Zid Lab

I am excited to share the main piece of work from my PhD! In this paper, we investigated the propensities of distinct transcripts in associating with biomolecular condensates, mainly focusing on how heat-induced mRNAs escape condensation and are properly translated.

www.biorxiv.org/content/10.6...

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

@science.org Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation | Science www.science.org/doi/10.1126/...

From MBoC… A systematic comparison of auxin-inducible degradation tools in yeast identifies optimal component combinations for fast, efficient protein depletion with low basal effects. https://www.molbiolcell.org/doi/10.1091/mbc.E25-12-0571

Construction of complex and diverse DNA sequences using DNA three-way junctions - Nature Sidewinder enables high-fidelity DNA assembly by separating the information that guides assembly from the final assembled sequence.

If you are looking for a distraction, this seems cool. Sticky ends++. If it works as advertised, seems like it could be a game-changer.
www.nature.com/articles/s41...

Our newest paper is out where we investigate how exogenous RNA triggers innate immune responses, such as PKR activation and stress granule assembly. rnajournal.cshlp.org/content/earl...

The Murphy Lab did our annual retreat this week. This year's theme was using AI (what it's good and bad for). I wanted to be open-minded to make sure we are not missing something we should be using it for, so we did a few exercises to test, and had presentations.

Mitochondrial hitch-hiking of Mapt mRNA maintains Tau levels in axons Hitch-hiking of transcripts on organelles, including mitochondria, has emerged as a common pathway to transport mRNAs into the axon to enable their local translation. However, the extent of mitochondr...

New preprint from my lab!!!
We took advantage of the MitoTag mouse line to study what mRNAs associate with mitochondria in axons in vivo, and we were in for a surprise! Other than our favorite Pink1, mainly cytoskeletal mRNAs hitch a ride and pave the way for axon growth. shorturl.at/rYe1U

Local mitochondrial physiology defined by mtDNA quality guides purifying selection Author summary Mitochondria are essential organelles in our cells that convert nutrients into usable cellular energy. They contain their own DNA, and mutations in this DNA can compromise mitochondrial...

How do cells assess mtDNA quality?

Local ATP and membrane-potential gradients reflect mtDNA integrity and drive intracellular purifying selection.

We introduce FAST, a scalable mtDNA QC assay in S. cerevisiae.

Great collaboration with the Schmoller Lab.

journals.plos.org/plosgenetics...
🧬⚡

Happy to share that the our manuscript "Cyclin CLB2 mRNA localization and protein synthesis link cell cycle progression to bud growth" is now finally out in its final form @natcomms.nature.com
www.nature.com/articles/s41...
Below a short🧵 with the key findings!

Really thrilled to have our work on mitochondrial presequence strength out today @jcb.org. We establish quantitative parameters to better define "strong" and "weak" presequences both in vitro and in vivo. This work was spearheaded by the ever talented Youmian Yan, a BBSB graduate student in my lab.

Mitochondrial position responds to glucose stimulation in a model of the pancreatic beta cell The compartmentalization of eukaryotic cells into membrane-bound organelles with specific subcellular positioning enables precise spatial and temporal control of cellular functions. Although functiona...

From the mukherjilab.com Mitochondrial position responds to glucose stimulation in a model of the pancreatic beta cell: Biophysical Journal www.cell.com/biophysj/ful...

Self-renewal of neuronal mitochondria through asymmetric division Mitochondrial ATP production is essential for life. Mitochondrial function depends on the spatio-temporal coordination of nuclear and mitochondrial genome expression, yet how this coordination occurs ...

⚡️Mitochondria make ATP, the energy that powers life. But in neurons, with axons up to a meter long, how do these tiny power plants stay functional in the right places? We went looking. 1/n www.biorxiv.org/content/10.6...

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

New paper from @zhixingchen2.bsky.social's lab!

It turns out that, in addition to its very low phototoxicity, PKmito Deep Red (PKMDR) directly reports on mitochondrial membrane potential (MMP) in live cells through its lifetime!

www.nature.com/articles/s41...

Excited to share that this work is now published in its final form!

link.springer.com/article/10.1...

TDP-43 directly inhibits mRNA accumulation in neurites through modulation of mRNA stability - The EMBO Journal The subcellular localization of many mRNAs to neuronal projections allows neurons to efficiently and rapidly react to spatially restricted external cues. However, for most of these RNAs, the mechanism...

A mechanism for controlling mRNA localization to neuronal projections:
Daniel Dominguez, Matthew Taliaferro @jmtali.bsky.social and collaborators implicated ALS-linked TDP-43 as inhibitor of mRNA accumulation in neurites, possibly by promoting their decay
link.springer.com/article/10.1...

Holy cow the Zhou lab at UCLA is cooking with Isonet 2 - www.biorxiv.org/content/10.6...

Averaging-free direct visualization of ribosome translational state! #teamtomo #cryoet

Announcing the 2026 edition of the EMBO workshop on RNA localization and local translation! This meeting will be held June 30 - July 4 near Porto, Portugal. Come for exciting updates in the field from both established investigators and trainees. See the link below for details!

What an honor to see @attychang.bsky.social’s work featured in @jcb.org The Year in Cell Biology 2025 collection! Even more special that it coincides with my first #cellbio2025 conference 🙂

s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social

#teamtomo #cellbio25

Chromosome duplication causes premature aging via defects in ribosome quality control Syndromes caused by chromosome amplification, such as Down syndrome, are characterized by premature aging, but the reason behind this is unclear. This study shows that chromosome amplification in yeas...

Our paper is out studying premature aging (a hallmark of Down syndrome) in aneuploid yeast. Who knew part of the problem is in Ribosome Quality Control. Congrats to Leah Escalante for leading this tour de force.

journals.plos.org/plosbiology/...

@attychang.bsky.social, @nanigrotjahn.bsky.social et al. show that cytoplasmic #ribosomes on #mitochondria alter the local membrane environment for protein import. rupress.org/jcb/article/...

📕 From The Year In Cell Biology: rupress.org/jcb/collecti...
#CellBio2025

Viral RNA blocks circularization to evade host codon usage control - Nature Rather than adapting to the codon usage of their host, viruses use viral 5′ untranslated regions to initiate translation, which allows them to produce viral proteins in host cells efficiently despite ...

ANOTHER PAPER from Yi Liu's lab. This one is a bit crazy - codon effects on mRNA translation happens at the initiation step and requires looping - viruses don't circularize their mRNAs and thus evade the requirement for common codons to have efficient mRNA translation.
www.nature.com/articles/s41...

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.

Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation Nature Structural & Molecular Biology - Mitochondrial translational activators (TAs) facilitate transcript-specific translation. Using selective ribosome profiling and cryo-electron microscopy,...

Our study on the molecular function of translational activators for mitochondrial protein synthesis is published:
rdcu.be/eSWxT
A great collaboration with @stirlingchurchman.bsky.social and @sshaolab.bsky.social with structural work from our @pelleeas.bsky.social
Funded by @kawresearch.bsky.social

Postdoctoral Researcher positions-Kapahi lab - Buck Institute - Career Page The Kapahi lab seeks postdocs to lead innovative projects exploring how circadian clocks & nutrient-responsive pathways influence eye & neuronal degeneration.

🚀 Postdoc opportunity!

The Kapahi Lab at Buck Institute for Research on Aging is hiring two postdoctoral researchers to lead cutting-edge studies on how nutrient signaling and circadian rhythms influence neurodegeneration & aging — combining fly, worm, and mammalian models with genomics. 📈

👉

We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.

It ships many new features, detailed below, but that are articulated around the following:

Polaroid snapshot of Omar Quintero-Carmonas and me (Ximena)

Beautiful green-yellow tree just outside of the Bottomley House at the University of Richmond against a pretty blue sky

A red brick building typical of University of Richmond campus

My seminar poster has my talk title "Cells Build Robust Organelles from Noisy Processes: Lessons from Algae and Yeast," plus information like the location and date of the talk

Had an amazing time visiting University of Richmond during peak foliage, learned about the innovative teaching and science we'd see more of around the country, and shared my own stochastic biophysics work, old and new. Thank you @omqu.bsky.social for my first ever dept seminar & campus visit

Metabolic environment-driven remodeling of mitochondrial ribosomes regulates translation and biogenesis Zheng et al. demonstrate that mitochondria remodel the structure and composition of mitochondrial ribosomes in response to metabolic state. This structural “gear-switching” mechanism fine-tunes mitoch...

Metabolic environment-driven remodeling of mitochondrial ribosomes regulates translation and biogenesis: Molecular Cell www.cell.com/molecular-ce...

Secretome translation shaped by lysosomes and lunapark-marked ER junctions - Nature Live-cell imaging of mRNA encoding secretome proteins and translated nascent peptide markers show that secretome translation occurs at endoplasmic reticulum junctions near lysosomes, requires lun...

www.nature.com/articles/s41...
Secretome translation shaped by lysosomes and lunapark-marked ER junctions

Neuronal compartmentalization results in impoverished axonal mitochondria https://www.biorxiv.org/content/10.1101/2025.10.27.684882v1