SMBE2026 Symposium 3 | Genome plasticity and evolutionary innovation
SMBE2026 Symposium 3 | Genome plasticity and evolutionary innovation
π¨ Abstract submission
smbe2026.org/abstracts
π Programme details
smbe2026.org/programme
#SMBE2026
Thrilled to be hosting this session with @henriklicht.bsky.social and @agesiorska.bsky.social π₯³
Already looking forward to @danielcroll.bsky.social's talk and the other talks and posters that'll form part of this session! π€©
Thanks, Jo! π€©
A great genomics paper from my friend and colleague @drandiwilson.bsky.social on the expansion of heat stress related proteins in Rhizina undulata bmcgenomics.biomedcentral.com/articles/10....
A schematic describing what happens to R. undulata pre-, during, and post-fire and which genes it potentially uses to survive and germinate after fire
We hypothesize the expansions of:
1) HSP20 = good at surviving heat π₯
2) GST = good at dealing with ROS generated during stress & in response to metabolism of PyOm β οΈ
3) ACD = good at metabolising PyOm π½
Taken together, R. undulata survives fire and then thrives in post-fire environments!
A figure showing the expansions of HSP20 and GST enzymes in R. undulata compared to other species
3 protein family expansions were discovered in R. undulata. The HSP20 expansion was present in the other fire-associates, but the 2 others were unique to R. undulata! This included GST and ACD enzymes. See below! π½
The different species considered in this study, including those with and without known associations with fire, particularly in post-fire environments.
Excited to share our newest article, out in BMC Genomics!
We looked at genomes of a bunch of Pezizomycetes without & without associations with fire to figure out how Rhizina undulata survives fire π₯
R. undulata needs high temperatures for germination = fire is important for its life cycle π₯
Aww, that's bad timing! But good luck in the lab, I hope it goes well β¨οΈπ§ͺ
A photo of my name tag in the auditorium.
Attending the annual #PlantBiologicalsNetworkMeeting in Copenhagen today β¨οΈ
A figure with three diagrams. The first is labeled "plan" and is a straight line of arrows from top to bottom. The second is labeled "process" and is a tree-like diagram, branching out from top to bottom, showing multiple different paths from one starting point to multiple end points. The third is labeled "publication" and is the same tree-like diagram from before, but with a single track highlighted to show what actually makes it into the publication
The most elegant diagram to explain what the scientific process and the average research project looks like β¨οΈ
So many side tracks that eventually don't make it into the final story, but are an integral part of the process.
From Yanai & Lercher (2025) in Nature Biotech
A photo of 56 eppendorf tubes in a red holder. Different coloured labels (blue, green, purple, pink, orange and yellow) are stuck on the lids of the tubes and indicate the sampleIDs
56 RNAseq samples done and ready to be shipped! π₯³π§¬π§«π§ͺπ¬
A selfie of me wearing a purple tshirt, with writing saying "CRISPR ENGINEER" and an image of a pair of scissors cutting a piece of DNA.
Seeing Jennifer Doudna speak this afternoon at the Black Diamond in Copenhagen π§¬π§«π¬
Appropriately dressed in my #CRISPREngineer shirt from @thermofishersci.bsky.social π§¬πββοΈ
A screenshot of a fb memory from 10 years ago, showing the publication of my first, first author paper in fungal genetics and biology. The title is "Unisexual reproduction in Huntiella moniliformis".
10 years ago, I published my first, first-author paper π€©
In some ways, it feels like just yesterday and I'm still a baby masters student π₯Ή
In other ways, it feels like this was 100 years ago π΅
Either way, the joy of seeing your work published never goes away β€οΈ
A photo of 24 small flasks, 12 of which have a dark liquid orange medium in them and 12 of which have a light yellow medium in them
Blood. Sweat. Tears.
Locust & root media.
π§ͺπ¬π§«
π¦πΎ
π§ͺ𧬠We acknowledge support from FABI, UCPH, The Novo Nordisk Foundation, and the NRF! And I thank my co-authors for their contributions to this manuscript ππ€©
Flow chart representing the protoplast extraction protocol. Factors that may require species-specific optimization are illustrated at each step, and optional steps that may improve protoplast yield and quality are included in light grey boxes.
π§ͺ𧬠We also provide a schematic and lots of in text details on how you can optimize this protocol for use in your own species! π§¬π§ͺ
Protoplasting of Sclerotinia sclerotiorum. (A) Unpigmented mycelia from S.sclerotiorum (CMW 60861) to be used as digestion starting material. (B) Extracted protoplasts after 3 hr of digestion. Scale bar, 10 ΞΌm. Inset shows a zoomed-in protoplast (B).
π§ͺ𧬠Protocol 5 is for Sclerotinia sclerotiorum- the fungus with a host range of more than 400 plant species! πΎππΏπ³ This protocol uses immature mycelium as a starting point
Protoplasting of Ophiostoma novo-ulmi. (A) Conidia from O.novo-ulmi (CMW 10573) to be used as the starting material for the digestion. (B) Protoplasts extracted after βΌ3 hr of digestion. Scale bars, 10 ΞΌm. Insets show a zoomed-in conidium (A) and a zoomed-in protoplast (B).
π§ͺ𧬠Protocol 4 is for Ophiostoma novo-ulmi, the Dutch elm disease pathogen π²π This protocol uses a DTT-EDTA pre-treatment and uses conidia as the starting material βοΈ
Protoplasting of Metarhizium species. (A) Conidia from Metarhizium acridum (ARSEF 3391). (B) Mature mycelium from Metarhizium brunneum (KVL 12-30) to be used as the starting material for the digestion. (C) Extracted protoplasts from Metarhizium acridum (ARSEF 3391) after βΌ1 hr; some cellular debris is also visible. Scale bars, 10 ΞΌm. Insets show a zoomed-in conidium (A) and two zoomed-in protoplasts (C).
π§ͺ𧬠Protocol 3 is for Metarhizium species- fungi that infect and cause death in insects, including various agricultural pests π¦ The protocol uses mature mycelium as a starting point.
Protoplasting of Fusarium circinatum. (A) A combination of conidia and mycelia from F. circinatum (CMW 350) after a 36-hr incubation in potato dextrose broth. This is the material to be used as the starting material for the digestion. (B) Extracted protoplasts after digestion for βΌ24 hr. Scale bars, 10 ΞΌm. Insets shows two zoomed-in conidia (A) and a zoomed-in protoplast (B), and arrows point at mycelium (A).
π§ͺ𧬠Protocol 2 is for Fusarium circinatum- the notorious pine pathogen that causes devastation in natural and managed forests π² This protocol describes extraction from a mixture of mycelium and conidia
Protoplasting of Ceratocystis species. (A) Maturemycelia grown fromC.fimbriata (CMW 14799) conidia, to be used as the starting material for the digestion. (B) Sorbitol overlay of the protoplasts, showing distinct layers. The region wherein the protoplasts are expected to settle (between 3 and 4 ml) is indicated by the white bracket. (C) Extracted protoplasts after βΌ3 hr of digestion and isolation. Scale bar, 10 ΞΌm. Inset shows a zoomed-in protoplast (C).
π§ͺ𧬠Protocol 1 is for Ceratocystis species and describes the extraction of protoplasts from mycelium, using a density gradient to purify the protoplasts ππ²
A screenshot of the article title and author list: "Extracting Protoplasts from Filamentous Fungi Using Extralyse, An Enzyme Used in the Wine Industry" Andi Wilson, Alida van Dijk, Bianke Marx, Deanne du Plessis, Grant Terblanche, SimonΓ© Bornman, P. Markus Wilken, Tuan A. Duong, Henrik H. De Fine Licht, and Brenda D. Wingfield
Super excited to share our newest paper, out in
Current protocols!
A collab btwn FABI & UCPH, we put together protoplast extraction protocols for 5 different fungal genera! π
With applications for genome editing & long read seq, we hope this will be super useful! π§ͺπ§¬
Basic Protocol 1: Protoplast extractions from Ceratocystis eucalypticola and Ceratocystis fimbriata Basic Protocol 2: Protoplast extractions from Fusarium circinatum Basic Protocol 3: Protoplast extractions from Metarhizium acridum, Metarhizium brunneum, and Metarhizium guizhouense Basic Protocol 4: Protoplast extractions from Ophiostoma novo-ulmi Basic Protocol 5: Protoplast extractions from Sclerotinia sclerotiorum
We present 5 protocols, each optimized in a different fungal genus, for species important in agriculture πΎ & forestry π²
We use an enzyme from the wine industry, #Extralyse, to overcome the reliance on cost-prohibitive lab-grade enzymes whose availability is unreliable π₯²π§ͺπ§¬
A selfie of me wearing a light blue migraine hat
It's taken a while, but I'm finally trying a #MigraineHat.. π
I've been an icepack girlie for a very long time, but this 360Β° cooling effect is π
Not to mention the sound and light dulling effect too π
#Migraine #ChronicMigraine
A photo of little piles of germinating barley seeds that are being transferred into ziplock germination pouches
And with that, another 4000-odd seeds have been sowed again π±πͺ
A photo of a green gloved hand holding a small petridish with bacteria growing all over it in tiny white colonies
This little plate and its tiny bacteria left me heartbroken on Wednesday evening π
After months of planning and preparing, a pre-pilot trial and a pilot trial, I started my large RNAseq experiment last week π₯³
If everything went to plan, I'd be done by 28 March. But biology had other plans... π§¬
Three photos: 1) barley seeds germinating from ziplock bag germination pouches, 2) barley plants with their leaves and roots exposed in a germination pouch, 3) a bottle of root-infused liquid
Three photos: 1) a locust sitting on a lettuce leaf, 2) freeze dried locusts in a glass beaker, 3) a bottle of locust-infused liquid
Wednesday was the first sampling day and... my root and locust media was contaminated by this bacteria left π§«
But after some tears and a restless night, I know what went wrong and how to fix it πͺ
Hopefully with the added experience, setting up Round 2 won't take as long! π€
A photo of open elevator doors. There is a liquid nitrogen flask on the floor and the safety tape closing the elevators.
Safety first β οΈ
#Mycology #MolecularBiology #RNAseq #LiquidNitrogen
A photo of 12 flat bottom flasks in the LAF bench. They have varying colours of amber-coloured medium in them
And I can finally say that my pilot experiment starts tomorrow πͺπ±π¦
If everything goes according to plan, the full experiment starts week after next!
Let's go! π€© #MycoSky #FungiSky #RNASeq
The hardest ~35g I've ever worked for π
π±
Harvesting roots for this experiment has been a challenge πͺ
Turns out that 360g of wet weight barley root = 36g dry weight π
But we've got the goods and the pilot experiment is underway!
