Biology subjects

Quevedo, C.

Publications and source records attributed to Quevedo, C..

3 recordsLinked to original sources

bioRxiv2025

Near telomere-to-telomere genome assembly of the Chilean jack mackerel Trachurus murphyi

The Chilean jack mackerel (Trachurus murphyi) is an economically important pelagic fish widely distributed across the South Pacific Ocean. Due to intense fishing pressure and the lack of high-quality genomic resources, the development of sustainable fisheries management strategies has been hindered. Here, we present a near telomere-to-telomere genome assembly of T. murphyi using PacBio and Hi-C sequencing data. The assembled genome spans 818.31 Mb, with a contig N50 length of 24.89 Mb and a scaffold N50 length of 34.34 Mb. The assembly is anchored on 24 pseudo-chromosomes, covering 95.80% of the genome. BUSCO analysis indicates a high level of completeness at 99.0%, and telomeres and centromeres were identified on pseudo-chromosomes. Repetitive sequences account for 24.24% of the total genome, and 47,734 protein-coding genes were annotated, 90.98% of them with assigned function. Comparative genomics analyses reveal strong synteny with its congeneric Trachurus species. This high-quality genome assembly serves as a valuable resource for studying the genetic diversity and population structure of the Chilean jack mackerel and provides a solid foundation for future management and conservation efforts.

genomics↗

bioRxiv2024

Longitudinal transcriptional changes reveal genes from the natural killer cell-mediated cytotoxicity pathway as critical players underlying COVID-19 progression

Patients present a wide range of clinical severities in response SARS-CoV-2 infection, but the underlying molecular and cellular reasons why clinical outcomes vary so greatly within the population remains unknown. Here, we report that negative clinical outcomes in severely ill patients were associated with divergent RNA transcriptome profiles in peripheral immune cells compared with mild cases during the first weeks after disease onset. Protein-protein interaction analysis indicated that early-responding cytotoxic NK cells were associated with an effective clearance of the virus and a less severe outcome. This innate immune response was associated with the activation of select cytokine-cytokine receptor pathways and robust Th1/Th2 cell differentiation profiles. In contrast, severely ill patients exhibited a dysregulation between innate and adaptive responses affiliated with divergent Th1/Th2 profiles and negative outcomes. This knowledge forms the basis of clinical triage that may be used to preemptively detect high-risk patients before life-threatening outcomes ensue. Highlights- Mild COVID-19 patients displayed an early transcriptional commitment with NK cell function, whereas severe patients do so with neutrophil function. - The identified co-expressed genes give insights into a coordinated transcriptional program of NK cell cytotoxic activity being associated with mild patients. - Key checkpoints of NK cell cytotoxicity that were enriched in mild patients include: KLRD1, CD247, and IFNG. - The early innate immune response related to NK cells connects with the Th1/Th2 adaptive immune responses, supporting their relevance in COVID-19 progression.

immunology↗

bioRxiv2023

Secretory and transcriptomic responses of mantle cells to low pH in the Pacific oyster (Crassostrea gigas)

Since the Industrial Revolution, the concentration of atmospheric carbon dioxide (CO2) due to anthropogenic activities has increased at unprecedented rates. One-third of the atmospheric anthropogenic CO2 emissions are dissolved in the oceans affecting the chemical equilibrium of seawater, which in turn leads to a decrease in pH and carbonate ion (CO32-) concentration, a phenomenon known as ocean acidification (OA). This chemical disequilibrium can be detrimental to marine organisms (e.g., mollusks) that fabricate mineralized structures based on calcium carbonate (CaCO3). Most studies on the effect of reduced pH in seawater have been conducted on the early developmental stages of shell-building invertebrates, neglecting how adult individuals face OA stress. Here, we evaluate histological, secretory, and transcriptional changes in the mantle of adult oysters (Crassostrea gigas) exposure to ambient (8.0 {+/-} 0.2) and reduced (7.6 {+/-} 0.2) pH during 20 days. Most histological observations did not show differences in terms of mantle cell morphology. However, Alcian Blue/PAS staining revealed significant differences in the number of Alcian Blue positive cells in the mantle edge, suggesting a decrease in the secretory activity in this morphogenetic zone. Transcriptomic analysis revealed 172 differentially expressed genes (DEGs) between mantle tissues from adult oysters kept in normal and reduced pH conditions. Almost 18% of the DEGs encode secreted proteins that are likely to be contributing to shell fabrication and patterning. 17 of 31 DEGs encoding secreted proteins correspond to oyster-specific genes, highlighting the fact that molluscan shell formation is underpinned by a rapidly evolving secretome. The GO analysis of DEGs encoding secreted proteins showed that they are involved in the cellular response to stimulus, response to stress, protein binding, and ion binding, suggesting these biological processes and molecular functions are altered by OA. This study demonstrates that histology and gene expression profiling can advance our understanding of the cellular and molecular mechanisms underlying adult oyster tolerance to low pH conditions.

molecular biology↗