Mary Mirvis

Your go-to tutorial for simulating mesoscale membranes is here. Look no further for:
-Understanding the state of the field
-A guide for creating new models for your science
-Hands-on tutorials to simulate your very own membranes
See tinyurl.com/punk3tcu and the below 🧵 start your journey 💻

In another exciting development our new preprint is online:
www.biorxiv.org/cgi/content/...

This is the work of my brilliant graduate student Katerina Kourkoulou in collaboration with Maggie Liu and Arnold Mathijssen. Here is a video of the subject of our study:

Metascience 2025 recordings are now available! #Metascience25 gathered researchers, funders, policymakers & more to explore how the research process can improve. The program included preconference symposia & plenary sessions on topics from policy change to AI in research.

🎥 cassyni.com/s/metasc...

📢 Abstract submission deadline reminder for 'Cell biology of the nucleus'!

Before packing your bags and leaving for your summer vacation, there is one important task left to do: submit your abstract for #EESNucleus ✍️

Deadline is 26 August: https://s.embl.org/ees25-07-bl

Theory and concepts in biology

So excited to be in Heidelberg for www.embl.org/about/info/c... ! This is going to be an awesome meeting, been looking forward to it for months! #EESTCBio

Unlawful grant terminations are harming young scientists and threatening innovation. ASCB joins leaders calling for immediate funding restoration.

www.ascb.org/society-news...

🚨New preprint!🚨 #teamtomo
We expanded Surface Morphometrics to quantify membrane thickness from cryo-ET—revealing local variation across organelles.

Led by the lab’s first grad student, @mmedina300kv.bsky.social (defending Monday! 🍾) w/ @attychang.bsky.social @hamid13r.bsky.social & @tomo.science

I’ll be there! Can’t wait!

Thanks! I think it’s just edge detection & 3D project plus a little B&C adjustment in FIJI 🙂

As a diversity grant dies, young scientists fear it will haunt their careers The Trump administration defunded the National Institute of Health's MOSAIC grant program, which launched the careers of scientists from diverse backgrounds.

Losing MOSAIC is such a senseless gut punch to so many deserving people like my lab mate @aralbright.bsky.social and science as a whole.

www.npr.org/sections/sho...

I agree, lately I increasingly prefer to frame gaps in knowledge as questions rather than these types of “little is known/poorly understood” statements, which are inherently vague and subjective. Questions are more engaging to a reader too imo

Nuclei (fire) and lipid droplets (black; seen by negative staining) are shown in adipocytes.

For #FluorescenceFriday, a GFP reporter shows nuclei (fire) nestled between lots of lipid droplets in this set of adipocytes 🔬 #Microscopy #CellBiology

This is incredibly cool: if you search for a condition that’s affected your family, the site returns stats on how much NIH has done for that disease, *and* a contact form for reaching out to tell your Members of Congress why you want to see them defend NIH.

Pass it on!

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ACTION ITEM-----ACTION ITEM

Implementation of Schedule F

This is what a lot of us have been worried about.

This allows for many civil service positions to replaced with political appointees. This could include NIH institute directors and even POs.

BUT THERE IS A COMMENT PERIOD...

1/n

Expansion microscopy micrograph of the choanoflagellate Choanoeca flexa, vaguely evocative of a cactus. Red = tubulin, green = actin, blue = DNA

Same with yellow = lipids (BODIPY)

A dream come true: the first expansion microscopy images of C. flexa 🤩 Generated by Mylan & Uzuki who learned from the best (@hiralshah.bsky.social @gautamdey.bsky.social @dudinlab.bsky.social). We will learn so much from these!

Come to the Annual Fletcher Lab Artshow on Friday May 9th, 2025! We host this event yearly as an opportunity for folks to display their artwork, come together with wine and cheese, and admire artwork!

Thanks Andrew! Yes that’s exactly the type of analysis I’m working on, defining “organization” in a way that can be compared between different cell types (I.e a specific set of morph metrics) is gonna be crucial

🙌

Many thanks to my co-author Brooke Weingard, my advisors Steve Goodman & @wallaceucsf.bsky.social , my Marshall lab mates and many others who have been supportive of this sort of oddball project. Now more than ever, I'm humbled by the absolute privilege of doing science! thanks for reading!
11/11

I'm excited for this chance to highlight the power of rigorous evidence synthesis for fundamental cell biology, something I hope to see more of and help develop in the future! If you're interested in the intersection of evidence/knowledge synthesis & fundamental bio please connect with me!
10/11

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Stay tuned for part two of this story which will dive into the linguistic and conceptual basis of "cell anatomy" throughout the corpus. We plan on keeping this corpus up to date & expanding its scope as a collaborative interactive resource (we call it a "living corpus" as a running joke )
9/11

We believe that the acceleration of whole-cell imaging tech & data in recent years represents the early stages of an emerging field. Hopefully this work will serve as a useful tool and catalyst for community discourse to standardize technical & conceptual norms.
8/11

But there are biases in the dataset! Namely small sample sizes, small cell types, non-mammalian cell types. This is a reflection of how technically challenging and costly whole-cell data is, even further highlighting the value of pooling datasets for research synthesis work.
7/11

This lights the way for lots of followup work e.g., which organelle-organelle relationships are more robust vs variable across perturbations? what geometric rules govern whole-cell patterns in eukaryotes?
6/11

overview of study: 89 studies, 118 datasets, 1689+ cells, 58 organelle combos, 13 imaging modalities, 12+ quantitative metrics, 80 cell types, 71 comparative conditions

Our corpus includes 89 studies published bw 2004-2024 screened from >11000 Pubmed results: nearly 1700 individual cells, 118 distinct datasets in 80 cell types using 13 volumetric imaging modalities, 71 comparative conditions, and at least 12 types of quantitative analyses.
5/11

gallery of example whole-cell images

To be included, studies had to show images and/or report measurements taken from complete single-cell reconstructions containing at least two clearly marked organelles in a eukaryotic system.
4/11

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Our scoping review methodology involves a robust search strategy for PubMed, strict inclusion criteria, and multiple rounds of screening and subsequent data extraction performed by multiple researchers in parallel, all fully reported and reproducible.
3/11

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We devised a synthesis approach to comprehensively curate whole-cell imaging data across the literature to enable comparative analysis of anatomical patterns across cell types & contexts.
2/11

Many thanks to my co-author Brooke Weingard, my advisors Steve Goodman & @wallaceucsf.bsky.social , my Marshall lab mates and many others who have been supportive of this sort of oddball project. Now more than ever, I'm humbled by the absolute privilege of doing science! thanks for reading!
11/11