RAMONA
We built Ramona to advance human health through live imaging that delivers unrivaled precision and scale

Our goals


Humans and other organisms are regularly exposed to chemical compounds that elicit toxicity through the aryl hydrocarbon receptor (AHR) signaling pathway. AHR agonists include polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and some natural products, pharmaceuticals, and endogenous compounds. Interindividual differences in sensitivity to AHR agonists exists. Several populations of Atlantic killifish (Fundulus heteroclitus) have independently evolved resistance to high levels of pollution. Genome-wide association studies suggested that variation in the AHR interacting protein (AIP) was associated with resistance to AHR ligands. AIP binds to AHR in the cytosol where it plays a role in stability and nuclear localization; however, its exact function is poorly understood. Two CRISPR-Cas9 generated aip mutant zebrafish (Danio rerio) lines were utilized. Homozygous mutants (aip−/− ) from either line died at 7–10-days post-fertilization (dpf), while no such effect is observed in ahr mutant lines. Larvae were exposed to four toxic AHR ligands from diverse chemical classes. aip−/− larvae exposed to PCB126, 5-nitroacenaphthene, and benzo(k) fluoranthene showed reduced sensitivity compared to both heterozygous (aip+/− ) and wildtype (aip+/+ ) larvae. However, changes in sensitivity were ligand-dependent. In contrast, aip−/− larvae demonstrated increased sensitivity to leflunomide. mRNA sequencing was performed at five dpf on unexposed larvae of all genotypes from both mutant lines. Approximately 1,000 differentially expressed genes and alternative splicing products were observed in aip−/− larvae. Gene sets and transcription factor binding motifs involved in cellular stress, apoptosis, innate immune response, proteolysis, replication, and metabolism were enriched. Single-cell deconvolution of the bulk RNA-seq results was performed using MuSiC, which estimated transcriptomic contributions from 28 different cell types, with significant shifts in transcriptional abundance estimated for cell types from structural tissues of mesodermal origin, neural tissues, immune cells, and metabolic organs. Our findings highlight the context-dependent nature of Aip in Ahr modulation and the critical roles that Aip plays in regulating cellular homeostasis.
Understanding the behavioral and morphological dynamics of moving model organisms like the zebrafish larvae requires accurate, high-throughput 3D analysis. However, traditional single-view 2D video tracking fails to capture the full scope of natural 3D movements and postural dynamics. Here, we present a novel high-throughput 24-camera array microscope with a co-designed “mirrored well plate" that allows for snapshot imaging of up to 48 wells over a 118 mm × 82 mm field of view from two orthogonal directions (i.e., a top-view and side-view). Accurate 3D position estimation and tracking is achieved with an efficient machine learning algorithm that scales well to high-throughput measurements. The proposed approach automates parallelized 3D model organism behavioral analysis, providing 3D skeletal tracking, swim bladder morphological dynamics, and kinematics of up to 48 swimming zebrafish larvae at up to several hundred frames per second. The result is an efficient and scalable solution for high-throughput 3D behavioral studies with broad compatibility with standard workflows across laboratories and procedures working with pharmacology, toxicology, and neuroscience.
Aggression is a nearly universal behavior used to secure food, territory, and mates across species, including the fruit fly Drosophila melanogaster. In fruit flies, both sexes display aggression through stereotypical motor patterns. This, along with their sophisticated genetic and molecular toolkit, makes Drosophila melanogaster an excellent model for studying aggression. While male- and female-specific aggressive motor programs have been qualitatively described, automated systems for quantifying these behaviors in freely moving flies remain limited in their ability to combine high-resolution analysis with high throughput. Here, we pair a high-resolution, high-throughput imaging system (Kestrel) with DeepLabCut pose estimation to create a pipeline that tracks multiple freely moving fly pairs and quantifies social dynamics with high fidelity. We validated the system’s high-throughput performance and body-part tracking accuracy through manual scoring and established Drosophila behavioral phenotypes. The platform reliably reproduced a known phenotype: heightened female aggression following activation of cholinergic pC1 neurons. It also revealed a previously uncharacterized neuronal population labeled by R72A10-GAL4 that promotes courtship in males without affecting aggression. Pose-based analysis further detected locomotive differences between experimental and control groups, and subtle genotype-specific variations in aggression and courtship. By providing a high-fidelity readout of circuit-specific manipulations, this workflow enables mechanistic dissection of social behaviors.
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