Biology subjects

Small, J.

Publications and source records attributed to Small, J..

7 recordsLinked to original sources

bioRxiv2026

SARM1 is required for macrophage immunophenotype switching that is essential for nerve repair

SARM1 is a key executor of Wallerian degeneration in axons. Global knockout of sarm1 in mice delays degeneration for several weeks. Recently, we reported that Schwann cell reprogramming, inflammation, and axon regeneration are also delayed in these animals. Several studies have also indicated that SARM1 has essential regulatory functions in macrophages (M{phi}). However, the role of SARM1 in M{phi} in the context of peripheral nerve injury remains unknown. Here, we report that loss of sarm1 impairs splenic M{phi} from adopting immunological stimuli driven immunophenotypes in culture. Through a combination of cell culture, Western blotting, gene expression analysis, in vivo injection of M{phi} into sciatic nerves, and generation of cell specific sarm1 conditional knockout mouse lines, we found that SARM1 is required for proper immunophenotypes in M{phi}. Loss of sarm1 in macrophages increases neurite length of sensory neurons in culture but delays regeneration in a model of peripheral nerve injury. We identified dysregulation of several inflammatory and anti-inflammatory immunological stimuli pathways and altered regulation of both iNOS and Arginase-1 in Sarm1-/- M{phi}. In culture, Sarm1-/- M{phi} display difficulty phagocytosing and clearing myelin debris and this was recapitulated in vivo with a M{phi} specific sarm1 knockout line. Generation of M{phi} and neuronal sarm1 conditional knockout mice further indicated that SARM1 is required in both cell types for an efficient response to peripheral nerve injury. This study provides the first evidence that SARM1 signaling in M{phi} is required for injury induced inflammation, degeneration, and axon regeneration.

neuroscience↗

bioRxiv2026

Contrasting effects of geographic distance, environmental distance, and intraspecific diversity on the performance of a marine invertebrate in common gardens

Restoration and management of natural populations often assume that local genotypes are best suited for transplantation to their local environment. Prioritizing a single local genotype, however, contrasts with the framework of maximizing intraspecific diversity to increase population resilience to environmental change. Local populations may also become maladapted to a rapidly changing environment, motivating alternative frameworks that instead minimize environmental distance between source and transplantation sites. Here, we tested the predictive power of the local is best, maximize intraspecific diversity, and minimize environmental distance frameworks on the survival and growth of Eastern oyster (Crassostrea virginica) genotypes in field common gardens that differed in salinity and disease pressure. Although a genome scan revealed patterns of adaptation to disease, heat stress, and salinity among source populations, we did not find strong support for the local is best framework: geographically distant southern genotypes performed comparably to local selection lines and a local wild population. Higher genetic diversity within monocultures was associated with higher survival, yet highly diverse polycultures survived at lower rates than the best-performing monocultures, providing mixed support for the maximize intraspecific diversity framework. Temperature and salinity of the environments-of-origin of parents predicted the survival of their offspring in common gardens, but the relationship between survival and environmental distance was context-dependent, leading to mixed support for the minimize environmental distance framework. Together, these results demonstrate that no single framework reliably predicted transplantation success, suggesting that effective management strategies may need to integrate genomic and environmental lines of evidence to guide genotype selection.

evolutionary biology↗

bioRxiv2026

Range-wide genetic population structure and environmental adaptation in the eastern oyster (Crassostrea virginica) provides insight for aquaculture

Selective breeding in aquaculture is necessary to establish food security and meet demand for sustainably produced protein. An informed selective breeding program requires understanding how population structure, environmental adaptation, and human activities shape natural genetic variation in wild conspecifics. Unfortunately, wild variation remains poorly characterized for many commercially important aquaculture species. Here, we conduct the first range-wide study of genomic population structure for the eastern oyster (Crassostrea virginica) across thousands of miles (Texas, USA to Eastern Canada) using a 200K SNP array. We integrate population structure analyses, genotype-environmental associations, and structural variant detection to identify adaptive loci and quantify human-mediated genetic impacts. Our data confirms two ancestral clusters with a phylogeographic break between the Gulf and Atlantic (FST = 0.06) and highlights patterns of substructure within each region. We find evidence of unexpected patterns of genomic variation in two locations: evidence of Gulf ancestry in a mid-Atlantic estuary (Chesapeake Bay), and evidence of Atlantic ancestry in a Gulf estuary (Apalachicola Bay). While we cannot definitively determine the causes of these unexpected patterns, we show that they are consistent with direct and indirect human impacts in these estuaries. Genotype-environment association analyses with in situ temperature and salinity measurements were used to identify putatively adaptive loci, including SNPs within large structural variants (>1Mb). Our results identified genomic targets for aquaculture breeding programs aimed at climate resilience, reveal complex patterns of human impacts in managed systems, and demonstrate how seascape genomics can be used to improve aquaculture outcomes.

evolutionary biology↗

bioRxiv2025

From Blue to Pink: Resazurin as a High-Throughput Proxy for Metabolic Rate in Oysters

Metabolic rate assays are critical tools for assessing organismal stress and resilience, yet their widespread application in aquaculture and ecological monitoring is limited. Improving these assays is essential for hatchery managers, farmers, and scientists seeking to identify resilient stocks and monitor stress in shellfish populations. Resazurin, a redox-sensitive dye commonly used in cell viability assays, offers a promising, high-throughput assay for metabolic rate assessment, but its application at the whole-organism level remains under explored. This study evaluates the efficacy of a resazurin-based metabolic assay in oysters (Crassostrea gigas and Crassostrea virginica) through four experimental approaches: (1) adaptation of the resazurin assay to measure oyster metabolism, (2) examination of temperature effects on oyster metabolism, (3) characterization of acute thermal stress responses, (4) examination of genetic variability in metabolism, and (5) correlations between metabolism and predicted performance in a selective breeding case study. Our findings confirm that resazurin fluorescence is correlated with oxygen consumption, validating its use as a measure of metabolism. Thermal performance assays reveal expected metabolic responses to temperature, including identification of optima and tipping points where metabolic stimulation shifts to depression under temperature stress. Acute thermal stress experiments demonstrate that oysters exhibiting greater metabolic depression are more likely to survive, supporting metabolism as a predictor of mortality. Further, genetic variation in stress responses is detected as family-level variation in metabolism. Metabolism of 50 families (C. virginica) selectively bred for performance in varying environments was measured and significantly correlated with predicted performance. By establishing resazurin as an additional reliable and scalable method for metabolic assessment, this study lays the groundwork for its broader adoption in aquaculture and conservation. Implementing this approach may provide a tool to enhance stock selection, improve hatchery management practices, and support adaptive strategies in the face of climate variability and increased environmental stress in coastal oceans.

physiology↗

bioRxiv2023

FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity

Cellular exposure to free fatty acids (FFA) is implicated in the pathogenesis of obesity-associated diseases. However, studies to date have assumed that a few select FFAs are representative of broad structural categories, and there are no scalable approaches to comprehensively assess the biological processes induced by exposure to diverse FFAs circulating in human plasma. Furthermore, assessing how these FFA- mediated processes interact with genetic risk for disease remains elusive. Here we report the design and implementation of FALCON (Fatty Acid Library for Comprehensive ONtologies) as an unbiased, scalable and multimodal interrogation of 61 structurally diverse FFAs. We identified a subset of lipotoxic monounsaturated fatty acids (MUFAs) with a distinct lipidomic profile associated with decreased membrane fluidity. Furthermore, we developed a new approach to prioritize genes that reflect the combined effects of exposure to harmful FFAs and genetic risk for type 2 diabetes (T2D). Importantly, we found that c-MAF inducing protein (CMIP) protects cells from exposure to FFAs by modulating Akt signaling and we validated the role of CMIP in human pancreatic beta cells. In sum, FALCON empowers the study of fundamental FFA biology and offers an integrative approach to identify much needed targets for diverse diseases associated with disordered FFA metabolism. HighlightsO_LIFALCON (Fatty Acid Library for Comprehensive ONtologies) enables multimodal profiling of 61 free fatty acids (FFAs) to reveal 5 FFA clusters with distinct biological effects C_LIO_LIFALCON is applicable to many and diverse cell types C_LIO_LIA subset of monounsaturated FAs (MUFAs) equally or more toxic than canonical lipotoxic saturated FAs (SFAs) leads to decreased membrane fluidity C_LIO_LINew approach prioritizes genes that represent the combined effects of environmental (FFA) exposure and genetic risk for disease C_LIO_LIC-Maf inducing protein (CMIP) is identified as a suppressor of FFA-induced lipotoxicity via Akt-mediated signaling C_LI

cell biology↗

bioRxiv2022

Development and evaluation of a formulation of probiont Phaeobacter inhibens S4 for themanagement of vibriosis in bivalve hatcheries

Larval eastern oysters (Crassostrea virginica) grown in shellfish hatcheries are susceptible to bacterial diseases, particularly vibriosis. Probiotics are microbes that confer health benefits to the host and have been identified as promising tools to manage diseases in aquaculture. The marine bacterium Phaeobacter inhibens S4 (S4) protects larval eastern oysters against challenge with the bacterial pathogen Vibrio coralliilyticus RE22 (RE22). A concentrated liquid formulation of probiont S4 that maintained high cell viability after long-term storage was developed for commercial use in shellfish hatcheries. The safety and efficacy of the formulation was tested in six different trials in two hatcheries. The S4 formulation was added to C. virginica larvae culture tanks daily at 104 colony forming units (CFU)/mL from day 1 post fertilization until day 6, 12, or 14, depending on the trial. Treatment of larvae in the hatchery with the S4 formulation did not significantly affect the survival and growth of the larvae. Formulated probiont S4 treatment in the hatchery led to a significant increase in Relative Percent Survival (RPS) when larvae were subsequently challenged with the pathogen RE22 (105 CFU/mL) for 24 hours in a laboratory challenge, as compared to probiotic-untreated RE22-challenged larvae (Relative Percent Survival increase of 46 - 74%, p < 0.05). These results suggest that this novel S4 formulation is a safe, easy to use, and effective tool in preventing larval losses due to vibriosis in hatcheries.

microbiology↗

bioRxiv2021

Intestinal Enteroid Monolayers Model the Human Intestinal Environment for Escherichia coli Infection

Enterohemorrhagic Escherichia coli O157:H7 is an enteric pathogen responsible for bloody diarrhea, hemolytic uremic syndrome, and in severe cases even death. The study of O157:H7 is difficult due to the high specificity of the bacteria for the human intestine, along with our lack of sufficiently complex human cell culture models. The recent development of human intestinal enteroids derived from intestinal crypt multipotent stem cells has allowed us to construct 2-dimensional differentiated epithelial monolayers grown in transwells that mimic the human intestine. Unlike previous studies, saline was added to the apical surface, while maintaining culture media in the basolateral well. The monolayers continued to grow and differentiate with apical saline. Apical infection with O157:H7 or commensal E. coli resulted in robust bacterial growth from 105 to over 108 over 24 hours. Despite this robust bacterial growth, commensal E. coli neither adhered to nor damaged the epithelial barrier over 30 hours. However, O157:H7 was almost fully adhered (>90%) by 18 hours with epithelial damage observed by 30 hours. O157:H7 contains the locus of enterocyte effacement (LEE) pathogenicity island responsible for attachment and damage to the intestinal epithelium. Previous studies report the ability of nutrients such as biotin, D-serine, and L-fucose to downregulate LEE gene expression. O157:H7 treated with biotin or L-fucose, but not D-serine displayed both decreased attachment and reduced epithelial damage over 36 hours. These data illustrate enteroid monolayers can serve as a suitable model for the study of O157:H7 pathogenesis, and identification of potential therapeutics. ImportanceO157:H7 is difficult to study due to its high specificity for the human intestine and the lack of sufficiently complex human cell culture models. The recent development of human intestinal enteroids derived from intestinal crypt multipotent stem cells has allowed us to construct 2-dimensional differentiated epithelial monolayers grown in transwells that mimic the human intestine. Our data illustrates enteroid monolayers can serve as a suitable model for the study of O157:H7 pathogenesis, and allow for identification of potential therapeutics.

microbiology↗