Matthaeus Schwarz-Schilling
@mattschwa.bsky.social
postdoc at the weizmann institute (bar-ziv lab) - tinkering with gene expression - bottom-up synthetic biology
When the evolutionary physiologist Christian Damsgaard analyzed bird eyes with microsensors, he noticed something surprising: Their retinas used no oxygen. How does this essential organ thrive without this essential element? www.quantamagazine.org/how-the-bird...
I’m very proud to share that I am a laureate of the Choose France for Science funding. This grant will help me build my lab over the next 3 years in France. Grateful to the @crpp-bordeaux.bsky.social, @cnrs.fr Chimie, @baretjc.bsky.social and others at the CRPP for their support.
We found a new mode by which bacteria deplete NAD+ to protect from phages. And then we found how phages overcome this defense Discovered by talented biochemist Dr Ilya Osterman, read the preprint: tinyurl.com/Narp-ap A thread 🧵
Bacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatases
Many bacterial defense systems restrict phage infection by breaking the molecule NAD+ to its constituents, adenosine diphosphate ribose (ADPR) and nicotinamide (Nam). To counter NAD+ depletion-mediated defense, phages evolved NAD+ reconstitution pathway 1 (NARP1), which uses ADPR and Nam to rebuild NAD+. Here we report a bacterial defense system called aRES, involving RES-domain proteins that degrade NAD+ into Nam and ADPR-1″-phosphate (ADPR-1P). This molecule cannot serve as a substrate for NARP1, so that NAD+ depletion by aRES defends against phages even if they encode NARP1. We further discover that some phages evolved an extended NARP1 pathway capable of overcoming aRES defense. In these phages, the NARP1 operon also includes a specialized phosphatase, which dephosphorylates ADPR-1P to form ADPR, a substrate from which NARP1 then reconstitutes NAD+. Other phages encode inhibitors that directly bind aRES proteins and physically block their active sites. Our study describes new layers in the NAD+-centric arms race between bacteria and phages and highlights the centrality of the NAD+ pool in cellular battles between viruses and their hosts. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, ERC-AdG GA 101018520 Israel Science Foundation, MAPATS grant 2720/22 Deutsche Forschungsgemeinschaft, SPP 2330, grant 464312965 Minerva Foundation with funding from the Federal German Ministry for Education and Research research grant from Magnus Konow in honor of his mother Olga Konow Rappaport Ministry of Aliyah and Immigrant Absorption, https://ror.org/05aycsg86 Clore Scholars Program
tinyurl.com
Now online! Mechanistic insights into RNA chaperoning by Ro60 and La autoantigens
Mechanistic insights into RNA chaperoning by Ro60 and La autoantigens
Structural and functional analyses elucidate the mechanisms by which two ATP-independent RNA chaperones, Ro60 and La, recognize and unfold misfolded RNAs. Diverse noncoding RNAs are associated with this chaperone machine, supporting a wide-ranging role in maintaining RNA homeostasis.
dlvr.it
Excited to share our new paper: we make 30 functional E. coli translation factors in a minimal system (PURE), find threshold concentrations to confirm nascent protein activity and use DNA-brushes to co-localize genes/ribosomes/proteins for simultaneous self-regeneration. doi.org/10.1038/s414...
Autonomous biogenesis of all thirty proteins of the Escherichia coli translation machinery - Nature Communications
The cell-free biogenesis of the protein translation machinery is essential for the creation of a self-regenerating synthetic cell. Here the authors synthesise all 30 E. coli translation proteins in a ...
doi.org
I learned about this dark side of syphilis when I took a history of medicine course. It is a remarkably resistant disease that brought armies to their knees and wrought tremendous societal damage. Ancient DNA Reveals Twisted Roots of Syphilis Go Back 5,500 share.google/V15zBbvnvlbf...
Ancient DNA Reveals Twisted Roots of Syphilis Go Back 5,500 Years
The first known outbreak of syphilis in Europe began at the turn of the 16th century, but on the distant continent of South America, the pathogen's history goes much deeper than that.
share.google
(1/2) Our work with @freddyfrischknecht.bsky.social on the chirality of malaria parasites has found its home in the January issue of @natphys.nature.com: www.nature.com/articles/s41... Moreover, we are very happy that it comes with a news and views article 👍❤️😀
Chirality of malaria parasites determines their motion patterns - Nature Physics
Malaria parasites move on helical trajectories when infecting their hosts. Now it is shown that they use right-handed chirality to control their motion patterns, and that this chirality is linked to t...
nature.com
A lot of the recent excitement around methods like AF3 (and followup methods which I often joking call YAAFCs: Yet Another Alpha Fold Clone) is the promise of modeling ligand-bound complexes from only a protein sequence + a small molecule SMILES string (movie from Charm Therapeutics)
A synthetic cell phage cycle www.nature.com/articles/s41...
A synthetic cell phage cycle - Nature Communications
The reconstitution of complex biological processes in cell-free systems can support the detailed characterisation of biochemical mechanisms which are difficult to probe in vivo. Here authors present a...
nature.com
PURE makes PURE: reconstitution of the PURE cell-free system from self-synthesized non-ribosomal proteins https://www.biorxiv.org/content/10.64898/2025.12.17.694911v1
Review: Cell-free protein synthesis in microcompartments towards cell–cell communication www.sciencedirect.com/science/arti...
I am happy to share that our review on the Controlled Protein Synthesis in Microfluidic Environments has been published 🎉 www.sciencedirect.com/science/arti... Thanks to @emmacrean.bsky.social, Imre Banlaki, @jankalkowski.bsky.social, and @hniederho.bsky.social for great teamwork!
A very cool paper from the Frey lab @physicsoflifelmu.bsky.social. Self-assembly governed by compartment geometry... Testing this in (surface-based) artificial cells would be exciting. Delay-facilitated self-assembly in compartmentalized systems | PNAS www.pnas.org/doi/10.1073/...
Delay-facilitated self-assembly in compartmentalized systems | PNAS
Self-assembly processes in biological and synthetic biomolecular systems are often governed by the spatial separation of biochemical processes. Whi...
pnas.org
Rapid and scalable purification of Escherichia coli active ribosomes using strong anion exchange spin columns. Biotechnol Bioproc E (2025). doi.org/10.1007/s122...
Rapid and scalable purification of Escherichia coli active ribosomes using strong anion exchange spin columns - Biotechnology and Bioprocess Engineering
Purification of active ribosomes is a prerequisite to studying ribosome functions. However, conventional purification methods such as ultracentrifugation, affinity tagging, and specialized chromatogra...
doi.org
3 more weeks to apply! 🧬 Fully funded PhD opportunity! 🧬 We are looking for a curious and motivated candidate to join our new team in Utrecht. Our goal is to develop biomimetic mechanisms for protein folding using DNA origami. More info: 🔗 www.uu.nl/en/organisat... 🗓️ Deadline: 15.08
Excited to share my first PhD student’s @biorxivpreprint.bsky.social! Tracking 5 dyes simultaneously Kavan Gor @embl.org tracks nascent #RNA folding during #ribosome assembly to correlate structural with functional information on single RNA molecules! Check it out! www.biorxiv.org/content/10.1...
Big news! I am starting my own research lab at the University of Bordeaux as a @cnrs.fr researcher. Excited to turn my dream job into a reality! I will join the @crpp-bordeaux.bsky.social and the fantastic team of @baretjc.bsky.social, Nicolas Martin and @lauraal.bsky.social. Check dupinlab.com.
Dupin Lab
dupinlab.com
Engineered orthogonal translation systems from metagenomic libraries expand the genetic code https://www.biorxiv.org/content/10.1101/2025.10.30.685624v1
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
Delighted to share my first first author paper, where we realized multi-μm membrane-like shells made entirely of DNA! Huge thanks to co-first author Christoph without whom this wouldn't be possible. This was born from his side-project involving Dipids, stay tuned for the soon-to-be-published paper!
bioRxiv Synthetic Biology@biorxiv-synthbio.bsky.social · 10mo agoVesicle-templated self-assembly of freestanding multi-μm DNA shells https://www.biorxiv.org/content/10.1101/2025.10.21.683722v1
Online monitoring of the mitochondrial respiration activity and protein formation in the Almost Living Cell-free Expression (ALiCE) system bmcbiotechnol.biomedcentral.com/articles/10....
Online monitoring of the mitochondrial respiration activity and protein formation in the Almost Living Cell-free Expression (ALiCE) system - BMC Biotechnology
Cell-free protein synthesis (CFPS) is one approach to address the increasing demand for complex recombinant proteins in various applications, especially in the pharmaceutical sector. CFPS offers a var...
bmcbiotechnol.biomedcentral.com
🚨Miao's and Weixiang's work on RNA transcription in DNA based condensates as nucleus mimics is now out in @natcomms.nature.com www.nature.com/articles/s41... #syncell #DNA #condensate #LLPS. Great work to understand transcription and LLPS in #crowded #viscoelastic environments @sfb1551.bsky.social
Constructing synthetic nuclear architectures via transcriptional condensates in a DNA protonucleus - Nature Communications
Nuclear biomolecular condensates are functional sub-compartments within the cell nucleus. Here, the authors develop a synthetic DNA protonucleus that enables RNA transcription and condensation into di...
nature.com
A paper in Nature suggests a quarter of heatwave events from 2000-23 would have been near impossible without anthropogenic climate change. The paper also indicates that major carbon emitters are responsible for around 50% of the increase in intensity of these events. ⚒️ 🧪
Systematic attribution of heatwaves to the emissions of carbon majors - Nature
Climate change made 213 historical heatwaves reported over 2000–2023 more likely and more intense, to which each of the 180 carbon majors (fossil fuel and cement producers) substantially contributed.
go.nature.com
We’ve developed the first-ever method to control nucleic acid activity and gene-expressing synthetic cells with a deeply tissue penetrating alternating magnetic field 🧬 🧪 🧲!!! Published in *Nature Chemistry* Led by Ellen Parkes @syncelleu.bsky.social #chemsky www.nature.com/articles/s41...
Magnetic activation of spherical nucleic acids enables the remote control of synthetic cells - Nature Chemistry
The programmability of synthetic cells, comprising lipid vesicles that are capable of imitating the structure and function of living cells, facilitates their application as drug delivery devices. Now,...
nature.com
Simultaneous in vitro expression of minimal 21 transfer RNAs by tRNA array method by Miyachi, R., Masuda, K., Shimizu, Y., Ichihashi, N. www.nature.com/articles/s41...
Simultaneous in vitro expression of minimal 21 transfer RNAs by tRNA array method - Nature Communications
tRNAs are essential for translating genetic information into proteins. Here, the authors develop a method to synthesize all 21 essential tRNAs from a single DNA in vitro, enabling protein production a...
nature.com
NextGen Voices: Rules all PIs should follow | Science www.science.org/doi/10.1126/...
Rules all PIs should follow
science.org
Inkscape plugin to rescale figures without distorting the text, and other useful features! github.com/burghoff/Sci...