Search results for "NR"
showing 10 items of 6911 documents
The HDAC6 Inhibitor tubacin induces release of CD133+ extracellular vesicles from cancer cells
2017
Tumor-derived extracellular vesicles (EVs) are emerging as an important mode of intercellular communication, capable of transferring biologically active molecules that facilitate the malignant growth and metastatic process. CD133 (Prominin-1), a stem cell marker implicated in tumor initiation, differentiation and resistance to anti-cancer therapy, is reportedly associated with EVs in various types of cancer. However, little is known about the factors that regulate the release of these CD133+ EVs. Here, we report that the HDAC6 inhibitor tubacin promoted the extracellular release of CD133+ EVs from human FEMX-I metastatic melanoma and Caco-2 colorectal carcinoma cells, with a concomitant dow…
Disease–Genes Must Guide Data Source Integration in the Gene Prioritization Process
2019
One of the main issues in detecting the genes involved in the etiology of genetic human diseases is the integration of different types of available functional relationships between genes. Numerous approaches exploited the complementary evidence coded in heterogeneous sources of data to prioritize disease-genes, such as functional profiles or expression quantitative trait loci, but none of them to our knowledge posed the scarcity of known disease-genes as a feature of their integration methodology. Nevertheless, in contexts where data are unbalanced, that is, where one class is largely under-represented, imbalance-unaware approaches may suffer a strong decrease in performance. We claim that …
Enhanced autophagic-lysosomal activity and increased BAG3-mediated selective macroautophagy as adaptive response of neuronal cells to chronic oxidati…
2019
Oxidative stress and a disturbed cellular protein homeostasis (proteostasis) belong to the most important hallmarks of aging and of neurodegenerative disorders. The proteasomal and autophagic-lysosomal degradation pathways are key measures to maintain proteostasis. Here, we report that hippocampal cells selected for full adaptation and resistance to oxidative stress induced by hydrogen peroxide (oxidative stress-resistant cells, OxSR cells) showed a massive increase in the expression of components of the cellular autophagic-lysosomal network and a significantly higher overall autophagic activity. A comparative expression analysis revealed that distinct key regulators of autophagy are upregu…
Discriminating graph pattern mining from gene expression data
2016
We consider the problem of mining gene expression data in order to single out interesting features that characterize healthy/unhealthy samples of an input dataset. We present and approach based on a network model of the input gene expression data, where there is a labelled graph for each sample. To the best of our knowledge, this is the first attempt to build a different graph for each sample and, then, to have a database of graphs for representing a sample set. Out main goal is that of singling out interesting differences between healthy and unhealthy samples, through the extraction of "discriminating patterns" among graphs belonging to the two different sample sets. Differently from the …
Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing
2018
AbstractAptamers have in recent years emerged as a viable alternative to antibodies. High-throughput sequencing (HTS) has revolutionized aptamer research by increasing the number of reads from a few (using Sanger sequencing) to millions (using an HTS approach). Despite the availability and advantages of HTS compared to Sanger sequencing, there are only 50 aptamer HTS sequencing samples available on public databases. HTS data in aptamer research are primarily used to compare sequence enrichment between subsequent selection cycles. This approach does not take full advantage of HTS because the enrichment of sequences during selection can be due to inefficient negative selection when using live…
Application of Graph Clustering and Visualisation Methods to Analysis of Biomolecular Data
2018
In this paper we present an approach based on integrated use of graph clustering and visualisation methods for semi-supervised discovery of biologically significant features in biomolecular data sets. We describe several clustering algorithms that have been custom designed for analysis of biomolecular data and feature an iterated two step approach involving initial computation of thresholds and other parameters used in clustering algorithms, which is followed by identification of connected graph components, and, if needed, by adjustment of clustering parameters for processing of individual subgraphs.
EFMviz
2020
Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge. In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes. The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (Escherichia coli, iAF1…
Data mining approaches to identify biomineralization related sequences.
2015
Proteomics is an efficient high throughput technique developed to identify proteins from a crude extract using sequence homology. Advances in Next Generation Sequencing (NGS) have led to increase knowledge of several non-model species. In the field of calcium carbonate biomineralization, the paucity of available sequences (such as the ones of mollusc shells) is still a bottleneck in most proteomic studies. Indeed, this technique needs proteins databases to find homology. The aim of this study was to perform different data mining approaches in order to identify novel shell proteins. To this end, we disposed of several publicly non-model molluscs databases. Previously identified molluscan she…
Network-Wide Adaptive Burst Detection Depicts Neuronal Activity with Improved Accuracy
2017
Neuronal networks are often characterized by their spiking and bursting statistics. Previously, we introducedan adaptive burst analysis methodwhich enhances the analysis power for neuronal networks with highly varying firing dynamics. The adaptation is based on single channels analyzing each element of a network separately. Such kind of analysis was adequate for the assessment of local behavior, where the analysis focuses on the neuronal activity in the vicinity of a single electrode. However, the assessment of the whole network may be hampered, if parts of the network are analyzed using different rules. Here, we test how using multiple channels and measurement time points affect adaptive b…
A new parallel pipeline for DNA methylation analysis of long reads datasets
2017
Background DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of the DNA sequence (Methyl-seq). Several software tools for methylation analysis have been proposed over recent years. However, the current trend is that the new sequencers and the ones expected for an upcoming future yield sequences of increasing length, making these software tools inefficient and obsolete. Results In this paper, we propose a new software based on a strategy for methylation analysis of Methyl-seq sequencing data that requires much shorter execution times while…