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Pyrosequencing

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https://www.readbyqxmd.com/read/28627648/characterization-of-a-blandm%C3%A2-1%C3%A2-harboring-plasmid-from-a-salmonella%C3%A2-enterica-clinical-isolate-in-china
#1
Jinwei Huang, Shanshan Deng, Jianmin Ren, Jianfei Tu, Meiping Ye, Minggui Wang
The plasmid-mediated transmission of antibiotic resistance genes has been reported to be involved in the development of antibiotic resistance in bacteria, and poses a serious threat for the success of bacterial infection treatment and human health worldwide. The present study used a 454 GS‑FLX pyrosequencing system to determine the ~140 kb nucleotide sequence of plasmid pHS36‑NDM, which was identified in a Salmonella Stanley isolate from the stool sample of an 11‑month‑old girl at Lishui Central Hospital, China, and which contains a New Delhi metallo‑β‑lactamase‑1 (NDM‑1) carbapenem resistance gene (blaNDM‑1)...
June 8, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28625654/line-1-hypomethylation-is-associated-to-specific-clinico-pathological-features-in-stage-i-non-small-cell-lung-cancer
#2
Andrea Imperatori, Nora Sahnane, Nicola Rotolo, Francesca Franzi, Elisa Nardecchia, Laura Libera, Chiara Romualdi, Maria Cattoni, Fausto Sessa, Lorenzo Dominioni, Daniela Furlan
OBJECTIVES: We hypothesize that selected genetic and/or epigenetic changes associated with advanced tumours may help identifying early non-small cell lung cancers (NSCLCs) that recur after resection. Among epigenetic changes, long interspersed nuclear element-1 (LINE-1) hypomethylation is seen early during carcinogenesis and may act in concert with genetic alterations to cancer progression. LINE-1 hypomethylation and gene mutations frequently involved in lung cancer, were analysed to evaluate their prognostic role in resected stage I NSCLC...
June 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28624728/nitrite-production-from-urine-for-sulfide-control-in-sewers
#3
Min Zheng, Zhiqiang Zuo, Yizhen Zhang, Yujia Cui, Qian Dong, Yanchen Liu, Xia Huang, Zhiguo Yuan
Most commonly used methods for sewer sulfide control involves dosing chemical agents to wastewater, which incurs high operational costs. Here, we propose and demonstrate a cost-effective and environmentally attractive approach to sewer sulfide control through urine separation and its subsequent conversion to nitrite prior to intermittent dosage to sewers. Urine collected from a male toilet urinal was fed to laboratory-scale sequencing batch reactors. The reactors stably converted roughly 50% of the nitrogen in urine to nitrite, with high abundance (at 17...
May 23, 2017: Water Research
https://www.readbyqxmd.com/read/28624699/toll-like-receptor-2-rs4696480-polymorphism-and-risk-of-oral-cancer-and-oral-potentially-malignant-disorder
#4
Camila de Barros Gallo, Xabier Marichalar-Mendia, Amaia Setien-Olarra, Amelia Acha-Sagredo, Naiara Garcia Bediaga, Maria Luisa Gainza-Cirauqui, Norberto Nobuo Sugaya, Jose Manuel Aguirre-Urizar
OBJECTIVES: The aim of this study was to identify the possible association between TLR polymorphisms and an increased risk of developing head and neck cancer, including oral (OSCC) and laryngeal squamous cell carcinoma (LSCC), and oral potentially malignant disorders, such as oral lichenoid disease (OLD), including oral lichen planus (OLP) and oral lichenoid lesions (OLL). DESIGN: This case-control study included 40 OSCC, 35 LSCC, 175 OLD (129 OLP and 46 OLL) patients and 89 healthy controls, all of them from the Basque Country, Spain...
June 6, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28623975/mitochondrial-dna-content-and-methylation-in-fetal-cord-blood-of-pregnancies-with-placental-insufficiency
#5
Chiara Novielli, Chiara Mandò, Silvia Tabano, Gaia M Anelli, Laura Fontana, Patrizio Antonazzo, Monica Miozzo, Irene Cetin
INTRODUCTION: Intrauterine growth restriction (IUGR) and preeclampsia (PE) are pregnancy disorders characterized by placental insufficiency with oxygen/nutrient restriction and oxidative stress, all influencing mitochondria functionality and number. Moreover, IUGR and PE fetuses are predisposed to diseases later in life, and this might occur through epigenetic alterations. Here we analyze content and methylation of mitochondrial DNA (mtDNA), for the first time in IUGR and PE singleton fetuses, to identify possible alterations in mtDNA levels and/or epigenetic control of mitochondrial loci relevant to replication (D-loop) and functionality (mt-TF/RNR1: protein synthesis, mt-CO1: respiratory chain complex)...
July 2017: Placenta
https://www.readbyqxmd.com/read/28623792/variations-in-microbial-community-and-ciprofloxacin-removal-in-rhizospheric-soils-between-two-cultivars-of-brassica-parachinensis-l
#6
Xian-Pei Huang, Ce-Hui Mo, Jiao Yu, Hai-Ming Zhao, Can Meng, Yan-Wen Li, Hui Li, Quan-Ying Cai, Ming-Hung Wong
Ciprofloxacin (CIP) is one of most used quinolone antibiotics detected frequently in agricultural soils and vegetables. In the present study, variations in microbial community and CIP removal in rhizospheric soils between two cultivars of Brassica parachinensis L. that accumulate higher and lower CIP (Sijiu and Cutai, respectively) were investigated under CIP stress (0mg/kg in CK, 2.94mg/kg in T1, and 67.11mg/kg in T2). The removal rates of CIP in rhizospheric soils of cultivar Sijiu were higher than those of cultivar Cutai, with a significant difference in T2 (48...
June 14, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28620196/integration-of-dna-methylation-and-gene-transcription-across-nineteen-cell-types-reveals-cell-type-specific-and-genomic-region-dependent-regulatory-patterns
#7
Binhua Tang, Yufan Zhou, Chiou-Miin Wang, Tim H-M Huang, Victor X Jin
Despite numerous studies done on understanding the role of DNA methylation, limited work has focused on systems integration of cell type-specific interplay between DNA methylation and gene transcription. Through a genome-wide analysis of DNA methylation across 19 cell types with T-47D as reference, we identified 106,252 cell type-specific differentially-methylated CpGs categorized into 7,537 differentially (46.6% hyper- and 53.4% hypo-) methylated regions. We found 44% promoter regions and 75% CpG islands were T-47D cell type-specific methylated...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28619164/impact-of-environmental-bacterial-communities-on-fish-health-in-marine-recirculating-aquaculture-systems
#8
Shuxia Xue, Wei Xu, Junli Wei, Jinsheng Sun
Marine cultured fish diseases caused by bacteria in recirculating aquaculture systems (RASs) greatly threaten fish aquaculture. To date, the dynamics of bacterial populations in RAS and their impacts to fish health remain largely unknown. In the present study, the bacterial communities in the water from two different marine RASs were analyzed using pyrosequencing technique. Fish disease syndromes and mortality had been reported from one RAS (RAS-d) while the fish in the other RAS remained healthy (RAS-h). The diversity of bacteria in each RAS and the abundance of each bacterium were identified based on sequencing the V4 hypervariable region of the 16S rRNA gene...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28618047/focal-b-catenin-mutation-identified-on-formalin-fixed-and-paraffin-embedded-inflammatory-hepatocellular-adenomas
#9
Joan Saldarriaga, Bettina Bisig, Gabrielle Couchy, Claire Castain, Jessica Zucman-Rossi, Charles Balabaud, Christine Sempoux, Paulette Bioulac-Sage
The identification of hepatocellular adenoma (HCA) with mutation in exon 3 of the CTNNB1 gene encoding for b-catenin is clinically relevant due to higher risk of malignant transformation. Inflammatory HCA (IHCA) can exhibit b-catenin activation (b-IHCA). We report 2 cases with multiple IHCA in which focal b-catenin activation has been found in one of the IHCA. In both cases, the diagnosis of IHCA was confirmed on the resected nodules by routine stains, immunohistochemical detection of C-reactive protein (CRP), and molecular biology on frozen material...
June 15, 2017: Histopathology
https://www.readbyqxmd.com/read/28612167/efficient-identification-of-snps-in-pooled-dna-samples-using-a-dual-mononucleotide-addition-based-sequencing-method
#10
Changchang Cao, Rongfang Pan, Jun Tan, Xiao Sun, Pengfeng Xiao
Identifying single nucleotide polymorphism (SNPs) from pooled samples is critical for many studies and applications. SNPs determined by next-generation sequencing results may suffer from errors in both base calling and read mapping. Taking advantage of dual mononucleotide addition-based pyrosequencing, we present Epds, a method to efficiently identify SNPs from pooled DNA samples. On the basis of only five patterns of non-synchronistic extensions between the wild and mutant sequences using dual mononucleotide addition-based pyrosequencing, we employed an enumerative algorithm to infer the mutant locus and estimate the proportion of mutant sequence...
June 13, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28611760/bacterial-composition-and-diversity-in-breast-milk-samples-from-mothers-living-in-taiwan-and-mainland-china
#11
Shiao-Wen Li, Koichi Watanabe, Chih-Chieh Hsu, Shiou-Huei Chao, Zheng-Hua Yang, Yan-Jun Lin, Chun-Chiang Chen, Yong-Mei Cao, Hsuan-Cheng Huang, Chuan-Hsiung Chang, Ying-Chieh Tsai
Human breast milk is widely recognized as the best source of nutrients for healthy growth and development of infants; it contains a diverse microbiota. Here, we characterized the diversity of the microbiota in the breast milk of East Asian women and assessed whether delivery mode influenced the microbiota in the milk of healthy breast-feeding mothers. We profiled the microbiota in breast milk samples collected from 133 healthy mothers in Taiwan and in six regions of mainland China (Central, East, North, Northeast, South, and Southwest China) by using 16S rRNA pyrosequencing...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28611750/nutrient-stoichiometry-shapes-microbial-community-structure-in-an-evaporitic-shallow-pond
#12
Zarraz M-P Lee, Amisha T Poret-Peterson, Janet L Siefert, Drishti Kaul, Ahmed Moustafa, Andrew E Allen, Chris L Dupont, Luis E Eguiarte, Valeria Souza, James J Elser
Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a mesocosm experiment was implemented in a stoichiometrically imbalanced pond, Lagunita, which has an average TN:TP ratio of 122 (atomic). The experiment had four treatments, each with five spatial replicates - unamended controls and three fertilization treatments with different nitrogen:phosphorus (N:P) regimes (P only, N:P = 16 and N:P = 75 by atoms)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28606963/a-single-nucleotide-polymorphism-in-the-ncf1-gene-leading-to-reduced-oxidative-burst-is-associated-with-systemic-lupus-erythematosus
#13
Lina M Olsson, Åsa C Johansson, Birgitta Gullstrand, Andreas Jönsen, Saedis Saevarsdottir, Lars Rönnblom, Dag Leonard, Jonas Wetterö, Christopher Sjöwall, Elisabet Svenungsson, Iva Gunnarsson, Anders A Bengtsson, Rikard Holmdahl
OBJECTIVES: Ncf1 polymorphisms leading to low production of reactive oxygen species (ROS) are strongly associated with autoimmune diseases in animal models. The human NCF1 gene is very complex with both functional and non-functional gene copies and genotyping requires assays specific for functional NCF1 genes. We aimed at investigating association and function of the missense single nucleotide polymorphism (SNP), rs201802880 (here denoted NCF1-339) in NCF1 with systemic lupus erythematosus (SLE)...
June 12, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/28601968/characteristics-and-diversity-of-endophytic-bacteria-in-moso-bamboo-phyllostachys-edulis-based-on-16s-rdna-sequencing
#14
Fang Liu, Zongsheng Yuan, Xintao Zhang, Guofang Zhang, Baogui Xie
To understand the diversity and distribution of endophytic bacteria in moso bamboo (Phyllostachys edulis), we used 16S rDNA sequencing to investigate the characteristics and diversity of endophytic bacteria in different moso bamboo tissues. After 454 pyrosequencing, we obtained 141,269 sequences from seven moso bamboo tissue samples. The taxonomic origins of unique sequences were identified using RDP classifier. The results showed that these sequences belonged to 26 bacterial orders, including the Actinomycetales, Rickettsiales, Burkholderiales, Enterobacteriales, and Rhizobiales...
June 10, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28600473/human-papillomavirus-dna-methylation-predicts-response-to-treatment-using-cidofovir-and-imiquimod-in-vulval-intraepithelial-neoplasia-3
#15
Sadie Esme Fleur Jones, Samantha Hibbitts, Christopher N Hurt, Dean Bryant, Alison N Fiander, Ned G Powell, Amanda J Tristram
Purpose <p>Response rates to treatment of vulval intraepithelial neoplasia (VIN) with imiquimod and cidofovir are approximately 57% and 61% respectively. Treatment is associated with significant side effects and, if ineffective, risk of malignant progression. Treatment response is not predicted by clinical factors. Identification of a biomarker that could predict response is an attractive prospect. This work investigated HPV DNA methylation as a potential predictive biomarker in this setting.</p> <p>Experimental design</p> <p>DNA from 167 cases of VIN 3 from the RT3 VIN clinical trial was assessed...
June 9, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28599225/performance-of-autotrophic-nitrogen-removal-from-digested-piggery-wastewater
#16
Shuang Wang, Lan Wang, Liangwei Deng, Dan Zheng, Yunhong Zhang, Yiqi Jiang, Hongnan Yang, Yunhui Lei
The performance of an autotrophic nitrogen removal process to treat digested piggery wastewater (DPW) was investigated by gradually shortening the HRT and enhancing the DPW concentration during 390days of operation. The results showed that the total nitrogen removal rate and efficiency reached 3.9kg-Nm(-3)day(-1) and 73%, which were significantly higher than the levels reported previously. A high relative abundance of Nitrosomonas (4.2%) and functional microbes (12.15%) resulted in a high aerobic ammonium oxidizing activity (1...
May 29, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28597254/changes-in-structure-and-function-of-bacterial-communities-during-coconut-leaf-vermicomposting
#17
Murali Gopal, Shrikant S Bhute, Alka Gupta, S R Prabhu, George V Thomas, William B Whitman, Kamlesh Jangid
To understand bacterial community dynamics during the vermicomposting of lignin-rich coconut leaves using an indigenous isolate of an epigeic earthworm, Eudrilus sp., we employed amplicon-based pyrosequencing of the V1 to V3 region of the 16S rRNA genes. Total community DNA was isolated from two separate vermicomposting tanks in triplicate at four different stages of the process: pre-decomposition (15th day), initial vermicomposting (45th day), 50-70% vermicomposting (75th day) and mature vermicompost (105th day)...
June 9, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28596594/magnifying-narrow-band-imaging-of-gastric-mucosal-morphology-predicts-the-h-pylori-related-epigenetic-field-defect
#18
Tomomitsu Tahara, Jumpei Yamazaki, Sayumi Tahara, Masaaki Okubo, Tomohiko Kawamura, Noriyuki Horiguchi, Takamitsu Ishizuka, Mitsuo Nagasaka, Yoshihito Nakagawa, Tomoyuki Shibata, Makoto Kuroda, Naoki Ohmiya
DNA methylation is associated with "field defect" in the gastric mucosa. To characterize "field defect" morphologically, we examined DNA methylation of non-neoplastic gastric mucosa in relation to their morphology seen by narrow-band imaging (NBI) with magnifying endoscopy. Magnifying NBI of non-neoplastic gastric body was classified as follows: normal-small and round pits with uniform subepithelial capillary networks; type 1-a little enlarged round pits with indistinct subepithelial capillary networks; type 2-remarkably enlarged pits with irregular vessels; and type 3-clearly demarcated oval or tubulovillous pits with bulky coiled or wavy vessels...
June 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28593503/global-level-of-plasma-dna-methylation-is-associated-with-overall-survival-in-patients-with-hepatocellular-carcinoma
#19
Chih-Ching Yeh, Abhishek Goyal, Jing Shen, Hui-Chen Wu, Joshua A Strauss, Qiao Wang, Irina Gurvich, Rachael A Safyan, Gulam A Manji, Mary V Gamble, Abby B Siegel, Regina M Santella
BACKGROUND: The impact of folate deficiency on global DNA methylation is uncertain. It also is unclear whether global DNA methylation is associated with outcome in HCC. LINE-1 methylation levels, as a surrogate marker of global methylation, may be influenced by folate deficiency. However, the interaction between LINE-1 methylation and folate level on overall survival (OS) in hepatocellular carcinoma (HCC) patients is unknown. We evaluated whether LINE-1 hypomethylation and folate deficiency are associated with HCC prognosis...
June 7, 2017: Annals of Surgical Oncology
https://www.readbyqxmd.com/read/28592103/-association-of-etheno-dna-adduct-and-dna-methylation-level-among-workers-exposed-to-diesel-engine-exhaust
#20
M L Shen, Z N He, X Zhang, H W Duan, Y Niu, P Bin, M Ye, T Meng, Y F Dai, S F Yu, W Chen, Y X Zheng
Objective: To investigate the association between etheno-DNA adduct and the promoter of DNA methylation levels of cyclin dependent kinase inhibitor 2A (P16), Ras association domain family 1 (RASSF1A) and O-6-methylguanine-DNA methyltransferase (MGMT) in workers with occupational exposure to diesel engine exhaust (DEE). Methods: We recruited 124 diesel engine testing workers as DEE exposure group and 112 water pump operator in the same area as control group in Henan province in 2012 using cluster sampling. The demographic data were obtained by questionnaire survey; urine after work and venous blood samples were collected from each subject...
June 6, 2017: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
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