Month: February 2017

SynBio Newsreel, February 2017

I’ll put the videos up here as well once they upload. Enjoy!

Blogs and community news

  • PLOS Synbio has an excellent interview with Christina Agapakis, creative director at Ginkgo.
  • STAT profiles Jeantine Lunshof, the bioethicist embedded in George Church’s lab who makes sure they don’t rush too quickly into ethically questionable research.
  • SynBioBeta highlights five women CEOs of synbio companies.
  • Keith Robison of OmicsOmics has an excellent perspective piece on Gen9’s acquisition by Ginkgo and the challenges of the high throughput DNA synthesis business, with a bonus appearance by Gen9 CEO Kevin Munnelly in the comments section.
  • Bioscentric argues that synthetic biology can bridge the coming ‘protein gap’ (disparity between available supply of protein and demand for it by global middle class) by engineering plant-based meat substitutes to taste and feel more like the real thing.

Policy and Bioethics

  • The National Academy of Science’s report on the ethics of human embryo editing, a year in the making, argues for cautious use of germline editing, for diseases which have no “reasonable” therapeutic alternatives, and following much more research into safety and efficacy. Notably, while the report advocated against genome editing to enhance embryos ‘at this time,’ it rejected the argument that genetic enhancement would be likely to significantly increase societal inequality. This comes after the American College of Medical Genetics urged against clinical editing of embryo genomes, at least until further ethical and technical issues are addressed. NAS’s report seems to be running a little ahead of public sentiment, according to a recent Pew poll which showed a majority of Americans are more worried than enthusiastic about genome-edited babies.
  • The FDA curbs a biohacker’s plans to use CRISPR correct a genetic disease carried by purebred dalmatians. He may just do it anyway, though.
  • India doesn’t have an official government policy on synthetic biology, but that’s about to change.

Industry and Funding

  • The patent for using CRISPR in eukaryotes belongs to the Broad institute, according to the Patent and Trademark Office. Expect UC Berkeley to appeal, but this is a major blow to their legal claim that gene editing with CRISPR in eukaryotes is an obvious extension of Doudna and Charpentier’s work in vitro and in bacteria. Berkeley professor and soon-to-be Senate candidate Michael Eisen wrote a scathing critique of the decision, and of University patent rights generally.
  • Meanwhile, the Innovative Genomics Institute (run by UC Berkeley and UCSF) intends to invest $125 million into gene editing research on crops and microbiomes. That’s a lot of CRISPR!
  • IndieBio graduates its fourth class of startups (full demo day video here). Among them are companies specializing in DNA data storage, enzyme engineering, high-throughput embryo editing, and microfluidic cell culture devices.
  • A year later, Twist Bioscience responds to Agilent’s lawsuit alleging IP theft.
  • You can now buy CRISPR-Cpf1 for gene editing from IDT.

Books, Longreads, Podcasts

  • Society needs to prepare for The End of Sex (for reproductive purposes), according to the book of the same name written by Stanford Law professor Hank Greely. Greely predicts this shift will be causes by the convergence of two technologies, in vitro generation of gametes from induced pluripotent stem cells and pre-implantation genetic diagnosis (PGD). These technologies will soon combine into a simple procedure called Easy PGD that enables parents to generate thousands of zygotes in vitro, implanting only those which have been sequenced, screened and edited to prevent genetic disorders (and, potentially, select for non-disease traits). The book provides a good overview of the scientific progress on both technologies, and extensively explores the legal, ethical and social implications of Easy PGD. I highly recommend it.

Biosecurity

  • Devang Mehta argues in an excellent PLOS Synbio post that biosecurity threats from DIY biohackers are overblown (for now), while threats from state actors are potentially more serious.
  • Former Ventria Biosciences employee Weiqiang Zhang is convicted of attempting to steal a genetically modified rice strain.

Now, on to the research papers!

Biomolecule engineering

  • Pu et al. use continuous, directed evolution to build a split RNA polymerase whose activity is dependent on the dimerization of modular protein-protein and small molecule binding domains. Basically, constructing a genetic sensing/actuation circuit from two interacting or molecule-binding protein domains just got a lot easier. Really cool.
  • Does Baker lab just publish a Science paper every month at this point? Marcos et al. have figured out how to build proteins from scratch with surface cavities structured around distorted beta sheets.
  • The last restriction enzyme you’ll ever buy? Enghiad and Zhao use a thermostable, DNA-guided nuclease called PfAgo to generate artificial restriction enzymes which can cleave any sequence while leaving sticky ends of any sequence at the cut sites. Summary in GEN.
  • Quagliela et al. use Golden Gate cloning to combine multiple different mutagenesis strategies in a single protein engineering library.

Genetic circuits and Metabolic Engineering

  • Gupta et al. apply quorum sensing to metabolic engineering, constructing strains of E. coli that switch off essential glycolytic enzymes when they reach a high enough density, thereby increasing the output of chosen metabolites derived from central carbon metabolism. Summary in MIT News.
  • Engelen et al. augment the field of DNA-based computing by debuting antibody-templated strand exchange, a process by which antibodies initiate the strand displacement reactions of peptide-functionalized DNA strands. They show how antibodies and their cognate antigens can now be used as inputs for DNA computing circuits.
  • Wearable computing is cool, but how about wearable, living computing? Liu et al. use a printed silicone/hydrogel combination material to construct simple wearable devices into which engineered E. coli can be embedded and subsequently sense small molecules on the surface of the skin.
  • Want to learn more about optogenetic control of gene expression in budding yeast? Then this review by Salinas et al. is for you.

Photosynthetic Synbio

  • Higo et al. build RNA-based, small molecule-inducible genetic circuits in cyanobacteria, thereby adding a modular and portable tool to the sparse cyanobacterias toolbox.
  • Song et al. show that new, fast-growing cyanobacterium UTEX 2793 can be engineered to produce more sucrose and glycogen than any strain before it. This is actually a paper from last year that got caught in my NCBI crawler, but it was relevant to Quentin’s November presentation so I thought it was worth adding.

Computational biology

  • Model and build biology to understand it! Moreno-Fenoll et al. explore how microbial communities that rely on commonly produced resources can survive the emergence of ‘cheaters,’ which consume the common resource without producing it. The show through mathematical modeling and engineering a synthetic microbial community with ‘cheater’ and ‘cooperator’ strains of E. coli that spatial division of the community into many random sub-populations promotes recovery of the cooperators after a cheater-induced population crash.

The strains, they are a changin’

  • Agmon et al. generate biocontained yeast by placing several essential genes under small molecule-inducible promoters, such that the strains won’t grow in the absence of, for instance, estradiol. They also demonstrate a strategy to dope in ‘decoy’ small molecules which don’t affect cell viability but make it harder for biopirates to figure out which small molecules are required to make the strains grow.
  • Two papers on improving the expansion of the genetic code, both from UT Austin labs! First, Monk et al. showcase a dual fluorescent protein reporter which can rapidly quantify the activity and specificity of non-standard amino acid (nsAA) incorporation by orthogonal tRNAs, and also an evolved, faster growing variant of the amber-codon-lacking recoded E. coli strain developed in Church lab. Maranhao and Ellington simultaneously debuted a new positive/negative selection strategy to develop more active and specific orthogonal tRNAs. They also show that non-recoded E. coli expressing their improved tRNAs grow faster than strains expressing the original tRNAs (recoded E. coli grows the same either way).

Therapeutic synbio