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https://www.readbyqxmd.com/read/28432442/smokeless-tobacco-products-harbor-diverse-bacterial-microbiota-that-differ-across-products-and-brands
#1
Eoghan M Smyth, Prachi Kulkarni, Emma Claye, Stephen Stanfill, Robert Tyx, Cynthia Maddox, Emmanuel F Mongodin, Amy R Sapkota
Smokeless tobacco products contain numerous chemical compounds, including known human carcinogens. Other smokeless tobacco constituents, including bacteria, may also contribute to adverse health effects among smokeless tobacco users. However, there is a lack of data regarding the microbial constituents of smokeless tobacco. Our goal was to characterize the bacterial microbiota of different smokeless tobacco products and evaluate differences across product types and brands. DNA was extracted from 15 brands of smokeless tobacco products (including dry snuff, moist snuff, snus, and Swedish snus) and 6 handmade products (e...
April 22, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28427571/targeted-deep-sequencing-reveals-high-diversity-and-variable-dominance-of-bloom-forming-cyanobacteria-in-eutrophic-lakes
#2
Yongguang Jiang, Peng Xiao, Yang Liu, Jiangxin Wang, Renhui Li
Cyanobacterial blooms in eutrophic lakes are severe environmental problems worldwide. To characterize the spatiotemporal heterogeneity of cyanobacterial blooms, a high-throughput method is necessary for the specific detection of cyanobacteria. In this study, the cyanobacterial composition of three eutrophic waters in China (Taihu Lake, Dongqian Lake, and Dongzhen Reservoir) was determined by pyrosequencing the cpcBA intergenic spacer (cpcBA-IGS) of cyanobacteria. A total of 2585 OTUs were obtained from the normalized cpcBA-IGS sequence dataset at a distance of 0...
April 2017: Harmful Algae
https://www.readbyqxmd.com/read/28424066/short-term-exposure-to-pm2-5-and-vanadium-and-changes-in-asthma-gene-dna-methylation-and-lung-function-decrements-among-urban-children
#3
Kyung Hwa Jung, David Torrone, Stephanie Lovinsky-Desir, Matthew Perzanowski, Joshua Bautista, Jacqueline R Jezioro, Lori Hoepner, Jamie Ross, Frederica P Perera, Steven N Chillrud, Rachel L Miller
BACKGROUND: Both short and long-term exposure to traffic-related air pollutants have been associated with asthma and reduced lung function. We hypothesized that short-term indoor exposure to fine particulate matter <2.5 μm (PM2.5) and vanadium (V) would be associated with altered buccal cell DNA methylation of targeted asthma genes and decreased lung function among urban children in a nested subcohort of African American and Dominican children. METHODS: Six day integrated levels of air pollutants were measured from children's homes (age 9-14; n = 163), repeated 6 months later (n = 98)...
April 19, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28423869/protective-effects-of-bacillus-subtilis-against-salmonella-infection-in-the-microbiome-of-hy-line-brown-layers
#4
Ju Kyoung Oh, Edward Alain B Pajarillo, Jong Pyo Chae, In Ho Kim, D-K Kang
Objective: This study investigated the effects of Bacillus subtilis CSL2 administration before Salmonella challenge on the fecal microbiota and microbial functionality of Hy-line Brown (HLB) laying hens. Methods: Fecal samples were collected from control (CON), Salmonella-infected (SAL) and Salmonella-infected, probiotic-treated (PRO) groups before and after Salmonella challenge for microbiome analysis using 16S rRNA gene pyrosequencing. Results: Infection with Salmonella led to decreased microbial diversity in hen feces; diversity was recovered with Bacillus administration...
April 19, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28422737/generation-of-lung-cancer-cell-lines-harboring-egfr-t790m-mutation-by-crispr-cas9-mediated-genome-editing
#5
Mi-Young Park, Min Hee Jung, Eun Young Eo, Seokjoong Kim, Sang Hoon Lee, Yeon Joo Lee, Jong Sun Park, Young Jae Cho, Jin Haeng Chung, Cheol Hyeon Kim, Ho Il Yoon, Jae Ho Lee, Choon-Taek Lee
Tyrosine kinase inhibitors (TKIs) such as gefitinib and erlotinib are effective against lung adenocarcinomas harboring epidermal growth factor receptor (EGFR) mutations. However, cancer cells can develop resistance to these agents with prolonged exposure; in over 50% of cases, this is attributable to the EGFR T790M mutation. Moreover, additional resistance mutations can arise with the use of new drugs. Cancer cell lines with specific mutations can enable the study of resistance mechanisms. In this study, we introduced the EGFR T790M mutation into the PC9 human lung cancer cell line-which has a deletion in exon 19 of the EGFR gene-by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas)9-mediated genome editing...
March 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/28419547/perinatal-dna-methylation-at-cdkn2a-is-associated-with-offspring-bone-mass-findings-from-the-southampton-women-s-survey
#6
Elizabeth M Curtis, Robert Murray, Philip Titcombe, Eloïse Cook, Rebecca Clarke-Harris, Paula Costello, Emma Garratt, Joanna D Holbrook, Sheila Barton, Hazel Inskip, Keith M Godfrey, Christopher G Bell, Cyrus Cooper, Karen A Lillycrop, Nicholas C Harvey
Poor intrauterine and childhood growth has been linked with the risk of osteoporosis in later life, a relationship which may in part be mediated through altered epigenetic regulation of genes. We previously identified a region within the promoter of the long non-coding RNA ANRIL encoded by the CDKN2A locus, at which differential DNA methylation at birth showed correlations with offspring adiposity. Given the common lineage of adipocytes and osteoblasts, we investigated the relationship between perinatal CDKN2A methylation and bone mass at ages 4 and 6 years...
April 17, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28418084/epstein-barr-virus-infection-induces-genome-wide-de-novo-dna-methylation-in-non-neoplastic-gastric-epithelial-cells
#7
Keisuke Matsusaka, Sayaka Funata, Masaki Fukuyo, Yasuyuki Seto, Hiroyuki Aburatani, Masashi Fukayama, Atsushi Kaneda
Epstein-Barr virus (EBV)-positive gastric cancer (GC) shows a higher DNA methylation epigenotype. EBV infection can causally induce genome-wide aberrant DNA methylation, as previously demonstrated by in vitro infection experiments in the low-methylation GC cell line MKN7. However, whether EBV exerts DNA methylation remodelling properties in non-neoplastic epithelial cells remains unclear. We here performed post-infection time-series DNA methylation analyses using the immortalised normal gastric epithelial cell line, GES1...
April 18, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28417460/effect-of-high-fat-diet-and-growth-stage-on-the-diversity-and-composition-of-intestinal-microbiota-in-healthy-bovine-livestock
#8
Shengyin Jiao, Hui Cao, Yue Dai, Junhui Wu, Jia Lv, Renjia Du, Bei Han
BACKGROUND: This study aimed to investigate the composition of bacteria in the bovine rectum and their functions during growth, in relation to different diets. Fecal samples were collected from 6-, 12-, 18- and 24-month cattle fed high-fat diet, and healthy female parents fed regular-diet. Total DNA was amplified (V3-V4 of 16S rRNA) and submitted to barcode-DNA-pyrosequencing. Then, intestinal microbiota profiles and functions were analysed. RESULTS: A total of 114,512 OTUs were detected from the 1,802,243 sequences obtained...
April 18, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28417144/the-effect-of-reconstruction-works-on-planktonic-bacterial-diversity-of-a-unique-thermal-lake-revealed-by-cultivation-molecular-cloning-and-next-generation-sequencing
#9
Gergely Krett, Attila Szabó, Tamás Felföldi, Károly Márialigeti, Andrea K Borsodi
The aim of this study was to gain detailed information about the diversity of planktonic bacterial communities of a worldwide special peat bedded natural thermal spa lake, and to reveal the effect of a lake wall reconstruction work. To compare the efficiency of different methods used for analyzing bacterial diversity, cultivation, molecular cloning and pyrosequencing were applied simultaneously. Despite the almost unchanged physical-chemical parameters and cell count values of lake water, remarkable differences were observed in the planktonic bacterial community structures during and after the reconstruction by all applied microbiological approaches...
April 17, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28416970/dna-methylation-profiling-in-peripheral-lung-tissues-of-smokers-and-patients-with-copd
#10
Isaac K Sundar, Qiangzong Yin, Brian S Baier, Li Yan, Witold Mazur, Dongmei Li, Martha Susiarjo, Irfan Rahman
BACKGROUND: Epigenetics changes have been shown to be affected by cigarette smoking. Cigarette smoke (CS)-mediated DNA methylation can potentially affect several cellular and pathophysiological processes, acute exacerbations, and comorbidity in the lungs of patients with chronic obstructive pulmonary disease (COPD). We sought to determine whether genome-wide lung DNA methylation profiles of smokers and patients with COPD were significantly different from non-smokers. We isolated DNA from parenchymal lung tissues of patients including eight lifelong non-smokers, eight current smokers, and eight patients with COPD and analyzed the samples using Illumina's Infinium HumanMethylation450 BeadChip...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28415613/promoter-dna-methylation-analysis-reveals-a-combined-diagnosis-of-cpg-based-biomarker-for-prostate-cancer
#11
Yuanyuan Tang, Shusuan Jiang, Yinmin Gu, Weidong Li, Zengnan Mo, Yuanjie Huang, Tianyu Li, Yanling Hu
BACKGROUND: Prostate cancer (PCa) is the most common tumor in elderly men. However, the specificity and sensitivity of serum prostate-specific antigen levels in PCa diagnosis are controversial. This study aims to reveal a novel diagnosis biomarker in PCa. MATERIALS AND METHODS: The differential methylated CpG sites between 423 primary PCa and 39 adjacent samples from The Cancer Genome Atlas (TCGA) on Illumina HumanMethylation 450 platform were analyzed. The diagnostic methylation markers were mined using the Prediction Analysis of Microarrays package in Bioconductor...
March 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28410788/independence-of-gut-bacterial-content-and-neonatal-necrotizing-enterocolitis-severity
#12
Lauren K Barron, Barbara B Warner, Phillip I Tarr, William D Shannon, Elena Deych, Brad W Warner
INTRODUCTION: Necrotizing enterocolitis (NEC) is a common and devastating gastrointestinal disease of premature infants. NEC severity varies widely. Recent data have demonstrated a strong link between gut microbial dysbiosis and development of NEC. We tested the hypothesis that alterations in the gut microbiome at the time of diagnosis predict the severity of NEC. METHODS: We used prospectively collected fecal samples from very low birth weight infants who developed NEC, stratifying by NEC severity...
April 5, 2017: Journal of Pediatric Surgery
https://www.readbyqxmd.com/read/28410402/unexpected-associated-microalgal-diversity-in-the-lichen-ramalina-farinacea-is-uncovered-by-pyrosequencing-analyses
#13
Patricia Moya, Arántzazu Molins, Fernando Martínez-Alberola, Lucia Muggia, Eva Barreno
The current literature reveals that the intrathalline coexistence of multiple microalgal taxa in lichens is more common than previously thought, and additional complexity is supported by the coexistence of bacteria and basidiomycete yeasts in lichen thalli. This replaces the old paradigm that lichen symbiosis occurs between a fungus and a single photobiont. The lichen Ramalina farinacea has proven to be a suitable model to study the multiplicity of microalgae in lichen thalli due to the constant coexistence of Trebouxia sp...
2017: PloS One
https://www.readbyqxmd.com/read/28407475/fungal-endophytes-of-wild-and-hybrid-vitis-leaves-and-their-potential-for-vineyard-biocontrol
#14
Gavin Kernaghan, Michael Mayerhofer, Amanda Griffin
Plants are colonized by diverse assemblages of fungal endophytes that have potential as biocontrol agents for a variety of crops, including grapevine. Although the diversity of symbionts can be very high in wild plants, the fungal endophytes of wild Vitis plants have not yet been investigated. We surveyed the fungal endophytes of six wild populations of Vitis riparia, as well as a cold tolerant, hybrid grapevine in five vineyards (one certified organic), using 454 pyrosequencing. We detected between 43 and 235 OTUs per sample, with the highest richness and diversity in the wild, the lowest in conventional vineyards, and intermediate levels in the organic vineyard...
April 13, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28407014/prevalence-of-macrolide-and-fluoroquinolone-resistance-mediating-mutations-in-mycoplasma-genitalium-in-five-cities-in-russia-and-estonia
#15
Elena Shipitsyna, Tatiana Rumyantseva, Daniel Golparian, Guzel Khayrullina, Amaya C Lagos, Inna Edelstein, Kai Joers, Jörgen S Jensen, Alevtina Savicheva, Natalia Rudneva, Larisa Sukhanova, Roman Kozlov, Alexander Guschin, Magnus Unemo
BACKGROUND AND OBJECTIVE: Resistance in the sexually transmitted bacterium Mycoplasma genitalium to all recommended therapeutic antimicrobials have rapidly emerged. However, to date, internationally reported resistance surveillance data for M. genitalium strains circulating in Eastern Europe are entirely lacking. The aim of this study was to estimate the prevalence of macrolide and fluoroquinolone resistance-associated mutations in M. genitalium in four cities in Russia and one in Estonia, 2013-2016...
2017: PloS One
https://www.readbyqxmd.com/read/28406998/structure-and-dynamics-of-the-gut-bacterial-microbiota-of-the-bark-beetle-dendroctonus-rhizophagus-curculionidae-scolytinae-across-their-life-stages
#16
Carlos Iván Briones-Roblero, Juan Alfredo Hernández-García, Roman Gonzalez-Escobedo, L Viridiana Soto-Robles, Flor N Rivera-Orduña, Gerardo Zúñiga
Bark beetles play an important role as agents of natural renovation and regeneration in coniferous forests. Several studies have documented the metabolic capacity of bacteria associated with the gut, body surface, and oral secretions of these insects; however, little is known about how the bacterial community structure changes during the life cycle of the beetles. This study represents the first comprehensive analysis of the bacterial community of the gut of the bark beetle D. rhizophagus during the insect's life cycle using 454 pyrosequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28406159/sensitivity-and-accuracy-of-high-throughput-metabarcoding-methods-for-early-detection-of-invasive-fish-species
#17
Chelsea Hatzenbuhler, John R Kelly, John Martinson, Sara Okum, Erik Pilgrim
High-throughput DNA metabarcoding has gained recognition as a potentially powerful tool for biomonitoring, including early detection of aquatic invasive species (AIS). DNA based techniques are advancing, but our understanding of the limits to detection for metabarcoding complex samples is inadequate. For detecting AIS at an early stage of invasion when the species is rare, accuracy at low detection limits is key. To evaluate the utility of metabarcoding in future fish community monitoring programs, we conducted several experiments to determine the sensitivity and accuracy of routine metabarcoding methods...
April 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28406068/clinical-and-hematological-relevance-of-jak2-v617f-and-calr-mutations-in-bcr-abl-negative-et-patients
#18
N Limsuwanachot, B Rerkamnuaychoke, S Chuncharunee, T Pauwilai, R Singdong, P Rujirachaivej, T Chareonsirisuthigul, T Siriboonpiputtana
BACKGROUND: Classical BCR-ABL1-negative myeloproliferative neoplasms (MPNs) including polycythemia vera, essential thrombocythemia (ET), and primary myelofibrosis frequently harbor JAK2, MPL, and CALR somatic mutations. METHODS: AS-PCR for JAK2 V617F, pyrosequencing for MPL W515L/K, and PCR-fragment analysis for CALR exon 9 mutations were established to analyze genomic DNA isolated from peripheral blood samples of 58 newly diagnosed ET patients in Thailand. RESULTS: JAK2 V617F was detected in 41 patients (71%) and CALR exon 9 mutation was positive in eight patients (14%), whereas no mutation of MPL W515L/K was observed in this study...
April 13, 2017: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/28404884/dfna5-promoter-methylation-a-marker-for-breast-tumorigenesis
#19
Lieselot Croes, Ken Op de Beeck, Patrick Pauwels, Wim Vanden Berghe, Marc Peeters, Erik Fransen, Guy Van Camp
BACKGROUND: Identification of methylation markers that are sensitive and specific for breast cancer may improve early detection. We hypothesize that DFNA5 promoter methylation can be a valuable epigenetic biomarker, based upon strong indications for its role as tumor suppressor gene and its function in regulated cell death. RESULTS: Statistically different levels of methylation were seen, with always very low levels in healthy breast reduction samples, very high levels in part of the adenocarcinoma samples and slightly increased levels in part of the normal tissue samples adjacent the tumor...
March 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28403884/idh1-r132c-mutation-is-detected-in-clear-cell-hepatocellular-carcinoma-by-pyrosequencing
#20
Jung Hee Lee, Dong Hoon Shin, Won Young Park, Nari Shin, Ahrong Kim, Hyun Jung Lee, Young Keum Kim, Kyung Un Choi, Jee Yeon Kim, Young Il Yang, Chang Hun Lee, Mee Young Sol
BACKGROUND: Isocitrate dehydrogenase 1 (IDH1) mutation is common in low-grade glioma (approximately 80%) and acute myeloid leukemia (approximately 10%). Other than brain tumor or hematologic malignancies, intrahepatic cholangiocarcinoma (iCC) is a well-known solid tumor with IDH1 mutation (6.8-20%). Histologically, poor differentiation and clear cell change are associated with IDH1 mutation in iCC. Since hepatocellular carcinoma (HCC) shares histologic features with iCC, some specific subtypes of HCC might show a higher IDH1 mutation rate than reported before (0...
April 12, 2017: World Journal of Surgical Oncology
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