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, September

Lots of news this month. We’ll post a link to the video version of the newsreel later this week. Enjoy!

Synbio community news

Biosecurity

Industry news

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

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

Genetic circuits

CRISPR/gene editing

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

Therapeutic synbio

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 in biology is about to get significantly faster.

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

May Newsreel (a little late)

Here are all the links from the May meeting’s newsreel. Enjoy!

—Isaac

Non-research articles:

1. Gen9 and Arzeda sign DNA synthesis deal. In related news, Twist Bioscience partners with Microsoft on DNA data storage. But how big is the synthetic DNA market? Rob Carlson’s perspective.

2. Synthetic biology tackles the antivenin shortage.

3. DIY bio lab in Brooklyn gets a profile in The Guardian.

Research articles:

4. Modeling competition between genes for expression machinery.

5. De novo design of protein structures which associate via hydrogen bond networks (as opposed to hydrophobic effects).

6. DNA nanostructures encoded and self-assembled in living bacteria.

7. Computationally designed protein enables biomineralization of cadmium chloride nanocrystal.

8. Moss assembles DNA in vivo (like yeast!).

9. Targeted isolation and cloning of 100 kb microbe genome fragments through Cas9-assisted technique.

10. DNA-guided genome editing with Natronobacter gregoryi Argonaute (NgAgo)—comparable in vitro editing to Cas9, but uses guide DNA rather than RNA, and doesn’t require a PAM sequence!

Human Genome Project: Write

On May 10th, a group of scientists led by George Church met in a closed-door, invitation only session to discuss the possibility of synthesizing the human genome. The intent was to publish a proposal outlining the need for human genome synthesis. That perspective piece was recently published in Science, and now has its own website. Among the goals and applications for human genome synthesis are:

 

  • To drive demand for large-scale DNA synthesis, and thus lower costs
  • To understand basic biology by re-creating noncoding DNA regions
  • To construct specific genotypes to study disease
  • To construct artificial chromosomes with all-included developmental pathways (minimal human cells, anyone?)
  • For gene therapy applications: improve safety by removing viral and cancer susceptibility, etc.
  • To recoding human cells for safety and biocontainment in manufacturing
  • To create a homozygous “pan-human” reference genome for drug testing

Drew Endy was invited but chose not to attend, instead exposing the meeting to the public and co-authoring an opinion piece on the ethics of human genome synthesis with our own Laurie Zoloth. Concerns raised in their piece include:

  • The secrecy and lack of public dialog severely damage public trust
  • The individuals involved have a financial conflict of interest
  • A non-human model organism genome synthesis project can provide the same demand to fuel low-cost DNA synthesis
  • No ethical analysis has been undertaken
  • A large potential for unintended consequences, especially on funding for the entire field of synthetic biology

What do you think? Join the discussion below!