From the Community: GeneMods September Newsreel

This post can be originally found at this link, and is from the Northwestern University synthetic biology club called GeneMods. This is part of their monthly SynBio Newsreel.

Synbio community news

• NASA sequences DNA, in space! They’re up to 1 billion bases and counting. Oxford Nanopore is awesome as always.
• DIY Bio labs all over the world are trying to print biomaterials. This article in Makezine is a good summary of their progress.
• Dominic Berry wrote a guest post on PLOS SynBio about studying the evolution of the synthetic biology community. From it, I learned about Engineering Life, a sociological study of synthetic biology labs in the UK, which runs an absolutely fascinating blog about historian’s perspectives on synbio research and policy.
• GEN surveys the protein engineering field, highlighting recent successes in computational design and directed evolution.
• NSF announces $24 million plan to build “blue sky” bioengineering center at UCSF.

Biosecurity

• The White House announces a major update to how biotechnology is regulated, the first such update since 1992. SynBioBeta has the summary.
• DARPA announces an initiative to develop tools for preventing or reversing gene editing. Digital Rights Management for the genome?
• Most Floridians want to use sterile GM mosquitos to combat Zika. Certainly better than South Carolina’s response. 
• Ecologists in Hawaii want to use sterile mosquitos (and are open to deploying gene drives) to protect native bird species from the avian malaria that is wiping them out. Now, Kevin Esvelt and others debate whether and how to use gene drives to protect endangered species at the International Union for the Conservation of Nature.
• NIH announces $20 million in prizes for groups that develop rapid diagnostics of antibiotic-resistant infections.
• Informative review on Motherboard of the history of bioweapons development/use/policy, and of contemporary bioerror (not terror) near-misses. Aaron Dy correctly points out, however, that while the article uses this historical review to discuss the threat of genetically modified bioweapons, all of the past cases involved unmodified pathogens.

Industry news

• Oxford Nanopore settles Illumina’s lawsuit over protein nanopore patents.
• Ginkgo Bioworks announces partnership with Arthur Daniels Midland, the Chicago-based food conglomerate.
• Monsanto licenses CRISPR from the Broad Institute—but is forbidden from using it for gene drives.
• Nice profile of Ginkgo Biosciences and its history in MIT News.
• The judges in biotech patent cases generally aren’t scientists. The Wall Street Journal proposes a separate patent court staffed by scientific experts to remedy this.

Longreads

• The snakebite crisis is escalating. Synbio could help—but it needs to avoid distracting from lower-tech initiatives, like scaling antivenom production in Africa and giving farmers boots.
• A thought-provoking history of DNA data storage, which also outlines the challenges and opportunities ahead for the field.
• In-depth analysis of the medical/pharmaceutical biotech investment ecosystem, from Brady Huggett.
• Freeman Dyson writes an inspiring vision of biology’s place in space exploration.
• The Summer 2016 edition of BioCoder is out (free PDF download if you register). Read it if you’re interested in DIYBio and synthetic biology from the perspective of hackers and makers.

Video

• SynbiCITE, the UK’s synbio industry organization, produces Nature Knows Best, a 24 minute documentary about industrial synbio applications in the UK. Enjoyed the Hall of the Mountain King soundtrack!
• Jennifer Doudna sits down with Dan Rather for a 40 minute conversation on CRISPR and her own backstory, filmed by iBiology.

Non-synbio blog of the month

• Genotopia is Professor Nathaniel Comfort’s blog about bio, genetics, medicine, history, and hype in biotech. His recent trilogy of posts about going to Yellowstone hot springs to study the origin of life is definitely worth reading.

Now, on to the research papers!

Biomolecule engineering

• Howarth lab generates more stable proteins by making them circular, ligating the N and C terminus using their SpyTag-SpyCatcher system.
• Mishler and Barrick labs develop a fast, cheap platform for evaluating non-standard amino acid incorporation using fluorescent proteins in recoded E. coli. Hopefully this will lead to improved synthetic tRNA/tRNA synthetase pairs!
• Baker lab is really on a roll! This month they accurately design small, stable, constrained peptides (similar to the peptides in snake/scorpion venom). They can incorporate D-amino acids and cyclic peptides, too. Summary of the research article here.
• The Coming Age of de-novo Protein Design is a review of advances in, well, you know.
• Simmel lab debuts a rationally designed transmembrane channel made of DNA.
• Pollard lab makes TALE construction easier with a Gibson Assembly-based protocol.

Genetic circuits

• Chang lab develops a genetic circuit which decouples E. coli growth from production of desired metabolite, leading to higher growth and yields.
• Selling lab builds a bistable genetic circuit using a Lactose/IPTG importer under control of a Lac repressor.

CRISPR/gene editing

• Bhatia lab at MIT controls CRISPR with light, by chemically sequestering the guide RNAs until UV light shines on them. There’s also a summary in MIT News.

Metabolic engineering

• Fairly comprehensive review of synthetic biology opportunities in plant metabolic engineering.

Building biology to understand it

• Yizhi Cai and Roy Walker summarize the results from the Fifth Annual Sc2.0 meeting, providing updates on the Synthetic Yeast Genome Project, and renewed debates about the Human Genome Project-Write.
• Review article argues that synbio could help to predict new biochemical innovations life may experience in the next few billion years. It’s an interesting perspective through which to view the field, and discusses cool work on improving photosynthesis and rewiring central carbon metabolism.

Autotrophs and agriculture

• Powering enzymatic nitrogen fixation using light and cadmium sulfide nanorods? Pretty cool. Legume Laboratory has a summary article.
• Bibby lab rewires cyanobacterial photosynthesis to increase efficiency and degrade a pesticide. EurekAlert has the summary.

Therapeutic synbio

• Collins lab shows that their freeze-dried, cell-free (FD-CF) paper platform can produce vaccine antigens, antimicrobial peptides and even small molecule therapeutics.
• Huang lab builds Salmonella strain which accumulates in tumors and secretes angiogenic inhibitor proteins.
• Quick mini-review of the ways synthetic biology is being used to diagnose disease.

The strains, they are a changin’

• A team led by Dan Gibson engineers Vibrio natriegens, which grows 2-3 times faster than E. coli, into a platform for plasmid cloning and protein expression. The design-build-test cycle is about to get significantly faster.