High-throughput zebrafish phenotyping platform

Tha lab’s first zebrafish paper “Assessment of Autism Zebrafish Mutant Models Using a High-Throughput Larval Phenotyping Platform” was published in a special topic of Frontiers in Cell and Developmental Biology: Zebrafish Models for Human Disease Studies led by postdoc Alexandra Colón-Rodríguez with support from present and former Dennis lab members José Uribe Salazar, KaeChandra Weyenberg, Aditya Sriram, Alejandra Quezada, Gulhan Kaya, Emily Jao, and Brittany Radke, as well as collaborator Pam Lein. Amazingly, co-authors included three undergrads and a high school student!

Some highlights:

  • Tested impacts on larval development of a high-throughput platform allowing morphological measurements using the VAST imaging system coupled with motion-tracking using DanioVision to detect drug-induced seizures.

  • Identified developmental defects (altered brain and eye sizes) and enhanced seizures for CRISPR mutants targeting orthologs of autism genes, SYNGAP1 and SLC7A5.

  • Established defects could be detected in both mosaic and stable mutant lines, opening up the possibility to increase throughput of genes screened.

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Farewell to team members KaeChandra, Aditya, and Elizabeth and updates

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The Dennis lab wants to congratulate junior specialist KaeChandra Weyenberg as she departs to pursue her master’s degree in Public Health from East Tennessee University.

We are also happy to send off graduating undergrads Aditya Sriram and Elizabeth Roberts. Aditya is headed to the University of Washington to pursue a master’s degree in Epidemiology and Elizabeth will pursue research at the Broad Institute in the Lander lab as she prepares to apply to grad school in the future.

We are also celebrating the news of several former Dennis lab undergrads:

  • Maram Bader has accepted an offer of admission to San Jose State University’s master’s in Microbiology and Molecular Biology program.

  • Dhriti Jagannathan plans to join the Genetic Counseling master’s program at the University of Minnesota.

  • Juliann Wang will start medical school at the University of Alabama at Birmingham School of Medicine.

2020 TAGC virtual conference

Third year IGG grad student José Uribe Salazar and PI Megan represented the Dennis lab at The Allied Genetic Conference (TAGC) this past week, showcasing two zebrafish projects ongoing in the group. José presented in the Zebrafish Neurogenetics session on a human-duplicated SRGAP2 zebrafish model and Megan presented in the Zebrafish Technologies session on a parallel-phenotyping platform to screen for multiple neurodevelopmental features in larvae. Talks were recorded and available (with conference registration) until mid-May via the TAGC website.

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Structural variant discovery in chimpanzees using long-read sequencing

The Dennis lab has published its first lead-authored paper “Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing” in a special issue of Genes: A Tale of Genes and Genomes, led by IGG PhD students Daniela Soto and Colin Shew with support from lab members, including research specialists Mira Mastoras and Gulhan Kaya, the UC Davis Genome Center core (Ruta Sahasrabudhe), as well as collaborator Aida Andrés and her group.

Some highlights:

  • Identified deletions and inversions (SVs) in two chimpanzees vs. a human reference using nanopore and optical mapping, including 88 novel deletions and 36 novel inversions.

  • Coupled with RNA-seq and Hi-C data from LCLs and IPSCs, we found SVs to be enriched for differentially-expressed genes between human and chimpanzee and depleted for TAD boundaries, recapitulating work from others.

  • Generated TAD maps directly comparing human and chimpanzee that show how inversions and deletion can perturb the chromatin landscape.

  • Highlighted genes found impacted uniquely in chimpanzees, that may play a role in species-specific traits (including some exhibiting signature of positive/balancing selection).

  • This represents the first nanopore sequencing of a chimpanzee (a western female) and, importantly, all our data is available for download (Illumina, ONT, bionano, and Hi-C) on our github page here.

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UC Davis Human Genomics symposium

Congratulations to junior research specialist KaeChandra Weyenberg for winning a poster award at the UC Davis Human Genomics symposium on her work using zebrafish to characterize genes important in neurodevelopmental disorders (her first ever presented research poster!).

Also, the Dennis lab was represented by excellent presentations from additional lab members, including grad student Daniela Soto and undergrad Matangi Kumar. It was a fun, information-packed day full of impressive human genomic research ongoing at UC Davis!

Alex on Capitol Hill


Alex took part in the 12th annual Society for Neuroscience Capitol Hill Day on March 8th as part of a group of scientists who met with senators and representatives to advocate for a more consistent and robust increase in funding for the NIH, NSF and the BRAIN Initiative. Her visit included meeting with 3 senators, including Kamala Harris, and 5 representatives, including Nancy Pelosi.

SfN California trainees with Jackie Speier, representative for California's 14th district. Alex is pictured third from the right.

SfN California trainees with Jackie Speier, representative for California's 14th district. Alex is pictured third from the right.