Synbio Newsreel, May 2017 | GeneMods

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, May 2017

Want to write about synbio?

• There are three online publications (that I know of) that cater specifically to essays/articles about synthetic biology/biohacking: BioCoder, the PLOS Synthetic Biology blog, and the GeneMods blog. BioCoder has an open call for submissions to its June newsletter, while PLOS SynBio and GeneMods welcome guest writers.

The Means of Production

• How do you turn more people into scientists? Make it cheaper to do science. How do you make it cheaper to do science? Teach people to build their own equipment. An excellent essay on The Conversation analyzes the intersection of citizen science and the Open Hardware movement, which seeks to develop free manuals for cheaply building all sorts of useful (often scientific) equipment. I particularly liked how the essay argued that making instruments cheaper changes the kinds of experiments people can conduct—science becomes something that can be performed by and for the specific benefit of small, local communities.

Blogs and Community News

• Fastco Design reviews the latest work from artist Robert Zhao Renhui, a book about the animals humans have modified or changed throughout history.
• Daniela Quagliela over at PLOS Synbio interviews chemist, protein engineer and directed evolution wizard Frances Arnold.
• Aaron Dy at PLOS Synbio looks at crowdfunding in synthetic biology, from the failure of Glowing Plant to the success of smaller iGEM crowdfunding campaigns, and proposes guidelines that might make crowdfunded synbio projects more likely to succeed.
• Is cell-free synthetic biology about to take off? Steven Burgess highlights some of the advances, advantages and challenges of engineering biology without cell membranes.
• Antonio Regalado at Technology Review summarizes the recent advances and ambitions surrounding DNA data storage. Most exciting part for me: Church lab is working on enzymatic DNA synthesis, and plans to have an announcement about it later this year!

Policy and Bioethics

• GP-Write organized its second annual meeting. They’ve shifted away from immediately synthesizing a human genome, broadening the focus to large genomes generally. Funding remains a challenge, but one pilot project to synthesize a prototrophic human cell has received a $500,000 DARPA grant.
• The FDA is seeking advice on how to regulate genome editing technologies, and has extended the public comment period through June 19. So if you have any valuable input (when, if ever, might genome edited plants/animals be riskier than those bred or engineered with older techniques? At what point does a small-time bioentrepreneur hacking a new plant/animal need to seek regulatory approval? Can they avoid oversight by using certain biosafety precautions or accepted model organisms?), let the FDA know!

Industry and Funding

• I think this extended 2012 article about the rise and fall of Amyris is essential reading for anyone interested in the synbio industry. Many things to learn from the successes and mistakes of the first generation of synbio companies.
• Hey, Open Hardware again! The open source liquid handler OpenTrons gets an upgrade: it can now do everything two times faster. Gotta get one of these for Northwestern!
• The Economist publishes an enthusiastic essay about cell-free bioengineering. Worth a read to get a sense of all the companies operating in this space!
• RebelBio, Ireland’s biotech accelerator, has launched its fourth class of startups, including an STD biosensor, a cell-free synbio kit, and microbial fuel cell that runs on wastewater.
• DNA sequencing is coming to the classroom, courtesy of PlayDNA, a new startup that uses Oxford Nanopore’s MinION sequencer to teach middle schoolers about biology.

Books, Videos, Podcasts

• Jennifer Doudna is (co-) writing a CRISPR book! Actually, she already wrote it, and it’s coming out in a month or so. The Curious Wavefunction offers an enthusiastic review and synopsis of the book, A Crack in Creation.
• I just read (well, listened to) Life at the Speed of Light, by J. Craig Venter. It’s a short book packed with Venter’s thought-provoking perspectives about the nature of biology, the history of the life sciences, the Human Genome Project and his transition to synthetic genomics. It also provides entertaining insights into Venter’s personality—namely, that he’s a little obsessed with Nobel prizes, and isn’t above using his book to settle decades-old scores with doubters, competitors and the press.

Now, on to the research papers!

The Digital to Biological Converter

• It’s finally happened: a team led by J. Craig Venter and Dan Gibson have built a digital to biological converter (DBC): a machine which, when fed a digital gene sequence (up to 6000 bases), will print, assemble, and express that gene sequence, all without a human touching it. They use their DBC to make GFP, antibody fragments, and influenza proteins for potential use in vaccine development. This is the first prototype and it’s bulky and expensive, but expect smaller, cheaper DBCs to start showing up in the coming years. This may be the beginning of the end for cloning DNA by hand.

Biomolecule Engineering

• High throughput measurement of engineered protein-protein interactions using…sexual agglutination?
• Savage lab uses recombineering to make protein engineering easier/faster/cheaper.
• Measure that protein! Kawasaki et al built RNA sensors to quantify protein concentrations in mammalian cells.
• Build those cassettes! Andreou and Nakayama design a new (better?) Golden Gate cloning system.

Genetic Circuits

• ‘Essentializer’ and ‘Cryodeath:’ Silver lab’s either building genetic kill switches or starting several metal bands.
• Voigt lab pulls a Voigt lab, and refactors+simplifies the entire Salmonella Type III secretion system.
• Weenink et al. rationally design 5’UTRs of yeast genes to fine-tune expression.
• Modular is better! Orthogonal ribosome subunits decouple gene circuits from normal cell processes.

Computational Biology

• Buzzword bingo! Cuperus et al. apply deep learning to synbio, to predict and design the expression regulation of yeast 5’UTRs.

CRISPR and Gene Editing

• NgAgo? Uh oh. Nature Biotechnology notes that no one can replicate 2016’s DNA-guided gene editing paper.
• Harrington et al. in Doudna lab report a thermostable Cas9 with increased stability in human serum.

Therapeutic SynBio

• Where would YOU stick your subcutaneous capsule of therapeutic cells to treat insulin insensitivity? I vote under the clavicle.

The Strains, They Are A-Changin’

• Watch out, E. coli! Church lab reports recombineering in Vibrio natriegens.
• Recombineering is everywhere this month! Silver lab reports that it works in Salmonella, with massive recoding (1557 Leu->Leu)!

Not synbio, but cool

• Olivia Judson developed an eloquent model of how life got better at exploiting energy over time. This is not technically synbio, but it’s very useful for thinking about how efficiently different organisms can grow/exploit energy.

Pore’s Law

• Oxford Nanopore’s annual DNA sequencing conference, London Calling, was amazing. Nanopore sequencing is getting faster, cheaper, smaller, larger, more accurate, and higher throughput all at once. Other sequencing companies had better look out. If you want to quickly catch up on everything presented, James Hadfield of Enseqlopedia covered both Day 1 and Day 2 of the conference extensively. Keith Robison over at OmicsOmics had probably the most comprehensive summary and perspective on Clive Brown’s keynote about the Oxford Nanopore’s progress and future plans.
• My favorite nanopore sequencing preprint thus far: Jain et al. report the sequencing and de novo assembly of a human reference genome using only MinION nanopore sequencers. My favorite part: they tried sequencing extra-long DNA fragments and out popped an 885 kb single read—~1000 times longer than the best read you could get from Sanger sequencing.
• If you want to really get in the weeds and understand how Oxford’s Nanopore sequencer works, this review on BioRxiv is worth a read.
• Lastly, science communication news! DNA sequencing is coming to the classroom, courtesy of PlayDNA and Oxford Nanopore.