Amir Mitchell

The pivot penalty in research - Nature An analysis of millions of scientific papers and patents reveals a ‘pivot penalty’ when researchers shift direction, with the impact of studies decreasing rapidly the further they move from their prev...

The (very real) cost of changing your research field. Absolutely true! But the freedom to pivot is one of the greatest things in this profession.
www.nature.com/articles/s41...

Great opportunity to participate in scientific outreach!

YouTube video by MicrobeTV Matters Microbial #89: Can AI Point Us to New Antibiotics

Had a fantastic time with @markowenmartin.bsky.social’s on his #MattersMicrobial podcast (@microbetv.bsky.social). We discussed how to uncover the killing mechanisms of hundreds of antibacterials simultaneously and how #AI can transform the search for new antibiotics 🧪🦠💊
youtu.be/Wa0zd-TRCO8?...

Yo, micro/evo/qbio/physics of living systems/astrobiology/renegade cell bio folks- if you are interested in starting a feed, reply/repost this. Let's get the crew back together!

Fascinating shift in the geography of drug development (excellent writing too!)

The inherent stochasticity of biological systems 😉

Interested in Antimicrobial Resistance & Quantitative Bio? Join a 3-day meeting+workshop with some of my favorite #AMR #QBio scientists this April (University of Exeter, UK). Register here: tinyurl.com/QAMR2025reg 🧪🦠

Amazing book, shaped my worldview on Science. Kuhn’s genius was also in claiming that “paradigm shifts” are not purely logical, but are tainted by social & psychological factors. He claimed that established scientists are often conservatives resisting such shifts.

It was all code written in Matlab

Sure, email me I can attach a copy

The drug-drug similarity networks are based on how these drugs impact a library of E. coli mutants (profiles of resistance or sensitivity). We in fact show the chemical similarity fails to capture many of these similarities.

Beautiful detective work disentangling what is the actual trigger for cell death upon transcriptional arrest 🧪

12 Days of OpenAI - YouTube 12 days. 12 livestreams. A bunch of new things, big and small.

Never-have-I-ever seen technology racing forward as fast as #LMMs in the past two years. Watching the #openAI releases coming out in real-time in their twelves-days series is jaw dropping! 🤖🌊
www.youtube.com/playlist?lis...

My only complain is that I feel a bit like Cassandra, from the greek mythology, barely anyone listens 😞

Microscopy image of fluorescent colonies of E. coli after automatic image segmentation

The ability of LMMs (chatGPT here) to *assist* in generating useful code for biologists a mind-blowing power multiplier 🤯! My advice to biologists at all career stages: Learn to code, its a superpower 🦸‍♀️🦹‍♂️ (simple example, counting fluorescent colonies isolated from mouse gut microbiome) 🧪🦠

There is also a lot to be said about doing a "proper" postdoc in a good lab. It opens your eyes to different research directions, lab techniques, mentoring style, institutions, and so much more!

I absolutely agree!! So many of these positions end up going nowhere. They make sense only in *very* few use cases (5-10%): it's a *real* program with real legacy of successful PIs, the candidate continues on their phd research trajectory, and the candidate is scientifically mature (rare).

Credit for this work goes to my former student Dr Emily Lowry. Emily literally submitted the revised version of this manuscript at the very last minute before leaving the lab 🥳 (9/9)

I love this work since it a wonderful demonstration of (1) Serendipity in research – it started unexpectedly when we saw an active reporter even in non-contacting colonies and (2) it shows the power of simple experiments and quantitative microscopy (8/9)

Traces of DNA-damage reporter decay with distance from colibactin producers

Careful quantification revealed that the damage decay curves are identical in contacting and non-contacting colonies. Therefore, direct contact is not only not required, but it doesn’t even increase the level of toxicity beyond what is expected by proximity (7/9)

Experiment setup for monitoring colibactin induced DNA damage in neighboring colonies.

Next, we monitored colibactin damage in separated colonies. This setup allowed us not only to validate contact independence, but also to accurately quantify how DNA-damage decays across distance (6/9)

Diagram of experiment setup. Colony of a colibactin producing cell is placed on a lawn of DNA-damage reporter cells. The yellow halo around the colony marks DNA damage

Microscopy imaging revealed that DNA damage is observed even hundreds of microns (YFP halo) away from the secreter front (mCherry) suggesting that direct cell-cell is not needed for toxicity (5/9)

Diagram showing the plasmids used for cloning the colibactin producing strain and the DNA-damage reporter strain

We cloned a YFP DNA-damage reporter in E. coli and tested how far colibactin induced damage “travels” across a lawn of cells (we tagged secreters and responders with constitutive mCherry and CFP to tell them apart) (4/9)

Colibactin mode of delivery is still under debate, with common models claiming delivery requires direct cell-cell contact. While contact certainly improves toxicity (see great recent work by the Lars Vereecke lab), does it add anything beyond what is expected by proximity alone? (3/9)

Colibactin is deeply studied in human cells due to its involvement in colorectal cancers, yet far less is known in the context of microbial communities. Our first study with @daganlab.bsky.social revealed self-inflicted DNA-damage in colibactin producers (2/9)
genome.cshlp.org/content/earl...

Cartoon of two bacteria on a petri dish

Our second paper on the bacterial toxin colibactin is now out on mBio, this time we critically evaluated the claim that colibactin toxicity necessitates cell-cell contact 🧪🦠🧵(1/9)
journals.asm.org/doi/10.1128/...

Great list. Please add me too 🙏

Thank you for the resource, can you please add me to the list too?

Thank you for the resource. Please include me in the second pack 🙏

Fantastic resource. Thanks for putting this together Georgia!