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Will Shaw @willshaw.bsky.social · 11/06/2026

The paper has many more insights that I hope will help make plant transformation easier and more predictable. biorxiv.org/content/10.6... And we’ll make the plasmids available through Addgene as ASAP! Huge thanks to everyone involved in @mokhalil.bsky.social and Mary Gehring labs!! 16/16

biorxiv.org

Rational design of T-DNA vectors enables predictable, single-copy integration in Arabidopsis thaliana

Agrobacterium-mediated transformation is the dominant method for plant transgenesis, yet it frequently produces multi-copy, structurally complex T-DNA insertions associated with transgene silencing, u...

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Will Shaw @willshaw.bsky.social · 11/06/2026

Beyond Arabidopsis, we believe this work establishes an important, outcome-focused framework for the rational, host-optimised design of next-generation T-DNA vectors, providing a foundation for more predictable and efficient plant transformation across diverse species. 15/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

By considering transformation outcomes holistically, and balancing the key criteria for successful transgenesis, we believe the T1 vectors will help reduce a major bottleneck in Arabidopsis research. 14/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

What to expect with the T1 vectors: A single 12 cm selection plate with 5,000 seeds yields ~25 transformants. Using low-effort genotyping, we mapped around one-third as single-copy insertions free from vector backbone sequence. 13/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

We combined these advanced to form the T1 vector series, an Arabidopsis-optimised T-DNA vector system. The T1 vectors enable clean, single-copy, and readily mappable transgene integration with predictable expression in the first generation after transformation. 12/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

We didn’t stop there! We also developed a simple genomic mapping method using inverse PCR, NsiI restriction sites, and iPCR barcodes next to each T-DNA border. Using this we are able to easily map clean, single-copy T-DNA insertions in Arabidopsis. 11/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

The Arabidopsis EF1A3 promoter worked well for selection marker expression while avoiding unwanted enhancer activity. This supports more predictable cell-type-specific and conditional transgene expression. 10/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

We also tackled a common issue with T-DNA vectors: the 35S promoter often used for selection markers has strong enhancer activity that can drive ectopic expression of adjacent transgenes. To avoid this, we screened Arabidopsis promoters for better alternatives. 9/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

As shown previously, this transformation boost also works in Arabidopsis. However, it also caused a large increase in T-DNA copy number. Here, more plants are not necessarily better, because more screening is needed to find stable, single-copy transgenic lines. 8/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

We also tested the effects of increasing T-DNA vector copy number in Agrobacterium, inspired by the excellent work of Szarzanowicz et al. Using a high-copy pVS1 replicon mutation, we confirmed improved transient transformation in Nicotiana. 7/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

We designed three T-DNA vectors with low, medium, and high transformation efficiency. The medium-efficiency design, RB-Mid, provided the best balance: good transformation efficiency, lower copy number, and reduced vector backbone transfer. 6/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

Using this reporter, we screened T-DNA border variants in a conventional vector similar to pCAMBIA. Altering the virulence-enhancing overdrive sequence revealed major differences in transformation efficiency and the fraction of plants expressing RUBY. 5/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

We developed a visual reporter for screening of predominantly single-copy insertions, based on RUBY transgene silencing seen in plants with more than ~1 T-DNA. Combined with simple genotyping, this allowed us to assess transformation outcomes beyond efficiency at scale. 4/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

Researchers often focus on improving transformation efficiency, but other outcomes are equally if not more important. Transgene copy number and expression stability all determine whether a transformant is useful. Screening these properties is laborious and time-consuming. 3/16

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Will Shaw @willshaw.bsky.social · 11/06/2026

In this paper, we set out to address one of the major bottlenecks in plant science - challenges associated with transformation. T-DNA integration is often multi-copy and structurally complex. This leads to a lot of variability, and often transgene silencing. 2/16

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Reposted by Will Shaw

Tom Ellis @proftomellis.bsky.social · 11/08/2025

New paper from our lab on synthetic genome work in yeast is out - Iterative SCRaMbLE for Engineering Synthetic Genome Modules and Chromosomes. Exciting project led by Jane (Xinyu) Lu in our group, now online. t.co/0LuGwgAWlA

t.co

https://www.nature.com/articles/s41467-025-62356-y

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Reposted by Will Shaw

Tom Ellis @proftomellis.bsky.social · 11/07/2025

Online now @ Cell is the yeast multicellular engineering paper from Fankang Meng - the fruits of his productive PhD in our group. He developed modular synthetic biology tools to bring multicellular behaviours to yeast - specific adhesion, juxtacrine signalling and more. www.cell.com/cell/fulltex...

cell.com

Engineering yeast multicellular behaviors via synthetic adhesion and contact signaling

By designing synthetic toolkits for contact-based signaling (MARS) and cell-cell adhesion (SATURN), we program yeast to form multicellular structures and perform complex tasks, like building logic cir...

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Reposted by Will Shaw

Sarah Guiziou @sarah-guiziou.bsky.social · 15/04/2025

🚨 PhD project alert: Engineering a soil bacteria to sense and record soil health. 🦠 🪴 🥼 🧑‍💻 🌍 Fully funded PhD studenship in my group, open for international students. @earlhaminst.bsky.social Please share widely! Deadline: 14th of May www.earlham.ac.uk/studentship/...

earlham.ac.uk

Sentinel bacteria: engineering a soil bacteria to sense and record soil health

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Will Shaw @willshaw.bsky.social · 18/03/2025

Thrilled to share that I will be moving back to the UK later in the year to start my next chapter as a Career Development Fellow at the Earlham Institute! 🌱🧬

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Reposted by Will Shaw

Eric Topol @erictopol.bsky.social · 12/01/2025

Publications in the past week built substantially on our knowledge of the brain's waste disposal system—glymphatics—and the implications on sleep and brain aging. Featuring exceptional work by Nedergaard Lab and @jonykipnis.bsky.social erictopol.substack.com/p/our-sleep-... open-access

erictopol.substack.com

Our Sleep, Brain Aging, and Waste Clearance

How sleep prevents "dirty" brains that age faster

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Reposted by Will Shaw

Satyaki PRV @satyakirv.bsky.social · 21/12/2024

Do you want an EMS-like drug that you can easily use in your lab or your garden shed to generate structural variation in your favorite plant? We show here that the topo2 inhibitor & common chemotherapy drug etoposide works really well to generate structural variation .

biorxiv.org

A simple method to efficiently generate structural variation in plants

Phenotypic variation is essential for the selection of new traits of interest. Structural variants, consisting of deletions, duplications, inversions, and translocations, have greater potential for ph...

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Reposted by Will Shaw

Mary Williams @PlantTeaching @plantteaching.bsky.social · 11/12/2024

Judge blocks rule that eased U.S. reviews of biotech crops Some plant researchers fear the setback could last years and will stifle innovation. (From Science) #PlantScience www.science.org/content/arti...

science.org

Judge blocks rule that eased U.S. reviews of biotech crops

Some plant researchers fear the setback could last years and will stifle innovation

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Reposted by Will Shaw

Tom Ellis @proftomellis.bsky.social · 08/12/2024

Latest preprint from Jane (Xinyu Lu) in our group explores what happens when we build a synthetic genome cluster in yeast for Histidine biosynthesis and SCRaMbLE it to see whether selected-for gene rearrangements can guide better design.

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