Gozde Demirer

Gozde Demirer

@prof-gozde.bsky.social

Assistant Prof @Caltech | Nanotechnology, synthetic biology, plant genetic engineering, plant-microbe interactions 🌱 🍅 🧬🧪 | she/her

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Gozde Demirer
@prof-gozde.bsky.social

We inserted a 5kb, 3-enzyme RUBY pathway: visible red pigment at ~1 copy/genome. Since efficiency didn't drop from 2 to 5kb, there's likely room for larger DNA. It worked across 3 species: Arabidopsis, N. benthamiana, and tomato. Bonus: inserted payloads stayed unmethylated and expression persisted.

Gozde Demirer
@prof-gozde.bsky.social

The R2 system is designed to slot into your existing pipeline: swap in the R2 protein + payload plasmid in place of your Cas9/donor and give it a try for targeted, multi-kb insertion at the rDNA safe harbor in plants. 🌱 If you are interested in testing the system, feel free to reach out.📩

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Gozde Demirer
@prof-gozde.bsky.social

Getting it to work in plants took geminiviral replicons and introns to boost R2 levels, a minimal-homology RNA payload, optimized 5′ and 3′ UTRs, and an HDV ribozyme for a clean 3′ end. The payoff: precise mCherry insertion went from ~0.5% of cells in the first screen to ~24% of transformed cells.

Gozde Demirer
@prof-gozde.bsky.social

1 integrated copy per genome on average, with> 90% being full-length insertions. At the same rDNA site, R2 is 30× more efficient than Cas9 HDR. >96% of recovered insertions mapped to 25S rDNA sites. 5′ junctions were seamless “anneal-type” (97.7%), confirmed by Nanopore long-read mapping.

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Gozde Demirer
@prof-gozde.bsky.social

25S rDNA is a natural genomic "safe harbor": many copies, highly transcribed, no essential genes nearby. As inserted genes sit away from regulatory elements, they get predictable, high expression. 👀Spoiler: we're making the R2 insertion site reprogrammable to target any locus. Stay tuned! 🔮

Gozde Demirer
@prof-gozde.bsky.social

The mechanism is double-strand break-free. The R2 ribonucleoprotein nicks one strand, primes off it, and reverse-transcribes the RNA payload directly into the genome, sidestepping the double-strand breaks (and the deletions/rearrangements they can cause) that Cas9-based insertion depends on.

Gozde Demirer
@prof-gozde.bsky.social

The problem: most plant engineering relies on Agrobacterium, which drops DNA in at random. That means variable expression, silencing, and generations of screening to find a good line. Targeted methods like Cas9 HDR and prime editing help but are limited in efficiency or payload size.🧬

Gozde Demirer
@prof-gozde.bsky.social

Our approach: the R2 protein from the zebra finch (Taeniopygia guttata) is a natural retroelement that inserts itself into the 28S/25S ribosomal DNA using its own RNA as the template, via target-primed reverse transcription. We adapted it to do the same in plants but to insert our cargoes.

Gozde Demirer reposted

Evan Groover
@evangroover.bsky.social

Excited to see the major chapter of my PhD in print! We present a massively-parallel approach for screening CRISPR edits in plants to speed up agricultural test cycles + benchmark genomic LMs. Thanks to my fantastic co-authors and advisors. Link below!

Savage Lab@savagecatsonly.bsky.social

Can CRISPR edits enable precise tuning of plant gene expression? We think: yes. In our newest manuscript, we measured the effects of >30,000 CRISPR-like promoter mutations in sorghum protoplasts.

Gozde Demirer
@prof-gozde.bsky.social

We're hiring a postdoctoral researcher in plant genome engineering with expertise in synthetic biology, gene editing, and omics, with an interest in developing next-generation technologies for plants.🪴🧬 Available immediately. If interested, send your CV! Feel free to share with your networks.

demirerlab.comHome | Demirer Lab

Gozde Demirer reposted

Tatsuya Nobori
@tatsuyanobori.bsky.social

ECRs in plant–microbe interactions: Join us in Norwich for an intensive, interactive 1.5-week Summer Conference at TSL (20–31 July). Lots of opportunities for networking and deep discussions. (We also plan to offer hands-on practical sessions using our technologies 🔬🧬)

The Sainsbury Laboratory@thesainsburylab.bsky.social

Join us in Norwich this July for the TSL Summer Conference in Plant-Microbe Interactions! ☀️🌱🧬 Discuss the latest approaches & discoveries in plant health with international keynote and local speakers. APPLY by 30 March '26 ⬇️ Click link for more info www.tsl.ac.uk/tsl-summer-c...

tsl.ac.ukTSL Summer Conference in Plant-Microbe Interactions, 20th – 31st July…Inviting Early Career Researchers to join international experts in discussing the latest approaches and discoveries in Plant-Microbe Interactions …

Gozde Demirer reposted

Brady Lab
@bradylabs.bsky.social

Interested in learning about the latest and greatest research in how plants respond to excess salt, too little or too much water? Come to the GRC in Salt and Water Stress in Switzerland. Lots of opportunities for all career levels. www.grc.org/salt-and-wat.... Please repost!

grc.org2026 Salt and Water Stress in Plants Conference GRCThe 2026 Gordon Research Conference on Salt and Water Stress in Plants will be held in Les Diablerets, Vaud (fr) Switzerland. Apply today to reserve your spot.

Gozde Demirer reposted

Nature Reviews Molecular Cell Biology
@natrevmcb.nature.com

Our cover indicates that while we celebrate the past we're looking ahead to the future - with the help of a Viewpoint! 13 researchers offer a glimpse of what their research field might look like in 2050 🔮 👉 go.nature.com/4neNdYU

go.nature.comVisions of the future of molecular cell biology - Nature Reviews Molecular Cell BiologyTo celebrate the journal’s 25th anniversary, we asked 13 researchers to offer a glimpse of what their research field might look like in 2050. They consider how technological breakthroughs — for example, artificial intelligence-powered virtual cells — could transform our understanding of how molecules, organelles and cells behave in different contexts, revolutionize therapies and enable the design of resilient crops.
Nature Reviews Molecular Cell Biology@natrevmcb.nature.com

Hello Bluesky! We're celebrating ✨25th years of NRMCB✨ with our October Issue - out now! It offers a glimpse into our journal's scope - cell death, enhancers, cell cycle, migration, transposable elements, membrane contact sites & AI! go.nature.com/4nJUz6w

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Gozde Demirer
@prof-gozde.bsky.social

3️⃣ Vacuum and sonication treatment (VAST) enables efficient transient gene expression in various monocot and eudicot plant seedlings: A transient expression method that dramatically improves gene expression efficiency and uniformity across several monocot and eudicot seedlings. tinyurl.com/38p2ud6w

doi.orgVacuum and sonication treatment enables efficient transient gene expression in various monocot and eudicot plant seedlingsTransient gene expression in intact plants is essential for rapidly addressing biological questions, where the current toolkit can be improved for higher efficiencies and broader plant species range. ...
Gozde Demirer
@prof-gozde.bsky.social

4️⃣ A 3D-Printed Capillary Tube Holder for High-Throughput Chemotaxis Assays: We developed a 3D-printed capillary tube holder that enables 384 simultaneous chemotaxis assays, making it possible to rapidly profile bacterial responses to root exudates and other chemoeffectors. tinyurl.com/3nw9haes

tinyurl.comA 3D-Printed Capillary Tube Holder for High-Throughput Chemotaxis AssaysBacterial chemotaxis is an important behavior to study to understand spatial segregation of species in mixed communities and the assembly of host microbiomes. This is particularly relevant in the rhiz...
Gozde Demirer
@prof-gozde.bsky.social

1️⃣ Extracellular contractile injection systems for high efficiency protein delivery to plants: We adapted bacterial PVC nanomachines to deliver proteins (Cre recombinase) to plants with 40% efficiency. DNA-free genome engineering with potential for cell-type specific targeting. tinyurl.com/mrx4d878

tinyurl.comExtracellular contractile injection systems for high efficiency protein delivery to plantsEfficient delivery of functional proteins into plant cells remains a major barrier in plant biotechnology. Extracellular contractile injection systems (eCISs) are phage tail-like nanomachines evolved ...
Gozde Demirer
@prof-gozde.bsky.social

2️⃣ Optimized R2 Retroelement Complexes Enable Precise and Efficient DNA Insertion into Plant Genomes: We engineered R2 protein to insert multi-kb DNA precisely into a safe harbor site in plants achieving 24% efficiency and 1 copy insertion per genome. Compact, precise, powerful! tinyurl.com/5n73za6h

doi.orgOptimized R2 Retroelement Complexes Enable Precise and Efficient DNA Insertion into Plant GenomesPrecise, targeted insertion of multi-kilobase DNA sequences is critical for studying gene function, ensuring robust transgene expression, and stacking traits in crops, but remains difficult to achieve...

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