Biology subjects

Gonzales, P.

Publications and source records attributed to Gonzales, P..

3 recordsLinked to original sources

bioRxiv2025

Unraveling IGK Locus in Dog Breeds: IMGT(R) New Insights into Canine Immunogenetics.

Over millennia, the selective breeding of dogs (Canis lupus familiaris) has generated remarkable genetic diversity among breeds, highlighting the need for comprehensive genomic and immunogenetic studies. This research provides detailed immunoglobulin kappa light chain locus (IGK) analysis across multiple dog breeds. It aims to uncover breed-specific genetic variations and their implications for immunology and veterinary medicine. The primary objectives were to do the biocuration of the IGK locus in nine canine genome assemblies, investigate structural variations, polymorphisms, and gene diversity, and to enrich the IMGT(R) database with comprehensive IGK data from diverse breeds, creating a more inclusive genetic resource. Our extensive annotation of breeds, including the Bernese Mountain Dog, Boxer, Cairn Terrier, Labrador Retriever, Great Dane, Basenji, and German Shepherd, identified 40 genes and 97 alleles, revealing both conserved genes and unique variants across these breeds, with in silico validation through Sanger sequencing. Notably, we analyzed discrepancies in the first reference assembly from the Boxer breed (Canfam3.1), highlighting potential errors in assembly, challenges in gene and allele nomenclature, and a low-density region within the canine IGK locus. This study not only refines the understanding of IGK locus diversity but also contributes to the IMGT(R) databases, advancing future research on immunogenetic variability, somatic mutations, and immune response dynamics in canine health and disease.

immunology↗

bioRxiv2021

Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood

Numerous reports have suggested that infectious agents could play a role in neurodegenerative diseases, but specific etiological agents have not been convincingly demonstrated. To search for candidate agents in an unbiased fashion, we have developed a bioinformatic pipeline that identifies microbial sequences in mammalian RNA-seq data, including sequences with no significant nucleotide similarity hits in GenBank. Effectiveness of the pipeline was tested using publicly available RNA-seq data. We then applied this pipeline to a novel RNA-seq dataset generated from a cohort of 120 samples from amyotrophic lateral sclerosis (ALS) patients and controls, and identified sequences corresponding to known bacteria and viruses, as well as novel virus-like sequences. The presence of these novel virus-like sequences, which were identified in subsets of both patients and controls, were confirmed by quantitative RT-PCR. We believe this pipeline will be a useful tool for the identification of potential etiological agents in the many RNA-seq data sets currently being generated.

bioinformatics↗

bioRxiv2018

Heat Shock in C. elegans Induces Downstream of Gene Transcription and Accumulation of Double-Stranded RNA

We observed that heat shock of Caenorhabditis elegans leads to the formation of nuclear double-stranded RNA (dsRNA) foci, detectable with a dsRNA-specific monoclonal antibody. These foci significantly overlap with nuclear HSF-1 granules. To investigate the molecular mechanism(s) underlying dsRNA foci formation, we used RNA-seq to globally characterize total RNA and immunoprecipitated dsRNA from control and heat shocked worms. We find antisense transcripts are generally increased after heat shock, and a subset of both sense and antisense transcripts enriched in the dsRNA pool by heat shock overlap with dsRNA transcripts enriched by deletion of tdp-1, which encodes the C. elegans ortholog of TDP-43. Interestingly, transcripts involved in translation are over-represented in the dsRNAs induced by either heat shock or deletion of tdp-1. Also enriched in the dsRNA transcripts are sequences downstream of annotated genes (DoGs), which we globally quantified with a new algorithm. To validate these observations, we used fluorescence in situ hybridization (FISH) to confirm both antisense and downstream of gene transcription for eif-3.B, one of the affected loci we identified.

molecular biology↗