Nitish Dua

Super exciting to see this preprint come out! It’s been a wonderful opportunity to be a part of this story and to apply Surface Morphometrics tooling to a fascinating system. Congratulations to all authors @wilflinglab.bsky.social
#teamtomo

Our new paper (with @biotay.bsky.social) is out and on the cover story of @currentbiology.bsky.social !!!! Veronika, a Carinthian mountain cow flexibly uses a “multi-purpose tool” to scratch herself. A video and more information will follow in the comments.
www.cell.com/current-biol...

Happy new year #teamtomo! We've resumed our OHSU tomo journal club, and this year I am going to be sharing it on bluesky. This week we did a roundtable, where attendees each brought a paper and did a 3-5 minute discussion of what they thought was cool about it. Here are the papers they discussed!

Medina, Chang et al. of the @nanigrotjahn.bsky.social lab introduce a new method based on the Surface Morphometrics pipeline to measure global and local thicknesses of organellar #membranes from cellular cryo-electron tomography data. rupress.org/jcb/article/...

#CryoET

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

Variability in intrinsic promoter strength underlies the temporal hierarchy of the Caulobacter SOS response induction The bacterial SOS response unfolds in a defined temporal order, but the determinants of this hierarchy are unclear. This study shows that intrinsic promoter strength, modulated in part by sigma factor...

1/Now published! We identify a novel regulatory layer underlying SOS response dynamic. Find a short summary about our findings below.
journals.plos.org/plosbiology/...
#MicroSky

🔬🥟 What do empanadas and #mitochondria have in common?
More than you'd think. Our "empanada-shaped" cells just helped uncover hidden subpopulations of mitochondria in your everyday, unpolarized cell lines. Curious how mitochondrial trafficking shapes network health?

Extremely grateful to have had the opportunity to present my CryoET adventures in the grotjahn lab at #cellbio2025. We can all agree that the CryoEM and CryoET session was the best. It was wonderful to meet old mito besties, NCBS besties and make new besties. 😌

Oxidative phosphorylation complexes contain subunits encoded by both the nuclear and mitochondrial genomes. How do cells coordinate the synthesis and assembly of these complexes at the inner membrane? We teamed up with Martin Ott (@mitolab.bsky.social) to address this in two recent papers.

Just installed Doppio on our Linux machine. This is awesome work making relion more accessible and easy to run. I haven't tried submitting jobs yet but it is already making our live easier!

I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!

An inherited mitochondrial DNA mutation remodels inflammatory cytokine responses in macrophages and in vivo in mice @natcomms.nature.com @ryanlab.bsky.social @tcddublin.bsky.social @universitypress.cambridge.org
www.nature.com/articles/s41...

CryoSift is now out @actacrystf.iucr.org doi.org/10.1107/S205... Thanks to all involved. Happy processing!

Exciting !

I’m excited to announce that my paper describing non-canonical mitotic mechanisms in the early mouse embryo is out in @science.org ! (link at end of 🧵)

StayRose: a photostable StayGold derivative red-shifted by genetic code expansion Photobleaching of fluorescent proteins often limits the acquisition of high-quality images in microscopy. StayGold, a novel dimeric green fluorescent protein recently monomerised through sequence engi...

mStayRose is published in JBC 🥳🎉

Congratulations @wsctt.bsky.social @sporemohan.bsky.social and team for the monumental effort to make a non-natural amino acid incorporating fluorescent protein accessible. It's based on mStayGold, bright, and photostable:

www.jbc.org/article/S002...

Last weeks #immunometabolism discoveries @biomednews.bsky.social ⬇️⬇️⬇️

biomed.news/bims-imicid/...

Lots of excellent work inside incl.

Backtracking metabolic dynamics in single cells predicts bacterial replication in human macrophages.

Structural basis of T-loop–independent recognition and activation of CDKs by the CDK-activating kinase Cyclin-dependent kinases (CDKs) are prototypical regulators of the cell cycle. The CDK-activating kinase (CAK) acts as a master regulator of CDK activity by catalyzing the activating phosphorylation o...

Now out in Science! Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle. In @vcushing.bsky.social's magnum opus, we use #cryoEM to figure out how the CDK-activating kinase recognises CDKs to fully activate them - a key step in cell cycle control.
www.science.org/doi/10.1126/...

Mitochondrial transfer

www.nature.com/articles/s42...

The Origin and Diversification of Mitochondria Moving beyond the simplistic view of mitochondria as the power house of the cell, Roger et al. present the immense diversity of mitochondria and mitochondrial functions across eukaryotes, and bring th...

Feeling mitochondrially challenged lately?

Here are two classic reviews on #mitochondria that should help.

www.cell.com/current-biol...

www.cell.com/current-biol...

📣📣📣📣

Bacterial ICMs exhibit internal invaginations that resemble eukaryotic cristae. (A)TEM images showing tubular cristae-like ICM compartments in free-living Desulfobacterota, and similar cristae-like ICM tubules in Desulfovibrio carbinolicus strains. The eukaryotic model organism S. cerevisiae exhibits tubular cristae structures, whereas the commonly used HEK293 cell line exhibits predominantly lamellar cristae structures. Scale bars: 500 nm. (B) Eukaryotic mitochondria tend to exhibit lamellar, tubular or discoidal cristae morphology, whereas orders of the class alphaproteobacteria exhibit a range of ICM morphologies. Lamellar-like ICMs, which exhibit parallel cytoplasmic protrusions that do not contact the inner membrane, are commonly observed in nitrogen-fixing and several methanotrophic alphaproteobacteria. (C) This simplified and non-exhaustive cladogram indicates the two domains of life – bacteria and archaea – with proto-mitochondria emerging in early alphaproteobacteria. Eukaryogenesis is marked by the horizontal transfer (red dotted arrow) from Bacteria to Hordarchaeales in Asgard archaea. §, †, #, * and ‡ connect species listed in B to their respective clades in C.

Kailash Venkatraman, Nicolas-Frédéric Lipp & @ibudin.bsky.social examine the similarities between prokaryotic intracytoplasmic membranes & mitochondrial IMs, & discuss whether cristae evolution has driven specialisation of the #mito lipidome.
journals.biologists.com/jcs/article/...
#JCSMitoSI

I had some absolutely incredible papers come online this week, and I need to take a minute to post about each of them. First, let me tell you about the CarboTag probes for imaging plant cell walls! From the Sprakel lab (a short thread) www.nature.com/articles/s41...

So excited for this work to be out!! Thanks to @attychang.bsky.social, @hamid13r.bsky.social, blue sky less Daniel Fuentes, @nanigrotjahn.bsky.social and @tomo.science!!!

🚨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

#invertefest needs some more marine representation, so here are 2 Liriope sp. hydrozoan and a teeny ctenophore amongst numerous copepods. Data recorded (5 fps) via a benchtop shadowgraph camera from a non-filtering end plankton net tow.

Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social,
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social

🔗 Preprint here tinyurl.com/3a74uanv

I know print journals aren't exactly on everyone's radar these days, but we’re still geeking out that our latest study—led by the brilliant @attychang.bsky.social—landed the cover of the April issue of JCB! 🤩

@zidlab.bsky.social @tomo.science @hamid13r.bsky.social

Live tracking of replisomes reveals nutrient-dependent regulation of replication elongation rates in Caulobacter crescentus Adhikashreni et al. use quantitative live-cell imaging to track cell-cycle dynamics in hundreds of individual bacteria. They observe nutrient-dependent regulation of replication elongation rates that ...

Happy to share Asha Joseph and Inchara Adhikashreni's latest work from the lab, describing replisome speed variation in Caulobacter!

www.cell.com/current-biol...

Retromer promotes the lysosomal turnover of mtDNA Lysosomal uptake of mtDNA controls mitochondrial quality.

Excited to share our latest paper in Science Advances! We finally dissected a new pathway for mitochondrial quality control upon mtDNA replication stress! Let’s start a short thread! 🧵

www.science.org/doi/10.1126/...

Drosophila follicle showing retrotransposons (pink & yellow) expressed in somatic cells infecting the oocyte

1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇