Zid Lab
UC San Diego Biochemistry studying RNA localization and mitochondria
- Reposted by Zid LabFrom MBoC… A systematic comparison of auxin-inducible degradation tools in yeast identifies optimal component combinations for fast, efficient protein depletion with low basal effects. molbiolcell.org/doi/10.1091/mbc.E25…
- Reposted by Zid LabIf 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...
- Reposted by Zid LabOur 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...
- Reposted by Zid LabThe 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 LabNew 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
- Reposted by Zid LabHow 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... 🧬⚡
- Reposted by Zid LabHappy 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!
- Reposted by Zid LabReally 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/...
- 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...
- Reposted by Zid LabOrganelles 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
- Organelles harbour pH gradients biorxiv.org/content/10.64898/20…
- Reposted by Zid LabNew 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...
- Reposted by Zid LabExcited to share that this work is now published in its final form! link.springer.com/article/10.1...
- Reposted by Zid LabA 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...
- Reposted by Zid LabHoly 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
- Reposted by Zid LabAnnouncing 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 LabWhat 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
- @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
- Reposted by Zid LabOur 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/...
- 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
- Reposted by Zid LabANOTHER 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...
- Reposted by Zid LabOxidative 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 LabOur 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
- 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. 📈 👉
- Reposted by Zid LabWe 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:
- Reposted by Zid LabHad 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 LabMetabolic environment-driven remodeling of mitochondrial ribosomes regulates translation and biogenesis: Molecular Cell www.cell.com/molecular-ce...
- Reposted by Zid Labwww.nature.com/articles/s41... Secretome translation shaped by lysosomes and lunapark-marked ER junctions
- Reposted by Zid LabNeuronal compartmentalization results in impoverished axonal mitochondria biorxiv.org/content/10.1101/202…
- Reposted by Zid LabAmazing paper from collaborators Schraga Schwartz and Moran Shalev-Benami at Weizmann. Nucleotide resolution sequencing of 16 RNA modifications from diverse organisms cultured under basal and 'extreme' conditions + enzymology, structure, synthesis, and biophysics. www.cell.com/cell/fulltex...
- Reposted by Zid LabOur collab w. V Goel, @nicholas-aboreden.bsky.social , J Jusuf, G Blobel, L Mirny, @irate-physicist.bsky.social out in @natsmb.nature.com www.nature.com/articles/s41... Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon Brief thread 👇
- been lurking here a while but time to spend less time in the bad place Here's my latest work in collab w/ Viraat Goel, @andersshansen.bsky.social, Leonid Mirny, Nick Aboreden, Gerd Blobel et al. Dynamics of microcompartment formation at the mitosis-to-G1 transition www.biorxiv.org/content/10.1...
- Reposted by Zid LabAnd it's out! Our paper on the optimization of smFISH to quantify cytokine mRNAs in T cells is published in EMBO Journal. Using this protocol, we gathered interesting insights on cytokine mRNAs co-expression and localization in these teeny tiny human cells. www.embopress.org/doi/full/10....
- I am super proud that this paper is now out in EMBO Journal lnkd.in/ev843k7P What did we do? we optimized imaging of single molecules, in our case cytokine mRNAs with smFISH in primary human T cells.
- Reposted by Zid LabFrom MBoC: Timothy J. Stasevich, Colorado State University, developed All Probes Plasmids (APPs) to simplify single-mRNA translation imaging—just 2 plasmids for multicolor, long-term tracking. www.molbiolcell.org/doi/10.1091/... #CellBiology
- Reposted by Zid LabI am thrilled to share our latest story led by the incredibly talented Brooke D’Arcy and Camila Musso. We discover a rich world of local gene expression in radial glia, essential neural and glial precursors, and develop a new method for sub-cellular mRNA manipulation. www.biorxiv.org/content/10.1...
- Reposted by Zid LabOnline now - the Review "Interconnectivity of mitochondrial protein biogenesis and quality control" from @mitolab.bsky.social et al. #ProteinImport #Proteaes #Proteolysis #Proteostasis Read it here: authors.elsevier.com/sd/article/S...
- Reposted by Zid LabMallory is a postdoc in Alexis Komor's lab. She brings gene editing to high schools, showing them what a future in science looks like. Without funding from the NSF, this outreach would not be possible. #BehindEveryBreakthrough
- Reposted by Zid Lab🚀 Our new paper is out @natmethods.nature.com! Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells. 🔗 www.nature.com/articles/s41... 🧬 www.addgene.org/John_Ngo/
- Reposted by Zid LabWonderful to see our paper on the #organelle signatures of #neurons and #astrocytes out in final form - congratulations, Shannon Rhoads and team!🎉 t.co/BPxKlbU6Ou
- Reposted by Zid LabVery excited to share new work out today in @natchembio.nature.com on a new approach - FACES - for selectively imaging of phospholipids and other biomolecules at spatial resolutions down to individual membrane leaflets (1/n) www.nature.com/articles/s41...
- Reposted by Zid LabOur new pre-print from the Greenberg and Churchman labs shows that activity-dependent modulation of RNA stability is a major, and underappreciated, mechanism of gene regulation in neurons. Tutorial below! www.biorxiv.org/content/10.1... (1/11)
- Reposted by Zid LabThrilled to announce our #preprint on a new factor in the last line of defense in #translation quality control out on #bioRXiv! Spearheaded by fantastic PhD student @kaushikiyer.bsky.social, supported by Chloé Walter, Alina Kraft, Max Müller and Lena Tittel.
- Jlp2 is an RQC complex-independent release factor acting on aberrant peptidyl-tRNA, protecting cells against translation elongation stress biorxiv.org/content/10.1101/202…
- Reposted by Zid LabProximity-specific ribosome profiling using LOV-BirA reveals two distinct strategies for mitochondrially-localized translation: one for long coding sequences and one for short. It was a pleasure to contribute to this beautiful work from Jonathan Weissman @weissmanlab.bsky.social and Jingchuan Luo
- Reposted by Zid Lab🚨 Preprint alert! 🚨 My first first-author manuscript is out on bioRxiv! We developed a new method to monitor mtDNA quality control in yeast, and found that a functional respiratory chain is crucial for the process. @osman-lab.bsky.social #mtDNA #mitochondria www.biorxiv.org/content/10.1...
- Reposted by Zid Lab(Yet another) shout-out to @joachimgoedhart.bsky.social and colleagues for their ongoing technical service to the cell biology community – in this case, the yeast cell biology community. Special kudos for making all the key plasmids available on @addgene.bsky.social. Stellar work all around!
- Reposted by Zid LabThe 4 chemically targeted Laurdan derivatives (for mitochondria, ER, lyso/endosomes, and the Golgi) that we published last year are now available (at a pretty reasonable price) from Avanti Polar Lipids (cat #880194, 880197, 880193, 880196). These have been very popular! pubs.acs.org/doi/full/10....
- Reposted by Zid LabIncredibly honored to be named a 2025 Pew Scholar in the Biomedical Sciences! 🧬 Grateful to Pew Trusts for this recognition and support, and to my awesome lab team, mentors and colleagues at @ucsdhealthsci.bsky.social Excited for what's ahead! www.pew.org/en/about/new...
- Reposted by Zid LabExcited to share our latest work developing molecular glue degraders of ZBTB11, now out in @natchembio.nature.com www.nature.com/articles/s41...
- Reposted by Zid LabThis preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...
- Reposted by Zid LabThis is quite relevant - RNA triggers chronic stress during neuronal aging Thanks @frezzalab.bsky.social for the hint!!! www.biorxiv.org/content/10.1...
- Reposted by Zid LabI nice little story from the lab: dx.plos.org/10.1371/jour...
- Reposted by Zid LabFirst copies of my book are here!! As a new faculty member, I realized that in addition to my research job, I also had a leadership job…and I wasn’t prepared for that. This book is the guide I wish I’d had then, with the goal of helping others now. jenheemstra.com/book
- Reposted by Zid LabBeyond excited to share our #NewPaper in @cellcellpress.bsky.social! Inflamed environments acidify intracellular #pH. BRD4 senses this via transcriptional condensates, tuning #macrophage responses to match demand and consequences of #inflammation authors.elsevier.com/sd/article/S...
