Search results for "bioinformatics"
showing 10 items of 1632 documents
Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates
2021
Due to the widespread of the COVID-19 pandemic, the SARS-CoV-2 genome is evolving in diverse human populations. Several studies already reported different strains and an increase in the mutation rate. Particularly, mutations in SARS-CoV-2 spike-glycoprotein are of great interest as it mediates infection in human and recently approved mRNA vaccines are designed to induce immune responses against it. We analyzed 1,036,030 SARS-CoV-2 genome assemblies and 30,806 NGS datasets from GISAID and European Nucleotide Archive (ENA) focusing on non-synonymous mutations in the spike protein. Only around 2.5% of the samples contained the wild-type spike protein with no variation from the reference. Among…
Evaluation of Epigenetic and Radiomodifying Effects during Radiotherapy Treatments in Zebrafish
2021
Radiotherapy is still a long way from personalizing cancer treatment plans, and its effectiveness depends on the radiosensitivity of tumor cells. Indeed, therapies that are efficient and successful for some patients may be relatively ineffective for others. Based on this, radiobiological research is focusing on the ability of some reagents to make cancer cells more responsive to ionizing radiation, as well as to protect the surrounding healthy tissues from possible side effects. In this scenario, zebrafish emerged as an effective model system to test for radiation modifiers that can potentially be used for radiotherapeutic purposes in humans. The adoption of this experimental organism is fu…
Management of painful bone metastases.
2007
PURPOSE OF REVIEW: This review examines recent data on the pathophysiology and mechanisms of bone pain; it highlights the use of multiple and interdisciplinary treatments rather than sole use of traditional analgesics. RECENT FINDINGS: Bone pain has been shown to have a unique pathophysiology. Recent experimental (animal) models have revealed that, parallel to increased bone destruction, ipsilateral spinal cord segments that receive primary input from the cancerous femur exhibit several notable neurochemical changes. These mandate the use of opioid doses sufficient to inhibit the observed nociceptive behaviours; these doses are greater than those required to alleviate pain behaviours of com…
Dynamics and reactivity in Thermus aquaticus N6-adenine methyltransferase.
2014
M.TaqI is a DNA methyltransferase from Thermus aquaticus that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine to the N6 position of an adenine, a process described only in prokaryotes. We have used full atomistic classical molecular dynamics simulations to explore the protein–SAM–DNA ternary complex where the target adenine is flipped out into the active site. Key protein–DNA interactions established by the target adenine in the active site are described in detail. The relaxed structure was used for a combined quantum mechanics/molecular mechanics exploration of the reaction mechanism using the string method. According to our free energy calculations the reaction takes…
Monitoring Stemness in Long-Term hESC Cultures by Real-Time PCR
2009
Human embryonic stem cells (hESC) involve long-term cultures that must remain undifferentiated. The real-time PCR (RT-PCR) technique allows the relative quantification of target genes, including undifferentiation and differentiation markers when referred to a housekeeping control with the addition of a calibrator that serves as an internal control to compare different lots of reactions during the time. The main aspects will include a minimal number of cells to be analyzed, genes to be tested, and how to choose the appropriate calibrator sample and the reference gene. In this chapter, we present how to apply the RT-PCR technique, protocols for its performance, experimental set-up and softwar…
Epigenetic regulation of stemness maintenance in the neurogenic niches
2015
In the adult mouse brain, the subventricular zone lining the lateral ventricles and the subgranular zone in the dentate gyrus of the hippocampus are two zones that contain neural stem cells (NSCs) with the capacity to give rise to neurons and glia during the entire life of the animal. Spatial and temporal regulation of gene expression in the NSCs population is established and maintained by the coordinated interaction between transcription factors and epigenetic regulators which control stem cell fate. Epigenetic mechanisms are heritable alterations in genome function that do not involve changes in DNA sequence itself but that modulate gene expression, acting as mediators between the environ…
A new Multi-Layers Method to Analyze Gene Expression
2007
In the paper a new Multi-Layers approach (called Multi-Layers Model MLM) for the analysis of stochastic signals and its application to the analysis of gene expression data is presented. It consists in the generation of sub-samples from the input signal by applying a threshold technique based on cut-set optimal conditions. The MLM has been applied on synthetic and real microarray data for the identification of particular regions across DNA called nucleosomes and linkers. Nucleosomes are the fundamental repeating subunits of all eukaryotic chromatin, and their positioning provides useful information regarding the regulation of gene expression in eukaryotic cells. Results have shown a good rec…
Role of non-coding RNAs as biomarkers of deleterious cardiovascular effects in sepsis.
2021
The mechanisms occurring during sepsis that produce an increased risk of cardiovascular (CV) disease (CVD) are poorly understood. Even less information exists regarding CV dysfunction as a complication of sepsis, particularly for sepsis-induced cardiomyopathy. However, recent research has demonstrated that non-coding RNAs, including microRNAs, long non-coding RNAs, and circular RNAs, play a crucial role in genetic reprogramming, gene regulation, and inflammation during the development of CVD. Here we describe experimental findings showing the importance of non-coding RNAs mediating relevant mechanisms underlying CV dysfunction after sepsis, so contributing to sepsis-induced cardiomyopathy. …
Genomic insights into the different layers of gene regulation in yeast.
2011
The model organism Saccharomyces cerevisiae has allowed the development of new functional genomics techniques devoted to the study of transcription in all its stages. With these techniques, it has been possible to find interesting new mechanisms to control gene expression that act at different levels and for different gene sets apart from the known cis-trans regulation in the transcription initiation step. Here we discuss a method developed in our laboratory, Genomic Run-On, and other new methods that have recently appeared with distinct technical features. A comparison between the datasets generated by them provides interesting genomic insights into the different layers of gene regulation …
RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures
2020
The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class > Topology > Fold) with two new lev…