Super fun project working with the Zorya team. Lots of interesting discussions and crazy biology, still lots to explore!
Very happy our paper on Zorya anti-phage defense system is now published in
@Nature! 🥳 Big congrats to first authors
@HaidaiHu and @__jphilipp and all other authors! Wonderful collab with @Salmo_Lab
and @SimonJacksonNZ #cryoEM @UCPH_CPR @koebenhavns_uni nature.com/articles/s4158…
0
5
29
1,935
Fantastic summary 🧵of our most recent #phagedefence work at @microtago a bonanza of new systems to study. Congrats @leighton_payne for another stella effort. The new systems are public on the PADLOC webserver PADLOC.otago.ac.nz
🚨📄PREPRINT ALERT! "New antiviral defences are genetically embedded within prokaryotic immune systems" ⚔️🦠 #phage biorxiv.org/content/10.110…
0
1
14
1,172
>150 predicted new #phage defense systems! We validated some examples but there are too many to test them all, so we've released the Phage Defence Candidate (Pdc) systems publicly for others to explore.... PADLOC 2.0 brings an updated system definition format and new features.
Hard to believe it's been 2 years since we released PADLOC v1.0.0 😱. To celebrate, here's a new major release – 📦 PADLOC v2.0.0, with lots of new systems! 🔥 (available from GitHub/Conda and the PADLOC web server: padloc.otago.ac.nz) 🧵 1/n
1
18
74
8,111
A fantastic opportunity to work with great people and lots of support from MWC to have a positive impact across the motu.
We are inviting MWC ECRs to join their MWC Early Career Steering Committee, where you will generate ideas & help coordinate MWC initiatives to support NZ ECRs & drive the future direction of the committee. Submit your application to join by 20th May 5pm forms.office.com/r/FbQf3wNTAU 🤩
0
2
3
SimonJackson retweeted
We are inviting MWC ECRs to join their MWC Early Career Steering Committee, where you will generate ideas & help coordinate MWC initiatives to support NZ ECRs & drive the future direction of the committee. Submit your application to join by 20th May 5pm forms.office.com/r/FbQf3wNTAU 🤩
0
5
7
Fantastic example of curiosity driven research. What a journey from the first 'weird' result through to the RNAseq jackpot revealing the cryptic system. Great to see Nils' hard work and determination now out, plus a bonus thread featuring @britneyspears
Very pleased to share our ✨New Paper✨ about an epigenetic conflict between a restriction–modification system and a methylation-dependent nuclease.
Want to know how that pans out? Continue reading here 🧵👇🏻 or head over to @NAR_Open for the full story: academic.oup.com/nar/advance-ar…
0
1
18
Massive shout-out to @NeSI_NZ for supporting our HPC compute needs, an excellent resource. 294,118 CPU hours in 2021 for this and several other projects related to #phage #host bioinformatics... might be time to plant a couple of trees.
We've updated the precomputed #phage defence results on the PADLOC server padloc.otago.ac.nz to RefSeq version 209. This release includes 234,098 bacteria and archaea genomes encoding 2,387,656 proteins involved anti-phage/plasmid/virus systems.
2
0
11
Thanks to @rafapinilla92 and twitterless Shiraz Shah, we've also added the SiAgo Argonaute system from their recent preprint doi.org/10.1101/2021.1…
We've rolled out PADLOC 2.0 to the server padloc.otago.ac.nz The user registration/login is gone (results now persist during your browser session) and we added a few features to increase the user experience. Bug reports & feedback welcome. Happy #phagedefence hunting.
1
1
10
Can everyone please take a break from discovering new systems while we go on holiday?...
Looking for Retron, Viperin, BREX, DISARM and Phosphorothioate-based #phagedefence systems?
The second PADLOC update this week is now out! 150+ subtypes and counting...
padloc.otago.ac.nz
Big effort by @leighton_payne & thanks to @pentamorfico & @ntoroga for the retron HMMs
1
1
47
An exciting week for the Argonaute family! Several past bioinformatic studies identified multiple types of multi-gene pAgo systems, now a trio of preprints show the function of effector proteins in these:
doi.org/10.1101/2021.1…
doi.org/10.1101/2021.1…
doi.org/10.1101/2021.1…
doi.org/10.1101/2021.1…
doi.org/10.1101/2021.1…
doi.org/10.1101/2021.1…
The latest PADLOC #phagedefence system update is out on padloc.otago.ac.nz including Pycsar, deaminases, Argonaute and PIWI-RE, Stk2 and Nhi systems! Including updates to CBASS to split out the Pycsar systems. Last but not least also the #CRISPR Lon/T accessory effectors.
0
0
18
SimonJackson retweeted
New vacancy for an ARF position to work on mycobacterial genetics (below). otago.taleo.net/careersection/…
0
17
11
Super proud of Leighton @leighton_payne and the first paper from his PhD exploring #phagedefense systems. A massive effort and congrats to all involved!
🎉 Proud to share my 1st first-author paper! Introducing our new tool for defence system identification: PADLOC academic.oup.com/nar/advance-ar… @NAR_Open 📰 (1/10)
0
1
18
The latest PADLOC #phage #defence locator update update includes 27 CRISPR-Cas subtypes comprised of 320 protein families! Precomputed results for >200,000 RefSeq genomes are open-access on the PADLOC webserver, or you can upload and run new genomes padloc.otago.ac.nz 1/3
📢 We've just added #CRISPR to the PADLOC webserver! Don't forget to follow @padlocbio to stay updated as we add more systems 👀
1
6
19
We’ve included CRISPR-associated proteins, #accessorynucleases and a bunch of predicted CARF and SAVED domain proteins. Several overlaps between predicted CRISPR accessory proteins and other #phagedefense systems have been resolved. 2/3
1
0
0
We’ve suggested two new type III CRISPR-Cas subtypes: III-G (signature Csx26) and III-H (Csx25). The PADLOC database allows easy updating of protein assignments, so we can keep up-to-date with names for all the exciting new cOA-activated CRISPR RNases/DNases and Proteases? 3/3
0
0
3
Well done @leighton_payne on bringing together PADLOC the Prokaryotic Antiviral Defence LOCator. Our webserver is live and includes several new Doron system subtypes we discovered in collaboration with @NobregaFL and team, @PeterFineran, @clive_ronson and @Benji_JP @microtago
PADLOC (padloc.otago.ac.nz) is ready for you to find phage defence systems in your favourite microbial genomes! You can currently identify CBASS, 'deity' systems and several new deity variants that we've discovered. Updates will be posted here, new systems to be added soon!
1
6
18
@leighton_payne @NobregaFL @PeterFineran @clive_ronson @Benji_JP @microtago Follow @padlocbio for updates on new systems, including unpublished types of phage defence systems. The PADLOC webserver include a list of pre-run RefSeq genomes, or you can uploaded genomes for analysis.
padloc.otago.ac.nz
padloc.otago.ac.nz
0
2
4
SimonJackson retweeted
Covid has highlighted the need to end age of austerity in science funding stuff.co.nz/science/125445…
1
5
22
SimonJackson retweeted
Want to talk about bench ready projects in NZ? Making sure the next generation of research leaders is supported to maintain critical capacity would be a good priority. nature.com/articles/d4158…
1
11
34
SimonJackson retweeted
A new discussion paper released today highlights some of the key issues and concerns of Aotearoa's #ECR population, while providing discussion points for how to safegaurd roles and support early career researchers in the current COVID-19 situation. bit.ly/3ktFlCW
6
41
43