Fernandez, M. E. | Search bioRxiv

bioRxiv2025

Deep and Quantitative Proteomic Profiling of Low Volume Mouse Serum Across the Lifespan

Assessing and validating circulating biomarkers is essential for the development of pre-clinical biomarkers that predict biological aging and aging-phenotypes in mice. However, comprehensive proteomics of serum, especially in longitudinal mouse studies, are limited by low volumes of samples. In this study, we develop a workflow for comprehensive and quantitative proteomic analysis of low volume mouse serum and demonstrate its utility and performance in identifying and evaluating key associations with aging phenotypes. Notably, a nanoparticle (NP)-based serum processing workflow coupled to mass spectrometry (MS) increases proteomic coverage by 3 to 6-fold across a range of volumes and provides a quantitative and reproducible (CV < 10%) pipeline for NP-based studies. In a study of 30 mice (aged 12, 24, and 30 months), we uncovered 3992 protein groups across all samples (2235 on average) in 20 {micro}L of serum and highlight novel insights into aging-associated changes in serum and associations with glucose and body composition. With 1 {micro}L additional serum, a 48-cytokine assay quantified 39 additional proteins not identified by MS. This study establishes a powerful workflow that enables deep quantitative proteomics of biologically relevant proteins in volumes feasibly obtained from mice (21 {micro}L of serum) and presents fundamental insights into the aging serum proteome.

biochemistry↗

bioRxiv2022

Context- and scale-dependent effects of thymol bioactivity on biological networks: contributions from quail under heat stress

A defining feature of healthy function is adaptability, the capacity to dynamically respond to novel and/or unpredictable factors, such as exposition to environmental challenges. Here we explore the role of context (i.e., order in which factors are applied) on the configuration of networks of behavioral and physiological traits from Japanese quail that were supplemented dietary thymol prior, jointly or after onset of a chronic heat stress protocol (i.e., supplementation strategies). Basal diet and standard environmental temperature were used as controls. We begin by showing that each supplementation strategy evolved differently over the 5-week experimental period in regard to body weight and feed- intake. At the end of this experimental period, context-dependency was also observed in the non- trivial functional relationships among 27 traits from 4 subsystems from distinct spatial-temporal scales. When considered separately, whole-organism level subsystems (i.e. somatic maintenance and egg production traits), are predominantly functionally related to environmental temperature. Conversely, at the molecular level, the live[r]s antioxidant system response is fundamentally dominated by the supplementation strategy. Interestingly, the serums antioxidant system shows an intermediate response, not dominated by a given factor. Overall, network configurations were highly dependent on context, and could be associated with specific induced physiological states. Our work constitutes the first study that includes network, integrative, and experimentally comparative analyses applied to the field of dietary supplementation under environmental challenges. This perspective could help understand complex biological responses important for developing efficient and welfare orientated supplementation protocols for farm animals and for interpreting the background in this field.

physiology↗