Michael Raissig
@michaelraissig.bsky.social
Plant developmental geneticist, football fanatic, parent
Associate Prof @unibern
equity, fairness, transparency, posts my own, he/him
Associate Prof @unibern
equity, fairness, transparency, posts my own, he/him
7/ Finally—our community tool 🌾
shiny.ips.unibe.ch
The B. distachyon Leaf Gene Expression Viewer allows visualization of any gene across the whole leaf, epidermal, or stomatal subsets. Interactive UMAPs and ggPlantmap provide an eFP-browser-like experience for grass developmental biology.
shiny.ips.unibe.ch
The B. distachyon Leaf Gene Expression Viewer allows visualization of any gene across the whole leaf, epidermal, or stomatal subsets. Interactive UMAPs and ggPlantmap provide an eFP-browser-like experience for grass developmental biology.
November 5, 2025 at 12:32 PM
7/ Finally—our community tool 🌾
shiny.ips.unibe.ch
The B. distachyon Leaf Gene Expression Viewer allows visualization of any gene across the whole leaf, epidermal, or stomatal subsets. Interactive UMAPs and ggPlantmap provide an eFP-browser-like experience for grass developmental biology.
shiny.ips.unibe.ch
The B. distachyon Leaf Gene Expression Viewer allows visualization of any gene across the whole leaf, epidermal, or stomatal subsets. Interactive UMAPs and ggPlantmap provide an eFP-browser-like experience for grass developmental biology.
6/ As a proof of concept we functionally analyzed two novel marker genes, one that is expressed in dividing leaf cells and another one that is expressed in the developing stomatal lineages.
November 5, 2025 at 12:32 PM
6/ As a proof of concept we functionally analyzed two novel marker genes, one that is expressed in dividing leaf cells and another one that is expressed in the developing stomatal lineages.
5/ Gene regulatory network analysis of the stomatal clusters identifies top transcription factors per clusters and could distinguish the targetome of co-expressed yet functionally distinct stomatal transcription factors BdMUTE and BdFAMA
November 5, 2025 at 12:32 PM
5/ Gene regulatory network analysis of the stomatal clusters identifies top transcription factors per clusters and could distinguish the targetome of co-expressed yet functionally distinct stomatal transcription factors BdMUTE and BdFAMA
4/ Pseudotime analysis reconstructs the guard cell lineage trajectory, mapping the sequential activation of key transcription factors and identifying novel stage-specific marker genes. Again, RNA-FISH validates sequential activity of the novel markers along developmental stages.
November 5, 2025 at 12:32 PM
4/ Pseudotime analysis reconstructs the guard cell lineage trajectory, mapping the sequential activation of key transcription factors and identifying novel stage-specific marker genes. Again, RNA-FISH validates sequential activity of the novel markers along developmental stages.
3/
Focusing on the epidermis, we resolved most cell lineages of the grass leaf epidermis including stomatal guard cells and subsidiary cells, hair cells and silica cells. We used known and novel marker genes and multiplexed, RNA-FISH to confirm the in silico clusters in the actual leaf epidermis
November 5, 2025 at 12:32 PM
3/
Focusing on the epidermis, we resolved most cell lineages of the grass leaf epidermis including stomatal guard cells and subsidiary cells, hair cells and silica cells. We used known and novel marker genes and multiplexed, RNA-FISH to confirm the in silico clusters in the actual leaf epidermis
2/ Our Brachypodium leaf atlas spans all major tissues.
UMAPs resolve epidermal, mesophyll, vascular, and meristematic compartments.
Known markers define cluster identities—revealing a coherent developmental continuum across the vegetative leaf.
November 5, 2025 at 12:32 PM
2/ Our Brachypodium leaf atlas spans all major tissues.
UMAPs resolve epidermal, mesophyll, vascular, and meristematic compartments.
Known markers define cluster identities—revealing a coherent developmental continuum across the vegetative leaf.
1/ Preprint alert:
🌾 The developing leaf of the wild grass Brachypodium distachyon at single-cell resolution
👉 doi.org/10.1101/2025...
A 70k-cell single-cell RNA-seq atlas of the developing grass leaf—from the shoot meristem to mature leaf tissues. @cerealcell.bsky.social @lbmountain.bsky.social
🌾 The developing leaf of the wild grass Brachypodium distachyon at single-cell resolution
👉 doi.org/10.1101/2025...
A 70k-cell single-cell RNA-seq atlas of the developing grass leaf—from the shoot meristem to mature leaf tissues. @cerealcell.bsky.social @lbmountain.bsky.social
November 5, 2025 at 12:32 PM
1/ Preprint alert:
🌾 The developing leaf of the wild grass Brachypodium distachyon at single-cell resolution
👉 doi.org/10.1101/2025...
A 70k-cell single-cell RNA-seq atlas of the developing grass leaf—from the shoot meristem to mature leaf tissues. @cerealcell.bsky.social @lbmountain.bsky.social
🌾 The developing leaf of the wild grass Brachypodium distachyon at single-cell resolution
👉 doi.org/10.1101/2025...
A 70k-cell single-cell RNA-seq atlas of the developing grass leaf—from the shoot meristem to mature leaf tissues. @cerealcell.bsky.social @lbmountain.bsky.social
🌿🌱 We’re hiring a tenure-track Assistant Professor (potentially open rank) at the Institute of Plant Sciences
@unibe.ch in Plant Population Ecology 🌻🌳
Be our colleague and join us in beautiful Bern, Switzerland
Apply by Jan 23 2026 👉 ohws.prospective.ch/public/v1/jo...
@unibe.ch in Plant Population Ecology 🌻🌳
Be our colleague and join us in beautiful Bern, Switzerland
Apply by Jan 23 2026 👉 ohws.prospective.ch/public/v1/jo...
October 30, 2025 at 3:55 PM
🌿🌱 We’re hiring a tenure-track Assistant Professor (potentially open rank) at the Institute of Plant Sciences
@unibe.ch in Plant Population Ecology 🌻🌳
Be our colleague and join us in beautiful Bern, Switzerland
Apply by Jan 23 2026 👉 ohws.prospective.ch/public/v1/jo...
@unibe.ch in Plant Population Ecology 🌻🌳
Be our colleague and join us in beautiful Bern, Switzerland
Apply by Jan 23 2026 👉 ohws.prospective.ch/public/v1/jo...
Happy to share our recent thoughts on how grasses form and pattern stomata
doi.org/10.1016/j.pb...
🌾From fate establishment, through within-file patterning to dumbbell formation🌾
Congrats to
@lbmountain.bsky.social
on getting two publications out in a single day - a first for the lab!
doi.org/10.1016/j.pb...
🌾From fate establishment, through within-file patterning to dumbbell formation🌾
Congrats to
@lbmountain.bsky.social
on getting two publications out in a single day - a first for the lab!
October 13, 2025 at 8:07 AM
Happy to share our recent thoughts on how grasses form and pattern stomata
doi.org/10.1016/j.pb...
🌾From fate establishment, through within-file patterning to dumbbell formation🌾
Congrats to
@lbmountain.bsky.social
on getting two publications out in a single day - a first for the lab!
doi.org/10.1016/j.pb...
🌾From fate establishment, through within-file patterning to dumbbell formation🌾
Congrats to
@lbmountain.bsky.social
on getting two publications out in a single day - a first for the lab!
Using cell wall immunostainings, Alex found differential staining of LM6, which stains arabinans. B. distachyon showed strong staining in subsidiary cells, and this staining was absent in B. stacei.
October 10, 2025 at 2:53 PM
Using cell wall immunostainings, Alex found differential staining of LM6, which stains arabinans. B. distachyon showed strong staining in subsidiary cells, and this staining was absent in B. stacei.
Anna therefore looked at the subcellular features of these stomatal complexes using TEM and found no striking differences between B. stacei and B. distachyon. Nonetheless, Anna saw the huge symplastic connections between the grass guard cells and shared vacuoles (a feature specific to grass stomata)
October 10, 2025 at 2:53 PM
Anna therefore looked at the subcellular features of these stomatal complexes using TEM and found no striking differences between B. stacei and B. distachyon. Nonetheless, Anna saw the huge symplastic connections between the grass guard cells and shared vacuoles (a feature specific to grass stomata)
When comparing stomatal gas exchange dynamics and capacity, however, B. hybridum and B. distachyon performed similarly, but B. stacei severely underperformed despite showing the same stomatal anatomical properties as B. distachyon.
October 10, 2025 at 2:53 PM
When comparing stomatal gas exchange dynamics and capacity, however, B. hybridum and B. distachyon performed similarly, but B. stacei severely underperformed despite showing the same stomatal anatomical properties as B. distachyon.
We analysed stomatal anatomy and physiology and found that the allotetraploid B. hybridum forms bigger but fewer stomata compared to their diploid parent species B. distachyon and B. stacei (not very surprising).
October 10, 2025 at 2:53 PM
We analysed stomatal anatomy and physiology and found that the allotetraploid B. hybridum forms bigger but fewer stomata compared to their diploid parent species B. distachyon and B. stacei (not very surprising).
Our paper comparing stomata of the three annual Brachypodium species is out 🌾
bmcplantbiol.biomedcentral.com/articles/10....
A great collaborative effort between @lbmountain.bsky.social, & our friends at University of Silesia (Alexander Betekhtin and Anna Milewska-Hendel). Funded by @dfg.de and NAWA
bmcplantbiol.biomedcentral.com/articles/10....
A great collaborative effort between @lbmountain.bsky.social, & our friends at University of Silesia (Alexander Betekhtin and Anna Milewska-Hendel). Funded by @dfg.de and NAWA
October 10, 2025 at 2:53 PM
Our paper comparing stomata of the three annual Brachypodium species is out 🌾
bmcplantbiol.biomedcentral.com/articles/10....
A great collaborative effort between @lbmountain.bsky.social, & our friends at University of Silesia (Alexander Betekhtin and Anna Milewska-Hendel). Funded by @dfg.de and NAWA
bmcplantbiol.biomedcentral.com/articles/10....
A great collaborative effort between @lbmountain.bsky.social, & our friends at University of Silesia (Alexander Betekhtin and Anna Milewska-Hendel). Funded by @dfg.de and NAWA
What a community, what a welcoming and inclusive atmosphere, what a location! Thank you @snsf.ch, CSF @ethz.ch, @newphyt.bsky.social, @biologists.bsky.social and @cerealcell.bsky.social for supporting us.
🌾Brachypodium 2025 was a blast🌾
Grazie mille - Thank you so much
Forza Brachy - Go Brachy
🌾Brachypodium 2025 was a blast🌾
Grazie mille - Thank you so much
Forza Brachy - Go Brachy
July 10, 2025 at 1:27 PM
What a community, what a welcoming and inclusive atmosphere, what a location! Thank you @snsf.ch, CSF @ethz.ch, @newphyt.bsky.social, @biologists.bsky.social and @cerealcell.bsky.social for supporting us.
🌾Brachypodium 2025 was a blast🌾
Grazie mille - Thank you so much
Forza Brachy - Go Brachy
🌾Brachypodium 2025 was a blast🌾
Grazie mille - Thank you so much
Forza Brachy - Go Brachy
IBRC2025 #Brachy2025 is about to start on Monte Verità 🌾
I am very excited for four full days of Brachypodium love ♥️
www.brachypodium2025.org
I am very excited for four full days of Brachypodium love ♥️
www.brachypodium2025.org
July 6, 2025 at 1:57 PM
IBRC2025 #Brachy2025 is about to start on Monte Verità 🌾
I am very excited for four full days of Brachypodium love ♥️
www.brachypodium2025.org
I am very excited for four full days of Brachypodium love ♥️
www.brachypodium2025.org
🥳Congratulations, Dr. Cheng!🥳
PhD student #4, who pioneered work with the leaf succulent Kalanchoë laxiflora in our lab 🌵🔬
See Xin's #preprint www.biorxiv.org/content/10.1...
I don't think I will ever get used to mentees leaving the lab.
Best of luck, Xin, you will be missed 💚
PhD student #4, who pioneered work with the leaf succulent Kalanchoë laxiflora in our lab 🌵🔬
See Xin's #preprint www.biorxiv.org/content/10.1...
I don't think I will ever get used to mentees leaving the lab.
Best of luck, Xin, you will be missed 💚
July 4, 2025 at 7:27 PM
🥳Congratulations, Dr. Cheng!🥳
PhD student #4, who pioneered work with the leaf succulent Kalanchoë laxiflora in our lab 🌵🔬
See Xin's #preprint www.biorxiv.org/content/10.1...
I don't think I will ever get used to mentees leaving the lab.
Best of luck, Xin, you will be missed 💚
PhD student #4, who pioneered work with the leaf succulent Kalanchoë laxiflora in our lab 🌵🔬
See Xin's #preprint www.biorxiv.org/content/10.1...
I don't think I will ever get used to mentees leaving the lab.
Best of luck, Xin, you will be missed 💚
The final program of #Brachy2025 is online www.brachypodium2025.org/program2
This will be a fantastic meeting set in the Mediterranean beauty of the Lago Maggiore Area.
I am excited to welcome the Brachypodium aficionados to Switzerland, 10 years after my first Brachy meeting
This will be a fantastic meeting set in the Mediterranean beauty of the Lago Maggiore Area.
I am excited to welcome the Brachypodium aficionados to Switzerland, 10 years after my first Brachy meeting
June 11, 2025 at 10:14 AM
The final program of #Brachy2025 is online www.brachypodium2025.org/program2
This will be a fantastic meeting set in the Mediterranean beauty of the Lago Maggiore Area.
I am excited to welcome the Brachypodium aficionados to Switzerland, 10 years after my first Brachy meeting
This will be a fantastic meeting set in the Mediterranean beauty of the Lago Maggiore Area.
I am excited to welcome the Brachypodium aficionados to Switzerland, 10 years after my first Brachy meeting
What an honour to witness data feminism scholar and activist Prof. Catherine D’Ignazio @kanarinka.bsky.social of MIT receive @unibe.ch’s Emily Jäger Award. Thank you for persisting despite being blacklisted by the federal government for holding a “woke” NSF grant ✊♀️
May 14, 2025 at 3:47 PM
What an honour to witness data feminism scholar and activist Prof. Catherine D’Ignazio @kanarinka.bsky.social of MIT receive @unibe.ch’s Emily Jäger Award. Thank you for persisting despite being blacklisted by the federal government for holding a “woke” NSF grant ✊♀️
Happy Birthday, Stomatal Biology group @unibe.ch 🥳
Hard to believe it's been 7 years already. This year, a big shout out to our group members joining us from around the world and doing amazing science on our favorite models, the grass B. distachyon 🌾 and leaf succulent K. laxiflora🌵. Thank you!
Hard to believe it's been 7 years already. This year, a big shout out to our group members joining us from around the world and doing amazing science on our favorite models, the grass B. distachyon 🌾 and leaf succulent K. laxiflora🌵. Thank you!
May 1, 2025 at 7:48 PM
Happy Birthday, Stomatal Biology group @unibe.ch 🥳
Hard to believe it's been 7 years already. This year, a big shout out to our group members joining us from around the world and doing amazing science on our favorite models, the grass B. distachyon 🌾 and leaf succulent K. laxiflora🌵. Thank you!
Hard to believe it's been 7 years already. This year, a big shout out to our group members joining us from around the world and doing amazing science on our favorite models, the grass B. distachyon 🌾 and leaf succulent K. laxiflora🌵. Thank you!
🌾 One week until registration deadline 🌾
Join us in stunning Monte Verità in the Italian-speaking part of Switzerland for what will be a great meeting on grass biology. Fantastic line-up www.brachypodium2025.org/speaker2 & a great community
Register until May 5 www.brachypodium2025.org/registration
Join us in stunning Monte Verità in the Italian-speaking part of Switzerland for what will be a great meeting on grass biology. Fantastic line-up www.brachypodium2025.org/speaker2 & a great community
Register until May 5 www.brachypodium2025.org/registration
April 28, 2025 at 11:40 AM
🌾 One week until registration deadline 🌾
Join us in stunning Monte Verità in the Italian-speaking part of Switzerland for what will be a great meeting on grass biology. Fantastic line-up www.brachypodium2025.org/speaker2 & a great community
Register until May 5 www.brachypodium2025.org/registration
Join us in stunning Monte Verità in the Italian-speaking part of Switzerland for what will be a great meeting on grass biology. Fantastic line-up www.brachypodium2025.org/speaker2 & a great community
Register until May 5 www.brachypodium2025.org/registration
Registration is open for the
International Brachypodium Research Conference 2025 (IBRC2025) #Brachy2025
July 6 - 10, 2025 in Monte Verità, Switzerland
www.brachypodium2025.org/registration
Registration deadline is May 5
🌾 Join us if you love grass biology 🌾
International Brachypodium Research Conference 2025 (IBRC2025) #Brachy2025
July 6 - 10, 2025 in Monte Verità, Switzerland
www.brachypodium2025.org/registration
Registration deadline is May 5
🌾 Join us if you love grass biology 🌾
February 19, 2025 at 4:13 PM
Registration is open for the
International Brachypodium Research Conference 2025 (IBRC2025) #Brachy2025
July 6 - 10, 2025 in Monte Verità, Switzerland
www.brachypodium2025.org/registration
Registration deadline is May 5
🌾 Join us if you love grass biology 🌾
International Brachypodium Research Conference 2025 (IBRC2025) #Brachy2025
July 6 - 10, 2025 in Monte Verità, Switzerland
www.brachypodium2025.org/registration
Registration deadline is May 5
🌾 Join us if you love grass biology 🌾
Brachy2025 in Switzerland - amazing line-up
most beautiful place in Switzerland
Hanging out with peers that share my love for Brachypodium
www.brachypodium2025.org
most beautiful place in Switzerland
Hanging out with peers that share my love for Brachypodium
www.brachypodium2025.org
January 2, 2025 at 5:02 PM
Brachy2025 in Switzerland - amazing line-up
most beautiful place in Switzerland
Hanging out with peers that share my love for Brachypodium
www.brachypodium2025.org
most beautiful place in Switzerland
Hanging out with peers that share my love for Brachypodium
www.brachypodium2025.org
🌵Preprint alert 🌵
5y in the works & extremely proud of this one. Xin Cheng & @heikelindner.bsky.social established the eudicot leaf succulent Kalanchoë laxiflora as a dev model.
Like in grasses, MUTE makes Kalanchoë’s stomatal subsidiary cells! 1/n
www.biorxiv.org/content/10.1...
BSKY-tutorial 👇
5y in the works & extremely proud of this one. Xin Cheng & @heikelindner.bsky.social established the eudicot leaf succulent Kalanchoë laxiflora as a dev model.
Like in grasses, MUTE makes Kalanchoë’s stomatal subsidiary cells! 1/n
www.biorxiv.org/content/10.1...
BSKY-tutorial 👇
December 28, 2024 at 2:43 PM
🌵Preprint alert 🌵
5y in the works & extremely proud of this one. Xin Cheng & @heikelindner.bsky.social established the eudicot leaf succulent Kalanchoë laxiflora as a dev model.
Like in grasses, MUTE makes Kalanchoë’s stomatal subsidiary cells! 1/n
www.biorxiv.org/content/10.1...
BSKY-tutorial 👇
5y in the works & extremely proud of this one. Xin Cheng & @heikelindner.bsky.social established the eudicot leaf succulent Kalanchoë laxiflora as a dev model.
Like in grasses, MUTE makes Kalanchoë’s stomatal subsidiary cells! 1/n
www.biorxiv.org/content/10.1...
BSKY-tutorial 👇
It was a pleasure to have the cerealstemcells.de/index.php research unit in Bern @unibern.bsky.social - wonderful science, great people and, of course, Swiss Cheese Fondue 🌾🇨🇭
December 19, 2024 at 3:47 PM
It was a pleasure to have the cerealstemcells.de/index.php research unit in Bern @unibern.bsky.social - wonderful science, great people and, of course, Swiss Cheese Fondue 🌾🇨🇭