SynBio Newsreel, July

There was a lot of news this month. Enjoy!

Northwestern News:

• The Communicating Science Convention (ComSciCon) in Chicago is coming up! If you’re in Chicago on Saturday August 6, I highly recommend you attend the keynote, where Emily Graslie will talk about how she and her team at the Field Museum engage with the public about science online.

Protein engineering:

• Ellington lab engineers a proof-reading reverse transcriptase. This is awesome.
• Baker lab designs a super-stable 60-subunit protein icosahedron, with optional 60 to 120 GFP attached.
• Precise optogenetic control of gene expression in E. coli enabled by an engineered blue-light-dependent DNA binding protein.
• How do you improve photosynthesis? A review. Reminds me of this talk about plans to convert plants from C3 to C4 photosynthesis.
• Interesting paper on “smart” growth media systems with delayed-release nutrients, and simpler high-yield protein expression protocols.

Genetic circuits:

• Control theory meets synthetic biology: an excellent and rigorous review on designing biological circuits which perform more robustly/predictably.
• Gene expression gets noisier/more stochastic in crowded macromolecular environments. Good thing to keep in mind when, say, prototyping genetic circuits with a dilute cell-free platform.
• Keasling lab engineers new acid-inducible promoters in yeast. 10-fold induction, and they get 10-fold higher production of lactic acid from them.
• Want to tune gene expression? Stick two promoters next to each other and start tweaking. Key phrase: RNA polymerase collision.
• In applied circuit news: Engineered Salmonella grow and explode in cyclic waves within tumors, increase survival in mouse cancer models. This paper also got a write-up in The Atlantic from my favorite science writer, Ed Yong.
• An integral feedback circuit, modeled and implemented in DNA.
• Rewiring native riboswitches to recognize new molecules. If you want to make new riboswitches, this article is a good place to start.

CRISPR/Gene Editing:

• Battle of the rationally designed transcriptional regulators: which performs better, dCas9 or TALEs? TALEs, as it turns out.
• Daisy chain gene drives proposed, which would only propagate a short. Esvelt also wrote a piece on Medium about daisy drives, informing the public about the idea.
• Cpf1 is more specific than Cas9, as determined by off-target cleavage tests in cells.
• A new biobrick assembly standard which uses Cpf1 digestion. Con: less efficient. Pro: don’t have to worry about restriction sites in your parts anymore.
• Church lab sequences and start building tools to engineer Vibrio natriegens, a saltwater bacterium that grows ~twice as fast as E. coli. Includes CRISPRi system for studying genes’ function.

Computational/Bioinformatics

• BioPartsDB: software that helps you design and build your own large DNA sequences from overlapping oligos.
• ATLAS of Biochemistry: an online map of all known and predicted metabolites, and all known and predicted enzymatic pathways to produce them.

Building biology to understand it

• Yeast engineered to be “multicellular” provide insight into the reason for the distinction between clonally reproducing germ cells and differentiated, non-dividing somatic cells.

Industry news:

• Synthorx gets $10 million Series B financing to expand the genetic code.
• CRISPR Therapeutics raises additional $38 million, bringing their total Series B financing to ~$140 million.
• AI Biosciences adapts a cheap 3D printer into a combination sample handler/ thermocycler.
• Microsoft and UW Seattle partner with Twist to store 200 MB of data, including an OK Go music video, in DNA.

Synbio community news:

• PLOS SynBio Community and EBRC’s Engineering Biology Times are great sources for synbio news.
• “Building with Biology:” reflections on SynBio outreach by Aaron Dy.
• Big picture post on why plant/photoautotroph synthetic biology matters. But, plant synbio isn’t easy. Remember glowing plant? 3 years on, it hasn’t delivered to its Kickstarter backers. MIT Technology Review discusses why.
• NSF awards a $300,000 grant for UPenn to develop synbio classes for high school students. It’s part of the NSF’s initiative to facilitate DIY technology.
• Slightly less controversial “Heroes of CRISPR” piece, about the grad students and post-docs who did the actual experiments.
• Chinese scientists to run first human CRISPR trial next month—a cancer immunotherapy treatment using Cas9-modified cells.
• Not to be outdone, American researchers at UPenn apply for a similar CRISPR cancer immunotherapy trial.
• De-extinction…while a species is still alive? How re-introducing dead alleles could help the black footed ferret.
• Nasa prepares for its first sequencing experiment in space. Oxford Nanopore is awesome.

Cool iGEM projects

• CosmoCrops—Co-culture cyanobacteria and B. subtilis. Cyanobacteria makes sugar, B. subtilis uses sugar to make other things (University of Copenhagen).
• Purdue iGEM team proposes to sequester phosphorus from wastewater and grow nano-wires in E. coli, and raises $3000 on experiment.com to do it.
• Our very own Northwestern iGEM team is tackling the non-viral delivery of Cas9 into bacteria by packaging into Outer Membrane Vesicles (OMVs).