Biology subjects

Shaw, C.

Publications and source records attributed to Shaw, C..

14 recordsLinked to original sources

bioRxiv2026

Metatranscriptomic Profiling Reveals Species-Level Microbial Shifts and Metabolic Remodeling in Feline Oral Inflammatory Disease

Progressive oral mucosal inflammatory diseases are common among mammals. Cats are a valuable natural model for these conditions because they frequently develop oral diseases with varying severity, yet causative microbes remain unidentified in part because longitudinal studies are challenging and sampling is difficult. The lack of individual pathobionts suggests community-scale taxonomic and functional remodeling of the microbiome may be a contributor to oral disease. This study evaluated the microbiome composition and function of 33 cats across three cohorts with different levels of inflammation: healthy, aggressive periodontitis, and feline gingivostomatitis. Ultradeep metatranscriptomic sequencing was used to assign microbial taxonomy and examine functional changes via differential gene expression analysis to reveal genera that maintained stable relative abundance across all three disease states, including Porphyromonas and Treponema, while others had more subtle shifts in species activity, including multiple members of Moraxella and Mycoplasmopsis. Disease status was marked by co-occurring changes in low activity species accompanied by microbiome-level changes in protein, arginine, and nitrogen metabolism. Cats with aggressive periodontitis and gingivostomatitis displayed microbiome shifts in species that correlated to disease state. Microbial differential expression analysis revealed induction of stress-related genes and metabolic genes involved in amino acid metabolism, polyamine production, and nitric oxide production. Together, species identification and functional profiling suggest oral inflammation was correlated to shifts in the activity of multiple species that were involved with NO and polyamines. These coordinated metabolic signatures represent potential diagnostic targets for feline oral inflammatory disease.

microbiology↗

bioRxiv2025

In utero lipid nanoparticle delivery achieves robust editing in hematopoietic stem cells.

Efficient delivery of genome editing reagents to hematopoietic stem cells (HSCs) has limited the development of in vivo gene editing therapies for hematologic disease. Here, we exploit developmental hematopoiesis to enable HSC targeting using clinically scalable lipid nanoparticles (LNPs). During fetal development, HSCs reside in the liver, a tissue that is efficiently accessed by LNPs. We show that in utero delivery of LNPs carrying Cre recombinase or CRISPR-Cas9 components results in transfection and genome editing of bona fide long-term repopulating HSCs. Edited HSCs maintain multilineage reconstitution capacity following transplantation, demonstrating preserved stem cell function. Comparative studies reveal that both fetal and early neonatal delivery permit HSC editing, with greater efficiency during fetal liver hematopoiesis. We further identify an LNP formulation that enhance HSC targeting and enable robust neonatal HSC editing without antibody-mediated targeting. Finally, combined delivery of Cas9 via LNPs and a repair template via adeno-associated virus in neonatal mice enables in vivo homology-directed repair in multiple tissues. Together, these findings establish the perinatal period as a therapeutic window for in vivo HSC genome editing and provide a scalable strategy for treating severe early-onset hematologic diseases.

cell biology↗

bioRxiv2025

Cellular Respiration and Amino Acid Metabolism Is Altered by Dietary Oligosaccharides in Salmonella During Epithelial Association

Dietary prebiotic oligosaccharides are common in peoples diets; however, little is known about how different prebiotics alter the enteric epithelium and microbiome. Here we show two structurally different prebiotic oligosaccharides, human milk oligosaccharides (HMO) and mannanoligosaccharides (MOS), alter the metabolism of colonic epithelial cells and Salmonella enterica sv. Typhimurium in ways specific to each prebiotic. Initially, HMO and MOS addition decreased S. Typhimurium association with epithelial cells. However, gene expression analysis revealed significantly induced expression of Specific Pathogenicity Island (SPI) 1 and 2 with HMO treatment opposed to increased fimbriae expression with MOS treatment. MOS treatment induced the expression of genes for amino acid metabolism in both the host cells and in S. Typhimurium, a metabolic shift that was not observed in the HMO treated cells. MOS treatment also altered respiration metabolism in S. Typhimurium to be more closely aligned to those observed in vivo during gut inflammation, which is opposed to colonization-type expression with HMO. Alteration of virulence observed was found to be prebiotic specific and dose dependent, indicating that some dietary substrates likely alter specific pathogens to change their virulence potential in unanticipated ways that lead to multiple outcomes to potentiate or attenuate enteric infections.

microbiology↗

bioRxiv2024

Sex-specific DNA methylation differences in Amyotrophic lateral sclerosis

Sex is an important covariate in all genetic and epigenetic research due to its role in the incidence, progression and outcome of many phenotypic characteristics and human diseases. Amyotrophic lateral sclerosis (ALS) is a motor neuron disease with a sex bias towards higher incidence in males. Here, we report for the first time a blood-based epigenome-wide association study meta-analysis in 9274 individuals after stringent quality control (5529 males and 3975 females). We identified a total of 226 ALS saDMPs (sex-associated DMPs) annotated to a total of 159 unique genes. These ALS saDMPs were depleted at transposable elements yet significantly enriched at enhancers and slightly enriched at 3UTRs. These ALS saDMPs were enriched for transcription factor motifs such as ESR1 and REST. Moreover, we identified an additional 10 genes associated with ALS saDMPs through chromatin loop interactions, suggesting a potential regulatory role for these saDMPs on distant genes. Furthermore, we investigated the relationship between DNA methylation at specific CpG sites and overall survival in ALS using Cox proportional hazards models. We identified two ALS saDMPs, cg14380013 and cg06729676, that showed significant associations with survival. Overall, our study reports a reliable catalogue of sex-associated ALS saDMPs in ALS and elucidates several characteristics of these sites using a large-scale dataset. This resource will benefit future studies aiming to investigate the role of sex in the incidence, progression and risk for ALS.

genomics↗

bioRxiv2024

Heritable intraspecific variation among prey in size and movement interact to shape predation risk and potential natural selection

O_LIPredator and prey traits are important determinants of the outcomes of trophic interactions. In turn, the outcomes of trophic interactions shape the evolution of predator and prey traits. How species traits are likely to respond to selection from trophic interactions depends crucially on whether and how heritable species traits are and their genetic correlations. Of the many traits potentially influencing the outcomes of trophic interactions, body size and movement traits have emerged as universally key traits. Yet, how these traits shape and are shaped by trophic interactions is generally unclear, as few studies have simultaneously measured the impacts of these traits on the outcomes of trophic interactions, their heritability, and their correlations within the same system. C_LIO_LIWe used outcrossed and then clonally propagated lines of the ciliate protist Paramecium caudatum from natural populations to examine variation in morphology and movement behavior, the extent to which this variation was heritable, and how intraspecific differences among lines altered Paramecium susceptibility to predation by the copepod Macrocyclops albidus. C_LIO_LIWe found that the Paramecium lines exhibited heritable variation in body size and movement traits. In contrast to expectations from interspecific allometric relationships, body size and movement speed showed little covariance among clonal lines. The proportion of Paramecium consumed by copepods was positively associated with Paramecium body size and velocity, however, we also found evidence of an interaction such that greater velocities led to greater predation risk for large body-sized paramecia but did not alter predation risk for smaller body-sized paramecia. The proportion of paramecia consumed was not related to copepod body size. These patterns of predation risk and heritable trait variation in paramecia suggest that copepod predation may act as a selective force operating independently on movement and body size and generating the strongest selection against large, high-velocity paramecia. C_LIO_LIOur results illustrate how the interactions between ecology and genetics can shape the potential natural selection on prey traits through the outcomes of trophic interactions. Further simultaneous measures of predation outcomes, traits, and their quantitative genetic characteristics will provide insights into the evolutionary ecology of species interactions and their eco-evolutionary consequences. C_LI

ecology↗

bioRxiv2023

Plant-like heliotropism in a photosymbiotic animal

Being photosynthetic sessile organisms, plants established heliotropism to track the suns position across the sky and allow their vegetative parts to orient accordingly. Here, we report plant-like heliotropic movement in a photosymbiotic sea anemone Anemonia viridis. Like plants, photosynthesis represents a key energy source in endosymbiotic cnidarians bearing microalgae. We observed that A. viridis in their natural habitats under sunlight displayed heliotropism or solar tracking by pointing their tentacles towards the sun while remaining sessile, facing east at dawn and west at dusk as they track the suns relative position through the day, a phenomenon previously only observed in plants. Solar tracking movements in A. viridis are driven by a light wavelength that prompts photosynthesis in their endosymbionts. The heliotropic response was absent in both bleached (aposymbiotic) A. viridis and in symbiotic A. viridis with chemically inhibited photosynthesis. We revealed a direct correlation between heliotropism and endosymbiont oxygen production in A. viridis. Our findings suggest that photosymbiotic A. viridis has likely evolved plant-like heliotropism as an effective way to modulate exposure to solar irradiation for photosynthesis. The study exemplifies how photosynthetic organisms such as plants and photosymbiotic sea anemones, display similar behaviour in response to similar environmental pressures.

animal behavior and cognition↗

bioRxiv2022

MRI-to-Synthetic 3D Gel Brain: Proof-of-Concept Fabrication For Intra-Parenchymal Diffusion Studies

Bioprinting technologies utilize hydrogel-based biomaterials to more accurately depict in vivo physical conditions within in vitro studies, yet, manufacturing the human brain from soft, poroelastic hydrogels remains a fundamental challenge. Conventional manufacturing routes to fabricate hydrogel brain models using techniques, i.e., 3D printing, seems challenging. This study aims to demonstrate an inverse replica molding fabrication technique that can overcome these challenges while maintaining the complex shape of an individual subjects brain in a miniaturized model--allowing for a more robust hydrogel model that can capture the interactions between diffusing molecules and brain boundaries. This is done by taking a subjects magnetic resonance imaging (MRI) scan and reconstructing the outer pial surface into a mesh surface. The mesh was then converted to an STL and printed out using an extrusion printer. A silicon mold was made from this print into which agarose was gelled. Once fully gelated, the synthetic gel brain was then carefully removed. Two infusion trials were run in the gel brain, each using a different infusion site. Then a diffusion profile was established and compared to a simple gel infusion model. The result shows different diffusion profiles at each location and between the simple and complex models. This model can better represent the interference the complex shape of the brain has on particle movement compared to simple gel models.

bioengineering↗

bioRxiv2022

In Silico, Brain Mesh Platform for Computing Topographic Dependent Internal Facets

Individualized and anatomically correct computational models of the brain can be leveraged to improve knowledge of drug dispersal following simulation of drug delivery. Using a patients magnetic resonance image (MRI) scans, we were able to reconstruct the pial surface of the brain of the left hemisphere with strong anatomic accuracy. We then established the major internal features, including the lateral ventricle, a tumor, and drug delivery catheters. These were able to include relevant tissue characteristics such as porosity and permeability in the Multiphysics platform COMSOL to create a platform for brain modeling. To test the performance of this platform, we simulated direct drug infusion in both a healthy patient brain and a diseased patient model, focusing on glioblastoma (GBM). Using this platform, we simulated perturbed convection enhanced delivery of a cancer medication (similar to temozolomide (TMZ) but modeled using methylene blue) to the tumor. Consequently, with our patient derived model, we are able to simulate solute dispersal and fluid flow representative of in vivo conditions.

bioengineering↗

bioRxiv2022

Convection-enhanced diffusion and directed withdrawal of methylene blue in agarose hydrogel using finite element analyses

Precision drug delivery for optimized therapeutic targeting requires knowledge of momentum transport and molecular diffusion of molecules within the patients interstitial tissue, especially for tumor treatment within the brain. Dispersion in the interstitial space is impacted by delivery method, tissue material properties, individual-specific fluid flow, and particle size of the input solute. Knowledge of a drugs dispersion allows for optimizing solute delivery, concentration, and flow rates to maximize drug distribution and biomarker recovery. For delivering drugs, increased knowledge of drug location after delivery can improve therapeutic treatment by optimizing the dosing of healthy and unhealthy tissue. Finite element methods (FEM) tools, such as COMSOL Multiphysics, can simulate molecular distribution inside-individual specific shapes and porous material properties. Furthermore, an additional unmet need is delivery methods that can be adjusted to manipulate diffusion regions through tissue via techniques such as directed flow. This would be especially valuable in targeted drug delivery within tumors to increase the cancerous surface area covered while limiting damage to surrounding tissues. In this project, the directed flow was induced by perfusing the injected solution at an input probe while withdrawing fluid at an output probe, enabling targeted flow through the desired region. FEM computation faithfully replicated these conditions and could be used to determine the effective concentrations perfused over the region of interest. We leveraged COMSOL Multiphysics to perform a computational study simulating convection-enhanced delivery (CED) with an output probe pulling the concentration profile over the region of interest. This simulation system can be applied to therapeutics targeting, vaccine subcutaneous injection, and waste and media diffusion in tissue engineering.

bioengineering↗

bioRxiv2020

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 hours in nylon bags within the rumen of cannulated dairy cows. Across a gene catalogue covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of polysaccharides such as hemicellulose, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8 and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggests that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

microbiology↗

bioRxiv2019

Integrated Sequencing & Array Comparative Genomic Hybridization in Familial Parkinson’s Disease

BackgroundParkinsons disease (PD) is a genetically heterogeneous condition; both single nucleotide variants (SNVs) and copy number variants (CNVs) are important genetic risk factors. We examined the utility of combining exome sequencing and genome-wide array-based comparative genomic hybridization (aCGH) for identification of PD genetic risk factors. MethodsWe performed exome sequencing on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated exome sequencing and array comparative genomic hybridization data for pathogenic SNVs and CNVs at Mendelian PD gene loci. SNVs were confirmed via Sanger sequencing. CNVs were confirmed with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing. ResultsUsing exome sequencing, we discovered individuals with known pathogenic single nucleotide variants in GBA (p.E365K, p.T408M, p.N409S, p.L483P) and LRRK2 (p.R1441G and p.G2019S). Two subjects were each double heterozygotes for variants in GBA and LRRK2. Based on aCGH, we additionally discovered cases with an SNCA duplication and heterozygous intragenic GBA deletion. Five additional subjects harbored both SNVs (p.N52fs, p.T240M, p.P437L, p.W453*) and likely disrupting CNVs at the PARK2 locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors. ConclusionsIntegrated exome sequencing and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for SNCA and PARK2 CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.

genetics↗

bioRxiv2019

SPiQE: an automated analytical tool for detecting and characterising fasciculations in amyotrophic lateral sclerosis

OBJECTIVESFasciculations are a clinical hallmark of amyotrophic lateral sclerosis (ALS). Compared to concentric needle EMG, high-density surface EMG (HDSEMG) is non-invasive and records fasciculation potentials (FPs) from greater muscle volumes over longer durations. To detect and characterise FPs from vast data sets generated by serial HDSEMG, we developed an automated analytical tool.\n\nMETHODSSix ALS patients and two control patients (one with benign fasciculation syndrome and one with multifocal motor neuropathy) underwent 30-minute HDSEMG from biceps and gastrocnemius monthly. In MATLAB we developed a novel, innovative method to identify FPs amidst fluctuating noise levels. One hundred repeats of 5-fold cross validation estimated the models predictive ability.\n\nRESULTSBy applying this method, we identified 5,318 FPs from 80 minutes of recordings with a sensitivity of 83.6% (+/-0.2 SEM), specificity of 91.6% (+/-0.1 SEM) and classification accuracy of 87.9% (+/-0.1 SEM). An amplitude exclusion threshold (100V) removed excessively noisy data without compromising sensitivity. The resulting automated FP counts were not significantly different to the manual counts (p=0.394).\n\nCONCLUSIONWe have devised and internally validated an automated method to accurately identify FPs from HDSEMG, a technique we have named Surface Potential Quantification Engine (SPiQE).\n\nSIGNIFICANCELongitudinal quantification of fasciculations in ALS could provide unique insight into motor neuron health.\n\nHighlightsO_LISPiQE combines serial high-density surface EMG with an innovative signal-processing methodology\nC_LIO_LISPiQE identifies fasciculations in ALS patients with high sensitivity and specificity\nC_LIO_LIThe optimal noise-responsive model achieves an average classification accuracy of 88%\nC_LI

neuroscience↗

bioRxiv2019

Identification of functional variants for platelet CD36 expression by Massively Parallel Reporter Assay.

CD36 is a platelet membrane glycoprotein whose engagement with oxidized low-density lipoprotein (oxLDL) results in platelet activation. The CD36 gene has been associated with platelet count, platelet volume, as well as lipid levels and CVD risk by genome-wide association studies. Platelet CD36 expression levels have been shown to be associated with both the platelet oxLDL response and an elevated risk of thrombo-embolism. Several genomic variants have been identified as associated with platelet CD36 levels, however none have been conclusively demonstrated to be causative. We screened 81 expression quantitative trait loci (eQTL) single nucleotide polymorphisms (SNPs) associated with platelet CD36 expression by a Massively Parallel Reporter Assay (MPRA) and analyzed the results with a novel Bayesian statistical method. Ten eQTLs located in a 35kb region upstream of the CD36 transcriptional start site demonstrated significant transcription shifts between their minor and major allele in the MPRA assay. Of these, rs2366739 and rs1194196, separated by only 20bp, were confirmed by luciferase assay to alter transcriptional regulation. In addition, electromobility shift assays demonstrated differential DNA:protein complex formation between the two alleles of this locus. Furthermore, deletion of the genomic locus by CRISPR/Cas9 in K562 cells results in upregulation of CD36 transcription. These data indicate that we have identified a variant that regulates expression of CD36, which in turn affects platelet function. To assess the clinical relevance of our findings we used the PhenoScanner tool, which aggregates large scale GWAS findings; the results reinforce the clinical relevance of our variants and the utility of the MPRA assay. The study demonstrates a generalizable paradigm for functional testing of genetic variants to inform mechanistic studies, support patient management and develop precision therapies. Author SummaryPlatelets are anucleate cells that are best known as regulators of vascular hemostasis and thrombosis but also play important roles in cancer, angiogenesis, and inflammation. CD36 is a platelet surface marker that can activate platelet in response to oxidized low density lipoprotein (oxLDL). CD36 has been associated with numerous cardiovascular traits in human including blood lipid levels, platelet count, and cardiovascular disease prevalence in human genetic studies. Human variability in platelet CD36 levels are associated with the platelet response to oxLDL. However, the genetic mechanisms responsible for the variability of CD36 levels are unknown. We examined 81 genetic variants associated with CD36 levels for functionality using a high-throughput assay. Of the ten variants that were identified in that assay, one doublet, rs2366739 and rs1194196, were confirmed using additional molecular and cellular assays. Deletion of the genomic region containing rs2366739 and rs1194196 resulted in overexpression of CD36 in a cell culture system. This finding indicates a control locus which can serve as a potential target in modulating CD36 expression and altering platelet function in cardiovascular disease.

genomics↗

bioRxiv2018

Enrichment of rare protein truncating variants in amyotrophic lateral sclerosis patients

To discover novel genetic risk factors underlying amyotrophic lateral sclerosis (ALS), we aggregated exomes from 3,864 cases and 7,839 ancestry matched controls. We observed a significant excess of ultra-rare and rare protein-truncating variants (PTV) among ALS cases, which was primarily concentrated in constrained genes; however, a significant enrichment in PTVs does persist in the remaining exome. Through gene level analyses, known ALS genes, SOD1, NEK1, and FUS, were the most strongly associated with disease status. We also observed suggestive statistical evidence for multiple novel genes including DNAJC7, which is a highly constrained gene and a member of the heat shock protein family (HSP40). HSP40 proteins, along with HSP70 proteins, facilitate protein homeostasis, such as folding of newly synthesized polypeptides, and clearance of degraded proteins. When these processes are not regulated, misfolding and accumulation of degraded proteins can occur leading to aberrant protein aggregation, one of the pathological hallmarks of neurodegeneration.

genomics↗