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https://www.readbyqxmd.com/read/27911317/alzheimer-s-disease-histological-and%C3%A2-behavioral-manifestations-in%C3%A2-transgenic-mice-correlate-with%C3%A2-specific%C3%A2-gut-microbiome-state
#1
Liang Shen, Lu Liu, Hong-Fang Ji
Alzheimer's disease (AD) is a neurodegenerative brain disease and is the most common form of dementia. In recent years, many studies indicated the association of gut microbiota changes with metabolic diseases. However, the gut microbiota of AD has not been investigated. The present study aims to compare the gut microbiota in APP/PS1 transgenic mice of AD and C57/Bl6 wild-type (WT) mice by pyrosequencing the V3 and V4 regions of the bacterial 16S ribosomal RNA genes. The 3-, 6-, and 8-month-old APP/PS1 and WT mice were used to explore the effects of age on the gut microbiota...
November 28, 2016: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/27910234/luminal-contents-from-the-gut-of-colicky-infants-induce-visceral-hypersensitivity-in-mice
#2
H Eutamène, C L Garcia-Rodenas, S Yvon, E d'Aldebert, F Foata, B Berger, J Sauser, V Theodorou, G Bergonzelli, E Mas
BACKGROUND: The pathophysiology of infantile colic is poorly understood, though various studies report gut microbiota dysbiosis in colicky infants. We aimed to test the hypothesis that colic-related dysbiosis is associated with visceral hypersensitivity triggered by an altered luminal milieu. METHODS: Fecal samples from seven colicky and seven non-colicky infants were studied. Fecal supernatants (FS) were infused into the colons of C57/Bl6 mice (n=10/specimen). Visceral sensitivity was subsequently assessed in the animals by recording their abdominal muscle response to colorectal distension (CRD) by electromyography (EMG)...
December 1, 2016: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/27909430/bacterial-active-community-cycling-in-response-to-solar-radiation-and-their-influence-on-nutrient-changes-in-a-high-altitude-wetland
#3
Verónica Molina, Klaudia Hernández, Cristina Dorador, Yoanna Eissler, Martha Hengst, Vilma Pérez, Chris Harrod
Microbial communities inhabiting high-altitude spring ecosystems are subjected to extreme changes in solar irradiance and temperature throughout the diel cycle. Here, using 16S rRNA gene tag pyrosequencing (cDNA) we determined the composition of actively transcribing bacteria from spring waters experimentally exposed through the day (morning, noon, and afternoon) to variable levels of solar radiation and light quality, and evaluated their influence on nutrient recycling. Solar irradiance, temperature, and changes in nutrient dynamics were associated with changes in the active bacterial community structure, predominantly by Cyanobacteria, Verrucomicrobia, Proteobacteria, and 35 other Phyla, including the recently described Candidate Phyla Radiation (e...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27905861/sodium-bisulfite-pyrosequencing-revealed-that-developmental-exposure-to-environmental-contaminant-mixtures-does-not-affect-dna-methylation-of-dna-repeats-in-sprague-dawley-rats
#4
Daniel Desaulniers, Cathy Cummings-Lorbetskie, Nanqin Li, Gong-Hua Xiao, Leonora Marro, Nasrin Khan, Karen Leingartner
Hypomethylation of DNA repeats has been linked to diseases and cancer predisposition. Human studies suggest that higher blood concentrations of environmental contaminants (EC) correlate with levels of hypomethylation of DNA repeats in blood. The objective of this study was to examine the effect of in utero and/or lactational exposure to EC on the methylation of DNA repeats (LINE-1 and identifier element) in Sprague-Dawley rat pups at birth, at postnatal day (PND) 21, and in adulthood (PND78-86). From gestation day 0 to PND20, dams were exposed to a mixture "M" of polychlorinated biphenyls (PCB), pesticides, and methylmercury (MeHg), at 0...
December 1, 2016: Journal of Toxicology and Environmental Health. Part A
https://www.readbyqxmd.com/read/27904989/respirometric-response-and-microbial-succession-of-nitrifying-sludge-to-m-cresol-pulses-in-a-sequencing-batch-reactor
#5
Alberto Ordaz, Mariana Sánchez, Rodrigo Rivera, Rafael Rojas, Alejandro Zepeda
A nitrifying consortium was kinetically, stoichiometrically and molecularly characterized via the in situ pulse respirometric method and pyrosequencing analysis before and after the addition of m-cresol (25 mg C L(-1)) in a sequencing batch reactor (SBR). Five important kinetic and stoichiometric parameters were determined: the maximum oxygen uptake rate, the maximum nitrification rate, the oxidation yield, the biomass growth yield, and the substrate affinity constant. An inhibitory effect was observed in the nitrification process with a recovery of this by up to eight SBR cycles after m-cresol was added to the system...
November 30, 2016: Biodegradation
https://www.readbyqxmd.com/read/27904883/interactions-of-respiratory-viruses-and-the-nasal-microbiota-during-the-first-year-of-life-in-healthy-infants
#6
Insa Korten, Moana Mika, Shkipe Klenja, Elisabeth Kieninger, Ines Mack, Maria Teresa Barbani, Meri Gorgievski, Urs Frey, Markus Hilty, Philipp Latzin
Traditional culture techniques have shown that increased bacterial colonization is associated with viral colonization; however, the influence of viral colonization on the whole microbiota composition is less clear. We thus aimed to understand the interaction of viral infections and the nasal microbiota in early life to appraise their roles in disease development. Thirty-two healthy, unselected infants were included in this prospective longitudinal cohort study within the first year of life. Biweekly nasal swabs (n = 559) were taken, and the microbiota was analyzed by 16S rRNA pyrosequencing, and 10 different viruses and 2 atypical bacteria were characterized by real-time PCR (combination of seven duplex samples)...
November 2016: MSphere
https://www.readbyqxmd.com/read/27901632/methane-oxidation-in-a-landfill-cover-soil-reactor-changing-of-kinetic-parameters-and-microorganism-community-structure
#7
Zhi L Xing, Tian T Zhao, Yan H Gao, Xu Yang, Shuai Liu, Xu Y Peng
Changing of CH4 oxidation potential and biological characteristics with CH4 concentration was studied in a landfill cover soil reactor (LCSR). The maximum rate of CH4 oxidation reached 32.40 mol d(-1) m(-2) by providing sufficient O2 in the LCSR. The kinetic parameters of methane oxidation in landfill cover soil were obtained by fitting substrate diffusion and consumption model based on the concentration profile of CH4 and O2. The values of [Formula: see text] (0.93-2.29%) and [Formula: see text] (140-524 nmol kgsoil-DW(-1)·s(-1)) increased with CH4 concentration (9...
November 30, 2016: Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances & Environmental Engineering
https://www.readbyqxmd.com/read/27901123/hill-number-as-a-bacterial-diversity-measure-framework-with-high-throughput-sequence-data
#8
Sanghoon Kang, Jorge L M Rodrigues, Justin P Ng, Terry J Gentry
Bacterial diversity is an important parameter for measuring bacterial contributions to the global ecosystem. However, even the task of describing bacterial diversity is challenging due to biological and technological difficulties. One of the challenges in bacterial diversity estimation is the appropriate measure of rare taxa, but the uncertainty of the size of rare biosphere is yet to be experimentally determined. One approach is using the generalized diversity, Hill number (Na), to control the variability associated with rare taxa by differentially weighing them...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900438/start-up-and-bacterial-community-compositions-of-partial-nitrification-in-moving-bed-biofilm-reactor
#9
Tao Liu, Yan-Jun Mao, Yan-Ping Shi, Xie Quan
Partial nitrification (PN) has been considered as one of the promising processes for pretreatment of ammonium-rich wastewater. In this study, a kind of novel carriers with enhanced hydrophilicity and electrophilicity was implemented in a moving bed biofilm reactor (MBBR) to start up PN process. Results indicated that biofilm formation rate was higher on modified carriers. In comparison with the reactor filled with traditional carriers (start-up period of 21 days), it took only 14 days to start up PN successfully with ammonia removal efficiency and nitrite accumulation rate of 90 and 91%, respectively, in the reactor filled with modified carriers...
November 30, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27899917/insights-into-the-regulation-of-rhizosphere-bacterial-communities-by-application-of-bio-organic-fertilizer-in-pseudostellaria-heterophylla-monoculture-regime
#10
Linkun Wu, Jun Chen, Hongmiao Wu, Xianjin Qin, Juanying Wang, Yanhong Wu, Muhammad U Khan, Sheng Lin, Zhigang Xiao, Xiaomian Luo, Zhongyi Zhang, Wenxiong Lin
The biomass and quality of Pseudostellariae heterophylla suffers a significant decline under monoculture. Since rhizosphere miobiome plays crucial roles in soil health, deep pyrosequencing combined with qPCR was applied to characterize the composition and structure of soil bacterial community under monoculture and different amendments. The results showed compared with the 1st-year planted (FP), 2nd-year monoculture of P. heterophylla (SP) led to a significant decline in yield and resulted in a significant increase in Fusarium oxysporum but a decline in Burkholderia spp...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27897454/considerations-for-standardizing-predictive-molecular-pathology-for-cancer-prognosis
#11
Michelangelo Fiorentino, Marina Scarpelli, Antonio Lopez-Beltran, Liang Cheng, Rodolfo Montironi
Molecular tests that were once ancillary to the core business of cyto-histopathology are becoming the third most relevant workload in pathology departments after histopathology/cytopathology and before autopsies. This has resulted from innovations in molecular biology techniques, which have developed at an incredibly fast pace. Areas covered: Most of the current widely used techniques in molecular pathology such as FISH, direct sequencing, pyrosequencing, and allele-specific PCR will be replaced by massive parallel sequencing that will not be considered next generation, but rather, will be considered to be current generation sequencing...
November 29, 2016: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/27896069/evaluation-of-de-novo-assembly-technique-in-the-south-african-abalone-haliotis-midae-transcriptome-a-comparison-from-illumina-and-454-systems
#12
Barbara Picone, Clint Rhode, Rouvay Roodt-Wilding
Next generation sequencing platforms have recently been used to rapidly characterize transcriptome sequences from a number of non-model organisms. The present study compares two of the most frequently used platforms, the Roche 454-pyrosequencing and the Illumina sequencing-by-synthesis (SBS), on the same RNA sample obtained from an intertidal gastropod mollusc species, Haliotis midae. All the sequencing reads were deposited in the Short Read Archive (SRA) database are retrievable under the accession number [SRR071314 (Illumina Genome Analyzer II)] and [SRR1737738, SRR1737737, SRR1737735, SRR1737734 (454 GS FLX)] in the SRA database of NCBI...
December 2016: Genomics Data
https://www.readbyqxmd.com/read/27895805/blood-based-dna-methylation-as-biomarker-for-breast-cancer-a-systematic-review
#13
REVIEW
Qiuqiong Tang, Jie Cheng, Xue Cao, Harald Surowy, Barbara Burwinkel
Multiple studies have investigated global DNA methylation profiles and gene-specific DNA methylation in blood-based DNA to develop powerful screening markers for cancer. This systematic review summarizes the current evidence on methylation studies that investigated methylation level of blood-derived DNA of breast cancer (BC) patients in comparison to healthy controls by conducting a systematic literature review in PubMed and Web of Science. Essential results, such as methylation levels of BC cases and healthy controls, p values, and odds ratios, were extracted from these studies by two investigators independently...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27895716/widespread-recovery-of-methylation-at-gametic-imprints-in-hypomethylated-mouse-stem-cells-following-rescue-with-dnmt3a2
#14
Avinash Thakur, Sarah-Jayne Mackin, Rachelle E Irwin, Karla M O'Neill, Gareth Pollin, Colum Walsh
BACKGROUND: Imprinted loci are paradigms of epigenetic regulation and are associated with a number of genetic disorders in human. A key characteristic of imprints is the presence of a gametic differentially methylated region (gDMR). Previous studies have indicated that DNA methylation lost from gDMRs could not be restored by DNMT1, or the de novo enzymes DNMT3A or 3B in stem cells, indicating that imprinted regions must instead undergo passage through the germline for reprogramming. However, previous studies were non-quantitative, were unclear on the requirement for DNMT3A/B and showed some inconsistencies...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27892678/characterization-and-prognosis-significance-of-jak2-v617f-mpl-and-calr-mutations-in-philadelphia-negative-myeloproliferative-neoplasms
#15
Roongrudee Singdong, Teerapong Siriboonpiputtana, Takol Chareonsirisuthigul, Adcharee Kongruang, Nittaya Limsuwanachot, Tanasan Sirirat, Suporn Chuncharunee, Budsaba Rerkamnuaychoke
Background: The discovery of somatic acquired mutations of JAK2 (V617F) in Philadelphia-negative myeloproliferative neoplasms (Ph-negative MPNs) including polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF) has not only improved rational disease classification and prognostication but also brings new understanding insight into the pathogenesis of diseases. Dosage effects of the JAK2 (V617F) allelic burden in Ph-negative MPNs may partially influence clinical presentation, disease progression, and treatment outcome...
January 10, 2016: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/27889811/bacterial-diversity-patterns-differed-in-two-developing-ecosystems
#16
Shankar G Shanmugam, Zenaida V Magbanua, Mark A Williams, Kamlesh Jangid, William B Whitman, Daniel G Peterson, William L Kingery
Microbial diversity patterns have been surveyed in many different soils and ecosystems, but we are unaware of studies comparing similar soils developing from similar parent materials in contrasting climates. In 2008, developmental chronosequences with ages ranging from 105 to 500,000 years across Georgia (GA) and Michigan (MI) were studied to investigate how bacterial community composition and diversity change as a result of local environmental gradients that develop during pedogenesis. Geographic factors were studied between and within locations spanning two scales: (1) regionally between 0...
November 26, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27889144/exploring-the-microbiota-of-the-red-brown-defect-in-smear-ripened-cheese-by-454-pyrosequencing-and-its-prevention-using-different-cleaning-systems
#17
Raffaele Guzzon, Ilaria Carafa, Kieran Tuohy, Gonzalo Cervantes, Luca Vernetti, Andrea Barmaz, Roberto Larcher, Elena Franciosi
Red-brown pigmentation can occasionally form in smeared-ripened cheese such as Fontina during the ripening process. This reaction is due to over-development of the typical microbiota present on the rind. Previous studies have demonstrated the relationship between red-brown pigmentation and the traditional utilization of wooden shelves during cheese ripening. The first part of the paper focuses on the characterisation of yeast and bacterial microbiota: plate counts and 454-pyrosequencing were performed in spoiled (n = 6) and non-spoiled cheeses (n = 6) and on the wooden shelves used during ripening...
April 2017: Food Microbiology
https://www.readbyqxmd.com/read/27889142/the-microbiota-of-marketed-processed-edible-insects-as-revealed-by-high-throughput-sequencing
#18
Cristiana Garofalo, Andrea Osimani, Vesna Milanović, Manuela Taccari, Federica Cardinali, Lucia Aquilanti, Paola Riolo, Sara Ruschioni, Nunzio Isidoro, Francesca Clementi
Entomophagy has been linked to nutritional, economic, social and ecological benefits. However, scientific studies on the potential safety risks in eating edible insects need to be carried out for legislators, markets and consumers. In this context, the microbiota of edible insects deserves to be deeply investigated. The aim of this study was to elucidate the microbial species occurring in some processed marketed edible insects, namely powdered small crickets, whole dried small crickets (Acheta domesticus), whole dried locusts (Locusta migratoria), and whole dried mealworm larvae (Tenebrio molitor), through culture-dependent (classical microbiological analyses) and -independent methods (pyrosequencing)...
April 2017: Food Microbiology
https://www.readbyqxmd.com/read/27888456/soil-ph-and-electrical-conductivity-are-key-edaphic-factors-shaping-bacterial-communities-of-greenhouse-soils-in-korea
#19
Jeong Myeong Kim, An-Sung Roh, Seung-Chul Choi, Eun-Jeong Kim, Moon-Tae Choi, Byung-Koo Ahn, Sun-Kuk Kim, Young-Han Lee, Jae-Ho Joa, Seong-Soo Kang, Shin Ae Lee, Jae-Hyung Ahn, Jaekyeong Song, Hang-Yeon Weon
Soil microorganisms play an essential role in soil ecosystem processes such as organic matter decomposition, nutrient cycling, and plant nutrient availability. The land use for greenhouse cultivation has been increasing continuously, which involves an intensive input of agricultural materials to enhance productivity; however, relatively little is known about bacterial communities in greenhouse soils. To assess the effects of environmental factors on the soil bacterial diversity and community composition, a total of 187 greenhouse soil samples collected across Korea were subjected to bacterial 16S rRNA gene pyrosequencing analysis...
December 2016: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/27886370/epigenetic-alterations-of-the-bdnf-gene-in-combat-related-post-traumatic-stress-disorder
#20
T Y Kim, S J Kim, H G Chung, J H Choi, S H Kim, J I Kang
OBJECTIVE: Brain-derived neurotrophic factor (BDNF) plays a crucial role in modulating resilience and vulnerability to stress. The aim of this study was to investigate whether epigenetic regulation of the BDNF gene is a biomarker of post-traumatic stress disorder (PTSD) development among veterans exposed to combat in the Vietnam War. METHODS: Using the Clinician-Administered PTSD Scale, combat veterans were grouped into those with (n = 126) and without (n = 122) PTSD...
November 25, 2016: Acta Psychiatrica Scandinavica
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