Search results for "ICO"
showing 10 items of 30544 documents
In silico prediction of Leishmania major -specific CD8+ epitopes
2017
Infections with Leishmania (L.) major induce protective IFN-γ-dependent Th1/Tc1 immunity in C57BL/6 mice as well as in immunocompetent humans. Even though antigen-specific immunity provides lifelong immunity against reinfection, a vaccine against this pathogen does not yet exist. Here, we compared the results obtained from in silico predictions of murine CD8-specific L. major peptides using the algorithm SYFPEITHI with the number and predicted affinity of known proteins/peptides. Our results indicate that the majority of "immunodominant" epitopes of L. major have not been identified so far; thus, computer-based prediction algorithms may aid the development of an effective vaccine.
In Silico Typing of Classical and Non-classical HLA Alleles from Standard RNA-Seq Reads
2018
Next-Generation Sequencing (NGS) enables the rapid generation of billions of short nucleic acid sequence fragments (i.e., "sequencing reads"). Especially, the adoption of gene expression profiling using whole transcriptome sequencing (i.e., "RNA-Seq") has been rapid. Here, we describe an in silico method, seq2HLA, that takes standard RNA-Seq reads as input and determines a sample's (classical and non-classical) HLA class I and class II types as well as HLA expression. We demonstrate the application of seq2HLA using publicly available RNA-Seq data from the Burkitt's lymphoma cell line DAUDI and the choriocarcinoma cell line JEG-3.
Conservation status and historical relatedness of Italian cattle breeds
2018
Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Ou…
In Situ, Light-Guided Axon Growth on Biomaterials via Photoactivatable Laminin Peptidomimetic IK(HANBP)VAV
2018
The ability to guide the growth of neurites is relevant for reconstructing neural networks and for nerve tissue regeneration. Here, a biofunctional hydrogel that allows light-based directional control of axon growth in situ is presented. The gel is covalently modified with a photoactivatable derivative of the short laminin peptidomimetic IKVAV. This adhesive peptide contains the photoremovable group 2-(4′-amino-4-nitro-[1,1′-biphenyl]-3-yl)propan-1-ol (HANBP) on the Lys rest that inhibits its activity. The modified peptide is highly soluble in water and can be simply conjugated to -COOH containing hydrogels via its terminal -NH 2 group. Light exposure allows presentation of the IKVAV adhesi…
N-(2-methyl-indol-1H-5-yl)-1-naphthalenesulfonamide : a novel reversible antimitotic agent inhibiting cancer cell motility
2016
Este es el post-print que se ha publicado de forma definitiva en: https://www.sciencedirect.com/science/article/abs/pii/S0006295216301423 A series of compounds containing the sulfonamide scaffold were synthesized and screened for their in vitro anticancer activity against a representative panel of human cancer cell lines, leading to the identification of N-(2-methyl-1H-indol-5-yl)-1-naphthalenesulfonamide (8e) as a compound showing a remarkable activity across the panel, with IC50 values in the nanomolar-to-low micromolar range. Cell cycle distribution analysis revealed that 8e promoted a severe G2/M arrest, which was followed by cellular senescence as indicated by the detection of senescen…
A unique view of SARS-CoV-2 through the lens of ORF8 protein
2021
Immune evasion is one of the unique characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) attributed to its ORF8 protein. This protein modulates the adaptive host immunity through down-regulation of MHC-1 (Major Histocompatibility Complex) molecules and innate immune responses by surpassing the host's interferon-mediated antiviral response. To understand the host's immune perspective concerning the ORF8 protein, a comprehensive study of the ORF8 protein and mutations possessed by it have been performed. Chemical and structural properties of ORF8 proteins from different hosts, such as human, bat, and pangolin, suggest that the ORF8 of SARS-CoV-2 is much closer to OR…
In Silico Insights towards the Identification of NLRP3 Druggable Hot Spots
2019
NLRP3 (NOD-like receptor family, pyrin domain-containing protein 3) activation has been linked to several chronic pathologies, including atherosclerosis, type-II diabetes, fibrosis, rheumatoid arthritis, and Alzheimer’s disease. Therefore, NLRP3 represents an appealing target for the development of innovative therapeutic approaches. A few companies are currently working on the discovery of selective modulators of NLRP3 inflammasome. Unfortunately, limited structural data are available for this target. To date, MCC950 represents one of the most promising noncovalent NLRP3 inhibitors. Recently, a possible region for the binding of MCC950 to the NLRP3 protein was described but no details were …
Assessing data analysis performance in research contexts: An experiment on accuracy, efficiency, productivity and researchers’ satisfaction
2018
[EN] Any knowledge generation process involves raw data comprehension, evaluation and inferential reasoning. These practices, common to different disciplines, are known as data analysis, and represent the most important set of activities in research contexts. Researchers use data analysis software methods and tools for generating new knowledge in their daily data analysis. In recent years, data analysis software has been incorporating explicit references in modelling of cognitive processes, in order to improve the assistance offered in data analysis tasks. However, data analysis software commercial suites are still resisting this inclusion, and there is little empirical work done in knowing…
Myofilament function and body mass index.
2017
Body mass is reported to influence myocardial performance. Recent studies have emphasised the importance of negative inotropic adipocyte-derived factors and their impact on cardiac contractile function. However, the underlying mechanisms remain unclear. We aimed to determine whether body mass impacts cardiac force development on the level of the contractile apparatus. We examined the influence of body mass index (BMI) (3 groups: group I >25, group II 25–30, group III >30) on the myocardial performance of skinned muscle fibres. Right atrial tissue preparations of 70 patients undergoing aortocoronary bypass operation (CABG, 48 patients, group a) and aortic valve replacement (AVR, 22 patients,…
Iflavirus increases its infectivity and physical stability in association with baculovirus
2016
Virus transmission and the prevalence of infection depend on multiple factors, including the interaction with other viral pathogens infecting the same host. In this study, active replication of an iflavirus, Spodoptera exigua iflavirus 1 (order Picornavirales) was observed in the offspring of insects that survived following inoculation with a pathogenic baculovirus, Spodoptera exigua multiple nucleopolyhedrovirus. Tracking the origin of the iflavirus suggested the association of this virus with the occlusion bodies of the baculovirus. Here we investigated the effect of this association on the stability and infectivity of both viruses. A reduction in baculovirus pathogenicity, without affect…