Search results for " sequencing"
showing 10 items of 976 documents
Genomics and Proteomics Analyses Revealed Novel Candidate Pesticidal Proteins in a Lepidopteran-Toxic Bacillus thuringiensis Strain
2020
Discovery and identification of novel insecticidal proteins in Bacillus thuringiensis (Bt) strains are of crucial importance for efficient biological control of pests and better management of insect resistance. In this study, the Bt strain KhF, toxic for Plodia interpunctella and Grapholita molesta larvae, underwent genomics and proteomics analyses to achieve a better understanding of the bases of its pathogenicity. The whole-genome sequencing results revealed that the KhF strain contained nine coding sequences with homologies to Bt insecticidal genes. The lepidopteran toxic mixture of spores and crystals of this Bt strain was subjected to liquid chromatography and tandem mass spectrometry …
Clinical Delineation Of A Subtype Of Frontonasal Dysplasia With Creased Nasal Ridge And Upper Limb Anomalies: Report Of Six Unrelated Patients
2017
IF 2.259; International audience; Frontonasal dysplasias are rare congenital malformations of frontonasal process-derived structures, characterized by median cleft, nasal anomalies, widely spaced eyes, and cranium bifidum occultum. Several entities of syndromic frontonasal dysplasia have been described, among which, to date, only a few have identified molecular bases. We clinically ascertained a cohort of 124 individuals referred for frontonasal dysplasia. We identified six individuals with a similar phenotype, including one discordant monozygous twin. Facial features were remarkable by nasal deformity with creased ridge and depressed or absent tip, widely spaced eyes, almond-shaped palpebr…
Association of Variants in the SPTLC1 Gene with Juvenile Amyotrophic Lateral Sclerosis
2021
Key Points Question What genetic variants are associated with juvenile amyotrophic lateral sclerosis (ALS)? Findings In this family-based genetic study, exome sequencing was performed in 3 patients diagnosed with juvenile ALS and failure to thrive; this identified de novo variants in SPTLC1 (p.Ala20Ser in 2 patients and p.Ser331Tyr in 1 patient). Variants in SPTLC1 are a known cause of hereditary sensory and autonomic neuropathy, type 1A, and these data extend the phenotype associated with this gene. Meaning De novo variants in the SPTLC1 gene are associated with juvenile ALS, a fatal neurological disorder.
5-methylcytosine modification of an Epstein–Barr virus noncoding RNA decreases its stability
2020
Many cellular noncoding RNAs contain chemically modified nucleotides that are essential for their function. The Epstein–Barr virus expresses two highly abundant noncoding RNAs called EBV-encoded RNA 1 (EBER1) and EBER2. To examine whether these viral RNAs contain modified nucleotides, we purified native EBERs from EBV-infected cells and performed mass spectrometry analysis. While EBER2 contains no modified nucleotides at stoichiometric amounts, EBER1 was found to carry 5-methylcytosine (m5C) modification. Bisulfite sequencing indicated that a single cytosine of EBER1 is methylated in ∼95% of molecules, and the RNA methyltransferase NSUN2 was identified as the EBER1-specific writer. Intrigui…
Artificial Chromosomes to Explore and to Exploit Biosynthetic Capabilities of Actinomycetes
2012
Actinomycetes are an important source of biologically active compounds, like antibiotics, antitumor agents, and immunosuppressors. Genome sequencing is revealing that this class of microorganisms has larger genomes relative to other bacteria and uses a considerable fraction of its coding capacity (5–10%) for the production of mostly cryptic secondary metabolites. To access actinomycetes biosynthetic capabilities or to improve the pharmacokinetic properties and production yields of these chemically complex compounds, genetic manipulation of the producer strains can be performed. Heterologous expression in amenable hosts can be useful to exploit and to explore the genetic potential of actinom…
Effect of organic loading rate on the production of Polyhydroxyalkanoates from sewage sludge
2023
The aim of this work was to study the effect of organic loading rate on the production of Polyhydroxyalkanoates (PHA) from sewage sludge. Synthesis of PHA using sewage sludge as platform was achieved in this work. Three pilot-scale selection-sequencing batch reactors (S-SBR) were used for obtaining a culture able to accumulate PHA following a strategy of aerobic dynamic feeding (ADF) at different volumetric organic-loading-rate (vOLR): 1.3, 1.8 and 0.8 g COD L-1 d-1 for S-SBR 1, S-SBR 2 and S-SBR 3, respectively. Decreasing the vOLR enhanced the general performance of the process as for organic matter removal (from 99.2% ± 0.3% in S-SBR-3 to 92 ± 2 in S-SBR-2) while the opposite trend was r…
Ancient human DNA.
2011
The contribution of palaeogenetic data to the study of various aspects of hominin biology and evolution has been significant, and has the potential to increase substantially with the widespread implementation of next generation sequencing techniques. Here we discuss the present state-of-the-art of ancient human DNA analysis and the characteristics of hominin aDNA that make sequence validation particularly complex. A brief overview of the development of anthropological palaeogenetic analysis is given to illustrate the technical challenges motivating recent technological advancements.
Parallelized short read assembly of large genomes using de Bruijn graphs
2011
Abstract Background Next-generation sequencing technologies have given rise to the explosive increase in DNA sequencing throughput, and have promoted the recent development of de novo short read assemblers. However, existing assemblers require high execution times and a large amount of compute resources to assemble large genomes from quantities of short reads. Results We present PASHA, a parallelized short read assembler using de Bruijn graphs, which takes advantage of hybrid computing architectures consisting of both shared-memory multi-core CPUs and distributed-memory compute clusters to gain efficiency and scalability. Evaluation using three small-scale real paired-end datasets shows tha…
An Unexplained Congenital Disorder of Glycosylation-II in a Child with Neurohepatic Involvement, Hypercholesterolemia and Hypoceruloplasminemia
2017
We report on a 12-year-old adopted boy with psychomotor disability, absence seizures, and normal brain MRI. He showed increased (but initially, at 5 months, normal) serum cholesterol, increased alkaline phosphatases, transiently increased transaminases and hypoceruloplasminemia with normal serum and urinary copper. Blood levels of immunoglobulins, haptoglobin, antithrombin, and factor XI were normal. A type 2 serum transferrin isoelectrofocusing and hypoglycosylation of apoCIII pointed to a combined N- and O-glycosylation defect. Neither CDG panel analysis with 79 CDG-related genes, nor whole exome sequencing revealed the cause of this CDG. Whole genome sequencing was not performed since th…