Mikel Lavilla-Puerta's Avatar

Mikel Lavilla-Puerta

@mikellavi.bsky.social

Oxygen, yeast, SynBio and sometimes, plants. Postdoc at Oxford Biology, PhD at Scuola Superiore Sant'Anna. I also sing and am very fond of my village.

117 Followers  |  145 Following  |  12 Posts  |  Joined: 11.02.2024  |  1.9108

Latest posts by mikellavi.bsky.social on Bluesky

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#ThrowbackThursday to last week Thursday at #ISPLORE2025JP where we took a group picture of our fantastic community. Missing those conferences vibes? Scroll back through the #ISPLORE2025JP hashtag for some of the best moments ๐ŸŒฑ๐ŸŒŠ

01.10.2025 22:32 โ€” ๐Ÿ‘ 13    ๐Ÿ” 7    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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#ISPLORE2025JP is over.. but not before a comedy performance and closing ceremony by the organizers Mikio Nakazono and Moto Ashikari ๐Ÿ˜†

Thanks so much to all organisers and sponsors for making this edition possible. It was truly amazing!

Next edition reveal by @djgibbs.bsky.social: #ISPLORE2028UK

26.09.2025 05:08 โ€” ๐Ÿ‘ 14    ๐Ÿ” 5    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 1
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Coming to you live from #ISPLORE2025JP Fresh preprint from my lab showing that leaves progressively oxygenate and how this is important for their morphogenesis.Thanks to our collaborators from @Fra_LicO2si lab. #plantscience
www.biorxiv.org/content/10.1...

22.09.2025 06:46 โ€” ๐Ÿ‘ 67    ๐Ÿ” 31    ๐Ÿ’ฌ 3    ๐Ÿ“Œ 1
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We finish this #ISPLORE2025JP session with exceptional talks by @mikellavi.bsky.social, Daai Zhang, @vinayshukla.bsky.social and Lina Zhou ๐ŸŒฑ๐ŸŒŠ Check out @beagiuntoli.bsky.social's recent preprint #plantscience

www.biorxiv.org/content/10.1...

23.09.2025 08:57 โ€” ๐Ÿ‘ 10    ๐Ÿ” 8    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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The speed of hypoxia: great talk by @mikellavi.bsky.social at the @isplore.bsky.social conference in Nagoya!

23.09.2025 07:33 โ€” ๐Ÿ‘ 10    ๐Ÿ” 5    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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A synthetic ERFVII-dependent circuit in yeast sheds light on the regulation of early hypoxic responses of plants Plants face hypoxic conditions either chronically, as particular tissues are characterized by fluctuating or stable low oxygen levels, or acutely, when flooded. In vascular plants, transcriptional ada...

A synthetic ERFVII-dependent circuit in yeast sheds light on the regulation of early hypoxic responses of plants | Preprint from @mikellavi.bsky.social @beagiuntoli.bsky.social @syno2xis.bsky.social #N-degron #hypoxia www.biorxiv.org/content/10.1...

08.09.2025 10:15 โ€” ๐Ÿ‘ 7    ๐Ÿ” 4    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

Yep! it's been a few years in the making, but after some upgrades, now it seems definitely worth the wait. See you in Japan indeed! Can't wait.

05.09.2025 16:53 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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A synthetic ERFVII-dependent circuit in yeast sheds light on the regulation of early hypoxic responses of plants Plants face hypoxic conditions either chronically, as particular tissues are characterized by fluctuating or stable low oxygen levels, or acutely, when flooded. In vascular plants, transcriptional adaptive responses to hypoxia are rapidly mounted by Ethylene Response Factors VII (ERFVIIs), regulated by Plant Cysteine Oxidases (PCOs) through the cysteine branch of the N-degron pathway (Cys-NDP) for oxygen sensing. However, this relatively simple regulatory circuit, consisting of both constitutively expressed as well as hypoxia-inducible ERFVIIs and PCOs, interacts with diverse signalling cues and pathways invoked by hypoxia. To understand the share of the PCO-mediated oxygen sensing mechanism in the production of hypoxia responses, we insulated the PCO/ERFVII circuit from Arabidopsis thaliana and adapted it to Saccharomyces cerevisiae . Using a reporter gene to monitor the output of the circuit allowed us to compare the speed and amplitude of response to hypoxia in the engineered yeast and the source organism. Hypoxia triggered ERFVII stabilization both in Arabidopsis and yeast, leading to a similarly fast transcriptional response that was however larger in plants. A simple hypoxia-inducible feedback loop improved the amplitude of response in yeast, demonstrating the importance of this regulation in the endogenous PCO/ERFVII circuit. Finally, computational modelling of the yeast circuit enabled us to identify promoter competition and presence of hypoxia-inducible PCOs as key parameters that shape early hypoxia responses in plant cells. ### Competing Interest Statement The authors have declared no competing interest. UK Research and Innovation, CBR00770

www.biorxiv.org/content/10.1...

05.09.2025 16:46 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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A synthetic ERFVII-dependent circuit in yeast sheds light on the regulation of early hypoxic responses of plants Plants face hypoxic conditions either chronically, as particular tissues are characterized by fluctuating or stable low oxygen levels, or acutely, when flooded. In vascular plants, transcriptional adaptive responses to hypoxia are rapidly mounted by Ethylene Response Factors VII (ERFVIIs), regulated by Plant Cysteine Oxidases (PCOs) through the cysteine branch of the N-degron pathway (Cys-NDP) for oxygen sensing. However, this relatively simple regulatory circuit, consisting of both constitutively expressed as well as hypoxia-inducible ERFVIIs and PCOs, interacts with diverse signalling cues and pathways invoked by hypoxia. To understand the share of the PCO-mediated oxygen sensing mechanism in the production of hypoxia responses, we insulated the PCO/ERFVII circuit from Arabidopsis thaliana and adapted it to Saccharomyces cerevisiae . Using a reporter gene to monitor the output of the circuit allowed us to compare the speed and amplitude of response to hypoxia in the engineered yeast and the source organism. Hypoxia triggered ERFVII stabilization both in Arabidopsis and yeast, leading to a similarly fast transcriptional response that was however larger in plants. A simple hypoxia-inducible feedback loop improved the amplitude of response in yeast, demonstrating the importance of this regulation in the endogenous PCO/ERFVII circuit. Finally, computational modelling of the yeast circuit enabled us to identify promoter competition and presence of hypoxia-inducible PCOs as key parameters that shape early hypoxia responses in plant cells. ### Competing Interest Statement The authors have declared no competing interest. UK Research and Innovation, CBR00770

Thanks for the shoutout Sjon! Here's the updated link: www.biorxiv.org/content/10.1...
Hope you like it!

05.09.2025 16:45 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
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A synthetic ERFVII-dependent circuit in yeast sheds light on the regulation of early hypoxic responses of plants Plants face hypoxic conditions either chronically, as particular tissues are characterized by fluctuating or stable low oxygen levels, or acutely, when flooded. In vascular plants, transcriptional adaptive responses to hypoxia are rapidly mounted by Ethylene Response Factors VII (ERFVIIs), regulated by Plant Cysteine Oxidases (PCOs) through the cysteine branch of the N-degron pathway (Cys-NDP) for oxygen sensing. However, this relatively simple regulatory circuit, consisting of both constitutively expressed as well as hypoxia-inducible ERFVIIs and PCOs, interacts with diverse signalling cues and pathways invoked by hypoxia. To understand the share of the PCO-mediated oxygen sensing mechanism in the production of hypoxia responses, we insulated the PCO/ERFVII circuit from Arabidopsis thaliana and adapted it to Saccharomyces cerevisiae . Using a reporter gene to monitor the output of the circuit allowed us to compare the speed and amplitude of response to hypoxia in the engineered yeast and the source organism. Hypoxia triggered ERFVII stabilization both in Arabidopsis and yeast, leading to a similarly fast transcriptional response that was however larger in plants. A simple hypoxia-inducible feedback loop improved the amplitude of response in yeast, demonstrating the importance of this regulation in the endogenous PCO/ERFVII circuit. Finally, computational modelling of the yeast circuit enabled us to identify promoter competition and presence of hypoxia-inducible PCOs as key parameters that shape early hypoxia responses in plant cells. ### Competing Interest Statement The authors have declared no competing interest. UK Research and Innovation, CBR00770

Find it here! www.biorxiv.org/content/10.1...

05.09.2025 16:44 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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Big thanks to everyone involved! @yuminghe.bsky.social @beagiuntoli.bsky.social @syno2xis.bsky.social et al.!
Several years in the making and a lot of people met, but finally out as a preprint!

05.09.2025 16:32 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
The synthetic circuit, plus a hypoxia-inducible feedback loop with PCO1 and a copy of RAP. Parameter analysis shows that PCO's features (affinity for oxygen, RAP, etc.) Dictate how fast responses are!

The synthetic circuit, plus a hypoxia-inducible feedback loop with PCO1 and a copy of RAP. Parameter analysis shows that PCO's features (affinity for oxygen, RAP, etc.) Dictate how fast responses are!

3] The role of hypoxia-inducible PCOs: why make more of an enzyme in hypoxia, where it has negligible activity..? Well, they actually do something! And they may be the key to engineer faster hypoxic responses

05.09.2025 16:32 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
The synthetic circuit is fast! 5 min in, hypoxia is already activating the reporter output!

The synthetic circuit is fast! 5 min in, hypoxia is already activating the reporter output!

Responses in plants aren't slower! And how fast they are has actually a lot to do with how many HRPEs they have in their promoters

Responses in plants aren't slower! And how fast they are has actually a lot to do with how many HRPEs they have in their promoters

Thanks to this yeast system we understood:
1] The Cys-NDP is responsible for these responses in plants happening in only 5-10min.
2] HRPE elements (in hypoxic promoters) compete for ERFVII TFs when these are limited. The more HRPEs, the faster the response!

05.09.2025 16:32 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
Synthetic yeast Cys-NDP strategy

Synthetic yeast Cys-NDP strategy

Growth controlled by the synthetic circuit: PCOs and oxygen slow yeast down!

Growth controlled by the synthetic circuit: PCOs and oxygen slow yeast down!

The Cys N-Degron Pathway (which controls plant responses to hypoxia) works in coordination with many, many other processes that finely tune low O2 responses.
We took it.
Put it in yeast, where no such regulation exists.
And it still works! So the Cys-NDP is self-sufficient...

05.09.2025 16:32 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
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a cartoon of spongebob wearing a hat with the letter f on it ALT: a cartoon of spongebob wearing a hat with the letter f on it

Preprint alert! ๐Ÿ—ž
We used SynBio to "simplify" the plant oxygen sensing pathway and implement it in yeast๐Ÿ„.
We can now control yeast growth through oxygen!
But most importantly,
Here's a very short recap of what we understood thanks to it:
biorxiv.org/content/10.110โ€ฆ

05.09.2025 16:32 โ€” ๐Ÿ‘ 4    ๐Ÿ” 3    ๐Ÿ’ฌ 3    ๐Ÿ“Œ 0
Mikel Lavilla-Puerta (he/him) is the First Author of Designed to breathe: synthetic biology applications in plant hypoxia published 02 December 2024. He is a Postdoctoral Research Assistant at Oxford University. Education background includes: 2022 Ph.D in Agrobiosciences at Scuola Superiore Sant'Anna / 2018 MSc in Industrial and Environmental Biotechnology at Complutense University of Madrid / 2016 BSc in Biology at Complutense Univesrity of Madrid. Research interests include Synthetic Biology, Oxygen, Plant Physiology Personal interests include Reading, Music.

Mikel Lavilla-Puerta (he/him) is the First Author of Designed to breathe: synthetic biology applications in plant hypoxia published 02 December 2024. He is a Postdoctoral Research Assistant at Oxford University. Education background includes: 2022 Ph.D in Agrobiosciences at Scuola Superiore Sant'Anna / 2018 MSc in Industrial and Environmental Biotechnology at Complutense University of Madrid / 2016 BSc in Biology at Complutense Univesrity of Madrid. Research interests include Synthetic Biology, Oxygen, Plant Physiology Personal interests include Reading, Music.

โ€œI come from a rural area where agriculture and natural spaces coexist.โ€ academic.oup.com/plphys/artic...

#WeAreASPB

01.08.2025 17:15 โ€” ๐Ÿ‘ 2    ๐Ÿ” 1    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 1

Congrats Vinay!! So exciting! Very happy for you

04.09.2025 14:51 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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Honoured & excited that โ€˜Breathing Undergroundโ€™ has been funded by the ERC!
This will let me explore one of the most fundamental questions of plant life: how roots breathe underground? @erc.europa.eu

04.09.2025 14:48 โ€” ๐Ÿ‘ 89    ๐Ÿ” 25    ๐Ÿ’ฌ 16    ๐Ÿ“Œ 0
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The diverse aspects of hypoxia. The size of the oxygen bubble correlates with concentration. This collection highlights the importance of hypoxia for plant development and environmental adaptation such as during flooding, in compacted or poorly aerated soils, high altitudes, and within meristematic tissues. Image credit: Moe Abbas.

The January 2025 issue of Plant Physiology is now online! Read this Focus Issue on Hypoxia and Plants here: https://academic.oup.com/plphys/issue @ASPB @OxUniPress #PlantSci

02.01.2025 18:16 โ€” ๐Ÿ‘ 21    ๐Ÿ” 7    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 11

The real deal on the topic of plant hypoxia, SynBio and orthogonality. How to use these three concepts to build new oxygen-sensitive circuits? Don't miss the thread below!

16.12.2024 09:11 โ€” ๐Ÿ‘ 2    ๐Ÿ” 1    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

Preprint alert, please share!!
With our new study, we engineered an orthogonal hypoxia-responsive system in plants inspired by mammalian HIF protein degradation. We demonstrated that this system could control protein stability and activity, enabling modulation of Oxygen sensing outputs. Here's how:

15.12.2024 17:45 โ€” ๐Ÿ‘ 53    ๐Ÿ” 28    ๐Ÿ’ฌ 6    ๐Ÿ“Œ 2

Added many more ISPLORE researchers to our starter pack, including @theplantlab.bsky.social, @mikellavi.bsky.social @freddietheodoulou.bsky.social, @gunjansharma88.bsky.social. Welcome to BlueSky!

13.12.2024 10:51 โ€” ๐Ÿ‘ 1    ๐Ÿ” 1    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
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Designed to breathe: synthetic biology applications in plant hypoxia Novel biosensors and concepts from engineering biology expand the toolbox for plant low oxygen biology research

First Bluesky post to share our review with the world! Is there anything, beyond oxygen biosensors, that SynBio can provide to the world of plant hypoxia? Check it out here! @plantphys.bsky.social academic.oup.com/plphys/advan...

05.12.2024 20:51 โ€” ๐Ÿ‘ 16    ๐Ÿ” 10    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 1

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