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Enrico Orsi

@eorsi.bsky.social
498 followers 36 following 51 posts

Bolognese 🇮🇹 in Copenhagen 🇩🇰 I engineer and optimize the metabolism of nonmodel C1-trophic bacteria for novel biotechnological applications Metabolic Engineering | Green Economy | CO2 valorization | DTU Biosustain

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Reposted by Enrico Orsi
bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 10/07/2026
A microbial growth-coupled platform for in vivo interrogation of Rubisco oxygenase activity www.biorxiv.org/content/10.64898/20…
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Enrico Orsi @eorsi.bsky.social · 12/07/2026
🧬 Even Earth's most abundant enzyme makes mistakes. Rubisco fixes CO₂ for nearly all life but wastes ~20% of potential crop yield on a 3-billion-year-old side reaction. We built a microbial sensor that finally makes it visible & tinkerable in living cells. www.biorxiv.org/content/10.6...
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Enrico Orsi @eorsi.bsky.social · 02/07/2026
@sheilaijensen.bsky.social is hiring for several cool positions! Check the vacancies
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Enrico Orsi @eorsi.bsky.social · 02/02/2026
10 years ago today, Italian PhD student Giulio Regeni was found murdered after being kidnapped and tortured by Egyptian security services. Egypt has never cooperated with Italian prosecutors to identify those responsible www.channeldraw.org/2026/01/24/g...
channeldraw.org
Giulio Regeni. Until There Is Justice - ChannelDraw
An artistic journey at the heart of an open wound
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Reposted by Enrico Orsi
Nico Claassens @nicoc-micsynmet.bsky.social · 25/11/2025
Newest preprint from our lab: a new family of promising synthetic CO2 fixation cycles that may outcompete the Calvin cycle and that Vittorio Rainaldi realized to a great extent in E. coli! Up to 11 heterologous enzymes in a cascade supporting CO2 fixation & growth! www.biorxiv.org/content/10.1...
biorxiv.org
Modular in vivo engineering of the reductive methylaspartate cycles for synthetic CO2 fixation
Biological carbon fixation is currently limited to seven naturally occurring pathways. Synthetic carbon fixation pathways have the potential to surpass aerobic natural pathways in efficiency, but none...
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Reposted by Enrico Orsi
Pablo Ivan Nikel @pabnik.bsky.social · 03/11/2025
Growth-coupled microbial biosynthesis of the animal pigment xanthommatin — Led by Leah Bushin, featuring M. Gracia Alvan, @danielvolke.bsky.social @oscarpuiggene.bsky.social in a fantastic collaboration w/Brad Moore @labnikel.bsky.social @natbiotech.nature.com 🦑 www.nature.com/articles/s41...
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Reposted by Enrico Orsi
labnikel.bsky.social @labnikel.bsky.social · 09/11/2025
How does Pseudomonas putida keep its redox balance steady across different metabolic states? Our new preprint shows that two transhydrogenases -membrane-bound PntAB and soluble SthA - act together as a flexible, reversible system to control NAD(H)/NADP(H) ratios. www.biorxiv.org/content/10.1...
biorxiv.org
Integrated control of redox and energy metabolism by the membrane-bound and soluble transhydrogenases of Pseudomonas putida across metabolic regimes
Redox homeostasis is central to microbial physiology and stress adaptation, yet the functional roles of transhydrogenases remain poorly understood beyond a few organisms. In this study, we systematica...
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Reposted by Enrico Orsi
Sebastian Wenk @sebwenk.bsky.social · 24/10/2025
🔥🔥🔥 Friday Evening, Paper Out, Feierabend 🔥🔥🔥 When evolution and enzyme engineering team up, they can convince microbes to assimilate sustainable carbon substrates preparing them for a life in a circular bioeconomy. doi.org/10.1016/j.ym...
doi.org
Redirecting
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Enrico Orsi @eorsi.bsky.social · 22/09/2025
Thanks! First challenge is to expand the substrate acceptance range in the cell factory
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Enrico Orsi @eorsi.bsky.social · 12/09/2025
Please repost! Postdoc in adaptive laboratory evolution and C1 synthetic metabolism! Location: DTU Biosustain 🦠🧬🔬 Starting in 01/2026! Fell free to reach out if you have questions! efzu.fa.em2.oraclecloud.com/hcmUI/Candid...
efzu.fa.em2.oraclecloud.com
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Enrico Orsi @eorsi.bsky.social · 10/07/2025
🔬 Start: Jan 2026 | 1-year funded 🏭 Work with AMBR + 10–30L reactors 📈 TRY optimization | in vivo polymerization | TEA & LCA 💼 Great stepping stone to fellowships (NNF, EU, etc.) LinkedIn post with more info: www.linkedin.com/posts/enrico...
linkedin.com
🚨 We're hiring a #Postdoc in #Bioprocess #Engineering! | Enrico Orsi
🚨 We're hiring a #Postdoc in #Bioprocess #Engineering! 🌱 📍 Location: DTU Biosustain 📅 Start: January 2026 | 🕐 Duration: 1 year (with potential extension) Are you a recent PhD graduate excited b...
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Enrico Orsi @eorsi.bsky.social · 10/07/2025
🧪 We're hiring a #Postdoc in Bioprocess Engineering! Excited about scaling CO₂-based biomanufacturing from bench to pilot scale? Join our group working on converting CO₂ + renewable electricity → polymers 💡🌱 👇
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Reposted by Enrico Orsi
Gerrich @gerrich.bsky.social · 16/06/2025
#ME16 This is quite subjective , but imo @helenasm.bsky.social just gave the most impressive talk of the conference so far and she is "only" in the third year of her PhD. If you are interested in synthetic pathway engineering or C1 fixation you should check out her research.
scholar.google.com
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Enrico Orsi @eorsi.bsky.social · 03/06/2025
🎉 Excited to share that I’ve received an Emerging Investigator Grant from the Novo Nordisk Foundation! I’ll start my research group in Jan 2026 to develop universal cell factories for P2X & CO₂-based biomanufacturing 🌱🔬 👉 researchleaderprogramme.com/recipients/e...
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Enrico Orsi @eorsi.bsky.social · 26/05/2025
www.sciencenews.dk/en/designed-... Piece from ScienceNews.dk on our glyoxylate and glycolate sensor strains
sciencenews.dk
Designed bacteria can detect specific molecules
Researchers have developed a computer-guided method for designing and engineering bacteria that can detect the presence of specific molecules in the environment. This method will advance the use...
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Reposted by Enrico Orsi
Ari Satanowski @ari-satanowski.bsky.social · 04/04/2025
Excited to share a main project from my PhD, out now in @naturecomms.bsky.social! 📝 We've designed and brought to life the “CORE cycle” – a new-to-nature pathway that provides a novel route for biological CO2 capture 🦠🌱 nature.com/articles/s41... Take a look! Thread below... 🧵
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Reposted by Enrico Orsi
labnikel.bsky.social @labnikel.bsky.social · 04/04/2025
Interested in engineering bacteria to turn #C1feedstocks into high-value chemicals for #bioproduction? Here is a thread summarizing our latest review on the roadblocks and how we might bio-hack our way past them 🧵 1/n academic.oup.com/femsre/advan...
academic.oup.com
Seven Critical Challenges in Synthetic One-Carbon Assimilation and Their Potential Solutions
Abstract. Synthetic C1 assimilation holds the promise of facilitating carbon capture while mitigating greenhouse gas emissions, yet practical implementatio
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Reposted by Enrico Orsi
Trends in Biotechnology @cp-trendsbiotech.bsky.social · 16/03/2025
Online now: Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system
dlvr.it
Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system
This study developed two simple, efficient, and rapid genome editing tools termed Self-splicing Intron-Based Riboswitch-Cas9 (SIBR-Cas9) and SIBR2.0-Cas12a, for editing the genome of the industrially relevant microbial strain Cupriavidus necator H16.…
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Reposted by Enrico Orsi
Constantinos Patinios @copabio.bsky.social · 14/03/2025
Excited to see our SIBR work out in Trends in Biotechnology :) doi.org/10.1016/j.ti... This is the first study I have coordinated from start to finish, and it brings me immense satisfaction to see it published. For a brilliant description of the tech check this: www.linkedin.com/feed/update/...
doi.org
Redirecting
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Enrico Orsi @eorsi.bsky.social · 14/03/2025
We had great support from our labs in developing this toolkit. Thanks to @pabnik.bsky.social, @nicoc-micsynmet.bsky.social, Sjoerd, Luc, Angela, Chase, Harrison, Raymond, John, and Wei! The plasmids will be available on Addgene. Feel free to reach out in case you want to try them!
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Enrico Orsi @eorsi.bsky.social · 14/03/2025
These results demonstrates that a new state-of-the-art is available for making gene deletions in this promising bug. With a turnaround time that is 50% shorter than the current systems available, we believe that SIBR-Cas9 and SIBR2.0-Cas12a will help using C. necator in new P2X applications! 8/n
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Enrico Orsi @eorsi.bsky.social · 14/03/2025
SIBR2.0 was then functional and we moved testing it for Cas12a. The new architectures revealed to be tight, allowing precise and controllable induction of cas12a as well, with similar efficiencies to the ones observed for Cas9! 7/n
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Enrico Orsi @eorsi.bsky.social · 14/03/2025
Here is where SIBR2.0 comes into place. Simona and Costas developed a script for strategically moving the intron position within the CDS to get rid of such hidden translation initiation starts. This was tested first in E. coli using GFP as readout. 6/n
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Enrico Orsi @eorsi.bsky.social · 14/03/2025
Then, we moved at testing if SIBR would work also on Cas12a. To our surprise, induction during the targeting assay revealed a leaky cas12a expression despite the presence of the intron with the STOP codon. This was because of a hidden translation start site that required some adjustments. 5/n
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Enrico Orsi @eorsi.bsky.social · 14/03/2025
We started by testing the SIBR setup on Cas9. This was because we already had evidence that it worked before, although poorly www.sciencedirect.com/science/arti... Targeting worked fine & by combining SIBR w/ Cas9, we achieved high editing efficiencies of >80% in two loci! Great start! 4/n
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Enrico Orsi @eorsi.bsky.social · 14/03/2025
Teaming up with Simona and Costas, we decided to apply the SIBR technology that Costas developed during his PhD to "pause" Cas counter-selection and allow endogenous homologous recombination (HR) to happen first. Our suspect was that C. necator is also poor at HR academic.oup.com/nar/article/... 3/n
academic.oup.com
Streamlined CRISPR genome engineering in wild-type bacteria using SIBR-Cas
Abstract. CRISPR-Cas is a powerful tool for genome editing in bacteria. However, its efficacy is dependent on host factors (such as DNA repair pathways) an
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Enrico Orsi @eorsi.bsky.social · 14/03/2025
C. necator holds potential for the conversion and valorization of CO2 for its ability to grow on this substrate using power-to-X feedstocks (like hydrogen or formate). However, making gene deletions in this organism has always been a pain due to its limited gene deletion toolkit 2/n
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Enrico Orsi @eorsi.bsky.social · 14/03/2025
Our brand new CRISPR/Cas toolkit for genome editing of Cupriavidus necator is out🦠🧬 A joint effort w/ @dellavallesimo.bsky.social and Costas (and many more!) Check 🧵 our long journey for developing a new state-of-the-art for the manipulation of this promising bug 1/n www.cell.com/trends/biote...
cell.com
Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system
This study developed two simple, efficient, and rapid genome editing tools termed Self-splicing Intron-Based Riboswitch-Cas9 (SIBR-Cas9) and SIBR2.0-Cas12a, for editing the genome of the industrially ...
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Reposted by Enrico Orsi
Qian Cheng @qchengx1e3.bsky.social · 12/03/2025
📑📑📑#synthetic_biology @eorsi.bsky.social @pabnik.bsky.social present a workflow for designing versatile auxotrophic metabolic sensors for glyoxylate and glycolate detection @naturecomms.bsky.social www.nature.com/articles/s41...
nature.com
Computation-aided designs enable developing auxotrophic metabolic sensors for wide-range glyoxylate and glycolate detection - Nature Communications
Auxotrophic metabolic sensors (AMS) are vital for bioengineering but are often time-consuming to develop. Here, the authors present a workflow for designing versatile AMS, demonstrating their use for ...
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Reposted by Enrico Orsi
labnikel.bsky.social @labnikel.bsky.social · 09/03/2025
The utilization of #C1-feedstocks, such as methanol, by non-model bacteria demands an in-depth analysis of design alternatives, a modular strategy to identify bottlenecks and efficient solutions within the host #metabolism of the chosen host... www.biorxiv.org/content/10.1...
biorxiv.org
Systematic engineering of synthetic serine cycles in Pseudomonas putida uncovers emergent topologies for methanol assimilation
The urgent need for a circular carbon economy has driven research into sustainable substrates, including one-carbon (C1) compounds. The non-pathogenic soil bacterium Pseudomonas putida is a promising ...
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Reposted by Enrico Orsi
Beau Dronsella @beaubd.bsky.social · 06/03/2025
Check out Sebastians crazy effort to engineer E. coli to grow on formate via the synthetic Serine-Threonine-Cycle. In contrast to the rGlyp the STC works even at ambient CO2!🔥
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Reposted by Enrico Orsi
Lennart Schada von Borzyskowski @lennartschada.bsky.social · 06/03/2025
Only one week left to apply for this exciting PhD position, supervised by @gillesvanwezel.bsky.social and me! Please apply if you are interested in microbial biochemistry and have a solid background in enzymes, metabolic pathways, and bacterial genetics. www.universiteitleiden.nl/en/vacancies...
universiteitleiden.nl
PhD aminosugar metabolism
The Faculty of Science / the Institute for Biology is looking for a :PhD Candidate , Aminosugar metabolism and control of growth and development in bacteriaVacancy number: 15487 PhD project descriptio...
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Reposted by Enrico Orsi
Sebastian Wenk @sebwenk.bsky.social · 06/03/2025
Interested in Sustainability, Metabolic Engineering and Evolution? Check out how we convinced E. coli to grow on the CO2-derived substrate formic acid using the synthetic Serine Threonine Cycle! ♻️🌱🦠 OPEN ACCESS publication to be found here: 🚨 doi.org/10.1016/j.ym... 🚨 #MEvoSky #microsky (1/🧵)
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labnikel.bsky.social @labnikel.bsky.social · 05/03/2025
🚀 The SEM Group (Lab Nikel) is officially on Bluesky! We’re kicking things off with our latest paper: an end-to-end journey on designing, implementing & applying auxotrophic metabolic sensors for bioengineering! 🧬🔬 @naturecomms.bsky.social Check it out: www.nature.com/articles/s41...
nature.com
Computation-aided designs enable developing auxotrophic metabolic sensors for wide-range glyoxylate and glycolate detection - Nature Communications
Auxotrophic metabolic sensors (AMS) are vital for bioengineering but are often time-consuming to develop. Here, the authors present a workflow for designing versatile AMS, demonstrating their use for ...
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Reposted by Enrico Orsi
Michele Partipilo @michelepartipilo.bsky.social · 05/03/2025
With great collaborations come great outcomes! A fine example from @eorsi.bsky.social from @pabnik.bsky.social's lab et collaborators of how to design, build and develop cell biosensors for value-added chemicals (related to synthetic C1 assimilation, of course)! 🧪
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
The sensor strains are available for the community who is interested in growth-coupled designs around glyoxylate. We are happy to share them😎! Thanks to all collaborators, @pabnik.bsky.social, Tobi Erb, Arren Bar-Even, Steffen Lindner, Ari Satanowski, Elad Noor, Hai He, Charles Cotton, etc... /end
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
Last, we assessed if we could sense glycolate for environmental monitoring purposes. We simulated phytoplankton blooms in the lab 🌞🌊(known to release glycolate) and used the sensors to detect any glycolate in the medium. We confirmed w/ HPLC that sensitive sensors worked for this purpose! 7/
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
Now, moving to applications🏭. The most obvious one is in vivo enzyme screening. We did so by testing a small library of Mtk and Mcl (involved in CO2 fixating and carbon-conserving pathways) for testing their best expression levels. We identified the optimal RBS combination to support carbon flux 6/
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
Then, the masterpiece from @helenasm.bsky.social who characterized these strains under incremental concentrations of glyoxylate🦠. Overall, they ranged from uM to mM spanning 3 orders of magnitude🔍! We also left the possibility for the strains to sense glycolate, which was also confirmed 5/
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
We deleted these genes in E. coli strains to convert them into metabolic sensors (few more KOs were needed). Great work here by Charlie, Ari, and Helena (and co) who did a great quality experimental job w/ impressive results. First, we confirmed the tightness of these deletions using 13C labeling 4/
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
Here, Elad and Hai applied their recently developed medium-scale model to identify a set of KOs that can lead to auxotrophies for glyoxylate, a central metabolic hub around which is not trivial to design growth-coupled selection schemes. They identify 5/6 designs w/ increasing glyoxylate demand 😎 3/
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
Let's be frank: correctly identifying deletionsto design tight and reliable auxotrophs is extremely challenging😫. Often, implementing a single auxotroph strain takes several months and trial-and-error iterations... 🤯2/
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
We just #published an end-to-end work for the computer-aided design💻, construction🛠️, validation✅, characterization🔬 & application💪 of #auxotroph metabolic sensors, the work-horses of in vivo growth-coupled selection screening systems-using glycolate as test case. 🧵👇1/ www.nature.com/articles/s41...
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
The sensor strains are available for the community who is interested in growth-coupled designs around glyoxylate. We are happy to share them😎! Thanks to all collaborators, @pabnik.bsky.social, Tobi Erb, Arren Bar-Even, Steffen Lindner, Ari Satanowski, Elad Noor, Hai He, Charles Cotton, etc... /end
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
Last, we assessed if we could sense glycolate for environmental monitoring purposes. We simulated phytoplankton blooms in the lab 🌞🌊(known to release glycolate) and used the sensors to detect any glycolate in the medium. We confirmed w/ HPLC that sensitive sensors worked for this purpose! 7/
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
Now, moving to applications🏭. The most obvious one is in vivo enzyme screening. We did so by testing a small library of Mtk and Mcl (involved in CO2 fixating and carbon-conserving pathways) for testing their best expression levels. We identified the optimal RBS combination to support carbon flux 6/
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
Then, the masterpiece from @helenasm.bsky.social who characterized these strains under incremental concentrations of glyoxylate🦠. Overall, they ranged from uM to mM spanning 3 orders of magnitude🔍! We also left the possibility for the strains to sense glycolate, which was also confirmed 5/
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
We deleted these genes in E. coli strains to convert them into metabolic sensors (few more KOs were needed). Great work here by Charlie, Ari, and Helena (and co) who did a great quality experimental job w/ impressive results. First, we confirmed the tightness of these deletions using 13C labeling 4/
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
Here, Elad and Hai applied their recently developed medium-scale model to identify a set of KOs that can lead to auxotrophies for glyoxylate, a central metabolic hub around which is not trivial to design growth-coupled selection schemes. They identify 5/6 designs w/ increasing glyoxylate demand 😎 3/
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
Let's be frank: correctly identifying deletionsto design tight and reliable auxotrophs is extremely challenging😫. Often, implementing a single auxotroph strain takes several months and trial-and-error iterations... 🤯2/
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