Biology subjects

Johnson, K. F.

Publications and source records attributed to Johnson, K. F..

3 recordsLinked to original sources

bioRxiv2025

Mapping mesenchymal diversity in the developing human intestine and organoids

The organization of diverse mesenchymal populations during human intestinal development is critical for tissue architecture and function yet remains poorly defined. To construct a comprehensive, tissue-scale map of the developing human small intestine, we leveraged single-cell RNA-sequencing data to build a custom Xenium spatial transcriptomics gene panel covering the diversity of cell types in the human intestine. Analysis was focused on the developing mesenchyme populations (also referred to as fibroblasts or stroma) given the lack of spatiotemporal information about these cell populations. We defined 5 broad mesenchymal populations occupying discrete anatomical locations within the lamina propria and submucosa - the subepithelial cells (SEC), lamina propria fibroblasts (LPF), submucosal fibroblasts (SMF), smooth muscle cells (SMC), and CXCL13+ fibroblasts. Our data reveal dynamic spatial remodeling of fibroblast communities during development and establish molecular markers to distinguish these populations. We leverage this high-resolution atlas to benchmark pluripotent stem cell-derived human intestinal organoids and to demonstrate how this foundational resource can be used to dissect intestinal stromal signaling in a spatial manner, with broad implications for modeling development, regeneration, and disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/665939v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@46299borg.highwire.dtl.DTLVardef@55a014org.highwire.dtl.DTLVardef@180a104org.highwire.dtl.DTLVardef@1cb42b2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA spatial atlas of fibroblast heterogeneity in the human intestine C_LIO_LIPopulations include subepithelial, submucosal, lamina propria, and CXCL13+ fibroblasts C_LIO_LIFibroblast position in the developing intestine is maintained into adulthood C_LIO_LIOrganoids largely recreate the spatial organization of the human intestine C_LI

developmental biology↗

bioRxiv2025

Spatiotemporal Models Reveal Dynamic Growth Patterns in U.S. West Coast Groundfish

Variability in somatic growth of marine fish affects their reproductive potential and survival, and therefore, the productivity of a population. Understanding how growth might vary among species with similar traits can improve predictions of population status and responses to environmental change. We used geostatistical models to characterize spatiotemporal variability in growth rate and body condition, two interrelated traits associated with somatic growth, of nine commercially important U.S. West Coast groundfish species with a range of life-history traits and depth distributions. Our models uncover spatiotemporal variability in growth rate and body condition in all nine groundfish species with limited trends shared among species with similar traits, suggesting a greater influence from niche partitioning acting on local scales. Such interspecific differences in growth rate and body condition responses also occurred at regional scales, with some species exhibiting positive responses while others declined. These findings reveal the dynamic nature of somatic growth among groundfish species and provide insight into potential mechanisms of its variability that could be considered within climate-enhanced assessments of population status for marine fish.

ecology↗

bioRxiv2025

'surveyjoin': A Standardized Database of Fisheries Bottom Trawl Surveys in the Northeast Pacific Ocean

Fisheries management faces challenges due to political, spatial, and ecological complexities, which are further exacerbated by variation or shifts in species distributions. Effective management depends on the ability to integrate fisheries data across political and geographic boundaries. However, such efforts may be hindered by inconsistent data formats, limited data sharing, methodological differences in sampling, and regional governance differences. To address these issues, we introduce the surveyjoin R package, which combines and provides public access to bottom trawl survey data collected by NOAA Fisheries and Fisheries and Oceans Canada in the Northeast Pacific Ocean. This initial database integrates over 3.3 million observations from 14 bottom trawl surveys spanning Alaska, British Columbia, Washington, Oregon, and California from the 1980s to present. This effort standardizes variables such as catch-per-unit-effort (CPUE), haul data, and in-situ measurements of bottom temperature. We demonstrate the utility of this database through three case studies. Our first case study develops a coastwide biomass index for Pacific hake (Merluccius productus) using geostatistical index standardization, comparing results to independent acoustic survey estimates. The second case study examines changes in the spatial distribution of groundfish species across marine heatwave and non-heatwave years, highlighting species-specific and community-level responses to warming events. Our third example applies spatially varying coefficient models to assess sablefish (Anoplopoma fimbria) biomass trends, identifying regional variability in increases in occurrence and biomass. Together, these case studies demonstrate how the surveyjoin R package and database may improve species and ecosystem assessments by providing insights into population trends across geopolitical boundaries. This database and package represent an important step toward offering a scalable framework that can be extended to include additional data types, surveys, and species. By fostering collaboration, transparency, and data-driven decision-making, surveyjoin supports international efforts to sustainably manage shared marine resources under dynamic environmental conditions.

ecology↗