#platynereis — Public Fediverse posts

At long last, the version of record of our paper on the #Platynereis #connectome

"Whole-body connectome of a segmented annelid larva"
is out.

Explore the rich online presentation with all the videos, figures and source data here:

https://doi.org/10.7554/eLife.97964

@eLife #neuroscience

At long last, the version of record of our paper on the #Platynereis #connectome

"Whole-body connectome of a segmented annelid larva"
is out.

Explore the rich online presentation with all the videos, figures and source data here:

https://doi.org/10.7554/eLife.97964

@eLife #neuroscience

At long last, the version of record of our paper on the #Platynereis #connectome

"Whole-body connectome of a segmented annelid larva"
is out.

Explore the rich online presentation with all the videos, figures and source data here:

https://doi.org/10.7554/eLife.97964

@eLife #neuroscience

Happy to be involved in UNICIL, our new Wellcome Trust Discovery project coordinated by @micromotility.bsky.social

We will study ciliary dynamics across scales and organisms. A long-term #postdoc position will be available at Heidelberg University @uniheidelberg shortly.

@uniofexeter press release:

https://news.exeter.ac.uk/living-systems-institute/multi-million-project-to-crack-the-code-of-cilia-tiny-structures-with-big-impact-on-human-health/

#biology #microscopy #vEM #cilia #platynereis

The revised version of our #Platynereis #connectome paper is now out:

https://elifesciences.org/reviewed-preprints/97964

Cell-type-level annotation of the whole organisms, including synaptic and desmosomal connectomes. Can be explored with CATMAID here:
https://catmaid-jekelylab.cos.uni-heidelberg.de
#larva #marine #neuroscience #vEM

The revised version of our #Platynereis #connectome paper is now out:

https://elifesciences.org/reviewed-preprints/97964

Cell-type-level annotation of the whole organisms, including synaptic and desmosomal connectomes. Can be explored with CATMAID here:
https://catmaid-jekelylab.cos.uni-heidelberg.de
#larva #marine #neuroscience #vEM

The revised version of our #Platynereis #connectome paper is now out:

https://elifesciences.org/reviewed-preprints/97964

Cell-type-level annotation of the whole organisms, including synaptic and desmosomal connectomes. Can be explored with CATMAID here:
https://catmaid-jekelylab.cos.uni-heidelberg.de
#larva #marine #neuroscience #vEM

We published a new preprint on the biophysics of ciliary metachronal waves in the Platynereis larva. https://www.biorxiv.org/content/10.1101/2025.02.10.637311v2 In collaboration with @micromotility.bsky.social and Rebecca Poon #cilia #biology #biophysics #platynereis 1/6

New preprint from Rebecca's PhD! did you know that the ciliary band metachronal wave in #Platynereis is a series of tiny waves within each multiciliated cell! What happens if you ablate some cilia?? 🌊😱 Cool #cilia collab w/ @jekely.biologists.social.ap.brid.gy! Revealed here doi.org/10.1101/2025...

New paper from Ikeda et al. on the biogenesis of chitin bristles in the annelid #Platynereis with nice #vEM reconstructions and a chitin synthase knockout.
Bristles are formed in a process of biological 3D printing. @biology
#microscopy
https://www.nature.com/articles/s41467-024-48044-3

.@SoerenHaefker @FRKT_labs &co reveal high individual diversity in #circadian behavioral patterns in the marine #annelid #Platynereis, showing that behavioral rhythmicity is not correlated with oscillations in core clock genes. @maxperutzlabs #PLOSBiology https://plos.io/49wKz9q

We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures

https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1

All the analyses, plots and figures should be reproducible in #rstats with the code provided:

https://zenodo.org/doi/10.5281/zenodo.10825370

@zenodo_org

by querying our public #CATMAID database:

https://catmaid.jekelylab.ex.ac.uk

#neuroscience @biology #volumeEM
@biorxivpreprint

We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures

https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1

All the analyses, plots and figures should be reproducible in #rstats with the code provided:

https://zenodo.org/doi/10.5281/zenodo.10825370

@zenodo_org

by querying our public #CATMAID database:

https://catmaid.jekelylab.ex.ac.uk

#neuroscience @biology #volumeEM
@biorxivpreprint

We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures

https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1

All the analyses, plots and figures should be reproducible in #rstats with the code provided:

https://zenodo.org/doi/10.5281/zenodo.10825370

@zenodo_org

by querying our public #CATMAID database:

https://catmaid.jekelylab.ex.ac.uk

#neuroscience @biology #volumeEM
@biorxivpreprint

We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures

https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1

All the analyses, plots and figures should be reproducible in #rstats with the code provided:

https://zenodo.org/doi/10.5281/zenodo.10825370

@zenodo_org

by querying our public #CATMAID database:

https://catmaid.jekelylab.ex.ac.uk

#neuroscience @biology #volumeEM
@biorxivpreprint

We have now published a new and massively extended/reworked preprint of the whole-body #Platynereis larval #connectome with over 50 figures

https://www.biorxiv.org/content/10.1101/2024.03.17.585258v1

All the analyses, plots and figures should be reproducible in #rstats with the code provided:

https://zenodo.org/doi/10.5281/zenodo.10825370

@zenodo_org

by querying our public #CATMAID database:

https://catmaid.jekelylab.ex.ac.uk

#neuroscience @biology #volumeEM
@biorxivpreprint

EM stack of a golgi ribbon in a glial cell of #Platynereis, from Benvenuto et al.,:
"Evolution of the ribbon-like organization of the Golgi apparatus"
with small contribution from our lab.
https://www.sciencedirect.com/science/article/pii/S2211124724001190?via%3Dihub
#CellBiology #volumeEM #cell

How This Marine #Worm Can Tell Moonglow From Sunbeams
https://www.quantamagazine.org/how-this-marine-worm-can-tell-moonglow-from-sunbeams-20231219/

A marine #cryptochrome with an inverse photo-oligomerization mechanism https://www.nature.com/articles/s41467-023-42708-2

"The marine #bristleworm #Platynereis dumerilii syncs its reproductive cycle with the phases of the #moon. #Scientists recently uncovered the structure of a #protein that helps it sense #moonlight."

Our favourite #Platynereis #opsin now in the mammalian brain as a new #optogenetic tool!

"Here we ... found that the Platynereis dumerilii ciliary opsin ... is an efficient, versatile, light-activated bistable GPCR that can suppress synaptic transmission in mammalian neurons with high temporal precision in-vivo "

https://www.biorxiv.org/content/10.1101/2023.07.01.547328v1

#neuroscience #GPCR

Our favourite #Platynereis #opsin now in the mammalian brain as a new #optogenetic tool!

"Here we ... found that the Platynereis dumerilii ciliary opsin ... is an efficient, versatile, light-activated bistable GPCR that can suppress synaptic transmission in mammalian neurons with high temporal precision in-vivo "

https://www.biorxiv.org/content/10.1101/2023.07.01.547328v1

#neuroscience #GPCR

Our favourite #Platynereis #opsin now in the mammalian brain as a new #optogenetic tool!

"Here we ... found that the Platynereis dumerilii ciliary opsin ... is an efficient, versatile, light-activated bistable GPCR that can suppress synaptic transmission in mammalian neurons with high temporal precision in-vivo "

https://www.biorxiv.org/content/10.1101/2023.07.01.547328v1

#neuroscience #GPCR

Our favourite #Platynereis #opsin now in the mammalian brain as a new #optogenetic tool!

"Here we ... found that the Platynereis dumerilii ciliary opsin ... is an efficient, versatile, light-activated bistable GPCR that can suppress synaptic transmission in mammalian neurons with high temporal precision in-vivo "

https://www.biorxiv.org/content/10.1101/2023.07.01.547328v1

#neuroscience #GPCR

Euro #EvoDevo 2024 will include the following satellite meetings:
#Amphioxus
#Platynereis
#ArthropodEvolution (that's a lot of species for a satellite meeting!)
#FishEvolution
#Crustacean
https://ecoevo.social/@EED2024/110219897240880479

Hydrostatic pressure is a dominant cue in the sea and many aquatic organisms are known to respond to changes in pressure, however the neuronal mechanisms have remained unclear.
We studied the larvae of the marine #annelid #Platynereis and found that they respond to increases in pressure by increased upward swimming.
#neuroscience
2/9

Our lab presentations at #SICB2023

Ranny’s talk: Comparative transcriptomics reveals sex-specific differences in #Platynereis dumerilii (Tomorrow, Jan 4th)

Bria’s talk: The cost or payout of #regeneration on growth and sexual maturation in Platynereis dumerilii (Tomorrow, 4th)

Duygu’s talk: Single-cell transcriptomics reveal specific gut regions in a freshwater #annelid (Thursday, 5th)

Ryan’s poster: Automating design of #fluorescent in situ probes for big data sets (Friday, 6th)

For all electron microscopists out there:

"Crosshair, semi-automated targeting for electron microscopy with a motorised ultramicrotome"

Kimberly Meechan et al. 2022 @eLife from Yannick Schwab's lab at EMBL in collaboration with The Crick institute. https://elifesciences.org/articles/80899

Presents a new method for reliably and "selectively targeting small regions of interest in a resin block by trimming with an ultramicrotome", powered by "user-friendly software to convert X-ray images of resin-embedded samples into angles and cutting depths for the ultramicrotome."

Reviewed by three outstanding electron microscopists: Christel Genaud, Song Pang, and Michaela Wilsch-Bräuninger.

#electronmicroscopy #microCT #Platynereis #science #methods #EMBL #TheCrick

@manlius Yes, a lot, but generated mostly with #CATMAID which is more purpose-built for #connectomics.

An early reconstruction of a neural circuit done with #TrakEM2 was by Davi Bock et al. 2011 on the mouse visual cortex, "Network anatomy and in vivo physiology of visual cortical neurons" https://www.nature.com/articles/nature09802

Another one with #TrakEM2 was by Dan Bumbarger et al. 2013 "System-wide rewiring underlies behavioral differences in predatory and bacterial-feeding nematodes" where they compared #celegans with another nematode, #pristionchus pacificus that has the exact same amount of neurons but connected differently https://www.sciencedirect.com/science/article/pii/S0092867412015000

Later ones with #CATMAID include:

The polychaete worm #Platynereis by @jekely 's group, "Whole-animal #connectome and cell-type complement of the three-segmented Platynereis dumerilii larva" Verazto et al. 2020 https://www.biorxiv.org/content/10.1101/2020.08.21.260984v2.abstract

And all of ours in #Drosophila larva. See the #VirtualFlyBrain server which hosts the #vEM of the whole central nervous system and lists all the neurons included in each published paper (currently 23), shared among the papers and all connecting to each other: https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=108250&yp=82961.59999999999&xp=54210.799999999996&tool=tracingtool&sid0=1&s0=2.4999999999999996&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)

The 24th will come soon, featuring the complete whole #Drosophila larval brain with ~2,500 neurons. It's under review.

What can you do with a #CATMAID server? Say, let's look at the #Drosophila (vinegar fly, often referred to as fruit fly) larval central nervous system, generously hosted by the #VirtualFlyBrain https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=108250&yp=82961.59999999999&xp=54210.799999999996&tool=tracingtool&sid0=1&s0=2.4999999999999996&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6) or the #Platynereis (a marine annelid) server from the Jekely lab https://catmaid.jekelylab.ex.ac.uk/

First, directly interact by point-and-click: open widgets, find neurons by name or annotations, fire up a graph widget and rearrange neurons to make a neat synaptic connectivity diagram, or an adjacency matrix, or look at neuron anatomy in 3D. Most text–names, numbers–are clickable and filterable in some way, such as regular expressions.

Second, interact from other software. Head to r-catmaid https://natverse.org/rcatmaid/ (part of the #natverse suite by Philipp Schlegel @uni_matrix, Alex Bates and others) for an R-based solution from the Jefferis lab at the #MRCLMB. Includes tools such as #NBLAST for anatomical comparisons of neurons (see paper by Marta Costa et al. 2016 https://www.sciencedirect.com/science/article/pii/S0896627316302653 ).

If R is not your favourite, then how about #python: the #navis package, again by the prolific @uni_matrix, makes it trivial, and works also within #Blender too for fancy 3D renderings and animations. An earlier, simpler version was #catpy by @csdashm https://github.com/ceesem/catpy , who also has examples on access from #matlab.

Third, directly from a #psql prompt. As in, why not? #SQL is quite a straightforward language. Of course, you'll need privileged access to the server, so this one is only for insiders. Similarly privileged is from an #ipython prompt initialized via #django from the command line, with the entire server-side API at your disposal for queries.

Fourth, and one of my favourites: from the #javascript console in the browser itself. There are a handful of examples here https://github.com/catmaid/CATMAID/wiki/Scripting but the possibilities are huge. Key utilities are the "fetchSkeletons" macro-like javascript function https://github.com/catmaid/CATMAID/wiki/Scripting#count-the-number-of-presynaptic-sites-and-the-number-of-presynaptic-connectors-on-an-axon and the NeuronNameService.getInstance().getName(<skeleton_id>) function.

Notice every #CATMAID server has its /apis/, e.g., at https://l1em.catmaid.virtualflybrain.org/apis/ will list all GET or REST server access points. Reach to them as you please. See the documentation: https://catmaid.readthedocs.io/en/stable/api.html

In short: the data is there for you to reach out to, interactively or programmatically, and any fine mixture of the two as you see fit.