Visualizing contigs in draft assemblies - I coin this a "mallard plot"

written by "Bill Nye the Science Guy", for those of us from those generations www.ms.now/opinion/arte...

the sensitivity of "tagIMseq" will be broadly useful for CRISPR-associated transposon work. Ruling out off-target insertions in resuspended colonies with minimal effort and cost investment is critical because targeting isn't always perfect.

A new paper from @dorruss12.bsky.social and Jeff Dangl on two flagellins in plant-associated Sphingomonas used for motility or host colonization.

www.biorxiv.org/content/10.6...

What if plant immunity doesn’t stop bacteria from arriving - but from staying?
Excited to share our new Dangl Lab paper (doi.org/10.1073/pnas.2535583123), asking a fundamental co-evolutionary question: which flagellar function is targeted by plant immunity?
#Coevolution #Plant-Microbiome #PNAS
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A quick thread summarizing our new bioRxiv preprint on using CASTs for DNA barcoding to tell "look-alike" bacteria apart (Sphingomonas edition)!! Enjoy the read! ✨

Thanks especially to @kawresearch.bsky.social and all co-authors. This is so far my only research publication where I am the most senior of all authors... not such a flex maybe, since it kind of also just means I'm getting older, but a major milestone for me nonetheless!

Future directions… bigger and better syncoms to study bacterial natural variation and molecular mechanisms beyond model strains, at the genus/population level.

a man in a suit and tie is running in front of a blue background that says too long did n't read ALT: a man in a suit and tie is running in front of a blue background that says too long did n't read

Three major insights:
1) CAST-based barcoding and gene disruption is straightforward, but requires screening and groundwork for quantitative use.
2) The Tn7 insertion locus, when it exists, needs critical evaluation.
3) “tagIMseq” is a versatile, rapid, and easy transposon mapping method

We confirmed rpoZ 3’ UTR insertion had no fitness penalty on plants, and targeted rpoZ in an uncharacterized bacterial pool with a triple tandem guide. After screening colonies (tagIMseq), we subcultured and sequenced genomes from positives, adding perfectly-tagged novel strains to our collection.

We targeted the rpoZ 3’ UTR in a Sphingomonad. We developed a rapid transposon mapping method, “tagIMseq”, leveraging tagmentation and @plasmidsaurus.bsky.social. It even works without a DNA prep on a resuspended colony! Most colonies were good, but many were not, so screening was important.

CASTs can target almost anywhere, so we searched for improved conserved “safe” sites as Tn7 alternatives. Regions between convergently terminating genes downstream of rpoZ in Sphingomonas, or pyrD in Pseudomonas, seemed much better. Both had conserved regions for efficient guides.

But we noticed something uncomfortable about the widely-used “safe” Tn7 site in Sphingomonas. In the majority of cases, insertions there would probably disrupt the next gene, because it was either too close or co-directional. We noticed the same situation in Pseudomonas.

The system let us detect and quantify our tagged strains simultaneously with the uncharacterized bacterial background in a complex host-associated environment.

Amplicon seq quantitatively captured the barcodes (colors) and the native 16S (grey) of the strains. Fascinating that each barcode had a different amplification efficiency (a phenomenon previously reported), requiring empirically-determined correction factors.

We designed our RNA guides within conserved areas so each could be recycled for use on many different strains. We managed insertions in diverse strains, and we could even hit the right target with 5 mismatches in the guide!

In new work led by @ezgiboz.bsky.social, we adapted a single-vector CAST, and made a tag featuring a random DNA barcode between unique and 16S priming sites. We planned “neutral” tags at the Tn7 site downstream of glmS, and “disruptive” tags in a carotenoid gene. www.biorxiv.org/content/10.6...

When organisms look similar, you can use a tag to tell them apart. We wanted to tag our collection of diverse Sphingomonas bacteria with DNA barcodes to distinguish them. We planned to use Tn7, until we saw new reports about CRISPR-associated transposons (CASTs).

yeah two manys softwearses...

There are too many independent softwares called "targetfinder"...

Any academic folks on H1B visas (even with stamps in passports) please get legal advice from your University attorneys before leaving the US.

There’s a leak - and a conceptual artist - at the Max Planck 👌

Bioinformaticians / computational biologists take note - know where you should take your OS tool chain from and do not introduce backdoors.

there only are data for the actual numbers (linked in the first post). reasons why is only thoughtful speculation

Increased ERC funding for top global researchers moving to Europe now confirmed The European Research Council (ERC) decision to increase its support for leading researchers moving to Europe has today been formally adopted. On top of its standard grants, the ERC offers additional ...

Not sure about a push to lead, but everyone sees opportunity to get the top talent no longer interested in the USA. ERC grants, for example, added a bonus for those joining Europe from outside. 2M bonus on a 1.5M starter grant, for example. erc.europa.eu/news-events/...

yeah, they go where the money is..

record 17,058 Marie Curie proposals in 2025 vs. 10,360 in 2024!!! the reason is pretty obvious, but wow that is a huge jump marie-sklodowska-curie-actions.ec.europa.eu/news/msca-po...

Job Alert! The University of Tübingen is hiring a FULL PROFESSOR (W3) in FUNCTIONAL ECOLOGY! Come and join our institute, and maybe our new excellence clusters @terra-cluster.org and @greenrobust.de. @gfoesoc.bsky.social @britishecologicalsociety.org @ecologicalsociety.bsky.social Please repost!

nicely done Sebastian!

In my experience, conference speakers are generally people who know stuff worth hearing, and not people who are great at public speaking. Listening to the content while ignoring whatever annoys you about the delivery is a good skill to cultivate, and you owe it to your intellect.