Seth Tomchik

A spring sunrise over Hickory Hill Park in Iowa City, about 3 miles (4.8 km) away from the University of Iowa. The hill in the foreground is West Prairie, where a controlled burn was recently carried out. Green shoots are just beginning to sprout again, making for a pretty contrast with the fire-charred landscape.

Lower foreground shows a prairie hill, darkened and cleared from a recent controlled burn, with shoots of green foliage just starting to regrow. In mid-image across the horizon is a line of trees. The top of the image shows the sunrise just breaking the horizon into a blue sky streaked with clouds.
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Seth Tomchik boosted
Lili

I spent some time working on making a setup to image muscle activity in walking flies. The leg moves out of the field of the view often, so we set up a light field microscope. It's just like a normal microscope, but with a microlens array filter added so the image comes out with a bunch of tiny lenslets. You can use to reconstruct a full volume from a single image!

We found the light field framework oLaF to work really well in reconstructing the volume (as you can see on the right image). It would take 20 minutes per image though, which would take too long for processing whole videos.

So I've made pyolaf! github.com/lambdaloop/pyolaf

It's a port of oLaF from Matlab to Python, with some optimizations to make it use the GPU effectively. With this, it can run at least 20x faster!

#neuroscience #microscopy #imaging

Raw image from light field microscope, showing the 10k+ lenslets in the microlens array. It shows a two legs of a fly, with fluorescent muscles.
GIF
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Cori Bargmann

@biorxivpreprint Elias Scheer’s thesis work is up on bioRxiv! It uncovers links between different foraging behaviors, including a classical ethological decision, abandoning a patch of food.

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Lili

The full connectome of the fruit fly is slowly being mapped out.
But how do we make sense of it? Sometimes the anatomy is highly suggestive of a function, but more often than not there are much more connections than we expect and the interpretation is complicated.

I've been slowly collecting papers that try to link a simulation of the connectome with a fly behavior.

Here, I'd like to share one such paper, which uses modeling and connectomics to study the link between development and fly preferences for a particular odor.

The paper is:
"Neural correlates of individual odor preference in Drosophila"
Churgin & Lavrentovich et al
(senior author @debivort )
biorxiv.org/content/10.1101/20

I presented the paper in the @tuthill journal club this week and wanted to share it here while it's still in my head! 🧵

#modeling #connectomics #Drosophila #neuroscience #PaperThread #JournalClub

Summary of the paper: 1) authors measured behavioral variability in odor preferences 2) behavioral variability is explained by variability in PN neuron responses 3) authors setup a simulation of neural dynamics with developmental variance 4) PN synapse density and ORN connection variability contribute to odor preferences
The hemibrain dataset encompasses the part of the fly brain highlighted here in blue. (The blue region covers about 40% of the brain.) This region includes neurons involved in leraning, navigation smell, vision, and many other functions.
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Carlo de Blasio

Parisian street 1935. Strada parigina 1935. Photo: Gilbert de Chambertrand. #BlackAndWhitePhotography.

B/w picture of a line of light coming from the only open view between two buildings in the very moment a passerby shows up at the same junction in Paris 1935. Immagine in bianconero di una linea di luce che arriva dall'unico spazio aperto tra due edifici nel momento preciso in cui un passante appare nello stesso punto a Parigi 1935. Photo: Gilbert de Chambertrand.
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Annika Reads

Every time someone says they did a GWAS for a complex trait, my eyes roll so hard you can *hear* them. But every now and again, people do serious validation! A PA-TX collab finds GPI anchor biosynthesis as a regulator of sleep in flies and fish. doi.org/10.1126/sciadv.abq0844

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omi

Silent snow. Location Kyoto. #followfriday #streetphotography #photography

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WeatherMatrix (Jesse Ferrell)

PHOTO BLOG: Earlier this month, a storm chaser from the Netherlands took a wonderful photo showing several textbook ice halos, including a 46-degree halo, a 22-degree halo with parhelion (sun dogs), and an upper tangent arc. accuweather.com/en/leisure-rec

Photo of a snowy mountain in Germany. A snow-covered tree is in the center with a person standing next to it. And in the sky are several ice halos, an outer halo, an inner halo with false suns on either side, and a bird-shaped arc on top.
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Seth Tomchik boosted
Panos Symvoulidis

RT @quorumetrix
I’ve made this video as an intuition pump for the density of #synapses in the #brain. This volume ~ grain of sand, has >3.2 million synapses (orange cubes). Peeling them away leaves only inputs on 2 #neurons. Zooming in, we see the synapses localized to the dendritic spines.
#b3d

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Seth Tomchik boosted
Jack Lowe

135 years ago, James Blyth dreamed of a future in which every house would be lit by a wind turbine, and argued that wind power was good for the environment and cheaper than fossil fuels.

Blyth was ahead of his time but, unfortunately, not on the money:

theguardian.com/environment/20

#JamesBlyth #ClimateCrisis #RenewableEnergy #WindPower #renewables #wind

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Seth Tomchik

Registration is open for the Mushroom Body Meeting 2023 in Göttingen, organized by André Fiala, Ilona Grunwald Kadow, and Yoshi Aso.

Meeting site and registration:
mushroom-body-meeting.org/

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Seth Tomchik boosted
Albert Cardona

3,013 neurons, half a million synapses: the complete #connectome of the whole #Drosophila larval brain!

Winding, Pedigo et al. 2022. "The connectome of an insect brain" biorxiv.org/content/10.1101/20

We’ve mapped and analysed its circuit architecture, from sensory neurons to brain output neurons, as reconstructed from volume electron microscopy, and here is what we found. 1/

#neuroscience #connectomics #vEM #volumeEM

Rendering of all 3,013 neurons that make up the brain of the larva of the vinegar fly, Drosophila melanogaster.
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Jen Cross

Atlantic Puffins float on the ocean near Machias Seal Island. International Waters between Maine and Canada, summer 2022

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Carl T. Bergstrom

I wrote a piece for the New York Times about how scientists used Twitter during the Covid pandemic and about what comes next.

nytimes.com/2022/11/19/opinion

Illustration accompanying the New York Times article: Twitter logos wearing masks
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*
Mastodon Migration

An Incredible Day In Internet History

It started with the Twitter lockout. 10,000 new users per hour. A QUARTER MILLION people migrated to Mastodon in one day. The servers struggled. Remarkably, admins all over the world built up capacity in real time. New users were patient. The system held.

It's running better now. There will be more hard days ahead, but people powered social media has arrived.

#twittermigration #NewUsers #Welcome

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Seth Tomchik boosted
Darren Obbard is on Bluesky

Happy FlyDay everyone! (11/18)

#Drosophila

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Soragni:Lab

My very first "tootorial", we have a new preprint out, so here goes nothing!

Here's the thing about benign tumors. While they may not spread and metastasize, they still can bring about substantial, and sometimes unappreciated, health issues, particularly when they number in the hundreds, or more. In our latest work, we focus on cutaneous neurofibromas in Neurofibromatosis type 1 syndrome

biorxiv.org/content/10.1101/20

A rapid platform for 3D patient-derived cutaneous neurofibroma organoid establishment and screening

Localized cutaneous neurofibromas (cNFs) are benign tumors that arise in the dermis of patients affected by Neurofibromatosis Type 1 syndrome (NF1). cNFs are fundamentally benign lesions: they do not undergo malignant transformation or metastasize. Nevertheless, in NF1 patients, they can cover a significant proportion of the body, with some individuals developing hundreds to thousands of lesions. cNFs can cause pain, itching, and disfigurement with substantial socio-emotional repercussions. To date, surgical removal or laser desiccation are the only treatment options, but can result in scarring and the leave a potential for regrowth. To support drug discovery efforts focused on identifying effective systemic therapies for cNF, we introduce an approach to routinely establish and screen cNF tumor organoids. We optimized conditions to support ex vivo growth of genomically-diverse cNFs. Patient-derived cNF organoids closely recapitulate the molecular and cellular heterogeneity of these tumors as measured by immunohistopathology, DNA methylation, RNA-seq and flow cytometry. Our tractable patient-derived cNF organoid platform enables rapid screening of hundreds of compounds in a patient- and tumor-specific manner. ### Competing Interest Statement The authors have declared no competing interest.

www.biorxiv.org
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Alexey Veraksa

PSA and reminder: abstract submission deadline for #Dros23 in Chicago is November 17:
genetics-gsa.org/drosophila-20

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Seth Tomchik boosted
Kristin Branson

More plotting of flies! I call this one "Fruit fly snow angel"

Colorful plot showing the distribution of tracked points on fruit flies whose positions are aligned based on their thoraxes.
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Seth Tomchik boosted
Kristin Branson

Reminder for those in the US to vote today!
You can look up your polling location and sample ballot here: vote.org/ .
20 states + DC allow you to register and vote at the same time: ncsl.org/research/elections-an
Bonus! You get a sticker. My county has stickers with a cow and grapes and Dulles airport and an artichoke (I think??)!
Don't forget to bring your iD!

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