Jarno Mäkelä

Congrats!

We have a tenure-track Assistant Professor position open at Aalto University in the area of Living State Physics with a focus on molecular and cellular biophysics, biophotonics, non-equilibrium phenomena, or biological engineering.
www.aalto.fi/en/open-posi...
Pls share! 🦠🔬🧪🧫

Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli - Nature Communications The authors describe BoltzNet, a neural network that learns the energy of transcription factor (TF)-DNA binding from genomic data and can be used to design new binding sites. They report the in vivo mapping and BoltzNet modeling of 139 E. coli TFs.

Mapping of DNA-binding sites for 139 E. coli transcription factors

and

A neural network that predicts binding energy from DNA sequence and can be used to design new binding sites

#NeuralNetworks #MachineLearning #Genomics

How does your favorite species elongate? 🧵 "Phenotypic plasticity in bacterial elongation among closely related species". Happy to see this paper in print @natcomms.nature.com. Nice work by @mariedelaby.bsky.social, Liu Yang et al. See original 🧵, different colours, same data and conclusions.

A palette of bridged bicycle-strengthened fluorophores - Nature Methods A suite of bridged rhodamine dyes (BriDyes) offers excellent brightness, solubility, photostability, and tunable cell permeability along with resistance to photoblueing, making them exceptional all-pu...

Here come our new palette of fluorescent dyes. The BD dyes endeaves to balance glowy brightness, robust photostability, and biocompatibility. Let's boost 4D dynamic super-resolution imaging!!!
www.nature.com/articles/s41...
@spirochrome.com

Dynamics of bacterial operons during genome-wide stresses is influenced by premature terminations and internal promoters Internal promoters in operons are critical in genome-wide stress responses, compensating for frequent premature RNAP falloffs.

How do internal promoters within operons shape bacterial stress responses? 🦠🧫
Contributing to a study with @andreribeirolbd.bsky.social, we show non-monotonic spatial expression patterns across operons in E. coli, B. subtilis, C. glutamicum, and H. pylori. www.science.org/doi/10.1126/...

The nucleoid of rapidly growing Escherichia coli localizes close to the inner membrane and is organized by transcription, translation, and cell geometry - Nature Communications The mechanisms underlying bacterial chromosome configuration are not fully understood. Here, Spahn et al. show that the Escherichia coli nucleoid adopts a condensed, membrane-proximal configuration du...

"E. coli nucleoid adopts a condensed, membrane-proximal configuration during rapid growth, an active role of transertion (coupled transcription, translation, and membrane insertion) in nucleoid organization" #microsky www.nature.com/articles/s41...

Robust and resource-optimal dynamic pattern formation of Min proteins in vivo Nature Physics - Oscillatory Min protein patterns prevent abnormal bacterial cell division. Now it is shown that Min pattern formation is resource efficient and involves wavelength-invariant...

Our paper on the E. coli Min system in vivo with @physicsoflifelmu.bsky.social & Judy Kim (UCSD) has been published in Nature Physics today. Tight integration of experiment and theory, and physiology and biophysics. Incredible perseverance of our young students. rdcu.be/ekIpO

Tissue-like multicellular development triggered by mechanical compression in archaea The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once in archaea. We show that uniaxial compression induces clonal mul...

Striking new study from @archaeon-alex.bsky.social's lab just out in @science.org on multicellular development induced by compression in Archaea: www.science.org/doi/10.1126/...

Please share with all your colleagues and friends! The more the merrier! 👇👇👇 more info on smlms.org!

Bright and photostable yellow fluorescent proteins for extended imaging - Nature Communications Yellow fluorescent proteins (YFPs) photobleach rapidly, restricting microscopy experiments. Here, the authors report mGold2s and mGold2t, YFPs that extend imaging durations up to 25 times longer than ...

Bright and photostable yellow fluorescent proteins for extended imaging by François St-Pierre and team:
www.nature.com/articles/s41...

Live tracking of replisomes reveals nutrient-dependent regulation of replication elongation rates in Caulobacter crescentus Adhikashreni et al. use quantitative live-cell imaging to track cell-cycle dynamics in hundreds of individual bacteria. They observe nutrient-dependent regulation of replication elongation rates that ...

Happy to share Asha Joseph and Inchara Adhikashreni's latest work from the lab, describing replisome speed variation in Caulobacter!

www.cell.com/current-biol...

We are looking for a postdoc with microbiology background for #superresolution #singlemolecule #ERC tracking project. Apply by 27.4.2025. 🦠🔬🧫
Pls share!

www.aalto.fi/en/open-posi...

New preprint from our lab!
Story started long ago that took many years in the making.

Great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social groups.

Generously funded by BBSRC @ukri.org & @leverhulme.bsky.social

How do #archaea segregate their chromosome?
#microsky #archaeasky

Congrats to Dr. Ana Andjelković from our and @richterlab.bsky.social lab for winning 2nd place in the Huygens Image Contest! 🎉🏆 Live STED imaging shows the cristae dynamics in a pathophysiological condition. svi.nl/imagecontest... #ScienceArt #ImageContest

Assistant Professor in Biophysics

#Jobs We are looking for a new colleague! Tenure Track Assistant Professor in Biophysics in the domains of functional imaging and biophysics. More info here: www.wur.nl/en/vacancy/a...

The Escherichia coli replication initiator DnaA is titrated on the chromosome DNA replication initiation is orchestrated in many prokaryotes by the replication initiator DnaA. Two models for regulation of DnaA activity in Escherichia coli have been proposed: the switch between ...

New preprint spear headed by the amazing #LorenzoOlivi: "The Escherichia coli replication initiator DnaA is titrated on the chromosome" using, among many other techniques, #sptPALM to determine growth dependent mobilities of DnaA diffusing in live cells. doi.org/10.1101/2024.10.07.617004 1/n

A dynamic 3D polymer model of the Escherichia coli chromosome driven by data from optical pooled screening The DNA of bacterial cells is organized in a highly dynamic chromosome structure. To guarantee its propagation, the chromosome must replicate, segregate, and accommodate other biological processes lik...

I’m excited to share the first preprint from my postdoc at
@johan_elf_
lab together with Konrad Gras. 🧬🦠
biorxiv.org/content/10.1...
(1/14)

📢Job Alert!📢
We are looking for 2 PhD students with biophysics or computational biology background for #SuperResolution #singlemolecule tracking project.
More information: tinyurl.com/5b58y9kd
Apply by 31.10.24. 🦠🔬🧫
Pls share!

Three-year postdoc available on anti-phage defense systems and phage biocontrol of phytopathogenic Ralstonia solanacearum at Helsinki (FIN) in collaboration with @hauryliuk.bsky.social and gemmaatkinson.bsky.social. Application deadline 29.2.2024. #phagesky #microsky jobs.helsinki.fi/job/Helsinki...

This is a phenomenal piece of work from Andreas Wagner et al - A rugged yet easily navigable fitness landscape www.science.org/doi/10.1126/... #EvoSky #MicroSky

Only two days to apply to ERC Research funded PhD and postdoc positions in our #TEMPADAPT project. 🦠🔬🧪More info: tinyurl.com/2zy95b5z tinyurl.com/3z6bja2x tinyurl.com/mpmwj5y4