Syn Bio Newsreel, December 2017 (a lot late)

Hi everyone, while we’re doing a backlog of blog posts, here’s the news from December! Enjoy!

GeneMods Podcast

-In this month’s podcast, we interview Karmella Haynes about her lab’s work in chromatin engineering to control gene expression. You won’t want to miss it!

Blogs and Community News

-The iGEM Jamboree was a huge success! Read here about the winners, particularly first place Vilnius’ on a novel way of regulating plasmid copy number in cells. Also, check out PLOS SynBio Community for a judge’s first-hand account of the competition.

-SynBioBeta reports on “Five Wild Biotech Products That Will Touch Our Lives in the Near Future”. We’re ready for you, cow-free cow milk and post-animal burgers. Mushroom lamps…maybe not.

Policy and Bioethics

–        In MIT’s Technology Review, Emily Mullen outlines all the CRISPR clinical trials set to happen in the US in 2018. CRISPR Therapeutics, the company founded by Doudna, Charpentier, et. al., will aim to use the genome editing technology to treat sickle cell anemia.

Industry and Funding

–        With its latest 275 million dollars in venture capital, Ginkgo Bioworks is now the first synthetic biology “unicorn” valued over a billion dollars.

–        An economic analysis of the feasibility of microbe-brewed spider silk reveals that E. coli­-sourced protein could one day get as cheap as $23/kg. That same mass requires more than 5,000 silkworms to produce.

–        Also speaking of spider silk, Wired frequently has some good syn bio coverage; here’s an article about Bolt Threads’s 100 spider silk beanies (which sold out immediately).

Cell-Free Synthetic Biology

–        PURE Express is great, but purifying each of the individual components for transcription and translation means that it carries a heavy price tag. This month, a group has published on engineering synthetic microbial communities that specialize in producing each of the components in bulk, greatly speeding up the purification process and, hopefully, tamping down that price tag.

  –        Then again, if you do want to mess around with messy extract systems (and who wouldn’t?), Jim Swartz and Jeffrey Varner have pre-published a useful summary on BioRxiv for independent sequence-specific modelling of transcription and translation in cell-free conditions.

Biomolecular Engineering

–        In the culmination of 20 years of effort, Floyd Romesberg’s group at Scripps has managed to create a strain of E. coli that can stably maintain a pair of unnatural nucleotides (labelled “X” and “Y”) in a plasmid and transcribe and translate them into a protein containing a nonstandard amino acid. A follow-up paper in JACS reveals that the mutations can be stably inherited on the bacterial chromosome.

–        There are protein scaffolds, DNA scaffolds, RNA scaffolds, but how about lipids? A new paper out of the Silver lab shows that you can colocalize metabolic enzymes to synthetic lipid assemblies to enhance yield of indigo.

Gene Circuits

–        Liu et. al. discuss just how tricky it is to get copy number right to prevent metabolic burden when expressing even simple AND gene circuits in E. coli. Can RNA-seq be a useful diagnostic tool to help?

–        Not sure about the acronyms, but the concept is pretty dang cool; Stanley Qi’s lab has reworked their previous Tango system to design ChaCha, a way of fusing diverse G-protein coupled receptors to a functional output based on dCas9 repression of a target gene.

–        The Smolke lab has applied miRNA switching to a real therapeutic target: T-cell proliferation. Adding a small molecule drug turns on cytokine signaling pathways. Read about it here:

De novo Protein Design

–        Enzyme design just keeps getting better and better; this month, Nature Communications reports the design of 4 alpha-helix bundles for a highly active and promiscuous oxidoreductase.

–        Not to be outdone, David Baker’s Nature paper of the month involves the engineering of a synthetic viral capsid that encapsulates its own DNA. These capsids had similar packaging efficiency to adenoviruses commonly used for gene delivery. Crazy stuff.

Build-a-Bear… with DNA???

–        December was a great month for DNA origami. First, we found out about a simple way to make mg-scale amount of DNA in standard 1L lab fermenters using phage and self-cleaving DNA sequences interwoven between arbitrary DNA sequences. Then, Peng Yin’s group showed that gigadalton-scale assemblies of 10,000 DNA parts can be achieved by using 13-nucleotide binding domains. What was the first thing they chose to make? A teddy bear, of course.

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