NEWSLETTER

Synthetic Spider Silk & Morphogen Gradients

This Week in Synthetic Biology (Issue #12)

Niko McCarty
Oct 16 · 10 min read
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Synthetic Spider Silk (Review)

Every once in awhile, a review comes along that makes me fall in love (again). I’ve always been intrigued by synthetic spider silk, but a review from Eriko Takano’s group, at the University of Manchester, has taken my obsession to new heights. This new review explores all the wondrous ways that living organisms — including, but not limited to, spiders — can be coaxed into producing synthetic silk. Takano and the other authors offer an exciting scientific journey through the challenges of producing, and harvesting, silk spidroin proteins from Salmonella bacteria, mammalian cells, rice (!), other plants (including Nicotiana tabacum) and even mice. I didn’t know that so many different critters could produce silk, nor did I understand just how big of a factor pH plays in the silk spinning process within a spider’s glands. This review, which is open access, was published in Trends in Biotechnology. Link

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Source: Tumblr

Synthetic Morphogen Gradients Come of Age

Two back-to-back studies, published in the Oct. 16 issue of Science, have demonstrated tunable, synthetic morphogen gradients — one in an in vitro system, and the other in living fruit flies.

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Source: Giphy

Mini Cannonballs, Grown & Tweaked Inside of Cells

Some organisms produce iron oxide nanoparticles, which are basically balls of magnetite (Fe3O4) that range in diameter from 1 to 100 nanometers. The applications for these “miniature cannonballs” (not a real scientific term, I assure you) are immense: they can be used as contrast agents for MRI, for example, or as gene carriers for genetic therapies. But, until now, it has been tough to coax cells — like M. magneticuminto producing iron oxide nanoparticles of a consistent size.

The Mystery of Overlapping Genes in Phages

One of the wonders of viruses is that a lot of features can be packed into an itty-bitty genome. The sum total genetic information of SARS-CoV-2, the virus that causes COVID-19, for example, consists of a measly 30,000 base pairs. For context, that’s 1/100,000th of the size of the human genome. And yet, SARS-CoV-2 can wreak utter destruction on the human body.

🧫 Rapid-Fire Highlights

More research & reviews worth your time

  • Fankang Meng and Tom Ellis wrote a review on “the second decade of synthetic biology”, spanning advancements from 2010 to the present. It’s a nice piece that covers the major milestones in this field. If you’re new to synthetic biology, or just want to relive the highlights, it’s a must read. Nature Communications (Open Access). Link
  • Even if a genetic cure were offered for sickle cell disease, would people expose themselves to genome editing? An important study takes a look at this issue. One fascinating result, that I noticed, was that “individuals with [sickle cell disease] demonstrated higher levels of genetic literacy than estimated by physicians.” AJOB Empirical Bioethics (Open Access). Link & Press Release
  • It’s exceedingly difficult to chemically synthesize long RNA sequences. Now, a new method enables “routine solid phase synthesis of long RNA strands”. The authors used this method to synthesize a 76-nt long tRNA and a 101-nt long sgRNA. bioRxiv (Open Access). Link
  • An online calculator can perform “techno-economic analysis” for scaling up a metabolic engineering project. Specifically, the calculator computes the “impact of fermentation level metrics on the commercial potential of a bioprocess for the production of a wide variety of organic molecules.” It is called the BioProcess TEA calculator, is freely available, and was developed by Michael Lynch at Duke University. bioRxiv (Open Access). Paper & Calculator
  • A wide-ranging perspective, from Ron Milo’s group at the Weizmann Institute, looks at carbon dioxide conversion in engineered organisms, especially algae, and how they can be used to feed a growing population. Cell Reports Physical Science (Open Access). Link
  • Even genetically identical cells behave differently, and so tools that probe metabolic flux, in single cells, are very desirable. A new study reports an RNA-based sensor for fructose-1,6-bisphosphate, an intermediate product in glycolysis, that “can be used to sense the glycolytic rate in single cells.” bioRxiv (Open Access). Link
  • Mikhail Shapiro’s group, at Caltech, has been at the forefront of synthetic biology and in vivo ultrasound technologies. Now, they’ve written a review that is very much worth your time; it covers the basic science behind ultrasound and discusses how engineered microbes can be used for in vivo imaging. Neuron (Open Access). Link
  • To determine a protein’s identity, within a cell, researchers often turn to an incredibly laborious method called mass spectrometry. A new study presents a method to fuse proteins to their mRNA transcript, enabling nucleic acid sequencing to be used for protein identification. This method could revolutionize proteomics. PNAS (Open Access). Link
  • Plants around the world produce thousands of different benzylisoquinoline alkaloids (yes, that’s a mouthful), chemical compounds that are widely used as antibacterial and anticancer drugs. Metabolic engineers have long been interested in producing these compounds in living yeast cells. Unfortunately, one of the enzymes that is required to produce these alkaloids — called norcoclaurine synthase — is toxic when present in the cytosol of yeast cells. A new study has found that, by targeting this enzyme to the peroxisome compartment, toxicity is reduced and titers for producing the alkaloids can be increased. Nature Chemical Biology. Link
  • I did not know this, but Vitamin E compounds can actually consist of eight different molecules; four tocotrienols and four tocopherols (which differ in their chemical structures). It turns out that tocotrienols can have really important health benefits, but are often left out of Vitamin E supplements. Now, a new study has engineered Baker’s yeast to produce tocotrienols by supplementing some native metabolic pathways in yeast with genes taken from photosynthetic organisms. Nature Communications (Open Access). Link
  • GFP is great to “light up” the insides of cells, but it has a problem: fluorescent proteins, in many cases, take several minutes to mature, or produce light, after they are produced in a cell. A new study has remedied this problem, reporting a “genetically encoded fluorescent biosensor” that, amazingly, enables the “detection of protein expression within seconds in live bacteria.” ACS Synthetic Biology. Link
  • A new study has, to some degree, standardized how genes can be expressed in cell-free systems. A paper from scientists at LanzaTech and Northwestern University reports a “modular vector system that allows for T7 expression of desired enzymes for cell-free expression and direct Golden Gate assembly into Clostridium expression vectors.” The new system enables scientists to quickly test genes in cell-free extracts, and then export those designs to living cells. Synthetic Biology (Open Access). Link
  • Plants, it turns out, are really good at producing antibodies against SARS-CoV-2. A new study has produced “milligram amounts of six different recombinant monoclonal antibodies against SARS-CoV-2 in Nicotiana benthamiana.” bioRxiv (Open Access). Link

📰 #SynBio in the News

  • The EBRC’s Student & Postdoc Association is looking for new members. Any trainees working in synthetic biology or adjacent fields are welcome to join. Membership is free and non-competitive, and members also get a few perks for professional networking: a mentorship program, an internship program, a Slack workspace, a LinkedIn page, and a few other things. Follow the link to join. Link
  • Mark Temple, at Western Sydney University, has “sonified” the coronavirus genome, turning its nucleotides into an hour-long musical composition. Mark has since written an article, for The Conversation, that explains the project’s inception, methods, and artistic merits. Link (To read the original study, click here).
  • A DIY “biohacker” made a COVID-19 vaccine in his house, tested it, and isn’t sure how to interpret the results. I am especially fond of this line from the article: “Zayner said his turn at vaccine testing has tempered his appetite for DIY human experimentation.” Hilarious. Link
  • Portable DNA sequencers enable researchers to collect genetic material and sequence it from (almost) anywhere in the world. Carlos de Rojas reports for Labiotech.eu. Link
  • If this is interesting to you, also check out Glen Gowers & co’s “off-grid” sequencing expedition in Vatnajökull, Iceland, which was published last year. Link
  • As ‘Chief of Staff’ roles become more common in biotech companies, an article in Bioeconomy.xyz takes a look at what this role actually does. Link
  • Spectrum and Science ran a piece on gene therapy, and whether it’s ready to treat some forms of autism. Link
  • Synthetic proteins, engineered to target the coronavirus, have been made in a lab. Scientific American takes a closer look. Link
  • Making breast milk, “without the breast”. A deep piece of reporting, at least relative to articles that have previously been written on this topic, was published in Future Human. Link

🐦 Tweet of the Week

Before a synthetic biologist even touches a cell, it is often useful to first build models that predict, among other things, which genes should be altered to produce a given response, or chemical, or phenotype. And then, once those genes are identified, the researcher must carefully tune and tweak and prod and control the genes to get them at an expression level that is juuuuuuust right for his or her purpose.

Bioeconomy.XYZ

Innovation for the Bioeconomy

Niko McCarty

Written by

Science journalism at NYU. Previously Caltech, Imperial College. #SynBio newsletter: https://synbio.substack.com Web: https://nikomccarty.com

Bioeconomy.XYZ

The Medium publication for biotechnology and everyone involved in the revolution. The best brought to you by the brightest. Founded by @1AlexanderTitus for you.

Niko McCarty

Written by

Science journalism at NYU. Previously Caltech, Imperial College. #SynBio newsletter: https://synbio.substack.com Web: https://nikomccarty.com

Bioeconomy.XYZ

The Medium publication for biotechnology and everyone involved in the revolution. The best brought to you by the brightest. Founded by @1AlexanderTitus for you.

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