lone flowering branch.. somatic mutation, or "guerilla grafting"? Living in the same city as @charlesmelnyk.bsky.social , one can't assume natural causes...

5 weeks today. after a second inquiry the chief editor identified a "technical glitch". Without the inquiry I guess we could have been "under evaluation" for years.

Derek Severi Lundberg@derekseveri.bsky.social · 3mo ago

> 1 month initial decision on whether to send for review or desk reject is killing us. Never waited this long pre-review before...

> 1 month initial decision on whether to send for review or desk reject is killing us. Never waited this long pre-review before...

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.

Derek Severi Lundberg@derekseveri.bsky.social · 4mo ago

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.

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 🧵1/8

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! ✨

Derek Severi Lundberg@derekseveri.bsky.social · 4mo ago

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).

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).

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.

James Bonfield@jbonfield.bsky.social · 11mo ago

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned

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!

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.

The “problem” with vaccines? They so effective at preventing deaths that they create generations of people that question whether disease was a problem in the first place because they have never experienced the horrors of a world without vaccines.

this is so strange!!!!!!!

Nature@nature.com · 11mo ago

A common type of ant in Europe breaks a fundamental rule in biology: its queens can produce male offspring that are a whole different species go.nature.com/4mOb5T9

@nature.com I love this article - but WHY are the only share options to X and Facebook when the whole point of the article is that science-based posts get more shares here? www.nature.com/articles/d41...

Research posts on Bluesky are more original — and get better engagement

Bluesky posts about science garner more likes and reposts than similar ones on X.

nature.com

reviewing for a major international journal and 1 in 6 refs are papers written in Chinese. Titles, journal names, and abstracts are English, so you don't realize it from the ref. list.("Journal of Plant Nutrition and Fertilizers".) I can't judge these.. Journal updating policy on ref language.

SynCom of maize root bacteria: in team work, they detox differently. Interacting they redirect the metabolisation to an alternative degradation product. Credits: @lisathoenen.bsky.social, Dr. Christine Pestalozzi & teams @unibas.ch and @unibe.ch. journals.asm.org/doi/10.1128/...

Synthetic communities of maize root bacteria interact and redirect benzoxazinoid metabolization | mSphere

We investigated how maize root bacteria—alone or in community—tolerate and metabolize antimicrobial compounds of their host plant. We found that the capacity to metabolize such a compound impacts bact...

journals.asm.org

this seems like a very good idea actually

1/2 What's best: a field-first or lab-first approach? No easy answers but differences between lab and field should not be seen as failure but motivate further inquiry and allow complementary discovery. Read our thoughts on this here: www.sciencedirect.com/science/arti...

Lab to field: Challenges and opportunities for plant biology

Plant-microbe research offers many choices of model and strain and whether a field-first or lab-first approach is best. However, differences between l…

sciencedirect.com

www.sciencedirect.com/science/arti... How much environmental chaos to embrace in plant-microbe research, and to what end? A commentary on setting (with all choices OK as long as all options considered) w/ bergelsonlab.org, @fabriceroux7.bsky.social, @plantevolution.bsky.social, tkarasovlab.org

This extension turns off google AI on the chrome browser, for any others who don't want to read the often-wrong AI overview! chromewebstore.google.com/detail/bye-b...

Bye Bye, Google AI: Turn off Google AI Overviews, Discussions and Ads - Chrome Web Store

Filter Google search results to hide AI overviews, ads, discussions or videos. You choose.

chromewebstore.google.com

Know an Evolutionary Genomicist looking for a faculty position? Join us in EEB @utknoxville.bsky.social Position is open for studying any organism, but personally I have some botany bias. 🌱 Apply before Sept 19 for full consideration. apply.interfolio.com/170735 Please share widely. Thanks!

1/3 New preprint led by Shanshan Wang, in collaboration with the Timmermans lab. Several groups have presented sc/snRNA-seq analyses of Arabidopsis leaves after bacterial infection before. Is there anything left to discover? Turns out: Yes. #plantscience www.biorxiv.org/content/10.1...

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements. Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal. journals.asm.org/doi/10.1128/... 🧵

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems

In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

journals.asm.org

Come join EEB at the University of Tennessee at Knoxville. Evolutionary Genomics, Assistant Professor, Ecology & Evolutionary Biology, Fall 2026 apply.interfolio.com/170735 functional and evolutionary genomics in any system 🌱, 🦠, or 🦌 (including 👫)