Search results for "rnaseq"
showing 10 items of 13 documents
Exposure to environmental radionuclides is associated with altered metabolic and immunity pathways in a wild rodent
2019
Wildlife inhabiting environments contaminated by radionuclides face putative detrimental effects of exposure to ionizing radiation, with biomarkers such as an increase in DNA damage and/or oxidative stress commonly associated with radiation exposure. To examine the effects of exposure to radiation on gene expression in wildlife, we conducted a de novo RNA sequencing study of liver and spleen tissues from a rodent, the bank vole Myodes glareolus. Bank voles were collected from the Chernobyl Exclusion Zone (CEZ), where animals were exposed to elevated levels of radionuclides, and from uncontaminated areas near Kyiv, Ukraine. Counter to expectations, we did not observe a strong DNA damage resp…
Unraveling the Molecular Mechanism of Action of Empagliflozin in Heart Failure With Reduced Ejection Fraction With or Without Diabetes
2019
Visual Abstract
Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite
2023
The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called “RNASeq” and “VariantSeq” to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, “RNASeq” and “VariantSeq” are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Serv…
Differentially methylated genes in proliferative verrucous leukoplakia reveal potential malignant biomarkers for oral squamous cell carcinoma
2021
Objectives: To explore the pathophysiology of proliferative verrucous leucoplakia (PVL) through a methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) case-control study. Materials and & nbsp; Methods: Oral biopsies from ten PVL patients and five healthy individuals were obtained and used to compare their epigenetic patterns. Network biology methods and integrative analyses of MeDIP-seq and RNAseq data were applied to investigate functional relations among differentially methylated genes (DMGs). The value of selected genes as malignant biomarkers was evaluated in a large cohort of oral squamous cell carcinoma (OSCC) patients from TCGA.& nbsp; Results: A total of 464…
Single-cell RNA sequencing of SARS-CoV-2 cell entry factors in the preconceptional human endometrium.
2021
Abstract STUDY QUESTION Are SARS-CoV-2 canonical cell entry machinery, consisting of ACE2, TMPRSS2, NRP1 and LY6E, or alternative potential cell entry machinery, consisting of BSG, ANPEP, CD209, CLEC4G, TMPRSS4, TMPRSS11A, FURIN, CTSB, CTSL and IFITM1, expressed in the human endometrium across the menstrual cycle? SUMMARY ANSWER Analysis of cell entry factors for SARS-CoV-2 by single-cell RNA-sequencing (scRNAseq) in the preconceptional human endometrium reveals low risk of infection. WHAT IS KNOWN ALREADY Gene expression datasets from bulk endometrial tissue show no significant expression of the SARS-CoV-2 receptor ACE2 and TMPRSS2. This is in contrast to reported expression of ACE2 at the…
Functional genomic analysis of the response to hypoxic and oxidative stress in Candida albicans
2017
Candida albicans es el patógeno humano más prevalente. A pesar de ser un organismo comensal, también es un hongo oportunista que puede causar infecciones de seria gravedad en personas inmunodeprimidas. Aunque los principales factores de virulencia han sido caracterizados, el proceso exacto de patogénesis en Candida todavía se desconoce. Los mecanismos de adaptación a los distintos ambientes a los que se enfrenta durante la invasión del cuerpo humano todavía no están suficientemente caracterizados. En este trabajo se usaron análisis genómicos funcionales para el estudio de la respuesta global de C. albicans a dos estreses que encuentra durante la invasión del cuerpo humano: estrés oxidativo …
Réponse transcriptionnelle de différents porte-greffes de vigne à l’inoculation par le champignon mycorhizien à arbuscules Rhizophagus irregularis
2022
La vigne (Vitis vinifera) est l'une des cultures arboricoles les plus importantes au monde. Cependant, la vigne est soumise à de multiples stress biotiques et abiotiques liés, entre autres, au changement climatique. La mycorhize à arbuscules, est une symbiose mutualiste entre la majorité des plantes terrestre (>80%) et certains champignons telluriques. Du fait de son système racinaire de faible densité et constitué de racines relativement épaisses, la vigne est une plante fortement dépendante de la symbiose mycorhizienne à arbuscule (SMA) pour sa croissance et son développement. Dans cette étude, nous avons conduit une étude transcriptomique par RNAseq pour analyser les effets de la colonis…
The Impact of Moyamoya Disease and
2019
Moyamoya disease (MMD) is a rare cerebrovascular disorder characterized by occlusion of bilateral internal carotid and intracerebral arteries with the compensatory growth of fragile small vessels. MMD patients develop recurrent infarctions in the basal ganglia and subcortical regions. Symptoms include transient ischemic attack or stroke, seizures, and headaches, which may occur suddenly or in a stepwise progression. Mutations in Ring Finger Protein 213 (RNF213), a Zinc ring finger protein, have been identified in some MMD patients but the etiology of MMD is still largely unknown. To gain insight into the pathophysiology of MMD, we characterized the impact of the RNF213 mutations on plasma p…
Establecimiento de organoides derivados de pacientes con carcinoma colorrectal como modelo para cribado de drogas con acción antitumoral
2022
El cáncer colorrectal (CCR) es la segunda causa de muerte por cáncer a nivel mundial, y es el tercero en incidencia. En los últimos años se han realizado grandes avances para entender mejor los aspectos clínico-patológicos y moleculares del CCR lo que ha conducido a una mejora de las terapias y aumentado la supervivencia de los pacientes. Sin embargo, pese a estos avances muchos pacientes no se benefician de los tratamientos, lo que evidencia la necesidad de búsqueda de nuevos biomarcadores de respuesta y modelos preclínicos adecuados que permitan avanzar hacia una medicina más personalizada. En este contexto, la tecnología de los organoides ha revolucionado el estudio in vitro del cáncer, …
Transcriptional Rewiring, Adaptation, and the Role of Gene Duplication in the Metabolism of Ethanol of Saccharomyces cerevisiae
2020
Ethanol is the main by-product of yeast sugar fermentation that affects microbial growth parameters, being considered a dual molecule, a nutrient and a stressor. Previous works demonstrated that the budding yeast arose after an ancient hybridization process resulted in a tier of duplicated genes within its genome, many of them with implications in this ethanol “produce-accumulate-consume” strategy. The evolutionary link between ethanol production, consumption, and tolerance versus ploidy and stability of the hybrids is an ongoing debatable issue. The implication of ancestral duplicates in this metabolic rewiring, and how these duplicates differ transcriptionally, remains unsolved. Here, we …