Sign in

Zid Lab

@zidlab.bsky.social
1.8K followers 237 following 10 posts

UC San Diego Biochemistry studying RNA localization and mitochondria

PostsRepliesMedia
Reposted by Zid Lab
José Díaz Maldonado @josediazm.bsky.social · 24/09/2026
Local translation couples synaptic activity to mitochondrial adaptation in dendrites www.biorxiv.org/content/10.6...
biorxiv.org
Local translation couples synaptic activity to mitochondrial adaptation in dendrites
Neurons rely on localized protein synthesis to rapidly adapt synaptic function to activity, yet how dendritic translation regulates mitochondrial remodeling during synaptic plasticity remains poorly u...
083
Reposted by Zid Lab
RNA modification papers @rnamod.bsky.social · 18/09/2026
Transcript-wide m6A methylation defines the efficiency of cap-independent translation initiation RNA (New York, N.Y.) · Smolin et al. doi.org/10.1261/rna.081017.126 #RNAsky #RNAmods
doi.org
Transcript-wide m6A methylation defines the efficiency of cap-independent translation initiation
Here, we combined ribosome profiling under conditions of mTOR inhibition and m⁶A mapping to identify distinct subsets of mRNAs that differ in their sensitivity to the suppression of cap-dependent initiation.
056
Reposted by Zid Lab
Sonya Neal @neal-lab.bsky.social · 11/09/2026
So exciting to see our work featured by @jcb.org ! 🎉 This study brings together proteomics, zebrafish & rhomboid biology. New in the final paper: Dr. Kvido Strisovsky Rhbdl2 inhibitor beautifully phenocopied the R2 KO. So proud of Saroj and grateful to co-authors and collaborators! 💕
1369
Reposted by Zid Lab
Anupam Patgiri @apatgiri.bsky.social · 28/08/2026
RNA-dependent association of the pyruvate dehydrogenase complex with mtDNA-containing assemblies supports mitochondrial translation www.biorxiv.org/content/10.6...
biorxiv.org
RNA-dependent association of the pyruvate dehydrogenase complex with mtDNA-containing assemblies supports mitochondrial translation
Mitochondrial DNA (mtDNA) encodes core subunits of the oxidative phosphorylation machinery, and its expression is spatially organized, with the genome packaged into nucleoids around which transcriptio...
093
Reposted by Zid Lab
bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 24/08/2026
Kinetic Control of Nuclear-encoded Mitochondrial mRNA Localization and Local Translation www.biorxiv.org/content/10.64898/20…
0107
Reposted by Zid Lab
Alex Guseman @alexguseman.bsky.social · 21/08/2026
Come be my colleague! We are hiring a structural biologist. I have thoroughly enjoyed starting my career here and both department(s) are full of exceptional scientists. apol-recruit.ucsd.edu/JPF04589
apol-recruit.ucsd.edu
Assistant Professor in Structural Biochemistry
University of California, San Diego is hiring. Apply now!
35662
Reposted by Zid Lab
bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 17/08/2026
Presequences of non-imported mitochondrial proteins serve as quality control elements in the cytosol www.biorxiv.org/content/10.64898/20…
064
Reposted by Zid Lab
Matthew Taliaferro @jmtali.bsky.social · 12/08/2026
Excited to share our newest work! We asked whether RNA molecules need to be in a specific place in the cell to do their job. We found that a single RNA must reach the midbody, the structure that pinches two dividing cells apart, for cell division to finish efficiently. 🧵⬇️
612143
Reposted by Zid Lab
Alex Guseman @alexguseman.bsky.social · 11/08/2026
Im looking for a postdoc to help with protein engineering efforts. If you know who could be a good fit send them my way! see details below:
02425
Reposted by Zid Lab
Yasemin Sancak @yasesancak.bsky.social · 05/08/2026
Excited to share our new preprint! biorxiv.org/content/10.6... We know that mitochondria make contacts with organelles, but determining whether these contacts establish functionally distinct mitochondrial populations has been challenging.
biorxiv.org
A Modular Platform for Purification of Organelle-associated Mitochondria Reveals Functional Specialization at Organelle Contact Sites
Mitochondria perform diverse metabolic and signaling functions, yet how these activities are spatially organized within the mitochondrial network of cells remains poorly understood. Organelle contact ...
12511
Reposted by Zid Lab
Stella Hurtley @smhsci.bsky.social · 31/07/2026
Out now in @science.org Atlas of lysosomal aging reveals a metabolite signature shared with lysosomal storage disorders | Science www.science.org/doi/10.1126/...
science.org
Atlas of lysosomal aging reveals a metabolite signature shared with lysosomal storage disorders
Lysosomal dysfunction is a well-recognized feature of aging. Here, we used a suite of tools for rapid lysosomal isolation to construct a multitissue atlas of the metabolite changes lysosomes undergo d...
1279
Reposted by Zid Lab
David McQuarrie @davidmcquarrie.bsky.social · 01/08/2026
A multivalent RNA affinity tag enables selective purification of tagged RNAs and bound proteins doi.org/10.1093/nar/...
doi.org
A multivalent RNA affinity tag enables selective purification of tagged RNAs and bound proteins
Abstract. Efficient purification of specific RNAs from lysates remains a major challenge. Existing methods, such as MS2 tagging or oligonucleotide hybridiz
05722
Reposted by Zid Lab
Stirling Churchman @stirlingchurchman.bsky.social · 28/07/2026
RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...
biorxiv.org
Analog intrinsic recoding measures RNA dynamics without chemical conversion
Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...
215361
Reposted by Zid Lab
Yury Bykov @yurabykov.bsky.social · 24/07/2026
A big milestone for our group: the first research paper submitted! We found that cytosolic translation stress disrupts mitochondrial homeostasis and investigated cytosolic RQC and mitochondrial factors that save it. Preprint: www.biorxiv.org/content/10.6...
192
Reposted by Zid Lab
Jeff Coller @jmcoller.bsky.social · 22/07/2026
New from my lab - Congrats to Dr. Suhee Chang. Nascent chain folding status modulates ribosome dynamics and mRNA stability through the ribosome-associated chaperone Zuo1: Molecular Cell www.cell.com/molecular-ce...
cell.com
Nascent chain folding status modulates ribosome dynamics and mRNA stability through the ribosome-associated chaperone Zuo1
Chang et al. show that co-translational protein misfolding feeds back to ribosomes, slowing translation elongation and triggering mRNA decay. The ribosome-associated chaperone Zuo1 mediates this respo...
0189
Reposted by Zid Lab
Alex Guseman @alexguseman.bsky.social · 15/07/2026
Well I guess I no longer have ESI status.... because its NoA day! I am thrilled my R35 application was funded by NIGMS! I
11904
Reposted by Zid Lab
Nitish Dua @nitishdua.bsky.social · 27/06/2026
Really hyped to share our pre-print on mtDNA replication-fission ! @nanigrotjahn.bsky.social (doi: doi.org/10.64898/202...) 🧵with details below ⤵️
doi.org
ATAD3A structurally links mtDNA replication and mitochondrial fission
Mitochondrial function depends on the maintenance of its genome, and disruptions in copy number and distribution are hallmarks of mitochondrial disorders. Mitochondrial DNA (mtDNA) replication is spat...
25622
Reposted by Zid Lab
Maria Barna @mbarnalab.bsky.social · 24/06/2026
Registration is now open for this very exciting meeting on Ribosome Heterogeneity and Translation Control @stowersinstitute.bsky.social . Come join us! There will be open slots for talks.
063
Reposted by Zid Lab
Anders Sejr Hansen @andersshansen.bsky.social · 22/06/2026
(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...
215276
Reposted by Zid Lab
Nikolai Slavov @slavov-n.bsky.social · 24/06/2026
Since the 1960s, the genetic code has been used to predict protein sequences from DNA and mRNA sequences. Our @nature.com article demonstrates that these predictions miss thousands of protein sequences present in human tissues. www.nature.com/articles/s41... 1/
28337
Reposted by Zid Lab
Slavov Laboratory @slavovlab.bsky.social · 24/06/2026
This discovery has been a long and exhilarating journey! It started in 2019 and proceeded through many challenges and thrilling highs. A journey that has opened new perspectives that we long to explore !
066
Reposted by Zid Lab
Yury Bykov @yurabykov.bsky.social · 19/06/2026
ER has a co-translational protein import mechanism known for decades. But how about mitochondria? Surprisingly, there is still a lot of debate about it! We wrote a comprehensive review on this topic. I hope it is useful :) onlinelibrary.wiley.com/doi/10.1002/...
091
Reposted by Zid Lab
Jeremy Berg @jeremymberg.bsky.social · 16/06/2026
Podcast with @ctmurphy1.bsky.social at Princeton is up, talking about longevity research in model organisms and people and the role of NIH-supported research. chw.princeton.edu/news/podcast...
chw.princeton.edu
PODCAST: The Science of Aging (And Why Research May Hold the Key to Longevity)
The Princeton Pulse Podcast shares breakthroughs in genetics, molecular biology, and genomics that are helping researchers understand how we can live longer and healthier.
02112
Reposted by Zid Lab
Michael Feldbrügge @mfeldbruegge.bsky.social · 15/06/2026
Just in time for the RNA localisation conference, we uploaded a manuscript describing the link between endosomal mRNA transport and local mitochondrial activity. Great collaboration during MibiNet www.biorxiv.org/cgi/content/... @mibinet.bsky.social #EMBOrnaLocalization
Model for regulation of local mitochondrial activity
03511
Reposted by Zid Lab
bioRxivpreprint @biorxivpreprint.bsky.social · 13/06/2026
Endosomal mRNA transport coordinates local mitochondrial bioenergetics during polar fungal growth www.biorxiv.org/content/10.64898/20…
034
Reposted by Zid Lab
Matthew Taliaferro @jmtali.bsky.social · 11/06/2026
New paper! How do RNAs "know" where to go inside a cell? We dug into the sequence elements that route RNAs to the right place. It turns out that, in mammals, they're surprisingly massive (>200 nt), multipartite, and wonderfully complicated. 🧵
816565
Reposted by Zid Lab
Maria Barna @mbarnalab.bsky.social · 21/05/2026
’m thrilled to share that our paper is out in Molecular Cell! We developed Ribo-Tweezer, a new technology that lets us rapidly and reversibly remove specific proteins from mature ribosomes to ask what they actually do in translation.
1227
Reposted by Zid Lab
UC San Diego @ucsandiego.bsky.social · 21/05/2026
A $5M investment in people and possibility. UC San Diego’s NIH-funded FIRST program is helping early-career faculty thrive and drive the future of biomedical research. bit.ly/43lRSzW #Research #UCSanDiego
bit.ly
UC San Diego Receives $5 Million Renewal for Prestigious Faculty Recruitment and Training Program
UC San Diego received a $5 million NIH renewal for its FIRST program, supporting faculty recruitment, mentorship and career development for 12 rising biomedical researchers.
032
Reposted by Zid Lab
Leon Strenger @lstrngr.bsky.social · 19/05/2026
I'm very excited to announce that my PhD work is out on biorxiv! pyTrance is a computational method to predict and quantify subcellular RNA co-localization from spatial transcriptomics data. www.biorxiv.org/content/10.6...
biorxiv.org
1115
Reposted by Zid Lab
Ahmad Jomaa @jomaalab.bsky.social · 13/05/2026
Excited to share our work uncovering SNOR, a ribosome-associated factor that promotes translation restart after dormancy published in Nature!! This was, as usual, a wonderful collaborative effort between our group and the Mattei Lab @simonemattei.bsky.social @embl.org www.nature.com/articles/s41...
514758
Reposted by Zid Lab
Marvin Tanenbaum @marvintanenbaum.bsky.social · 13/05/2026
For 40 years the 8-nt ‘Kozak Sequence’ was thought to mark sites of translation initiation. In a new study, we revise this model by identifying an ~80-nt sequence—the extended Translation Initiation Sequence (eTIS)— that guides ribosomes to correct start sites. 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
317878
Reposted by Zid Lab
Itay Budin @ibudin.bsky.social · 01/05/2026
What membrane properties do cells maintain through regulation of lipid metabolism? In a new paper, we identify intrinsic curvature stress as one such parameter and show how different (eukaryotic) cell types employ different lipids to do that www.cell.com/cell-reports...
cell.com
Active regulation of intrinsic curvature by eukaryotic phospholipid metabolism
Cells maintain membrane function by actively balancing the molecular shape of their lipids. Milshteyn et al. find that, when subjected to high hydrostatic pressure, yeast and human cells, but not bact...
18430
Reposted by Zid Lab
Kurianlab @kurianlab.bsky.social · 23/04/2026
www.sciencedirect.com/science/arti...
sciencedirect.com
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces
RNA-binding proteins (RBPs) orchestrate post-transcriptional processes, including splicing, cleavage and polyadenylation, and translation. Our updated…
096
Reposted by Zid Lab
allen institute @alleninstitute.org · 23/04/2026
Spend less time processing cell images with the Allen Cell Structure Segmenter. This #OpenScience python-based toolkit helps #cellscience researchers navigate complex images by automatically capturing the boundaries of structures. Access at: lnkd.in/gpWA7xWH
03516
Reposted by Zid Lab
Sam Lewis, Ph.D. @samlewis.bsky.social · 13/04/2026
Excited to share a new collaborative paper with Lena Koslover's team, fueled by @chanzuckerberg.bsky.social Metabolism Across Scales Program 🧪 1/ www.pnas.org/doi/10.1073/...
pnas.org
Diffusive spreading across dynamic mitochondrial network architectures | PNAS
In eukaryotic cells, mitochondria form networks that range from highly fused interconnected structures to fragmented populations of individual orga...
13515
Reposted by Zid Lab
Molecular Cell @cp-molcell.bsky.social · 19/04/2026
Mitochondrial translation elongation controls OXPHOS biogenesis by coordinating synthesis and folding of mitochondrially encoded proteins
dlvr.it
Mitochondrial translation elongation controls OXPHOS biogenesis by coordinating synthesis and folding of mitochondrially encoded proteins
Xie et al. show that mitochondrial translation elongation rate influences OXPHOS biogenesis. In the filamentous fungus Neurospora crassa, MRM1 slows elongation speed independently of its methyltransferase activity by simultaneously binding mitoribosomes and mRNAs, thereby coordinating synthesis with folding and membrane insertion of mitochondrially encoded OXPHOS subunits.
0174
Reposted by Zid Lab
Sergey Kryazhimskiy @skryazhi.bsky.social · 10/04/2026
It looks like there will be an open postdoc position in my lab soon. I'll be looking for someone with substantial wet-lab experience in microbiology / microbial ecology / evolution / physiology. If everything goes well, an ad will be coming. But if you know someone, ask them to reach out already.
02930
Reposted by Zid Lab
José Díaz Maldonado @josediazm.bsky.social · 03/04/2026
U2AF regulates the translation and localization of nuclear-encoded mitochondrial mRNAs. www.cell.com/molecular-ce...
cell.com
U2AF regulates the translation and localization of nuclear-encoded mitochondrial mRNAs
Garcia et al. identify a non-canonical function of the splicing factor U2AF1 in translation and localization of nuclear-encoded mitochondrial RNAs. An oncogenic missense mutation leads to pervasive ch...
073
Reposted by Zid Lab
Cell Biology J-Club @cellclub.bsky.social · 02/04/2026
Pearling drives mitochondrial DNA nucleoid distribution | Science www.science.org/doi/10.1126/...
science.org
Pearling drives mitochondrial DNA nucleoid distribution
The distribution of mitochondrial DNA–containing nucleoids is essential for mitochondrial function and genome inheritance; however, no known mechanisms can explain nucleoid segregation or their regula...
0228
Reposted by Zid Lab
Furqan Fazal @furqanmfazal.bsky.social · 02/04/2026
Excited to share our @natprot.nature.com paper on using RNA proximity labeling to map subcellular RNA transcriptomes. We’ve been working in this area for a while and wanted to create a resource paper to guide the uninitiated reader. rdcu.be/fblvI
rdcu.be
APEX-seq maps transcriptome-wide subcellular RNA localization in living cells
Nature Protocols - This Protocol describes the transcriptome-wide labeling of RNAs in a particular subcellular compartment using proximity biotinylation by localized APEX2 enzyme and subsequent...
27227
Reposted by Zid Lab
Alicia Kowaltowski @aliciakowaltowski.bsky.social · 31/03/2026
Our newest paper is out online! An Open-Source Code to Analyze Mitochondrial Intracellular Distribution from Fluorescence Microscopy Images Congrats @giologia.bsky.social! portlandpress.com/bioscirep/ar...
portlandpress.com
An Open-Source Code to Analyze Mitochondrial Intracellular Distribution from Fluorescence Microscopy Images
Mitochondria have a plethora of roles in cells, many of which are related to dynamic changes in their size, shape, and intracellular location. Mitochondrial morphology is commonly assessed by microsco...
1167
Reposted by Zid Lab
anil oza @aniloza.bsky.social · 19/03/2026
lots of jarring statistics and heartbreaking stories I could share from this story, but this particular anecdote made me tear up when @jonathanwosen.bsky.social first shared this story with me For more details from our survey of ~1000 nih-funded researchers, read the report below
screenshot of story reading, "It wasn’t enough to save her three-person team. Sweetwyne still let go of a laboratory technician, and another left on their own. She’s had to return to the bench to help the one remaining staffer with experiments. Sweetwyne expects she’ll have to shut down the lab by the end of this year. And as a non-tenure-track researcher with 95% of her salary coming from grants, Sweetwyne said she’s at risk of losing her position at UW altogether. 

While she tries not to bring her worries home, her 6-year-old daughter has noticed. Each morning, she hands Sweetwyne a pair of coins and asks, “Is this going to be enough?” Sweetwyne always says yes, and, at the end of each day, hides the pennies and quarters around her house for the child to find again so that she doesn’t run out of change."
6136101
Reposted by Zid Lab
Osman Lab @osman-lab.bsky.social · 15/03/2026
We have officially launched our new lab website. 🥳 The site includes the automated literature curation on #mtDNA quality control and copy number regulation, which will appear on Mondays and Thursdays. Listen to the latest #NotebookLM generated podcast. 🧬 Explore the new site: osman-lab.de
osman-lab.de
The Osman Lab | LMU Munich
Mitochondrial research and genome maintenance at Ludwig-Maximilians-University.
0136
Reposted by Zid Lab
Jordy F. Botello @jbotello.bsky.social · 10/03/2026
Some molecular machines, like ribosomes, can persist for long periods of time in cells. Could molecular aging of ribosomes shape how proteins are made? In our new preprint we track ribosomes as they age in cells and uncover unexpected effects on translation (1/10) www.biorxiv.org/content/10.6...
412851
Reposted by Zid Lab
Páll Melsted @pmelsted.bsky.social · 06/03/2026
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result
618887
Reposted by Zid Lab
Journal of Cell Biology @jcb.org · 03/03/2026
“I’m grateful to be included in a journal with such a strong legacy in defining and advancing the field of cell biology.”— Dr. Danielle Grotjahn (@nanigrotjahn.bsky.social). JCB is where the world meets your research. Learn more. hubs.la/Q0442hKP0
192
Reposted by Zid Lab
Cell Biology J-Club @cellclub.bsky.social · 02/03/2026
RNA-specific local translation is patterned by condensates for multinucleate cell growth www.nature.com/articles/s41...
nature.com
RNA-specific local translation is patterned by condensates for multinucleate cell growth - Nature Cell Biology
Geisterfer, Jalihal et al. show spatially distinct effects of Whi3 condensates on target translation in Ashbya syncytia. In vitro, translation is enriched at condensate–solute interfaces but repressed...
0146
Reposted by Zid Lab
Sarah Cohen @cohenlaboratory.bsky.social · 16/02/2026
Cells come in many shapes and sizes, with diverse physiological functions. But how do #organelles and their interaction networks remodel during #differentiation of stem cells into different cell types? Here’s what we discovered about neuronal differentiation: 1/13
48838
Reposted by Zid Lab
Eduardo Tassoni Tsuchida @eduardotassoni.bsky.social · 12/02/2026
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...
biorxiv.org
1163