SynBio Newsreel, June 2017

GeneMods has a podcast now!

  • For the first episode, we interviewed Professor Danielle Tullman-Ercek about synthetic biology in space. We also run through some of the May newsreel, gameshow-style!

Other Podcasts

  • In Our Time, the BBC’s history podcast, devotes a whole episode to enzymes: how they were discovered, why they’re amazing, and what we use them for. Well worth a listen.

Videos

  • Josiah Zayner, biohacker extraordinaire, gave a riveting opening presentation at the Festival of Genomics in San Diego. Three thoughts after watching it: I want to know how he built a fully furnished lab for only $5000; I want to see the data confirming that he’s been able to genetically modify his skin cells; and I really felt iffy about the part where he implied that he was helping a guy treat his wife’s cancer.

Books

  • I just read (well, listened to) Change Agent, a new thriller by Daniel Suarez set in a biotech dystopia. An interpol officer in charge of hunting black market embryo editors in Southeast Asia gets dosed with a Change Agent, and finds his appearance and DNA fingerprint transformed into that of the very kingpin he has been chasing. It’s a richly imagined world and a fun read for anyone interested in synbio. The ‘mirror man’ assassin is my favorite character–you’ll have to read it to find out why!
  • Haven’t read the whole thing yet, but the first chapter of Cory Doctorow’s new scifi/spec-fic novel Walkaway opens with a party serving genemod fluorescent beer (which is already a thing, thanks to Josiah Zayner). On my reading list!
  • John Cumbers of SynBioBeta is teaming up with Karl Schmieder to write What’s Your Bio Strategy, a book about the massive advances in bioengineering and the synthetic biology entrepreneurs these advances are enabling. The book isn’t available yet but the site linked above contains numerous excerpts, comprising interviews with leaders in the synbio industry. One to watch for!

Big Conferences

  • SB7.0, the 7th iteration of the largest meeting in the field, took place in Singapore. There haven’t been a lot of recaps posted online, but I’m sure there will be more in July. The most exciting announcement I saw came from bionet, the organization Drew Endy helped start to facilitate the open sharing and modification of biological molecules, tools and protocols. The Biobricks Foundation is partnering with Twist Bioscience to synthesize and share, free of charge, 10,000 genes with the entire synthetic biology community. This unprecedented biotechnological commons will be available to anyone to use, modify, share and sell through the bionet license. Which 10,000 genes? You decide! Bionet will create a forum through which the whole synbio community can advocate for parts to go into the commons (perhaps through this subreddit). You can bet that GeneMods will do what it can to help build this new resource. I can’t wait to get started.
  • Busy month for synbio conferences! The week after SB7.0 in Singapore, Vancouver hosted the Synthetic Biology: Engineering Evolution and Design (SEED) conference. Many GeneMods members attended, and this month’s meeting includes a recap of their favorite SEED talks.
  • CRISPR 2017 happened in Big Sky, Montana. Michael Chao wrote a good overview in Nature Microbiology. The conference apparently featured positive mouse data from Locus and Eligo Biosciences, two companies trying to redirect CRISPR to kill antibiotic-resistant bacteria.

Blogs and Community News

  • The always-excellent Daniela Quagliela over at PLOS Synbio interviewed Julie Legault, the founder and CEO of bioengineering-in-a-box company Amino Labs.

Industry and Funding

Now, on to the research papers!

Small, Cheap, and Open

  • Microfluidics are going open-source. Kong et al. debut Metafluidics, a site for sharing and modding designs and synthesis protocols for microfluidic devices, such as the controller/mixer part they use to assemble genetic elements at much smaller scale than pipetting would allow. It’s halfway between Github and Thingiverse, and aimed specifically at shrinking and democratizing the hardware required for synthetic biology. Summary in MIT News.

Build More Biohackers!

  • An article in Nature Biotech argues for increased high school participation in iGEM, and tracks the growth of and lessons learned from Canadian high school iGEM teams. and similar competitions (BIOMOD? BioTreks? News to me).

Who Needs Cells?

Biomolecule Engineering

  • Another tour-de-force Baker lab collaboration: Strauch et al. designed a protein inhibitor of influenza that matches both the geometry and the binding pockets in hemagglutinin, and which can protect mice from influenza the day before or after exposure. Summary in Science.
  • Northwestern alert! Alam et al. design a split fluorescent RNA aptamer that lights up in cells expressing both halves of the aptamer, and can be tagged onto other RNA sequences.

Genetic Circuits

Computational Biology

  • Want to build genomes from scratch, but not a programmer? Then Genome Partitioner, a new web tool from Christen et al. for breaking huge DNA constructs into synthesizable chunks, might be right for you.
  • Want to massively engineer existing genomes? Try Millstone, a web-based toolset from Goodman et al. for designing MAGE experiments in any microbe with a reference genome.
  • Design and build (highly symmetric) biomolecules from scratch with ISAMBARD! Nice open source tool from Wood et al.

CRISPR and Gene Editing

  • Pineda et al. have a very useful review of the challenges facing CRISPR gene editing therapies, and the approaches to solve them.

The Strains, They Are A-Changin’

Metabolic Engineering

Useful Parts Galore

  • Rapidly explore vast genetic design spaces with Woodruff et al.’s new Registry in a Tube: a strategy to make giant pools of standard, barcoded genetic parts, which can then be rapidly extracted and combinatorially assembled into an enormous number of composite devices.
  • What if you want to assemble all your parts-in-a-tube, but don’t want to buy restriction enzymes or Gibson master mix? Liang et al. have a solution: a twin-primer assembly method that requires only DNA primers (with overhangs) and polymerase for PCR.
  • Did you know gut fungi digest lignocellulose using massive complexes of carbohydrate binding and degrading enzymes called cellulosomes? I didn’t. But now Haitjema et al. have figured out a minimal set of genes for scaffolding and assembling fungal cellulosome enzymes. Watch out, cellulosic biomass!

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

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

Genetic Circuits

Computational Biology

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

The Strains, They Are A-Changin’

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 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. Best 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.

SynBio Newsreel, April 2017

Blogs and community news

Policy and Bioethics

  • In an about-face, the FDA has approved 23andMe to supply users with information about their risks for various diseases. Previously, 23andMe was only allowed to provide information on diseases the users might be carriers for.
  • Researchers are taking more seriously the idea that humans will need to be genetically modified in order to colonize Mars and the rest of the solar system.
  • In the future, will some forms of gene editing be required? Intriguing article in The Atlantic draws comparisons between the prosecution of Christian Scientist parents for the avoidable deaths of their children, and a potential future in which parents are held accountable for not editing deadly diseases out of their children’s genomes.

Industry and Funding

  • At their London conference, SynBioBeta founder John Cumbers announces a new synthetic biology venture fund in partnership with Data Collective. If you need money for your synbio startup, now there’s one more place to apply.
  • The biohacking project to build a glowing plant has run out of money and had to stop. They’re still working on making a fragrant moss, however.

Books, Videos, Podcasts

  • Drew Endy’s keynote at SynBioBeta London was something else. No one can accuse him of not dreaming big.
  • The Naked Scientists (perhaps my favorite general science podcast) devote an episode to organs-on-chips. And if you don’t like listening, you can read the transcript.

Biosecurity

  • The SB7.0 conference is offering a Biosecurity Fellowship. Only a 1 page application, but it’s due on April 28th, so apply fast!
  • Labs are trying to use CRISPR as an antibiotic, delivered via bacteriophage to chop up the pathogenic bacteria’s DNA. It’s an interesting idea, but I wonder: if you’ve found a phage to deliver CRISPR into target bacteria, why not just use the phage to kill the bacteria?

Now, on to the research papers! Fewer than most months; I’ll try to find more in May.

Detection and Genetic circuits

  • Belkin et al. can find landmines from a distance with E. coli, in a field trial. Summary in The Guardian (though the paper is really short, so a summary is almost unnecessary).
  • Gottenberg et al. reveal SHERLOCK, a CRISPR/C2c2-dependent strategy to detect minuscule concentrations of specific RNA and DNA sequences. Summary in MIT News.

Therapeutic synbio

SynBio Newsreel, March 2017

Lots of things happened in March!

Blogs and community news

  • Aaron Dy discusses how the bionic leaves being developed in Pam Silver’s lab could aid in the colonization of Mars.
  • Daniela Quagliela interviews the founders of UK synbio company Synthace about Antha, the high-level programming language they developed to speed up and simplify automated bioengineering protocols.
  • Indiebio’s blog now has interviews with most of their portfolio companies. A great place to find synbio companies doing cool work!
  • Policy and Bioethics
  • Induced pluripotent human stem cells can now be patterned to generate structures that look a lot like early embryos. These synthetic human entities with embryo-like features (SHEEFs) will force us to rethink the decades-old rules surrounding human embryo research.
  • In ever greater numbers, parents are starting foundations and companies to develop gene therapies for the rare diseases that afflict their children.

Industry and Funding

  • Forbes profiles Craig Venter—what he’s done, what he’s doing, and what he hopes to do in the future.
  • eGenesis raises $38 million to engineer pigs that can serve as organ donors to humans.
  • Wired profiles two startups—Venomyx and VenomAB—that are trying to make cheap, recombinant snake antivenom. But will their approach be able to tackle antivenom’s distribution challenges?
  • Twist raises an extra $33 million to expand its gene synthesis, and DNA data storage and pharmaceutical discovery strategies.
  • If February was a great month for Broad in the CRISPR patent fight, March looks a bit tougher. The European Patent Office granted a broad (not Broad) CRISPR patent to University of California and University of Vienna (Doudna and Charpentier’s institutions), for developing the single guide RNA to guide Cas9.

Books, Videos, Podcasts

  • Radiolab devotes an entire episode to an update about CRISPR and gene drives, including interviews with Jennifer Doudna, Kevin Esvelt and the best (well, only) audio representation of a bacterial CRISPR repeat I’ve ever heard.
  • George Church gave an hour-long talk to the Innovative Genomics Institute. Worth watching!

Biosecurity

  • Bill Gates publishes an op-ed arguing that bioterrorism is a serious threat to global security, and that to counter this threat we must strengthen public health infrastructure in the developing world, increase our ability to rapidly generate new vaccines, openly share health/epidemiological data between countries, and ‘prepare for pandemics the way the military prepares for war.’ Interestingly, these steps are very similar to the global health goals his foundation has been pursuing for a while, just repackaged to emphasize the economic and security arguments for them. Perhaps this reframing will persuade the current US government to maintain or increase spending on global health?

Now, on to the research papers!

Genetic circuits

  • If most synbio takes steps toward making biology easier to engineer, Weinberg et al. just took a giant leap. They use recombinase-based genetic circuits to reliably build over 100 complex logic gates in mammalian cells, including a 6-input AND gate, and even adder and subtracter modules. It’s like Endy lab’s reliable, stable genetic programs in E. coli—but bigger, and in mammals! Summary in Wired.

Biomolecule engineering

  • Running out of colors to paint your cells for fluorescent imaging? Frances Arnold’s lab has your back. Herwig and Rice et al. engineered an opsin protein to accept a synthetic chromophore, so that it now fluoresces brightly in the infrared. Works in both bacteria and mammalian cells, too.
  • Bedbrook and Rice et al. from Arnold lab also take aim at engineering new light-activated ion channels for optogenetics, using recombination of diverse channelrhodopsin sequences to generate new proteins with distinct expression, localization, and light-induced activation patterns.
  • Praetorius and Dietz report DNA origami, with TAL effector staples!

Computational biology

  • Data storage in DNA just got much more feasible. Erlich and Zielinski combine fountain codes (a robust encoding strategy from mobile video streaming applications) and automated, iterative oligo sequence optimization to store 72 MB of data in easily sequenced DNA. They achieve unprecedented retrieval fidelity (100%), lossless copying capacity (a quadrillion replications), and storage density (250 petabytes per gram), approaching the theoretical limit for data storage in DNA.

Gene Drives and CRISPR (also, preprints are cool)

  • One of the primary ethical challenges confronting gene drives is that, even if the population of one region supports drive use, the drive could easily spread to areas where people don’t want it. In a new preprint, Min et al. from Kevin Esvelt’s lab propose a technical solution to this problem of universal consent: a daisy quorum gene drive. This system combines the limited spread of a daisy chain gene drive with a genetic ‘quorum sensing’ capability, so that after the daisy drive runs out of gas, the drive modifications are only stable in regions where most of the target organisms have already been modified. This architecture also enables a second gene drive to revert a modified population to the wild genotype, increasing the potential reversibility of gene drives.
  • Efficient editing with CRISPR is a challenge, so it would be great if you could just select for the cells that have been edited. Well, now you can! Agudelo et al. report on Biorxiv a method to select for edited cells by co-delivering guide RNAs which generate toxin-resistant mutations in a sodium/potassium pump gene.

The strains, they are a changin’

  • Saccaromyces cerevisiae 2.0, the yeast with a synthetic genome, is more than halfway complete. 7 articles detailing Boeke and company’s progress appeared simultaneously in Science. Pretty frickin’ cool.

SynBio Newsreel, February 2017

I’ll put the videos up here as well once they upload. Enjoy!

Blogs and community news

  • PLOS Synbio has an excellent interview with Christina Agapakis, creative director at Ginkgo.
  • STAT profiles Jeantine Lunshof, the bioethicist embedded in George Church’s lab who makes sure they don’t rush too quickly into ethically questionable research.
  • SynBioBeta highlights five women CEOs of synbio companies.
  • Keith Robison of OmicsOmics has an excellent perspective piece on Gen9’s acquisition by Ginkgo and the challenges of the high throughput DNA synthesis business, with a bonus appearance by Gen9 CEO Kevin Munnelly in the comments section.
  • Bioscentric argues that synthetic biology can bridge the coming ‘protein gap’ (disparity between available supply of protein and demand for it by global middle class) by engineering plant-based meat substitutes to taste and feel more like the real thing.

Policy and Bioethics

  • The National Academy of Science’s report on the ethics of human embryo editing, a year in the making, argues for cautious use of germline editing, for diseases which have no “reasonable” therapeutic alternatives, and following much more research into safety and efficacy. Notably, while the report advocated against genome editing to enhance embryos ‘at this time,’ it rejected the argument that genetic enhancement would be likely to significantly increase societal inequality. This comes after the American College of Medical Genetics urged against clinical editing of embryo genomes, at least until further ethical and technical issues are addressed. NAS’s report seems to be running a little ahead of public sentiment, according to a recent Pew poll which showed a majority of Americans are more worried than enthusiastic about genome-edited babies.
  • The FDA curbs a biohacker’s plans to use CRISPR correct a genetic disease carried by purebred dalmatians. He may just do it anyway, though.
  • India doesn’t have an official government policy on synthetic biology, but that’s about to change.

Industry and Funding

  • The patent for using CRISPR in eukaryotes belongs to the Broad institute, according to the Patent and Trademark Office. Expect UC Berkeley to appeal, but this is a major blow to their legal claim that gene editing with CRISPR in eukaryotes is an obvious extension of Doudna and Charpentier’s work in vitro and in bacteria. Berkeley professor and soon-to-be Senate candidate Michael Eisen wrote a scathing critique of the decision, and of University patent rights generally.
  • Meanwhile, the Innovative Genomics Institute (run by UC Berkeley and UCSF) intends to invest $125 million into gene editing research on crops and microbiomes. That’s a lot of CRISPR!
  • IndieBio graduates its fourth class of startups (full demo day video here). Among them are companies specializing in DNA data storage, enzyme engineering, high-throughput embryo editing, and microfluidic cell culture devices.
  • A year later, Twist Bioscience responds to Agilent’s lawsuit alleging IP theft.
  • You can now buy CRISPR-Cpf1 for gene editing from IDT.

Books, Longreads, Podcasts

  • Society needs to prepare for The End of Sex (for reproductive purposes), according to the book of the same name written by Stanford Law professor Hank Greely. Greely predicts this shift will be causes by the convergence of two technologies, in vitro generation of gametes from induced pluripotent stem cells and pre-implantation genetic diagnosis (PGD). These technologies will soon combine into a simple procedure called Easy PGD that enables parents to generate thousands of zygotes in vitro, implanting only those which have been sequenced, screened and edited to prevent genetic disorders (and, potentially, select for non-disease traits). The book provides a good overview of the scientific progress on both technologies, and extensively explores the legal, ethical and social implications of Easy PGD. I highly recommend it.

Biosecurity

  • Devang Mehta argues in an excellent PLOS Synbio post that biosecurity threats from DIY biohackers are overblown (for now), while threats from state actors are potentially more serious.
  • Former Ventria Biosciences employee Weiqiang Zhang is convicted of attempting to steal a genetically modified rice strain.

Now, on to the research papers!

Biomolecule engineering

  • Pu et al. use continuous, directed evolution to build a split RNA polymerase whose activity is dependent on the dimerization of modular protein-protein and small molecule binding domains. Basically, constructing a genetic sensing/actuation circuit from two interacting or molecule-binding protein domains just got a lot easier. Really cool.
  • Does Baker lab just publish a Science paper every month at this point? Marcos et al. have figured out how to build proteins from scratch with surface cavities structured around distorted beta sheets.
  • The last restriction enzyme you’ll ever buy? Enghiad and Zhao use a thermostable, DNA-guided nuclease called PfAgo to generate artificial restriction enzymes which can cleave any sequence while leaving sticky ends of any sequence at the cut sites. Summary in GEN.
  • Quagliela et al. use Golden Gate cloning to combine multiple different mutagenesis strategies in a single protein engineering library.

Genetic circuits and Metabolic Engineering

  • Gupta et al. apply quorum sensing to metabolic engineering, constructing strains of E. coli that switch off essential glycolytic enzymes when they reach a high enough density, thereby increasing the output of chosen metabolites derived from central carbon metabolism. Summary in MIT News.
  • Engelen et al. augment the field of DNA-based computing by debuting antibody-templated strand exchange, a process by which antibodies initiate the strand displacement reactions of peptide-functionalized DNA strands. They show how antibodies and their cognate antigens can now be used as inputs for DNA computing circuits.
  • Wearable computing is cool, but how about wearable, living computing? Liu et al. use a printed silicone/hydrogel combination material to construct simple wearable devices into which engineered E. coli can be embedded and subsequently sense small molecules on the surface of the skin.
  • Want to learn more about optogenetic control of gene expression in budding yeast? Then this review by Salinas et al. is for you.

Photosynthetic Synbio

  • Higo et al. build RNA-based, small molecule-inducible genetic circuits in cyanobacteria, thereby adding a modular and portable tool to the sparse cyanobacterias toolbox.
  • Song et al. show that new, fast-growing cyanobacterium UTEX 2793 can be engineered to produce more sucrose and glycogen than any strain before it. This is actually a paper from last year that got caught in my NCBI crawler, but it was relevant to Quentin’s November presentation so I thought it was worth adding.

Computational biology

  • Model and build biology to understand it! Moreno-Fenoll et al. explore how microbial communities that rely on commonly produced resources can survive the emergence of ‘cheaters,’ which consume the common resource without producing it. The show through mathematical modeling and engineering a synthetic microbial community with ‘cheater’ and ‘cooperator’ strains of E. coli that spatial division of the community into many random sub-populations promotes recovery of the cooperators after a cheater-induced population crash.

The strains, they are a changin’

  • Agmon et al. generate biocontained yeast by placing several essential genes under small molecule-inducible promoters, such that the strains won’t grow in the absence of, for instance, estradiol. They also demonstrate a strategy to dope in ‘decoy’ small molecules which don’t affect cell viability but make it harder for biopirates to figure out which small molecules are required to make the strains grow.
  • Two papers on improving the expansion of the genetic code, both from UT Austin labs! First, Monk et al. showcase a dual fluorescent protein reporter which can rapidly quantify the activity and specificity of non-standard amino acid (nsAA) incorporation by orthogonal tRNAs, and also an evolved, faster growing variant of the amber-codon-lacking recoded E. coli strain developed in Church lab. Maranhao and Ellington simultaneously debuted a new positive/negative selection strategy to develop more active and specific orthogonal tRNAs. They also show that non-recoded E. coli expressing their improved tRNAs grow faster than strains expressing the original tRNAs (recoded E. coli grows the same either way).

Therapeutic synbio

SynBio Newsreel, January 2017

Happy new year, synbio community! And also happy first anniversary of this blog, approximately. Joe Muldoon gave an excellent summary of the newsreel at today’s meeting; watch below, and then continue to the full linkstorm!

Synbio community news

Synbio profiles

  • Ginkgo Bioworks co-founder Tom Knight appears in Forbes. Main takeaway: it’s never too late to go back to school and learn a new field.

Industry news

  • Editas licenses CRISPR-Cpf1 exclusively from the Broad institute for therapeutic applications, and non-exclusively to Monsanto for agricultural applications. Meanwhile the Doudna-Charpentier CRISPR teams have pooled their resources, with Intellia, Caribou, CRISPR Therapeutics and ERS Genomics all signing a mutual patent sharing and protection agreement.
  • Oh snap! Ginkgo Bioworks acquires Gen9. This insightful Boston Globe commentary explains that the acquisition happened in large part because Gen9 ran out of funding in the cutthroat DNA synthesis market. Meanwhile, it looks like Ginkgo is trying to become the first vertically integrated synbio company. What will this mean for Twist Bioscience, now that their largest customer has bought its own DNA synthesis company?

Books, Longreads, Podcasts

  • Nick Lane’s The Vital Question, which tackles the origins of both life and eukaryotes, is excellent. Fun fact from the book: multicellularity has independently evolved over 30 times, but endosymbiosis between prokaryotes (the origin of eukaryotes) has only given rise to complex cells once, as far as we know.
  • Clarkesworld Magazine’s podcast is just what any sci-fi fan could want—a new short story (~20-90 minutes), read into your ears, every week. Lots of synbio speculative fiction here; I particularly enjoyed a recent episode (text version here) about two friends who make counterfeit steaks in China using high-end cell culture.

And now onto the research articles!

The strains, they are a-changin’

Biomolecule engineering

Genetic circuits and Metabolic Engineering

  • To increase bioplastic production, He et al. engineer a genetic circuit that turns on only when high density (measured by quorum sensing) and stationary phase are reached.
  • Crocker et al. use TALE protein fused to activator and repressor domains to develop a fully synthetic transcriptional regulation system in fruit flies. They then use this platform to explore the function of the pioneer/transcriptional enhancer Zelda, and to determine the best genetic architecture for generating sharp boundaries at the intersection of two developmental signaling factor gradients.
  • Maurer et al. compare lab yeast with industrial yeast using quantitative trait loci (QTL) mapping, figure out the alleles which matter most for the industrial yeast’s productivity, and use CRISPR to put those alleles into lab yeast. The result is a lab yeast strain which outperforms the original industrial strain!

Plant Synbio

CRISPR/gene editing

  • Anti-CRISPR proteins discovered by Rauche et al. inhibit spCas9 activity, and may facilitate biocontainment and reduce off-target effects of CRISPR applications. GenomeWeb has the summary.
  • Two new, compact CRISPR systems, dubbed CasX and CasY, discovered in uncultured archaea by a team including Jennifer Doudna. Their biochemistry and potential for genome editing applications should follow shortly, so watch this space! GenomeWeb has the summary.
  • This is genetics on CRISPR. Peters et al. use an inducible CRISPRi library to produce a powerhouse study of essential gene knockdown and function in B. subtilis. One of those fun papers where the new results barely fit even in a Cell paper.

Computational biology

  • Obertorner et al. from the Joint Genome Institute debut BOOST, a web design program for genetic parts that can modify sequences to make them easier/cheaper for for DNA synthesis companies to build.
  • Gumulya and Gilliam present a really cool review of how sequence data from diverse evolutionary branches of life can be used to reconstruct approximate ‘ancestral’ enzymes, which are useful both for evolutionary biology and as starting points for protein engineering studies.

Engineering mammals

SynBio Newsreel, November

Hey look, we figured out how to embed video! Now you can watch a newsreel summary first, and then read any of the papers that sounded particularly interesting. There are fewer links this month because work in November+December was crazy, but rest assured the January newsreel will be just as exhaustive as usual!

Synbio community news

  • Who needs CRISPR gene drives when you have Wolbachia? Scientists have successfully engineered the microbe, which lives in insect cells and spreads to all female offspring (while killing males), to render mosquitos inhospitable to dengue virus.
  • The GP-Write white paper came out. STAT summarized it.
  • iGEM happened! Many cool things. Grand prize winner was Imperial College London’s team, which engineered different strains of E. coli to co-culture at different population ratios.
  • This year’s iGEM saw the launch of bionet, a P2P sharing platform for biological materials developed through the Biobricks foundation and a Drew Endy-led team.
  • The Wyss Institute’s work on replacing animal drug testing models with human organoids on chips gets a write-up in Wired.
  • UK researchers apply to perform field trials on wheat that has been modified to photosynthesize more efficiently, boosting yields 20% (in a greenhouse).

Industry news

  • The Guardian profiles BioAmber and Bolt Threads, two companies trying to develop yeast-based pipelines for succinic acid and spider silk fabrics, respectively.
  • PacBio sues Oxford Nanopore for infringing patents related to reading a single DNA molecule twice. OmicsOmics argues this lawsuit probably won’t damage Oxford Nanopore’s business, and is more an act of desperation from PacBio.

Now, on to the research papers!

Biomolecule engineering

CRISPR/gene editing

SynBio Newsreel, August

We have more of a newsletter than a newsreel this month, since there’s no summary video. However, that was because we devoted our entire monthly meeting to a thought-provoking critique and discussion of the Human Genome Project-Write, led by Professor Laurie Zoloth. With that said, enjoy the newsreeletter!

Synbio community news:

Industry news:

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:

Genetic circuits:

CRISPR/Gene Editing:

Metabolic Engineering

Building biology to understand it

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:

Genetic circuits:

CRISPR/Gene Editing:

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

Industry news:

Synbio community news:

Cool iGEM projects

April Newsreel (a lot late)

As long as I’m posting the May links, the April links should go up too. Enjoy!

–Isaac

Research articles:

  1. Synthetic mammalian gene circuits
  2. Expanding DNA Polymerase function
  3. Synthetic biochemistry module produces valuable chemicals from glucose
  4. Programming IPSC differentiation with a genetic circuit
  5. Cellular device for liver protection
  6. Rapid and efficient incorporation of long DNA fragments into E. coli genomes
  7. A step towards rational dynamic control of gene expression
  8. Research Highlight: A minimal synthetic cell.
  9. Research highlight: Automated genetic circuit design.

Non-research stuff

  1. ComSciCon is awesome! Chicago meeting’s in August, come to the keynote.
  2. The Foundry (DNA factory) Opens in the UK
  3. Perspective article on biosafety in DIY bio communities
  4. Oxford Nanopore responds to Illumina lawsuit
  5. Tech Museum Synthetic Biology Exhibit
  6. GM Mushroom escapes US Regulations
  7. Sean Parker starts $250 million cancer immunotherapy institute