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Pyrosequencing

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https://www.readbyqxmd.com/read/28525852/absolute-quantification-of-dna-methylation-using-microfluidic-chip-based-digital-pcr
#1
Zhenhua Wu, Yanan Bai, Zule Cheng, Fangming Liu, Ping Wang, Dawei Yang, Gang Li, Qinghui Jin, Hongju Mao, Jianlong Zhao
Hypermethylation of CpG islands in the promoter region of many tumor suppressor genes downregulates their expression and in a result promotes tumorigenesis. Therefore, detection of DNA methylation status is a convenient diagnostic tool for cancer detection. Here, we reported a novel method for the integrative detection of methylation by the microfluidic chip-based digital PCR. This method relies on methylation-sensitive restriction enzyme HpaII, which cleaves the unmethylated DNA strands while keeping the methylated ones intact...
May 12, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28522997/biogeographic-comparison-of-lophelia-associated-bacterial-communities-in-the-western-atlantic-reveals-conserved-core-microbiome
#2
Christina A Kellogg, Dawn B Goldsmith, Michael A Gray
Over the last decade, publications on deep-sea corals have tripled. Most attention has been paid to Lophelia pertusa, a globally distributed scleractinian coral that creates critical three-dimensional habitat in the deep ocean. The bacterial community associated with L. pertusa has been previously described by a number of studies at sites in the Mediterranean Sea, Norwegian fjords, off Great Britain, and in the Gulf of Mexico (GOM). However, use of different methodologies prevents direct comparisons in most cases...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28521213/phylogenetic-analysis-of-an-epidemic-outbreak-of-acute-hepatitis-c-in-hiv-infected-patients-by-ultra-deep-pyrosequencing
#3
Noelia Caro-Pérez, María Martínez-Rebollar, Josep Gregori, Josep Quer, Patricia González, Martina Gambato, Neris García-González, Fernando González-Candelas, Josep Costa, Juan Ignacio Esteban, Josep Mallolas, Xavier Forns, Montse Laguno, Sofía Pérez-Del-Pulgar
BACKGROUND: The incidence of acute hepatitis C (AHC) among HIV-infected men who have sex with men (MSM) has increased significantly in the last 10 years. Several studies point to a social and sexual network of HIV-positive MSM that extends internationally. OBJECTIVES: The aim of our study was to investigate the dynamics of HCV transmission in an outbreak of AHC in HIV-infected MSM in Barcelona by ultra-deep pyrosequencing. STUDY DESIGN: Between 2008 and 2013, 113 cases of AHC in HIV-infected MSM were diagnosed in the Infectious Diseases Unit, Hospital Clínic, Barcelona...
May 10, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28521159/distribution-and-genetic-diversity-of-microbial-populations-in-the-pilot-scale-biofilter-for-simultaneous-removal-of-ammonia-iron-and-manganese-from-real-groundwater
#4
Qingfeng Cheng, Lichao Nengzi, Linlin Bao, Yang Huang, Shengyu Liu, Xiuwen Cheng, Bo Li, Jie Zhang
A pilot-scale biofilter treating real groundwater was developed in this study, which showed that ammonia, iron and manganese were mainly removed at 0.4, 0.4 and 0.8 m of the filter bed, respectively, and the corresponding removal efficiencies were 90.82%, 95.48% and 95.90% in steady phase, respectively. The variation of microbial populations in the biofilter during start-up process was also investigated using high-throughput pyrosequencing (HTP). Results indicated that the main functional microbes for ammonia, iron and manganese removal were Nitrosomonas, Crenothrix and Crenothrix, respectively, which was mainly distributed at 0...
May 13, 2017: Chemosphere
https://www.readbyqxmd.com/read/28520754/effects-of-milk-product-intake-on-thigh-muscle-strength-and-nfkb-gene-methylation-during-home-based-interval-walking-training-in-older-women-a-randomized-controlled-pilot-study
#5
Shizue Masuki, Kensei Nishida, Shigenari Hashimoto, Mayuko Morikawa, Satoshi Takasugi, Masashi Nagata, Shun'ichiro Taniguchi, Kazuhito Rokutan, Hiroshi Nose
BACKGROUND: Muscle atrophy with aging is closely associated with chronic systemic inflammation and lifestyle-related diseases. In the present study, we assessed whether post-exercise milk product intake during 5-month interval walking training (IWT) enhanced the increase in thigh muscle strength and ameliorated susceptibility to inflammation in older women. METHODS: Subjects [n = 37, 66±5 (standard deviation) yrs] who had been performing IWT for >6 months participated in this study...
2017: PloS One
https://www.readbyqxmd.com/read/28517029/carbon-driven-enrichment-of-the-crucial-nitrate-reducing-bacteria-in-limed-peat-soil-microcosms
#6
Ying Zhu, Xiaoyuan Zhang, Xiaogang Wu, Guanzhou Chen, Lars R Bakken, Liping Zhao, Åsa Frostegård, Xiaojun Zhang
Bacteria of Dechloromonas were recognized as potential functional important denitrifiers in a long term shell sand amended peat soil. Different microcosms in a solid matrix and slurry systems with the addition of carbon and nitrogen sources, e.g., clover leaves, glutamate, and nitrate, were established. The bacterial community structures were analyzed by pyrosequencing of the 16S rRNA gene to select the conditions for enriching bacteria of Dechloromonas. The results showed that a relatively even bacterial community in the initial soil shifted to communities dominated by a few types of nitrate reducing bacteria after the incubation, which strongly responded to the carbon substrates addition and consumption...
May 18, 2017: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/28516344/defining-optimal-cutoff-value-of-mgmt-promoter-methylation-by-roc-analysis-for-clinical-setting-in-glioblastoma-patients
#7
Guoqiang Yuan, Liang Niu, Yinian Zhang, Xiaoqing Wang, Kejun Ma, Hang Yin, Junqiang Dai, Wangning Zhou, Yawen Pan
Resistance to temozolomide (TMZ) chemotherapy poses a significant challenge in the treatment of glioblastoma (GBM). Hypermethylation in O(6)-methylguanine-DNA methyltransferase (MGMT) promoter is thought to play a critical role in this resistance. Pyrosequencing (PSQ) has been shown to be accurate and robust for MGMT promoter methylation testing. The unresolved issue is the determination of a cut-off value for dichotomization of quantitative MGMT PSQ results into "MGMT methylated" and "MGMT unmethylated" patient subgroups as a basis for further treatment decisions...
May 17, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28514767/glutathione-peroxidase-7-suppresses-cancer-cell-growth-and-is-hypermethylated-in-gastric-cancer
#8
Zheng Chen, Tianling Hu, Shoumin Zhu, Kenichi Mukaisho, Wael El-Rifai, Dun-Fa Peng
Gastric cancer (GC) is one of the most common cancers in the world, and remains the third leading cause of cancer-related deaths worldwide. Glutathione peroxidase 7 (GPX7) is a member of GPX family which is downregulated in some cancer types. In this study, we investigated the expression, regulation, and molecular function of GPX7 in gastric cancer using 2D and 3D in vitro models and de-identified human tissue samples. Quantitative real-time RT-PCR, immunofluorescence, Western blot, 3D organotypic cultures, and pyrosequencing assays were used...
April 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28510800/structural-modulation-of-gut-microbiota-in-bama-minipigs-in-response-to-treatment-with-a-growth-promoting-agent-salbutamol
#9
Chenyang Lu, Jun Zhou, Yanyan Li, Dijun Zhang, Zuzhong Wang, Ye Li, Lingzhi Cheong, Chundan Zhang, Xiurong Su
Even though salbutamol (SAL) had remarkable effects on the enhancement of growth rate and carcass composition in different livestock species such as cattle, pigs, sheep and poultry, it was banned as a growth promoter because of its adverse effects on health. However, the specific mechanism by which salbutamol enhances growth efficiency remains unknown. In this study, Bama pigs were randomly allocated to receive salbutamol (5 mg/kg) for 30 or 60 days and were compared with untreated pigs. Pigs treated with salbutamol demonstrated enhanced growth rates and carcass composition; however, they showed deterioration in blood biochemical indices and organ development...
May 16, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28502968/prokaryotic-communities-at-different-depths-between-soils-with-and-without-tomato-bacterial-wilt-but-pathogen-present-in-a-single-greenhouse
#10
Chol Gyu Lee, Toshiya Iida, Yasuhiro Inoue, Yasunori Muramoto, Hideki Watanabe, Kazuhiro Nakaho, Moriya Ohkuma
The characterization of microbial communities that promote or suppress soil-borne pathogens is important for controlling plant diseases. We compared prokaryotic communities in soil with or without the signs of tomato bacterial wilt caused by Ralstonia solanacearum. Soil samples were collected from a greenhouse at two different depths because this pathogen is present in deep soil. We used samples from sites in which we detected phcA, a key gene regulating R. solanacearum pathogenicity. The pyrosequencing of prokaryotic 16S rRNA sequences in four soil samples without disease symptoms but with phcA and in two soil samples with disease symptoms indicated that community richness was not significantly different between these two soils; however, microbial diversity in the lower soil layer was higher in soil samples without disease symptoms but with phcA...
May 13, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28502757/the-placental-imprinted-dlk1-dio3-domain-a-new-link-to-pre-and-postnatal-growth-in-humans
#11
Anna Prats-Puig, Gemma Carreras-Badosa, Judit Bassols, Patricia Cavelier, Agnés Magret, Cristina Sabench, Francis de Zegher, Lourdes Ibáñez, Robert Feil, Abel López-Bermejo
BACKGROUND: The developmentally important DLK1-DIO3 imprinted domain on human chromosome 14 is regulated by two differentially methylated regions(DMRs), the IG-DMR and the MEG3 DMR. OBJECTIVES: The aim was to determine the natural variation in DNA methylation at these DMRs in human placentas, and to determine its link to gene expression levels at the domain. Second, to explore whether the domain's methylation and gene expression correlate with pre- and early-postnatal growth of the conceptus...
May 11, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28501592/endoscopic-and-molecular-characterization-of-colorectal-sessile-serrated-adenoma-polyps-with-cytological-dysplasia
#12
Yoshihito Tanaka, Hiro-O Yamano, Eiichiro Yamamoto, Hiro-O Matushita, Hironori Aoki, Kenjiro Yoshikawa, Ryo Takagi, Eiji Harada, Michiko Nakaoka, Yuko Yoshida, Makoto Eizuka, Tamotsu Sugai, Hiromu Suzuki, Hiroshi Nakase
BACKGROUND AND AIMS: Sessile serrated adenoma/polyps (SSA/Ps), which are precursor lesions of colorectal cancer (CRC) with BRAF mutation and the CpG island methylator phenotype (CIMP), develop cytological dysplasia (CD) during the progression of colorectal tumorigenesis. In the present study, we aimed to clarify the endoscopic and molecular signatures of SSA/Ps, with and without CD. METHODS: A series of 208 serrated lesions, including 41 hyperplastic polyps (HPs), 90 SSA/Ps, 33 SSA/Ps with CD and 44 traditional serrated adenomas (TSAs), were observed and resected using magnifying endoscopy...
May 10, 2017: Gastrointestinal Endoscopy
https://www.readbyqxmd.com/read/28500655/discovery-and-validation-of-candidate-host-dna-methylation-markers-for-detection-of-cervical-precancer-and-cancer
#13
Megan A Clarke, Patricia Luhn, Julia C Gage, Clara Bodelon, S Terence Dunn, Joan Walker, Rosemary Zuna, Stephen Hewitt, J Keith Killian, Liying Yan, Andrew Miller, Mark Schiffman, Nicolas Wentzensen
Human papillomavirus (HPV) testing has been recently introduced as an alternative to cytology for cervical cancer screening. However, since most HPV infections clear without causing clinically relevant lesions, additional triage tests are required to identify women who are at high risk of developing cancer. We performed DNA methylation profiling on formalin-fixed, paraffin-embedded tissue specimens from women with benign HPV16 infection and histologically confirmed cervical intraepithelial neoplasia grade 3 (CIN3), and cancer using a bead-based microarray covering 1,500 CpG sites in over 800 genes...
May 13, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28498804/increased-s100a15-expression-and-decreased-dna-methylation-of-its-gene-promoter-are-involved-in-high-metastasis-potential-and-poor-outcome-of-lung-adenocarcinoma
#14
Yung-Che Chen, Meng-Chih Lin, Chang-Chun Hsiao, Yi-Xin Zheng, Kuang-Den Chen, Ming-Tse Sung, Chung-Jen Chen, Ting-Ya Wang, Yong-Yong Lin, Huang-Chih Chang, Yu-Mu Chen, Jen-Chieh Chang
PURPOSE: This study aims to determine the functional role of S100A15 and its promoter DNA methylation patterns in lung cancer progression. EXPERIMENTAL DESIGN: We analyzed 178 formalin-fixed paraffin embedded specimens from lung cancer patients, including 24 early stage and 91 advanced stage adenocarcinoma. S100A15 protein expression was evaluated by immunohistochemistry stain, and its DNA methylation levels were measured by pyrosequencing. RESULTS: S100A15 nuclear staining was increased in lung adenocarcinoma patients with distant metastasis versus those without distant metastasis...
April 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28498466/elevated-slc26a4-gene-promoter-methylation-is-associated-with-the-risk-of-presbycusis-in-men
#15
Jin Xu, Jiachen Zheng, Wanjing Shen, Lili Ma, Ming Zhao, Xubo Wang, Jiyuan Tang, Jihong Yan, Zhenhua Wu, Zuquan Zou, Shizhong Bu, Yang Xi
Presbycusis affects approximately one-third of people over the age of 65 and is a worldwide health problem. In the current study, whether the methylation level of solute carrier family 26 member 4 (SLC26A4) predicted an increased risk of presbycusis was investigated. Peripheral blood samples from 102 patients with presbycusis and 104 controls were collected, and the methylation of the CpG sites of SLC26A4 was measured by applying pyrosequencing technology combined with sodium bisulfate DNA conversion chemistry...
May 10, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28496167/effect-of-trichoderma-harzianum-on-maize-rhizosphere-microbiome-and-biocontrol-of-fusarium-stalk-rot
#16
Kandasamy Saravanakumar, Yaqian Li, Chuanjin Yu, Qiang-Qiang Wang, Meng Wang, Jianan Sun, Jin-Xin Gao, Jie Chen
Fusarium stalk rot (FSR) caused by Fusarium graminearum (FG) significantly affects the productivity of maize grain crops. Application of agrochemicals to control the disease is harmful to environment. In this regard, use of biocontrol agent (BCA) is an alternative to agrochemicals. Although Trichoderma species are known as BCA, the selection of host-pathogen specific Trichoderma is essential for the successful field application. Hence, we screened a total of 100 Trichoderma isolates against FG, selected Trichoderma harzianum (CCTCC-RW0024) for greenhouse experiments and studied its effect on changes of maize rhizosphere microbiome and biocontrol of FSR...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28494084/the-use-of-high-throughput-dna-sequence-analysis-to-assess-the-endophytic-microbiome-of-date-palm-roots-grown-under-different-levels-of-salt-stress
#17
Mahmoud W Yaish, Ibtisam Al-Harrasi, Aliya S Alansari, Rashid Al-Yahyai, Bernard R Glick
Date palms are able to grow under diverse abiotic stress conditions including in saline soils, where microbial communities may be help in the plant's salinity tolerance. These communities able to produce specific growth promoting substances can enhance date palm growth in a saline environment. However, these communities are poorly defined. In the work reported here, the date palm endophytic bacterial and fungal communities were identified using the pyrosequencing method, and the microbial differential abundance in the root upon exposure to salinity stress was estimated...
September 2016: International Microbiology: the Official Journal of the Spanish Society for Microbiology
https://www.readbyqxmd.com/read/28493414/investigating-niche-partitioning-of-ectomycorrhizal-fungi-in-specialized-rooting-zones-of-the-monodominant-leguminous-tree-dicymbe-corymbosa
#18
Matthew E Smith, Terry W Henkel, Gwendolyn C Williams, M Catherine Aime, Alexander K Fremier, Rytas Vilgalys
Temperate ectomycorrhizal (ECM) fungi show segregation whereby some species dominate in organic layers and others favor mineral soils. Weak layering in tropical soils is hypothesized to decrease niche space and therefore reduce the diversity of ectomycorrhizal fungi. The Neotropical ECM tree Dicymbe corymbosa forms monodominant stands and has a distinct physiognomy with vertical crown development, adventitious roots and massive root mounds, leading to multi-stemmed trees with spatially segregated rooting environments: aerial litter caches, aerial decayed wood, organic root mounds and mineral soil...
May 11, 2017: New Phytologist
https://www.readbyqxmd.com/read/28489894/analysis-of-global-dna-methylation-changes-in-primary-human-fibroblasts-in-the-early-phase-following-x-ray-irradiation
#19
Anna Maierhofer, Julia Flunkert, Marcus Dittrich, Tobias Müller, Detlev Schindler, Indrajit Nanda, Thomas Haaf
Epigenetic alterations may contribute to the generation of cancer cells in a multi-step process of tumorigenesis following irradiation of normal body cells. Primary human fibroblasts with intact cell cycle checkpoints were used as a model to test whether X-ray irradiation with 2 and 4 Gray induces direct epigenetic effects (within the first cell cycle) in the exposed cells. ELISA-based fluorometric assays were consistent with slightly reduced global DNA methylation and hydroxymethylation, however the observed between-group differences were usually not significant...
2017: PloS One
https://www.readbyqxmd.com/read/28489329/differential-responses-of-soil-bacteria-fungi-archaea-and-protists-to-plant-species-richness-and-plant-functional-group-identity
#20
Sigrid Dassen, Roeland Cortois, Henk Martens, Mattias de Hollander, George A Kowalchuk, Wim H van der Putten, Gerlinde B De Deyn
Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454-pyrosequencing to analyse the soil microbial community composition in a long-term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1-60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil...
May 10, 2017: Molecular Ecology
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