Search results for "computational"
showing 10 items of 5884 documents
NOseq: amplicon sequencing evaluation method for RNA m6A sites after chemical deamination
2020
Abstract Methods for the detection of m6A by RNA-Seq technologies are increasingly sought after. We here present NOseq, a method to detect m6A residues in defined amplicons by virtue of their resistance to chemical deamination, effected by nitrous acid. Partial deamination in NOseq affects all exocyclic amino groups present in nucleobases and thus also changes sequence information. The method uses a mapping algorithm specifically adapted to the sequence degeneration caused by deamination events. Thus, m6A sites with partial modification levels of ∼50% were detected in defined amplicons, and this threshold can be lowered to ∼10% by combination with m6A immunoprecipitation. NOseq faithfully d…
Numerical simulations demonstrate that the double tapering of the spatualae of lizards and insects maximize both detachment resistance and stability
2011
Many biological attachment devices of insects, spiders and geckos consist of arrays of hairs (setae), which are terminated by contact elements of different shapes. However, the most frequently observed shape is a thin plate-like spatula. In spite of a rather wide range of sizes, most spatulae of different animals are not uniform, but rather possess a gradient in thickness and width. Here we show that the spatulae of insects and geckos become gradually thinner and wider approaching the end. This geometrical effect is explained in the present paper, by using a numerical approach for the modelling of the van der Waals adhesion and friction between the contact elements and the substrate. The ap…
A computational model of postprandial adipose tissue lipid metabolism derived using human arteriovenous stable isotope tracer data
2019
Given the association of disturbances in non-esterified fatty acid (NEFA) metabolism with the development of Type 2 Diabetes and Non-Alcoholic Fatty Liver Disease, computational models of glucose-insulin dynamics have been extended to account for the interplay with NEFA. In this study, we use arteriovenous measurement across the subcutaneous adipose tissue during a mixed meal challenge test to evaluate the performance and underlying assumptions of three existing models of adipose tissue metabolism and construct a new, refined model of adipose tissue metabolism. Our model introduces new terms, explicitly accounting for the conversion of glucose to glyceraldehye-3-phosphate, the postprandial …
Confined But-2-ene catalytic isomerization inside H-ZSM-5 models: A DFT study
2015
The isomerization of cis-but-2-ene to trans-but-2-ene within a 22T H-ZSM-5 zeolite model, also in the presence of two adsorbed Pd atoms, has been studied by DFT calculations. The results obtained allow us to state that the cis/trans but-2-ene isomerization can easily proceed inside unsupported zeolite cavities. In this case, differently than in the gas phase reaction, the trans-but-2-ene is less stable than the cis-but-2-ene, when adsorbed on the zeolite inner surface. Excluding the adsorption-desorption steps, the isomerization process involves two intermediates and three transition states, whose energy content is always very low with respect to that of reagents and intermediate species. T…
iGEMS: an integrated model for identification of alternative exon usage events.
2016
Abstract DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2.0 and performance was validated using RT-qPCR. First, AEU was studied in adipocytes treated with (n = 9) or without (n = 8) the anti-diabe…
Flexible switching of feedback control mechanisms allows for learning of different task dynamics.
2013
To produce skilled movements, the brain flexibly adapts to different task requirements and movement contexts. Two core abilities underlie this flexibility. First, depending on the task, the motor system must rapidly switch the way it produces motor commands and how it corrects movements online, i.e. it switches between different (feedback) control policies. Second, it must also adapt to environmental changes for different tasks separately. Here we show these two abilities are related. In a bimanual movement task, we show that participants can switch on a movement-by-movement basis between two feedback control policies, depending only on a static visual cue. When this cue indicates that the …
Development of primary early-onset colorectal cancers due to biallelic mutations of the FANCD1/BRCA2 gene
2013
International audience; Fanconi anaemia (FA) is characterized by progressive bone marrow failure, congenital anomalies, and predisposition to malignancy. In a minority of cases, FA results from biallelic FANCD1/BRCA2 mutations that are associated with early-onset leukaemia and solid tumours. Here, we describe the clinical and molecular features of a remarkable family presenting with multiple primary colorectal cancers (CRCs) without detectable mutations in genes involved in the Mendelian predisposition to CRCs. We unexpectedly identified, despite the absence of clinical cardinal features of FA, a biallelic mutation of the FANCD1/BRCA2 corresponding to a frameshift alteration (c.1845_1846del…
Genome-based in silico identification of new Mycobacterium tuberculosis antigens activating polyfunctional CD8+ T cells in human tuberculosis.
2011
Although CD8(+) T cells help control Mycobacterium tuberculosis infection, their M. tuberculosis Ag repertoire, in vivo frequency, and functionality in human tuberculosis (TB) remains largely undefined. We have performed genome-based bioinformatics searches to identify new M. tuberculosis epitopes presented by major HLA class I supertypes A2, A3, and B7 (covering 80% of the human population). A total of 432 M. tuberculosis peptides predicted to bind to HLA-A*0201, HLA-A*0301, and HLA-B*0702 (representing the above supertypes) were synthesized and HLA-binding affinities determined. Peptide-specific CD8(+) T cell proliferation assays (CFSE dilution) in 41 M. tuberculosis-responsive donors ide…
Single-Nucleotide Polymorphism Array-Based Karyotyping of Acute Promyelocytic Leukemia
2014
Acute promyelocytic leukemia (APL) is characterized by the t(15;17)(q22;q21), but additional chromosomal abnormalities (ACA) and other rearrangements can contribute in the development of the whole leukemic phenotype. We hypothesized that some ACA not detected by conventional techniques may be informative of the onset of APL. We performed the high-resolution SNP array (SNP-A) 6.0 (Affymetrix) in 48 patients diagnosed with APL on matched diagnosis and remission sample. Forty-six abnormalities were found as an acquired event in 23 patients (48%): 22 duplications, 23 deletions and 1 Copy-Neutral Loss of Heterozygocity (CN-LOH), being a duplication of 8(q24) (23%) and a deletion of 7(q33-qter) (…
1q gain and CDT2 overexpression underlie an aggressive and highly proliferative form of Ewing sarcoma
2012
12 páginas, 6 figuras, 1 tabla.-- et al.