From the Community: GeneMods August 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:

• Steven Burgess steps down as managing editor at the PLOS SynBio Community. His parting review is typically excellent.
• Great piece on Oxitec’s sterile mosquitos, and the human challenge of testing them in Key West.
• NIH reconsiders its moratorium on human-animal chimera research.
• A PBS article on using CRISPR in grapes turns into a remarkably comprehensive overview of the opportunities and challenges in editing agricultural plants.
• Is NgAgo’s gene editing reproducible? Jury’s still out, but preliminary evidence isn’t good.
• DARPA launches an Engineered Living Materials initiative, with the goal of designing biomaterials that grow into the shape of whatever structure/component. Open for proposals through September!
• Interesting warning about over-hyping technology: a piece on embryonic stem cells and the challenges of treating disease with them.
• If you’re in New York and want to build stuff with bio, you can now take a crash course in making custom biomaterials, put on by New York’s Genspace DIYbio lab.
• If you find yourself in Cambridge, check out Cafe Synthetique, the local synbio salon. Sounds like a GeneMods sister organization!
• Cool profile in STAT of David Baker and co.’s plans to solve problems in the world (mostly diseases, in this piece) with computationally designed proteins.
• Highlights from the 2016 BioDesign Challenge (from last month, but good enough to post anyway).

Industry news:

• Engineered Cas9 with lower off-target effects goes commercial: high-fidelity Cas9 variant from Joung lab licensed to Editas.
• Total cost of CRISPR patent fight exceeds $20 million and counting.
• DOD gives Ginkgo $2 million to develop probiotic vaccine for traveler’s diarrhea.

Books and Longreads

• I just discovered BioCoder, a quarterly newsletter about synthetic biology from technology media company O’Reilly Media, and I’m really enjoying it.
• Carl Zimmer gets his genome sequenced and analyzed by some of the best researchers in the field. A Game of Genomes chronicles his adventure. A must-read.
• Ed Yong’s fantastic book about the microbes that precede, surround, live on, and comprise us, I Contain Multitudes, came out. I cannot recommend enough that you get your hands (or ears, it’s on Audible!) on this book.

Now, onto the research papers!

Protein engineering:

• Easily and quickly sensing the presence of small molecules is one of the rate-limiting challenges in metabolic engineering. Now, Savage Lab reports rapid construction of metabolite biosensors using domain insertion profiling.
• Baker Lab does it again, reporting rationally designed, two-component, 120 subunit, icosahedral protein complexes..
• Electrochemical across membranes fundamentally underly pretty much all biological energy production. Fotiadis Lab has now engineered a photo-switchable, light-driven proton pump. 

Genetic circuits:

• A Lu Lab collaboration programs yeast and builds a mini bioreactor to produce single doses of multiple biological therapeutics on command.

CRISPR/Gene Editing:

• A Joung Lab collaboration relaxes Staphylococcus aureus Cas9’s PAM specificity, expanding the sites this smaller programmable nuclease can target. 
• It’s been a bumper crop month for making molecular recordings in the genomes of cells. Science published three papers (summarized here): Church Lab reported molecular recordings produced using the actual CRISPR parts of CRISPR (as opposed to Cas9); Lu Lab used recombinases to build state machines in living cells; and a collaboration between Shendure and Schier Labs used Cas9 to record the differentiation and trace the lineage of all the cells in a zebrafish. Then, Lu Lab developed a method to continuously record the presence of Cas9 in human cells using a self-targeting guide RNA.

Metabolic Engineering

•  Jewett Lab takes a step toward easier natural product mining by expressing non-ribosomal peptide synthetases and producing small-molecule peptides in a cell-free lysate system.

Building biology to understand it

• A massively recoded, 57-codon E. coli? Not quite yet, but Church Lab computationally designs the genome, synthesizes the parts, and makes progress on assembling and testing them.
• Venter Institute edits and interrogates bacterial ribosome genes, on a synthetic bacterial genome in yeast. GenomeWeb has a summary if you don’t have time to read the whole paper.
• Review article in ACS SynBio argues that mammalian artificial chromosomes (MACs) are the way of the future.