Scott Saunders
@s_h_saunders
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Distinguished Fellow @UTSWNews / 🧬 Bacterial genetics enthusiast 🧫 / Caltech PhD (biofilms & redox) / Open & reproducible science (he/him)
Dallas, TX
Joined January 2018
The “ORBIT for E. coli” paper is out in Nucleic Acids Research! **Perform genetics (e.g. deletions) without any PCR / cloning – just transform an oligo!**. The paper demonstrates benefits over λ Red & shows how oligos scale to high throughput libraries.
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Dallas is also a nice place to live - 4th largest metro area in US, so there's a huge diversity of people, neighborhoods, food and jobs. There's 1 week left to apply. Please reach out to us if you have any questions or concerns!. 4/4
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Beyond our corner of the 11th floor, UTSW is an amazing place to do basic science. There are excellent grad programs, very nice core facilities, and top notch faculty (including practicing MDs)!. E.g. Dave Greenberg, Erdal Toprak, @CaoXinyun, @kvnforsberg, Boyuan Wang. 3/4
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We see many different types of science fitting under "systems biology" - the key is work that combines wet lab & dry lab (computation/theory) efforts. Interests might include genetics, physiology, syn bio, communities, or evolution. We are open minded!. 2/4
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Please help me amplify a special faculty search. We're looking for someone in "Microbial Systems Biology" to join me and @kimreynolds_lab at UT Southwestern Systems Bio / Bioinformatics. There is an empty lab space right next to us waiting for you!. 1/4
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We just had our dept retreat this week at the @PerotMuseum. Pretty awesome to have a poster session with the dinosaurs!. Thanks to everyone that helped plan! @Papu_Sci @LHBioinf_UTSW @gabrielgihana @MiloLinLab @kimreynolds_lab
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RT @aliciakrogers: 🎉🪱🎉 Congratulations to Victor Ambros and Gary Ruvkun! Everyday is a great day to be part of the Worm Small RNA Community….
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Come join us at UT Southwestern! . It's a very nice place to do science. There's an extremely strong basic science community and there are interesting opportunities to connect to the clinical side of the institution.
Announcing a new tenure-track faculty search in microbial systems biology! Come be my neighbor and join a fantastic ecosystem of systems biologists and informaticians. Application deadline is Nov 29.
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RT @jkpfeiff: Faculty search announcement: Tenure-Track Assistant Professor in Microbiology at UT Southwestern. We seek candidates working….
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RT @aliciakrogers: Excited to share the first Rogers lab paper is officially out at Nucleic Acids Research! . RNAi….
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RT @kvnforsberg: I couldn't be happier for @luis840alberto, who was named one of 50 #GilliamFellows by @HHMINEWS. I'm very grateful that L….
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Looks awesome David! Very nice way to get around bottlenecking.
"InducTn-seq, which leverages inducible mutagenesis for temporal control of Tn5 transposition. InducTn-seq generates millions of transposon mutants from a single colony."
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Congrats! Very cool way to do in vivo biochemistry.
Physical protein interactions constrain interface sequence. But what about non-binding "biochemical" interactions in metabolism? We used deep mutational scanning to map sequence constraints for two enzymes that catalyze consecutive metabolic reactions:
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Thanks again to the many people that have interacted with me on this ORBIT adventure. Here are some of them that are on Twitter!. @kimreynolds_lab.@mrazomej.@TRoeschinger.@gdchure.@DavidWBasta.@LHBioinf_UTSW.@aliciakrogers
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If you want advice for getting ORBIT to work in your system, or you potentially want to collaborate, or you just think this stuff is cool – please don’t hesitate to reach out!.
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I’m quite excited about oligo genetics and I think there’s huge potential for performing genetics in diverse bacteria! I also believe this will be useful for making very interesting mutant libraries.
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…and we have tried to compile more info on the lab website, including protocols and FAQs. We really want ORBIT to be accessible to any lab, so we will do our best to update this page with helpful info.
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We have some quick “Targeting Oligo Design App” tutorials on YouTube….
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To help users design oligos, there’s an app! Just click on a gene and get an oligo - ready to order!. A new feature outputs the modified locus, so users can easily check strains (w PCR / Sanger). Aside from MG1655, this could be a useful learning tool.
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Nearly all the ORBIT plasmids are now available on Addgene!. To get started, order at least one helper plasmid and one integrating plasmid. We recently created a temperature sensitive pHelper (TS_V2_ampR) that works beautifully – I highly recommend it.
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My original thread on the preprint explains how ORBIT works in detail and walks through the paper. I just have a few updates in the thread below.
Our 1st preprint!. We developed a genetic toolkit for E. coli that directly uses cheap DNA oligos to specify kb scale mutations. No PCR/cloning to delete genes!. The paper demonstrates benefits over λ Red & gets fancy w/ pooled mutant libraries. 1/15.
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