Search results for " Genes"
showing 10 items of 322 documents
Detection of condition-specific marker genes from RNA-seq data with MGFR
2019
The identification of condition-specific genes is key to advancing our understanding of cell fate decisions and disease development. Differential gene expression analysis (DGEA) has been the standard tool for this task. However, the amount of samples that modern transcriptomic technologies allow us to study, makes DGEA a daunting task. On the other hand, experiments with low numbers of replicates lack the statistical power to detect differentially expressed genes. We have previously developed MGFM, a tool for marker gene detection from microarrays, that is particularly useful in the latter case. Here, we have adapted the algorithm behind MGFM to detect markers in RNA-seq data. MGFR groups s…
Wolbachia (alphaproteobacteria: rickettsiales) infections in isolated aphid populations from oceanic islands of the Azores archipelago: revisiting th…
2019
Aphids (Hemiptera: Aphididae) have provided a suitable model to study endosymbionts, their community, and dynamics since the discovery of the obligate endosymbiont Buchnera aphidicola in these organisms. In previous studies, Wolbachia was found in some aphid species. In the present study, we report the prevalence of Wolbachia in aphids sampled from a geographically isolated region (Azores Islands), aiming at a better understanding and characterization of the two newly reported supergroups, M and N. The description of the supergroup M was based on 16S rRNA as well as some protein-coding genes. However, the assignment of the supergroup N was according to 16S rRNA gene sequences of a very few …
Profiling the physiological and molecular response to sulfonamidic drag in Procambarus clarkii
2014
Sulfamethoxazole (SMZ) is one of the most widely employed sulfonamides. Because of the widespread use of SMZ, a considerable amount is indeed expected to be introduced into the environment. The cytotoxicity of SMZ relies mainly on arylhydroxylamine metabolites (S-NOH) of SMZ and it is associated with the production of reactive oxygen species (ROS). There is limited information about the toxic potential of SMZ at the cellular and molecular levels, especially in aquatic and/or non-target organisms. In the present study, the red swamp crayfish (Procambarus clarkii), being tolerant to extreme environmental conditions and resistant to disease, was used as a model organism to profile the molecula…
miR-29b negatively regulates human osteoclastic cell differentiation and function: Implications for the treatment of multiple myeloma-related bone di…
2013
Skeletal homeostasis relies upon a fine tuning of osteoclast (OCLs)-mediated bone resorption and osteoblast (OBLs)-dependent bone formation. This balance is unsettled by multiple myeloma (MM) cells, which impair OBL function and stimulate OCLs to generate lytic lesions. Emerging experimental evidence is disclosing a key regulatory role of microRNAs (miRNAs) in the regulation of bone homeostasis suggesting the miRNA network as potential novel target for the treatment of MM-related bone disease. Here, we report that miR-29b expression decreases progressively during human OCL differentiation in vitro. We found that lentiviral transduction of miR-29b into OCLs, even in the presence of MM cells,…
Influence of Age on Cerebral Housekeeping Gene Expression for Normalization of Quantitative Polymerase Chain Reaction after Acute Brain Injury in Mice
2015
To prevent methodological errors of quantitative PCR (qPCR) normalization with reference genes is obligatory. Although known to influence gene expression, impact of age on housekeeping gene expression has not been determined after acute brain lesions such as traumatic brain injury (TBI). Therefore, expression of eight common control genes was investigated at 15 min, 24 h, and 72 h after experimental TBI in 2- and 21-month-old C57Bl6 mice. Expression of β2-microglobulin (B2M), β-actin (ActB), and porphobilinogen deaminase (PBGD) increased after TBI in both ages. β2M demonstrated age-dependent differences and highest inter- and intragroup variations. Expression of cyclophilin A, glyceraldehyd…
Associations of common breast cancer susceptibility alleles with risk of breast cancer subtypes in BRCA1 and BRCA2 mutation carriers
2014
Introduction More than 70 common alleles are known to be involved in breast cancer (BC) susceptibility, and several exhibit significant heterogeneity in their associations with different BC subtypes. Although there are differences in the association patterns between BRCA1 and BRCA2 mutation carriers and the general population for several loci, no study has comprehensively evaluated the associations of all known BC susceptibility alleles with risk of BC subtypes in BRCA1 and BRCA2 carriers. Methods We used data from 15,252 BRCA1 and 8,211 BRCA2 carriers to analyze the associations between approximately 200,000 genetic variants on the iCOGS array and risk of BC subtypes defined by estrogen re…
Impact of Different Selection Approaches for Identifying Lynch Syndrome-Related Colorectal Cancer Patients: Unity Is Strength
2022
Lynch syndrome (LS) is an inherited genetic condition associated with increased predisposition to colorectal cancer (CRC) and other tumors and is caused by germline mutations in Mismatch Repair (MMR) or EPCAM genes. The identification of LS carriers is currently based on germline testing of subjects with MMR-deficient (dMMR) tumors or fulfilling clinical criteria, but the most efficient strategies to select patients who should be offered genetic testing are yet not well defined. In order to assess the most suitable selection mode to identify LS-related CRC patients, we retrospectively collected and analyzed all clinical and molecular information of 854 CRC patients, recruited from 2013 to 2…
Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color
2020
Simple Summary In order to assess sources of variation related to Polverara breed plumage color (black vs. white), we carried out genome-wide analyses to identify the genomic regions involved in this trait. The present work has revealed new candidate genes involved in the phenotypic variability in local chicken populations. These results also contribute insights into the genetic basis for plumage color in poultry, and confirm the great complexity of the mechanisms that control this trait. Abstract Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is a…
Genetic analysis of dyslexia candidate genes in the European cross-linguistic NeuroDys cohort
2013
The work conducted at the WTCHG was supported by Wellcome Trust grants [076566/Z/05/Z] and [075491/Z/04]; the work in Zurich partly by an SNSF grant [32-108130]. We also thank MAF (Mutation Analysis core Facility) at the Karolinska Institute, Novum, Huddinge. The French part of the project was funded by Agence Nationale de la Recherche (ANR-06-NEURO-019-01 GENEDYS) and Ville de Paris. S Paracchini is a Royal Society University Research Fellow. D Czamara was supported by the Deutsche Forschungsgemeinschaft (German Research Foundation) within the framework of the Munich Cluster for Systems Neurology (EXC 1010 SyNergy). Dyslexia is one of the most common childhood disorders with a prevalence o…
THE ROLE OF INFLAMMATION IN TYPE A AORTIC DISSECTION: A PILOT STUDY
2013
Type A aortic dissection (TAAD) is a severe cardiovascular disease with high mortality rates. Current evidence suggests inflammation as the main mechanism of its complex pathophysiology. Accordingly, in this study the eventual presence of inflammatory cells in aorta specimens and any contribution of these cells in both apoptosis and metalloproteinase levels were assessed. The potential relationship between plasma inflammatory molecules and TAAD was also detected. In addition, implication in TAAD susceptibility of ten common and functional single nucleotide polymorphisms (SNP)s of six candidate genes (CCR5, TLR4, ACE, eNOs, MMP-9 and −2) was determined. Thus, histo-pathological and immunois…