Selected Grantee Publications
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- Other Animal Models
- Aquatic Vertebrate Models
Precise Visuomotor Transformations Underlying Collective Behavior in Larval Zebrafish
Harpaz et al., Nature Communications. 2021.
https://www.nature.com/articles/s41467-021-26748-0
Sensory signals from neighbors, analyzed in the visuomotor stream of animals, is poorly understood. The authors studied aggregation behavior in larval zebrafish and found that over development larvae transition from over dispersed groups to tight shoals. Young larvae turn away from virtual neighbors by integrating and averaging retina-wide visual occupancy within each eye, and by using a winner-take-all strategy for binocular integration. Observed algorithms accurately predict group structure over development. These findings allow testable predictions regarding the neuronal circuits underlying collective behavior in zebrafish. Supported by ORIP (R43OD024879, R44OD024879) and NINDS.
Negative Inotropic Mechanisms of β-cardiotoxin in Cardiomyocytes by Depression of Myofilament ATPase Activity without Activation of the Classical β-Adrenergic Pathway
Lertwanakarn et al., Scientific Reports. 2021.
https://www.nature.com/articles/s41598-021-00282-x
Beta-cardiotoxin (β-CTX) from the king cobra venom (Ophiophagus hannah) was previously proposed as a novel β-adrenergic blocker. However, the involvement of β-adrenergic signaling by this compound has never been elucidated. The objectives of this study were to investigate the underlying mechanisms of β-CTX as a β-blocker and its association with the β-adrenergic pathway. Healthy Sprague Dawley rats were used for cardiomyocytes isolation. In summary, the negative inotropic mechanism of β-CTX was discovered. β-CTX exhibits an atypical β-blocker mechanism. These properties of β-CTX may benefit in developing a novel agent aid to treat hypertrophic cardiomyopathy. Supported by ORIP (P40OD010960) and NHLBI.
Collective Behavior Emerges from Genetically Controlled Simple Behavioral Motifs in Zebrafish
Harpaz et al., Science Advances. 2021.
https://www.science.org/doi/10.1126/sciadv.abi7460
Harpaz et al. report that zebrafish regulate their proximity and alignment with each other at early larval stages. Two visual responses (one measuring relative visual field occupancy and one accounting for global visual motion), account for emerging group behavior. Mutations in genes known to affect social behavior in humans perturb these reflexes in individual larval zebrafish and change their emergent collective behaviors. Model simulations show that changes in these two responses in individual mutant animals predict well the distinctive collective patterns that emerge in a group. Hence, group behaviors reflect in part genetically defined primitive sensorimotor “motifs” evident in young larvae. Supported by ORIP (R43OD024879, R44OD024879) and NINDS.
Whole-Organism 3D Quantitative Characterization of Zebrafish Melanin by Silver Deposition Micro-CT
Katz et al., eLife. 2021.
https://www.biorxiv.org/content/10.1101/2021.03.11.434673v1
This research team combined micro-computed tomography (CT) with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. The resulting images enabled whole-body, computational analyses of regional melanin content and morphology. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy and allowed direct quantitative comparisons of melanin content. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, 3D computational phenomic analysis of a specific cell type at cellular resolution. Advances such as this in whole-organism, high-resolution phenotyping provide superior context for studying the phenotypic effects of genetic, disease, and environmental variables. Supported by ORIP (R24OD018559).
MIC-Drop: A Platform for Large-scale In Vivo CRISPR Screens
Parvez et al., Science. 2021.
https://pubmed.ncbi.nlm.nih.gov/34413171/
CRISPR screens in animals are challenging because generating, validating, and keeping track of large numbers of mutant animals is prohibitive. These authors introduce Multiplexed Intermixed CRISPR Droplets (MIC-Drop), a platform combining droplet microfluidics, single-needle en masse CRISPR ribonucleoprotein injections, and DNA barcoding to enable large-scale functional genetic screens in zebrafish. In one application, they showed that MIC-Drop could identify small-molecule targets. Furthermore, in a MIC-Drop screen of 188 poorly characterized genes, they discovered several genes important for cardiac development and function. With the potential to scale to thousands of genes, MIC-Drop enables genome-scale reverse genetic screens in model organisms. Supported by ORIP (R24OD017870), NIGMS, and NHLBI.
The Bowfin Genome Illuminates the Developmental Evolution of Ray-Finned Fishes
Thompson et al., Nature Genetics. 2021.
https://www.nature.com/articles/s41588-021-00914-y
The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here the authors present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era. Supported by ORIP (R01OD011116).
TGF-β1 Signaling Is Essential for Tissue Regeneration in the Xenopus Tadpole Tail
Nakamura et al., Biochemical and Biophysical Research Communications. 2021.
https://www.sciencedirect.com/science/article/pii/S0006291X21008731
Amphibians, such as Xenopus tropicalis, exhibit a remarkable capacity for tissue regeneration after traumatic injury. Nakamura et al. show that inhibition of TGF-β1 function prevents tail regeneration in Xenopus tropicalis tadpoles. CRISPR-mediated knock-out (KO) of tgfb1 retards tail regeneration; the phenotype of tgfb1 KO tadpoles can be rescued by injection of tgfb1 mRNA. Cell proliferation, critical for tissue regeneration, is downregulated in tgfb1 KO tadpoles; tgfb1 KO reduces the expression of phosphorylated Smad2/3 (pSmad2/3). These results show that TGF-β1 regulates cell proliferation through the activation of Smad2/3. They propose that TGF-β1 plays a critical role in TGF-β receptor-dependent tadpole tail regeneration in Xenopus. Supported by ORIP (P40OD010997, R24OD030008).
Deep Learning-Based Framework for Cardiac Function Assessment in Embryonic Zebrafish from Heart Beating Videos
Naderi et al., Computers in Biology and Medicine. 2021.
https://www.sciencedirect.com/science/article/pii/S0010482521003590
Zebrafish is a powerful model system for a host of biological investigations, cardiovascular studies, and genetic screening. However, the current methods for quantifying and monitoring zebrafish cardiac functions involve tedious manual work and inconsistent estimations. Naderi et al. developed a Zebrafish Automatic Cardiovascular Assessment Framework (ZACAF) based on a U-net deep learning model for automated assessment of cardiovascular indices, such as ejection fraction (EF) and fractional shortening (FS) from microscopic videos of wildtype and cardiomyopathy mutant zebrafish embryos. The framework could be widely applicable with any laboratory resources, and the automatic feature holds promise to enable efficient, consistent, and reliable processing and analysis capacity. Supported by ORIP (R44OD024874)
A Symphony of Destruction: Dynamic Differential Fibrinogenolytic Toxicity by Rattlesnake (Crotalus and Sistrurus) Venoms
Seneci et al., Comparative Biochemistry and Physiology Part C. 2021.
https://pubmed.ncbi.nlm.nih.gov/33766656/
This study adopts rattlesnakes as a model group to investigate the evolutionary history of venom coagulotoxicity in the context of phylogenetics, natural history, and biology. Venom-induced clotting of human plasma and fibrinogen was determined and mapped onto the rattlesnake phylogenetic tree to reconstruct the evolution of coagulotoxicity across the group. Results indicate that venom phenotype is often independent of phylogenetic relationships in rattlesnakes, suggesting the importance of diet and/or other environmental variables. This study is the most comprehensive effort to date to characterize the evolutionary and biological aspects of coagulotoxins in rattlesnake venom. Further research at finer taxonomic levels is recommended. Supported by ORIP (P40OD010960).
Loss of Gap Junction Delta-2 (GJD2) Gene Orthologs Leads to Refractive Error in Zebrafish
Quint et al., Communications Biology. 2021.
https://pubmed.ncbi.nlm.nih.gov/34083742/
Myopia is the most common developmental disorder of juvenile eyes. Although little is known about the functional role of GJD2 in refractive error development, the authors find that depletion of gjd2a (Cx35.5) or gjd2b (Cx35.1) orthologs in zebrafish cause changes in eye biometry and refractive status. Their immunohistological and scRNA sequencing studies show that Cx35.5 (gjd2a) is a retinal connexin; its depletion leads to hyperopia and electrophysiological retina changes. They found a lenticular role; lack of Cx35.1 (gjd2b) led to a nuclear cataract that triggered axial elongation. The results provide functional evidence of a link between gjd2 and refractive error. Supported by ORIP (R24OD026591), NIGMS, and NINDS.