Jarno Mäkelä

Jarno Mäkelä

@jmakela.bsky.social

Assist. Prof. of Biophysics at Aalto Univ. | Temperature adaptation | Super-resolution microscopy | Single molecule tracking | #ERCStG https://www.aalto.fi/en/department-of-neuroscience-and-biomedical-engineering/single-molecule-dynamics-in-cells

625 followers414 following8 posts

Jarno Mäkelä
@jmakela.bsky.social

Excited to share our new bioRxiv preprint, led by the fantastic #AdaPajari! We used live-cell #single-molecule tracking to watch bacterial #Hsp70 DnaK survey the proteome and rapidly shift into longer-lived client engagement during heat shock. 🔬🦠🧪 doi.org/10.64898/2026.07.01.735817

doi.orgBacterial Hsp70 DnaK transiently samples the proteome to rapidly capture stress-induced misfolding.Protein-quality-control systems are essential for cells to maintain protein homeostasis during both steady-state growth and acute stress. Yet, how individual chaperone molecules dynamically reorganize...
Jarno Mäkelä
@jmakela.bsky.social

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! 🦠🔬🧪🧫

aalto.fiAssistant professor in Living state physics | Aalto UniversityAalto University is where science and art meet technology and business. We shape a sustainable future by making research breakthroughs in and across our disciplines, sparking the game changers of tomorrow and creating novel solutions to major global challenges. Our community is made up of 120 nationalities, 14 000 students, 400 professors and close to 5000 faculty and staff working on our dynamic campus in Espoo, Greater Helsinki, Finland. Diversity is part of who we are, and we actively work to ensure our community’s diversity and inclusiveness. This is why we warmly encourage qualified candidates from all backgrounds to join our community.

Jarno Mäkelä reposted

Nature Communications
@natcomms.nature.com

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

bit.lyPredictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli - Nature CommunicationsThe 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.

Jarno Mäkelä reposted

Yves Brun lab
@brunlabcaulo.bsky.social

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.

nature.comPhenotypic plasticity in cell elongation among closely related bacterial speciesNature Communications - Multiple types of cell elongation have been described in bacteria, but little is known about how these strategies vary across species. Here, the authors use fluorescent...
Yves Brun lab@brunlabcaulo.bsky.social

How does your favorite species elongate? 🧵 "Phenotypic plasticity in bacterial elongation among closely related species" by @mariedelaby.bsky.social, Liu Yang et al https://buff.ly/48Kw96x. How do cells elongate, all over, poles, middle? Close species do it the same way right? Not quite! #Microsky

Jarno Mäkelä reposted

Zhixing Chen
@zhixingchen2.bsky.social

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

nature.comA palette of bridged bicycle-strengthened fluorophores - Nature MethodsA 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...
Jarno Mäkelä
@jmakela.bsky.social

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/...

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

Jarno Mäkelä reposted

Zeynep Baharoglu
@zeynepbaharoglu.bsky.social

"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...

nature.comThe nucleoid of rapidly growing Escherichia coli localizes close to the inner membrane and is organized by transcription, translation, and cell geometry - Nature CommunicationsThe 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...

Jarno Mäkelä reposted

Suckjoon Jun’s lab at UCSD
@junlab.bsky.social

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

rdcu.beRobust and resource-optimal dynamic pattern formation of Min proteins in vivoNature 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...

Jarno Mäkelä reposted

Thibaut Brunet
@thibautbrunet.bsky.social

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/...

science.orgTissue-like multicellular development triggered by mechanical compression in archaeaThe 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...

Jarno Mäkelä reposted

Joachim Goedhart
@joachimgoedhart.bsky.social

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

nature.comBright and photostable yellow fluorescent proteins for extended imaging - Nature CommunicationsYellow 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 ...

Jarno Mäkelä reposted

Johannes Hohlbein
@hohlbeinlab.bsky.social

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

doi.orgThe Escherichia coli replication initiator DnaA is titrated on the chromosomeDNA 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 ...

Jarno Mäkelä reposted

Dvir Schirman
@dvirschirman.bsky.social

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)

biorxiv.orgA dynamic 3D polymer model of the Escherichia coli chromosome driven by data from optical pooled screeningThe 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...

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