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DNA sequencing Research

14:01 EDT 17th October 2018 | BioPortfolio

Analysis of differentially expressed circular RNAs for the identification of a coexpression RNA network and signature in colorectal cancer.

Circular RNAs (circRNAs) play an important regulatory role in tumorigenesis. The aim of the present study was to analyze the circRNA expression network and elucidate its potential implications in colorectal cancer (CRC). The circRNA expression profile was analyzed in CRC tissues by RNA sequencing, and the functions of differentially expressed genes were analyzed by Gene Ontology (GO) and Kyoto Enc...

Transcriptom analysis revealed regulation of dexamethasone induced microRNAs in chicken thymus.

Stress-induced immunosuppression is one of the serious threats to the poultry industry, especially obvious for young chicken. However, the molecular mechanism of stress-induced immunosuppression has not been clear in chicken. Here, we established an immunosuppression model of 7-day-old chickens with injecting dexamethasone (Dex) to analyze the molecular regulation in the chicken thymus. The micro...

Meningococcal B (4CMenB) vaccine : uptodate and recommendations.

Neisseria meningitidis is the cause of relatively rare invasive infections, but with very important morbi-mortality. Vaccines are already available for serogroups A, C, W, Y. A new vaccine against meningococcus B is on the Belgian market since March 2017. Serogroup B is the most prevalent in Western countries. The target populations are children and teenager, since it is at this age that peaks in ...

Altered Levels of Long NcRNAs Meg3 and Neat1 in Cell and Animal models of Huntington's Disease.

Altered expression levels of protein-coding genes and microRNAs have been implicated in the pathogenesis of Huntington's disease (HD). The involvement of other ncRNAs, especially long ncRNAs (lncRNA), is being realized recently and the related knowledge is still rudimentary. Using small RNA sequencing and PCR arrays we observed perturbations in the levels of 12 ncRNAs in HD mouse brain, eight of w...

A synonymous RET substitution enhances the oncogenic effect of an in-cis missense mutation by increasing constitutive splicing efficiency.

Synonymous mutations continue to be filtered out from most large-scale cancer genome studies, but several lines of evidence suggest they can play driver roles in neoplastic disease. We investigated a case of an aggressive, apparently sporadic medullary thyroid carcinoma (MTC) harboring a somatic RET p.Cys634Arg mutation (a known MTC driver). A germ-line RET substitution (p.Cys630=) had also been f...

Streptococcal Lancefield polysaccharides are critical cell wall determinants for human Group IIA secreted phospholipase A2 to exert its bactericidal effects.

Human Group IIA secreted phospholipase A2 (hGIIA) is an acute phase protein with bactericidal activity against Gram-positive bacteria. Infection models in hGIIA transgenic mice have suggested the importance of hGIIA as an innate defense mechanism against the human pathogens Group A Streptococcus (GAS) and Group B Streptococcus (GBS). Compared to other Gram-positive bacteria, GAS is remarkably resi...

Transcriptomics-based identification and characterization of 11 CYP450 genes of Panax ginseng responsive to MeJA.

Cytochromes P450 (CYP450s), a superfamily of mono-oxygenases, are essential to generate highly functionalized secondary metabolites in plants and contribute to the diversification of specialized triterpenoid biosynthesis in eudicots. However, screening and identifying the exact CYP450 genes in ginsenoside biosynthesis is extremely challenging due to existence of large quantities of members in CYP4...

Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP.

GBS-SNP-CROP is a bioinformatics pipeline originally developed to support the cost-effective genome-wide characterization of plant genetic resources through paired-end genotyping-by-sequencing (GBS), particularly in the absence of a reference genome. Since its 2016 release, the pipeline's functionality has greatly expanded, its computational efficiency has improved, and its applicability to a broa...

MetaSMC: A Coalescent-based Shotgun Sequence Simulator for Evolving Microbial Populations.

High-throughput sequencing technology has revolutionized the study of metagenomics and cancer evolution. In a relatively simple environment, a metagenomics sequencing data is dominated by a few species. By analyzing the alignment of reads from microbial species, single nucleotide polymorphisms can be discovered and the evolutionary history of the populations can be reconstructed. The ever-increasi...

Cross-sectional whole-genome sequencing and epidemiological study of multidrug-resistant Mycobacterium tuberculosis in China.

The increase in MDR-TB severely hampers TB prevention and control in China, a country with the second highest MDR-TB burden globally. The first nationwide drug-resistant TB surveillance program provides an opportunity to comprehensively investigate the epidemiological/drug-resistance characteristics, potential drug-resistance mutations, and effective population changes of Chinese MDR-TB.

SCALOP: sequence-based antibody canonical loop structure annotation.

Canonical forms of the antibody complementarity-determining regions (CDRs) were first described in 1987 and have been redefined on multiple occasions since. The canonical forms are often used to approximate the antibody binding site shape as they can be predicted from sequence. A rapid predictor would facilitate the annotation of CDR structures in the large amounts of repertoire data now becoming ...

CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes.

Identification of conserved syntenic blocks across microbial genomes is important for several problems in comparative genomics such as gene annotation, study of genome organization and evolution, and prediction of gene interactions. Current tools for syntenic block discovery do not scale up to the large quantity of prokaryotic genomes available today.

Impact of next generation sequencing defined HIV pre-treatment drug resistance on virological outcomes in the ANRS 12249 treatment as prevention trial.

Previous studies in HIV-positive individuals on thymidine analogue backbone antiretroviral therapy (ART) with either nevirapine or efavirenz have suggested poorer virological outcomes in the presence of pretreatment drug resistance (PDR). We assessed the impact of PDR on virological suppression (VS) [

Emergent Behavior of IBD-Associated Escherichia coli During Disease.

Inflammatory bowel diseases are becoming increasingly common throughout the world, both in developed countries and increasingly in rapidly developing countries. Multiple lines of evidence point to a role for the microbial composition of the gastrointestinal tract in the etiology of IBD, but to date, attempts to define a specific microbial cause for IBD have proved unsuccessful. Microbial 16S rRNA ...

The fascinating world of non-coding RNA and how it may help to unravel the mysteries of tooth movement regulation.

The innovative study presented by Huang and co-workers in this issue of the European Journal of Orthodontics is one of the first giving insight into the mostly disregarded world of non-coding ribonucleic acids in orthodontics. In other fields of science non-coding ribonucleic acids have been shown to play a major role in the regulation of cell metabolism as well as the aetiology of diseases such a...

The genomic basis of tumor regression in Tasmanian devils (Sarcophilus harrisii).

Understanding the genetic basis of disease-related phenotypes, such as cancer susceptibility, is crucial for the advancement of personalized medicine. Although most cancers are somatic in origin, a small number of transmissible cancers have been documented. Two such cancers have emerged in the Tasmanian devil (Sarcophilus harrisii ) and now threaten the species with extinction. Recently, cases of ...

Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition.

Phase-variation of Type I restriction-modification systems can rapidly alter the sequence motifs they target, diversifying both the epigenetic patterns and endonuclease activity within clonally descended populations. Here, we characterize the Streptococcus pneumoniae SpnIV phase-variable Type I RMS, encoded by the translocating variable restriction (tvr) locus, to identify its target motifs, mecha...

Host developmental toxicity of BPA and BPA alternatives is inversely related to microbiota disruption in zebrafish.

Host-associated microbiota can biotransform xenobiotics, mediate health effects of chemical exposure, and play important roles in early development. Bisphenol A (BPA) is a widespread environmental chemical that has been associated with adverse endocrine and neurodevelopmental effects, some of which may be mediated by microbiota. Growing public concern over the safety of BPA has resulted in its rep...

DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells.

DNMT3L (DNMT3-like), a member of the DNMT3 family, has no DNA methyltransferase activity but regulates de novo DNA methylation. While biochemical studies show that DNMT3L is capable of interacting with both DNMT3A and DNMT3B and stimulating their enzymatic activities, genetic evidence suggests that DNMT3L is essential for DNMT3A-mediated de novo methylation in germ cells but is dispensable for de ...

Antibody discovery and the arrow of time.

RetroRules: a database of reaction rules for engineering biology.

RetroRules is a database of reaction rules for metabolic engineering (https://retrorules.org). Reaction rules are generic descriptions of chemical reactions that can be used in retrosynthesis workflows in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors. The use of such rules is becoming increasingly important in the context of synthetic biology ap...

New approach for understanding genome variations in KEGG.

KEGG (Kyoto Encyclopedia of Genes and Genomes; https://www.kegg.jp/ or https://www.genome.jp/kegg/) is a reference knowledge base for biological interpretation of genome sequences and other high-throughput data. It is an integrated database consisting of three generic categories of systems information, genomic information and chemical information, and an additional human-specific category of healt...

Actinomadura vinacea isolated from a nonhealing cutaneous wound in a cat.

A 6-year-old, spayed female, domestic shorthair cat was presented to the University of Georgia Veterinary Teaching Hospital for a 3-year history of a nonhealing wound on the right tarsus. The wound temporarily resolved with medical management, but intermittently recurred when antimicrobials were discontinued. At presentation, the wound had become refractory to antimicrobial therapy. Physical exami...

Neuronal and vascular deficits following chronic adaptation to high altitude.

We sought to understand the mechanisms underlying cognitive deficits that are reported to affect non-native subjects following their prolonged stay and/or work at high altitude (HA). We found that mice exposed to a simulated environment of 5000 m exhibit deficits in hippocampal learning and memory accompanied by abnormalities in brain MR imaging. Exposure (1-8 months) to HA led to an increase ...

Intratumoral Heterogeneity in Recurrent Metastatic Squamous Cell Carcinoma of the Oral Cavity: New Perspectives Afforded by Multiregion DNA Sequencing and mtDNA Analysis.

Improvements in sequencing technologies have shown that genetic differences among neoplastic cells can reflect clonal expansion. Intratumor heterogeneity (ITH) has been suggested to explain differences in prognosis and treatment response, indicating that personalized medicine is the goal of the future. This study evaluated ITH in 5 patients with recurrent metastatic oral squamous cell carcinoma (O...

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