Understanding the pathways and biological processes underlying differential gene expression is fundamental for characterizing gene expression changes in response to an experimental condition. Zebrafish, with a transcriptome closely mirroring that of humans, are frequently utilized as a model for human development and disease. However, a challenge arises due to the incomplete annotations of zebrafish pathways and biological processes, with more comprehensive annotations existing in humans. This incompleteness may result in biased functional enrichment findings and loss of knowledge. danRerLib, a versatile Python package for zebrafish transcriptomics researchers, overcomes this challenge and provides a suite of tools to be executed in Python including gene ID mapping, orthology mapping for the zebrafish and human taxonomy, and functional enrichment analysis utilizing the latest updated Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. danRerLib enables functional enrichment analysis for GO and KEGG pathways, even when they lack direct zebrafish annotations through the orthology of human-annotated functional annotations. This approach enables researchers to extend their analysis to a wider range of pathways, elucidating additional mechanisms of interest and greater insight into experimental results.

Embryogenesis is a well-coordinated process relying on precise cues and environmental signals that direct spatiotemporal embryonic patterning. Quite often, when one error in this process occurs, others tend to co-occur. We posit that investigating the co-occurrence of these abnormalities over time would yield additional information about the mode of toxicity for chemicals. Here, we use the environmental contaminant tris(4-chlorophenyl)methanol (TCPMOH) as a model toxicant to assess the relationship between exposures and co-occurrence of developmental abnormalities in zebrafish embryos. We propose a dynamic network modeling approach to study the co-occurrence of abnormalities, including pericardial edema, yolk sac edema, cranial malformation, spinal deformity, delayed/failed swim bladder inflation, and mortality induced by TCPMOH exposure. TCPMOH-exposed samples revealed increased abnormality co-occurrence when compared to controls. The abnormalities were represented as nodes in the dynamic network model. Abnormalities with high co-occurrence over time were identified using network centrality scores. We found that the temporal patterns of abnormality co-occurrence varied between exposure groups. In particular, the high TCPMOH exposure group experienced abnormality co-occurrence earlier than the low exposure group. The network model also revealed that pericardial and yolk sac edema are the most common critical nodes among all TCPMOH exposure levels, preceding further abnormalities. Overall, this study introduces a dynamic network model as a tool for assessing developmental toxicology, integrating structural and temporal features with a concentration response.

Magnetic resonance (MR) imaging has demonstrated that CF subjects have a significantly higher lung density (e.g., fluid content) when compared with healthy control subjects, but, at present, there are no techniques to quantify the spatial presentation of these lung abnormalities. The excess fluid in MR lung images for CF subjects with mild (n = 4), moderate (n = 5), and severe (n = 4) disease and age- and sex-matched healthy controls (n = 13) in both the right and left lungs was identified and quantified using a thresholding-based image segmentation technique using healthy controls as a baseline. MR lung images were categorized into one of three spatial presentation groups based on their regional and global percent area of the lung covered by excess fluid (i.e., spatial distribution): (i) generalized for sparse, (ii) localized diffuse for a moderate focality, and (iii) localized for a strong focality. A total of 96% of the controls presented as generalized. CF subjects populated all three presentation groups and an individual’s right and left lungs did not always categorize identically. The developed metrics for categorization provide a quantification method to describe the spatial presentation of CF disease and suggests the heterogeneous nature of the disease.

Optimal embryonic development plays a major role in the health of an individual beyond the developmental stage. Nutritional perturbation during development is associated with cardiovascular and metabolic disease later in life. With both nutritional uptake and overall growth being risk factors for eventual health, it is necessary to understand not only the behavior of the processes during development but also their interactions. In this study, we used differential equations, image analyses, curve fittings, parameter estimation and laboratory experiments to quantify the rate of yolk absorption and its effect on early development of a vertebrate model (Danio rerio). Findings from this study establish a nonlinear functional relationship between nutrient absorption and early fish growth. We found that the rate of change in fish length and yolk utilization is logistic, that is the yolk decays rapidly for a period of time before leveling out. An interesting finding from this study is that yolk utilization reaches its maximum at 84 h post-fertilization. We validated our mathematical models against experimental observations, making them powerful tools for replication and future simulations.

Tris(4-chlorophenyl)methanol (TCPMOH) is a water contaminant with unknown etiology, but is believed to be a byproduct of DDT manufacturing. It is highly persistent in the environment, and bioaccumulates in marine species. TCPMOH has also been measured in human breast milk, which poses a risk for developing infants. However, almost no toxicity data is currently available. In this study, we investigate the hazard posed by developmental TCPMOH exposures using the zebrafish model (Danio rerio). Zebrafish (Danio rerio) embryos were exposed to 0, 0.1, 0.5, 1, or 5 µM TCPMOH beginning at 24 h post fertilization (hpf). Embryonic mortality and incidence of morphological deformities increased in a concentration-dependent manner with TCPMOH exposure. RNA sequencing assessed changes in gene expression associated with acute (4 hour) exposures to 50 nM TCPMOH. Developmental exposure to TCPMOH decreased expression of ahr2, as well as metabolic enzymes cyp1a1, cyp1b1, cyp1c1, cyp1c2, and cyp2y3 (p<0.05). These findings were concordant with decreased Cyp1a1 induction measured by the ethoxyresorufin-O-deethylase (EROD) assay (p<0.05). Pathways associated with xenobiotic metabolism, lipid metabolism, and transcriptional and translational regulation were decreased. Pathways involved in DNA replication and repair, carbohydrate metabolism, and endocrine function were upregulated. Overall, this study demonstrates that TCPMOH is acutely toxic to zebrafish embryos at elevated concentrations.

This study was designed to explore the role of acetylcholine (ACh) in pulmonary viral infection and recovery. Inflammatory control is critical to recovery from respiratory viral infection. ACh secreted from non-neuronal sources, including lymphocytes, plays an important, albeit underappreciated, role in regulating immune-mediated inflammation. ACh and lymphocyte cholinergic status in the lungs were measured over the course of influenza infection and recovery. The role of ACh was examined by inhibiting ACh synthesis in vivo. Pulmonary inflammation was monitored by Iba1 immunofluorescence, using a novel automated algorithm. Tissue repair was monitored histologically. Pulmonary ACh remained constant through the early stage of infection and increased during the peak of the acquired immune response. As the concentration of ACh increased, cholinergic lymphocytes appeared in the BAL and lungs. Cholinergic capacity was found primarily in CD4 T cells, but also in B cells and CD8 T cells. The cholinergic CD4+ T cells bound to influenza-specific tetramers and were retained in the resident memory regions of the lung up to 2 months after infection. Histologically, cholinergic lymphocytes were found in direct physical contact with activated macrophages throughout the lung. Inflammation was monitored by ionized calcium-binding adapter molecule 1 (Iba1) immunofluorescence, using a novel automated algorithm. When ACh production was inhibited, mice exhibited increased tissue inflammation and delayed recovery. Histologic examination revealed abnormal tissue repair when ACh was limited. These findings point to a previously unrecognized role for ACh in the transition from active immunity to recovery and pulmonary repair following respiratory viral infection.

The article by Poole, Turner, and Maher-Boulis (2020) describes one way in which undergraduates have been used to support the SUMMIT-P goal of investigating examples of how mathematics and statistics are applied in partner discipline courses. Two other universities in the SUMMIT-P consortium, San Diego State University and Oregon State University, also use undergraduates in different ways to support the work of integrating science applications into math classes. In this article, we compare and contrast these three uses to further highlight this somewhat untapped resource.