Dvir Schirman

Dvir Schirman

@dvirschirman.bsky.social

@EMBOFellows postdoc in @johan_elf_ lab, @UU_University. Chromosome organization in bacteria. Combining microscopy and large synthetic libraries to study genotype-to-phenotype. alumnus of @TPilpel lab

427 followers566 following34 posts

Dvir Schirman reposted

José Aguilar-Rodríguez
@jaguilarrod.bsky.social

One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential. www.biorxiv.org/content/10.1...

biorxiv.orgMassively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptationThe nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...
Dvir Schirman
@dvirschirman.bsky.social

I tried the previous version on my preprint, and the feedback was pretty impressive and useful 🧐🔬

Oded Rechavi@odedrechavi.bsky.social

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

Dvir Schirman
@dvirschirman.bsky.social

This is how you revolutionize science 🕺 #TCTeAC

Elise Cutts@elisecutts.bsky.social

@odedrechavi.bsky.social says he wants to change science for the better. How? I’m still not quite sure. But 1.5 days into #TCTeAC, the plan seems to involve, among other things, walk-up songs, jumping, dancing, and a hefty serving of joy.

Dvir Schirman reposted

Itai Yanai
@itaiyanai.bsky.social

Woodstock Night Science is trending more than Trump AND Nature! #TCTEAC

Trending Tags (Beta)@trendtags.bsky.social

🚀 Trending Now on BlueSky (Last 15 minutes): #Photography #art #gay #nsfw #ss954 #AIart #FotoVorschlag #gamedev #Nude #TCTeAC #AIイラスト #Trump #nature #indiedev #ai Trends refresh every 15 minutes.

Dvir Schirman reposted

Itai Yanai
@itaiyanai.bsky.social

There's a lot of joy in doing science and Woodstock Night Science (June 10-13 in Prague) will be a celebration of the science that we know and love. Many exciting talks & innovations that will push the boundaries of what a scientific conference can really do. woodstock.img.cas.cz Only 40 spots left!

Dvir Schirman reposted

Séamus Holden 🔬🦠🧫
@seamusholden.bsky.social

Fellow bacterial cell biologists, message me if you use @thermofishersci.bsky.social Gene Frames for microscopy! Thermo are planning to discontinue these in September but have indicated they will look into this further. If I make list of labs using them Thermo might not kill the product Please RT🔬🦠

jove.comLive Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae using Automated Time-lapse Microscopy42.1K Views. University of Groningen. This protocol provides a step-by-step procedure to monitor single cell behavior of different bacteria in time using automated fluorescence time-lapse microscopy....

Dvir Schirman reposted

Will Ratcliff
@wcratcliff.bsky.social

1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social. www.nature.com/articles/s41...

nature.comGenome duplication in a long-term multicellularity evolution experiment - NatureIn the Multicellularity Long Term Evolution Experiment, diploid yeast evolve to be tetraploid under selection for larger multicellular size, revealing how whole-genome duplication can arise due to its...

Dvir Schirman reposted

Sri Kosuri
@srikosuri.bsky.social

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

Dvir Schirman reposted

Di Jiang
@dijiang319.bsky.social

This week @science.org Sarfatis, Moffitt et al. from @bostonchildrens.bsky.social @harvardmed.bsky.social @broadinstitute.org Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/... #microsky #microbial #microbiology #genomics #transcriptomic 🦠🧫

science.orgHighly multiplexed spatial transcriptomics in bacteriaSingle-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...

Dvir Schirman reposted

Grainger Lab
@graingerlab.bsky.social

If you're interested in chromosome biology (DNA folding, gene regulation, replication, polymer modelling and more) we're organising the below this autumn. It'd be great to see you there. Please share if you can. :-)

Dvir Schirman reposted

Arne Elofsson
@handle.invalid

We are excited to announce that the call for the new SciLifeLab PULSE postdoctoral program is now open! This unique program invites talented researchers to propose individually designed projects see : www.scilifelab.se/research/pul.... The deadline for applications is March 31, 2025.

scilifelab.sePULSESciLifeLab PULSE: Program for Future Leaders in Life Science SciLifeLab PULSE is a comprehensive postdoctoral program, that will train 48 future leaders in life sciences. PULSE focuses on innovative, ...

Dvir Schirman reposted

Arnaud Krebs
@arnaudkr.bsky.social

New conference that will explore gene regulation mechanisms at molecular resolution. We bring bring together a fine crowd that uses microscopy, genomics and theory to chart the future of the booming fields of #singlemoleculegenomics and #singlemoleculemicroscopy. Join us July 15-18th 2025 at EMBL

Dvir Schirman
@dvirschirman.bsky.social

We are constructing a new and much bigger strain library with two labels in each strain. This will allow us to measure actual pairwise distances and get a more accurate view of chromosome dynamics. (14/14)

Dvir Schirman
@dvirschirman.bsky.social

Second, we wish to integrate all this data into one physical simulation of a replicating chromosome. So we simulate the chromosome as beads-on-a-string polymer model which replicates as the cell grows. We then restrain using our imaging data (11/14)

Dvir Schirman
@dvirschirman.bsky.social

From this model, we extract a pairwise distance map at each cell size. This dynamic distance map reproduces known macrodomains of the E. coli chromosome and also shows that the left-arm and right-arm macrodomains form dynamically at a certain stage of the cell cycle. (12/14)

Dvir Schirman
@dvirschirman.bsky.social

Using this system we get the spatial distribution of 68 different sites as a function of time. First, we get a dynamic global image of chromosome dynamics both at the cell’s long axis and radial axis. (10/14)

Dvir Schirman
@dvirschirman.bsky.social

So, to measure all of them in a single experiment our lab developed a system for running microscopy experiments on a strain library in a single experiment. We do that by loading the library onto a microfluidic device called a “mother machine”. (7/14)

Dvir Schirman
@dvirschirman.bsky.social

Where bacterial cells are growing in narrow growth channels, and each channel contains only the daughter cells of a single mother cell. Meaning, all cells in a growth channel have the same genotype. (8/14)

Dvir Schirman
@dvirschirman.bsky.social

To track the chromosome in live cells we can insert a fluorescent label into the chromosome which we can track in 3D under the microscope. But to track the whole chromosome dynamics we would need to label many sites along the chromosome. (5/14)

Dvir Schirman
@dvirschirman.bsky.social

We achieve that by cloning a strain library of 68 strains each of them with a label at a different site. But no one wants to conduct 68 different experiments (each of them takes a whole day)… (6/14)

Dvir Schirman
@dvirschirman.bsky.social

In bacteria, to make sure the genome propagates to the next generations, the chromosome must be replicated and the two new copies must segregate to two halves of the cell before division (which can happen within 20 minutes). (3/14)

Dvir Schirman
@dvirschirman.bsky.social

We wish to find the relationships between chromosome organization and biological function in these bacteria. Since the chromosome organization is constantly changing, to do that, we must track how it develops over time. (4/14)

Dvir Schirman
@dvirschirman.bsky.social

We follow chromosome dynamics in E. coli using live cell imaging, and build a dynamic simulation of a replicating chromosome which helps us to get a glimpse into the dynamic nature of chromosome architecture. (2/14)

Dvir Schirman reposted

Rike Stelkens
@stelkens.bsky.social

Thinking about moving (now more than ever?): Here’s a great postdoc funding opportunity if you’d like to join the academic community in Sweden. Happy to act as your host lab, if you’re interested in evolution and genomics in yeast www.scilifelab.se/research/pul...

scilifelab.seAbout the PULSE programAbout the PULSE program PULSE builds upon and further leverages the unique SciLifeLab community, fostering excellence in biology-, technology-, and data-driven research. The program emphasises key res...

Dvir Schirman reposted

Will Ratcliff
@wcratcliff.bsky.social

New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30

You are up to date.