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https://www.readbyqxmd.com/read/28337413/draft-genome-sequence-of-thermoanaerobacterium-sp-strain-psu-2-isolated-from-thermophilic-hydrogen-producing-reactor
#1
Sompong O-Thong, Peerawat Khongkliang, Chonticha Mamimin, Apinya Singkhala, Poonsuk Prasertsan, Nils-Kåre Birkeland
Thermoanaerobacterium sp. strain PSU-2 was isolated from thermophilic hydrogen producing reactor and subjected to draft genome sequencing on 454 pyrosequencing and annotated on RAST. The draft genome sequence of strain PSU-2 contains 2,552,497 bases with an estimated G + C content of 35.2%, 2555 CDS, 8 rRNAs and 57 tRNAs. The strain had a number of genes responsible for carbohydrates metabolic, amino acids and derivatives, and protein metabolism of 17.7%, 14.39% and 9.81%, respectively. Strain PSU-2 also had gene responsible for hydrogen biosynthesis as well as the genes related to Ni-Fe hydrogenase...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28336495/genetic-variation-and-epigenetic-modification-of-the-prodynorphin-gene-in-peripheral-blood-cells-in-alcoholism
#2
Claudio D'Addario, Klementy Shchetynsky, Mariangela Pucci, Carlo Cifani, Agneta Gunnar, Vladana Vukojević, Leonid Padyukov, Lars Terenius
Dynorphins are critically involved in the development, maintenance and relapse of alcoholism. Alcohol-induced changes in the prodynorphin gene expression may be influenced by both gene polymorphisms and epigenetic modifications. The present study of human alcoholics aims to evaluate DNA methylation patterns in the prodynorphin gene (PDYN) promoter and to identify single nucleotide polymorphisms (SNPs) associated with alcohol dependence and with altered DNA methylation. Genomic DNA was isolated from peripheral blood cells of alcoholics and healthy controls, and DNA methylation was studied in the PDYN promoter by bisulfite pyrosequencing...
March 20, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28335783/svr-rates-of-hcv-infected-population-under-peg-ifn-%C3%AE-r-treatment-in-northwest-china
#3
Yanhua Li, Jiuping Wang, Juan Wang, Yunfeng Xiao, Bin Xu, Hongwei Li, Liu Yang, Xiaoke Hao, Yueyun Ma
BACKGROUND: Chronic HCV Patients taking PEG-IFN-α/R from different ethnic groups have different probabilities of reaching a sustained viral response (SVR). There are many influence factors, such as HCV genotype, IL-28B single-nucleotide polymorphisms (SNP), Fibrosis 4 index (FIB-4), and aspartate aminotransferase-to-platelet ratio index (APRI) score. But the baseline factors in relation to treatment outcome was still not much clear. METHODS: We evaluated data from 231 chronic HCV patients with or without liver fibrosis and their antiviral efficacy after treatment with pegylated interferon plus ribavirin (PEG-IFN-α/R) for 24-48 weeks...
March 23, 2017: Virology Journal
https://www.readbyqxmd.com/read/28334663/microbial-communities-change-in-an-anaerobic-digestion-after-application-of-microbial-electrolysis-cells
#4
Beom Lee, Jun-Gyu Park, Won-Beom Shin, Dong-Jie Tian, Hang-Bae Jun
Microbial electrolysis cells (MECs) are being studied to improve the efficiency of anaerobic digesters and biogas production. In the present study, we investigated the effects of electrochemical reactions in AD-MEC (anaerobic digester combined with MECs) on changes in the microbial communities of bulk sludge through 454-pyrosequencing analysis, as well as the effect of these changes on anaerobic digestion. Methanobacterium beijingense and Methanobacterium petrolearium were the dominant archaeal species in AD, while Methanosarcina thermophila and Methanobacterium formicicum were dominant in AD-MEC at steady-state...
February 8, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28331950/how-do-elevated-co2-and-nitrogen-addition-affect-functional-microbial-community-involved-in-greenhouse-gas-flux-in-salt-marsh-system
#5
Seung-Hoon Lee, Patrick J Megonigal, Hojeong Kang
Salt marshes are unique ecosystem of which a microbial community is expected to be affected by global climate change. In this study, by using T-RFLP analysis, quantitative PCR, and pyrosequencing, we comprehensively analyzed the microbial community structure responding to elevated CO2 (eCO2) and N addition in a salt marsh ecosystem subjected to CO2 manipulation and N addition for about 3 years. We focused on the genes of microbes relevant to N-cycling (denitrification and nitrification), CH4-flux (methanogens and methanotrophs), and S-cycling (sulfate reduction) considering that they are key functional groups involved in the nutrient cycle of salt marsh system...
March 22, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28326064/contribution-of-ultra-deep-sequencing-in-the-clinical-diagnosis-of-a-new-fungal-pathogen-species-basidiobolus-meristosporus
#6
Emilie Sitterlé, Christophe Rodriguez, Roman Mounier, Julien Calderaro, Françoise Foulet, Michel Develoux, Jean-Michel Pawlotsky, Françoise Botterel
Some cases of fungal infection remained undiagnosed, especially when the pathogens are uncommon, require specific conditions for in vitro growth, or when several microbial species are present in the specimen. Ultra-Deep Sequencing (UDS) could be considered as a precise tool in the identification of involved pathogens in order to upgrade patient treatment. In this study, we report the implementation of UDS technology in medical laboratory during the follow-up of an atypical fungal infection case. Thanks to UDS technology, we document the first case of gastro-intestinal basidiobolomycosis (GIB) due to Basidiobolus meristosporus...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28320414/epidermal-growth-factor-receptor-and-epididymis-invasion-as-prognostic-biomarkers-in-clinical-stage-i-testicular-germ-cell-tumours
#7
Miguel F Sanmamed, E Esteban, E Uriol, R Zarate, M Capelan, C Muriel, G Crespo, J P Berros, P Pardo-Coto, Q Perez, C Alvarez-Fernández, P Jiménez Fonseca, M Luque, A Astudillo
BACKGROUND: Inguinal orchiectomy is curative in 70-80% of clinical stage I testicular germ cell tumours (CS I TGCT). The identification of patients who are at low risk of relapse is critical to avoid unnecessary treatment. The aim of this study is to explore EGFR, hMLH-1/hMSH-2 and microsatellite instability (MSI) as potential prognostic factors of recurrence in CS I TGCT. METHODS: Fifty-six CS I TGCT patients who underwent inguinal orchiectomy were included in this study...
March 20, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28320391/quantification-of-resistant-alleles-in-the-%C3%AE-tubulin-gene-of-field-strains-of-gastrointestinal-nematodes-and-their-relation-with-the-faecal-egg-count-reduction-test
#8
Myriam Esteban-Ballesteros, Francisco A Rojo-Vázquez, Philip J Skuce, Lynsey Melville, Camino González-Lanza, María Martínez-Valladares
BACKGROUND: Benzimidazole (BZ) resistance in gastrointestinal nematodes is associated with a single nucleotide polymorphism (SNP) at codons 167, 198 and 200 in the isotype 1 of beta-tubulin gene although in some species these SNPs have also been associated with resistance to macrocyclic lactones. In the present study we compared the levels of resistance in Teladorsagia circumcincta and Trichostrongylus colubriformis by means of the faecal egg reduction test (FECRT) and the percentage of resistant alleles obtained after pyrosequencing...
March 20, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28317363/-periodontal-inflammation-affects-the-mechanical-and-immune-barrier-functions-of-mice-gut
#9
Xie Meilian, Yu Ting, Zhuo Ying, Huang Xin, Xie Baoyi, Xuan Dongying, Zhang Jincai
OBJECTIVE: To explore the effects of periodontal inflammation on the functions of gut barrier (ecological barrier, mechanical barrier, and immune barrier) in mice. METHODS: Twenty male C57BL/6J mice were randomly divided into perio-dontitis (P) or control (C) groups. The P group was subjected under a 10-day ligation with Porphyromonas gingivalis to induce periodontitis, whereas the C group was ligated with sham. Maxillae were obtained to assess alveolar bone loss...
August 1, 2016: Hua Xi Kou Qiang Yi Xue za Zhi, Huaxi Kouqiang Yixue Zazhi, West China Journal of Stomatology
https://www.readbyqxmd.com/read/28306743/characterization-of-spatial-distribution-of-the-bacterial-community-in-the-south-sea-of-korea
#10
Ji-Hui Seo, Ilnam Kang, Seung-Jo Yang, Jang-Cheon Cho
In order to investigate the importance of spatial and environmental factors on the structure and diversity of bacterial communities, high-resolution 16S rRNA gene tag pyrosequencing was applied to bacterial communities in the littoral sea. Seawater samples were prepared from seven different stations in the South Sea of Korea, the marginal sea in the western Pacific Ocean, and were divided into three groups according to distances from the coastline. The majority of 19,860 sequences were affiliated with Alphaproteobacteria (58...
2017: PloS One
https://www.readbyqxmd.com/read/28302031/hif1a-is-overexpressed-in-medulloblastoma-and-its-inhibition-reduces-proliferation-and-increases-epas1-and-atg16l1-methylation
#11
Gustavo Alencastro Veiga Cruzeiro, Maristella Bergamo Dos Reis, Vanessa Silva Silveira, Régia Caroline Peixoto Lira, Carlos Gilberto Carlotti, Luciano Neder, Ricardo Santos Oliveira, José Andres Yunes, Silvia Regina Brandalise, Simone Aguiar, Agda Karina Eterovic, Luiz Gonzaga Tone, Carlos Alberto Scrideli, Elvis Terci Valera
BACKGROUND: Genetic and epigenetic modifications are closely related to tumor initiation and progression and can provide guidance for understanding tumor functioning, potentially leading to the discovery of new therapies. Studies have associated hypoxia-related genes to tumor progression and chemo/radioresistance in brain tumors. Information on the expression profile of hypoxia-related genes in pediatric medulloblastoma, although scarce, may reveal relevant information that could support treatment decisions...
March 15, 2017: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/28300071/hypomethylation-of-interleukin-6-il-6-gene-increases-the-risk-of-essential-hypertension-a-matched-case-control-study
#12
S-Q Mao, J-H Sun, T-L Gu, F-B Zhu, F-Y Yin, L-N Zhang
Essential hypertension (EH) is a chronic disease with clear epigenetic component. Inflammation and endothelial dysfunction have a great role in the development of persistent blood pressure elevation. The aim of this study was to explore an association between EH and DNA methylation in pro-inflammation cytokine gene interleukin-6 (IL-6) during the inflammatory process. We performed methylation analysis of peripheral blood DNA using bisulphite pyrosequencing technology between 96 EH patients and 96 age- and gender-matched healthy controls...
March 16, 2017: Journal of Human Hypertension
https://www.readbyqxmd.com/read/28298607/human-herpesvirus-6b-induces-hypomethylation-on-chromosome-17p13-3-correlating-with-increased-gene-expression-and-virus-integration
#13
Elin Engdahl, Nicky Dunn, Pitt Niehusmann, Sarah Wideman, Peter Wipfler, Albert J Becker, Tomas J Ekström, Malin Almgren, Anna Fogdell-Hahn
Human herpesvirus 6B (HHV-6B) is a neurotropic beta-herpesvirus that achieves latency by integrating its genome into host cell chromosomes. Several viruses can induce epigenetic modifications in their host cells, but no study has investigated the epigenetic modifications induced by HHV-6B. This study analyzed methylation with Illumina 450K array comparing HHV-6B infected and uninfected Molt-3 T cells three days post infection. Bisulfite pyrosequencing was used to validate Illumina results and investigate methylation over time in vitro Expression of genes was investigated using qPCR, and virus integration was investigated with PCR...
March 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28296930/seasonal-changes-in-the-digesta-adherent-rumen-bacterial-communities-of-dairy-cattle-grazing-pasture
#14
Samantha J Noel, Graeme T Attwood, Jasna Rakonjac, Christina D Moon, Garry C Waghorn, Peter H Janssen
The complex microbiota that resides within the rumen is responsible for the break-down of plant fibre. The bacteria that attach to ingested plant matter within the rumen are thought to be responsible for initial fibre degradation. Most studies examining the ecology of this important microbiome only offer a 'snapshot' in time. We monitored the diversity of rumen bacteria in four New Zealand dairy cows, grazing a rye-grass and clover pasture over five consecutive seasons, using high throughput pyrosequencing of bacterial 16S rRNA genes...
2017: PloS One
https://www.readbyqxmd.com/read/28293696/intestinal-microbial-community-dynamics-of-white-tailed-deer-odocoileus-virginianus-in-an-agroecosystem
#15
M Lisette Delgado, Pallavi Singh, Julie A Funk, Jennifer A Moore, Emily M Cannell, Jeannette Kanesfsky, Shannon D Manning, Kim T Scribner
The intestinal microbiota has important functions that contribute to host health. The compositional dynamics of microbial communities are affected by many factors, including diet and presence of pathogens. In contrast to humans and domestic mammals, the composition and seasonal dynamics of intestinal microbiota of wildlife species remain comparatively understudied. White-tailed deer (Odocoileus virginianus) is an ecologically and economically important wildlife species that inhabits agricultural ecosystems and is known to be a reservoir of enteric pathogens...
March 14, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28293326/line-1-is-preferentially-hypomethylated-within-adenomatous-polyps-in-the-presence-of-synchronous-colorectal-cancer
#16
Alice Chu Jiang, Lela Buckingham, William Barbanera, Amoah Yeboah Korang, Faraz Bishesari, Joshua Melson
BACKGROUND: Conventional tubular adenomas are frequently detected in patients undergoing average risk screening colonoscopy and are over-represented in patients who will develop colorectal cancer (CRC). Whether features of adenomas could serve as predictors of synchronous CRC is not known. Here, we investigate whether global methylation markers, including LINE-1, differ within adenomas in patients with and without synchronous CRC. METHODS: Colorectal tubular/tubulovillous adenomatous polyps in the absence (P group, n = 45) and in the presence of synchronous CRC (PC group, n = 32) were identified...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28289585/the-mefv-gene-pathogenic-variants-and-phenotype-genotype-correlation-in-children-with-familial-mediterranean-fever-in-the-%C3%A3-anakkale-population
#17
F Battal, F Silan, N Topaloğlu, H Aylanç, Ş Yıldırım, F Köksal Binnetoğlu, M Tekin, N Kaymaz, O Ozdemir
The aim of the current study was to determine the frequency of the Mediterranean fever (MEFV) gene pathogenic variants in 60 children diagnosed with familial Mediterranean fever (FMF) and to compare the phenotype-genotype correlation. Genomic DNA was isolated by the spin-column method from peripheral blood samples (collected in vacutainers containing EDTA) and buccal smears. The MEFV gene profiles for the current FMF cohort were genotyped by pyrosequencing and direct Sanger sequencing techniques for the target pathogenic variants...
December 1, 2016: Balkan Journal of Medical Genetics: BJMG
https://www.readbyqxmd.com/read/28289404/different-types-of-diatom-derived-extracellular-polymeric-substances-drive-changes-in-heterotrophic-bacterial-communities-from-intertidal-sediments
#18
Julio Bohórquez, Terry J McGenity, Sokratis Papaspyrou, Emilio García-Robledo, Alfonso Corzo, Graham J C Underwood
Intertidal areas support extensive diatom-rich biofilms. Such microphytobenthic (MPB) diatoms exude large quantities of extracellular polymeric substances (EPS) comprising polysaccharides, glycoproteins and other biopolymers, which represent a substantial carbon pool. However, degradation rates of different EPS components, and how they shape heterotrophic communities in sediments, are not well understood. An aerobic mudflat-sediment slurry experiment was performed in the dark with two different EPS carbon sources from a diatom-dominated biofilm: colloidal EPS (cEPS) and the more complex hot-bicarbonate-extracted EPS...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28285217/transformation-of-chlorpyrifos-in-integrated-recirculating-constructed-wetlands-ircws-as-revealed-by-compound-specific-stable-isotope-csia-and-microbial-community-structure-analysis
#19
Xiaoyan Tang, Yang Yang, Wenda Huang, Murray B McBride, Jingjing Guo, Ran Tao, Yunv Dai
Carbon isotope analysis and 454 pyrosequencing methods were used to investigate in situ biodegradation of chlorpyrifos during its transport through three model integrated recirculating constructed wetlands (IRCWs). Results show that plant and Fe-impregnated biochar promoted degradation of chlorpyrifos and its metabolite 3,5,6-trichloro-2-pyridinol (TCP). Carbon isotope ratios in the IRCWs shifted to -31.24±0.58‰ (IRCW1, plant free), -26.82±0.60‰ (IRCW2, with plant) and -24.76±0.94‰ (IRCW3, with plant and Fe-biochar)...
February 20, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28284085/detection-of-turner-syndrome-using-x-chromosome-inactivation-specific-differentially-methylated-cpg-sites-a-pilot-study
#20
Qiang Zhang, Xiaohong Guo, Tian Tian, Teng Wang, Qiaoli Li, Lei Wang, Yun Liu, Qinghe Xing, Lin He, Xinzhi Zhao
BACKGROUND: Early diagnosis of Turner syndrome (TS) may improve preventive measures and treatment. X-chromosome inactivation specific differentially methylated CpG sites (XIDMSs) that are high methylated in inactive X chromosomes (Xi) and unmethylated in active X chromosomes (Xa) may be potential makers for TS detection. METHODS: The candidate XIDMSs were screened from 9 male and 12 female DNA samples with normal karyotypes using the Illumina 450k array and validated by bisulfite sequencing PCR and pyrosequencing assay...
March 8, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
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