Simon Kozlov MIT generative AI for desiccation resistant proteins. Generative AI rarely produces proteins better than nature, can this be improved by giving it feedback rapidly increasing the DBTL cycle in #synbio

Synthetic tunable promoters for optimizing defense by Anuradha Dhingra - cool idea incorporating information about time of day to help modulate defenses #plantsynbio

Next Matt Szarzanowicz Shih Lab on making agrobacterium transformation better, noting recent pub on improved binary vectors: www.nature.com/articles/s41... #plantsynbio

Final morning pitches from ECRs! Dan Hong Gunn lab from Cornell on using #synbio to improve rubisco. Looking for a 'unicorn' that is both fast and specific, highlights hornwort enzyme www.nature.com/articles/s41... challenge of chaperones remain

Use of plant metabolite biosensors to modulate bacterial gene expression - making bacteria nitrogen sensitive pubs.acs.org/doi/10.1021/...
#plantsynbio. and really importantly - now working on syncomms to address rhizosphere interactions with engineered bacteria

@jeanmichelane.bsky.social on the near term prospects of improving biological nitrogen fixation for crops by engineering diazotrophs to become ammonium excretory by modulating gene expression of nitrogenase and metabolism #plantsynbio
linkinghub.elsevier.com/retrieve/pii...

Recurring theme - field trails are essential for crop engineering because of limited correlation with lab. Also liked this analogy - people don't necessarily need to endlessly spin the hamster wheel of DBTL cycle.

@johnathan-n.bsky.social on engineering omega-3-fatty acids in plants.
- Engineering plants takes decades
- ~100 person years to prototype
- screening 100s of events.
- Camelina - only crop can transform by floral dip
- very likely most T-DNAs are multimetized
#PlantSynbio

Jessica Rutkoski UIUC provided great overview of a public breeding program. Gene edited wheat is a no go, also challenging as most trait quantitative, but if pushed she highlights some challenges #synbio could help - verbalization, lodging, creation of double haploids.

Veena Veena from Danforth explaining transgenic pipelines. "Very exciting times to be [in this field]

1. Try different promoters with your CRISPR/Cas9.
2. Less than 10% agro transformations contain intact T-DNA.
3. Industry need many, many events to create a suitable product.

Great start to the #PlantSynbio workshop in Gainesville today. Tracey Chapman Pairwise, talking about limited success of prime editing in plants and introducing REDRAW as an alternative for template editing www.biorxiv.org/content/10.1...

Through all the noise we did identify some signs of genetic differences, but the effects were small. Even with all the caveats of crop models, plugging in this variation suggested at most a 1.6% daily increase in CO2 assimilation. Which is less than before but could be cumulative 9/n

I work with some very talented people and they were able to help us try to parse out what was going on using a battery of statistics and models. Probably most consistent effect was daily VPD (evaporative demand) 7/n

So we sampled at 7 developmental stages over two years - in a nutshell things were fairly stable (at a field level) with many genotypes responding similarly to environment. Time to senescence has big impact at end of season 6/n

spoiler alert - it's bad... very bad.. why should you care? there is ample evidence that without proper QC checks or experimental controls you can get incorrect results e.g. doi.org/10.1007/s105...

They went on to overexpress this gene in poplar and arabidopsis and saw increased growth and improved photosynthesis. The later was eventually shown to be caused by increased accumulation of rubisco. We have no idea how this is working - but has been fascinating to explore.

We really started taking notice when there appeared to be a difference in efficiency of photosynthesis between genotypes with high and low expression of an orphan gene dubbed bstr by my colleagues...

We used chlorophyll fluorescence analysis which is a sensitive measure of photosynthesis and can be impacted by many processes. In the list of hits we found something unusual. A number of 'orphan genes' - unique to poplar were picked out. These are formed by integration of small fragments of .. 2/n

Very proud moment - Ignacio - labs first grad student successfully passed his prelims today. He's been excellent. Hopefully there will be some exciting work coming out in the next few years #plantsynbio