nonsynonymous changes were identified as putative pathogenic variants, including 4 truncating mutations produced by three frameshifts (MT-ATP6 8628 insC; MT-ND5 13475 T-del, and MT-CYB 14984 insA) and 1 nonsense mutation in MT-CO3 9253 G>A...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29111407/application-of-reverse-transcriptase-pcr-dgge-as-a-rapid-method-for-routine-determination-of-vibrio-spp-in-foods
#18
Kanchana Chahorm, Cheunjit Prakitchaiwattana
The aim of this research was to evaluate the feasibility of PCR-DGGE and Reverse Transcriptase-PCR-DGGE techniques for rapid detection of Vibrio species in foods. Primers GC567F and 680R were initially evaluated for amplifying DNA and cDNA of ten references Vibrio species by PCR method. The GC-clamp PCR amplicons were separated according to their sequences by the DGGE using 10% (w/v) polyacrylamide gel containing 45-70% urea and formamide denaturants. Two pair of Vibrio species, which could not be differentiated on the gel, was Vibrio fluvialis - Vibrio furnissii and Vibrio parahaemolyticus - Vibrio harveyi...
October 12, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29101771/modifications-at-k31-on-the-lateral-surface-of-histone-h4-contribute-to-genome-structure-and-expression-in-apicomplexan-parasites
#19
Fabien Sindikubwabo, Shuai Ding, Tahir Hussain, Philippe Ortet, Mohamed Barakat, Sebastian Baumgarten, Dominique Cannella, Andrés Palencia, Alexandre Bougdour, Lucid Belmudes, Yohann Couté, Isabelle Tardieux, Cyrille Y Botté, Artur Scherf, Mohamed-Ali Hakimi
An unusual genome architecture characterizes the two related human parasitic pathogens Plasmodium falciparum and Toxoplasma gondii. A major fraction of the bulk parasite genome is packaged as transcriptionally permissive euchromatin with few loci embedded in silenced heterochromatin. Primary chromatin shapers include histone modifications at the nucleosome lateral surface close to the DNA but their mode of action remains unclear. We now identify versatile modifications at Lys31 within the globular domain of histone H4 that crucially determine genome organization and expression in Apicomplexa parasites...
November 4, 2017: ELife
https://www.readbyqxmd.com/read/29099169/real-time-study-of-the-interaction-between-g-rich-dna-oligonucleotides-and-lead-ion-on-dna-tetrahedron-functionalized-sensing-platform-by-dual-polarization-interferometry
#20
Shuang Wang, Shasha Lu, Jiahui Zhao, Jianshe Huang, Xiurong Yang
G-quadruplex plays roles in numerous physiological and pathological processes of organisms. Due to the unique properties of G-quadruplex (e.g., forming G4/hemin complexes with catalytic activity and electron acceptability, binding with metal ions, proteins, fluorescent ligands, and so on), it has been widely applied in biosensing. But the formation process of G-quadruplex is not yet fully understood. Here, a DNA tetrahedron platform with higher reproducibility, regenerative ability, and time-saving building process was coupled with dual polarization interferometry technique for the real-time and label-free investigation of the specific interaction process of guanine-rich singled-stranded DNA (G-rich ssDNA) and Pb(2+)...
November 14, 2017: ACS Applied Materials & Interfaces
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