Sliced brains and open science

Evolution of nervous systems

mollusk

Kilias, 1985

planarian

Kellogg, 1903

vertebrate

Jefferys, 1763

Evolution - a historical science

Population genetics approach (the flowers)
vs.
Structuralist approach (rest of the tree)

The Structuralist Approach

Geology
Fossil Record

Dickinsonia costata

Phylogeny
Comparative biology

Theory
Transition Analysis

Marine animal models

Nematostella

Hydra

Macrostomum

Platynereis

Trichoplax

Our marine animal facility @329

Neuronal signalling substances are released by vesicle fusion

Basic Neurochemistry: Molecular, Cellular and Medical Aspects

vesicle fusion at the synapse
small-transmitter release (Glu, GABA, ACh, Gly)
synaptic or extrasynaptic release of neuropeptides
synaptic or extrasynaptic release of monoamines (serotonin, noradrenaline etc.)

Biosynthesis of monoamines

Phylogeny of monoamine GPCRs

GPCRs are activated by ligands as predicted by the tree

A new model of neurotransmitter evolution

Neurotransmitter systems in cnidarians

Neuropeptide transmitter systems in cnidarians

mass spec for small neuropeptides
64 peptides derived from 33 neuropeptide precursors
no homology to bilaterian neuropeptides

Neuropeptide transmitter systems in cnidarians

over 1000 GPCRs in the Nematostella genome
screened 161 Nematostella GPCRs
31 receptors specifically activated by one of 14 peptides

FDSS/μCELL Kinetic Plate Imager

Independent diversification of receptor-peptide systems

at least 8 ancestral cnidarian families of peptide GPCRs
independent divergence from bilaterian receptors
prediction of ligands across many cnidarians

The multilayer peptidergic connectome of Nematostella

every node is a cell type from scRNAseq data
links connect peptide-expressing with receptor-expressing cells
different colours represent different peptide-receptor pairs
highly peptidergic nervous systems

The multilayer peptidergic connectome of Nematostella

Platynereis dumerilii

breeding culture
genome sequence
microinjection, transgenesis
neuron-specific promoters
knock-out lines
neuronal connectome
neuronal activity imaging

Volume EM with Array Tomograpy

Array tomography workflow

Whole-body vEM reconstruction

Synaptic connectome

Ciliary photoreceptors in the Platynereis larva

Circuitry of ciliary photoreceptors

UV response in Platynereis larvae

Pressure response in Platynereis larvae

Ciliary photoreceptor cells sense Δ pressure

Microscopy pressure chamber

Calcium imaging

Photoreceptor responses to pressure are graded

Pressure increases ciliary beating through serotonergic cells

Circuitry of ciliary photoreceptors

NOS mutants have altered cPRC response

Volume-EM reconstruction of the ctenophore apical organ

Bruno C. Vellutini

Kei Jokura

Ctenophore balancer organ

Tamm, 2014

Noda & Tamm, 2014

Ctenophore balancer organ

Ctenophore balancer organ - ciliary photoreceptors

Connectome of the ctenophore apical organ

lateral view

oral view

Open Science @COS

How do we keep track of all the data and analyses?
We need reproducible workflows!
Do you use Excel, Prism, Word, Illustrator, Powerpoint to write your papers (thesis, etc.)?
Import data to Excel, make plot, change axis labels, legend, colour etc. manually -> export plot as png.jpg -> Open Illustrator (or worse, Powerpoint) -> import image, add labels -> export figure -> open MS Word, write text, import figure
Oh, there is a new measurement and new data points…
repeat the steps
Oh, my supervisor wants the plot in cyan with large caps… sh.t…
repeat…

Wouldn’t it be nice…

to have a program that can do all of this in one?
that can analyse data, make plots, work as a text editor and allow the embedding of figures?
that supports version control to keep track of all changes
that allows to develop projects that can be easily shared with anyone?
that enables one-click publication of the entire workflow?
that is free and open-source?
that would even allow me to prepare slides for my progress report…