Petr Šulc

While this work presents a first step towards 'decoding the repeatome' in human genome, it also presents a fast an accessible framework to assess stimulatory potential of transcripts coming from various experimental datasets.

Complementary to this hypothesis, it is also possible that maintaining these patterns is also beneficial for the repeat families, as we argue in the case of the highly studied family of LINE-1 repeats, where high CpG content might help prevent their deleterious effect on organism's fitness.

We argue that these repeats might have been co-opted to trigger innate immune system response upon translational dysregulation, such as in cancer cells. We checked experimentally that repeat transcripts that we marked as anomalous do bind to pattern recognition receptors of innate immune system.

It allows us to quantify how anomalous given sequence is with respect to what one would expect from a typical transcript from human genomes. The two chosen motifs, CpG content and double-stranded regions,are hallmarks of RNA viruses and our immune system recognizes them as immunostimulatory targets.

In our work, we instead focus on developing statistical mechanics-based framework to identify anomalous sequence (CpGf) and structure (long double-stranded segment) motifs in transcripts of these regions, which are known to be recognized by innate immune system receptors.

A majority of our genome does not code for proteins nor has any established regulatory function. These regions are sometimes called 'junk DNA'. Their function, or lack of, is a very active topic of research.

Repeats mimic pathogen-associated patterns across a vast evolutionary landscape An emerging hallmark of disease is transcription of pathogen-associated molecular patterns from within the genome–known as viral mimicry. We propose a statistical physics framework to measure “selecti...

🧪 In our new work (just published in Cell Genomics) with Benjamin Greenbaum , John LaCava, Daniel De Carvalho, PhD , Simona Cocco and Remi Monasson labs, we venture into the dark matter of human genome:
www.cell.com/cell-genomic...

🧵A shot thread summary below in comments:⬇️

On this first day of #DNA31, reminder for the mol pro community that I put together this feed which picks up the last 3 days of posts from our community! Enjoy the meeting! 🧬

A great effort to chart possible future paths for the molecular programming field

The predictions were verified experimentally. Our results have implications for DNA/RNA molecular computing, design of DNA computing systems that interface with RNA triggers, and as we show in our presented model, it can also have implications for predicting the kinetics in CRISPR-based systems.

It shows that just by permuting the distribution of bases in the duplex (while keeping AT / CG base pair number constant), the kinetics of the reaction can be altered by orders of magnitude, stemming from the details of differences in stability between hybrid and canonical bases in DNA/RNA systems.

It is also of importance for biological systems like CRISPR-Cas9. In this collaboration, Eryk Ratajczyk supervised by Louis, Doye and Turberfield groups from Oxford, uses our new oxDNA-oxRNA hybrid coarse-grained model to study the strand displacement RNA invades DNA duplex.

Controlling DNA–RNA strand displacement kinetics with base distribution | PNAS DNA–RNA hybrid strand displacement underpins the function of many natural and engineered systems. Understanding and controlling factors affecting D...

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Our new paper is just out in PNAS:
www.pnas.org/doi/10.1073/...

It is about nucleic acid strand displacement, which is a key reaction in molecular computation, and part of the success of the oxDNA model comes from the fact it can efficiently simulate this process.

1/4🧵

Great work by our student Navraj and Subhajit, building on top of the ground work of previous database by @floppleton.bsky.social and Michael Matthies

Just in time for #FNANO conference in Snowbird, UT, our updated and improved version of nanobase.org server is online. Just like the PDB database helped to share protein structures, we want to create a community resource for the DNA/RNA/protein nanotechnology design researchers to share their work

4/4: Our crystal example thus provides a falsifiability test for classical nucleation theory, showing need for also taking into account structural fluctuations.

Excellent work by Camilla Beneduce and Diogo Pinto from John Russo's group in Rome!

3/4 However, we find that one of the three possible crystal phases is strongly preferred, due to the crystal lattice ordering being similar to the local ordering in the liquid phase.

2/4: The assumptions of CNT rely on the free energy difference between bulk phase and the melt, and the interfacial free energy. In this work, we look at a two component system that forms a polymorph: it can nucleate into three different lattices with same interfacial and bulk free-energy.

🧪In our new paper (journals.aps.org/prl/abstract...) in collaboration with Russo, Romano, Rovigatti and Sciortino groups in Rome / Venice, we look at Classical Nucleation Theory: a popular model of nucleation process, n is a key phenomena in self-assembly, self-organization and phase transitions.

Thank you Ulrich, it was a pleasure visiting Heidelberg and meeting you. Many thanks to the amazing group of @kgoepfrich.bsky.social for hosting me!

Great collaboration with @laklab-tubs.bsky.social , simulations carried out by my student Josh Evans

If you change something in the candano file, it has to be loaded again from scratch into oxview. The scadnano tool has recently been expanded to also allow for visualization in embedded oxview window. Having an interactive cadnano-like interface inside oxView is currently on our TBD wishlist

How We Simulate DNA Origami This tutorial provides a detailed step-by-step description on how to import DNA origami designs into the oxDNA model and characterize the origami's properties (such as equilibrium shape and flexibili...

🧬 A new tutorial article from our student Sarah, walking step by step through DNA origami simulation using oxDNA model, with the help of oxview.org and oxdna.org free tools. No prior experience assumed, and also accompanied by a video: youtu.be/5-rgMekX8gE
onlinelibrary.wiley.com/doi/10.1002/...

Thank you!

Thank you!

Ceny Neuron 2024: Seznamte se s letošními laureáty | Nadace Neuron Věda je plná emocí a práce vědce představuje rébus, hru, touhu po poznání, vášeň, radost i lásku. Prozkoumejte krásu těchto emocí prostřednictvím laureátů Ceny Neuron.

I am very grateful to Neuron Foundation, considered among the most prestigious awards for Czech Scientists, for awarding me Promising Scientist award in Physics yesterday at a ceremony in Prague. Many thanks goes to my family, collaborators and students: www.nadaceneuron.cz/novinky/ceny...

Automating Blueprints for the Assembly of Colloidal Quasicrystal Clusters One of the frontiers of nanotechnology is advancing beyond the periodic self-assembly of materials. Icosahedral quasicrystals, aperiodic in all directions, represent one of the most challenging target...

🧪🧬 New article with J Russo, D. Pinto and F. Sciortino out is @acspublications.bsky.social ACS Nano: pubs.acs.org/doi/10.1021/...
We use our #SAT Assembly method to design particles that assemble into 3D quasicrystal clusters, paving a way to their experimental realization with DNA nanostructures

YouTube video by Sapienza soft matter group SATa CLAUSE: When magic snow falls, a enchanted meadow blossoms

In our Christmas tradition with John Russo's lab at Sapienza university of Rome, here is a Christmas-themed video highlighting a current research project based on our #SAT-assembly method, this time chiral crystals self-assembly (made by C. Beneduce): www.youtube.com/watch?v=0A7x...

Glad you find it useful!

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Thank you so much to whoever put this very comprehensive list of #science Bsky starter packs together. This is just amazing: docs.google.com/document/d/1...