same handle at other places sometimes
re: yeast genetics, dumb cloning tricks, life in the shell, pipelines, methodz and liberation, ๐CFUs๐ colonizing
Questions or comments? Please try the discussion options on the preprint so everyone can see it, and/or email me
Email on preep, also ppiseq AT-THE-DOMAIN-OF rhesis SEPARATED-BY-DOT com
Here's methods for pooled gen of PPI-screening split-tag yeast assay libraries
tldr; is gateway&gibson, then longread+Nextflow(w/ itermae), then select and shortread seq, fitness with FitSeq (fork) - a lotta PPI quants
Also: ~4x your yeast transforms with this one simple trick
Pooled PPIseq: screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform https://t.co/HEGq7whzi2 #biorxiv_sysbio
What do we find? Expressed in yeast, Nsp4 seems to stick to KDELR* - that could be part of mechanism for replication foci formation via retrograde, ORF7B seems to stick to taste-receptors ๐ค, and many more.
Not complete screen, but methods ready for non-specialist applications!
"As our Arab and Muslim neighbors are beaten and silenced, we fear the atmosphere in Germany has become more dangerousโfor Jews and Muslims alikeโthan at any time in the nationโs recent history. We condemn these acts committed in our names."
Check it if you want a pipeline on @gitlab for doing de novo plasmid assembly of long-read data separated out by barcode. Yeah random-fragmentation works and you don't need to know the barcodes ahead of time (but that probably helps)
@nextflow + @SingularityApp
Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries
https://t.co/VjJd0LPSHE
#biorxiv_synbio
Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries
https://t.co/VjJd0LPSHE
#biorxiv_synbio
@mossomest@markowenmartin Thanks for mention. I'd be down to help folks (students etc) work on standardizing a design, just for kicks. It's really cheap, basically a ministat (TM) with the IR LED & sensor setup
Probably start with a batch reactor, do the perturbations manually to show nutrient shifts
@skryazhi@_miloj@s_venkataram Also, I hope the community around the @varianteffects can engage with it. I think there's obviously a lot of methods/skills transfer, and they may have more niche applications to develop on top of and around the work
@skryazhi@_miloj@s_venkataram It looks really good. I haven't had a chance to go through it in detail, but y'all hit on pretty much everything, and I am looking forward to getting into it with a journal club next week. This is going to help a lotta people - good work!
Nice to see this out!
https://t.co/nGoFGiJ1uP
This was such an enjoyable collaboration with @_miloj and @s_venkataram. I learned so much in the process. Thank you guys!
Also thanks to @darachm for giving us valuable feedback on the preprint!
@kevinfolta@MIT@kesvelt 589 cases are vax derived. Esvelt point stands that virus genomes mutates a lot (to simplify), but this is not a sign of someone who is experienced or deeply familiar in what they are talking about.
@kevinfolta@MIT@kesvelt So identifying and studying viruses is valuable because zoonotic spillover is the source of new viral threats, and yes a ranked order list is important for prioritizing limited research bucks, and yes you can get useful research done without it circulating in a pandemic