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Savage Lab

@SavageCatsOnly

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Compartmentalizing your metabolism, and y’know, CRISPR stuff. Account managed by grad students and postdocs 🤙 @UCBerkeley @berkeleyMCB @igisci @HHMINEWS

Berkeley, CA
Joined May 2016
Don't wanna be here? Send us removal request.
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@SavageCatsOnly
Savage Lab
6 months
What limits rubisco function? Is it the chemical mechanism? Evolution? In an updated pre-print @prywes et. al explore this question by assaying >99% of single amino acid mutants in Form II rubisco (1/7)
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@SavageCatsOnly
Savage Lab
5 years
From our lab to yours, Happy Halloween! May your 260/280 always be ~1.8 and your 260/230 fall within 2.0-2.2 🎃🧬🧪 @QIAGEN
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@SavageCatsOnly
Savage Lab
6 months
Former Amgen scholar @caroguerrero522 enjoyed her summer in the Savage lab so much she decided to come back for more. Excited to welcome this Savage Cat back to the lab as a grad student!
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@SavageCatsOnly
Savage Lab
3 years
New collabo with @theJensenLab out now!!
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@theJensenLab
Jensen Lab
3 years
Check out our new @biorxivpreprint with @SavageCatsOnly on RuBisCO lattices in α-carboxysomes:
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@SavageCatsOnly
Savage Lab
6 years
New work out from Savage Cats! “CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification” congrats to Ben, Christoff, Harneet, Kian, Rayka et al!!!!
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@SavageCatsOnly
Savage Lab
4 years
Please RT! We’re looking to hire a postdoc interested in CRISPR biochemistry with a focus on diagnostics! Interested candidates can DM this account or email savage @berkeley .edu with a CV & cover letter.
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@SavageCatsOnly
Savage Lab
5 months
🥳🥳🥳
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@berkeleyMCB
UC Berkeley MCB
5 months
Congrats to MCB's David Savage  @SavageCatsOnly on his promotion to Professor of Biochemistry, Biophysics and Structural Biology! 👏🥂
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@SavageCatsOnly
Savage Lab
3 years
Like and RT this tweet to congratulate Savage Cat @BW_Thornton for passing her qualifying exam and ascending to PhD Candidate! @berkeleyMCB 🥳
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@SavageCatsOnly
Savage Lab
4 years
Our #preprint on MISER, a new technique for minimizing proteins is up on @biorxivpreprint ! Tweetsplainer thread by @realarikshams below, including some neat insights on #CRISPR -Cas9 ⬇️
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@SavageCatsOnly
Savage Lab
3 years
good data is the best high 🤙📈
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@SavageCatsOnly
Savage Lab
5 years
“Onwards and upwards” to a nap!!!
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@SavageCatsOnly
Savage Lab
3 years
the lab is in shambles rn
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@SavageCatsOnly
Savage Lab
3 years
We’ve had much cause to celebrate lately, including bidding a bittersweet farewell to Eli Dugan, our amazing lab manager who is starting his PhD at @UCSF Tetrad in the Fall! 🥳 Also 👏🏾 to our commander-in-chief #Dave ( @dfsavage ) for TEN YEARS at @UCBerkeley 😳😮‍💨🔟
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@SavageCatsOnly
Savage Lab
4 years
Welcome to our newest Savage Cats, Brittney Thornton ( @BW_Thornton ) and Julia Tartaglia ( @juliaamber10 )! Look for great things to come 👩‍🔬🧬 @berkeleyMCB
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@SavageCatsOnly
Savage Lab
5 years
Congratulations to @Nichols_NTA for Best Grad Student Talk at the @berkeleyMCB BBS retreat! 🦠
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@SavageCatsOnly
Savage Lab
5 years
Some #savage #whiteboardwisdom for the new week y’all
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@SavageCatsOnly
Savage Lab
2 years
Our newest Cats have the #synbio community SHOOK! We’re thrilled to welcome @florazhiqiwang , @rachelfweissman , and @rodriguezje1991 to the lab!
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@SavageCatsOnly
Savage Lab
6 years
Introducing the #Savagest BoyBand #42degrees
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@SavageCatsOnly
Savage Lab
3 years
Here’s the tweet you’ve all been waiting for: We’re thrilled to welcome @berkeleyMCB grad student Muntathar Al-Shimary to the lab! 🧬🧑‍🔬😼
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@SavageCatsOnly
Savage Lab
3 years
We are looking to hire a Science Research Associate to work with us at the interface of protein design + CRISPR/Cas + applied gene editing! Please share broadly!
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@SavageCatsOnly
Savage Lab
6 months
Rubisco is, after all, an enzyme, so we wanted to biochemically characterize each mutation. By repeating the assay over CO2 titration, key biochemical parameters (e.g. Vmax, Kc) are estimated for each mutant! (5/7)
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@SavageCatsOnly
Savage Lab
4 years
Huge congrats to our very own Rob Nichols @Nichols_NTA - just posted his paper on the discovery and characterization of a whole new sulfur-metabolizing branch of the bacterial nanocompartment family - "family 2 encapsulins." Rewarding collabo with @bjlafrance and @NogalesLab
@Nichols_NTA
Bobby Digit4L Nichols
4 years
So happy to see our pre-print online!! We discovered an characterized a new prokaryotic organelle - a novel family of encapsulins! With the help of @bjlafrance and the @NogalesLab we determined the structure of the compartment to 2.2 Angstrom resolution!!
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@SavageCatsOnly
Savage Lab
4 years
Incredibly proud of our collaborator, @igisci neighbor, and @berkeleyMCB faculty Jennifer Doudna @doudna_lab for this historic achievement! #CRISPR #WomenInSTEM #GoBears
@NobelPrize
The Nobel Prize
4 years
BREAKING NEWS: The 2020 #NobelPrize in Chemistry has been awarded to Emmanuelle Charpentier and Jennifer A. Doudna “for the development of a method for genome editing.”
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@SavageCatsOnly
Savage Lab
3 years
top o’ the morning, top o’ the morning, top o’ the morning, top o’ the morning, top o’ the morning, top o’ the morning, top o’ the morning
@HHMINEWS
HHMI
3 years
HHMI News: We are proud to announce our 33 new #HHMIInvestigators . These individuals have the potential to make transformative discoveries over time and we look forward to seeing where their ideas lead them.
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@SavageCatsOnly
Savage Lab
6 years
Julia’s qualsified! Come party w us and enjoy some of her EtOH. 4th floor EBB.
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@SavageCatsOnly
Savage Lab
5 years
It’s been a big year for E. coli - she graduated from heterotrophy school and has been learning a lot of new metabolisms! Congrats to Bar-Even lab on the culmination of many years of work!!
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@SavageCatsOnly
Savage Lab
4 years
Resident baller @Nichols_NTA gives his thesis research presentation to start off this year’s virtual MCB TheRPs. Great talk Rob!
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@SavageCatsOnly
Savage Lab
7 months
Qualified✅ NSF GRFP ✅ Join us in congratulating PhD candidate @CynthiaTerrace on passing her qualifying and being awarded the NSF GRFP! 🎉 🎉🎉
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@SavageCatsOnly
Savage Lab
5 years
A huge congrats to Sean and @flamholz ! Onwards and upwards!!
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@SavageCatsOnly
Savage Lab
1 year
Three brand new savage cats ready to hit the lab. We're thrilled to welcome @CynthiaTerrace (and her feline friends) to the Savage lab! 🥽🥼🧪🙀
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@SavageCatsOnly
Savage Lab
5 years
Behind ⁦ @Jjdesmarais2 ⁩ new hot off the presses paper: DAB family transporters are everywhere in prokaryotes!
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@SavageCatsOnly
Savage Lab
4 years
Every day in the Savage Lab we ask ourselves, "what's new with #carboxysome engineering?" If you find yourself new to this line of thinking, fear not! Our own @JuliaBorden has authored a #review on the topic for your reading pleasure! 👇 #synbiothoughts
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@SavageCatsOnly
Savage Lab
1 year
But wait, there's more! New work by Turnšek et al. identifies key residues that drive this assembly, shows the effects of mutation in vivo, and probes the biochemistry in vitro with reconstituted carboxysomes!
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@SavageCatsOnly
Savage Lab
2 years
Congrats to our Certified Fresh™️ PhD candidate Muntathar Al-Shimary on #crushing his qualifying exam! @berkeleyMCB @doudna_lab
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@SavageCatsOnly
Savage Lab
4 years
Big week for #synbio at the Savage Lab!! @flamholz , Eli, @cblikstad , and @MiloLabWIS ’s paper on reconstituting a CO2 concentrating mechanism in E. coli is out in @eLife ! 🦠
@flamholz
Avi Flamholz
4 years
It's alive!!!
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@SavageCatsOnly
Savage Lab
1 year
In the first preprint of the weekend, @loltrogge et al. find that the size of α-carboxysomes is strongly specified by CsoS2 and, in particular, the relative abundance of M- and C-type peptide repeats. ⬇️
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@SavageCatsOnly
Savage Lab
6 months
Small changes in sequence can have big consequences in function, and not only negatively! We hope that this data is useful to other enzyme engineers and that this result expands our view of what is possible with even small changes. (7/7)
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@SavageCatsOnly
Savage Lab
4 years
The year of the encapsulin CONTINUES with our new paper w/ @bjlafrance , Caleb Cassidy-Amstutz, and @NogalesLab . We show that a nanocompartment shell binds flavin, suggesting it could participate in redox chemistry... This one is HOT- call it Thermatoga!
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@SavageCatsOnly
Savage Lab
5 years
. @Flamholz ’s heartfelt farewell address to the lab. “Eat the pizza” —Avi Flamholz, PhD.
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@SavageCatsOnly
Savage Lab
6 months
To address this, @prywes et al developed an assay to estimate the fitness of 99% of single mutations in a high-throughput E. coli screen. E. coli growth rate is linked to enzyme behavior! (3/7)
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@SavageCatsOnly
Savage Lab
4 years
Things our beloved postdoc @cblikstad will miss about California, in ascending order: - the CA sea and sun - working with CArboxysomes - her wonderful labmates, the Savage CAts Please join us in wishing Cissi well as she starts her own group in @chem_angstrom at @uppsalauni ! 🧑‍🔬
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@SavageCatsOnly
Savage Lab
2 years
🌼 𝓕𝓵𝓸𝓻𝓪𝓵 𝓕𝓻𝓲𝓭𝓪𝔂 🌼 at the Savage Lab 🌹🌸🌷🌺🐱🌻💐🌼🪷
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@SavageCatsOnly
Savage Lab
1 year
A light ☀️ read on a dark 🕶️ reaction enzyme. Everything you want to know about “one of the most pivotal enzymes to life on earth”. Brought to you by @NoamPrywes @NaiyaPhillips @owen_t_tuck @luisarchaeota Read it now @AnnualReviews ! 😍📖🔥
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@SavageCatsOnly
Savage Lab
3 years
Another day, another reason to celebrate in our lab. Congratulations to Savage Cat (and now PhD candidate) @juliaamber10 for passing her quals! 🥳🍾👩‍🔬
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@SavageCatsOnly
Savage Lab
6 months
As the entry-point for nearly all CO2 to the biosphere, rubisco is arguably one of the most important enzymes. Yet, Rubisco catalysis is slow. While there are 100s of biochemical measurements, our understanding of catalysis is limited by low-throughput in vitro assays (2/7)
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@SavageCatsOnly
Savage Lab
6 months
Several single AA mutations increased the CO2 affinity! Given sequence divergence and different oligomeric states of Form I & II, we were surprised to find single muts led to CO2 affinity outside of the range of Form II & at the edge of the distribution of plants and algae (6/7)
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@SavageCatsOnly
Savage Lab
5 years
Big congrats to our friends in the Milo Lab @WeizmannScience on publishing this huge achievement: "Conversion of Escherichia coli to Generate All Biomass Carbon from CO2"
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@SavageCatsOnly
Savage Lab
6 months
This assay neatly identified known structural, functional, and evolutionary effects, confirming the robustness of the screen. For example, key residues in Loop 6 and the active site, are mutation-intolerant (4/7)
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@SavageCatsOnly
Savage Lab
2 years
A bittersweet and fond farewell to our lab manager Shin Kim, as he embarks on his med school journey at UCLA!
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@SavageCatsOnly
Savage Lab
2 years
Our talented technician, Emily Meier ( @emileedle_ ), is off to @HopkinsCMDB for her PhD! Emily has been a wonderful and valuable member of the lab and the diagnostics team, and we’re excited for her adventures in Baltimore! 👩‍🔬🧬✌️
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@SavageCatsOnly
Savage Lab
3 years
Dave breaks a 10 year Twitter silence to shout out #woodgang 🌱🌳🪵
@dfsavage
Dave Savage
3 years
Planted 70 trees to celebrate dads ~70th at the home place in Iowa. Does this count for #chalkitdown ? @SavageCatsOnly
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@SavageCatsOnly
Savage Lab
6 years
Congrats Emeric on passing his qualifying exam!!!!!
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@SavageCatsOnly
Savage Lab
3 years
“what I cannot create, I do not understand. what I cannot understand, I must destroy.”
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@SavageCatsOnly
Savage Lab
6 years
Everyone should read this fabulous paper from Manajit Hayer-Hartl’s lab. We saw her speak about it recently and it is phenomenal work that explains a lot about beta carboxysome formation.
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@SavageCatsOnly
Savage Lab
3 years
Wowww, carboxysomes? 😯 Carbonic anhydrases?? 😮‍💨 RUBISCO??? 🤯 This preprint from Savage Cat @cblikstad (now Group Leader at @UU_University ) has it all!! Check out the thread below for an explainer. Congrats Cissi et alia! 🦠
@cblikstad
Cecilia Blikstad
3 years
Happy to share that our work on how carbonic anhydrase encapsulates into α-carboxysomes is now on Biorxiv. Tl;dr: We discovered a carbonic anhydrase-Rubisco supercomplex and solved a sub 2 Å cryoEM structure. @SavageCatsOnly @berkeleyMCB 1/
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@SavageCatsOnly
Savage Lab
4 years
BREAKING: Jason Derulo has fallen down the stairs at the remote BBS retreat on zoom
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@SavageCatsOnly
Savage Lab
4 years
🆒🆕 Super cool work by @patrick_pausch et. al. on the characterization of a new CRISPR protein, CasΦ, that can cut dsDNA despite being ~half the size of Cas9! 🧬✂️
@patrick_pausch
Patrick Pausch
4 years
Very excited to share my first postdoc paper. We experimentally characterized the hypercompact CRISPR-CasΦ system (type V-J). At half the size of Cas9, CasΦ is still able to cut dsDNA. Great collaboration with @themicrobeguy , @ScienceMagazine (1/6)
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@SavageCatsOnly
Savage Lab
6 years
Savage cats do Halloween. Costumes include: unicorn pusheen, triceratops, @scotusginsburg does science, and quite possibly the best Mario and Luigi you will ever see IRL!!! 🦄🐱🦖👩‍⚖️👨🏻‍🔧👨🏻‍🔧
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@SavageCatsOnly
Savage Lab
2 years
Whew, we've got a double-whammy preprint drop for you to peruse this weekend! @flamholz & Eli et al, along with Renee @Caltech GPS & @Nichols_NTA has a step-by-step guide on how to develop a superpower ⁽ᶦⁿ ᵇᵃᶜᵗᵉʳᶦᵃ⁾ 🦠💪⚡️ 1/3
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@SavageCatsOnly
Savage Lab
6 years
New work out by #SavageCat @3rdFloorTom ⁩ - Oblong structure of the complex I-like molecule NDH of oxygenic photosynthesis | Nature
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@SavageCatsOnly
Savage Lab
4 years
Thrilled to see what @scribetx (co-founded by Savage Lab alum @BenjaminLOakes ) has in store for the #CRISPR therapeutics space!
@scribetx
Scribe Therapeutics
4 years
1/ We are excited to take the wraps off Scribe Therapeutics - a molecular engineering company focused on building best-in-class in vivo therapies to permanently treat the underlying cause of disease. Read our launch press release:
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@SavageCatsOnly
Savage Lab
4 years
Congrats to Rob on a great PhD!!! 🍻🍻Rob set out to answer some of the great mysteries of the prokaryotic nanocompartments (AKA encapsulins) for his dissertation. Turns out there are a bunch of these systems and there are even more questions/ mysteries now!
@Nichols_NTA
Bobby Digit4L Nichols
4 years
Dr. Robert Nichols 🍾🤙
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@SavageCatsOnly
Savage Lab
5 years
Savagest beach day. Tough life out here.
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@SavageCatsOnly
Savage Lab
6 years
Pretty #Savage perspective out in Biochemistry describing recent work by Manajit Hayer-Hartl's lab showing that liquid-liquid phase separation of rubisco+ccmM underlies the formation of the beta carboxysome. Wise words by @cblikstad @flamholz and Luke
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@SavageCatsOnly
Savage Lab
4 years
Congratulations to @flamholz , Eli, @cblikstad and @MiloLabWIS collaborators - this paper is the culmination of many years of work, and many decades of collective effort studying bacterial CO2 concentrating mechanisms. So exciting to see it in the world!
@flamholz
Avi Flamholz
4 years
So happy that our new manuscript "Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli" is up on @bioRxiv
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@SavageCatsOnly
Savage Lab
3 years
Amazing work by @JoshCofsky of @doudna_lab figuring out how exactly DNA is interrogated by Cas9! If only we had this for all the engineered variants out there… 👀😮‍💨
@JoshCofsky
Josh Cofsky
3 years
New pre-print! While #CRISPR -Cas9 searches through the genome, how does it actually "read" DNA sequence information, which is normally hidden within the double helix? We determined structures of Cas9 in the act of DNA interrogation to find out! Thread below 👇 (1/8)
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@SavageCatsOnly
Savage Lab
5 years
Important application of CRISPR tech - isothermal 10 min detection of #covid19 . @mammothbiosci @igisci
@mammothbiosci
Mammoth Biosciences
5 years
We've updated our white paper, "A protocol for rapid detection of SARS-CoV-2 using CRISPR: SARS-CoV-2 DETECTR." Check it out to learn how our DETECTR platform could be used to detect SARS-CoV-2 #COVID ー19 #COVID19 #CRISPR #Diagnostics #CRISPRDx
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Savage Lab
6 years
Congrats to Daniella and the Merchant lab on publishing this amazingly comprehensive view of Chlamydomonas physiology and gene expression
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@SavageCatsOnly
Savage Lab
2 years
👑 Capping off the end of a successful summer CRISPRing plants with @AmgenFoundation Scholar Carolina Guerrero! Look out for her next year in a PhD program near you 👀 #amgenscholars 🌱
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@SavageCatsOnly
Savage Lab
1 year
Back at it with another double preprint drop 📝📝Starring the repetitive, disordered, and “mysterious” scaffold protein CsoS2 and its role in the α-carbozysome. Two (Twitter) threads incoming! 🤩
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@SavageCatsOnly
Savage Lab
5 years
Here's the updated preprint from @mammothbiosci
@mammothbiosci
Mammoth Biosciences
5 years
Read our @medrxivpreprint co-authored with @cychiu98 ’s lab @UCSF to see how our #CRISPR -based DETECTR lateral flow assay can precisely detect SARS-CoV-2 in real patient samples! #COVID19 #CoronaVirus
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@SavageCatsOnly
Savage Lab
6 years
After the climate apocalypse, when Earth atmosphere is all reduced again, Rubisco gonna party like its 3.2 bya.
@KingLabWOTD
Fossilized Word of the Day
6 years
Today, @SavageCatsOnly would like to remind you: quantity =/= quality. @Choano_Lab might have this Twitter the rest of the year, but we only need one week 💁‍♀️💁‍♂️. RuBisCO™️: trade name for the worst-tasting yet most abundant rhubarb-flavored cookies on the planet.
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Savage Lab
2 years
Woohoo! Now that it’s twitter-official, we can post this video from Maria’s celebration from >a month ago 🍾
@MariaLukarska
Maria Lukarska
2 years
Very honored that I have been awarded the @LSRFdtn postdoctoral fellowship! I'm really happy to join this community and grateful for my amazing lab @SavageCatsOnly and my mentor @dfsavage for their continued support!
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@SavageCatsOnly
Savage Lab
6 years
We find that our Monday experiments consistently run a little smoother when bacon, eggs, and mimosas are added to the reaction mixture 🤙
@KingLabWOTD
Fossilized Word of the Day
6 years
#SavageWeek is over! As @KingLabWOTD reverts back to its steady-state next week, we'll be honoring the @SavageCatsOnly tradition of Mimosa Mondays 🥂 with 96-well-format DIP. DIP-seq​ (n.)​: (alt. "dip-seek") A high-throughput strategy to locate the best dip for group meetings.
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@SavageCatsOnly
Savage Lab
3 years
I’m outside with the PCC, right outside, 6803
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@SavageCatsOnly
Savage Lab
6 years
Onwards and upwards Seanathan safety officer and protein engineer supreme! #graduation #savagecats
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@SavageCatsOnly
Savage Lab
3 years
Esteemed alum @3rdFloorTom making moves !! 💪👀
@LSRFdtn
Life Sciences Research Foundation
3 years
LSRF is pleased to announce our 2021 class of awardees! We thank our outstanding team of reviewers and, of course, the organizations and individuals providing the funding for these researchers. Congratulations! #BasicResearch , #LifeScience , #PostdocFundin
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@SavageCatsOnly
Savage Lab
5 years
Finally a structure of the cyanobacterial CO2 uptake complex! For those who don't know, cyanos can take up both CO2 and HCO3-, but the CO2 uptake mechanism is complex and mysterious. Amazing contribution to the CCM field. Congrats to @SchullerJm @TheKailaLab @NowaLab et alia.
@TheKailaLab
VilleKaila
5 years
We proudly present how cyanobacteria efficiently concentrate CO2 from the atmosphere with the remarkable photosynthetic complex I. Great collaboration with @NowaLab and @SchullerJm . @NatureComms @ERC_Research @2017Kaw100 @Stockholm_Uni
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Savage Lab
5 years
Important lessons on the history of the CRISPR revolution by one of our own @Nichols_NTA 🧬
@Nichols_NTA
Bobby Digit4L Nichols
5 years
I made a video about the CRISPR patent dispute. Parody of "Obedient Servant" from the musical Hamilton by Lin-Manuel Miranda.
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@SavageCatsOnly
Savage Lab
6 years
Mega congrats to our very own ⁦ @nicholsr2528 ⁩ on his lifetime #FolliesAchievement award jawn.
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@SavageCatsOnly
Savage Lab
6 years
Great BBS retreat this year @berkeleyMCB - excellent talks and posters, beautiful beaches, awesome food and people. Onwards and upwards!
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@SavageCatsOnly
Savage Lab
6 years
If you like our work on cas9, just wait for our work on the enigmatic #cas22b it’s #13b better! #synbio #incrementalism #wejustmakethesenamesup
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@SavageCatsOnly
Savage Lab
2 years
It’s time to 🌿BeReal🌿
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@NoamPrywes
Noam Prywes
2 years
Here at @SavageCatsOnly we are thrilled to present a review on rubisco. We focused on structure, mechanism, evolution and engineering attempts. We try, and fail, to conclusively answer the question "What exactly is holding this enzyme back?" 1/10
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@SavageCatsOnly
Savage Lab
6 years
FPbase is inspiring, super useful and not to be confused with fbpase, metabolism friends!
@TalleyJLambert
Talley Lambert
6 years
@FPbase is published in @naturemethods ! So very thrilled to see what started as a fun side project get released today in one of my favorite journals. Thank you @rita_strack for the encouragement.
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@SavageCatsOnly
Savage Lab
8 years
Congrats to Dana and Stacy! Check out their new paper on making metabolite biosensors!
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@SavageCatsOnly
Savage Lab
5 years
When our boy @evan_groover isn’t busy enough transforming plants he’s on the sax
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@SavageCatsOnly
Savage Lab
4 years
Just out from @3rdFloorTom - a really clear and comprehensive review of recent structures of photosynthetic NADH dehydrogenase-like complexes (NDH-1). Super clear figures and explanation of structure/function relationship for plants/cyanos/algae.
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@SavageCatsOnly
Savage Lab
6 years
Need a quick primer on #scicomm and #sciencetwitter ? You probably do. Our own @JuliaBorden wrote a Toolbox for the latest edition of @BerkeleySciRev ! Pick your copy up today! 🤙🤓 (We won’t comment on the fact that this account is not on the “suggested people to follow” list)
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@SavageCatsOnly
Savage Lab
5 years
#SavageCats aspire to celebrate all the news year. #ShanaTova
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