Biology subjects

Rivera, P.

Publications and source records attributed to Rivera, P..

5 recordsLinked to original sources

bioRxiv2026

Age-associated increases in inter-individual gene expression variability across human tissues

Aging involves progressive physiological decline, yet the underlying transcriptomic patterns remain poorly understood. Although differentially expressed genes (DEGs) have been the primary focus of previous studies, here we investigate differentially variable genes (DVGs) using a novel Gene Stability Score (GSS). In 30 tissue types from nearly 1,000 individuals in the Genotype-Tissue Expression (GTEx) project, age- and sex-related DVGs account for approximately 15% of overall expression variability between samples of the same tissue, with age-related DVGs specifically contributing 7.7%. We further show that DEGs and DVGs affect distinct biological pathways, and that inter-individual instability is significantly correlated with cell-to-cell transcriptional noise. Moreover, gene regulatory network analysis reveals that this variability is not random but is shaped by local network architecture. Finally, we identify robust reference genes, including TBP, PUM1, and TMEM199, for RT-qPCR experiments in studying age-related gene expression changes in humans. Together, our findings suggest that aging involves both coordinated transcriptional programs and increased stochasticity across individuals and cells.

genomics↗

bioRxiv2025

Distinct D-Box Motifs in SPD-2 Mediate APC/CFZR-1 -Dependent Degradation and Centrosomal Localization in Caenorhabditis elegans

Centrosome duplication must be tightly regulated to maintain genomic stability. In Caenorhabditis elegans, the APC/C and co-activator FZR-1 function as negative regulators of centrosome duplication by targeting specific substrates for proteolytic degradation. While C. elegans SAS-5 and ZYG-1 have been identified as substrates of APC/CFZR-1, the mechanism by which APC/CFZR-1-dependent degradation influences centrosome assembly remains unclear. Here, we identified SPD-2, the conserved homolog of human CEP192, as a substrate of APC/CFZR-1. We show that loss of APC/CFZR-1 increases both cellular and centrosomal SPD-2 levels, and that SPD-2 physically associates with FZR-1 in vivo. Functional analyses of canonical D-box motifs reveal that D-box1, D-box2, and D-box3 each contribute to SPD-2 degradation, each with different functional consequences. Mutation of D-box3 alone partially rescued zyg-1 mutant phenotypes by restoring centrosome duplication and embryonic viability through increased centrosomal SPD-2 and ZYG-1. In contrast, mutating D-box1 or D-box2 elevated cellular SPD-2 but did not rescue zyg-1, with the D-box1 mutation further reducing centrosomal SPD-2 and exacerbating duplication defects and lethality in zyg-1 mutants. Our results reveal a conserved mechanism for APC/CFZR-1-dependent degradation of SPD-2 and show that its degron motifs have dual functions in degradation and centrosomal localization, ensuring robust control of centrosome assembly during C. elegans embryogenesis.

genetics↗

bioRxiv2024

Chemogenetic control of GABAergic activity within the interpeduncular nucleus reveals dissociable behavioral components of the nicotine withdrawal phenotype

Chronic exposure to nicotine results in the development of a dependent state such that a withdrawal syndrome is elicited upon cessation of nicotine. The habenulo-interpeduncular (Hb-IPN) circuit contains a high concentration of nAChRs and has been identified as a main circuit involved in nicotine withdrawal. Here we investigated the contribution of two distinct subpopulations of IPN GABAergic neurons to nicotine withdrawal behaviors. Using a chemogenetic approach to specifically target Amigo1-expressing or Epyc-expressing neurons within the IPN, we found that activity of the Amigo1 and not the Epyc subpopulation of GABAergic neurons is critical for anxiety-like behaviors both in naive mice and in those undergoing nicotine withdrawal. Moreover, data revealed that stimulation of Amigo1 neurons in nicotine-naive mice elicits opposite effects on affective and somatic signs of withdrawal. Taken together, these results suggest that somatic and affective behaviors constitute dissociable components of the nicotine withdrawal phenotype and are likely supported by distinct subpopulations of neurons within the IPN.

neuroscience↗

bioRxiv2023

Acute resistance exercise induces mitophagy and mitophagomes on subsarcolemmal clefts in human skeletal muscle: Focus on BNIP3L/NIX40 as a mitophagy flux marker

ObjectiveMitochondrial dynamics and quality control in skeletal muscle are central to healthy metabolism. Resistance exercise is a recognized tool for improving skeletal muscle function; however, its effect on mitochondria is still not fully understood. We investigated the impact of resistance exercise on mitochondrial morphology and mitophagy in human skeletal muscle. MethodsEight healthy men performed resistance exercise on one leg, and muscle biopsies were subsequently obtained from the resting leg (Rest) and the exercised leg (Ex) to measure protein abundance and mitochondrial morphology. Additionally, muscle biopsies were obtained from twelve healthy men, and the abundance of BNIP3L protein was correlated with muscle cell and whole body health markers. ResultsEx increased p-Drp1 and decreased MFN2, Parkin, and BNIP3L protein levels. Electron microscopy indicated an increase in mitochondrial circularity, cristae abnormality, and mitophagosome structures in Ex, with a marked increase in subsarcolemmal mitophagosomes. We also identified mitophagosomes outside the muscle. Experiments in human myotubes showed a severe decrease in BNIP3L protein in response to CCCP-induced mitochondrial damage with and without bafilomycin. A positive correlation was found between BNIP3L and exercise RQ, HOMA index, while a negative correlation was found with mitophagosomes abundance and VO2max. ConclusionOur study describes the effect of resistance exercise on mitochondrial dynamics and mitophagy in skeletal muscle, demonstrating induction of mitochondrial fission and mitophagy in the exercised leg. Moreover, we propose BNIP3L as a potential regulator and marker of mitophagy flux.

physiology↗

bioRxiv2021

Developmental integration cannot explain major features of stomatal anatomical evolution in seed plants

Functional and developmental constraints on phenotypic variation may cause traits to covary over millions of years and slow populations from reaching their adaptive optima. Alternatively, trait covariation may result from selective constraint if some trait combinations are generally maladaptive. Quantifying the relative contribution of functional, developmental, and selective constraints on phenotypic variation is a longstanding goal of macroevolution, but it is often difficult to distinguish different types of constraints. The anatomy of leaves with stomata on both surfaces (amphistomatous) present a unique opportunity to test the importance of functional and developmental constraints on phenotypyic evolution. The key insight is that stomata on each leaf surface encounter the same functional and developmental constraints, but potentially different selective constraints because of leaf asymmetry in light capture, gas exchange, and other features. Independent evolution of stomatal traits on each surface imply that functional and developmental constraints alone likely do not explain trait covariance. Packing limits on how many stomata can fit into a finite epidermis and cell-size-mediated developmental integration are hypothesized to constrain variation in stomatal anatomy. The simple geometry of the planar leaf surface and knowledge of stomatal development make it possible to derive equations for phenotypic (co)variance caused by these constraints and compare them with data. We analyzed evolutionary covariance between stomatal density and length in amphistomatous leaves from 236 phylogenetically independent contrasts using a robust Bayesian model. Stomatal anatomy on each surface diverges partially independently, meaning that packing limits and developmental integration are not sufficient to explain phenotypic (co)variation. Hence, selective constraints, which require an adaptive explanation, likely contribute to (co)variation in ecologically important traits like stomata. We show how it is possible to evaluate the contribution of different constraints by deriving expected patterns of (co)variance and testing them using similar but separate tissues, organs, or sexes.

plant biology↗