iiinova — where your digital self keeps evolving

Alan Gerber @alangerber.bsky.social · 08/10/2026

PI at work: When you're not reading manuscripts or writing grants, you're poking holes in 0.5 mL tubes with annoyingly bendy 25G needles for your PhD student's gel extractions. When you have good students, that's apparently all they need you for... I miss lab work. 😅

Cluttered office desk with a laptop, coffee mugs, paperwork, and laboratory supplies. In the foreground, a box of 0.5 mL microcentrifuge tubes and 25G needles used to punch holes in the tubes for acrylamide gel extraction.

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Alan Gerber @alangerber.bsky.social · 28/09/2026

Roses are red, abundance is not dependency, and the same perturbation can mean very different things in different cells. We hope this platform will help dissect function of these genes much more systematically!

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Alan Gerber @alangerber.bsky.social · 28/09/2026

The same pattern extended to the Pol III machinery itself. Glioblastoma models were much less sensitive to perturbing dedicated Pol III factors. Sometimes they maintained the final gene product. Sometimes the product dropped... but the cells carried on anyway.

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Alan Gerber @alangerber.bsky.social · 28/09/2026

Even initiator methionine tRNA genes were interesting. One or more individual iMet tRNA genes emerged as fitness hits in 293T and BJ-hTERT cells BUT none did in two glioblastoma models we tested. Somewhat unexpected given the unique role of iMet tRNAs in translation initiation.

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Alan Gerber @alangerber.bsky.social · 28/09/2026

The largest contributors to a mature tRNA pool were not necessarily the most important ones. And some much less abundant loci still produced fitness phenotypes. At least for tRNAs with unique sequences, simply measuring abundance does not necessarily tell you which loci cells depend on...

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Alan Gerber @alangerber.bsky.social · 28/09/2026

Preprint alert 🚨: We built a CRISPRi screen for a part of the genome that is unusually awkward to perturb: the RNA Pol III transcriptome. Hundreds of tRNA genes, lots of sequence similarity, plenty of redundancy... Turns out the biology had a few surprises for us 👇 www.biorxiv.org/content/10.6...

biorxiv.org

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains uncl...

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Alex Palazzo @ribonucleicacids.bsky.social · 13/02/2026

Ever notice that when one gene is disrupted, its orthologs get upregulated? This phenomenon, known as transcriptional adaptation, has been controversial and mysterious - glad to see that we are starting to learn how it works.

science.org

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...

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Evelina Tutucci @anilevetu.bsky.social · 15/10/2025

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....

embopress.org

Single-molecule imaging of transcription dynamics, RNA localization and fate in human T cells | The EMBO Journal

imageimageT cells produce pro-inflammatory cytokines like IFN-γ and TNF. This study presents an optimized single-molecule FISH workflow in primary human T cells for studying how (post)-transcriptional...

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Evelina Tutucci @anilevetu.bsky.social · 26/02/2025

It's out! Beautiful work led by Loreto Oyarte Gálvez & @cbisot.bsky.social! Do you want to learn more about how Mycorrhizal fungi extraordinary networks form and function? Read the open-access publication! Link below 👇

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Evelina Tutucci @anilevetu.bsky.social · 21/12/2024

I am giving a lecture at the EMBO practical course: "FISHing for RNAs: classical to single molecule approaches" Check out this hands-on EMBO course!

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Anders Sejr Hansen @andersshansen.bsky.social · 20/12/2024

Excited to share @domenicnarducci.bsky.social 's paper now out in Mol Cell published back-to-back with the paper from @dewitlab.bsky.social‬ - despite lots of prior work, we find that ZNF143 has no looping function www.sciencedirect.com/science/arti... www.sciencedirect.com/science/arti...

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Alan Gerber @alangerber.bsky.social · 20/12/2024

Indeed, featuring the fusion of some letters (but not all) of the first word of the title of a paper we published last year and my last name. Quite an achievement 😅

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Alan Gerber @alangerber.bsky.social · 20/12/2024

MDPI & Frontiers journals blacklisted in Finland, I wonder if this will indeed spread further? Never considered any of these journals for publication, but MDPI surely send funny emails... Maybe I will introduce myself like this 👇 from now on 😂.

The picture shows a screenshot of an email from a MDPI journal creatively addressing me by fusing part of the title of a paper and my last name...

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Alejandro Montenegro @aemonten.bsky.social · 12/12/2024

"We report that numerous “miRNAs” previously reported in EMT and cancer contexts are not incorporated into RISC and are not capable of endogenously silencing target genes, despite the fact that hundreds of publications in the cancer field describe their roles" www.biorxiv.org/content/10.1...

biorxiv.org

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Yago Arribas @yarribas.bsky.social · 12/12/2024

Not easy to describe the emotions of seeing our work published in @cellpress.bsky.social ! We explored how novel isoforms emerge during evolution through the exonization of Transposable Elements. Exonized TEs modify the functions and structures of host proteins. www.cell.com/cell/fulltex...

cell.com

Transposable element exonization generates a reservoir of evolving and functional protein isoforms

Transposable element exonization by unannotated splicing events produces stable protein isoforms with acquired functions that are subject to evolutionary selection.

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Alexis A. Jourdain @jourdainlab.bsky.social · 16/12/2024

📢We're recruiting📢 Our lab at the University of Lausanne is looking for a postdoctoral associate to study #nucleotide metabolism in physiology and cancer in vivo! Please share #uridine #cancermetabolism #immunometabolism @unil.bsky.social 🔗(PDF): www.jourdainlab.org/wp-content/u...

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Olivier Duss @olivierduss.bsky.social · 11/12/2024

Excited to share our new work on the earliest steps of Pol-III transcription: We provide structural and kinetic insights into tRNA promoter engagement by yeast transcription factor TFIIIC ! Cool collaboration with the Müller and Eustermann Labs @embl.org ! academic.oup.com/nar/advance-...

academic.oup.com

Structural and kinetic insights into tRNA promoter engagement by yeast general transcription factor TFIIIC

Abstract. Transcription of transfer RNA (tRNA) genes by RNA polymerase (Pol) III requires the general transcription factor IIIC (TFIIIC), which recognizes

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Scott McGrath @smcgrath.phd · 09/12/2024

🧪 Your eyes may deceive you. A study of 3,387 life-science papers from 2023 found nearly 1/3 of bar charts distorted data, often by not starting the y-axis at zero or misusing log scales.

nature.com

Bad bar charts are pervasive across biology

Scientific ‘shorthand’ could be introducing data distortions into published papers.

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Alex Palazzo @ribonucleicacids.bsky.social · 26/11/2024

Very cool - snoRNA73 acts as a bridge between mRNAs and 7SL (i.e. the SRP ncRNA) to facilitate the synthesis of the encoded secreted protein.

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Molecular Biosystems Conference @molbiosystems.bsky.social · 25/11/2024

Did you know that at our conference, we record our Keynote Lectures and make them freely available? You can find them all in our Youtube page! To get started, check out the 2023 IUBMB Jubilee Lecture, given by Prof. Rachel Green.

youtube.com

Rachel Green - IUBMB Jubilee Lecture - 3rd Molecular Biosystems Conference (2023)

YouTube video by Molecular Biosystems Conference

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Reposted by Alan Gerber

Artem @rtviii.bsky.social · 25/11/2024

Post a non-religious photo you think of as holy. Not necessarily holy, just cool contrast between "then and now" in ribosome assembly landscape understanding. Nierhaus map from the 80s / AV Broeck & Sebastian Clinge in Science 2023.

https://www.science.org/doi/10.1126/science.adh3892?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed

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Alan Gerber @alangerber.bsky.social · 25/11/2024

Can you add me? Assistant prof at Amsterdam UMC. Thanks!

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Alan Gerber @alangerber.bsky.social · 25/11/2024

Could you add me? My group work on regulation of Pol III and tRNAs. Thanks!

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Alan Gerber @alangerber.bsky.social · 24/11/2024

Next time I speak with Bob, I'll let him know :-)

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Evelina Tutucci @anilevetu.bsky.social · 24/11/2024

This 👇 is happening. Change is coming!

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Alan Gerber @alangerber.bsky.social · 24/11/2024

Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4 by Ueli Laemmli! The paper which introduced SDS-page to the world!!! 💯

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Alan Gerber @alangerber.bsky.social · 24/11/2024

Not frog cells, sea urchin embryos

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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 24/11/2024

💯 February 14th 1969, RNA polymerases' day. The pioneering experiment that laid the foundation for the eukaryotic transcription field by Robert Roeder.

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Ben Long @botbml.bsky.social · 24/11/2024

Post a non-religious photo you think of as holy

A TEM image of structural carboxysomes in a tobacco chloroplast

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Alan Gerber @alangerber.bsky.social · 23/11/2024

Post a non-religious photo you think of as holy.

Figure showing the chromatographic resolution of the three nuclear DNA-dependent RNA polymerases from
Sea urchin embryos (Bob Roeder, 18 Feb 1969).

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Alan Gerber @alangerber.bsky.social · 23/11/2024

Hi, could you add me to this list? Thanks

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The Lewis Lab @peterlewislab.bsky.social · 22/11/2024

IDH-mutant gliomas evolve from slow-cycling OPC-like cells to proliferative NPC-like cells through chromatin reprogramming and genetic alterations. This transition reveals key mechanisms of tumor progression. www.nature.com/articles/s43...

nature.com

Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas - Nature Cancer

Wu et al. perform single-cell analyses to explore the switch from low-grade to high-grade isocitrate-dehydrogenase-mutant glioma and show that it is characterized by oligodendrocyte progenitor cell-li...

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Nils Blüthgen @molsysbio.bsky.social · 21/11/2024

How long does an mRNA stay in the nucleus? How long does it stay in the cytoplasm? In an amazing collaboration with @landthalerm.bsky.social, we used metabolic labeling, cell fractionation and mathematical modeling to quantify mRNA flow through the cell. Finally out in MSB: doi.org/10.1038/s443...

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Sam Rodriques @sgrodriques.bsky.social · 20/11/2024

New on BioRxiv: We report a new, endogenous molecular clock in unmodified human cells and tissues. It is ticking away right now in almost every cell in your body. Paper here: www.biorxiv.org/content/10.1... 1/

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Craig Kaplan @triggerloop.bsky.social · 21/11/2024

This is a very cool paper that I will add to my Mol Bio course. Specific tRNA recruitment of mRNA degradation complex to ribosome through the P site tRNA interactions with CCR4-NOT complex 1/ www.science.org/doi/10.1126/...

science.org

Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes

The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation....

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Will Allen @weallen1.bsky.social · 21/11/2024

In collaboration with Reuben Saunders, @jswlab.bsky.social, and Xiaowei Zhuang, we are very excited to release Perturb-Multi: a platform for pooled multimodal genetic screens in intact mammalian tissue. Check it out! www.biorxiv.org/content/10.1...

biorxiv.org

A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function

Organ function requires coordinated activities of thousands of genes in distinct, spatially organized cell types. Understanding the basis of emergent tissue function requires approaches to dissect the...

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Alan Gerber @alangerber.bsky.social · 19/11/2024

"Z-DNA isn't a thing... because it is not right-handed"

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Alan Gerber @alangerber.bsky.social · 19/11/2024

😂. The idea was massive parallel back translation of complex mix of proteins in the same sample. I still think this is (at least currently) unfeasible... As for evolution being smart, I guess "smart" enough for never requiring this...

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Alan Gerber @alangerber.bsky.social · 19/11/2024

Can I be added to this list as well? Thanks

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