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pathogen dna enrichment

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https://www.readbyqxmd.com/read/29138457/functional-annotation-of-structural-ncrnas-within-enhancer-rnas-in-the-human-genome-implications-for-human-disease
#1
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
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/29080873/-a-bioinformatic-pipeline-for-ngs-data-analysis-and-mutation-calling-in-human-solid-tumors
#6
K Yu Tsukanov, A Yu Krasnenko, D A Plakhina, D O Korostin, A V Churov, O S Druzhilovskaya, D V Rebrikov, V V Ilinsky
We aimed to develop a pipeline for the bioinformatic analysis and interpretation of NGS data and detection of a wide range of single-nucleotide somatic mutations within tumor DNA. Initially, the NGS reads were submitted to a quality control check by the Cutadapt program. Low-quality 3¢-nucleotides were removed. After that the reads were mapped to the reference genome hg19 (GRCh37.p13) by BWA. The SAMtools program was used for exclusion of duplicates. MuTect was used for SNV calling. The functional effect of SNVs was evaluated using the algorithm, including annotation and evaluation of SNV pathogenicity by SnpEff and analysis of such databases as COSMIC, dbNSFP, Clinvar, and OMIM...
October 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/29066549/selective-proteomic-analysis-of-antibiotic-tolerant-cellular-subpopulations-in-pseudomonas-aeruginosa-biofilms
#7
Brett M Babin, Lydia Atangcho, Mark B van Eldijk, Michael J Sweredoski, Annie Moradian, Sonja Hess, Tim Tolker-Nielsen, Dianne K Newman, David A Tirrell
Biofilm infections exhibit high tolerance against antibiotic treatment. The study of biofilms is complicated by phenotypic heterogeneity; biofilm subpopulations differ in their metabolic activities and their responses to antibiotics. Here, we describe the use of the bio-orthogonal noncanonical amino acid tagging (BONCAT) method to enable selective proteomic analysis of a Pseudomonas aeruginosa biofilm subpopulation. Through controlled expression of a mutant methionyl-tRNA synthetase, we targeted BONCAT labeling to cells in the regions of biofilm microcolonies that showed increased tolerance to antibiotics...
October 24, 2017: MBio
https://www.readbyqxmd.com/read/29061645/homologous-recombination-dna-repair-pathway-disruption-and-retinoblastoma-protein-loss-are-associated-with-exceptional-survival-in-high-grade-serous-ovarian-cancer
#8
Dale W Garsed, Kathryn Alsop, Sian Fereday, Catherine Emmanuel, Catherine Kennedy, Dariush Etemadmoghadam, Bo Gao, Val Gebski, Valérie Garès, Elizabeth L Christie, Maartje Ca Wouters, Katy Milne, Joshy George, Ann-Marie Patch, Jason Li, Gisela Mir Arnau, Timothy Semple, Sreeja R Gadipally, Yoke-Eng Chiew, Joy Hendley, Thomas Mikeska, Giada V Zapparoli, Kaushalya Amarasinghe, Sean Grimmond, John V Pearson, Nicola Waddell, Jillian Hung, Colin J R Stewart, Raghwa Sharma, Prue E Allan, Peter F Rambau, Nadia Traficante, Orla McNally, Linda Mileshkin, Anne L Hamilton, Sumitra Ananda, Marisa Grossi, Paul A Cohen, Yee C Leung, Robert M Rome, Philip J Beale, Penny Blomfield, Michael Friedlander, Alison Brand, Alexander Dobrovic, Martin Köbel, Paul Harnett, Brad H Nelson, David D L Bowtell, Anna DeFazio
PURPOSE: Women with epithelial ovarian cancer generally have a poor prognosis, however a subset of patients has an unexpected dramatic and durable response to treatment. We sought to identify clinical, pathological, and molecular determinants of exceptional survival in women with high-grade serous cancer (HGSC), a disease associated with the majority of ovarian cancer deaths. EXPERIMENTAL DESIGN: We evaluated the histories of 2,283 ovarian cancer patients and, after applying stringent clinical, and pathological selection criteria, identified 96 with HGSC that represented significant outliers in terms of treatment response and overall survival...
October 23, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29054799/systematic-evaluation-of-cell-selex-enriched-aptamers-binding-to-breast-cancer-cells
#9
Laia Civit, Seyed Mohammad Taghdisi, Anna Jonczyk, Silvana Haßel, Carsten Gröber, Michael Blank, H James Stunden, Marc Beyer, Joachim Schultze, Eicke Latz, Günter Mayer
The sensitive and specific detection of pathogenic cells is essential in clinical diagnostics. To achieve this, molecular tools are required that unequivocally recognise appropriate cell surface molecules, such as biomarkers that come along with disease onset and progression. Aptamers are short single-stranded oligonucleotides that interact with cognate target molecules with high affinity and specificity. Within the last years they have gained an increased attention as cell-recognition tools. Here, we report a systematic analysis of a cell-SELEX procedure, for the identification of aptamers that recognise breast cancer cells...
October 17, 2017: Biochimie
https://www.readbyqxmd.com/read/29044499/identification-of-the-first-homozygous-1-bp-deletion-in-gdf9-gene-leading-to-primary-ovarian-insufficiency-by-using-targeted-massively-parallel-sequencing
#10
M M França, M F A Funari, M Y Nishi, A M Narcizo, S Domenice, E M F Costa, A M Lerario, B B Mendonca
Targeted massively parallel sequencing (TMPS) has been used in genetic diagnosis for Mendelian disorders. In the past few years, the TMPS has identified new and already described genes associated with primary ovarian insufficiency phenotype. Here, we performed a targeted gene sequencing to find a genetic diagnosis in idiopathic cases of Brazilian POI cohort. A custom SureSelect(XT) DNA target enrichment panel was designed and the sequencing was performed on Illumina NextSeq sequencer. We identified one homozygous 1-bp deletion variant (c...
October 16, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29041965/enrichment-allows-identification-of-diverse-rare-elements-in-metagenomic-resistome-virulome-sequencing
#11
Noelle R Noyes, Maggie E Weinroth, Jennifer K Parker, Chris J Dean, Steven M Lakin, Robert A Raymond, Pablo Rovira, Enrique Doster, Zaid Abdo, Jennifer N Martin, Kenneth L Jones, Jaime Ruiz, Christina A Boucher, Keith E Belk, Paul S Morley
BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28956490/development-of-a-multiplex-pcr-for-simultaneous-detection-of-pasteurella-multocida-mannheimia-haemolytica-and-trueperella-pyogenes
#12
Wenlong Zhang, Xiaodan Liu, Mengcheng Liu, Bo Ma, Li Xu, Junwei Wang
Pasteurella multocida, Mannheimia haemolytica and Trueperella pyogenes are three bacterial pathogens closely associated with the bovine respiratory disease complex (BRDC). In the current study, a multiplex PCR for the simultaneous detection of these three bacteria in cultures was established. After serial optimisation, the detection limit of the method for the genomic DNA of the three bacteria was 40 pg/μl. The method could detect the genomic DNA of these three bacteria but not the genomic DNA of seven other bacterial strains...
September 2017: Acta Veterinaria Hungarica
https://www.readbyqxmd.com/read/28941453/development-of-a-dna-aptamer-for-screening-neisseria-meningitidis-serogroup-b-by-cell-selex
#13
Kimia Mirzakhani, Seyed Latif Mousavi Gargari, Iraj Rasooli, Samaneh Rasoulinejad
Background: Artificial oligonucleotides like DNA or RNA aptamers can be used as biodiagnostic alternatives for antibodies to detect pathogens. Comparing to antibodies, artificial oligonucleotides are produced easily at lower costs and are more stable. Neisseria meningitidis, the causative agent of meningitis, is responsible for about 1% of infections in an epidemic period. Specific DNA aptamers that bind to N. meningitidis serogroup B were identified by whole-cell Systemic Evolution of Ligands by EXponential Enrichment (SELEX)...
September 24, 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28939980/targeted-exome-sequencing-in-anti-factor-h-antibody-negative-hus-reveals-multiple-variations
#14
R W Thergaonkar, Ankita Narang, Bahadur Singh Gurjar, Pradeep Tiwari, Mamta Puraswani, Himanshi Saini, Aditi Sinha, Binuja Varma, Mitali Mukerji, Pankaj Hari, Arvind Bagga
BACKGROUND: Genetic susceptibility to atypical hemolytic uremic syndrome (aHUS) may lie within genes regulating or activating the alternate complement and related pathways converging on endothelial cell activation. METHODS: We tested 32 Indian patients of aHUS negative for antibodies to complement factor H for genetic variations in a panel of 15 genes, i.e., CFH, CFHR1-5, CFI, CFB, C3, CD46, MASP2, DGKE, ADAMTS13, THBD and PLG using next-generation DNA sequencing and for copy number variation in CFHR1-3...
September 22, 2017: Clinical and Experimental Nephrology
https://www.readbyqxmd.com/read/28932211/strain-level-streptococcus-colonization-patterns-during-the-first-year-of-life
#15
Meredith S Wright, Jamison McCorrison, Andres M Gomez, Erin Beck, Derek Harkins, Jyoti Shankar, Stephanie Mounaud, Edelwisa Segubre-Mercado, Aileen May R Mojica, Brian Bacay, Susan A Nzenze, Sheila Z M Kimaro, Peter Adrian, Keith P Klugman, Marilla G Lucero, Karen E Nelson, Shabir Madhi, Granger G Sutton, William C Nierman, Liliana Losada
Pneumococcal pneumonia has decreased significantly since the implementation of the pneumococcal conjugate vaccine (PCV), nevertheless, in many developing countries pneumonia mortality in infants remains high. We have undertaken a study of the nasopharyngeal (NP) microbiome during the first year of life in infants from The Philippines and South Africa. The study entailed the determination of the Streptococcus sp. carriage using a lytA qPCR assay, whole metagenomic sequencing, and in silico serotyping of Streptococcus pneumoniae, as well as 16S rRNA amplicon based community profiling...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28924154/a-dna-aptamer-efficiently-inhibits-the-infectivity-of-bovine-herpesvirus-1-by-blocking-viral-entry
#16
Jian Xu, Xixi Zhang, Shuanghai Zhou, Junjun Shen, Dawei Yang, Jing Wu, Xiaoyang Li, Meiling Li, Xiufen Huang, Joshua E Sealy, Munir Iqbal, Yongqing Li
Bovine herpesvirus 1 (BoHV-1) is an important pathogen of domestic and wild cattle responsible for major economic losses in dairy and beef industries throughout the world. Inhibition of viral entry plays a crucial role in the control of BoHV-1 infection and aptamers have been reported to inhibit viral replication. In this study, nine DNA aptamers that target BoHV-1 were generated using systemic evolution of ligands by exponential enrichment. Of the nine candidates, aptamer IBRV-A4 exhibited the highest affinity and specificity for BoHV-1, which bound to BoHV-1 with a Kd value of 3...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28919685/prevalence-of-listeria-monocytogenes-yersinia-enterocolitica-staphylococcusaureus-and-salmonella-enterica-typhimurium-in-meat-and-meat-products-using-multiplex-polymerase-chain-reaction
#17
C Latha, C J Anu, V J Ajaykumar, B Sunil
AIM: The objective of the study was to investigate the occurrence of Listeria monocytogenes, Yersinia enterocolitica, Staphylococcusaureus, and Salmonella enterica Typhimurium in meat and meat products using the multiplex polymerase chain reaction (PCR) method. MATERIALS AND METHODS: The assay combined an enrichment step in tryptic soy broth with yeast extract formulated for the simultaneous growth of target pathogens, DNA isolation and multiplex PCR. A total of 1134 samples including beef (n=349), chicken (n=325), pork (n=310), chevon (n=50), and meat products (n=100) were collected from different parts of Kerala, India...
August 2017: Veterinary World
https://www.readbyqxmd.com/read/28901631/equine-behavioral-enrichment-toys-as-tools-for-non-invasive-recovery-of-viral-and-host-dna
#18
Peter A Seeber, Sanatana E Soilemetzidou, Marion L East, Chris Walzer, Alex D Greenwood
Direct collection of samples from wildlife can be difficult and sometimes impossible. Non-invasive remote sampling for the purpose of DNA extraction is a potential tool for monitoring the presence of wildlife at the individual level, and for identifying the pathogens shed by wildlife. Equine herpesviruses (EHV) are common pathogens of equids that can be fatal if transmitted to other mammals. Transmission usually occurs by nasal aerosol discharge from virus-shedding individuals. The aim of this study was to validate a simple, non-invasive method to track EHV shedding in zebras and to establish an efficient protocol for genotyping individual zebras from environmental DNA (eDNA)...
September 2017: Zoo Biology
https://www.readbyqxmd.com/read/28899689/enhanced-expression-of-genes-related-to-xenobiotic-metabolism-in-the-skin-of-patients-with-atopic-dermatitis-but-not-with-ichthyosis-vulgaris
#19
Stefan Blunder, Sulev Kõks, Gea Kõks, Ene Reimann, Hubert Hackl, Robert Gruber, Verena Moosbrugger-Martinz, Matthias Schmuth, Sandrine Dubrac
Previous transcriptome analyses underscored the importance of immunological and skin barrier abnormalities in atopic dermatitis (AD). We sought to identify novel pathogenic pathways involved in AD by comparing the transcriptomes of AD patients stratified for filaggrin (FLG) null mutations to those of both healthy donors and patients with ichthyosis vulgaris (IV). We applied RNA-sequencing to analyze the whole transcriptome of nonlesional skin. Six-hundred and seven genes (476 up-regulated and 131 down-regulated by greater than 2-fold) and one-hundred and ninety-three genes (172 up-regulated and 21 down-regulated by greater than 2-fold) were differentially expressed when all AD or IV patients were compared to healthy donors, respectively...
September 9, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28882568/identification-of-pathogenic-genes-related-to-rheumatoid-arthritis-through-integrated-analysis-of-dna-methylation-and-gene-expression-profiling
#20
Lei Zhang, Shiyun Ma, Huailiang Wang, Hang Su, Ke Su, Longjie Li
The purpose of our study was to identify new pathogenic genes used for exploring the pathogenesis of rheumatoid arthritis (RA). To screen pathogenic genes of RA, an integrated analysis was performed by using the microarray datasets in RA derived from the Gene Expression Omnibus (GEO) database. The functional annotation and potential pathways of differentially expressed genes (DEGs) were further discovered by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Afterwards, the integrated analysis of DNA methylation and gene expression profiling was used to screen crucial genes...
November 15, 2017: Gene
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