Nikel SEM Group

Building synthetic metabolisms in bacteria for a sustainable future @DTUBiosustain · Views are our own + #Pseudomonas’ 🧬 ·

[Pablo Iván Nikel @pabnik.bsky.social @PabloINik]

Seven Critical Challenges in Synthetic One-Carbon Assimilation and Their Potential Solutions—led by @FavoinoGiusi & @OscarPuiggene @LabNikel @FEMSmicro #Microbiology #Reviews #SynBio #Metabolic #Engineering
https://t.co/J7an6ZeBxk

[Michele Partipilo @MichelePartipi3]

Ins and outs for designing bacterial metabolisms for C1-assimilation, from a multilevel perspective, now pieced together in this review from our @LabNikel! Check it out at https://t.co/FWpCjhyRX9

[Nikel SEM Group @LabNikel]

New paper out! Check our new CRISPR toolkit for Cupriavidus necator!

[Pablo Iván Nikel @pabnik.bsky.social @PabloINik]

Streamlined and efficient genome editing in #Cupriavidus necator H16 using an optimised SIBR-Cas system—spearheaded by @dellavallesimo & @enricoorsi & led by Costas Patinios + Wei Huang @TrendsinBiotech #SynBio
https://t.co/OW8LANTTn5

[Nikel SEM Group @LabNikel]

New paper out in collaboration w/ @mirbachh from @maxplanckpress and many more! Check Helena's thread for a detailed overview of the manuscript!👇

[Helena Schulz-Mirbach @mirbachh]

Really happy to share that our work on constructing six glyoxylate / glycolate sensors covering a three order of magnitude concentration range is out now in @NatureComms ! 🔥

Read below to see how we developed the sensors and what they are good for 🥳.

https://t.co/DEGQujQ8x9

[Helena Schulz-Mirbach @mirbachh]

Really happy to share that our work on constructing six glyoxylate / glycolate sensors covering a three order of magnitude concentration range is out now in @NatureComms ! 🔥

Read below to see how we developed the sensors and what they are good for 🥳.

https://t.co/DEGQujQ8x9

[Nikel SEM Group @LabNikel]

New paper out from our group!

[Pablo Iván Nikel @pabnik.bsky.social @PabloINik]

Computation-aided designs enable developing auxotrophic #metabolic #sensors for wide-range glyoxylate and glycolate detection—spearheaded by @enricoorsi w/a choral assembly of cool collaborators @LabNikel @NatureComms #SynBio #OpenAccess
https://t.co/IXyVsaurt2

[Pablo Iván Nikel @pabnik.bsky.social @PabloINik]

Preprint alert🚨Systematic #engineering of synthetic serine cycles in #Pseudomonas putida uncovers emergent topologies for #methanol assimilation · @biorxivpreprint led by @OscarPuiggene #SynBio #Methylotrophy #CircularEconomy @LabNikel
https://t.co/3gBucAfUz0

[Helena Schulz-Mirbach @mirbachh]

Super exciting work by @OscarPuiggene from @LabNikel on advancing #methanol use by Pseudomonas Putida by engineering #serinecycle variants! Many congratulations, excited to be a part of this !

[Nikel SEM Group @LabNikel]

Check our newest preprint 👇!

[Pablo Iván Nikel @pabnik.bsky.social @PabloINik]

#Preprint alert 🚨 Genetic dissection of cyclic di-GMP signaling in #Pseudomonas aeruginosa via diguanylate cyclase disruption―collaboration between @LabNikel & Andrea Smania's team in Argentina, led by @martino_RA & @Daniel__Volke @biorxiv_micrbio #CRISPR
https://t.co/LFYy7orWeg

[Pablo Iván Nikel @pabnik.bsky.social @PabloINik]

Engineering a phi15-based #expression system for stringent #gene expression in #Pseudomonas putida—led by @EvelineLammens, @Daniel__Volke in a nice collab between @LabNikel & @RobLavigne1's team
https://t.co/cdJJj24xyc

[Nikel SEM Group @LabNikel]

Congratulations @PabloINik on this great achievement!
We are thrilled to congratulate our group leader, @PabloINik, for being elected Fellow of ASM! A well-earned recognition of your outstanding contributions to our field! 🥳

[Pablo Iván Nikel @pabnik.bsky.social @PabloINik]

Honored to be elected as Fellow of the #American Academy of #Microbiology! This recognition reflects the incredible work of my past and present collaborators, students, and mentors. Deep gratitude to my nominators and the microbiology community for their support! @ASMicrobiology

[Pablo Iván Nikel @pabnik.bsky.social @PabloINik]

CIFR (Clone–Integrate–Flip-out–Repeat): A toolset for iterative #genome and pathway #engineering of Gram-negative #bacteria—our latest contribution led by @FilFederici & Francesco Luppino @LabNikel @DTUBiosustain #OpenAccess #SynBio
https://t.co/SnSjKlNh96

[Michele Partipilo @MichelePartipi3]

Amazing tool for multiple cycles of genetic engineering of Gram negative bacteria developed by @FilFederici and Francesco, now fully available! @LabNikel

[Pablo Iván Nikel @pabnik.bsky.social @PabloINik]

Leveraging engineered #Pseudomonas putida minicells for bioconversion of organic acids into short-chain methyl ketones by @KaterinaKozaeva, @ManuelNietoDom1, @maxi_prep et al. @ACSSynBio @LabNikel @DTUBiosustain #OpenAccess
https://t.co/rFm2ypWNYH

[Nikel SEM Group @LabNikel]

We hope this thread is helpful to everyone interested in synthetic biology and metabolic engineering, or simply curious about what our group has been up to in 2024. Have some relax in this break to charge your energies back! 🎉

[Nikel SEM Group @LabNikel]

Finally, this piece from @NicoKrink provides a guided overview of CRISPR-based editing tools for bacteria, offering orientation on their diverse applications, challenges, and improvements, inspired by The Hitchhiker’s Guide to the Galaxy
https://t.co/dHaezofHUN

[Nikel SEM Group @LabNikel]

And also Meliawati led this work on Paenibacillus polymyxafor isobutanol production by genes KO and KI, optimizing NADPH regeneration, and identifying key metabolic bottlenecks, offering insights for further biotechnological applications of this bacterium
https://t.co/IY9PPeEM39

[Nikel SEM Group @LabNikel]

Touching on new bugs, here @enricoorsi and @dellavallesimo led the work for creating a new CRISPR/Cas toolkit for the emerging C1 platform C. necator, showing unprecedented efficiencies and turnover times for gene deletions
https://t.co/B4IjEqcuqT

[Nikel SEM Group @LabNikel]

And in this chapter, w/ @DeMaria_SynBio they outline use of L-threonine aldolases (LTAs) from E.coli and P.putida to efficiently synthesize 4-F-L-threonine in vitro + protocols for adapting these activities to produce other fluorometabolites in vivo
10.1016/bs.mie.2024.02.016

[Nikel SEM Group @LabNikel]

@ManuelNietoDom1 explores here enzymatic synthesis of F-alanine enantiomers using few dehydrogenases, demonstrating efficient production with high enantiomeric excess, and introduces a novel fluorine biocatalysis method for trifluorinated alanine
https://t.co/rc6BgZMpl0

[Nikel SEM Group @LabNikel]

Going back to P. putida, this minireview w/ @vdlorenzo_CNB and @PabloINik traces the evolution of KT2440 from a model organism for biodegradation studies to a SynBio #chassis, highlighting its adaptability and importance in various applications
https://t.co/0eKs6Uw9fv

[Nikel SEM Group @LabNikel]

These types of sensors are ideal platform to harness for #evolution campaigns. Here, @enricoorsi led this #perspective article that proposes integration of ML, automation, high-throughput screenings and in vivo evolution to develop superior biocatalyst
https://t.co/hjCM1uIhCA