Top: A representative modeling example from Chimpanzee CPEB3 HDV-like ribozyme (PDB ID: 7QR3), with models predicted by four better-performing methods (blue cartoons) overlaid on experimental structure (gray cartoons). Left to right: DRFold2, DeepFoldRNA, AlphaFold3, RhoFold. Bottom: Structural visualization of the example from coxsackievirus B3 cloverleaf RNA (PDBID: 8DP3), showing experimental structure (left), AlphaFold3’s best prediction from 100 models (middle), and 5th model of DRfold2 (right), respectively. Structures are rainbow-colored from 5′ (blue) to 3′ (red) end.

Accurate RNA structure prediction remains a challenge, despite recent computational advances. This study presents DRFold2, a #DeepLearning framework that significantly enhances accuracy of de novo #RNAstructure prediction by increasing contact prediction precision @plosbiology.org 🧪 plos.io/4aoOQiX

Deciphering guanidine assimilation and riboswitch-based gene regulation in cyanobacteria for synthetic biology applications | PNAS Guanidine is well known as a denaturing agent. However, recent studies have demonstrated both the widespread synthesis of guanidine, e.g., in plant...

A new + interesting paper on the guanidine riboswitch in Synechocystis and other cyanobacteria:
"Deciphering guanidine assimilation and ri"boswitch-based gene regulation in cyanobacteria for synthetic biology applications" | PNAS www.pnas.org/doi/10.1073/...

The train station in Qingdao. A light-flooded palace for high-speed trains.

Inside the high-speed train Qingdao-Beijing in China. Riding at more than 300 km/h.

Riding a train in China, returning from the ISPP 2025 and the Green Carbon conference.

RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets Nature Communications - RNA-binding proteins play key roles in post-transcriptional gene regulation. Here, Hemm et al. developed RAPDOR, a widely applicable tool based on Jensen-Shannon Distance...

„RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics dataset“ rdcu.be/eImcr : 11 authors from 3 labs. Many thanks to all for making this possible!

To correctly determine a distance there, we used Jensen Shannon Divergence as a metric, which is a symmetrified version of the well-known Kullback–Leibler divergence for comparing distributions.
The GradR data can be searched online at synecho-rapdor.biologie.uni-freiburg.de
@meinbio.bsky.social

For the intuitive analysis + visualization of such datasets we introduce RAPDOR. In contrast to expression profiles, which are compared e.g. by correlation, the results of GradR and similar approaches are naturally displayed as distributions, as the protein fraction in each compartment is measured.

We have been searching for novel RNA-binding proteins and validated, among many candidates, Sll1967 (a possible RlmD homolog), Sll0726 (phosphoglucomutase), Ssl2245 (a putative antitoxin), Slr0711 (possible QueF homolog), and Sll0947 (ribosome-associated inhibitor RaiA/LrtA homolog) as binding RNA.

RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets Nature Communications - RNA-binding proteins play key roles in post-transcriptional gene regulation. Here, Hemm et al. developed RAPDOR, a widely applicable tool based on Jensen-Shannon Distance...

How to search for unknown RNA-binding proteins? We did GradR in the cyanobacterium Synechocystis 6803. And now our paper „RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics dataset“ is finally out in Nature Communications, here: rdcu.be/eImcr .

Figure on track 1.

The train is made to look nice. Forest items everywhere

Riding a train in Lithuania.

¡Muchas gracias, José!

Many thanks, Jörg! And it has been a pleasure to visit Göttingen recently!

RNA-binding proteins and photosynthesis: The RRM domain–containing protein Rbp3 interacts with ribosomes and the 3’ ends of mRNAs encoding photosynthesis proteins | PNAS www.pnas.org/doi/10.1073/...

Inorganic carbon levels regulate growth via SigC signaling cascade in cyanobacteria Cyanobacterial growth depends on inorganic carbon (Ci; CO2 and bicarbonate) concentration, but mechanism(s) adjusting photosynthesis and growth according to Ci remain unclear. ΔrpoZ cells lacking th...

Inorganic carbon levels regulate growth via SigC signaling cascade in cyanobacteria - Kurkela - New Phytologist - Wiley Online Library nph.onlinelibrary.wiley.com/doi/10.1111/...

Evidence for a CO2‐concentrating mechanism in the model streptophyte green alga Chara braunii Oxygenic photosynthesis in streptophytic algae, such as Charophyceae, is often impeded by low CO2 levels in aquatic habitats. Consequently, many algal groups evolved a CO2-concentrating mechanism (C...

Measuring carbon isotope discrimination and crucial gene expression changes indicated that C. braunii expresses a CO2-concentrating mechanism to cope with these challenges. Supported by @watertoland.bsky.social Details here: nph.onlinelibrary.wiley.com/doi/10.1111/...

They must cope with low CO2 solubility in water, which can limit the CO2 fixation by RubisCO. Moreover, the total pool of inorganic carbon is highly variable in this environment, depending on pH, temperature, and salinity.

How are fully submerged algae efficiently fixing carbon?
All organisms performing oxygenic photosynthesis fix CO2 in
the Calvin–Benson–Bassham cycle using RubisCO. But aquatic organisms have a challenge.

Out now: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA
cell.com/molecular-ce...

Most long-A pAgos interfere with invading DNA solo. Why then are cyanobacterial pAgos co-encoded with a Cas4-like protein?

Just three days left for the deadline for oral abstract submissions for the 15th Workshop on Cyanobacteria at Vanderbilt University (Nashville, TN, USA) - don't miss out!
Workshop dates: 4-7th June 2025. More information: web.cvent.com/event/3d0bd3.... Please share widely!

TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses RNA-guided systems provide remarkable versatility, enabling diverse biological functions. Through iterative structural and sequence homology-based mining starting with a guide RNA-interaction domain o...

TIGR-Tas: A new family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses: www.science.org/doi/10.1126/...

🚨 New #Breakthrough article from @holmqvist-lab.bsky.social: "ProQ prevents mRNA degradation through inhibition of poly(A) polymerase" #RNA #Stability #Degredation #mRNA 📖 Read the full article here: https://doi.org/10.1093/nar/gkaf103

Annegret Wilde (@freecyano.bsky.social) cyanobacteriologist from University Freiburg

Our new Opinion article, now out in Trends in Plant Science is the result of a great collaboration with Conrad Mullineaux and Annegret Wilde freecyano.bsky.social @cyanolab.bsky.social

Does mRNA targeting explain gene retention in chloroplasts? During their evolution from cyanobacteria, plastids have relinquished most of their genes to the host cell nucleus, but have retained a core set of ge…

Why did chloroplasts retain some genes from their free-living ancestors rather than transferring all of them to the nucleus following endosymbiosis? We suggest that mRNA targeting might play a role.
www.sciencedirect.com/science/arti...

Horizontal gene transfer of the functional archaellum machinery to Bacteria Motility in Archaea is driven by a nanomachinery called the archaellum. So far, archaella have been exclusively described for the archaeal domain; however, a recent study reported the presence of arch...

Would you expect that Bacteria use an archaellum for swimming? We didn't, but we found that some Chloroflexota do! Find the story here: www.biorxiv.org/content/10.1...

A little thread below 1/n

Highly multiplexed spatial transcriptomics in bacteria Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...

🅲🅾🅾🅻 🆃🅴🅲🅷🅽🅾🅻🅾🅶🆈

“Bacterial-MERFISH” provides ~1000-fold volumetric expansion of individual cells, charts gene expression in hundreds of thousands of cells, deciphering bacterial single-cell heterogeneity, intracellular transcriptome organization, and bacterial adaptation to µm-scale niches in vivo

This review has been put together by 12 authors working on multicellularity in bacteria. Many thanks to the DFG by supporting this research through the SPP priority program 2389 “Emergent Functions of Bacterial Multicellularity”.

Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges | Microbiology and Molecular Biology Reviews SUMMARYThe development of multicellularity represents a key evolutionary transition that is crucial for the emergence of complex life forms. Although multicellularity has traditionally been studied in...

Multicellularity is a key feature of complex life, but how to study multicellularity in bacteria and at the single cell level? Use advanced microscopy, MS imaging, flow cytometry, spatial and single-cell transcriptomics, advanced microfluidics and more. See here: journals.asm.org/doi/10.1128/...

Sharepic showing Date, Time and Place of Prof. Eilon Shani's CIBSS Seminar talk on "A Multi-targeted genome-scale CRISPR Toolbox to Overcome Functional Redundancy and Reveal Hidden Hormone Transport Mechanisms", Tuesday, January 14th 2025, Lecture Hall, Institute of Biology I, Hauptstr. 1, and online per Zoom.

Mark your calendars for next Tuesday: Tel Aviv University's Prof. Eilon Shani will present a #CRISPR -based toolkit that targets multiple genes at a genome-wide scale, addressing functional overlap in genetic systems and to uncover hidden mechanisms behind hormone transport.
kurzlinks.de/fprn

The conformational space of RNase P RNA in solution - Nature Using a deep neural network and statistical analyses of atomic force microscopy images of individual RNA molecules enables the mapping of RNA conformational space in solution.

The conformational space of RNase P RNA in solution using atomic force microscopy: www.nature.com/articles/s41...

R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning Abstract. RNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation of heterocysts in filamentous cyanobacteria i

PatR (Alr1700) is a previously not characterized protein that binds sRNAs and functions as a master regulator of heterocyst patterning and differentiation.
academic.oup.com/nar/advance-...

Not all bacteria, even of a single species, are created equal. Nor are they always unicellular. Some cyanobacteria develop heterocysts and fix nitrogen. GradR/R-DeeP analysis identified new RNA-binding proteins. Some were previously known for other functions. Others were completely uncharacterized.