The Integrative Life Sciences Research Showcase, part of VCU Research Weeks, was held on April 23, 2025 in the Student Commons. The event consisted of doctoral students presenting their research via presentations and in a poster session. The showcase abstracts include: 

Reactive oxygen species mediated Src family kinase signaling regulates definitive hematopoiesis in zebrafish – Brad Williams

Hematopoietic stem and progenitor cells (HSCs) make up the self-renewing reservoir of multipotent cells that produce myeloid and lymphoid cell lineages for the life of an organism. HSCs are the therapeutic unit of bone marrow transplantation and play a critical role in the development of blood disorders. Understanding the signaling mechanisms that govern their specification is therefore essential. In vertebrates, HSCs arise from hemogenicen dothelium-derived precursor cells, located primarily in the embryonic dorsal aorta (DA) during the process called the endothelial to hematopoietic transition (EHT). Nearby cells in the trunk of the embryo likely form an embryonic niche, providing extracellular signals that drive this process. Reactive oxygen species (ROS) have established roles in the regulation of developmental signaling pathways. Furthermore, they are known to modulate the activity of Src-family kinases (SFKs), a class of non-receptor tyrosine kinases. Wild type zebrafish (Danio rerio) embryos were treated with either ROS scavenger edaravone (MCI-186), or PP2, a pharmacological inhibitor of SFKs. Embryos were also injected with splice-blocking morpholino oligonucleotides targeting mRNA transcripts of zebrafish SFK yrk to knock down Yrk protein expression. Whole-mount in-situ hybridization for key HSC and endothelial cell marker genes was performed to examine the status of HSC and endothelial development under these conditions. An analysis of colocalization of phospho-Src antibody with endothelial markers was performed to highlight SFK activity in the vasculature. We observed defective HSC development in embryos treated with the pharmaceuticals and morpholinos, suggesting a model where ROS signaling is required for phosphorylation of SFK Yrk, which in turn plays a yet to be determined signaling role in the development of HSCs.

Facilitative and competitive interactions among dune grass species in monoculture and polyculture communities – Anne Sciolino

Coastal dunes are natural barriers between land and sea and are imperative to the protection and preservation of inland ecosystems and human infrastructure. However, due to global warming, seal level rise, and coastal development, coastal dunes are under constant threat of destruction. Restoration efforts have been implemented to rebuild the protective function of dunes through the planting of dune building grasses. Dune grasses build and maintain these vital sand dunes. However, little is known about facilitative and competitive relationships among the grasses. In order to maximize restoration efforts, research is needed to better understand the biotic interactions among restorative grass plantings. Our objective was to help fill this knowledge gap by quantifying the facilitative and competitive interactions of four common dune building grasses along the coast of the eastern United States in both polyculture and monoculture communities. To do so we designed plantings of common dune grasses, Ammophila breviligulata, Panicum amarum, Spartina patens, and Uniola paniculata, within polyculture plots to facilitate interspecies interactions and monoculture plots to allow intraspecies interactions along the coast of Hog Island, a Virginia barrier island along the Delmarva peninsula. We also designed a mirror planting of the same four grasses in a mesocosm. The mesocosm planting design included the same polyculture and monoculture combinations of grasses growing within plots.

However, each planting design was grown in both pots that allowed root interaction and pots that excluded root interaction though root compartmentalizing. We found that while many of the species were unaffected by planting designs, Panicum amarum had the highest yield in polyculture planting designs where interspecies below ground root interactions were allowed, indicating greater facilitation in polyculture plantings. With the current practice of planting dune grasses in monoculture communities, this research will provide coastal managers with planting designs that maximize the success rate of dune grass establishment and success.

Investigating the role of sphingolipid biosynthesis dysregulation in ALS8 – AnnaMari Stump

Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disorder that impairs the central nervous system through both upper and lower motor neuron degeneration. ALS impacts 5 per 100,000 people and results in death between 3-5 years after diagnosis. ALS has both genetic and environmental factors, the focus of my work is on VAPB, a gene which has a mutation causative of ALS8. VAPB is conserved through evolution with a homolog in yeast SCS2, SCS22 both homologs play key roles in ER structure and function, defects in VAPB lead to protein misfolding causing cellular transport dysfunction and aggregation to occur. Our lab has capitalized on those features by making a yeast model of ALS8 that recapitulates the same phenotype and preformed a genetic screen to identity suppressors of ALS8, three genes involved in sphingolipid biosynthesis were identified. My work involves studying roles of lipid regulation in ALS.

Time Since Deposition Signatures for Epithelial Cells Recovered from Aged Biological Samples: Implications for Front-End Separation and DNA Profiling of Biological Mixture Samples – Arianna DeCorte

With the increase in sensitivity of DNA profiling, activity-level questions related to how and when evidentiary DNA was deposited have become a driving issue in forensic cases. To address this, we have developed a novel method to determine time since deposition (TSD) of trace biological samples using morphological and autofluorescence profiles of individual epithelial cells that are measured in a non-destructive and high-throughput manner prior to DNA profiling. These signatures have been tested in a series of trace epithelial samples generated from both saliva and touch epidermal deposits over time periods ranging between one day and over one year. Results from this time series show linear changes in the intensity of autofluorescence for most donors (12 out of 15 donor scatter plots R2 > 0.80). Variation in the baseline levels of autofluorescence between some individuals limited the accuracy of a universal regression model for predicting TSD in blinded samples (R2 = 0.68). To overcome this, a binary prediction model was developed where cells were classified as having TSD as either less than or greater than a specific time threshold, e.g., sample was deposited less than one week ago or is older than one week. The accuracy of four different time thresholds were evaluated: 1 day, 1 week, 2 weeks, and 1 month. Results showed that false positive TSD estimates (i.e., a sample is classified as being younger than the time threshold but is actually older), were 10% and 4% at 1 day and 1 week, respectively. However, there were no false positive TSD estimates using 2 week or 1 month thresholds across all samples tested. Overall, this suggests that autofluorescence signatures can provide probative TSD estimates for epithelial cell populations from saliva and/or touch epidermal deposits. Current efforts are focused on integrating the workflow for generating TSD estimates into the operational constraints of a DNA caseworking laboratory and extending this method to other types of biological deposits including complex cell mixtures.

Unraveling forest composition and carbon storage dynamics in the face of biotic disturbances – Ariel Johnson

In many forested regions of the world, insect disturbances are increasing, impacting forest community composition and structure. The extent to which associated changes in forest composition and structure are coupled with the amount of carbon (C) stored annually in plant biomass, or net primary production (NPP), remains poorly understood. However, this foundational knowledge is vital for managing, remotely sensing, and modeling the effects of insect pests on C cycling processes. We used the Forest Resilience Threshold Experiment (FoRTE), a replicated study of disturbance orientation and severity, employing stem girdling to achieve four levels of gross defoliation: 0% control, 45%, 65% and 85%. Utilizing five years of species specific leaf litter and seedling data and portable canopy LiDAR data, we analyzed relationships between community composition, structure, and NPP following disturbance. Preliminary analysis suggests that disturbance severity and orientation affected species changes, but our hypotheses were incorrect in stating that early successional species would dominate in higher severity plots. Across disturbance severities, the canopy was predominantly occupied by Quercus and Populus species, but their expected dominance did not manifest in any of the seedling plots. Five years after disturbance initiation, middle successional Acer and Fagus species emerge as dominant following all disturbance severities and both disturbance orientations within the seedling and sapling strata. Additionally, our findings suggest that in the early stages of disturbance response, NPP resistance was not driven by a specific plant species, but by the ratio of early successional species to middle successional species within a given forested stand. As we manage forests for greater stability in the face of increasing disturbances and intensifying climate change, our analysis indicates that C cycling stability may be possible despite community compositional changes.

Exploring the Relationship between Genetic and Environmental Influences on the Initiation and Progression of Cannabis Use from Adolescence to Early Adulthood – Chao-Yi Lo

Introduction: Cannabis use has negative impacts on health and social functioning, and prevalence of current use is increasing among U.S. adolescents and adults. Twin studies have investigated initiation and progression of cannabis use as independent constructs, but evidence conceptualizing cannabis use as a multi-stage process is limited. Vulnerabilities for progression depend on those for initiation with relative genetic and environmental contributions to each stage, which may vary across age. Therefore, we explore the degree to which genetic and environmental factors contribute to variation in cannabis initiation and progression across adolescence and early adulthood.

Methods: Data from 1,385 twin pairs ages 12–18 years participating in the Virginia Twin Study of Adolescent Behavioral Development were analyzed along with two follow-up waves (1,183 pairs aged 18–27 years and 666 pairs aged 22–32 years). Cannabis initiation was defined as lifetime use, and progression as current use or lifetime use occurring more than 10 times per month. A causal-common-contingent (CCC) model was fitted separately for each age group to estimate genetic, shared and unique environmental contributions to the variance of and the correlation between initiation and progression.

Results: The prevalence of cannabis initiation (55.0%) and progression (43.1%) was highest in participants ages 18-27. As individuals transition from adolescence to young adulthood, heritability increased while the contribution of shared environmental factors decreased. The correlation between initiation and progression was only significant in young adults, with progression-specific variation completely environmental.

Identification of microRNA Biomarkers for Predicting Body Weight and Muscularity in Forensic Samples – Xiaomeng Yang

Background: Forensic DNA phenotyping (FDP) utilizes genetic markers to predict externally visible characteristics (EVCs) of unknown individuals, especially in cases lacking suspects or database matches. Recent studies suggest that microRNA (miRNA) expression is influenced by external factors such as metabolism and physical activity. This study introduces an innovative FDP approach exploiting miRNA expression profiles from blood and saliva to predict an individual’s body weight and muscularity classes.

Methods: Comprehensive body composition was assessed via bioelectrical impedance analysis. DNA extracts from whole blood and saliva were analyzed using reverse transcription-quantitative PCR (RT-qPCR) to evaluate miRNA expression. Additionally, high- throughput sequencing (HTS) of RNA extracts was performed to identify potential miRNA markers linked to body weight and muscularity.

Results: Analysis of 100 blood and saliva DNA extracts revealed associations between body weight categories and specific miRNAs, such as miR-145-5p and let-7i-5p. HTS of selected samples identified several differentially expressed miRNAs involved in metabolic regulation, exercise adaptation, and muscle cell differentiation, offering promising targets for further validation.

Conclusions: This study highlights the predictive ability of miRNAs and contributes to the development of prediction models for environmentally influenced EVCs. Notably, the ability to detect miRNAs from DNA extracts reduces sample consumption and processing time while providing investigators with more identity-related information. Future work will focus on increasing sample size and verifying identified miRNA markers to enhance the accuracy of prediction models.

Gene-based Analysis of Rare Variants for Alcohol Use Disorder in the All of Us Cohort – Masoud Edizadeh

Background: Alcohol Use Disorder (AUD) is a complex condition with genetic and environmental influences. The largest genome-wide association study (GWAS) on problematic alcohol use identified > 100 loci, highlighting the significant contribution of common single nucleotide variants (SNVs) to the condition. In contrast, studies investigating the role of rare SNVs have only reported a few genes for this disorder, largely due to the limited sample sizes with whole-genome sequencing data available. The All of Us (AOU) cohort provides a unique opportunity to investigate rare variants associated with AUD. Unlike disease-specific biobanks, AOU is a population-based biobank that enrolls individuals from diverse backgrounds and health statuses, making it challenging to accurately define phenotypes for complex disorders.

Methods: Cases were defined as individuals with an AUD diagnosis based on codes of the International Classification of Diseases, 9th or 10th version (ICD9-10, or Systematized Nomenclature of Medicine (SNOMED) codes in their electronic health records (EHRs) or those prescribed AUD medications such as Acamprosate or Disulfiram. Controls were individuals without an AUD diagnosis who had reported alcohol consumption at least once and had no AUD endorsements. Individuals with a history of naltrexone use but no AUD diagnosis were excluded, as naltrexone is also prescribed for opioid use disorder.

Covariates included sex ploidy estimations (from the AoU Dragen pipeline), ancestry, and age. Individuals with sex chromosome aneuploidies were excluded. A variant annotation file was created using AOU-provided annotation files, selecting only specific consequences in canonical transcripts and filtering out variants with allele frequencies exceeding 5% in The Genome Aggregation Database (gnomAD) or AOU. Gene-set and mask files were generated for analysis. Quality control (QC) on array data was performed using genotype and variant missingness (<10%), minor allele frequency (>1%), and Hardy-Weinberg equilibrium (HWE) threshold (1×10⁻⁷⁵). REGENIE was used for gene-set analysis in two steps: (1) common variants from array data and (2) rare exonic variants on chromosome 4.

Results: Manual querying of the AOU database identified 29,182 cases and 484,154 controls for AUD. Older individuals tended to have more AUD-related endorsements, indicating a correlation between age and depth of EHR. QC filtering retained 510,788 variants, removing 1,228,481 out of 1,739,269 present in the array (the InfiniumTM Global Diversity Array,). REGENIE gene-set analysis provided p-values for each gene, and a Manhattan plot of the results showed no genome-wide significant signals for chromosome 4.

Conclusion: Despite the comprehensive approach to defining AUD phenotypes and conducting rare variant analysis, no significant genetic associations were identified. Future work will refine case-control definitions and expand the analysis to additional genomic regions.

Statistical Analysis of Vessel Shipping in the Arctic: Backcasting Decision-Making with Vessel Speed to Quantify Environmental Risks – Mauli Pant

Background and Motivation: The Arctic Northwest Passage (NWP) presents new maritime opportunities but also significant risks due to dynamic environmental and ecological challenges. This study uses AIS data from 2010 to 2019 to analyze vessel speed as a key metric for backcasting decision-making. Environmental factors: sea ice concentration, wind patterns, and whale distribution are assessed for their influence on navigational risks. The findings establish a baseline for past risks, facilitating informed decision-making for future Arctic maritime operations.

Methods: Spatio-temporal kriging interpolates missing data on sea ice, wind, and bathymetry. Generalized Linear Mixed Models (GLMMs) quantify the impact of environmental factors on vessel speed, accounting for spatial and temporal dependencies. A Gamma distribution with a log link is applied to address excess zeros in speed data, with a dispersion model to account for heteroscedasticity.

Results: The spatio-temporal overlap between vessel and ice data facilitated the assessment of ice- related risks using the Arctic Climate Change Economy Society (ACCESS 2015) safe speed thresholds. Approximately 40% of vessels from 2010 to 2019 were exposed to ice-related risks. GLMMs reveal significant relationships between Speed Over Ground (SOG), ice concentration, and wind speed. The model explains 67% of SOG variability compared to Null model, with spatial random effects explaining the 31% of the variance. Vessel group interactions with ice concentration provided insights into how different vessels adjust speed to varying ice conditions. Furthermore, interactions between vessel status and bathymetry showed how navigational status and ocean depth influence SOG and navigational decisions.

Discussion and Future Work: Future research will integrate whale distribution data to assess collision and ship strike risks, contributing to an optimization model that minimizes Arctic shipping risks.

Cross-scale coupling of plant traits and carbon cycling processes in a restored tidal freshwater marsh – Mindy Priddy

Tidal freshwater wetlands are understudied and biogeochemically distinct from their saline coastal and freshwater interior counterparts. These ecosystems are relatively high sources of methane and vary in their capacity to sequester carbon; however, the mechanisms that underlie carbon dioxide and methane flux exchange across spatial scales are poorly understood but crucial to improving biogeochemical models. To address this knowledge gap, we are using chambers, eddy-covariance towers, and terrestrial and airborne remote sensing to characterize the leaf-to-landscape spectral, physiological, and morphological traits tied to carbon cycling processes, with the goal of identifying the biophysical drivers of fluxes in a restored tidal freshwater wetland in the Chesapeake Bay watershed. Our study site is the US-RRC (Rice Rivers Center) AmeriFlux Core Site facility, an early successional tidal freshwater wetland restored 15 years ago following nearly a century of inundation.

Our preliminary analyses suggest that methane and carbon dioxide fluxes are coupled to plant functional traits across spatial scales, providing a mechanistic basis for inferring and interpreting tidal freshwater carbon cycling processes from remotely sensed data. At 1 to 30 meter spatial scales, we observed distinct spectral signatures among plant functional types corresponding with different profiles of stomatal conductance, net carbon assimilation, leaf mass per area (LMA), and foliar nitrogen content. At larger landscape scales, net ecosystem exchange and methane fluxes were greater where fast-growing, physiologically active annual species dominate within the flux tower footprint, highlighting a spatial connection between smaller and larger spatial scales.

Our analysis has implications for multi-scale modeling, highlighting challenges and opportunities associated with the prediction of carbon dioxide and methane fluxes in a heterogeneous, dynamic system.

Utilizing large scale biobank data to examine copy number variant association in PTSD – Sydney Kramer

PTSD is moderately heritable, and genome-wide association studies (GWAS) have identified numerous common variants associated with PTSD. Yet, rare structural variation through copy number variant (CNV) associations are much less understood. We leverage short-read whole genome sequencing (srWGS) data from the All of Us (AoU) study to examine rare CNVs associated with PTSD. This study used data from the All of Us Research Program’s Controlled Tier Dataset v8, available to authorized users on the Researcher Workbench.

We conducted Firth’s regression using srWGS based genotypes with data from 49,879 individuals of European ancestry with cases defined as 2+ ICD 9 (309.81) and 10 (F43.1) codes for PTSD and controls defined as absence of these codes and adjusting for population structure, sex, and age. We examined the genome-wide total span of CNVs and CNVs overlapping individual genes. P-values were Bonferroni adjusted.

A total of 1483 cases and 48436 controls were identified. We tested the association of 584,029 CNVs with PTSD. One marginally significant duplication, q21.22 (z-stat=5.35, OR=17.91, SE=0.54, p=8.909e-08, adj p=0.05) was found in the THAP9 gene. A deletion, q22.2, was also suggestive (z-stat=5.19, OR=1.95, SE=0.13, adj p=0.06) in the DSCAM gene.

Two suggestive CNVs were identified as associated with PTSD case status even in a limited sample size. The duplication in THAP9 has been associated with neurodevelopmental disorders. Planned extensions will apply cross-ancestry pipelines, additional biobanks, and integrative common variant approaches to enhance power and further clarify the genetic architecture of PTSD.

Survival of wastewater-associated, antibiotic resistant bacteria within in situ mesocosms – Mary Coughter

Wastewater is a well-documented source of antibiotic resistance bacteria (ARB) and genes (ARG) to aquatic ecosystems, especially in urban environments impacted by sewage overflows and treatment plant discharge. Elevated levels of ARB and ARG have been detected in both treated and untreated wastewater, but few studies have quantified their survival and persistence after discharge into receiving water bodies. Our research utilized in situ mesocosms made of dialysis membranes to track ARB survival in a large river.

Specifically, dialysis membrane was used to create “microbial cages” containing wastewater microbial communities, which were suspended in a river system and sampled after 1, 4, and 7 days. Even after one week of in situ incubation, we found an elevated abundance of viable bacteria resistant to ciprofloxacin, sulfonamide, and cefotaxime. Die-off rates for ARBs were much slower than for Escherichia coli, which suggests that standard water- quality monitoring approaches may not be useful for assessing risk associated with antibiotic resistance. Quantitative PCR (qPCR) was used to track the abundance of corresponding ARGs over time. In addition, changes in bacterial community composition were assessed using full-length 16S rRNA gene sequencing (PacBio). Bacterial taxa characteristic of untreated wastewater, including several potentially pathogenic species, were still detected four days after discharge into the river. Together, these data are among the first available to quantify ARB survival and ARG persistence in natural environments, which is an essential step in developing a predictive mechanistic understanding of potential human health risks associated with wastewater discharge.

Comparative Analysis of VlsE Variants for Lyme Disease Detection in Horses – Jade Smith

Lyme disease is a significant concern in veterinary medicine. Horses are at a high risk of tick exposure and are thus susceptible to tick-borne pathogens, including the causative agent of Lyme disease, Borrelia burgdorferi. Clinical manifestations of LD in horses may include fever, intermittent lameness, encephalitis, uveitis, and infectious arthritis. Horses with long-term Infections may exhibit pronounced neurological disease. Clinical signs indicative of neurological Involvement includes hyperesthesia, ataxia, dysphagia, laryngeal dysfunction, cranial nerve deficits, muscle atrophy, and neck stiffness. Testing for infection and or exposure to the LD agent is most commonly accomplished using serological assays. In this report, we assess Ab responses to B. burgdorferi proteins that are widely used in serological tests, including OspC, OspA, VlsE, and OspF. C6 antibody- based tests and the Equine Lyme Multiplex Assay (Animal Health Diagnostic Center; Cornell University) are among the most widely used tests. The multiplex test detects Abs to OspA, OspC, and OspF. C6 peptide-based tests detect Abs to a conserved region of the VlsE protein. In this report, we have comparatively assessed Ab responses to the proteins that are currently used in equine LD diagnosis. The data suggest that care must be taken when interpreting diagnostic assay results, as varying Antibody responses among animals and natural variations in the amino acid sequence of the test antigens can affect the accuracy of these tests.

Avl9 contributes to recycling and sorting of endosomal cargos – Daniel Rioux

Trafficking of cargos between cellular compartments requires numerous proteins including Rabs and their activating regulators guanine nucleotide exchange factors (GEF). GEFs are characterized by numerous domains and motifs including a class known as DENNs (Differentially Expressed in Normal and Neoplastic tissue). Among these is the DENN-like protein Avl9, which has a poorly characterized role in trafficking and secretion. Here, we show that Avl9 characterizes puncta that display dynamic movement at the periphery of the cell near the PM along with movement of these puncta from the mother to the budneck and daughter cells. Further we show that Avl9 colocalizes with the Golgi marker Aur1 but not with Trans-Golgi Network marker Sec7, demonstrating a potential non-canonical role for Avl9 in secretion. We next demonstrate that loss of AVL9 results in defects in recycling of Snc1 but no changes to normal secretion of an endocytosis defective Snc1 mutant. This recycling defect is enhanced in combination with the loss of RCY1, SNX4, or VPS35 suggesting that Avl9 is acting separate from these pathways. Supporting this is a finding of growth defects in a rcy1∆ avl9∆ mutant but not in snx4∆ avl9∆ or vps35∆ avl9∆ mutants. These data suggest a model in which Avl9 contributes to a recycling pathway that operates early in the endolysosomal pathway independent of the TGN.