Search results for "Sequencing"
showing 10 items of 1087 documents
easyPAC: A Tool for Fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from Alignments or Consensus Sequences
2012
Video abstract A video abstract by the authors of this paper is available. video-abstract8870.mov
The Administration of Escherichia coli Nissle 1917 Ameliorates Development of DSS-Induced Colitis in Mice
2018
The beneficial effects of probiotics on immune-based pathologies such as inflammatory bowel disease (IBD) have been well reported. However, their exact mechanisms have not been fully elucidated. Few studies have focused on the impact of probiotics on the composition of the colonic microbiota. The aim of the present study was to correlate the intestinal anti-inflammatory activity of the probiotic Escherichia coli Nissle 1917 (EcN) in the dextran sodium sulfate (DSS) model of mouse colitis with the changes induced in colonic microbiota populations. EcN prevented the DSSinduced colonic damage, as evidenced by lower disease activity index (DAI) values and colonic weight/length ratio, when compa…
Interpretation of gut microbiota data in the ‘eye of the beholder’: A commentary and re‐evaluation of data from ‘Impacts of radiation exposure on the…
2021
1.Evidence that exposure to environmental pollutants can alter the gut microbiota composition of wildlife includes studies of rodents exposed to radionuclides. 2.Antwis et al. (2021) used amplicon sequencing to characterise the gut microbiota of four species of rodent (Myodes glareolus, Apodemus agrarius, A. flavicollis and A. sylvaticus) inhabiting the Chernobyl Exclusion Zone (CEZ) to examine possible changes in gut bacteria (microbiota) and gut fungi (mycobiota) associated with exposure to radionuclides and whether the sample type (from caecum or faeces) affected the analysis. 3.The conclusions derived from the analyses of gut mycobiota are based on data that represent a mixture of inges…
A New Feature Selection Methodology for K-mers Representation of DNA Sequences
2015
DNA sequence decomposition into k-mers and their frequency counting, defines a mapping of a sequence into a numerical space by a numerical feature vector of fixed length. This simple process allows to compare sequences in an alignment free way, using common similarities and distance functions on the numerical codomain of the mapping. The most common used decomposition uses all the substrings of a fixed length k making the codomain of exponential dimension. This obviously can affect the time complexity of the similarity computation, and in general of the machine learning algorithm used for the purpose of sequence analysis. Moreover, the presence of possible noisy features can also affect the…
The transcriptome analysis of Strongyloides stercoralis L3i larvae reveals targets for intervention in a neglected disease.
2012
Background: Strongyloidiasis is one of the most neglected diseases distributed worldwide with endemic areas in developed countries, where chronic infections are life threatening. Despite its impact, very little is known about the molecular biology of the parasite involved and its interplay with its hosts. Next generation sequencing technologies now provide unique opportunities to rapidly address these questions. Principal Findings: Here we present the first transcriptome of the third larval stage of S. stercoralis using 454 sequencing coupled with semi-automated bioinformatic analyses. 253,266 raw sequence reads were assembled into 11,250 contiguous sequences, most of which were novel. 8037…
Novel Mutations in the Asparagine Synthetase Gene (ASNS) Associated With Microcephaly
2018
Microcephaly is a devastating condition defined by a small head and small brain compared to the age- and sex-matched population. Mutations in a number of different genes causative for microcephaly have been identified, e.g., MCPH1, WDR62, and ASPM. Recently, mutations in the gene encoding the enzyme asparagine synthetase (ASNS) were associated to microcephaly and so far 24 different mutations in ASNS causing microcephaly have been described. In a family with two affected girls, we identified novel compound heterozygous variants in ASNS (c.1165G > C, p.E389Q and c.601delA, p.M201Wfs∗28). The first mutation (E389Q) is a missense mutation resulting in the replacement of a glutamate residue …
Neoantigens Generated by Individual Mutations and Their Role in Cancer Immunity and Immunotherapy
2017
Recent preclinical and clinical studies have proved the long-standing hypothesis that tumors elicit adaptive immune responses and that the antigens driving effective T-cell response are neoantigens, i.e., peptides that are generated from somatically mutated genes. Hence, the characterization of neoantigens and the identification of the immunogenic ones are of utmost importance for improving cancer immunotherapy and broadening its efficacy to a larger fraction of patients. In this review, we first introduce the methods used for the quantification of neoantigens using next-generation sequencing data and then summarize results obtained using these tools to characterize the neoantigen landscape…
Diagnosis of exon 12‐positive polycythemia vera rescued by NGS
2020
Abstract A JAK2V617F‐negative polycythemia associated with low serum epo needs to be tested for an exon 12 JAK2 mutation. When negative, due to potential serious complications in PV, a next generation sequencing is necessary to rule out false negative results.
SNPs detection by eBWT positional clustering
2019
Sequencing technologies keep on turning cheaper and faster, thus putting a growing pressure for data structures designed to efficiently store raw data, and possibly perform analysis therein. In this view, there is a growing interest in alignment-free and reference-free variants calling methods that only make use of (suitably indexed) raw reads data. We develop the positional clustering theory that (i) describes how the extended Burrows–Wheeler Transform (eBWT) of a collection of reads tends to cluster together bases that cover the same genome position (ii) predicts the size of such clusters, and (iii) exhibits an elegant and precise LCP array based procedure to locate such clusters in the e…
Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change
2017
The global biogeography of microorganisms remains poorly resolved, which limits the current understanding of microbial resilience toward environmental changes. Using high-throughput 16S rRNA gene amplicon sequencing, we characterized the microbial diversity of terrestrial and lacustrine biofilms from the Arctic, Antarctic and temperate regions. Our analyses suggest that bacterial community compositions at the poles are more similar to each other than they are to geographically closer temperate habitats, with 32% of all operational taxonomic units (OTUs) co-occurring in both polar regions. While specific microbial taxa were confined to distinct regions, representing potentially endemic popul…