Seth Blackshaw

Jan 19, 2025 | biorxiv.org | Ying Xin |Yang Jin |Cheng Qian |Seth Blackshaw

AbstractNon-peptide ligands (NPLs), including lipids, amino acids, carbohydrates, and non-peptide neurotransmitters and hormones, play a critical role in ligand-receptor-mediated cell-cell communication, driving diverse physiological and pathological processes. To facilitate the study of NPL-dependent intercellular interactions, we introduce MetaLigand, an R-based and web-accessible tool designed to infer NPL production and predict NPL-receptor interactions using transcriptomic data.

Oct 17, 2024 | nature.com | Kurt Weir |Natasha Sandoval Vega |Veronica F. Busa |Dana K. Merriman |Krzysztof Palczewski |Seth Blackshaw | +3 more

Torpor encompasses diverse adaptations to extreme environmental stressors such as hibernation, aestivation, brumation, and daily torpor. Here we introduce StrokeofGenus, an analytic pipeline that identifies distinct transcriptomic states and shared gene expression patterns across studies, tissues, and species. We use StrokeofGenus to study multiple and diverse forms of torpor from publicly-available RNA-seq datasets that span eight species and two classes. We identify three transcriptionally distinct states during the cycle of heterothermia: euthermia, torpor, and interbout arousal. We also identify torpor-specific gene expression patterns that are shared both across tissues and between species with over three hundred million years of evolutionary divergence. We further demonstrate the general sharing of gene expression patterns in multiple forms of torpor, implying a common evolutionary origin for this process. Although here we apply StrokeofGenus to analysis of torpor, it can be used to interrogate any other complex physiological processes defined by transient transcriptomic states.

Oct 2, 2024 | nature.com | Ingie Hong |Thomas Hainmueller |Dong Won Kim |Richard Johnson |Nathachit Limjunyawong |David Cheon | +7 more

AbstractThe brain helps us survive by forming internal representations of the external world1,2. Excitatory cortical neurons are often precisely tuned to specific external stimuli3,4. However, inhibitory neurons, such as parvalbumin-positive (PV) interneurons, are generally less selective5. PV interneurons differ from excitatory neurons in their neurotransmitter receptor subtypes, including AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors (AMPARs)6,7.

Jul 11, 2024 | onlinelibrary.wiley.com | Seth Blackshaw |Jiang Qian |David Hyde

CONFLICT OF INTEREST STATEMENT Seth Blackshaw receives research support from Genentech, and is a co-founder and shareholder of CDI Labs, LLC. REFERENCES 1, , , , & (2023). Molecular mechanisms controlling vertebrate retinal patterning, neurogenesis, and cell fate specification. Trends in Genetics: TIG, 39(10), 736–757. 2, & (2012). Cell fate determination in the vertebrate retina. Trends in Neurosciences, 35(9), 565–573. 3, , , , , , , , , , , , , & (2019).