Genemods June newsreel and new podcast
The Synbio Newsreel is guest contributed by Isaac Larkin from the Northwestern University synthetic biology club called GeneMods. This post can be originally found as part of their monthly SynBio Newsreel and you can follow them at @Genemods.
Synbio Newsreel, June 2017
GeneMods has a podcast now!
- For the first episode, we interviewed Professor Danielle Tullman-Ercek about synthetic biology in space. We also run through some of the May newsreel, gameshow-style!
- In Our Time, the BBC’s history podcast, devotes a whole episode to enzymes: how they were discovered, why they’re amazing, and what we use them for. Well worth a listen.
- Josiah Zayner, biohacker extraordinaire, gave a riveting opening presentation at the Festival of Genomics in San Diego. Three thoughts after watching it: I want to know how he built a fully furnished lab for only $5000; I want to see the data confirming that he’s been able to genetically modify his skin cells; and I really felt iffy about the part where he implied that he was helping a guy treat his wife’s cancer.
- I just read (well, listened to) Change Agent, a new thriller by Daniel Suarez set in a biotech dystopia. An interpol officer in charge of hunting black market embryo editors in Southeast Asia gets dosed with a Change Agent, and finds his appearance and DNA fingerprint transformed into that of the very kingpin he has been chasing. It’s a richly imagined world and a fun read for anyone interested in synbio. The ‘mirror man’ assassin is my favorite character–you’ll have to read it to find out why!
- Haven’t read the whole thing yet, but the first chapter of Cory Doctorow’s new scifi/spec-fic novel Walkaway opens with a party serving genemod fluorescent beer (which is already a thing, thanks to Josiah Zayner). On my reading list!
- John Cumbers of SynBioBeta is teaming up with Karl Schmieder to write What’s Your Bio Strategy, a book about the massive advances in bioengineering and the synthetic biology entrepreneurs these advances are enabling. The book isn’t available yet but the site linked above contains numerous excerpts, comprising interviews with leaders in the synbio industry. One to watch for!
- SB7.0, the 7th iteration of the largest meeting in the field, took place in Singapore. There haven’t been a lot of recaps posted online, but I’m sure there will be more in July. The most exciting announcement I saw came from bionet, the organization Drew Endy helped start to facilitate the open sharing and modification of biological molecules, tools and protocols. The Biobricks Foundation is partnering with Twist Bioscience to synthesize and share, free of charge, 10,000 genes with the entire synthetic biology community. This unprecedented biotechnological commons will be available to anyone to use, modify, share and sell through the bionet license. Which 10,000 genes? You decide! Bionet will create a forum through which the whole synbio community can advocate for parts to go into the commons (perhaps through this subreddit). You can bet that GeneMods will do what it can to help build this new resource. I can’t wait to get started.
- Busy month for synbio conferences! The week after SB7.0 in Singapore, Vancouver hosted the Synthetic Biology: Engineering Evolution and Design (SEED) conference. Many GeneMods members attended, and this month’s meeting includes a recap of their favorite SEED talks.
- CRISPR 2017 happened in Big Sky, Montana. Michael Chao wrote a good overview in Nature Microbiology. The conference apparently featured positive mouse data from Locus and Eligo Biosciences, two companies trying to redirect CRISPR to kill antibiotic-resistant bacteria.
Blogs and Community News
- The always-excellent Daniela Quagliela over at PLOS Synbio interviewed Julie Legault, the founder and CEO of bioengineering-in-a-box company Amino Labs.
Policy and Bioethics
- An article in Nature Biotech argues for increased high school participation in iGEM, and tracks the growth of and lessons learned from Canadian high school iGEM teams. and similar competitions (BIOMOD? BioTreks? News to me).
Industry and Funding
- CRISPR counter-punch! China sides with Europe, and grants foundational CRISPR patents to Jennifer Doudna and Emmanuelle Charpentier’s team. The US PTO’s decision granting the patent to Feng Zhang and the Broad is starting to look more like an outlier.
- Microsoft is doubling down on DNA data storage, purchasing 10 million more long oligonucleotides from Twist Bioscience.
- DNA synthesis company IDT has announced a new competitive grant for synthetic biology start-ups, the winners of which receive 100,000 base pairs of free DNA (and the runners-up 50,000). Get that DNA!
- Speaking of competitions: the X-Prize Foundation (of private spaceflight fame) is considering launching an X-prize for the first team to build a microbe that can survive, reproduce and make useful products under Martian conditions.
- Bolt Threads got $50 million in funding and a partnership with Patagonia. Recombinant spider silk jackets aren’t far off!
- Ecovocative, the company that makes packaging and furniture out of mushroom mycelium, just won a $9 million DARPA grant to develop living building materials!
- Nature Jobs published five rules for building a synthetic biology startup.
Now, on to the research papers!
Small, Cheap, and Open
- Microfluidics are going open-source. Kong et al. debut Metafluidics, a site for sharing and modding designs and synthesis protocols for microfluidic devices, such as the controller/mixer part they use to assemble genetic elements at much smaller scale than pipetting would allow. It’s halfway between Github and Thingiverse, and aimed specifically at shrinking and democratizing the hardware required for synthetic biology. Summary in MIT News.
Who Needs Cells?
- It’s been a good month for cell-free protein synthesis. Nieß et al. published a predictive model of cell-free protein synthesis which points the way towards increasing protein production rates. Also, Schoborg et al. from Jewett lab that figured out how to screen for transmembrane sugar-transferring enzymes in a cell-free context.
- Another tour-de-force Baker lab collaboration: Strauch et al. designed a protein inhibitor of influenza that matches both the geometry and the binding pockets in hemagglutinin, and which can protect mice from influenza the day before or after exposure. Summary in Science.
- Northwestern alert! Alam et al. design a split fluorescent RNA aptamer that lights up in cells expressing both halves of the aptamer, and can be tagged onto other RNA sequences.
- Riglar et al. in Pam Silver’s lab have built E. coli that can live and persist in mouse guts for long periods, and can switch on a stable reporter circuit in the presence of an inflammatory signaling molecule. Living gut diagnostics aren’t far away!
- That’s…much easier. Borkowski, Endy and Subsoontorn build a simple recombinase-based circuit that turns on protein expression when E. coli reach a certain density. No IPTG, quorum sensing, or autoinduction media needed!
- Bacterial vision gets an upgrade, courtesy of (who else) Voigt lab! Fernandez-Rodriguez et al. build a circuit that can sense and respond to red, green, and blue light independently. Summary on the PLOS SynBio blog.
- Maier et al. build an epigenetic memory circuit in bacteria (not eukaryotes! What?!). I bet the metabolic load for epigenetic memory is quite low.
- Gander et al. use dCas9 repression build the most complex genetic logic gates yet in a eukaryote.
- Want to build genomes from scratch, but not a programmer? Then Genome Partitioner, a new web tool from Christen et al. for breaking huge DNA constructs into synthesizable chunks, might be right for you.
- Want to massively engineer existing genomes? Try Millstone, a web-based toolset from Goodman et al. for designing MAGE experiments in any microbe with a reference genome.
- Design and build (highly symmetric) biomolecules from scratch with ISAMBARD! Nice open source tool from Wood et al.
CRISPR and Gene Editing
- Pineda et al. have a very useful review of the challenges facing CRISPR gene editing therapies, and the approaches to solve them.
The Strains, They Are A-Changin’
- Dalia et al. efficiently transform DNA into Vibrio natriegens, and do multiplex genome engineering for desired traits. It’s similar to last month’s Church lab recombineering preprint, but requires a co-selection marker.
- Yeast can now make waxy, very long chain fatty acids, courtesy of Yongjin and colleagues.
- From fat yeast to fat algae! After over a decade of work, a group from Synthetic Genomics have built a macroalgae strain which grows about as well as wild type and accumulates twice as much fat. Summary in Ars Technica.
Useful Parts Galore
- Rapidly explore vast genetic design spaces with Woodruff et al.’s new Registry in a Tube: a strategy to make giant pools of standard, barcoded genetic parts, which can then be rapidly extracted and combinatorially assembled into an enormous number of composite devices.
- Did you know gut fungi digest lignocellulose using massive complexes of carbohydrate binding and degrading enzymes called cellulosomes? I didn’t. But now Haitjema et al. have figured out a minimal set of genes for scaffolding and assembling fungal cellulosome enzymes. Watch out, cellulosic biomass!