Search results for " sequencing"

Complete genome sequence of the hydrogenotrophic Archaeon Methanobacterium sp Mb1 isolated from a production-scale biogas plant

2013

Methanobacterium sp. Mb1, a hydrogenotrophic methanogenic Archaeon, was isolated from a rural biogas plant producing methane-rich biogas from maize silage and cattle manure in Germany. Here we report the complete genome sequence of the novel methanogenic isolate Methanobacterium sp. Mb1 harboring a 2,029,766 bp circular chromosome featuring a GC content of 39.74%. The genome encodes two rRNA operons, 41 tRNA genes and 2021 coding sequences and represents the smallest genome currently known within the genus Methanobacterium. (C) 2013 Elsevier B.V. All rights reserved.

HECTOR : a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data

2014

Background Current-generation sequencing technologies are able to produce low-cost, high-throughput reads. However, the produced reads are imperfect and may contain various sequencing errors. Although many error correction methods have been developed in recent years, none explicitly targets homopolymer-length errors in the 454 sequencing reads. Results We present HECTOR, a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. In this algorithm, for the first time we have investigated a novel homopolymer spectrum based approach to handle homopolymer insertions or deletions, which are the dominant sequencing errors in 454 pyrosequencing reads. We have evaluat…

FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA.

2019

AbstractMethyl-5-uridine (m5U) is one the most abundant non-canonical bases present in cellular RNA, and in yeast is found at position U54 of tRNAs where modification is catalysed by the methyltransferase Trm2. Although the mammalian enzymes that catalyse m5U formation are yet to be identified via experimental evidence, based on sequence homology to Trm2, two candidates currently exist, TRMT2A and TRMT2B. Here we developed a genome-wide single-nucleotide resolution mapping method, Fluorouracil-Induced-Catalytic-Crosslinking-Sequencing (FICC-Seq), in order to identify the relevant enzymatic targets. We demonstrate that TRMT2A is responsible for the majority of m5U present in human RNA, and t…

Analyzing Illumina Gene Expression Microarray Data from Different Tissues: Methodological Aspects of Data Analysis in the MetaXpress Consortium

2012

Microarray profiling of gene expression is widely applied in molecular biology and functional genomics. Experimental and technical variations make meta-analysis of different studies challenging. In a total of 3358 samples, all from German population-based cohorts, we investigated the effect of data preprocessing and the variability due to sample processing in whole blood cell and blood monocyte gene expression data, measured on the Illumina HumanHT-12 v3 BeadChip array. Gene expression signal intensities were similar after applying the log(2) or the variance-stabilizing transformation. In all cohorts, the first principal component (PC) explained more than 95% of the total variation. Technic…

Microbial communities and novel taxa in « Continental Smokers » of northern Greece

2017

Analogously to the ocean-bottom black/white smokers, “continental smokers” have recently been defined as sites of mantle degassing through continental crust. The goal of this research, carried out within the Deep Carbon Observatory Community, is to investigate the role of deeplysourced fluids in niche ecosystem differentiation in European continental smokers. A 16S rRNA gene survey of microbial communities was carried out on 11 geothermal manifestations of northern Greece, all showing a distinct contribution of mantle fluids (R/Ra up to 1.2) that allow to classify them as continental smokers. The selected sites cover a wide range of temperatures (15-77 °C), pH (6.11-8.46), Eh (-289 – 40 mV)…

Recentrifuge

2019

Robust comparative analysis and contamination removal for metagenomics.

2020

The composition of phytoplankton community is the basis for environmental monitoring and assessment of the ecological status of aquatic ecosystems. Community composition studies of phytoplankton have been based on time-consuming and expertise-demanding light microscopy analyses. Molecular methods have the potential to replace microscopy, but the high copy number variation of ribosomal genes and the lack of universal primers for simultaneous amplification of prokaryotic and eukaryotic genes complicate data interpretation. In this study, we used our previously developed directional primer-independent high-throughput sequencing (HTS) approach to analyze 16S and 18S rRNA community structures. C…

2021

Amplicon sequencing of partial regions of the ribosomal RNA loci (rDNA) is widely used to profile microbial communities. However, the rDNA is dynamic and can exhibit substantial interspecific and intraspecific variation in copy number in prokaryotes and, especially, in microbial eukaryotes. As change in rDNA copy number is a common response to environmental change, rDNA copy number is not necessarily a property of a species. Variation in rDNA copy number, especially the capacity for large intraspecific changes driven by external cues, complicates analyses of rDNA amplicon sequence data. We highlight the need to (i) interpret amplicon sequence data in light of possible interspecific and intr…

Impact of Rocky Desertification Control on Soil Bacterial Community in Karst Graben Basin, Southwestern China

2021

Microorganisms play critical roles in belowground ecosystems, and karst rocky desertification (KRD) control affects edaphic properties and vegetation coverage. However, the relationship between KRD control and soil bacterial communities remains unclear. 16S rRNA gene next-generation sequencing was used to investigate soil bacterial community structure, composition, diversity, and co-occurrence network from five ecological types in KRD control area. Moreover, soil physical-chemical properties and soil stoichiometry characteristics of carbon, nitrogen and phosphorus were analyzed. Soil N and P co-limitation decreased in the contribution of the promotion of KRD control on edaphic properties. T…

Prevalence and distribution of human papillomavirus findings in swab specimens from gynaecology clinics of the east coast of Spain.

2010

The objective of this study was to determine the prevalence of human papillomavirus (HPV) among females in the east coast of Spain. A total of 1956 women visiting gynaecology clinics for routine check-ups were included in the study. Swabs were analyzed for HPV DNA by consensus polymerase chain reaction followed by direct sequencing. The overall HPV prevalence was 12.99%. HPV vaccine types 6, 11, 16 and 18 were detected in 6.13% of female participants.