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Hiromi Shiratori, Carmen Feinweber, Claudia Knothe, Jörn Lötsch, Dominique Thomas, Gerd Geisslinger, Michael J Parnham, Eduard Resch
DNA methylation is a major regulatory process of gene transcription, and aberrant DNA methylation is associated with various diseases including cancer. Many compounds have been reported to modify DNA methylation states. Despite increasing interest in the clinical application of drugs with epigenetic effects, and the use of diagnostic markers for genome-wide hypomethylation in cancer, large-scale screening systems to measure the effects of drugs on DNA methylation are limited. In this study, we improved the previously established fluorescence polarization-based global DNA methylation assay so that it is more suitable for application to human genomic DNA...
2016: PloS One
Siobhan Eustace Ryan, Fergus Ryan, Veronica O'Dwyer, Derek Neylan
PURPOSE: Approximately 95% of patients who are diagnosed with Leber's hereditary optic neuropathy (LHON) have one of three mitochondrial point mutations responsible for the disease, G3460A, G11778A, and T14484C. The purpose of this study was to develop a novel multiplex real-time amplification-refractory mutation system (ARMS) PCR combined with high-resolution melt curves to identify the individual mutations involved. The study aimed to provide a more robust, cost- and time-effective mutation detection strategy than that offered with currently available methods...
2016: Molecular Vision
S Combes, K Massip, O Martin, H Furbeyre, L Cauquil, G Pascal, O Bouchez, N Le Floc'h, O Zemb, I P Oswald, T Gidenne
Limiting the post-weaning intake of the young rabbit is known to improve its resistance to digestive disorders, whereas a degradation of its housing hygiene is assumed to have a negative impact on its health. This study aims at providing insights into the mechanism of digestive health preservation regarding both host (growth and immune response) and its symbiotic digestive microbiota. A 2×2 factorial design from weaning (day 28) to day 64 was set up: ad libitum intake or restricted intake at 70% of ad libitum, and high v...
October 17, 2016: Animal: An International Journal of Animal Bioscience
Xiao-Ming Lu, Chang Chen, Tian-Ling Zheng
Pyrosequencing and metagenomic profiling were used to assess the phylogenetic and functional characteristics of microbial communities residing in sediments collected from the estuaries of Rivers Oujiang (OS) and Jiaojiang (JS) in the western region of the East China Sea. Another sediment sample was obtained from near the shore far from estuaries, used for contrast (CS). Characterization of estuary sediment bacterial communities showed that toxic chemicals potentially reduced the natural variability in microbial communities, while they increased the microbial metabolic enzymes and pathways...
October 15, 2016: Microbial Ecology
John Moat, Athanasios Rizoulis, Graeme Fox, Mathew Upton
The domestic environment can be a source of pathogenic bacteria. We show here that domestic shower hoses may harbour potentially pathogenic bacteria and fungi. Well-developed biofilms were physically removed from the internal surface of shower hoses collected in four locations in England and Scotland. Amplicon pyrosequencing of 16S and 18S rRNA targets revealed the presence of common aquatic and environmental bacteria, including members of the Actinobacteria, Alphaproteobacteria, Bacteroidetes and non-tuberculous Mycobacteria...
October 2016: Journal of Water and Health
Emilio A Herrera, Francisca Cifuentes-Zúñiga, Esteban Figueroa, Cristian Villanueva, Cherie Hernández, René Alegría, Viviana Arroyo, Estefania Peñaloza, Marcelo Farías, Ricardo Uauy, Paola Casanello, Bernardo J Krause
In humans, intrauterine growth restriction (IUGR) is associated with vascular dysfunction, oxidative stress and signs of endothelial programming in umbilical vessels. We aimed to determine the effects of maternal antioxidant treatment with N-acetyl cysteine (NAC) on fetal endothelial function and eNOS programming in IUGR guinea pigs. IUGR was induced by implanting ameroid constrictors on uterine arteries of pregnant guinea pigs at mid gestation, receiving half of the sows NAC in the drinking water (from day 34 until term)...
October 14, 2016: Journal of Physiology
Claudia Minosse, Emanuela Giombini, Barbara Bartolini, Maria R Capobianchi, Anna R Garbuglia
Hepatitis C virus (HCV) is classified into seven phylogenetically distinct genotypes, which are further subdivided into related subtypes. Accurate assignment of genotype/subtype is mandatory in the era of directly acting antivirals. Several molecular methods are available for HCV genotyping; however, a relevant number of samples with indeterminate, mixed, or unspecified subtype results, or even with misclassified genotypes, may occur. Using NS5B direct (DS) and ultra-deep pyrosequencing (UDPS), we have tested 43 samples, which resulted in genotype 1 unsubtyped (n = 17), mixed infection (n = 17), or indeterminate (n = 9) with the Abbott RealTime HCV Genotype II assay...
October 7, 2016: International Journal of Molecular Sciences
Susanne A Bengesser, Eva Z Reininghaus, Nina Lackner, Armin Birner, Frederike T Fellendorf, Martina Platzer, Nora Kainzbauer, Bernhard Tropper, Christa Hörmanseder, Robert Queissner, Hans-Peter Kapfhammer, Sandra J Wallner-Liebmann, Robert Fuchs, Erwin Petek, Christian Windpassinger, Mario Schnalzenberger, Bernd Reininghaus, Bernd Evert, Andreas Waha
OBJECTIVES: The clock gene ARNTL is associated with the transcription activation of monoamine oxidase A according to previous literature. Thus, we hypothesised that methylation of ARNTL may differ between bipolar disorder (BD) and controls. METHODS: The methylation status of one CpG island covering the first exon of ARNTL (PS2) and one site in the 5' region of ARNTL (cg05733463) were analysed in patients with BD (n = 151) versus controls (n = 66). Methylation analysis was performed by bisulphite-conversion of DNA from fasting blood with the EpiTect Bisulfite Kit, PCR and pyrosequencing...
October 14, 2016: World Journal of Biological Psychiatry
Grazia Palomba, Valentina Doneddu, Antonio Cossu, Panagiotis Paliogiannis, Antonella Manca, Milena Casula, Maria Colombino, Annamaria Lanzillo, Efisio Defraia, Antonio Pazzola, Giovanni Sanna, Carlo Putzu, Salvatore Ortu, Mario Scartozzi, Maria Teresa Ionta, Giovanni Baldino, Giuseppina Sarobba, Francesca Capelli, Tito Sedda, Luciano Virdis, Michela Barca, Giulia Gramignano, Mario Budroni, Francesco Tanda, Giuseppe Palmieri
BACKGROUND: Activation of oncogenes downstream the EGFR gene contributes to colorectal tumorigenesis and determines the sensitivity to anti-EGFR treatments. The aim of this study was to evaluate the prognostic value of KRAS, BRAF, NRAS and PIK3CA mutations in a large collection of CRC patients from genetically-homogeneous Sardinian population. METHODS: A total of 1284 Sardinian patients with histologically-proven diagnosis of colorectal carcinoma (CRC) and presenting with metastatic disease were included into the study...
October 13, 2016: Journal of Translational Medicine
Elvira E Ziganshina, Dilyara M Sharifullina, Andrey P Lozhkin, Rustem N Khayrullin, Igor M Ignatyev, Ayrat M Ziganshin
Atherosclerosis is considered a chronic disease of the arterial wall and is the major cause of severe disease and death among individuals all over the world. Some recent studies have established the presence of bacteria in atherosclerotic plaque samples and suggested their possible contribution to the development of cardiovascular disease. The main objective of this preliminary pilot study was to better understand the bacterial diversity and abundance in human atherosclerotic plaques derived from common carotid arteries of individuals with atherosclerosis (Russian nationwide group) and contribute towards the further identification of a main group of atherosclerotic plaque bacteria by 454 pyrosequencing their 16S ribosomal RNA (16S rRNA) genes...
2016: PloS One
B Dréno, E Araviiskaia, E Berardesca, G Gontijo, M Sanchez Viera, L F Xiang, R Martin, T Bieber
The skin is a complex barrier organ made of a symbiotic relationship between microbial communities and host tissue via complex signals provided by the innate and the adaptive immune systems. It is constantly exposed to various endogenous and exogenous factors which impact this balanced system potentially leading to inflammatory skin conditions comprising infections, allergies or autoimmune diseases. Unlike the gut and stool microbiome which has been studied and described for many years, investigations on the skin or scalp microbiome only started recently...
October 13, 2016: Journal of the European Academy of Dermatology and Venereology: JEADV
Danyta I Tedjo, Agnieszka Smolinska, Paul H Savelkoul, Ad A Masclee, Frederik J van Schooten, Marieke J Pierik, John Penders, Daisy M A E Jonkers
Monitoring mucosal inflammation is crucial to prevent complications and disease progression in Crohn's disease (CD). Endoscopy is the current standard, but is invasive. Clinical activity scores and non-invasive biochemical markers do not correlate well with mucosal inflammation. Microbial perturbations have been associated with disease activity in CD. Therefore, we aimed to investigate its potential use to differentiate CD patients in remission from those with an exacerbation. From 71 CD patients repeated fecal samples were collected, resulting in 97 active disease and 97 remission samples based on a combination of biochemical and clinical parameters...
October 13, 2016: Scientific Reports
Rongfang Pan, Pengfeng Xiao
Molecular haplotyping is becoming increasingly important for studying the disease association of a specific allele because of its ability of providing more information than any single nucleotide polymorphism (SNP). Computational analysis and experimental techniques are usually performed for haplotypic determination. However, established methods are not suitable for analyzing haplotypes of massive natural DNA samples. Here we present a simple molecular approach to analyze haplotypes of conventional polymerase chain reaction (PCR) products quantitatively in a single sequencing run...
October 12, 2016: Analytical and Bioanalytical Chemistry
Hailong Zhao, Shuying Wang, Chengwei Song, Yunhong Zha, Li Li
BACKGROUND: The prognostic value of the status of O(6)-methylguanine-DNA methyltransferase (MGMT) promoter methylation measured by pyrosequencing assay (PSQ) among glioblastoma (GBM) patients was examined in meta-analysis. METHODS: Eligible studies that reported the association between the status of MGMT promoter methylation by PSQ and prognostic value of GBM patients from three electronic databases, like PubMed, EMBASE, and Cochrane library were involved in meta-analysis...
October 12, 2016: World Journal of Surgical Oncology
M Constanza Mannino, Máximo Rivarola, Alejandra C Scannapieco, Sergio González, Marisa Farber, Jorge L Cladera, Silvia B Lanzavecchia
BACKGROUND: Diachasmimorpha longicaudata (Hymenoptera: Braconidae) is a solitary parasitoid of Tephritidae (Diptera) fruit flies of economic importance currently being mass-reared in bio-factories and successfully used worldwide. A peculiar biological aspect of Hymenoptera is its haplo-diploid life cycle, where females (diploid) develop from fertilized eggs and males (haploid) from unfertilized eggs. Diploid males were described in many species and recently evidenced in D. longicaudata by mean of inbreeding studies...
October 12, 2016: BMC Genomics
H Diao, H L Yan, Y Xiao, B Yu, J Yu, J He, P Zheng, B H Zeng, H Wei, X B Mao, D W Chen
BACKGROUND: The present study was conducted to compare the differences in gut microbiota composition and gut-phenotypes among pig breeds, and determine whether these differences would transmit to mice colonized with fecal microbiota of different pig breeds. A total of 24 1-day-old germ-free BALB/C mice were divided into 3 groups (TFM, YFM and RFM), which were transplanted with intact fecal microbiota of Tibetan pig (TP), Yorkshire pig (YP) and Rongchang pig (RP), respectively. RESULTS: Results showed that different pig breeds exhibited distinct gut microbiota profile based on high-throughput pyrosequencing...
October 11, 2016: BMC Microbiology
Sebastian Maciak, Katarzyna Michalak, Shiv D Kale, Pawel Michalak
Nucleolar dominance is a dramatic disruption in the formation of nucleoli and the expression of ribosomal RNA (rRNA) genes, characteristic of some plant and animal hybrids. Here, we report that F1 hybrids produced from reciprocal crosses between 2 sister species of Xenopus clawed frogs, X. muelleri and X. borealis, undergo nucleolar dominance somewhat distinct from a pattern previously reported in hybrids between phylogenetically more distant Xenopus species. Patterns of nucleolar development, 45S rRNA expression, and gene copy inheritance were investigated using a combination of immunostaining, pyrosequencing, droplet digital PCR, flow cytometry, and epigenetic inhibition...
October 12, 2016: Cytogenetic and Genome Research
Ryu Suto, Chikako Ishimoto, Mikio Chikyu, Yoshito Aihara, Toshimi Matsumoto, Hirohide Uenishi, Tomoko Yasuda, Yasuyuki Fukumoto, Miyoko Waki
We investigated anammox with a focus on biofilm in 10 wastewater treatment plants (WWTPs) that use activated sludge treatment of swine wastewater. In three plants, we found red biofilms in aeration tanks or final sedimentation tanks. The biofilm had higher anammox 16S rRNA gene copy numbers (up to 1.35 × 10(12) copies/g-VSS) and higher anammox activity (up to 295 μmoL/g-ignition loss/h) than suspended solids in the same tank. Pyrosequencing analysis revealed that Planctomycetes accounted for up to 17.7% of total reads in the biofilm...
October 8, 2016: Chemosphere
Xin Wen, Jian Zhou, Yancheng Li, Xiaoxia Qing, Qiang He
In this study, a novel process combined simultaneous partial nitrification, anammox and denitrification (SNAD) with denitrifying phosphorus removal (DPR) was proposed for advanced nitrogen removal. Firstly simulating sewage was introduced to a sequencing batch reactor (SBR) for organic matter removal and anaerobic phosphorus release (stage 1). Then effluent of stage 1 with low COD was discharged to a sequencing biofilm batch reactor (SBBR) for partial nitrification, anammox and partial denitrification (stage 2)...
October 5, 2016: Bioresource Technology
Laura Delgado-Balbuena, Juan M Bello-López, Yendi E Navarro-Noya, Analine Rodríguez-Valentín, Marco L Luna-Guido, Luc Dendooven
Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E...
2016: PloS One
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