Biology subjects

da Silva, D.

Publications and source records attributed to da Silva, D..

4 recordsLinked to original sources

bioRxiv2025

Proteomic profiling of skeletal muscle ribosomes from higher versus lower responders to 10 weeks of resistance training

Ribosome biogenesis is a key driver of resistance training (RT)-induced skeletal muscle hypertrophy in humans. However, high resolution insight into RT-induced compositional alterations in ribosomes remain unexplored. Therefore, the purpose of this study was twofold: 1) develop a protocol sufficient to enrich and examine the ribosomal proteome from a small amount of human muscle tissue, and 2) determine if ribosomal protein composition differs between higher and lower responders to RT. Fourteen participants completed 10 weeks of RT (23 sessions) and were stratified into higher (n=7) and lower (n=7) responders based on changes in vastus lateralis muscle cross-sectional area (VL mCSA) and mean myofiber cross-sectional area (fCSA) from baseline (PRE) to after the 23rd RT session (POST). Participants then performed a twenty fourth RT session and biopsies were collected 24 hours post-RT (POST-24h) to examine acute bout (POST to POST-24h) ribosomal proteome alterations to RT. Ribosome enrichment and analysis included ultracentrifugation (100,000 g, 3h, 2{degrees}C) through 20% sucrose gradients followed by shotgun proteomics to quantify ribosomal protein composition. Our protocol produced exceptional ribosome enrichment, with 74 distinct ribosomal proteins being detected (92% coverage of the putative 80 cytosolic ribosomal proteins) as well as [~]164-fold and [~]71-fold increases in large (RPL) and small (RPS) protein subunit abundances, respectively, compared to conventional tissue homogenization. Despite robust phenotypic differences in hypertrophy between responder groups to the 10-week RT protocol (mCSA: +31% versus +3%; fCSA: +29% versus -2%, P<0.05 for both outcomes), ribosomal protein composition was not significantly different between groups (higher vs. lower responders), nor was there a significant time (POST to POST-24h) or a group*time interaction (P>0.028 for all comparisons). In conclusion, we present a highly effective ribosome enrichment protocol requiring minimal human muscle tissue. Though preliminary analyses indicate that ribosomal protein composition was similar between hypertrophic phenotypes in response to an acute RT session after a 10-week RT intervention, future research leveraging our techniques with more sampling time points are needed to provide more definitive conclusions.

molecular biology↗

bioRxiv2025

Risk reshapes amygdala representation of choice

Modifying behavior in response to changing environmental conditions is a crucial adaptive function. This capacity is exemplified when animals curtail pursuit of a valued outcome that risks being punished by aversive consequences, but the mediating brain mechanisms remain poorly understood. Here, using in vivo cellular-resolution calcium (Ca2+) imaging, optogenetics and chemogenetics, we show that risk of punishment dramatically alters animals choice between a large/risky and small- /safe reward and produces novel, causally necessary, patterns of activity in basolateral amygdala (BLA) neurons. We find that experience of a punished outcome generates a BLA representation that is selectively replayed when animals subsequently abort choice of the large/risky reward option. Additionally, we show that risk leads to the incorporation of newly encoding BLA neurons into the pre-choice representation, which predicts shifting away from the large/risky option. These findings reveal how dynamic reshaping of BLA representations underpins behavioral flexibility in the face of risk.

neuroscience↗

bioRxiv2024

Divergent gene expression in alcohol and opioid usedisorders results in consistent alterations in functional networks in the Dorsolateral Prefrontal Cortex

Substance Use Disorders (SUDs) manifest as persistent drug-seeking behavior despite adverse consequences, with Alcohol Use Disorder (AUD) and Opioid Use Disorder (OUD) representing prevalent forms associated with significant mortality rates and economic burdens. The co-occurrence of AUD and OUD is common, necessitating a deeper comprehension of their intricate interactions. While the causal link between these disorders remains elusive, shared genetic factors are hypothesized. Leveraging public datasets, we employed genomic and transcriptomic analyses to explore conserved and distinct molecular pathways within the dorsolateral prefrontal cortex associated with AUD and OUD. Our findings unveil modest transcriptomic overlap at the gene level between the two disorders but substantial convergence on shared biological pathways. Notably, these pathways predominantly involve inflammatory processes, synaptic plasticity, and key intracellular signaling regulators. Integration of transcriptomic data with the latest genome-wide association studies (GWAS) for problematic alcohol use (PAU) and OUD not only corroborated our transcriptomic findings but also confirmed the limited shared heritability between the disorders. Overall, our study indicates that while alcohol and opioids induce diverse transcriptional alterations at the gene level, they converge on select biological pathways, offering promising avenues for novel therapeutic targets aimed at addressing both disorders simultaneously.

neuroscience↗

bioRxiv2019

Spatial control of oxygen delivery to 3D cultures alters cancer cell growth and gene expression

Commonly used monolayer cancer cell cultures fail to provide a physiologically relevant environment in terms of oxygen delivery. Here, we describe a three-dimensional bioreactor system where cancer cells are grown in Matrigel in modified 6-well plates. Oxygen is delivered to the cultures through a polydimethylsiloxane (PDMS) membrane at the bottom of the wells, with microfabricated PDMS pillars to control oxygen delivery. The plates receive 3% oxygen from below and 0% oxygen at the top surface of the media, providing a gradient of 3% to 0% oxygen. We compared growth and transcriptional profiles for cancer cells grown in Matrigel in the bioreactor, 3D cultures grown in 21% oxygen, and cells grown in a standard hypoxia chamber at 3% oxygen. Additionally, we compared gene expression of conventional 2D monolayer culture and 3D Matrigel culture in 21% oxygen. We conclude that controlled oxygen delivery may provide a more physiologically relevant 3D system.

bioengineering↗