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https://www.readbyqxmd.com/read/28737436/dna-methylation-in-the-norepinephrine-transporter-gene-promoter-region-is-not-associated-with-depression-and-hypertension
#1
Lin Meng, Dongmei Chen, Fei Pei, Rutai Hui, Yang Zheng, Jingzhou Chen
OBJECTIVE: This study aims to detect the role of DNA methylation in norepinephrine transporter (NET) gene promoter region on the association between depression and hypertension. METHODS: A total of 162 subjects were categorized into four groups based on depression scores and blood pressure. DNA was extracted from peripheral white blood cells and methylation levels of nine CpG sites in NET gene promoter region were investigated by pyrosequencing. RESULTS: For each CpG site and the average value of nine CpG sites, there were no significant differences in DNA methylation of the NET gene promoter between healthy controls and patients with depression or hypertension...
July 24, 2017: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/28736954/the-impact-of-the-bovine-fecal-microbiome-on-escherichia-coli-o157-h7-prevalence-and-enumeration-in-naturally-infected-cattle
#2
M Kim, L A Kuehn, J L Bono, E D Berry, N Kalchayanand, H C Freetly, A K Benson, J E Wells
AIMS: The objective of this study was to determine if the fecal microbiome has an association with E. coli O157:H7 prevalence and enumeration. METHODS AND RESULTS: Pyrosequencing analysis of fecal microbiome was performed from feedlot cattle fed one of three diets: i) 94 heifers fed low concentrate (LC) diet, ii) 142 steers fed moderate concentrate (MC) diet, and iii) 132 steers fed high concentrate (HC) diet. A total of 322,585 OTUs were calculated from 2,411,122 high-quality sequences obtained from 368 fecal samples...
July 23, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28736819/evaluation-of-dna-methylation-of-inflammatory-genes-following-treatment-of-chronic-periodontitis-a-pilot-case-control-study
#3
Farah Asa'ad, Valentina Bollati, Giorgio Pagni, Rogerio M Castilho, Eleonora Rossi, Francesca Pomingi, Letizia Tarantini, Dario Consonni, William V Giannobile, Giulio Rasperini
OBJECTIVE: To evaluate the influence of periodontal therapy on DNA methylation in chronic periodontitis patients as compared to healthy individuals. MATERIALS & METHODS: Twenty patients were enrolled into two groups: 1) 10 diagnosed as clinically healthy; and 2) 10 diagnosed with chronic periodontitis. Clinical measures were recorded and gingival biopsies were harvested at baseline (both patient groups) and at 2 and 8 weeks post-baseline for diseased individuals...
July 24, 2017: Journal of Clinical Periodontology
https://www.readbyqxmd.com/read/28736228/dbz-is-a-putative-ppar%C3%AE-agonist-that-prevents-high-fat-diet-induced-obesity-insulin-resistance-and-gut-dysbiosis
#4
Pengfei Xu, Fan Hong, Jialin Wang, Jing Wang, Xia Zhao, Sheng Wang, Tingting Xue, Jingwei Xu, Xiaohui Zheng, Yonggong Zhai
BACKGROUND: The nuclear receptor PPARγ is an effective pharmacological target for some types of metabolic syndrome, including obesity, diabetes, nonalcoholic fatty liver disease, and cardiovascular disease. However, the current PPARγ-targeting thiazolidinedione drugs have undesirable side effects. Danshensu Bingpian Zhi (DBZ), also known as tanshinol borneol ester derived from Salvia miltiorrhiza, is a synthetic derivative of natural compounds used in traditional Chinese medicine for its anti-inflammatory activity...
July 20, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28735386/the-performance-and-microbial-communities-of-biodegradation-electron-transfer-with-sulfur-metabolism-integrated-process-for-flue-gas-desulfurization-wastewater-treatment
#5
Chao Wei, Wenjie He, Li Wei, Jun Ma, Chunying Li
The biodegradation-electron transfer with sulfur metabolism integrated (BESI(®)) process was used for the treatment of real flue gas desulfurization wastewater. The BESI(®) process consists of an anaerobic activated sludge reactor, an anoxic activated sludge reactor, and an aerobic bio-film reactor. The performance of the integrated process was evaluated by the removal efficiencies of organics and nitrogen pollutants. The sulfate in the wastewater was used as an abundant sulfur source to drive the integrated process...
July 22, 2017: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/28735303/acid-fast-bacterium-detection-and-identification-from-paraffin-embedded-tissues-using-a-pcr-pyrosequencing-method
#6
Jian R Bao, Richard B Clark, Ronald N Master, Kileen L Shier, Lynn L Eklund
AIMS: Acid-fast bacterium (AFB) identification from formalin-fixed paraffin-embedded (FFPE) tissues is challenging and may not be readily available to the clinical laboratory. A method to detect and identify AFB from FFPE tissues using PCR and pyrosequencing (PCR-Seq) was developed and evaluated. METHODS: The method was validated using spiked cell-clotted paraffin blocks before use with patients' specimens. DNA was extracted from tissue sections, and a 16S rRNA gene fragment was amplified and a signature sequence was produced on a PyroMark ID system...
July 22, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28734695/response-of-the-bacterial-community-in-an-on-farm-biopurification-system-to-which-diverse-pesticides-are-introduced-over-an-agricultural-season
#7
Peter N Holmsgaard, Simone Dealtry, Vincent Dunon, Holger Heuer, Lars H Hansen, Dirk Springael, Kornelia Smalla, Leise Riber, Søren J Sørensen
A biopurification system (BPS) is used on-farm to clean pesticide-contaminated wastewater. Due to high pesticide loads, a BPS represents a hot spot for the proliferation and selection as well as the genetic adaptation of discrete pesticide degrading microorganisms. However, while considerable knowledge exists on the biodegradation of specific pesticides in BPSs, the bacterial community composition of these systems has hardly been explored. In this work, the Shannon diversity, the richness and the composition of the bacterial community within an operational BPS receiving wastewater contaminated with various pesticides was, for the first time, elucidated over the course of an agricultural season, using DGGE profiling and pyrosequencing of 16S rRNA gene fragments amplified from total community DNA...
July 19, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28733028/bifidobacterium-longum-affects-the-methylation-level-of-forkhead-box-p3-promoter-in-2-4-6-trinitrobenzenesulphonic-acid-induced-colitis-in-rats
#8
Ming Zhang, Lixing Zhou, Shu Zhang, Yang Yang, Lei Xu, Zichun Hua, Xiaoping Zou
Bifidobacterium longum (B. Longum) is a common probiotic colonized in the human gut and against the development of chronic inflammation including inflammatory bowel disease (IBD). But the underlying mechanism remains unknown. The aim of this study was to evaluate the affection of B. longum on the methylation levels of forkhead box P3 (Foxp3) promoter. 2, 4, 6-trinitrobenzenesulphonic acid (TNBS)-induced colitis rat models were treated with B. longum or medium, respectively. The genomic DNA of spleen peripheral blood mononuclear cells (PBMC) cells was extracted...
July 18, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28729864/synechococcus-assemblages-across-the-salinity-gradient-in-a-salt-wedge-estuary
#9
Xiaomin Xia, Wang Guo, Shangjin Tan, Hongbin Liu
Synechococcus are the most abundant and widely distributed picocyanobacteria in the ocean. The salt-wedge type of estuary possesses the complete horizontal and vertical gradient of salinity together with other physical and chemical parameters. In order to reveal whether such a complex environmental gradient harbors a high diversity of Synechococcus, we investigated the abundance, taxonomic composition and pigment genetic diversity of Synechococcus in surface and bottom waters across the salinity gradient in a salt-wedge estuary by flow cytometric analysis and pyrosequencing of the rpoC1 gene and cpcBA operon (encoding phycocyanin)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28728121/effect-of-residual-h2o2-from-advanced-oxidation-processes-on-subsequent-biological-water-treatment-a-laboratory-batch-study
#10
Feifei Wang, Doris van Halem, Gang Liu, Karin Lekkerkerker-Teunissen, Jan Peter van der Hoek
H2O2 residuals from advanced oxidation processes (AOPs) may have critical impacts on the microbial ecology and performance of subsequent biological treatment processes, but little is known. The objective of this study was to evaluate how H2O2 residuals influence sand systems with an emphasis on dissolved organic carbon (DOC) removal, microbial activity change and bacterial community evolution. The results from laboratory batch studies showed that 0.25 mg/L H2O2 lowered DOC removal by 10% while higher H2O2 concentrations at 3 and 5 mg/L promoted DOC removal by 8% and 28%...
July 15, 2017: Chemosphere
https://www.readbyqxmd.com/read/28727822/dna-methylation-of-candidate-genes-in-peripheral-blood-from-patients-with-type-2-diabetes-or-the-metabolic-syndrome
#11
Sanne D van Otterdijk, Alexandra M Binder, Katarzyna Szarc Vel Szic, Julia Schwald, Karin B Michels
INTRODUCTION: The prevalence of type 2 diabetes (T2D) and the metabolic syndrome (MetS) is increasing and several studies suggested an involvement of DNA methylation in the development of these metabolic diseases. This study was designed to investigate if differential DNA methylation in blood can function as a biomarker for T2D and/or MetS. METHODS: Pyrosequencing analyses were performed for the candidate genes KCNJ11, PPARγ, PDK4, KCNQ1, SCD1, PDX1, FTO and PEG3 in peripheral blood leukocytes (PBLs) from 25 patients diagnosed with only T2D, 9 patients diagnosed with T2D and MetS and 11 control subjects without any metabolic disorders...
2017: PloS One
https://www.readbyqxmd.com/read/28725028/detection-and-quantitation-of-copy-number-variation-in-the-voltage-gated-sodium-channel-gene-of-the-mosquito-culex-quinquefasciatus
#12
Walter Fabricio Silva Martins, Krishanthi Subramaniam, Keith Steen, Henry Mawejje, Triantafillos Liloglou, Martin James Donnelly, Craig Stephen Wilding
Insecticide resistance is typically associated with alterations to the insecticidal target-site or with gene expression variation at loci involved in insecticide detoxification. In some species copy number variation (CNV) of target site loci (e.g. the Ace-1 target site of carbamate insecticides) or detoxification genes has been implicated in the resistance phenotype. We show that field-collected Ugandan Culex quinquefasciatus display CNV for the voltage-gated sodium channel gene (Vgsc), target-site of pyrethroid and organochlorine insecticides...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28725026/microbiome-analysis-and-confocal-microscopy-of-used-kitchen-sponges-reveal-massive-colonization-by-acinetobacter-moraxella-and-chryseobacterium-species
#13
Massimiliano Cardinale, Dominik Kaiser, Tillmann Lueders, Sylvia Schnell, Markus Egert
The built environment (BE) and in particular kitchen environments harbor a remarkable microbial diversity, including pathogens. We analyzed the bacterial microbiome of used kitchen sponges by 454-pyrosequencing of 16S rRNA genes and fluorescence in situ hybridization coupled with confocal laser scanning microscopy (FISH-CLSM). Pyrosequencing showed a relative dominance of Gammaproteobacteria within the sponge microbiota. Five of the ten most abundant OTUs were closely related to risk group 2 (RG2) species, previously detected in the BE and kitchen microbiome...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724248/exposure-to-particulate-air-pollution-during-early-pregnancy-is-associated-with-placental-dna-methylation
#14
Jing Cai, Yan Zhao, Pengcheng Liu, Bin Xia, Qingyang Zhu, Xiu Wang, Qi Song, Haidong Kan, Yunhui Zhang
Maternal exposure to particulate matter with aerodynamic diameter <10μm (PM10) during pregnancy results in adverse birth outcomes. Changes in placental DNA methylation might mediate those adverse effects. In this study, we examined the associations between prenatal PM10 exposure and DNA methylation of LINE1, HSD11B2 and NR3C1 in human placenta. One hundred and eighty-one mother newborn pairs (80 fetal growth restriction newborns, 101 normal newborns) participated in this study. The average PM10 exposure of each trimester and of the whole pregnancy was calculated using daily air pollution concentration data...
July 15, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28723626/positive-correlation-of-cg16672562-methylation-with-obesity-related-traits-in-childhood-obesity-and-its-independence-with-underlying-hif3a-hypoxia-inducible-factor-3a-genetic-background
#15
Suman Lee, Hyo Jin Kim, Sohee Han, Jae-Pil Jeon, Sang-Ick Park, Ho-Yeong Yu, Mi Yeong Hwang, Juyoung Lee
Differential methylations of the HIF3A (hypoxia-inducible factor 3a) gene have been linked to body mass index (BMI). To explore the association of these methylations to childhood obesity, we measured 5 CpG methylation sites (cg27146050, cg46801562, cg22891070, cg16672562 and cg46801675) in intron 1 of the HIF3A gene by pyrosequencing, in the Korean population (mean age: 13.9 yrs, 305 obese cases and 387 controls). Two CpG methylations, cg46801562 and cg16672562, had statistically significant association with childhood obesity (P = 2...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28722770/asbestos-associated-genome-wide-dna-methylation-changes-in-lung-cancer
#16
Eeva Kettunen, Hector Hernandez-Vargas, Marie-Pierre Cros, Geoffroy Durand, Florence Le Calvez-Kelm, Kristina Stuopelyte, Sonata Jarmalaite, Kaisa Salmenkivi, Sisko Anttila, Henrik Wolff, Zdenko Herceg, Kirsti Husgafvel-Pursiainen
Previous studies have revealed a robust association between exposure to asbestos and human lung cancer. Accumulating evidence has highlighted the role of epigenome deregulation in the mechanism of carcinogen-induced malignancies. We examined the impact of asbestos on DNA methylation. Our genome-wide studies (using Illumina HumanMethylation450K BeadChip) of lung cancer tissue and paired normal lung from 28 asbestos-exposed or non-exposed patients, mostly smokers, revealed distinctive DNA methylation changes...
July 19, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28722603/molecular-characterization-of-mycobacterium-tuberculosis-strains-with-tb-sprint
#17
Barbara Molina-Moya, Michel Kiréopori Gomgnimbou, Carmen Lafoz, Alicia Lacoma, Cristina Prat, Guislaine Refrégier, Sofia Samper, Jose Dominguez, Christophe Sola
We evaluated Tuberculosis-Spoligo-Rifampicin-Isoniazid Typing (TB-SPRINT), a microbead-based method for spoligotyping and detection of rifampicin and isoniazid resistance in Mycobacterium tuberculosis. For that, 67 M. tuberculosis complex strains were retrospectively selected. Membrane-based spoligotyping, restriction fragment length polymorphism, DNA sequencing/pyrosequencing of rpoB, katG, and inhA promoter, TB-SPRINT, and SNP typing were performed. Concordance between spoligotyping methods was 99.6% (2,785/2,795 spoligotype data points)...
July 10, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28720682/reducing-artifactual-egfr-t790m-mutations-in-dna-from-formalin-fixed-paraffin-embedded-tissue-by-use-of-thymine-dna-glycosylase
#18
Hongdo Do, Ramyar Molania, Paul L Mitchell, Rita Vaiskunaite, John D Murdoch, Alexander Dobrovic
BACKGROUND: False-positive EGFR T790M mutations have been reported in formalin-fixed lung tumors, but the cause of the false positives has not been identified. The T790M mutation results from a C>T change at the cytosine of a CpG dinucleotide. The presence or absence of methylation at this cytosine has different consequences following deamination, resulting in a thymine or uracil, respectively, both of which however result in an artifactual change. Uracil-DNA glycosylase (UDG) can be used to eliminate DNA templates with uracil residues but is not active against artifactual thymines...
July 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28719849/selective-cathodic-microbial-biofilm-retention-allows-a-high-current-to-sulfide-efficiency-in-sulfate-reducing-microbial-electrolysis-cells
#19
Guillermo Pozo, Yang Lu, Sebastien Pongy, Jürg Keller, Pablo Ledezma, Stefano Freguia
Selective microbial retention is of paramount importance for the long-term performance of cathodic sulfate reduction in microbial electrolysis cells (MECs) due to the slow growth rate of autotrophic sulfate-reducing bacteria. In this work, we investigate the biofilm retention and current-to-sulfide conversion efficiency using carbon granules (CG) or multi-wall carbon nanotubes deposited on reticulated vitreous carbon (MWCNT-RVC) as electrode materials. For ~2months, the MECs were operated at sulfate loading rates of 21 to 309gSO4 -S/m(2)/d...
July 12, 2017: Bioelectrochemistry
https://www.readbyqxmd.com/read/28719667/assessing-intragenomic-variation-of-the-internal-transcribed-spacer-two-adapting-the-illumina-metagenomics-protocol
#20
Lo'ai Alanagreh, Caitlin Pegg, Amritha Harikumar, Mark Buchheim
Primary and secondary structural data from the internal transcribed spacer two (ITS2) have been used extensively for diversity studies of many different eukaryotic organisms, including the green algae. Ease of amplification is due, at least in part, to the fact that ITS2 is part of the tandemly-repeated rRNA array. The potential confounding influence of intragenomic variability has yet to be addressed except in a few organisms. Moreover, few of the assessments of intragenomic variation have taken advantage of the deep sequencing capacity of sequence-by-synthesis protocols...
2017: PloS One
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