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!

Other Podcasts

  • 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.

Videos

  • 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.

Books

  • 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!

Big Conferences

  • 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.

Industry and Funding

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.

Build More Biohackers!

  • 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).

Who Needs Cells?

Biomolecule Engineering

  • 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.

Genetic Circuits

Computational Biology

  • 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’

Metabolic Engineering

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.
  • What if you want to assemble all your parts-in-a-tube, but don’t want to buy restriction enzymes or Gibson master mix? Liang et al. have a solution: a twin-primer assembly method that requires only DNA primers (with overhangs) and polymerase for PCR.
  • 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!
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GeneMods has a podcast now!

Excited to announce that the first episode of the GeneMods podcast, Synbio in Spaaaace!, is now live! Jordan Harrison and I interviewed Professor Danielle Tullman-Ercek about synthetic biology in space. We also run through some of the May newsreel, gameshow-style. Hope you all like it!

We’re just starting this thing so we’d love to know what you liked, things you’d change, or topics you want us to explore in future episodes. If you have feedback, you can reach us here or on the GeneMods Twitter account. Looking forward to hearing from you!