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
19.11.2025 05:13 — 👍 2 🔁 1 💬 0 📌 0
Neuronal compartmentalization results in impoverished axonal mitochondria https://www.biorxiv.org/content/10.1101/2025.10.27.684882v1
29.10.2025 19:15 — 👍 5 🔁 2 💬 0 📌 1
Our 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 👇
20.10.2025 18:36 — 👍 55 🔁 18 💬 2 📌 2
And 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....
15.10.2025 21:31 — 👍 29 🔁 11 💬 1 📌 0
From 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
13.10.2025 22:24 — 👍 27 🔁 9 💬 0 📌 0
I 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...
10.10.2025 22:28 — 👍 73 🔁 24 💬 4 📌 3
Online 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...
10.10.2025 15:55 — 👍 16 🔁 11 💬 0 📌 0
Mallory 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
08.10.2025 18:01 — 👍 8 🔁 4 💬 1 📌 0
🚀 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/
22.09.2025 18:27 — 👍 223 🔁 97 💬 6 📌 9
Wonderful to see our paper on the #organelle signatures of #neurons and #astrocytes out in final form - congratulations, Shannon Rhoads and team!🎉 t.co/BPxKlbU6Ou
17.09.2025 17:37 — 👍 99 🔁 40 💬 6 📌 1
Thrilled 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.
09.09.2025 18:17 — 👍 10 🔁 8 💬 1 📌 0
Proximity-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
27.08.2025 15:29 — 👍 32 🔁 7 💬 1 📌 2
Side-by-side systematic characterization of novel FPs in budding yeast
Fluorescent proteins (FPs) have become indispensable for biological research. Since the discovery of the first FP, Aequorea victoria green fluorescent protein (avGFP), new fluorescent proteins are con...
(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!
15.08.2025 20:39 — 👍 25 🔁 10 💬 1 📌 0
Organelle-Targeted Laurdans Measure Heterogeneity in Subcellular Membranes and Their Responses to Saturated Lipid Stress
Organelles feature characteristic lipid compositions that lead to differences in membrane properties. In cells, membrane ordering and fluidity are commonly measured using the solvatochromic dye Laurdan, whose fluorescence is sensitive to lipid packing. As a general lipophilic dye, Laurdan stains all hydrophobic environments in cells; therefore, it is challenging to characterize membrane properties in specific organelles or assess their responses to pharmacological treatments in intact cells. Here, we describe the synthesis and application of Laurdan-derived probes that read out the membrane packing of individual cellular organelles. The set of organelle-targeted Laurdans (OTL) localizes to the ER, mitochondria, lysosomes, and Golgi compartments with high specificity while retaining the spectral resolution needed to detect biological changes in membrane ordering. We show that ratiometric imaging with OTLs can resolve membrane heterogeneity within organelles as well as changes in lipid packing resulting from inhibition of trafficking or bioenergetic processes. We apply these probes to characterize organelle-specific responses to saturated lipid stress. While the ER and lysosomal membrane fluidity is sensitive to exogenous saturated fatty acids, that of mitochondrial membranes is protected. We then use differences in ER membrane fluidity to sort populations of cells based on their fatty acid diet, highlighting the ability of organelle-localized solvatochromic probes to distinguish between cells based on their metabolic state. These results expand the repertoire of targeted membrane probes and demonstrate their application in interrogating lipid dysregulation.
The 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....
15.08.2025 15:57 — 👍 47 🔁 14 💬 1 📌 1
Pew Awards 22 Researchers Biomedical Science Grants
Incredibly 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...
12.08.2025 16:59 — 👍 32 🔁 2 💬 3 📌 0
Picture of a smiling person holding up a copy of a book.
First 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
26.07.2025 17:35 — 👍 311 🔁 66 💬 12 📌 4
Beyond 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...
22.07.2025 13:24 — 👍 79 🔁 29 💬 6 📌 2
mRNA 3′UTRs chaperone intrinsically disordered regions to control protein activity
More than 2,700 human mRNA 3′UTRs have hundreds of highly conserved (HC) nucleotides, but their biological roles are unclear. Here, we show that mRNAs with HC 3′UTRs mostly encode proteins with long intrinsically disordered regions (IDRs), including MYC, UTX, and JMJD3. These proteins are only fully active when translated from mRNA templates that include their 3′UTRs, raising the possibility of functional interactions between 3′UTRs and IDRs. Rather than affecting protein abundance or localization, we find that HC 3′UTRs control transcriptional or histone demethylase activity through co-translationally determined protein oligomerization states that are kinetically stable. 3′UTR-dependent changes in protein folding require mRNA-IDR interactions, suggesting that mRNAs act as IDR chaperones. These mRNAs are multivalent, a biophysical RNA feature that enables their translation in network-like condensates, which provide favorable folding environments for proteins with long IDRs. These data indicate that the coding sequence is insufficient for the biogenesis of biologically active conformations of IDR-containing proteins and that RNA can catalyze protein folding. ### Competing Interest Statement The authors have declared no competing interest. Pershing Square Foundation, https://ror.org/04tce9s05 G. Harold & Leila Y. Mathers Foundation National Institutes of Health, DP1GM123454, R35GM144046 Memorial Sloan Kettering Cancer Center, https://ror.org/02yrq0923, P30 CA008748
New paper:
More than 2700 human 3′UTRs are highly conserved. These 3′UTRs are essential components in mRNA templates, as their deletion decreases protein activity without changing protein abundance. Highly conserved 3′UTRs help the folding of proteins with long IDRs.
www.biorxiv.org/content/10.1...
07.07.2025 14:28 — 👍 158 🔁 66 💬 4 📌 5
Exploring RNA & RBPs in cancer: from cell edges to the chromatin. Microscopy lover, proteomics newbie. Likes computer sciences, physics & photography. Also an illustrator and graphic designer for Science and Biology (see: @STEMDORADOscimag)
I help you excel in research and become more productive, organized, and successful using the newest academic tools, AI and workflows.
Weekly blog posts • 4 in-depth courses • Community of 1000s
https://effortlessacademic.com
Chief Technology Officer at ArrePath. Using Chemistry ML, imaging, and computer vision to accelerate antibiotic discovery and design. Formerly Zymergen, Nikon Imaging Center at UCSF.
Assistant Professor & CPRIT Scholar at Baylor College of Medicine | Biophysicist & RNA Aficionado | Mitochondria, Cancer, Translation, RNA Proximity Labeling | http://fazallab.org
RNA biologist at Johannes Gutenberg University Mainz, Germany: co-translational quality control - RNA modification - and beyond.
Lab url: ak-winz.pharmazie.uni-mainz.de
Assistant Professor, UCSD. Induced proximity, medicinal chemistry, chemical proteomics. https://fergusonlab.ucsd.edu
Professor and Chair of WashU Chemistry. I’m a researcher, but I’m a #MentorFirst. Author of Labwork to Leadership.
AP @BostonChildrens @harvardmed AM @broadinstitute
inflammation, tissue biology, quant.&systems immunology #1stGen #ImmigrantScientists #NewPI
RNA Biologist. Bioinformatician. Philadelphian.
Stanford Genetics PhD Student
Assistant Professor at Baylor College of Medicine and Texas Children's Hospital. Houston, TX
Science: disorder, condensates, repeats, cell stress, neurodegeneration, drug discovery, synbio Non-science: art, fashion, cooking
www.boeynaemslab.org
Senior Research Scientist in RIKEN. Ribosome, deep sequencing, local translation, phase separation.
RNA / PhD Student at UTokyo and RIKEN
https://orcid.org/0009-0008-3513-4507
Biomedical researcher studying mitochondrial disorders. PhD from Anu Suomalainen lab, Helsinki. Postdoc at Prokisch lab, Munich.
Research group at Karolinska Institute - SciLifeLab. Stockholm, Sweden. Managed by Vicent Pelechano.
Research group in the Biochemistry department @cambiochem.bsky.social at the University of Cambridge exploring the RNA Universe! 🧬✨ https://www.ericmiskalab.org/
Managed by lab members
Organisers of @cambridgerna.bsky.social
Assistant Professor at NYU | Neurobiologist | Mitochondria Enthusiast |K99/R00 fellow | she/her
www.gibbslabnyu.org
EMBLAustralia Group Leader @ UNSW Sydney| Ex Asst Prof IISc Bangalore | EMBO YI 2018 | MPI-CBG Dresden & BITS Pilani alumna | Co-founder @ biaswatchindia | Ally 🏳️🌈
PhD student in Grotjahn lab @Scripps Research
#Teamtomo #Mitochondria
