Hendrickx, A. | bioRxiv Science

bioRxiv2025

Cross-species proteomics quantification pipeline distinguishes donor versus host extracellular matrix in explanted biomaterials

Xenogenic biomaterial durability, including bioprosthetic heart valves (BPVs), is compromised by pathological extracellular matrix (ECM) remodeling, resulting in progressive structural degeneration. Mass spectrometry-based proteomics can help reveal BPV degeneration mechanisms; however, peptide sequence similarity between donor and host species complicates protein-level analysis. We present a cross-species proteomic analytical strategy for xenogenic biomaterials and cross-species proteomic datasets. In silico tryptic digestion of human and bovine protein databases identified over 400 overlapping proteins with a high protein percent identity. Explanted human BPV tissue was divided into macroscopically distinct regions of degeneration and analyzed by mass spectrometry. A peptide-level strategy quantified protein abundances in a species-delineated analysis. We highlighted degeneration region-specific depositions of key human ECM proteins and bovine ECM proteins whose abundance is time dependent. We demonstrated that single-species analysis of a cross-species proteome results in inaccurate quantification. This study highlights the importance of distinguishing between donor and host species proteomes for accurate protein quantification. While focused on clinically explanted biomaterials, our approach is broadly applicable to all forms of xenotransplantation and the use of xenogenic matrices.

bioengineering↗

bioRxiv2024

Leaf functional trait evolution and its putative climatic drivers in African Coffea species

Background and AimsLeaf traits are known to be strong predictors of plant performance and can be expected to (co)vary along environmental gradients. We investigated the variation, integration, environmental relationships, and evolutionary history of leaf functional traits in the genus Coffea L., typically a rainforest understory shrub, across Africa. A better understanding of the adaptive processes involved in leaf trait evolution can inform the use and conservation of coffee genetic resources in a changing climate. MethodsWe used phylogenetic comparative methods to investigate the evolution of six leaf traits measured from herbarium specimens of 58 African Coffea species. We added environmental data and data on maximum plant height for each species to test trait-environment correlations in various (sub)clades, and we compared continuous trait evolution models to identify variables driving trait diversification. Key ResultsA substantial leaf trait variation was detected across the genus Coffea in Africa, which was mostly interspecific. Of these traits, stomatal size and stomatal density exhibited a clear trade-off. We observed low densities of large stomata in early branching lineages and higher densities of smaller stomata in more recent taxa, which we hypothesise to be related to declining CO2 levels since the mid-Miocene. Brownian Motion evolution was rejected in favour of White Noise or Ornstein-Uhlenbeck models for all traits, implying these traits are adaptively significant rather than driven by pure drift. The evolution of leaf area was likely driven by precipitation, with smaller leaves in dryer climates across the genus. ConclusionsGenerally, Coffea leaf traits appear to be evolutionarily labile and governed by stabilising selection, though evolutionary patterns and correlations differ depending on the traits and clades considered. Our study highlights the importance of a phylogenetic perspective when studying trait relationships across related taxa, as well as the consideration of various taxonomic ranges.

evolutionary biology↗