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https://www.readbyqxmd.com/read/28931073/bacterial-and-diazotrophic-diversities-of-endophytes-in-dendrobium-catenatum-determined-through-barcoded-pyrosequencing
#1
Ou Li, Rong Xiao, Lihua Sun, Chenglin Guan, Dedong Kong, Xiufang Hu
As an epiphyte orchid, Dendrobium catenatum relies on microorganisms for requisite nutrients. Metagenome pyrosequencing based on 16S rRNA and nifH genes was used to characterize the bacterial and diazotrophic communities associated with D. catenatum collected from 5 districts in China. Based on Meta-16S rRNA sequencing, 22 bacterial phyla and 699 genera were identified, distributed as 125 genera from 8 phyla and 319 genera from 10 phyla shared by all the planting bases and all the tissues, respectively. The predominant Proteobacteria varied from 71...
2017: PloS One
https://www.readbyqxmd.com/read/28930610/rps6ka4-mir1237-and-aurkc-promoter-regions-are-differentially-methylated-in-wilms-tumor
#2
Hanna S Pereira, Sheila C Soares Lima, Paulo S de Faria, Leila Ca Cardoso, Hector N Seuanez
Wilms' tumor (WT) is the most frequent renal cancer in childhood, the occurrence of which is characterized by a relatively low frequency of associated mutations. While epigenetic alterations have been postulated to play a relevant role in the emergence of this tumor, the mechanisms involved in WT development remain largely unknown. In this study, the DNA methylation profile of WT was characterized with Beadchip array. Comparisons between WT with normal kidney identified 827 differentially methylated regions, most of which were attributable in hypermethylation in CpG islands...
January 1, 2018: Frontiers in Bioscience (Elite Edition)
https://www.readbyqxmd.com/read/28928877/mechanisms-of-breast-cancer-in-shift-workers-dna-methylation-in-five-core-circadian-genes-in-nurses-working-night-shifts
#3
Johanna Samulin Erdem, Øivind Skare, Marte Petersen-Øverleir, Heidi Ødegaard Notø, Jenny-Anne S Lie, Edyta Reszka, Beata Pepłońska, Shanbeh Zienolddiny
Shift work has been suggested to be associated with breast cancer risk, and circadian disruption in shift workers is hypothesized as one of the mechanisms of increased cancer risk. There is, however, insufficient molecular evidence supporting this hypothesis. Using the quantitative methodology of pyrosequencing, epigenetic changes in 5-methyl cytosine (5mC) in five circadian genes CLOCK, BMAL1, CRY1, PER1 and PER2 in female nurses working night shift work (278 breast cancer cases, 280 controls) were analyzed...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28928412/bacterial-communities-16s-rdna-fingerprinting-as-a-potential-tracing-tool-for-cultured-seabass-dicentrarchus-labrax
#4
Tânia Pimentel, Joana Marcelino, Fernando Ricardo, Amadeu M V M Soares, Ricardo Calado
Traceability of seafood has become crucial with market globalization and consumer's awareness. The present study used PCR-DGGE and 454 pyrosequencing to assess if bacterial communities fingerprint associated to seabass (Dicentrarchus labrax) skin mucus can be used to discriminate the geographic origin of fishes cultured in three semi-intensive fish farms. PCR-DGGE and pyrosequencing results were congruent and suggested that this molecular approach has the potential to trace fish farms with a spatial resolution <500 m...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28927259/generation-diversity-determination-and-application-to-antibody-selection-of-a-human-na%C3%A3-ve-fab-library
#5
Sangkyu Kim, Insoo Park, Seung Gu Park, Seulki Cho, Jin Hong Kim, Nagesh S Ipper, Sun Shim Choi, Eung Suk Lee, Hyo Jeong Hong
We constructed a large naïve human Fab library (3 x 1010 colonies) from the lymphocytes of 809 human donors, assessed available diversities of the heavy-chain variable (VH) and κ light-chain variable (VK) domain repertoires, and validated the library by selecting Fabs against 10 therapeutically relevant antigens by phage display. We obtained a database of unique 7,373 VH and 41,804 VK sequences by 454 pyrosequencing, and analyzed the repertoires. The distribution of VH and VK subfamilies and germline genes in our antibody repertoires slightly differed from those in earlier published natural antibody libraries...
September 20, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28923633/changes-in-dna-methylation-of-glucocorticoid-induced-tumor-necrosis-factor-receptor-and-its-ligand-in-liver-transplantation
#6
W Wang, G Ji, Y Chen, J Wang, J Sun, G Tang, Z Xie, H Zhao, G Liu, S Tan, G Chen, H Xue
Liver transplantation (LT) is the criterion standard of care in patients with end-stage liver disease and those with tumors of hepatic origin in the setting of liver dysfunction. Chronic immune rejection of the liver transplant can lead to bad prognosis for patients. Glucocorticoid-induced tumor necrosis factor receptor (GITR) play a key role in dominant immunologic self-tolerance maintained by CD25+/CD4+ regulatory T cells. Here, we investigated the DNA methylation variations of GITR and GITR ligand (GITRL) using pyrosequencing by analyzing blood DNA samples of patients after LT...
October 2017: Transplantation Proceedings
https://www.readbyqxmd.com/read/28922630/effects-of-iron-and-calcium-carbonate-on-contaminant-removal-efficiencies-and-microbial-communities-in-integrated-wastewater-treatment-systems
#7
Zhimiao Zhao, Xinshan Song, Yinjiang Zhang, Yufeng Zhao, Bodi Wang, Yuhui Wang
In the paper, we explored the influences of different dosages of iron and calcium carbonate on contaminant removal efficiencies and microbial communities in algal ponds combined with constructed wetlands. After 1-year operation of treatment systems, based on the high-throughput pyrosequencing analysis of microbial communities, the optimal operating conditions were obtained as follows: the ACW10 system with Fe(3+) (5.6 mg L(-1)), iron powder (2.8 mg L(-1)), and CaCO3 powder (0.2 mg L(-1)) in influent as the adjusting agents, initial phosphorus source (PO4(3-)) in influent, the ratio of nitrogen to phosphorus (N/P) of 30 in influent, and hydraulic retention time (HRT) of 1 day...
September 8, 2017: Chemosphere
https://www.readbyqxmd.com/read/28920403/comparison-of-bacterial-communities-in-leachate-from-decomposing-bovine-carcasses
#8
Seung-Hak Yang, Hee Kwon Ahn, Bong Soo Kim, Sun Sik Chang, Ki Yong Chung, Eun Mi Lee, Kwang Seok Ki, Eung Gi Kwon
Objective: Burial is associated with environmental effects such as the contamination of ground or surface water with biological materials generated during the decomposition process. Therefore, bacterial communities in leachates originating from the decomposing bovine carcasses were investigated. Methods: To understand the process of bovine (Hanwoo) carcass decomposition, we simulated burial using a lab-scale reactor with a volume of 5.15 m3. Leachate samples from 3 carcasses were collected using a peristaltic pump once a month for a period of 5 months, and bacterial communities in samples were identified by pyrosequencing of the 16S rRNA gene...
September 18, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28917719/polymorphisms-in-manganese-transporters-show-developmental-stage-and-sex-specific-associations-with-manganese-concentrations-in-primary-teeth
#9
Karin Wahlberg, Manish Arora, Austen Curtin, Paul Curtin, Robert O Wright, Donald R Smith, Roberto G Lucchini, Karin Broberg, Christine Austin
BACKGROUND: Manganese (Mn) is an essential metal that can become neurotoxic at elevated levels with negative consequences on neurodevelopment. We have evaluated the influence of single nucleotide polymorphisms (SNPs) in Mn transporter genes SLC30A10 and SLC39A8 on Mn concentrations in dentine, a validated biomarker that reflects Mn tissue concentrations early in life. METHODS: The study included 195 children with variable environmental Mn exposure. Mn concentrations in dentine representing fetal, early postnatal and early childhood developmental periods were measured using laser ablation-inductively coupled plasma mass spectrometry...
September 13, 2017: Neurotoxicology
https://www.readbyqxmd.com/read/28916278/microbial-reduction-of-vanadium-v-in-groundwater-interactions-with-coexisting-common-electron-acceptors-and-analysis-of-microbial-community
#10
Hui Liu, Baogang Zhang, Heyang Yuan, Yutong Cheng, Song Wang, Zhen He
Vanadium (V) pollution in groundwater has posed serious risks to the environment and public health. Anaerobic microbial reduction can achieve efficient and cost-effective remediation of V(V) pollution, but its interactions with coexisting common electron acceptors such as NO3(-), Fe(3+), SO4(2-) and CO2 in groundwater remain unknown. In this study, the interactions between V(V) reduction and reduction of common electron acceptors were examined with revealing relevant microbial community and identifying dominant species...
September 12, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28914591/mucosa-associated-microbiota-dysbiosis-in-colitis-associated-cancer
#11
Mathias L Richard, Giuseppina Liguori, Bruno Lamas, Giovanni Brandi, Gregory da Costa, Thomas W Hoffmann, Massimo Pierluigi Di Simone, Carlo Calabrese, Gilberto Poggioli, Philippe Langella, Massimo Campieri, Harry Sokol
Gut microbiota dysbiosis has been associated with inflammatory bowel diseases (IBD). In colorectal cancer, the gut microbiota has also been recognized as potentially involved in aggravating or favoring the tumor development. However, very little is known on the structure and role of the microbiota in colitis associated cancer (CAC), an important complication of IBD in human. Here we analyzed the bacterial and fungal composition of the mucosa associated microbiota of patients suffering CAC, sporadic cancer (SC) and of healthy subjects (HS) by barcode sequences analysis on the following cohort: 7 CAC patients, 10 SC patients and 10 HS using 16S (MiSeq) and ITS2 (pyrosequencing) sequencing, for bacteria and fungi respectively...
September 15, 2017: Gut Microbes
https://www.readbyqxmd.com/read/28912759/seasonality-affects-the-diversity-and-composition-of-bacterioplankton-communities-in-dongjiang-river-a-drinking-water-source-of-hong-kong
#12
Wei Sun, Chunyu Xia, Meiying Xu, Jun Guo, Guoping Sun
Water quality ranks the most vital criterion for rivers serving as drinking water sources, which periodically changes over seasons. Such fluctuation is believed associated with the state shifts of bacterial community within. To date, seasonality effects on bacterioplankton community patterns in large rivers serving as drinking water sources however, are still poorly understood. Here we investigated the intra-annual bacterial community structure in the Dongjiang River, a drinking water source of Hong Kong, using high-throughput pyrosequencing in concert with geochemical property measurements during dry, and wet seasons...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28910736/soil-microbial-community-responses-to-acid-exposure-and-neutralization-treatment
#13
Doyun Shin, Yunho Lee, Jeonghyun Park, Hee Sun Moon, Sung Pil Hyun
Changes in microbial community induced by acid shock were studied in the context of potential release of acids to the environment due to chemical accidents. The responses of microbial communities in three different soils to the exposure to sulfuric or hydrofluoric acid and to the subsequent neutralization treatment were investigated as functions of acid concentration and exposure time by using 16S-rRNA gene based pyrosequencing and DGGE (Denaturing Gradient Gel Electrophoresis). Measurements of soil pH and dissolved ion concentrations revealed that the added acids were neutralized to different degrees, depending on the mineral composition and soil texture...
September 11, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28906277/effect-of-cytomegalovirus-and-epstein-barr-virus-replication-on-intestinal-mucosal-gene-expression-and-microbiome-composition-of-hiv-infected-and-uninfected-individuals
#14
Sara Gianella, Antoine Chaillon, Ece A Mutlu, Phillip A Engen, Robin M Voigt, Ali Keshavarzian, John Losurdo, Prachi Chakradeo, Steven M Lada, Masato Nakazawa, Alan L Landay
BACKGROUND: HIV-infection is associated with dramatic changes in the intestinal mucosa. The impact of other viral pathogens is unclear. METHODS: One hundred and eight (108) biopsies from left and right colon (n = 79) and terminal ileum (n = 29) were collected from 19 HIV-infected and 22 HIV-uninfected participants. Levels of cytomegalovirus (CMV) and Epstein-Barr virus (EBV) DNA were measured by droplet digital PCR. Mucosal gene expression was measured via multiplex-assay...
September 24, 2017: AIDS
https://www.readbyqxmd.com/read/28903346/glutathione-peroxidase-7-suppresses-cancer-cell-growth-and-is-hypermethylated-in-gastric-cancer
#15
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...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28903182/molecular-estimation-of-alteration-in-intestinal-microbial-composition-in-hashimoto-s-thyroiditis-patients
#16
Hafiz Muhammad Ishaq, Imran Shair Mohammad, Hui Guo, Muhammad Shahzad, Yin Jian Hou, Chaofeng Ma, Zahid Naseem, Xiaokang Wu, Peijie Shi, Jiru Xu
The gut microbiota has a crucial effect on human health and physiology. Hypothyroid Hashimoto's thyroiditis (HT) is an autoimmune disorder manifested with environmental and genetic factors. However, it is hypothesized that intestinal microbes might play a vital role in the pathogenesis of HT. The aim of current was to investigate and characterize the gut microbial composition of HT patients both quantitatively and qualitatively. The fecal samples from 29 HT patients and 12 healthy individuals were collected...
September 9, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28900279/next-generation-sequencing-plus-ngs-with-y-chromosomal-markers-for-forensic-pedigree-searches
#17
Xiaoqin Qian, Jiayi Hou, Zheng Wang, Yi Ye, Min Lang, Tianzhen Gao, Jing Liu, Yiping Hou
There is high demand for forensic pedigree searches with Y-chromosome short tandem repeat (Y-STR) profiling in large-scale crime investigations. However, when two Y-STR haplotypes have a few mismatched loci, it is difficult to determine if they are from the same male lineage because of the high mutation rate of Y-STRs. Here we design a new strategy to handle cases in which none of pedigree samples shares identical Y-STR haplotype. We combine next generation sequencing (NGS), capillary electrophoresis and pyrosequencing under the term 'NGS+' for typing Y-STRs and Y-chromosomal single nucleotide polymorphisms (Y-SNPs)...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28899645/transcriptome-based-discovery-of-pathways-and-genes-related-to-reproduction-of-the-black-tiger-shrimp-penaeus-monodon
#18
Tanaporn Uengwetwanit, Pattareeya Ponza, Duangjai Sangsrakru, Duangdao Wichadakul, Supawadee Ingsriswang, Rungnapa Leelatanawit, Sirawut Klinbunga, Sithichoke Tangphatsornruang, Nitsara Karoonuthaisiri
The black tiger shrimp (Penaeus monodon) is an aquatic animal with considerable economic importance. Poor reproductive maturation in captivity impedes sustainable aquaculture production of this species. This study aims to provide transcriptomic information on reproductive organs using 454 pyrosequencing technology. The transcriptome analysis of ovaries and testes revealed 41,136 transcripts with 20,192 contigs. We found novel sets of transcripts completing several important reproductive pathways such as gonadotropin-releasing hormone (GnRH) signaling and progesterone-mediated oocyte maturation...
September 9, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28898288/long-term-no-till-a-major-driver-of-fungal-communities-in-dryland-wheat-cropping-systems
#19
Dipak Sharma-Poudyal, Daniel Schlatter, Chuntao Yin, Scot Hulbert, Timothy Paulitz
In the dryland Pacific Northwest wheat cropping systems, no-till is becoming more prevalent as a way to reduce soil erosion and fuel inputs. Tillage can have a profound effect on microbial communities and soilborne fungal pathogens, such as Rhizoctonia. We compared the fungal communities in long-term no-till (NT) plots adjacent to conventionally tilled (CT) plots, over three years at two locations in Washington state and one location in Idaho, US. We used pyrosequencing of the fungal ITS gene and identified 422 OTUs after rarefication...
2017: PloS One
https://www.readbyqxmd.com/read/28895358/-influence-of-oil-pollution-on-soil-microbial-community-diversity
#20
Xiaolou Li
Bacteria, actinomycetes and fungi are the three major groups of soil microbes. Soil microbes play a critical role in ecological and biodegradation processes in petroleum-contaminated soils. Based on the actual situation, this study took the oil polluted soil around the abandoned oil well in Shehong County, Suining City, Sichuan Province as the test soil. First, we determined the physiochemical properties of the tested soil; then we analyzed the changes of physiochemical properties and the three major microbes in petroleum contaminated soils...
June 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
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