Congratulations Dr. John!

Jan 23, 2022

We are most delighted that John Bear has just passed his PhD viva!

For his thesis, John investigated spectral processing in zebrafish retinal ganglion cells.

Thank you to Ryan MacDonald and George Kemenes for serving as examiners, and Kevin Staras for chairing!

 

John’s PhD publication:

Zhou M*, Bear J*, Roberts PA, Janiak FK, Semmelhack J, Yoshimatsu T, Baden T§. Zebrafish Retinal Ganglion Cells Asymmetrically Encode Spectral and Temporal Information Across Visual Space. Current Biology 30, 2927-2942. (bioRxiv version). direct link. pdf.

 

Boehringer Ingelheim-FENS Research Award 2022

Oct 18, 2021

“The Federation of European Neuroscience Societies (FENS) and Boehringer Ingelheim are delighted to announce the recipients of the Boehringer Ingelheim FENS Research Award 2022: Prof. Tom Baden (UK) and Prof. Tatjana Tchumatchenko (DE).

FENS and Boehringer Ingelheim would like to congratulate both winners for their outstanding scientific achievements. The award will be presented during the FENS Forum on 9-13 July 2022 in Paris, France, where the two awardees will jointly give the Boehringer-Ingelheim / FENS Research Award lecture.”

Winners of the Boehringer Ingelheim FENS Research Award 2022 announced

Two new papers

Oct 18, 2021

We are excited to see two related papers come out on the same day! The first (Yoshimatsu et al.) looks at spectral processing in zebrafish cones, while the second (Bartel et al.) then uses the same approach to study the next layer down in retinal bipolar cells.

Paper 1: Yoshimatsu T, Bartel P, Schroeder C, Janiak FK, St-Pierre F, Berens P, Baden T$. Ancestral circuits for vertebrate colour vision emerge at the first retinal synapse. Science Advances 7(24):eabj6815 (bioRxiv version). direct link. pdf.

Paper 2: Bartel P, Yoshimatsu T, Janiak FK, Baden T§. Spectral inference reveals principal cone-integration rules of the zebrafish inner retina. Current Biology 31 1-13. (bioRxiv version). direct link.  pdf.

Together, the papers reveal the principal rules by which the zebrafish retina breaks natural light into achromatic and chromatic components at the earliest possible site.

Paper 1

For colour vision, retinal circuits must separate information about intensity and wavelength. This requires circuit level comparison of at least two spectrally distinct photoreceptors. However, many vertebrates use four or more, and in those cases the nature and implementation of this computation remains poorly understood. Here, we establish the complete circuit architecture and function of outer retinal circuits underlying colour processing in the tetrachromatic larval zebrafish. Our findings reveal that the specific spectral tunings of the four cone types near optimally rotate the encoding of natural daylight in a principal component analysis (PCA)−like manner to yield one primary achromatic axis, two colour opponent axes as well as a secondary UV-achromatic axis for prey capture. We note that fruit flies − the only other tetrachromat species where comparable circuit-level information is available − use essentially the same strategy to extract spectral information from their relatively blue-shifted terrestrial visual world. Together, our results suggest that rotating colour space into achromatic and chromatic axes at the eye′s first synapse may be a fundamental principle of colour vision when using more than two spectrally well separated photoreceptor types.

Paper 2

Bartel P, Yoshimatsu T, Janiak FK, Baden T§. Spectral inference reveals principal cone-integration rules of the zebrafish inner retina. Current Biology 31 1-13. (bioRxiv version). direct link.  pdf.

The central goal of this study was to try and infer the total effective cone-integration logic of bipolar cells in larval zebrafish by way of linking highly resolved spectral tuning functions across these two populations of neurons.

We previously showed that the four zebrafish cones exhibit distinct but highly stereoypical tunings at the level of their output (paper 1). Accordingly, we used the same recording conditions to also obtain spectral tuning functions of the downstream neurons, the retinal bipolar cells (right).

We find that this works very well, allowing us to explain ~95% of the variance in bipolar cell responses based on linear cone-combinations. Based on this, we chart an overview of the total cone-integration logic in larval zebrafish, and relate these insights to spectral processing in mammalians.

 

New lab member

Sep 3, 2021

We are pleased to welcome to Chiara to the lab!

Chiara joins us on our Wellcome funded project on the retinal basis of vision in fish. She will be studying the cone-type dependence of various visual behaviours and their underlying circuits.

New paper about cone-integration on bioRxiv

Aug 11, 2021

Bartel P, Yoshimatsu T, Janiak FK, Baden T§. Spectral inference reveals principal cone-integration rules of the zebrafish inner retina. bioRxiv doi: 10.1101/2021.08.10.455697. direct link.  pdf.

The central goal of this study was to try and infer the total effective cone-integration logic of bipolar cells in larval zebrafish by way of linking highly resolved spectral tuning functions across these two populations of neurons.

We previously showed that the four zebrafish cones exhibit distinct but highly stereoypical tunings at the level of their output (Yoshimatsu et al. bioRxiv 2020). Accordingly, we used the same recording conditions to also obtain spectral tuning functions of the downstream neurons, the retinal bipolar cells (right).

We find that this works very well, allowing us to explain ~95% of the variance in bipolar cell responses based on linear cone-combinations. Based on this, we chart an overview of the total cone-integration logic in larval zebrafish, and relate these insights to spectral processing in mammalians.

 

Paper on ribbon-tuning now out at eLife

Jul 16, 2021

Schroeder C$, Oesterle J, Berens P*, Yoshimatsu T*, Baden T*$. Distinct Synaptic Transfer Functions in Same-Type Photoreceptors. eLife 10:e67851. (bioRxiv version).  direct link.  pdf.

With EM, 2p-imaging and computational modelling we show that on the synaptic level of single neuron types in the retina there exist highly specialized mechanisms which are advantageous for the encoding of different visual features. 

Already in EM we see different geometries of the ribbon depending on the location of the UV-cones.

We confirm these differences by “dual-color” 2-photon imaging of pre-synaptic calcium and glutamate release of the synapse.

We use these recordings to build a computational model of the ribbon synapse, which reproduces region-specific response properties. An interactive model tool can be found on #github and you can run it on #googlecolab here: http://www.tinyurl.com/h3avl1ga

By using simulation-based inference we get full posterior estimations of the parameter distributions and can compare these between different retinal regions.

Finally, the computational model allows us to extrapolate to new stimuli and predict response behaviours of different synapse configurations. Hereby we identify principles which are advantageous for the encoding of different visual features, which may be more relevant in different locations of the visual field.

This work builds on previous findings, where we showed fovea-like photoreceptor specializations in UV Cones in zebrafish, which drives prey-capture behavior: https://www.cell.com/neuron/pdf/S0896-6273(20)30313-5.pdf