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Biology subjects

Knoblich, S.

Publications and source records attributed to Knoblich, S..

3 recordsLinked to original sources

Spatio-temporal visualisation and manipulation of endogenous Yap1 in medaka

A key requirement to address fundamental questions in developmental biology is the ability to visualise and manipulate endogenous signalling proteins in vivo. Here we generate such an enabling experimental tool for the highly conserved Hippo pathway and its transcriptional effector Yap1, which converts mechanical and chemical cues into transcriptional output during embryogenesis and regeneration. We generate and characterise a Yap1- mGreenLantern (Yap1-mGL) endogenous CRISPR/Cas9-mediated knock-in line that enables 4D analysis of Yap1 dynamics in medaka. We resolve Yap1- mGL expression and nuclear/cytoplasmic localisation in real time, revealing the onset of reporter fluorescence before gastrulation, tissue and cell-type specific Yap1-mGL localisation during somitogenesis and injury-induced Yap1 upregulation during larval spinal cord regeneration. Using the nanobody-based degron system, we degrade the Yap1 protein in vivo, recapitulating the genetic loss-of-function mutant phenotype. Combining endogenous tags with nanobody-based degrons offers a powerful approach to visualise and acutely perturb endogenous protein function in vivo.

developmental biology↗

Quantitative mapping of heterochrony to species-specific phenotypes

The genetic program of animal development is conserved, but its rate of execution varies across species. Heterochrony, shifts in the relative timing of developmental events, generates phenotypic variation, but its prevalence and origin are unclear. Here, we compare two vertebrates with a 3-fold difference in developmental rate, zebrafish (Danio rerio) and medaka (Oryzias latipes) and characterize heterochrony with embryo-scale single-cell genomics. We generated an atlas of >1.2M single-cell transcriptomes of medaka from blastula to hatch and developed a new approach to represent medaka development in "zebrafish time", uncovering many cryptic, cell-level timing shifts not predicted by medakas slower development. We confirm a divergent heterochrony in the medaka notochord using in vivo imaging, revealing that coupled acceleration and delay of sister cell types shapes the species-specific morphology of this tissue. Our results point to cell type-specific timing deviations as a reservoir of phenotypic variation and we propose that species-specific developmental rate can emerge from these cell-level differences.

Developmental Biology↗

Multi-species community platform for comparative neuroscience in teleost fish

Studying neural mechanisms in complementary model organisms from different ecological niches in the same animal class can leverage the comparative brain analysis at the cellular level. To advance such a direction, we developed a unified brain atlas platform and specialized tools that allowed us to quantitatively compare neural structures in two teleost larvae, medaka (Oryzias latipes) and zebrafish (Danio rerio). Leveraging this quantitative approach we found that most brain regions are similar but some subpopulations are unique in each species. Specifically, we confirmed the existence of a clear dorsal pallial region in the telencephalon in medaka lacking in zebrafish. Further, our approach allows for extraction of differentially expressed genes in both species, and for quantitative comparison of neural activity at cellular resolution. The web-based and interactive nature of this atlas platform will facilitate the teleost communitys research and its easy extensibility will encourage contributions to its continuous expansion.

neuroscience↗