Vaccines On Demand (Wouldn't that be nice?) - 2021.02.08

Plus: All the research in synthetic biology this week.

Feb 08, 2021

☀️ Good morning.

Thanks to those of you who filled out last week’s survey. About 70% of respondents preferred this new format, so I’ll stick to it. Reach out to me if you have feedback.

Nature has explored only a tiny fraction of the life and life’s molecules that are possible. With evolution in our hands, with the ability to set genetic diversity and to tailor the forces of selection, we can now explore paths that Nature has left unexplored. -Frances Arnold

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On-Demand Vaccines for Bacterial Infections: A new study, published in Science Advances, describes a method to produce conjugate vaccines—which are used to prevent some of the leading causes of vaccine-preventable deaths, according to the World Health Organization—using ground up, freeze-dried bacteria. E. coli bacteria were first engineered to produce an antigen for a pathogenic microbe of choice. Then, the researchers ripped open the cells and added in a piece of DNA encoding a carrier protein, which attaches to those antigens and helps display them to the immune system. The team turned the whole mixture into a powder that could be transported and stored at room temperature. Then, to make a dose of vaccine, they just add water. The freeze-dried tube produces the vaccine, on demand, in about one hour. As a proof of concept, the researchers manufactured vaccines that protected mice against a disease-causing bacteria, Francisella tularensis. The work was authored by researchers at Northwestern University in Evanston, Illinois.

Why It Matters: Most vaccines need to be stored at cold temperatures. This makes it difficult to transport them to parts of the world without a temperature-controlled supply chain. This study could help make vaccines accessible to a greater number of people. The technique is also very general; it can be used to make just about any conjugate vaccine that is on the market today. Conjugate vaccines are already used to prevent a lot of childhood diseases, including multiple types of bacterial meningitis, which killed an estimated 300,000 people in 2016. That’s according to a 2018 study in The Lancet Neurology.

Cas13a Treats SARS-CoV-2 and Flu: DNA targeting CRISPR enzymes, including Cas9 and Cas12a, can manipulate genomes with ease. But there are also CRISPR proteins that target RNA, including the Cas13 ‘family.’ Since influenza and SARS-CoV-2 are both RNA-based viruses, Cas13 can be used to target, and chop up, their genetic material. For a new study, published in Nature Biotechnology, researchers at the Georgia Institute of Technology and Emory University, in Atlanta, used Cas13a to cut specific regions of the influenza and SARS-CoV-2 viruses. They first searched for guide RNAs that could cut these viruses in a cell culture model. Then, they packaged up an mRNA sequence encoding Cas13a, together with its ‘guides,’ and delivered them into mouse airways with a nebulizer (a device that converts liquid into a fine mist). In the mice, “Cas13a degraded influenza RNA in lung tissue efficiently when delivered after infection, whereas in hamsters, Cas13a delivery reduced SARS-CoV-2 replication and reduced symptoms.”

Why It Matters: Vaccines are great for fending off diseases. But knocking out a respiratory infection—after it has already happened—is much more challenging. This study shows that a CRISPR-based system can be programmed to target viruses, and can be easily delivered into airways with a nebulizer. This approach could likely be used to target other types of respiratory infections in the future.

Glucose Sensor Upgrade: For a new study, published in Nature Communications, researchers at the University of Toronto merged engineered cells with a standard glucose meter, expanding the number of molecules that can be measured with these common devices. Glucose test strips are typically coated with an enzyme, called glucose oxidase, that senses sugar and converts that signal into electricity. The researchers built a genetic circuit that can sense a wider array of molecules—like an antigen from a pathogenic microbe—and produce a commensurate amount of sugar. Standard glucose test strips can then be used to measure the concentration of those ‘sensed’ molecules in about an hour. The genetic circuit + glucose sensor combo was used to measure small molecules and synthetic RNAs, including “RNA sequences for typhoid, paratyphoid A and B, and related drug resistance genes” at attomolar concentrations.

Why It Matters: The ongoing pandemic has highlighted the need for scalable, rapid testing. By leveraging a household technology—glucose sensors—to detect a wider range of molecules, perhaps this study could be an entryway for synthetic biology; a way to get engineered cells into the hands of more people.

Open the Genetic Floodgates: There are many ways to “turn on” a single gene, but few options to do the same for many genes at once. The Cas12a protein, though, is uniquely suited to this purpose. For a new preprint, which was posted to bioRxiv and has not been peer-reviewed, researchers at the University of Edinburgh used a Cas12a protein from the bacterium, Francisella novicida, to activate six genetic targets at once. They encoded six crRNAs—nucleotide sequences that direct Cas12a to a genetic target—in a single piece of DNA, and swapped around their order to study how their position impacts the efficiency of gene editing. They found that the crRNA in the last position was produced in the lowest amount.

Why It Matters: Researchers have been activating specific genes in cells for decades. But only recently—in the last few years—has ‘multiplexed’ activation become simple; routine even. This new preprint is important, in my opinion, because of the depth of its experiments. The team played with the order of crRNAs, as I’ve already written, but they also tested the synergism of crRNAs. In other words, can you turn a gene on at even higher levels if you target it with two crRNAs instead of one? (Yes.)

CRISPR Clocks: The Cas9 protein cuts DNA at a steady pace. Cut…cut…cut, like a wobbly metronome. For a new study, published in Cell, researchers at the Yonsei University College of Medicine, in Seoul, Korea, used this “CRISPR clock” to record the timing of cellular events. They figured out how long it takes Cas9 to cut DNA (every DNA sequence takes a different amount of time to cut) and then sequenced the DNA to figure out the amount of time that had elapsed. The “clocks” were tested in HEK293T, a type of human liver cell, and also in mice. The clocks could be turned “on” by inflammation or heat. In one experiment, the researchers put cells with these clocks into mice, and then injected the animals with fat molecules that cause inflammation. They sequenced the cells, and found that they could determine the elapsed time, from genetic sequencing alone, with a mean error of just 7.6 percent.

Why It Matters: Biological clocks are useful for many reasons. The researchers said that their CRISPR clocks could be used to record when a pre-cancerous cell is turned into a cancer cell, for example. Scientists could expose cells to toxins, for example, and then measure the amount of time that it takes for cancerous growth to begin. The CRISPR clocks could be used to study these effects inside of living cells.

🧫 Other Studies Published This Week

Special Issue: 20 Years of the Human Genome

Science magazine’s issue, this week, was devoted to celebrating the “Human Genome at 20.” My recommendations: “Complicated legacies: The human genome at 20” and “Beyond DNA: The rest of the story.” Both are insightful. Link to Issue.

Biosensors

(Review) Transcription factor-based biosensor for dynamic control in yeast for natural product synthesis. Frontiers in Bioengineering and Biotechnology. Open Access. Link
A protein-based biosensor for detecting calcium by magnetic resonance imaging. bioRxiv. Open Access. Link

Fundamental Discoveries

A genome-wide screen in the mouse liver reveals sex-specific and cell non-autonomous regulation of cell fitness. bioRxiv. Open Access. Link
Photoactivatable CaMKII induces synaptic plasticity in single synapses. Nature Communications. Open Access. Link
Resolving phylogenetic and biochemical barriers to functional expression of heterologous iron-sulphur cluster enzymes. bioRxiv. Open Access. Link
Intercellular communication induces glycolytic synchronization waves between individually oscillating cells. PNAS. Open Access. Link
A comprehensive phenotypic CRISPR-Cas9 screen of the ubiquitin pathway uncovers roles of ubiquitin ligases in mitosis. Molecular Cell. Link

Genetic Circuits

Ultrasensitive molecular controllers for quasi-integral feedback. Cell Systems. Link

Genetic Engineering & Control

Small-molecule inhibitors of histone deacetylase improve CRISPR-based adenine base editing. Nucleic Acids Research. Open Access. Link
A piggyBac‐mediated transgenesis system for the temporary expression of CRISPR/Cas9 in rice. Plant Biotechnology Journal. Link
Expanding the SiMPl plasmid toolbox for use with spectinomycin/streptomycin. bioRxiv. Open Access. Link
Joint universal modular plasmids (JUMP): a flexible vector platform for synthetic biology. Synthetic Biology. Open Access. Link

Medicine and Diagnostics

Engineering advanced logic and distributed computing in human CAR immune cells. Nature Communications. Open Access. Link
A thermostable, flexible RNA vaccine delivery platform for pandemic response. bioRxiv. Open Access. Link
Toolkit for quickly generating and characterizing molecular probes specific for SARS-CoV-2 nucleocapsid as a primer for future coronavirus pandemic preparedness. ACS Synthetic Biology. Link

Metabolic Engineering

An artificial self-assembling nanocompartment for organising metabolic pathways in yeast. bioRxiv. Open Access. Link
Transport engineering for improving production and secretion of valuable alkaloids in Escherichia coli. bioRxiv. Open Access. Link
Autophagy‐inducing peptide increases CHO cell monoclonal antibody production in batch and fed‐batch cultures. Biotechnology and Bioengineering. Link
Quorum sensing-mediated protein degradation for dynamic metabolic pathway control in Saccharomyces cerevisiae. Metabolic Engineering. Link
(Review) Synthetic biology approaches to enhance microalgal productivity. Trends in Biotechnology. Open Access. Link
A biological route to conjugated alkenes: Microbial production of hepta-1,3,5-triene. ACS Synthetic Biology. Open Access. Link
(Review) Yeast-based biosynthesis of natural products from xylose. Frontiers in Bioengineering and Biotechnology. Open Access. Link

New Technology

Synthetic protein quality control to enhance full-length translation in bacteria. Nature Chemical Biology. Link
Scalable characterization of the PAM requirements of CRISPR–Cas enzymes using HT-PAMDA. Nature Protocols. Link
A platform for post-translational spatiotemporal control of cellular proteins. Synthetic Biology. Open Access. Link
An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine. Nature Communications. Open Access. Link

Protein Engineering

Computation-guided optimization of split protein systems. Nature Chemical Biology. Link
Efficient Lewis acid catalysis of an abiological reaction in a de novo protein scaffold. Nature Chemistry. Link
Periplasmic expression of SpyTagged antibody fragments enables rapid modular antibody assembly. Cell Chemical Biology. Link

Systems Biology and Modelling

A MATLAB toolbox for modeling genetic circuits in cell-free systems. Synthetic Biology. Open Access. Link
Enzyme kinetics of CRISPR molecular diagnostics. bioRxiv. Open Access. Link
Potential landscapes, bifurcations, and robustness of tristable networks. ACS Synthetic Biology. Link
Modeling of copy number variability in Pichia pastoris. Biotechnology and Bioengineering. Link

Have a great week.

— Niko