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https://www.readbyqxmd.com/read/28214969/attached-and-suspended-denitrifier-communities-in-pristine-limestone-aquifers-harbor-high-fractions-of-potential-autotrophs-oxidizing-reduced-iron-and-sulfur-compounds
#1
M Herrmann, S Opitz, R Harzer, K U Totsche, K Küsel
Oxygen and nitrate availability as well as the presence of suitable organic or inorganic electron donors are strong drivers of denitrification; however, the factors influencing denitrifier abundance and community composition in pristine aquifers are not well understood. We explored the denitrifier community structure of suspended and attached groundwater microorganisms in two superimposed limestone aquifer assemblages with contrasting oxygen regime in the Hainich Critical Zone Exploratory (Germany). Attached communities were retrieved from freshly crushed parent rock material which had been exposed for colonization in two groundwater wells (12...
February 18, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28214441/enhanced-treatment-of-fischer-tropsch-f-t-wastewater-using-the-up-flow-anaerobic-sludge-blanket-coupled-with-bioelectrochemical-system-effect-of-electric-field
#2
Dexin Wang, Hongjun Han, Yuxing Han, Kun Li, Hao Zhu
The coupling of bioelectrochemical system (BES) with an up-flow anaerobic sludge blanket (UASB) was established for enhanced Fischer-Tropsch (F-T) wastewater treatment while the UASB (control group) was operated in parallel. The presence of electric field could offer system a more reductive micro-environment that lower the ORP values and maintain the appropriate pH range, resulting in the higher chemical oxygen demand (COD) removal efficiency and methane production for BES-UASB (86.8% and 2.31±0.1L/(L·d)) while those values in control group were 72...
February 7, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28213734/dehalococcoides-and-general-bacterial-ecology-of-differentially-trichloroethene-dechlorinating-flow-through-columns
#3
Babur S Mirza, Darwin L Sorensen, Daniel J McGlinn, R Ryan Dupont, Joan E McLean
The diversity of Dehalococcoides mccartyi (Dhc) and/or other organohalide respiring or associated microorganisms in parallel, partial, or complete trichloroethene (TCE) dehalogenating systems has not been well described. The composition of Dhc populations and the associated bacterial community that developed over 7.5 years in the top layer (0-10 cm) of eight TCE-fed columns were examined using pyrosequencing. Columns biostimulated with one of three carbon sources, along with non-stimulated controls, developed into complete (ethene production, whey amended), partial (cis-dichloroethene (DCE) and VC, an emulsified oil with nonionic surfactant), limited (<5 % cis-DCE and 95 % TCE, an emulsified oil), and non- (controls) TCE dehalogenating systems...
February 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28213546/environmental-surveillance-of-norovirus-genogroups-i-and-ii-for-sensitive-detection-of-epidemic-variants
#4
Shinobu Kazama, Takayuki Miura, Yoshifumi Masago, Yoshimitsu Konta, Kentaro Tohma, Takafumi Manaka, Xiaofang Liu, Daisuke Nakayama, Takashi Tanno, Mayuko Saito, Hitoshi Oshitani, Tatsuo Omura
Sewage samples have been investigated to study the level of noroviruses concentration in sewage or the genotypes of noroviruses circulating in human populations. However, the statistical relationship between the concentration of the virus and the number of infected individuals, and the clinical importance of genotypes or strains detected in sewage are unclear. In this study, we carried out both environmental and clinical surveillance of noroviruses for three years: 2013-2016. We performed cross-correlation analysis between the concentrations of norovirus GI or GII in sewage samples collected weekly and the number of gastroenteritis cases...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28212707/astrobiological-implications-of-dim-light-phototrophy-in-deep-sea-red-clays
#5
Anindita Das, Tanya Singh, P A LokaBharathi, Prashant K Dhakephalkar, Sweta Mallik, Pranav R Kshirsagar, N H Khadge, B Nagender Nath, Satadru Bhattacharya, Aditya Kumar Dagar, Prabhjot Kaur, Dwijesh Ray, Anil D Shukla, Christabelle E G Fernandes, Sheryl O Fernandes, Tresa Remya A Thomas, Mamatha S S, Babu Shashikant Mourya, Ram Murti Meena
Red clays of Central Indian Basin (CIB) under influence of trace of Rodriguez Triple Junction exhibited chemoautotrophy, low temperature hydrothermal alterations and photoautotrophic potential. Seamount flank TVBC-08, hosting such signatures revealed dominance of aerobic anoxygenic phototroph Erythrobacter, with 93% of total 454 pyrosequencing tags. Subsequently, enrichments for both aerobic (Erythrobacter) and anaerobic anoxygenic phototrophs (green and purple sulphur bacteria) under red and white LED light illumination, with average irradiance 30...
February 2017: Life Sciences in Space Research
https://www.readbyqxmd.com/read/28210249/feeding-a-high-concentration-diet-induces-unhealthy-alterations-in-the-composition-and-metabolism-of-ruminal-microbiota-and-host-response-in-a-goat-model
#6
Canfeng Hua, Jing Tian, Ping Tian, Rihua Cong, Yanwen Luo, Yali Geng, Shiyu Tao, Yingdong Ni, Ruqian Zhao
There is limited knowledge about the impact of long-term feeding a high-concentrate (HC) diet on rumen microbiota, metabolome, and host cell functions. In this study, a combination of mass spectrometry-based metabolomics techniques, 454 pyrosequencing of 16S rDNA genes, and RT-PCR was applied to evaluate the changes of ruminal microbiota composition, ruminal metabolites, and related genes expression in rumen epithelial cells of lactating goats received either a 35% concentrate diet or a 65% concentrate diet for 4 or 19 weeks, respectively...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28208156/oncogenic-role-of-pdk4-in-human-colon-cancer-cells
#7
D Leclerc, D N T Pham, N Lévesque, M Truongcao, W D Foulkes, C Sapienza, R Rozen
BACKGROUND: Cancer cells maintain high rates of glycolysis. Pyruvate dehydrogenase kinases (PDK) contribute to this phenomenon, which favours apoptosis resistance and cellular transformation. We previously reported upregulation of PDK4 in normal mucosa of colorectal cancer (CRC) patients compared with controls and in preneoplastic intestine of our mouse model. Decreased methylation of four consecutive PDK4 CpGs was observed in normal mucosa of patients. Although other members of the PDK family have been investigated for transformation potential, PDK4 has not been extensively studied...
February 16, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28207957/phylogenetic-relatedness-explains-highly-interconnected-and-nested-symbiotic-networks-of-woody-plants-and-arbuscular-mycorrhizal-fungi-in-a-chinese-subtropical-forest
#8
Liang Chen, Yong Zheng, Cheng Gao, Xiang-Cheng Mi, Ke-Ping Ma, Tesfaye Wubet, Liang-Dong Guo
Elucidating symbiotic relationships between arbuscular mycorrhizal fungi (AMF) and plants contributes to a better understanding of their reciprocally dependent co-existence and community assembly. However, the main drivers of plant and AMF community assembly remain unclear. In this study, we examined AMF communities from 166 root samples of 17 woody plant species from 10 quadrats in a Chinese subtropical forest using 454 pyrosequencing of 18S rRNA gene to describe symbiotic AMF-plant association. Our results show the woody plant-AMF networks to be highly interconnected and nested, but in anti-modular and anti-specialized manners...
February 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28202002/viral-e6-is-overexpressed-via-high-viral-load-in-invasive-cervical-cancer-with-episomal-hpv16
#9
Die Hong, Jia Liu, Ying Hu, Xiaonan Lu, Baohua Li, Yang Li, Dongxiao Hu, Weiguo Lu, Xing Xie, Xiaodong Cheng
BACKGROUND: The integration of HR-HPV genome into host DNA is regarded as a key step for the development of cervical cancer. However, HR-HPV genome indeed exists as episome except for integrant. It may be alternative mechanisms in episome-associated carcinogenesis, although, by which HPV 16 episome induces cervical carcinogenesis is unclear now. METHODS: Ninety-three invasive cervical cancer tissues with HPV16 positive were collected. Viral physical status was calculated from comparing E2 to E6-copies and detection of viral load was made with realtime-PCR using copy numbers of E6...
February 15, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28199908/dna-methylation-analysis-of-the-egr3-gene-in-patients-of-schizophrenia
#10
Tsung-Ming Hu, Shih-Hsin Hsu, Su-Min Tsai, Min-Chih Cheng
DNA methylation has been implicated in the pathogenesis of schizophrenia. EGR3 is considered as a potential candidate gene for schizophrenia. We conducted in vitro DNA methylation reaction, Lucia luciferase activity assay, and pyrosequencing assay to assess the DNA methylation of the EGR3 expression underlying the pathophysiology of schizophrenia. We found that DNA methylation of the putative EGR3 regulatory regions attenuated Lucia luciferase activity. There was no difference in the DNA methylation pattern of EGR3 between in 50 schizophrenic patients and 47 controls...
February 8, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/28199766/dysbiosis-of-oral-buccal-mucosa-microbiota-in-patients-with-oral-lichen-planus
#11
Yuan He, Diping Gong, Cong Shi, Fangyang Shao, Jiahao Shi, Jian Fei
OBJECTIVE: The bacterial community structure of buccal mucosa in patients with oral lichen planus was evaluated and compared with healthy control. SUBJECTS AND METHODS: Buccal scraping samples have been taken on 43 oral lichen planus patients (21 erosive and 22 non-erosive) and 21 mucosal healthy volunteers. The V3 hypervariable 16S rDNA region were amplified and sequenced by high-throughput 454 pyrosequencing. RESULTS: 94.26% of the total buccal bacteria were classified into 15 abundant genera...
February 15, 2017: Oral Diseases
https://www.readbyqxmd.com/read/28199741/melatonin-prevents-obesity-through-modulation-of-gut-microbiota-in-mice
#12
Pengfei Xu, Jialin Wang, Fan Hong, Sheng Wang, Xi Jin, Tingting Xue, Li Jia, Yonggong Zhai
Excess weight and obesity are severe public health threats worldwide. Recent evidence demonstrates that gut microbiota dysbiosis contributes to obesity and its comorbidities. The body weight-reducing and energy balancing effects of melatonin have been reported in several studies, but to date, no investigations toward examining whether the beneficial effects of melatonin are associated with gut microbiota have been carried out. In this study, we show that melatonin reduces body weight, liver steatosis, and low-grade inflammation as well as improving insulin resistance in high fat diet (HFD)-fed mice...
February 15, 2017: Journal of Pineal Research
https://www.readbyqxmd.com/read/28199330/comparison-of-bacterial-communities-from-lava-cave-microbial-mats-to-overlying-surface-soils-from-lava-beds-national-monument-usa
#13
Kathleen H Lavoie, Ara S Winter, Kaitlyn J H Read, Evan M Hughes, Michael N Spilde, Diana E Northup
Subsurface habitats harbor novel diversity that has received little attention until recently. Accessible subsurface habitats include lava caves around the world that often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. To investigate these differences, we analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soil overlying each cave...
2017: PloS One
https://www.readbyqxmd.com/read/28198450/identification-of-methylation-driven-differentially-expressed-stxbp6-as-a-novel-biomarker-in-lung-adenocarcinoma
#14
Govinda Lenka, Mong-Hsun Tsai, Hsin-Chieh Lin, Jen-Hao Hsiao, Yi-Ching Lee, Tzu-Pin Lu, Jang-Ming Lee, Chung-Ping Hsu, Liang-Chuan Lai, Eric Y Chuang
DNA methylation is an essential epigenetic marker associated with the silencing of gene expression. Although various genome-wide studies revealed aberrantly methylated gene targets as molecular biomarkers for early detection, the survival rate of lung cancer patients is still poor. In order to identify methylation-driven biomarkers, genome-wide changes in DNA methylation and differential expression in 32 pairs of lung adenocarcinoma and adjacent normal lung tissue in non-smoking women were examined. This concurrent analysis identified 21 negatively correlated probes (r ≤ -0...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28197796/bacterial-community-shift-for-monitoring-the-co-composting-of-oil-palm-empty-fruit-bunch-and-palm-oil-mill-effluent-anaerobic-sludge
#15
Mohd Huzairi Mohd Zainudin, Norhayati Ramli, Mohd Ali Hassan, Yoshihito Shirai, Kosuke Tashiro, Kenji Sakai, Yukihiro Tashiro
A recently developed rapid co-composting of oil palm empty fruit bunch (OPEFB) and palm oil mill effluent (POME) anaerobic sludge is beginning to attract attention from the palm oil industry in managing the disposal of these wastes. However, a deeper understanding of microbial diversity is required for the sustainable practice of the co-compositing process. In this study, an in-depth assessment of bacterial community succession at different stages of the pilot scale co-composting of OPEFB-POME anaerobic sludge was performed using 454-pyrosequencing, which was then correlated with the changes of physicochemical properties including temperature, oxygen level and moisture content...
February 14, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28197780/erratum-to-development-of-a-robust-and-sensitive-pyrosequencing-assay-for-the-detection-of-idh1-2-mutations-in-gliomas
#16
Hideyuki Arita, Yoshitaka Narita, Yuko Matsushita, Shintaro Fukushima, Akihiko Yoshida, Hirokazu Takami, Yasuji Miyakita, Makoto Ohno, Soichiro Shibui, Koichi Ichimura
No abstract text is available yet for this article.
February 14, 2017: Brain Tumor Pathology
https://www.readbyqxmd.com/read/28194743/comparison-of-microbial-communities-from-different-jinhua-ham-factories
#17
Qingfeng Ge, Yubin Gu, Wangang Zhang, Yongqi Yin, Hai Yu, Mangang Wu, Zhijun Wang, Guanghong Zhou
Microbes in different aged workshops play important roles in the flavor formation of Jinhua ham. However, microbial diversity, community structure and age related changes in workshops are poorly understood. The microbial community structure and diversity in Jinhua ham produced in factories that have 5, 15, and 30 years of history in processing hams were compared using the pyrosequencing technique. Results showed that 571,703 high-quality sequences were obtained and located in 242 genera belonging to 18 phyla...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28193703/methylation-in-the-matrix-metalloproteinase-2-gene-is-associated-with-cerebral-ischemic-stroke
#18
Hsiu-Fen Lin, Edward Hsi, Ling-Chun Huang, Yi-Chu Liao, Suh-Hang H Juo, Ruey-Tay Lin
Matrix metalloproteinase-2 (MMP-2) is involved in the pathophysiology of stroke. Previous studies have shown that MMP-2 activity is increased in stroke; however, evidence of epigenetic regulation of the MMP-2 in stroke is still limited. We examined methylation of the MMP-2 promoter in patients with ischemic stroke. This study included 298 patients with ischemic stroke and 258 age-matched and sex-matched controls. MMP-2 promoter methylation levels were measured by pyrosequencing at eight potential cytosine-guanine (CpG) sites...
February 13, 2017: Journal of Investigative Medicine: the Official Publication of the American Federation for Clinical Research
https://www.readbyqxmd.com/read/28193149/taqman-probes-as-blocking-agents-for-enriched-pcr-amplification-and-dna-melting-analysis-of-mutant-genes
#19
Irina V Botezatu, Irina O Panchuk, Anna M Stroganova, Anastasia I Senderovich, Valentina N Kondratova, Valery P Shelepov, Anatoly V Lichtenstein
Asymmetric PCR and DNA melting analysis with TaqMan probes applied for mutation detection is effectively used in clinical diagnostics. The method is simple, cost-effective, and carried out in a closed-tube format, minimizing time, labor, and risk of sample cross-contamination. Although DNA melting analysis is more sensitive than Sanger sequencing (mutation detection thresholds are ~5% and 15%-20%, respectively), it is less sensitive than more labor-intensive and expensive techniques such as pyrosequencing and droplet digital PCR...
February 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28191262/maternal-intake-of-methyl-group-donors-affects-dna-methylation-of-metabolic-genes-in-infants
#20
Sara Pauwels, Manosij Ghosh, Radu Corneliu Duca, Bram Bekaert, Kathleen Freson, Inge Huybrechts, Sabine A S Langie, Gudrun Koppen, Roland Devlieger, Lode Godderis
BACKGROUND: Maternal nutrition during pregnancy and infant nutrition in the early postnatal period (lactation) are critically involved in the development and health of the newborn infant. The Maternal Nutrition and Offspring's Epigenome (MANOE) study was set up to assess the effect of maternal methyl-group donor intake (choline, betaine, folate, methionine) on infant DNA methylation. Maternal intake of dietary methyl-group donors was assessed using a food-frequency questionnaire (FFQ)...
2017: Clinical Epigenetics
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