SynBio Newsreel, April 2017

Blogs and community news

Policy and Bioethics

  • In an about-face, the FDA has approved 23andMe to supply users with information about their risks for various diseases. Previously, 23andMe was only allowed to provide information on diseases the users might be carriers for.
  • Researchers are taking more seriously the idea that humans will need to be genetically modified in order to colonize Mars and the rest of the solar system.
  • In the future, will some forms of gene editing be required? Intriguing article in The Atlantic draws comparisons between the prosecution of Christian Scientist parents for the avoidable deaths of their children, and a potential future in which parents are held accountable for not editing deadly diseases out of their children’s genomes.

Industry and Funding

  • At their London conference, SynBioBeta founder John Cumbers announces a new synthetic biology venture fund in partnership with Data Collective. If you need money for your synbio startup, now there’s one more place to apply.
  • The biohacking project to build a glowing plant has run out of money and had to stop. They’re still working on making a fragrant moss, however.

Books, Videos, Podcasts

  • Drew Endy’s keynote at SynBioBeta London was something else. No one can accuse him of not dreaming big.
  • The Naked Scientists (perhaps my favorite general science podcast) devote an episode to organs-on-chips. And if you don’t like listening, you can read the transcript.

Biosecurity

  • The SB7.0 conference is offering a Biosecurity Fellowship. Only a 1 page application, but it’s due on April 28th, so apply fast!
  • Labs are trying to use CRISPR as an antibiotic, delivered via bacteriophage to chop up the pathogenic bacteria’s DNA. It’s an interesting idea, but I wonder: if you’ve found a phage to deliver CRISPR into target bacteria, why not just use the phage to kill the bacteria?

Now, on to the research papers! Fewer than most months; I’ll try to find more in May.

Detection and Genetic circuits

  • Belkin et al. can find landmines from a distance with E. coli, in a field trial. Summary in The Guardian (though the paper is really short, so a summary is almost unnecessary).
  • Gottenberg et al. reveal SHERLOCK, a CRISPR/C2c2-dependent strategy to detect minuscule concentrations of specific RNA and DNA sequences. Summary in MIT News.

Therapeutic synbio

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SynBio Newsreel, March 2017

Lots of things happened in March!

Blogs and community news

  • Aaron Dy discusses how the bionic leaves being developed in Pam Silver’s lab could aid in the colonization of Mars.
  • Daniela Quagliela interviews the founders of UK synbio company Synthace about Antha, the high-level programming language they developed to speed up and simplify automated bioengineering protocols.
  • Indiebio’s blog now has interviews with most of their portfolio companies. A great place to find synbio companies doing cool work!
  • Policy and Bioethics
  • Induced pluripotent human stem cells can now be patterned to generate structures that look a lot like early embryos. These synthetic human entities with embryo-like features (SHEEFs) will force us to rethink the decades-old rules surrounding human embryo research.
  • In ever greater numbers, parents are starting foundations and companies to develop gene therapies for the rare diseases that afflict their children.

Industry and Funding

  • Forbes profiles Craig Venter—what he’s done, what he’s doing, and what he hopes to do in the future.
  • eGenesis raises $38 million to engineer pigs that can serve as organ donors to humans.
  • Wired profiles two startups—Venomyx and VenomAB—that are trying to make cheap, recombinant snake antivenom. But will their approach be able to tackle antivenom’s distribution challenges?
  • Twist raises an extra $33 million to expand its gene synthesis, and DNA data storage and pharmaceutical discovery strategies.
  • If February was a great month for Broad in the CRISPR patent fight, March looks a bit tougher. The European Patent Office granted a broad (not Broad) CRISPR patent to University of California and University of Vienna (Doudna and Charpentier’s institutions), for developing the single guide RNA to guide Cas9.

Books, Videos, Podcasts

  • Radiolab devotes an entire episode to an update about CRISPR and gene drives, including interviews with Jennifer Doudna, Kevin Esvelt and the best (well, only) audio representation of a bacterial CRISPR repeat I’ve ever heard.
  • George Church gave an hour-long talk to the Innovative Genomics Institute. Worth watching!

Biosecurity

  • Bill Gates publishes an op-ed arguing that bioterrorism is a serious threat to global security, and that to counter this threat we must strengthen public health infrastructure in the developing world, increase our ability to rapidly generate new vaccines, openly share health/epidemiological data between countries, and ‘prepare for pandemics the way the military prepares for war.’ Interestingly, these steps are very similar to the global health goals his foundation has been pursuing for a while, just repackaged to emphasize the economic and security arguments for them. Perhaps this reframing will persuade the current US government to maintain or increase spending on global health?

Now, on to the research papers!

Genetic circuits

  • If most synbio takes steps toward making biology easier to engineer, Weinberg et al. just took a giant leap. They use recombinase-based genetic circuits to reliably build over 100 complex logic gates in mammalian cells, including a 6-input AND gate, and even adder and subtracter modules. It’s like Endy lab’s reliable, stable genetic programs in E. coli—but bigger, and in mammals! Summary in Wired.

Biomolecule engineering

  • Running out of colors to paint your cells for fluorescent imaging? Frances Arnold’s lab has your back. Herwig and Rice et al. engineered an opsin protein to accept a synthetic chromophore, so that it now fluoresces brightly in the infrared. Works in both bacteria and mammalian cells, too.
  • Bedbrook and Rice et al. from Arnold lab also take aim at engineering new light-activated ion channels for optogenetics, using recombination of diverse channelrhodopsin sequences to generate new proteins with distinct expression, localization, and light-induced activation patterns.
  • Praetorius and Dietz report DNA origami, with TAL effector staples!

Computational biology

  • Data storage in DNA just got much more feasible. Erlich and Zielinski combine fountain codes (a robust encoding strategy from mobile video streaming applications) and automated, iterative oligo sequence optimization to store 72 MB of data in easily sequenced DNA. They achieve unprecedented retrieval fidelity (100%), lossless copying capacity (a quadrillion replications), and storage density (250 petabytes per gram), approaching the theoretical limit for data storage in DNA.

Gene Drives and CRISPR (also, preprints are cool)

  • One of the primary ethical challenges confronting gene drives is that, even if the population of one region supports drive use, the drive could easily spread to areas where people don’t want it. In a new preprint, Min et al. from Kevin Esvelt’s lab propose a technical solution to this problem of universal consent: a daisy quorum gene drive. This system combines the limited spread of a daisy chain gene drive with a genetic ‘quorum sensing’ capability, so that after the daisy drive runs out of gas, the drive modifications are only stable in regions where most of the target organisms have already been modified. This architecture also enables a second gene drive to revert a modified population to the wild genotype, increasing the potential reversibility of gene drives.
  • Efficient editing with CRISPR is a challenge, so it would be great if you could just select for the cells that have been edited. Well, now you can! Agudelo et al. report on Biorxiv a method to select for edited cells by co-delivering guide RNAs which generate toxin-resistant mutations in a sodium/potassium pump gene.

The strains, they are a changin’

  • Saccaromyces cerevisiae 2.0, the yeast with a synthetic genome, is more than halfway complete. 7 articles detailing Boeke and company’s progress appeared simultaneously in Science. Pretty frickin’ cool.