Synthetic Biology & Synthetic Genomics @ Imperial College London and the Sanger Institute. Bilingual in English and DNA. D-/L-
London
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My wife complains that I empty the egg box funny, but she won’t be laughing if our kitchen suddenly becomes a centrifuge.
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For those who follow these things; Ambros did his PhD with a Nobel winner, and postdoc with another Nobel winner. Ruvkun did his postdoc with a Nobel winner too.
BREAKING NEWS
The 2024 #NobelPrize in Physiology or Medicine has been awarded to Victor Ambros and Gary Ruvkun for the discovery of microRNA and its role in post-transcriptional gene regulation.
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Just gave a lecture on eukaryotic synthetic biology. Not my normal lecture set-up but seemed to work 😃 My daughter’s Frozen wand made a good pointer 💎
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Spare a thought for UPenn’s public relations team today trying to work out what to say about the Medicine Nobel Prize going to one of their Profs and another Prof they kicked out for not doing faculty-level research.
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Mirror image DNA polymerase has been engineered 🤯
Bioorthogonal information storage in L-DNA with a high-fidelity mirror-image Pfu DNA polymerase go.nature.com/3j1IbPF
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Cellulose shoes made by bacteria | Nature Biotechnology
short profile of our collaborators and friends at Modern Synthesis nature.com/articles/s41587-0…
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Why is Nanodrop so bad at giving the right concentration of our miniprepped plasmids? Look at the gel and table. We Qiaprepped 13 plasmids from NEB Turbo cells, read the conc. on 2 different Nanodrops and a Qubit and then did test digest and gel. Only Qubit matches the gel data🤷♀️
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In movies when an alien appears to threaten humankind, the whole world comes together to fight as one. In real life when 30kb of RNA threatens to collapse every country's healthcare system we can't even agree on what time to shut the pubs.
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Our paper on growing engineered living materials from a kombucha-inspired symbiotic culture of bacteria and yeast is published today in @NatureMaterials
Here comes a tweetstorm about it.... 🌪️
nature.com/articles/s41563-0…
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Wow. After years of planning and waiting our new lab space @ImperialBioeng is finally open.
🎉🎉🎉
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I've finally got to level-up my Twitter handle to @ProfTomEllis - my promotion to full professor has just been announced. 👨🎓 Hard to think that only 10 years ago I was a postdoc filling my application to @ImperialBioeng
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Lots of great living bioart from our undergrad teaching classes with carotene, violacein, lycopene, GFP and RFP yeast strains. Stay tuned for Voting for a winner.
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All the talk about what synthetic biology might achieve by 2040 spurred me to organise a online event to discuss one of the top 10 - control of evolution. I’ll tweet more details soon about this exciting event but for now save the date...
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Me: Why do you want to do a PhD? Student: I went to a journal club and saw a prof totally destroy a paper and it inspired me to go into academia.
Me: 😲
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My (short) take on the technology and research achievements of the synthetic biology community over the last decade.
TL;DR - we crushed it 👍
nature.com/articles/s41467-0…
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I'm sorry but this year it should be called "Lobby Universities, Funders and Governments To Actually Give a Damn About Postdocs Week" here's why... ⬇️
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End of our yeast synthetic lab series today and students are super excited to see their yeast living bio art plates. So many cool designs from their engineered strains making pigments and fluorescent proteins. 👏
Who wants to see some pretty plates? ⬇️
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Mega virtual synthetic biology conference - 18 days, 3 hrs per day from Dec 1st to Dec 18th. It's going to be like an online synbio advent calendar of talks from all the big names.
biodesign-conference.com/alb…
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This is getting quite a few RT so just for clarity I’m not saying it’s not important or not. It’s great work and fully deserving. Just been lots of chat recently about the network of Nobel prize winners being very interconnected and the lack of diversity in who gets the medals.
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Happy to share that our work engineering cellulose-producing bacteria to grow light-induced patterns and make melanin to grow black leather-like materials is now published OA in @NatureBiotech > Study led by the amazing Marcus Walker @Marcus_waal nature.com/articles/s41587-0…
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The annual joy of choosing winning yeast bioart from our synthetic biology undergrad module. The students. These are our top 10 out of 62 artworks made this year.
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Who else remembers this issue of Nature? To say it was an influence on my decision to do synthetic biology is a bit of an understatement. I literally quit my day job after reading this.
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Perfect day for Lecture 1 of my brand new Intro to Synthetic Biology module. Today’s topic is history of synbio and it happens to be exactly 20 years to the day since the first two papers came out.
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Sculpture to celebrate Cyanobacteria and all they’ve done for our planet. Thanks Cyanos! @ Eden Project, Cornwall
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An 1980 automated DNA synthesiser that adds dinucleotides at-a-time. 🧬This thing should be in a museum. 🏛 Oh wait, it is! @sciencemuseum
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After writing about the last 10 years of #synbio last year, myself and 2 @ImperialBioeng students - Hia Ming and Olivia Gallup - chose to write about the next decade. Our ideas for 10 future challenges for #syntheicbiology are now published online.
ietresearch.onlinelibrary.wi…
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Please tell me that this is a Nature paper where someone accidentally place an order for 100 kb of synthetic DNA in reverse instead of uploading the reverse complement.
Nature research paper: Synthetic reversed sequences reveal default genomic states go.nature.com/439chr3
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I gave FutureHouse's platform a go today, challenging the Falcon agent to try to explain some perplexing counter-intuitive lab results we just got and suggest experiments to work them out. I have to say I was very impressed. I'd rate it at ~70% as effective as me... (1/3)
Today, we are launching the first publicly available AI Scientist, via the FutureHouse Platform.
Our AI Scientist agents can perform a wide variety of scientific tasks better than humans. By chaining them together, we've already started to discover new biology really fast. With the platform, we are bringing these capabilities to the wider community. Watch our long-form video, in the comments below, to learn more about how the platform works and how you can use it to make new discoveries, and go to our website or see the comments below to access the platform.
We are releasing three superhuman AI Scientist agents today, each with their own specialization:
A general-purpose agent (Crow);
An agent to automate literature reviews (Falcon); and
An agent to answer the question “Has anyone done X before” (Owl).
We are also releasing an experimental agent, Phoenix, that has access to a wide variety of tools for planning experiments in chemistry. More on that below.
The three literature search agents (Crow, Falcon, and Owl) have benchmarked superhuman performance. They also have access to a large corpus of full scientific texts, which means that you can ask them more detailed questions about experimental protocols and study limitations that general-purpose web search agents, which usually only have access to abstracts, might miss. Our agents also use a variety of factors to distinguish source quality, so that they don’t end up relying on low-quality papers or pop-science sources. Finally, and critically, we have an API, which is intended to allow researchers to integrate our agents into their workflows.
Phoenix is an experimental project we put together recently just to demonstrate what can happen if you give the agents access to lots of scientific tools. It is not better than humans at planning experiments yet, and it makes a lot more mistakes than Crow, Falcon, or Owl. We want to see all the ways you can break it!
The agents we are releasing today cannot yet do all (or even most!) aspects of scientific research autonomously. However, as we show in the video, you can already use them to generate and evaluate new hypotheses and plan new experiments way faster than before. Internally, we also have dedicated agents for data analysis, hypothesis generation, protein engineering, and more, and we plan to launch these on the platform in the coming months as well. Within a year or two, it is easy to imagine that the vast majority of desk work that scientists do today will be accelerated with the help of AI agents like the ones we are releasing today.
The platform is currently free-to-use. Over time, depending on how people use it, we may implement pricing plans. If you want higher rate limits, especially for research projects, get in touch. @m_skarlinski, @andrewwhite01, @_tnadolski, Remo Storni, @semajazarb, @ludomitch, @MichaelaThinks, as well as @jasonjoyride and his team for making such fantastic videos of us!
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If your covid19 research is focused only on protein structure then this image should tell you why it’s failing - sugars everywhere.
Glycosylated SARS-Cov-2 Spike Trimer. Biantennary LacNAc N-glycans (18 per protomer) are shown in dark magenta. Protein is from Swiss-Model (based on 6VSB), glycans built using glycam.org. #glycotime #COVIDー19 @SWISS_MODEL @glycam
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That awkward moment when the old plasmid your lab made can't be found anywhere in the minus 80 but is available on @Addgene
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Today in @NatureComms , Will Shaw (@willmshaw) and I finally share our new work collaborating with Xiaozhou (David) Luo @ SIAT, developing a yeast-based biosensor & workflow for screening microbially-produced Δ9-tetrahydrocannbinol, better known as 𝗧𝗛𝗖🧵nature.com/articles/s41467-0…
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next they want to do a ribosome but first they need to make a DNase because nothing gets rid of their L-DNA once it’s made. #Mirrorworldproblems
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In our work on engineered living materials, a question we ask ourselves is ‘How can we use synthetic biology to make materials more sustainable?’ In our new preprint, Marcus Walker @Marcus_waal answers this with ‘Bacterial Black Sheep’.
How? Read on… 🧵⬇️
biorxiv.org/content/10.1101/…
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Navigating Tottenham Court Road station with a pushchair is like playing a level of Donkey Kong
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How about some nice news? I’m very proud of my dad who has won this year’s Michael Faraday medal 🥇 from the Institute of Physics. 🌌 🔭 ucl.ac.uk/news/2020/oct/ucl-…
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This new synthetic biology method / preprint from Caleb Bashor‘s team looks very exciting >> Ultra-high throughput mapping of genetic design space
biorxiv.org/content/10.1101/…
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Synthetic biology is starting to go off-patent. The genetic toggle switch patent expired last month, 20 years after its filing.
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The German iGEM meetup on Sunday challenged me to think of what sort of synthetic biology will happen over the next 10 to 20 years. Here's 10 things I thought of and discussed. What did I miss?
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Nice paper showing the use of engineered E.coli cell lysates as budget molbio reagents for PCR, qPCR, LAMP, Golden Gate | Producing molecular biology reagents without purification dx.plos.org/10.1371/journal.…
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We made a synthetic yeast chromsome! @BABlount and I just posted a preprint @biorxiv describing our contribution to Sc2.0: the 660kb SynXI chromosome.
1000s of synonmous mutations in coding genes caused no issues at all, unlike edits to non-coding DNA. 🧵
biorxiv.org/content/10.1101/…
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Paper is actually more mind-blowing than just that. Stable data storage and gene assembly all with L-chirality DNA They made an L-DNA dependent RNA polymerase too. Super impressive work.
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A paper where we get engineered bacteria to make the Imperial logo was finally accepted yesterday. Perfectly timed with the announcement from college that we are now all moving to a new logo. Typical! 🤣
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This is disgusting and scientifically backwards. As a matter of principle, I will now refuse to participate in international peer review of all ARC grants until the @arc_gov_au change this policy. I hope others in the international scientific community do the same.
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Guide to lab tipping:
1. For successful PCRs you should be giving 15-20% to the Thermocycler, although less is fine if the reactions didn’t work and you explain it clearly.
2. For thorough sterilisation the autoclave usually expects 15%+
3. Gels usually expect a dollar per run
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SynBio Turing patterns in E.coli. I've seen this amazing project progress over the last few years at Imperial and excited that it's now published. Well done to all involved! cell.com/cell-systems/fullte…
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An under-rated aspect of synthetic biology research is that we rarely need to care about stats and p-values because we build things where the change in cell behaviour is designed to obvious. Usually ‘log-scale obvious’.
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Plot line for Jurassic Park. Hope none of the astronauts have large spans of frog DNA in their chromosomes.
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£38700. There’s going to be a lot of UK universities who I bet will now be needing to reconsider their (embarrassingly low) postdoc salary scales.
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Paper submitted and paper accepted within the same hour! 🎉🎉 A great afternoon for the team 🎉🎉
Don’t worry they’re not the same paper (I’m not a PNAS member).
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It’s amusing to read all the biologists saying AI can only be awesome for biology if we collect lots more data, completely ignoring the fact that what we really lack is the ability to build and test at scale what the AI models predict. 🤔
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Another exciting new tool to engineer biology from the Jason Chin Lab >>> Establishing a synthetic orthogonal replication system enables accelerated evolution in E. coli | Science science.org/doi/10.1126/scie…
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We all thought Twitter was dying but looks like #scitwitter is back strong going through its usual monthly cycles. This month = people who use R think people who don’t use R are losers. Next month = why don’t they ask for reference letters AFTER shortlisting for interview?
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It's finally out... Will Shaw's awesome YTK add-on toolkit for rapid parallel yeast genome engineering is published today in @ACSSynBio @willmshaw @MoKhalilLab > If you do yeast synthetic biology, you're going to need this game-changing kit from @Addgene pubs.acs.org/doi/10.1021/acs…
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I think if committees put more conscious effort into looking beyond those that are part of obvious networks then medals and awards like these could be more rich in who and what work they celebrate.
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On the left - actual flowcharts from my institution about how to publish in journals and be OA compliant.
On the right - what I wish their advice could just be.
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What happens to bacterial genomes when they're cloned into yeast? Do they transcribe, do they get silenced, do they get packaged away from the rest of the DNA? This cool study congrats to the Koszul lab team at Pasteur for this great work science.org/doi/10.1126/scie…
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Question for microbiology twitter 🧫🔬
What mechanism/genes make our cellulose-producing bacteria arrange ~100 synthase complexes nicely in a line along the cell axis on one side? Anyone know of other bacteria able to align membrane-bound complexes in this fashion? 🤷♂️
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We're hiring! We're taking another big leap in using synthetic biology to engineer materials - this time for sustainable food and textiles. In the next few weeks, we've up to 4 postdoc positions opening up. I'd love to hear from anyone interested in joining us this year. Pls RT🔁
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I heard that the full annual energy bill for @imperialcollege is expected to be £20 Million more than usual this coming year.😮 Can someone tell leadership that running deep freezers at -70C saves 25% of the energy of running at -80C? We have hundreds of these on campus.
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Happy Sc2.0 day. 10 new papers published today in Cell Genomics, Cell and Molecular Cell. Telling the story of 8 more completed chromosomes (including ours) and a tRNA neochromosome and bringing more than half the syn genome together into a single cell.
cell.com/cell-genomics/curre…
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Okay Synbio Twitter, I want your opinions - What are the most important achievements in synthetic biology in the last 10 years? 2010 to 2020. Go! ⬇️
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Kind of crazy that @NatureProtocols puts a warning square about using Ethidium Bromide but no warning square about generating infectious new variants of a pandemic-causing virus.
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We’re back! After a whole year, our in-person teaching of #synbio for Bioengineers is happening again. On the menu for today, CRISPR genome editing and metabolic pathway Golden Gate.
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As a synthetic biologist I get asked a lot if you could ever release an engineered microbe in the EU. This paper gives an important account of efforts to do so by a team at Cambridge, and describes the legal labyrinth that makes it possible yet impossible. academic.oup.com/synbio/adva…
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Engineering GPCR signalling for tunable sensing > Our new paper now out in @CellCellPress chock full of great synthetic biology, genome engineering & modelling work led by @willmshaw in collaboration with @GpcrL & @AstraZeneca. #OA paper @bbsrc funded. cell.com/cell/fulltext/S0092…
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Just heard that some of our remote-learning undergrads have moved to an AirBnB in Portugal for the term as the rent is much less than London and it's the same timezone.
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Complained at the weekend about Profs leaving academia for $$$$$$ private institutes, and then today was on a panel of 8 external experts zooming for 5 hrs straight to assess a proposal worth just £150k total. Unpaid work of course.
Oh and we have to write a report too. 🤦
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Meet 𝐋𝐢𝐥𝐚 - an Automated Scientist built by the Amyris crew to do E.coli and Yeast metabolic engineering by DBTL cycles. Lila has made 100s of biosynthesis strains. Perhaps she is going to make your PhD students feel a bit sad
biorxiv.org/content/10.1101/…
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Bioluminescence occurs naturally in prokaryotes, animals, protists and even fungi too - but not plants.
Is it just a matter of time before we find natural bioluminescent plants? Or is there fundamental reason plants shouldn't glow?
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Imperial researchers engineered this tree to turn red in response to the stress of undergrads returning every October #biosensor
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A happy end to #SEED2024 back in London. Thanks @NEBiolabs for the gift. She loves it.
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If your lab has battle-hardened gel electrophoresis equipment that looks like it was bought when people used faxes for ordering, then please let me know the brand. So sick of the gel tanks we buy breaking within a year. Looking at you BioRad.
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After the DNA Nobel, Francis Crick replied to requests using this brilliant postcard. Would love to be this rude!
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while everyone else is preoccupied with the Chemistry Nobel Prize today, may I present to you Fluorescent Wombats
theguardian.com/science/2023…
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Personal opinion - if institutes like MIT and HHMI want to limit their exposure to future scandals, they might want to think hard about the risks of encouraging and rewarding big research groups.
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Synthetic biology and bioelectrochemical tools for electrogenetic system engineering > exciting new paper in Science Advances from my #synbio colleagues here at @IC_CSynBio Cool work that builds from our 2018 @imperialigem team. 👏👏
science.org/doi/10.1126/scia…
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Okay this is pretty cool. Voigt lab built a soil bacteria biosensor that produces a hyper-spectral molecule and showed that when put on sandpits they can be imaged from actual space…770 km away! 🤯. #SEED2024
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Engineered phage for the win! | UK Teenager recovers from near death in world-first GM virus treatment theguardian.com/science/2019…
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Vaccinating 2M a week in the UK should be our minimum. Why not aim higher? Last year, with only 6 weeks notice we organised >25 million people to vote in person in one day. UK should plan for this scale of operation immediately.
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Excited that we can finally announce this huge new centre based at Imperial funded by Bezos (yes.. that guy) where we will be using synthetic biology and other technologies to make food more sustainable. Congrats to @LedesmaAmaro for leading this amazing new initiative.
Our new Bezos Centre for Sustainable Protein has launched today! 🎉
@BezosEarthFund has granted us $30 million to establish the Centre. Together, we will transform our food systems and protect our planet 🌍💚
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As I tell my undergrads, there are only 2 rules in biology:
Rule 1: If people think there is a rule, then somewhere out there an organism or virus will be breaking it.
Rule 2: The person who finds that gets a paper in Cell
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Browsing @Addgene as a synthetic biologist is like a trip to the merchant in Zelda games. You want everything even if you have no idea how you might use it just yet.
“The shadow tyrosine kinase of the winds” - sounds important.
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Lots of great results for our undergrad bioengineering synthetic biology practicals. Successful yeast CRISPR ✅ Successful Golden Gate reactions ✅ Successful carotenoid biosynthesis ✅
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Come join us! I’m looking for 2 #synbio postdocs to join my group as soon as possible to work on synthetic genomics. Eukaryote/Yeast experience desired.
Posts can be at @imperialcollege London or @sangerinstitute Cambridge depending on applicant preference. Please RT.
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