Johnson, N. C. | Search bioRxiv

bioRxiv2026

Proteome-Driven Phenotyping of Identified Single Neurons in Intact Brain Tissue by Aspiration Patch Proteomics

Single-cell proteomics has advanced rapidly, but direct proteome measurements from identified neurons in intact brain tissue remain difficult because most workflows require cell isolation and recent patch-based studies have emphasized whole-soma retrieval. Here we show that aspiration-based patch proteomics enables deep proteome profiling of identified single neurons directly in acute mouse brain slices. We combined fluorescence-guided patch-clamp microsampling, minimal-loss bottom-up proteomics, and high-sensitivity capillary electrophoresis-timsTOF mass spectrometry to analyze partial somal aspirates from dopaminergic, parvalbumin, and serotonergic neurons in situ. The workflow identified more than 1,000 proteins from single-neuron samples under optimized conditions while consuming only about 0.25% of the processed digest per analysis. These proteomes were sufficient to separate biological replicates by neuronal phenotype, distinguish neuronal subtypes on the basis of protein expression alone, and define a conserved somal proteome shared across neuronal classes. Our results establish that controlled aspiration of partial somal material can support proteome-driven phenotyping without whole-soma retrieval, cell dissociation, or loss of native tissue context. Aspiration patch proteomics therefore provides an accessible route for subtype-level proteome phenotyping in intact brain tissue.

neuroscience↗

bioRxiv2025

Exploring eco-evolutionary and temporal patterns of arbuscular mycorrhizal fungal communities colonizing Sorghum bicolor across sites of contrasting land use history and climate

Societal Impact StatementSorghum bicolor is a globally important crop, having endpoint uses ranging from human food to animal feed to biofuel production. Sorghum is stress-tolerant and can be grown on marginal land that may be otherwise unsuitable for large-scale food production. Sorghum is therefore a promising candidate for agricultural strategies focused on maximizing production on these marginal lands through beneficial interactions with arbuscular mycorrhizal fungi and other microbes. This study investigates how sorghum genotypes and their interactions with the environment can be leveraged to foster particular AMF assemblages which can be investigated further for their effect on the host plant. Arbuscular mycorrhizal fungal (AMF) symbiosis can influence crop production, but can be variable across environmental conditions, host-partner complementarity and temporal dynamics. Understanding how these factors interact to shape AMF community assembly allows for the selection of crop genotypes that may maximally utilize AMF associations in agricultural systems. We assessed the development of AMF communities colonizing the roots of eight genetically diverse genotypes of Sorghum bicolor across a growing season. We used two field sites with contrasting environments and management histories. Sorghum cultivated in Arizona (AZ) contained low diversity AMF communities, while in Georgia (GA) sorghum harbored more diverse and evenly distributed AMF communities. We observed evidence of host-filtering of AMF communities, though with genotypes displaying more distinct associations in GA than AZ. AZ showed rapid shifts from early Funneliformis mosseae dominance to dominance by either Entrophospora etunicata or Diversispora aurantia. In GA, such drastic abundance shifts were not observed. Instead, consistent temporal turnover was associated more with higher level family abundance patterns driven by the combination of minor variations in multiple low-abundance taxa. Our findings demonstrate that there is potential for leveraging intra-species genetic variation in AMF community assembly as an extended plant phenotype.

ecology↗