iiinova — where your digital self keeps evolving

Derek Severi Lundberg @derekseveri.bsky.social · 17/05/2026

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

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Derek Severi Lundberg @derekseveri.bsky.social · 13/04/2026

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

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Derek Severi Lundberg @derekseveri.bsky.social · 07/04/2026

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

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Derek Severi Lundberg @derekseveri.bsky.social · 07/04/2026

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.

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Derek Severi Lundberg @derekseveri.bsky.social · 07/04/2026

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.

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Derek Severi Lundberg @derekseveri.bsky.social · 07/04/2026

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.

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Derek Severi Lundberg @derekseveri.bsky.social · 07/04/2026

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.

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Derek Severi Lundberg @derekseveri.bsky.social · 07/04/2026

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

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Derek Severi Lundberg @derekseveri.bsky.social · 07/04/2026

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.

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Derek Severi Lundberg @derekseveri.bsky.social · 07/04/2026

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!

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Derek Severi Lundberg @derekseveri.bsky.social · 07/04/2026

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...

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Derek Severi Lundberg @derekseveri.bsky.social · 07/04/2026

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).

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Derek Severi Lundberg @derekseveri.bsky.social · 05/12/2023

Uppsala, a pleasant student city, is only about 45 min from the capital Stockholm. Summers are amazing with nearly endless light and comfortable temperatures. Winters are cold and dark but are tolerable and some days are very beautiful!

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Derek Severi Lundberg @derekseveri.bsky.social · 05/12/2023

PhD students at @_SLU receive a salary according to this scale, which is definitely a livable wage. internt.slu.se/en/my-employ...

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Derek Severi Lundberg @derekseveri.bsky.social · 05/12/2023

The project will then generate plasmid-cured and partially-cured versions of several strains and “implant” genetic barcodes into them so we can tell them apart in mixed populations. Do plasmids offer any advantage, and why?

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Derek Severi Lundberg @derekseveri.bsky.social · 05/12/2023

Plasmids that are important may be difficult to remove, but we will try! We will use high-throughput methods to measure the stability of each plasmid in a panel of strains and to cure plasmids from these strains.

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Derek Severi Lundberg @derekseveri.bsky.social · 05/12/2023

Using a mixture of long and short-read sequencing, we will characterize Sphingomonas chromosomes and their associated plasmids - as many as possible - from plant-associated environments. This involves field work, molecular biology, and bioinformatics.

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Derek Severi Lundberg @derekseveri.bsky.social · 05/12/2023

The PhD project aims to explain the numerous and diverse plasmids found in plant-associated Sphingomonas bacteria. These bacteria are abundant on leaves and roots of many plants worldwide and can provide benefits to plants and soil - the plasmids likely help them adapt.

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Derek Severi Lundberg @derekseveri.bsky.social · 05/12/2023

A PhD position is available in my group at @_SLU starting in 2024 thanks to a new grant from @Vetenskapsradet. The application deadline is 31 Jan. 2024. The preferred start date is late spring or summer 2024. Apply via this link: www.slu.se/en/about-slu... More details in thread 👇

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Derek Severi Lundberg @derekseveri.bsky.social · 13/11/2023

Check out this absolute monstrosity!!! On a visit to FSU Jena. @parafilmm.bsky.social

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Derek Severi Lundberg @derekseveri.bsky.social · 26/09/2023

surprising before and after (Euphorbia ingens)

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