Lightnews — Scholar-powered news

Nicholas Southern

@neuroscinikolai.bsky.social

740 followers 1.8K following 23 posts

PhD Student @ https://niopeklab.de/ Engineering switchable proteins💡 Views and opinions are my own 🇺🇸 in 🇩🇪

niopeklab.de

Posts Media Videos Starter Packs

Pinned

Nicholas Southern @neuroscinikolai.bsky.social · Jun 13

Excited to share my main PhD work is finally out! 🥳

We built a phage-assisted evolution platform to evolve allosteric protein switches (POGO-PANCE) and introduce cumulative, targeted mutations/Indels (RAMPhaGE)!

See how we evolved ultra-strong, light-switchable AraC variants 🌚🌞

bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · Jun 13

Phage-Assisted Evolution of Allosteric Protein Switches https://www.biorxiv.org/content/10.1101/2025.06.12.659331v1

2 11 22

Nicholas Southern @neuroscinikolai.bsky.social · 2d

Since it’s binding based, it makes sense you can delete these regions but it is neat that you dont majorly affect positioning using the typical sgRNA length, though circular permutation might yield different results overall. Thanks for the detailed insights, and best of luck with your submission! 😄

Reposted by Nicholas Southern

Keri Martinowich @martinowk.bsky.social · 7d

New Hot Topics piece from @rphillips3.bsky.social and Stephanie Page in @npp-journal.bsky.social describing emerging insights on roles of molecularly-defined cell types in the lateral septum, which serves as a hub for coordinating diverse social behaviors.

www.nature.com/articles/s41...

Role of molecularly defined lateral septum cell types and circuits in social behaviors - Neuropsychopharmacology

Neuropsychopharmacology - Role of molecularly defined lateral septum cell types and circuits in social behaviors

www.nature.com

9 15

Nicholas Southern @neuroscinikolai.bsky.social · 8d

Also its so interesting seeing how robust these proteins are to large scale deletions like this, as you would imagine the spacing of the domains themselves to one another would greatly impact your ability to truncate them. Did you guys also consider playing w/ sgRNA content like in the OG paper? 😄

1 1

Nicholas Southern @neuroscinikolai.bsky.social · 8d

Hahaha also although you can’t edit, you can at least delete posts here as I am sure people on my feed noticed as I was writing on my preprint with the same typo 5 times in a row 🤦

Nicholas Southern @neuroscinikolai.bsky.social · 8d

Thanks for the full response Andrew! I suppose it makes sense you’re mostly optimising for ease/time here although you still need to order the sgRNA libraries. As for small deletions, I certainly agree but I also imagine having connective residues could help string deleted junctions together

1 2

Reposted by Nicholas Southern

Keri Martinowich @martinowk.bsky.social · 14d

In the early years of my PhD I remember being asked if we'd ever treat or cure diseases like HIV or Huntington's. I remember saying maybe, but not knowing if I believed. Seeing research pay off as real impact on human lives is - incredible.

www.bbc.com/news/article...

www.bbc.com/news/article...

Huntington's disease successfully treated for first time

One of the most devastating diseases finally has a treatment that can slow its progression and transform lives, tearful doctors tell BBC.

www.bbc.com

8 41 150

Reposted by Nicholas Southern

Jörg Vogel @jorg-vogel-lab.bsky.social · 28d

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

4 63 130

Nicholas Southern @neuroscinikolai.bsky.social · 29d

You know I liked this paper, but I was more curious why they went this route for library construction versus trying to improve their earlier MISER strategy given that recombineering efficiency has seen some advances since. Maybe someone @savagecatsonly.bsky.social can help me 😄

7 2

Nicholas Southern @neuroscinikolai.bsky.social · Sep 8

I’ll eventually get caught up, but I listen while pipetting so there’s a lot of “day science” to get through first (right now on recording 21 with Daniel Kahneman 😅😂)

Nicholas Southern @neuroscinikolai.bsky.social · Sep 8

Been having a lot of fun lately listening to the Night Science Podcast after stumbling on it from the article series by @itaiyanai.bsky.social and Martin Lercher, definitely recommend it if you have a passing interest in the creative aspects of how the scientific process is conducted 😄

1 2 10

Nicholas Southern @neuroscinikolai.bsky.social · Sep 5

Really interesting and impressive work!!!

Reposted by Nicholas Southern

Constantinos Patinios @copabio.bsky.social · Sep 4

🚀 New publication alert! 🚀

We just published in @natbiotech.nature.com:
👉 Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes
doi.org/10.1038/s415...

Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes - Nature Biotechnology

Append editing of ADP-ribosyl to thymine is used for precise modifications in bacteria and eukaryotes.

doi.org

3 10 22

Reposted by Nicholas Southern

Sorek Lab @soreklab.bsky.social · Sep 2

Preprint: De-novo design of proteins that inhibit bacterial defenses

Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications

Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵

Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection

Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...

www.biorxiv.org

2 70 140

Reposted by Nicholas Southern

bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · Aug 30

Growth, dissolution and segregation of genetically encoded RNA droplets by ribozyme catalysis https://www.biorxiv.org/content/10.1101/2025.08.29.673008v1

4 4

Reposted by Nicholas Southern

Martin Pacesa @martinpacesa.bsky.social · Aug 27

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.

www.nature.com/articles/s41...

14 110 300

Reposted by Nicholas Southern

John Skiles Skinner @skiles.blue · Aug 17

A terrorist targeted federal workers last week. There wasn’t much reporting on it. But I’m not finished thinking about it! 🧵

An anti-vaxxer fired more than 500 gunshots into CDC Atlanta, shattering 150 “blast-proof” windows on 6 buildings. Employees were pinned down in terror.

93 3.2K 7.4K

Reposted by Nicholas Southern

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Aug 13

De novo design of light-regulated dynamic proteins using deep learning https://www.biorxiv.org/content/10.1101/2025.08.12.669910v1

2 3

Reposted by Nicholas Southern

Jeremy Berg @jeremymberg.bsky.social · Aug 7

Well, this is a huge Executive Order power grab...

www.whitehouse.gov/presidential...

1/3

Improving Oversight of Federal Grantmaking

By the authority vested in me as President by the Constitution and the laws of the United States of America, and to improve the process of Federal

www.whitehouse.gov

52 240 440

Reposted by Nicholas Southern

Nature Methods @natmethods.nature.com · Aug 6

PANCS-Binders (phage-assisted noncontinuous selection of protein binders) screens multiple high-diversity protein libraries against a panel of dozens of targets for high-throughput binder discovery. @chembiobryan.bsky.social @mstyles-chembiol.bsky.social

www.nature.com/articles/s41...

1 14 23

Reposted by Nicholas Southern

Nature Methods @natmethods.nature.com · Aug 4

Work by @bene837.bsky.social @jmathony.bsky.social @dominikniopek.bsky.social @uniheidelberg.bsky.social

Nature Methods @natmethods.nature.com · Aug 4

ProDomino is a machine learning-based method that predicts domain insertion sites and helps guide the engineering of functional multi-domain proteins.

www.nature.com/articles/s41...

5 12

Reposted by Nicholas Southern

Jeremy Day @daylab.bsky.social · Jul 29

Pretty sure my grandfather, who was a NASA engineer that worked on Saturn and Apollo missions in Alabama in the 1960s and 1970s, would be alarmed to see what’s happening now. This is faded but here is a technical drawing he produced for fiber optic viewing of the liquid oxygen supply for Saturn V.

2 8 38

Reposted by Nicholas Southern

Martin Pacesa @martinpacesa.bsky.social · Jul 25

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

23 39 220

Reposted by Nicholas Southern

bioRxiv Bioengineering @biorxiv-bioeng.bsky.social · Jul 17

Engineering site-specific nucleic acid-protein conjugates by utilizing a natural RNAylation reaction https://www.biorxiv.org/content/10.1101/2025.07.11.664405v1

1 2

Reposted by Nicholas Southern

Hannah Ledvina Ph.D. @hannahledvina.bsky.social · Jul 2

Words cannot describe how excited I am to share the findings from the second half of my postdoc in @aaronwhiteley.bsky.social's lab where we discover that bacteria use functional amyloids to defend themselves from predatory bacteria. rdcu.be/euu5Y. See thread for details on this epic adventure 1/.

Functional amyloid proteins confer defence against predatory bacteria

Nature - Escherichia coli uses curli fibres, oligomers of the functional amyloid CsgA, as a barrier to protect against the predatory bacteria Bdellovibrio bacteriovorus and Myxococcus xanthus in a...

rdcu.be

6 52 160

Reposted by Nicholas Southern

Martin Pacesa @martinpacesa.bsky.social · Jun 30

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!

github.com/martinpacesa...

4 55 140