Biology subjects

Cool, J.

Publications and source records attributed to Cool, J..

4 recordsLinked to original sources

bioRxiv2025

An interpretable alphabet for local protein structure search based on amino acid neighborhoods

MotivationRecent advancements in protein structure prediction methods have vastly increased the size of databases of protein structures, necessitating fast methods for protein structure comparison. Search methods that find structurally similar proteins can be applied to find remote homologs, study the functional relationships among proteins, and aid in protein engineering tasks. The structure comparison method Foldseek represents each protein structure as a sequence of "3Di" characters and uses highly optimized sequence comparison software to search with this alphabet. An alternate alphabet encoding richer features has the potential to improve search accuracy while leaving the underlying search algorithm unchanged. ResultsWe design a "3Dn" structural alphabet that encodes the local neighborhoods around each amino acid in an interpretable way. In a search benchmark task, a combination of our alphabet and Foldseeks 3Di alphabet, outperforms each alphabet individually and ranks best among local search methods that do not require amino acid identity information. We provide software tools that enable the exploration of novel alphabets and combinations of alphabets for protein structure search. Availability and implementationThe code is freely available at https://github.com/spetti/structure_comparison.

bioinformatics↗

bioRxiv2023

Testis morphogenesis and fetal Leydig cell development are mediated through ERK signaling activated by platelet derived growth factor receptor alpha

Platelet derived growth factor receptor alpha (Pdgfra) plays a crucial role in the morphogenesis and differentiation of the fetal testis, but the molecular signaling involved in these processes remains unclear. Here, we use XY Pdgfra-null knock-in (KI) gonads to investigate the molecular mechanisms underlying Pdgfra-mediated testis cord formation and development of fetal Leydig cells (FLCs). The extracellular signal-regulated kinase (ERK) pathway, a well-known mitogen-activated protein kinase signaling pathway, was significantly inhibited in XY Pdgfra KI gonads, suggesting that ERK signaling is activated downstream of PDGFRA. Using ex vivo whole-organ culture, small interfering RNA (siRNA) cell culture methods, transwell assays and a genetic mouse model to disrupt ERK signaling in gonadal cells, we found that the ERK pathway promoted testis cord formation via early growth response 1 (Egr1)-mediated cell migration and regulated the expression of steroidogenic enzymes in FLCs via activating the transcription factor cAMP responsive element binding protein 1 (CREB; official name CREB1). These findings highlight the significance of PDGFRA and its downstream signaling in fetal testis morphogenesis and cellular differentiation, thus providing insights into the etiology of and potential therapeutic targets for disorders related to gonadal development.

developmental biology↗

bioRxiv2023

Integrated multimodal cell atlas of Alzheimer's disease

Alzheimers disease (AD) is the most common cause of dementia in older adults. Neuropathological and imaging studies have demonstrated a progressive and stereotyped accumulation of protein aggregates, but the underlying molecular and cellular mechanisms driving AD progression and vulnerable cell populations affected by disease remain coarsely understood. The current study harnesses single cell and spatial genomics tools and knowledge from the BRAIN Initiative Cell Census Network to understand the impact of disease progression on middle temporal gyrus cell types. We used image-based quantitative neuropathology to place 84 donors spanning the spectrum of AD pathology along a continuous disease pseudoprogression score and multiomic technologies to profile single nuclei from each donor, mapping their transcriptomes, epigenomes, and spatial coordinates to a common cell type reference with unprecedented resolution. Pseudo-progression analysis showed two major epochs corresponding with a slow early increase in pathology and a later exponential increase that correlated with cognitive decline. The early phase included inflammatory microglial and reactive astrocyte component, as well as a selective loss of Sst+ inhibitory neuron types in superficial cortical layers, loss of myelinating oligodendrocytes, and up-regulation of a re-myelination program by OPCs. The later phase involved loss of excitatory neurons and Pvalb and Vip neuron subtypes also predominantly in superficial layers. These cell vulnerabilities were also seen in prefrontal cortex and replicated by other independent studies when integrated with the BRAIN Initiative reference. Study data and exploratory tools are freely available to accelerate progress in AD research at SEA-AD.org.

genomics↗

bioRxiv2021

cellxgene: a performant, scalable exploration platform for high dimensional sparse matrices

Quickly and flexibly exploring high-dimensional datasets, such as scRNAseq data, is underserved but critical for hypothesis generation, dataset annotation, publication, sharing, and community reuse. cellxgene is a highly generalizable, web-based interface for exploring high dimensional datasets along categorical, continuous and spatial dimensions, as well as feature annotation. cellxgene is differentiated by its ability to performantly handle millions of observations, and bridges a critical gap by enabling computational and experimental biologists to iteratively ask questions of private and public datasets. In doing so, cellxgene increases the utility and reusability of datasets across the single-cell ecosystem. The codebase can be accessed at https://github.com/chanzuckerberg/cellxgene. For questions and inquiries, please contact cellxgene@chanzuckerberg.com.

systems biology↗