Zid Lab
@zidlab.bsky.social
UC San Diego Biochemistry studying RNA localization and mitochondria
Pinned
Zid Lab
@zidlab.bsky.social
· Nov 9
eIF5A controls mitoprotein import by relieving ribosome stalling at TIM50 translocase mRNA
eIF5A controls the mitochondrial protein import, and thus the mitochondrial function, by relieving ribosome stalling of mitochondrial surface-localized mRN
doi.org
🧪Happy to announce the newest work from our lab in collaboration with the Alepuz lab at the Univ of Valencia, exploring why decreased eIF5A activity leads to mitochondrial dysfunction! doi.org/10.1083/jcb....
#RNABiology #mitochondria
(1/7)
#RNABiology #mitochondria
(1/7)
Reposted by Zid Lab
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.
January 15, 2026 at 4:51 PM
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.
Reposted by Zid Lab
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
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
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...
shorturl.at
January 15, 2026 at 10:17 AM
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
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
Reposted by Zid Lab
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...
🧬⚡
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...
🧬⚡
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...
journals.plos.org
January 10, 2026 at 4:00 PM
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...
🧬⚡
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...
🧬⚡
Reposted by Zid Lab
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!
www.nature.com/articles/s41...
Below a short🧵 with the key findings!
January 10, 2026 at 6:54 PM
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!
www.nature.com/articles/s41...
Below a short🧵 with the key findings!
Reposted by Zid Lab
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.
Yan, @ianofbristol.bsky.social, @nieminm.bsky.social et al. define quantitative parameters underlying the strength of mitochondrial-targeting presequences, and demonstrate that yeast require strong presequences to facilitate select metabolic pathways in #mitochondria. rupress.org/jcb/article/...
January 8, 2026 at 5:47 PM
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.
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...
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...
www.cell.com
December 19, 2025 at 6:02 PM
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...
Reposted by Zid Lab
⚡️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...
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 ...
www.biorxiv.org
December 18, 2025 at 8:36 PM
⚡️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...
Reposted by Zid Lab
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
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
Organelles harbour pH gradients https://www.biorxiv.org/content/10.64898/2025.12.12.694065v1
December 17, 2025 at 12:46 AM
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
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
Reposted by Zid Lab
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...
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...
December 16, 2025 at 12:11 PM
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...
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...
Reposted by Zid Lab
Excited to share that this work is now published in its final form!
link.springer.com/article/10.1...
link.springer.com/article/10.1...
December 15, 2025 at 2:37 PM
Excited to share that this work is now published in its final form!
link.springer.com/article/10.1...
link.springer.com/article/10.1...
Reposted by Zid Lab
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...
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...
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...
link.springer.com
December 15, 2025 at 1:00 PM
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...
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...
Reposted by Zid Lab
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
Averaging-free direct visualization of ribosome translational state! #teamtomo #cryoet
December 12, 2025 at 3:53 PM
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
Averaging-free direct visualization of ribosome translational state! #teamtomo #cryoet
Reposted by Zid Lab
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!
December 8, 2025 at 4:40 PM
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!
Reposted by Zid Lab
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
s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social
#teamtomo #cellbio25
@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
📕 From The Year In Cell Biology: rupress.org/jcb/collecti...
#CellBio2025
December 7, 2025 at 8:10 PM
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
s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social
#teamtomo #cellbio25
Reposted by Zid Lab
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/...
journals.plos.org/plosbiology/...
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...
journals.plos.org
December 5, 2025 at 4:58 PM
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/...
journals.plos.org/plosbiology/...
Reposted by Zid Lab
@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
📕 From The Year In Cell Biology: rupress.org/jcb/collecti...
#CellBio2025
December 5, 2025 at 4:15 PM
@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
📕 From The Year In Cell Biology: rupress.org/jcb/collecti...
#CellBio2025
Reposted by Zid Lab
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...
www.nature.com/articles/s41...
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 ...
www.nature.com
December 4, 2025 at 9:10 PM
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...
www.nature.com/articles/s41...
Reposted by Zid Lab
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.
December 3, 2025 at 8:42 PM
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.
Reposted by Zid Lab
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
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
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,...
rdcu.be
December 3, 2025 at 1:39 PM
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
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
Reposted by Zid Lab
🚀 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. 📈
👉
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. 📈
👉
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.
buckinstitute.applytojob.com
November 30, 2025 at 2:09 AM
🚀 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. 📈
👉
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. 📈
👉
Reposted by Zid Lab
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:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 11:42 AM
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:
It ships many new features, detailed below, but that are articulated around the following:
Reposted by Zid Lab
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
November 19, 2025 at 5:13 AM
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
Reposted by Zid Lab
Metabolic environment-driven remodeling of mitochondrial ribosomes regulates translation and biogenesis: Molecular Cell www.cell.com/molecular-ce...
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...
www.cell.com
November 6, 2025 at 6:37 PM
Metabolic environment-driven remodeling of mitochondrial ribosomes regulates translation and biogenesis: Molecular Cell www.cell.com/molecular-ce...
Reposted by Zid Lab
www.nature.com/articles/s41...
Secretome translation shaped by lysosomes and lunapark-marked ER junctions
Secretome translation shaped by lysosomes and lunapark-marked ER junctions
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
November 5, 2025 at 5:03 PM
www.nature.com/articles/s41...
Secretome translation shaped by lysosomes and lunapark-marked ER junctions
Secretome translation shaped by lysosomes and lunapark-marked ER junctions
Reposted by Zid Lab
Neuronal compartmentalization results in impoverished axonal mitochondria https://www.biorxiv.org/content/10.1101/2025.10.27.684882v1
October 29, 2025 at 7:15 PM
Neuronal compartmentalization results in impoverished axonal mitochondria https://www.biorxiv.org/content/10.1101/2025.10.27.684882v1