Nikolaj Koch

Scientist @nash_lab, previously @BudisaNed and @rappsilberlab | synthetic biology | genetic code expansion | economics enthusiast

[Nikolaj Koch @KochNikolaj]

I am happy to share my last PhD project. In search for a better variant of the PylRS system we looked for psychrophilic homologs.
https://t.co/GYScYU2BCE
tl,dr: We discovered a far more efficient PylRS (at least in E. coli)

[Michael A. Nash @nash_lab]

Signatures of Electron–Hole Hopping in Myoglobin Peroxidase Activity Revealed by Deep Mutational Learning | ACS Catalysis https://t.co/qh0Sgy28iS

[Michael A. Nash @nash_lab]

Check out our latest work on engineering the substrate specificity of an enzyme using high-throughput methods!

https://t.co/cyDKnQFGsg

[Leah Roe @leahtangroe]

I created a protein backbone editing method and named it after my alma mater (x2)! Out now in Nature ChemBio, we show the first examples of a β2-, γ-, and δ-amino acid encoded into full length proteins expressed in cells. https://t.co/6j7QBpbAPJ

[bioRxiv Bioengineering @bioRxiv_bioE]

Decoding Substrate Specificity in a Promiscuous Biocatalyst by Enzyme Proximity Sequencing

https://t.co/cKkko3CvgV
#biorxiv_bioE

[Nikolaj Koch @KochNikolaj]

@RuxandraTeslo If this is a tool for everyone it doesn't matter if it has AI and whatnot. Per definition not everybody can beat the market, at least in the long run. That said I also don't get "the innovation".

[Green Research Group @GreenGroupMIB]

Very happy to announce that 'Efficient and selective energy transfer photoenzymes powered by visible light' is out today in Nature Chemistry! Congratulations to Rebecca, Ross and everyone else involved in this project! 🎉🎉🎉
https://t.co/mIYqmFCksO

[Raffael Schumann (@[email protected]) @RaffaelLucaSchu]

🚨 Our lab just rewrote life‘s operating system!
Together, we’ve built Syn57 - an E. coli with a synthetic genome running on a 57-codon genetic code!

https://t.co/T9JaQx7ACM

#SyntheticBiology #Syn57 #PhD #GeneticCode #GenomeEngineering #Biosecurity #FutureOfBiology

[European Research Council (ERC) @ERC_Research]

“Let me remind us all why governments around the world have a stake in supporting science & innovation. The arguments are well-established but often forgotten.”

Read Maria Leptin’s full speech @Researchirel’s event with stellar Irish ERC grantees.

https://t.co/jjLCwUEene
🇪🇺🇮🇪

[Sasha Gusev @SashaGusevPosts]

I wrote about how polygenic heritable conditions present in families and the liability threshold model. This has some counterintuitive implications for considering the risk of a condition in offspring as well as the impact of multi-generational selection. A 🧵:

[SeTh @EconomicEthics]

#Servicethread #AusGruenden
Weil mir in den letzten Tagen immer wieder etwas aus der #EconTwitter-Bubble zum Wohnungsmarkt in die TL gespült wurde, einmal ein paar ganz grundsätzliche Dinge dazu, wie problematisch die Behandlung von Wohnraum in VWL-Lehrbüchern sein kann.1/25

[bioRxiv Biophysics @biorxiv_biophys]

Force-dependent Reorganization and Mechanostability of the Izumo1:Juno Complex Involved in Human Fertilization https://t.co/EYvgQAPYT1 #biorxiv_biophys

[The Banfield Lab @BanfieldLab]

🚨 We discovered a new genetic code, "Genetic Code 34," sporadically distributed in archaea. Select archaea have genome-wide recoding of the TAG stop codon to pyrrolysine; the adoption of this code was likely driven by metabolic processes. (1/2) https://t.co/wzEKFpSPxE

[Prof. Nikolai Slavov @slavov_n]

The genetic code was worked out in vitro with synthetic RNAs.
◾️ We are beginning to explore the full scope of RNA decoding in mammals.
◾️ It results in stable proteins.

@shiri_tsour and a team from @SlavovLab led the way.

Alternatively translated proteins include TFs, ...
🧵

[Nikolaj Koch @KochNikolaj]

Great work from Jaime Fernández de Santaella (Dr. Fernández since yesterday :D) with whom I really enjoyed working together.

[Nikolaj Koch @KochNikolaj]

I am happy to share our newest work from the @Nash_lab where we combined genetic code expansion and bacterial surface display. Using an amber codon deep mutational scanning and sequencing workflow, we mapped S-allylcysteine incorporation efficiency across the hArg1 sequence.

[biorxiv_bioengineering @biorxiv_bioeng]

Amber Codon Mutational Scanning and Bioorthogonal PEGylation for Mapping Antibody Binding Sites on Human Arginase-1 https://t.co/2cvIsouFkK #biorxiv_bioeng

[Nikolaj Koch @KochNikolaj]

This provides insights into structural and sequence dependencies of S-allylcysteine incorporation. With this technique we also determined the binding epitope of a monoclonal antibody on the surface of hArg1.

[Michael A. Nash @nash_lab]

Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions | Journal of the American Chemical Society https://t.co/xSCBDbBeOm

Great collaboration with @rafaelcbernardi !

[Nikolaj Koch @KochNikolaj]

This is a really cool story. Could be very useful for some GCE applications

[Panke Lab @BPL_ethz]

Find out more about our system for importing non-natural molecules into E.coli. Here we tailor the substrate profile of the cargo release step.

Congratulations David and team!

https://t.co/aIEHXxbrd5

@ACSSynBio @emirodrob

[Anush Chiappino-Pepe @AnushChP]

1/ 🚨 Excited to share my Postdoc research with @geochurchlab at @harvadmed! Dive into our discoveries on the central dogma of biology, antibiotic resistance, #compbio designs, and #synbio. 🧬🔬 Check our paper: https://t.co/iGpCB5CFGI

[Akos Nyerges @AkosNyerges]

In our newest preprint,
• we explore the effects of synonymous genome recoding, and
• construct & troubleshoot a synthetic 57-codon E. coli genome using multi-omics, editing, and laboratory evolution.

1/n