Mark Budde
@markwbudde
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Co-founder and CEO - Plasmidsaurus & Primordium Labs. Prev work: Synthetic mammalian quorum-sensing and pop control; intMEMOIR to optically encode cell lineage.
Pasadena, CA
Joined June 2009
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Here is the full sequence of the Pfizer vaccine, courtesy of the WHO. 4284 nucleotide, 1273 amino acids. All U are 1-methyl-3'-pseudouridine. PolyA has strange structure, is broken up with GCAUAUGACU.
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On this day in 1977, Fred Sanger published the first paper demonstrating "Sanger sequencing", opening the doors to read DNA and earning him a 1980 Nobel prize. Absolutely revolutionary work🫡
The first Sanger sequencing image. Figure 1, PNAS 74:5463:5467 1977
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@pitdesi
It also has no date but doesn't say "ad". Some sort of special case to goose Mr. Beasts views on X.
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I'm excited to announce I'm leaving Caltech for my dream of building a synthetic biology company. Along with a great group of people, including the brilliant
@ElowitzLab
, we founded
@PrimordiumLabs
with the sole purpose of accelerating cutting-edge synthetic biology research. 1/
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Amazing testing results! Abbott PanBio Rapid Antigen Test: ZERO false positives in 1575 symptomatics. 96% sensitive for patients Ct<32, and 100% sensitive for patients Ct<28 (most infectious). 50¢ to manufacture and $7 in Germany. Banned in USA.
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This is scary. 50% of asymptomatic SARS-CoV-2 patients had abnormal lung CT scans.
Asymptomatics with
#COVID19
: 3 new publications today
@TheLancetInfDis
+
@NEJM
Diamond Princess-> Japan & Hong Kong
Asymptomatic persisted in >50%; mostly older age predicts; but 50% w/ abnormal CT scans
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@TenreiroDaniel
My favorite reverse gaslight: I'd like the worst thing on the menu. What do you think the worst thing on the menu is?
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Primordium is now offering everyone the chance to sample our full-plasmid sequencing service for FREE - never use Sanger sequencing again! Please retweet this message and we'll DM you a coupon to sequence 5 ENTIRE PLASMIDS 100% FREE, no CC or PO needed. 5/
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How can you reconstruct the lineage history of an organism without disrupting tissue organization? Introducing intMEMOIR - An optical lineage reconstruction technology developed as a collaboration with
@GraceKC
,
@ElowitzLab
, Alejandro Granados, Carlos Lois, and more. 1/
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Big day for me, now leading Plasmidsaurus! So many plans for the unified company and we need people to help us grow. Shoot me a DM or email if you love working on sequencing, bioinformatics, robotics (Opentrons), web development, or anything else that might interest us!
BIG NEWS! We are thrilled to share the news that
@PrimordiumLabs
and
@plasmidsaurus
have joined forces, forming a single company with a unified mission of accelerating scientific discovery through innovations in DNA sequencing!
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TODAY IS THE DAY! I’m unbelievably excited to announce that today I start leading a group
@Caltech
to apply synthetic biology circuits for human therapies w/
@elowitzlab
. And we are hiring.
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Synthetic biology for therapy will require control of population density. Can you design a quorum sensing system that enables cells to sense, respond to, and control their own population density? We designed one with a paradoxical control circuit. /1
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Are there any incredible biotech/ synbio/ molecular bio podcasts? They mostly seem focused on branding and promoting the guest, instead of interesting discussions.
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Charlie Munger live on Caltech seminar right now “I watched polio get totally killed by the vaccinations. The vaccines will spread over the world so fast it will make your head spin. This horrible COVID will then shrink to insignificance.”
Let’s hope so!
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My lovely wife
@elizabeth_budde
solved 3 medical emergencies on our flight to Germany (and didn't have time to work on her slides). 👩🏻⚕️🦸♀️
At the gate for the return flight, they alerted her of potential patient and that they would come to her right away if issues come up.
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Thanks to
@ATinyGreenCell
for sending these colored plasmids to play with. They really are this intense 🤩
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Plasmidsaurus cereal at the BioProcess conference in Boston. Can you decode the secret message?
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@ebennettlab
When posting on BioRxiv, I’m still excited about the work. When the paper goes live on the journal website, I am completely sick of the paper and dealing with reviews, and have mentally moved on to a different project.
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Beautiful. Simple. Elegant.
A few TFs enable complex synthetic transcriptional states. Each additional TF adds many potential transcriptional states without modifying the original TFs. Figure 4 will be a classic. Congrats
@RonZhu2015
&
@ElowitzLab
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Exposure to cutting edge research brought me to Twitter. Maybe I’m following the wrong people, but my feed is now just people complaining, mostly about academia. Is it just my feed, or has Twitter gotten worse?
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If you are running a company, or thinking about starting a company, you should be listening to
@FoundersPodcast
Incredible to hear
@lexfridman
recommend listening to Founders in his excellent conversation with
@JeffBezos
!!
(First 10 seconds of this clip!)
I love how Jeff points out the important role books and long form podcasts can play in increasing attention span and focus.
Lex
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My Biden story: Summer 2010, our family was simultaneously having our first child and closing on our house. On our way to the hospital, my wife added an email auto-reply to say she was on maternity leave. 🤰 1/ 7
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Me: Illustrate the fact that no primers are needed for whole plasmid sequencing, which makes the scientists super happy
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Postdocs are such an ideal asset. Smart, willing to work long hours for artificially depressed wages, and a proven track record of success. It’s great that a tight labor market means there is finally a real alternative. Love to see the postdoc shortage.
Is it me or are there 10x the postdoc openings as there are PhD graduates??? 🤔🤔🤔
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The perfect fortune for my colleague after I share the bench.
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This is revolutionary work - enabling new workflows in genome engineering. Thanks
@mgdurrant
and
@ntperry13
for sharing this work, can't wait to try it out. And thanks
@pdhsu
and
@arcinstitute
for continuing to accelerate bio!
Just shared at
@KeystoneSymp
a new
@ArcInstitute
discovery of the bridge RNA recombinase mechanism: a new class of natural RNA-guided systems that retains the key property of programmability from RNAi and CRISPR while enabling large-scale genome design beyond RNA and DNA cuts
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We'll start merging
@plasmidsaurus
and
@PrimordiumLabs
labs over the next month. Anything you would like to see?
(Also, we're looking for an all-star Front End Dev to build our next gen interface! Please email me mark
@plasmidsaurus
.com with cover letter and CV if interested)
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Cool new genome engineering tool from scientists at
@AstraZeneca
. Knocking your gene of interest into the Diphtheria Toxin Receptor locus, along a DT insensitive exon, creates population with homogenous gene expression. Useful for
#synbio
.
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Cas9-integrase fusion for inserting 36kb constructs into primary T cells? 🤩
This will be absolutely revolutionary if it holds up. And, given my experience with how amazing serine integrates are, I completely expect it will hold up. Can’t wait to try it!
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The descent of a COVID skeptic, in 10 steps:
1. 🙅♂️ Coronavirus isn’t real.
2. 🌅 Coronavirus will go away on its own from warm weather.
3. 🧪 Cases are increasing because of testing. More tests means more cases.
4. 🏥 Percent positive is going up because of targeted testing.
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Congrats to
@kkariko
&
@WeissmanLab
! They chose the original modifications, not because they were biologically significant, but because they could easily be ordered from
@TriLinkBioTech
. MAKE LIFE EASY FOR SCIENTISTS!
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Thanks to the
@PrimordiumLabs
and
@plasmidsaurus
team (and spouses) for merging our websites on Mother's day. Everyone can now access all services and dropboxes! This new website will enable us to rapidly push new features. Stay tuned!
Check it out:
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We spent the past year building Primordium Labs. Our first product, rapid whole-plasmid and long-PCR sequencing, aims to make full-plasmid sequencing as routine as a miniprep.
Bonus: NO SEQUENCING PRIMERS NEEDED.
Retweet the next tweet for a free trial 👇👇👇 4/
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Pretty sure we have the fastest and most innovative lab automation team in history at
@plasmidsaurus
🦖🦕🧬🤖
There is nothing more fun than working with a team of high-agency top performers to unlock new capabilities that others claim are impossible.
This team rocks! 🦾
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Has your science ever failed because of undetected mutations in your plasmids? For most people, the answer is likely "yes", but they might not know it. We're taught to only sequence the insert, but we have learned the hard way that backbone mutations commonly derail projects. 2/
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I’m old enough to remember when we called rCutSmart buffer “NEB Buffer 4 + 1/100 BSA”
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😳
Bioorthogonal information storage in L-DNA with a high-fidelity mirror-image Pfu DNA polymerase
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@OdedRechavi
Those same members watching the same joke, delivered by the university president:
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Who designed the horrible PMC layout, and why is Pubmed still using it? Raw LaTeX is more readable.
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@arjunrajlab
@ElowitzLab
constantly drilled into us the importance of clear, active sentences for slide titles. Not only helpful for the reader, but also clarifies what to put in the text.
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So happy to hear these stories. 😊
I’ve never worked so hard on my life. Eg, pulling all-nighters because a car-jacking on the bay bridge delayed our logistics and we live by fast results.
It’s great to hear the amazing science from our customers.
Worth it
@BJ_Greber
@plasmidsaurus
Had similar experience (mostly with large plasmids) and then switched to
@PrimordiumLabs
, works much better for me
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Are you a top-tier software engineer looking to solve real problems and accelerate biotech? Our talented and dynamic software team at Plasmidsaurus is pushing SynBio forward and we are looking for fun, super cracked colleagues. Interested?
(please RT)
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🤩Just learned about the new python string format system. This is amazing.
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What are your favorite rock-solid restriction enzymes? We are starting a new project that will use the same sites over and over. HindIII and EcoRI are good. What else?
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@TonyBurnetti
I think so. Earliest ref I can find is this BioNtech paper.
They cite their own review, which mentions how plasmids with >100 polyA are unstable, but doesn't mention the linker.
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@DaveLeeBBC
@elonmusk
It's almost like he knows how to use public support to pressure the govt to give him what he wants.
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Proud of the real Dr. Dr. Budde
@elizabeth_budde
for donating her entire Sunday to vaccinate thousands at the Pomona Fairplex. One step closer to this thing being over.👩🏻⚕️💉💪
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Thanks for your support and stay tuned as we announce more tools to accelerate the synthetic biology revolution.
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If you retweet within the first 48 hours, you will receive a DM from
@primordiumlabs
with your unique code and submission instructions.
*Note: you must either follow
@primordiumlabs
or have your DMs open, otherwise there is no way to send you the code. 6/
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@joanneintexas
@DrMattMcCarthy
@lrozen
There are plenty of masks in China. People have not been importing them because of regulatory fears. I imported 10,000 this week and gave them away to all public facing employees in my city.
Since the government was dragging their feet, I imported and delivered thousands of masks to all public facing businesses in Arcadia and Monrovia California. By preventing spread in our community, we will keep many people healthy.
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“Seaspiracy” on Netflix is a pretty good documentary about how all of the plastic in the ocean is from fishing, but the fishing industry funds the anti-oceanic-pollution campaigns, so we don’t hear about it. Instead we ban straws and keep eating wild caught fish.
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8. 👮♂️ People are dying, but the mitigation kills more people than the virus.
9. 🤒 Many people are dying, but it is not worse than a bad flu.
10. ☠️Everyone is dying. But everyone dies anyway. This is just survival of the fittest.
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About quantitative easing:
“We're in very uncharted waters. Nobody has ever gotten by with the kind of money printing we're doing now for a very extended period, without some trouble. And I think we're, we're very near the edge of playing with fire.”
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If you have the slightest interest in synbio, subscribe to the Cell Crunch newsletter RIGHT NOW! Don't miss out on tomorrow's synbio breakthroughs -
@NikoMcCarty
is KILLING IT!
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Promoters, LTRs/ITRs, antibiotic resistance genes, origins, etc, all commonly mutate.
Best case: an experiment gives misleading results.
Worst case: years are spent characterizing or publishing an artifact. This happens all the time and is completely avoidable. 3/
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Anecdote request: Ever found a plasmid mutation not in your insert that caused you problems?
For instance, your piggyBac vector didn’t work because the LTRs got messed up.
Or TC selection didn’t work - thought the insert was toxic, but selection marker was actually mutated.
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I'll never know what scientific barriers they are talking about. Clearly they aren't talking about barriers to access.
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I'm in SF this week setting up our new lab!👨🔬 Who should I meet?
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Amazing that off-the-shelf bispecific antibodies give the benefits of CAR-T without the hassle and improved safety profile.
Presented now by
@elizabeth_budde
at
#ASH23
: In a phase 1/2 trial, mosunetuzumab, a CD20-CD3
#bispecific
, + polatuzumab vedotin, an anti-CD79B
#ADC
, had an overall response rate of 59.2% in patients with r/r large B cell
#lymphoma
@JulioChavezMD
#lymsm
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Are there any in-person meetings this summer? I don’t even care about the topic, I’d give anything for a good old-fashioned science discussion with new friends.
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Have there been superconducter screens, similar to how biologists do genetics screens? Create tiny amounts of millions of different allows, place them over a magnet at increasingly low temperatures and blow away the non-diamagnetic materials? Analyze what remains and repeat.
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@millerlab
@mbeisen
You hear a lot about a “rogue postdoc”, but much less about the PI who insisted on producing impossible results.
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Oldest thing in our lab is a microscope Ed Lewis used for his Nobel Prize winning work on Hox genes.
Found this bottle of Triton that I reckon could be from the 70s??
What’s the oldest thing you’ve found in your lab? Points for not saying your PI! 🤣
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Everyone please stop saying there is 1000x viral load! That is only true at early timepoints, because it replicates faster. Max viral load is 2-4x.
Avoid the "Delta stress test"
1. This 🦠version is far more transmissible w/ >1000 X viral load than the original
2. Vaccines still are protecting well vs severe illness but we're seeing an increase in breakthroughs & disease
3. 😷 helps; 💉synergy
4. This wave will pass
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@EdwardJacksonD
Not so sure about selecting for candidates who want to use the office to maximize income.
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So please visit and learn how much simpler research can be. It can be more efficient, much cheaper, and more reliable - allowing you to focus on the scientific questions you care about rather than tracking down mutations you don't! 7/
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HUD took care of everything and the lawsuit settled. I wish it hadn't been needed, but we are still thankful to Joe Biden for getting the ball rolling. And I wish it wasn't needed, but hope he continues the fight for justice throughout his presidency!
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Dinosaur shaped cornbread at
@plasmidsaurus
and
@PrimordiumLabs
HQ. Watch for the meteor ☄️ 🦖🦕🧇
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Our (Elowitz and Cai labs) new proof-of-principle paper showing in situ lineage reconstruction in mammalian cells.
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@michaelmina_lab
@paulmromer
We need to make this available to everyone, ASAP!
Amazing testing results! Abbott PanBio Rapid Antigen Test: ZERO false positives in 1575 symptomatics. 96% sensitive for patients Ct<32, and 100% sensitive for patients Ct<28 (most infectious). 50¢ to manufacture and $7 in Germany. Banned in USA.
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Since the government was dragging their feet, I imported and delivered thousands of masks to all public facing businesses in Arcadia and Monrovia California. By preventing spread in our community, we will keep many people healthy.
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@jmaemontgomery
Woah, that's incredible! Did a company make a knockout pig? And more details on where you got it?
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5. 🧂 Rates are increasing because they are “salting” the numbers.
6. 👶 Infection is spreading, but only in young, healthy, low risk people.
7. 👴 Infection is spreading to everyone, but only kills people who would have died anyway.
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Amazing talk by
@KizzyPhD
on mRNA COVID vaccines. Some new info:
“The only reason it took 48 hours to design the sequence is because it was a weekend. It actually only took about an hour to come up with the vaccine sequence” -> 41 days for Moderna to ship first drug product. 1/4
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Heartfelt congratulations, Dr.
@ma_yitong
! Your remarkable achievement in enabling quorum sensing in mammalian cells during your PhD defense in synthetic biology is a testament to your hard work and dedication. It was a pleasure to work with you. Best wishes for a bright future!
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How cool is this? ZincFinger-KRAB targeting NaV1.7, a pain signal, provides pain relief for at least 105 days when delivered via AAV in mice. If we can solve immunogenicity issues, similar treatments could cure many (most?) chronic diseases.
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How are your kids doing? Mine haven’t been in school since March, haven’t seen most of their friends for a year, and it’s starting to get ugly. Zoom isn’t enough.
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@trvrb
While we don’t yet know, it might cause milder symptoms upon reinfection after antigen escape, becoming just another coronavirus. Time will tell.
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The entire web came from inside the spider, and is made from bugs caught in previous webs.
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@breakliquid
There is best way to do this: write plate name on the frosted top of the plate, pipette 100 ul of tx cells on the other end. Add about 10 glass beads. Then, hold the plate at about 45 degrees with the cells at the bottom and shake back and forth. You will get a nice gradient.
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Clicking “not interested in this tweet” on every frustrating tweet mostly fixed the problem. Give it a shot.
Exposure to cutting edge research brought me to Twitter. Maybe I’m following the wrong people, but my feed is now just people complaining, mostly about academia. Is it just my feed, or has Twitter gotten worse?
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@drugmonkeyblog
@mbeisen
💯💯💯💯 everyoneone should work an hourly job as a kid, it gives perspective. What has everyone else done?
Me:
-paperboy
-warehouse worker
-trophy assembler
-tropical fish sales
-rental care clerk
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If you want to use cutting-edge synthetic biology to improve human health, please check out our job postings. Feel free to contact me directly if you don’t think the job descriptions are a good fit. Please RT.
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@carlzimmer
I heard Charlie Munger say this yesterday, very hopeful.
Charlie Munger live on Caltech seminar right now “I watched polio get totally killed by the vaccinations. The vaccines will spread over the world so fast it will make your head spin. This horrible COVID will then shrink to insignificance.”
Let’s hope so!
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