iiinova — where your digital self keeps evolving

Mary Mirvis @marymirvis.bsky.social · 13/05/2026

1/13 So excited to share our new preprint!! How do organelles pack together in a crowded cytoplasm? we know organelles interact via contact sites, but how does competition for space contribute to organelle morphology and interactions? @wallaceucsf.bsky.social www.biorxiv.org/content/10.6...

Images of packed cellular interiors from Maritan et al 2022 and Heinrich et al 2021.

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Itai Yanai @itaiyanai.bsky.social · 19/12/2025

Doing a PhD is - at heart - one long discussion with your mentor. The discussion changes over time - with unexpected turns and ups & downs - but through it all is a pair of people discussing a topic endlessly to make sense of it. PhD students: choose someone you like to talk to!

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Yamuna Krishnan @krishnanyamuna.bsky.social · 17/12/2025

Organelles do NOT have a single uniform pH. And if you think they must, because “protons diffuse fast,” this paper is for you. A thread on why that assumption is wrong; and what we found instead. 🧵 1/n

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Paul & Virginie - Centriole Lab @centriolelab.bsky.social · 10/12/2025

🥳 Our new paper on C2CD3 is out in @plosbiology.org With the labs of @cellarchlab.com , @chgenoud.bsky.social , and @stearnslab.bsky.social , we revealed the mammalian centriole Distal Ring architecture by combining #UExM and in situ #CryoET. Big congrats to @ebertiaux.bsky.social and all involved.

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Connie Yan @connieyan.bsky.social · 08/12/2025

I'll be sharing my work on how cells know when to make missing structures at #cellbio2025 today! Come check out my poster (B406) and my talk in the Evolutionary Cell Bio mini symposium session which starts at 4pm.

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Wallace Marshall @wallaceucsf.bsky.social · 07/12/2025

The giant ciliate Stentor has a macronucleus that undergoes a dramatic shape change during cellular regeneration. In poster 038 at CellBio2025 Monday Dec 8, I present work by Isabella Ibalio showing that histone modifications correlate with these dramatic nuclear shape changes.

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Wallace Marshall @wallaceucsf.bsky.social · 07/12/2025

Stentor is a single cell that can regenerate missing pieces, but how does it know when something is missing? In poster 406 at CellBio2025 Monday Dec 8, Connie Yan shows that conserved cell cycle machinery plays a key role in triggering cellular regeneration.

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Wallace Marshall @wallaceucsf.bsky.social · 07/12/2025

Stentor is a single cell with a complex cortical pattern showing anterior/posterior polarization In poster 410 at CellBio2025 Monday Dec 8, Yina Hudnall shows a role for posterior-enriched mRNA that encoding DNA binding proteins.

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Wallace Marshall @wallaceucsf.bsky.social · 07/12/2025

Mitochondria form dynamic networks that can be represented as graphs. But the space of graphs is complex. In poster 376 at CellBio2025 Monday Dec 8, Raphie Mostov presents a mathematical approach to represent mitochondria far more simply.

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Wallace Marshall @wallaceucsf.bsky.social · 07/12/2025

The cell is a crowded place where organelles are packed together . In poster B365 at CellBio2025 Monday Dec 8 in the Quantitative Modeling session room 122, Mary Mirvis uses soft x-ray tomography to explore how packing interactions affect organelle shape and interaction.

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Wallace Marshall @wallaceucsf.bsky.social · 07/12/2025

The low Reynolds number of cytoplasmic flow which makes mixing hard. In poster 359 at the CellBio2025 meeting Sunday Dec 7, Ulises Diaz shows how giant cells leverage reversible actin gel assembly to drive rapid mixing of cytoplasm, faster even than "chaotic mixing" schemes.

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Wallace Marshall @wallaceucsf.bsky.social · 07/12/2025

Flagellar length control in Chlamydomonas is a paradigm for organelle size regulation. In poster 163 at CellBio2025 Sunday Dec 7, I present work by Hiro Ishikawa using a synthetic biology approach to test a length-sensing model based on diffusion of kinesin in flagella

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Wallace Marshall @wallaceucsf.bsky.social · 07/12/2025

Flagellar length control in Chlamydomonas is a paradigm for organelle size regulation. In poster 155 at the CellBio2025 meeting Sunday Dec 7, Ximena Garcia Arceo uses Lithium, which increases intraflagellar transport, as a tool to probe how length-altering mutants work.

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Wallace Marshall @wallaceucsf.bsky.social · 05/12/2025

Cells can hunt prey, solve mazes, and learn from past experience. Does this mean they can think, at some level? Find out more at our upcoming session on "Cell Behavior and Cognition" at the ASCB/EMBO #cellbio2025 meeting, Saturday 1-3 pm rm 115.

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Billie Meadowcroft @billiemeadowcroft.bsky.social · 22/10/2025

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 💻

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Guillermina Ramirez-SanJuan @guille-rochelle.bsky.social · 18/09/2025

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:

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Center for Open Science @cos.io · 12/08/2025

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...

cassyni.com

Cassyni | Science starts with a seminar

Seamlessly organise, run and publish academic research seminars. Get started in minutes.

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EMBL Events @events.embl.org · 31/07/2025

📢 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: s.embl.org/ees25-07-bl

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Mary Mirvis @marymirvis.bsky.social · 06/05/2025

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

embl.org

Theory and concepts in biology

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Danielle Grotjahn @nanigrotjahn.bsky.social · 01/05/2025

🚨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

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Mary Mirvis @marymirvis.bsky.social · 29/04/2025

I’ll be there! Can’t wait!

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Rachael Ott @rachaelott.bsky.social · 25/04/2025

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

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

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C.H. Romatowski @chromatowski.bsky.social · 21/04/2025

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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Jeremy Berg @jeremymberg.bsky.social · 23/04/2025

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

media.tenor.com

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Thibaut Brunet @thibautbrunet.bsky.social · 22/04/2025

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!

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

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Fletcher Lab @fletcherlabucb.bsky.social · 21/04/2025

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!

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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

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

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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

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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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

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

media.tenor.com

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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

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

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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

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

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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

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

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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

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

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

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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

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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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

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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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

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

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a group of pokemon standing next to each other with gotta catch 'em all written on the bottom

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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

New(ish) preprint! 📰What whole-cell patterns emerge from the arrangement, morphologies, and interactions of organelles in the 3D space of the cell? What would we see if we could gather ALL the whole-cell reconstruction data that's out there in one place? www.biorxiv.org/content/10.1... 🧵 1/11

biorxiv.org

A scoping study of the whole-cell imaging literature: a foundational corpus, potential for mesoscale data synthesis, and implications for standardization of an emerging field

The level of cellular organization bridging the mesoscale and whole-cell scale is coming into focus as a new frontier in cell biology. Great progress has been made in unraveling the complex physical a...

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Celeste Ng @pronounced-ing.bsky.social · 19/04/2025

Trump's team backing down in front of Harvard should embolden EVERYONE to stand up to them. Do not comply in advance. Instead say "Fuck you, make me."

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Vaishnavi Ananthanarayanan (She/Her) @vaishananth.bsky.social · 09/04/2025

How is mitochondrial volume maintained across successive generations of dividing cells? In our new preprint, we show how fission yeast cells use mitochondrial activity to control division timing and maintain mitochondrial homeostasis! (1/n) 📖 www.biorxiv.org/content/10.1...

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 08/04/2025

Bioimaging and bioimage analysis friends, some help if you have 2-3 mins; for a paper, we're trying to estimate the number of biologists trained in open source software or tools in the last ~5 years. (1/2) #bioimaging #microscopy #bioimageanalysis

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Jeremy Berg @jeremymberg.bsky.social · 02/03/2025

I am not going to call this a Bluetorial, because I do not want to sully that term (which, at least I, find joyful). Let’s call it a Orwellial.

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Jeremy Koster @jeremykoster.bsky.social · 19/02/2025

Upon learning that yesterday would be my last day as a program officer at the National Science Foundation, I shared this parting message with my colleagues. The next few months will be frenetic and stressful for them. Here are some things that you can do to help them with the mission ahead. (1)

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Josephine Kavanagh @ourhaus.bsky.social · 06/02/2025

Not certain what is happening with PubMed - see banner headline below. I hope 🤞 it's not going down - just a lot of people searching and downloading records important to their field. If PubMed does goes down use @europepmc.org it includes current PubMed abstracts plus a lot lot more. #PubMed

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Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · 28/01/2025

I just contacted my representatives about the nomination of RFK, Jr and the recent executive orders. Here is what I wrote in my email or said to the staffer on the phone: Hello- I am writing/calling on several topics:

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