Good morning! This week…

Undark examined the potential of gene editing to create meatier cattle, while STAT hosted a virtual CRISPR event featuring Alexis Thompson and David Liu. Meanwhile, Massive Science compared cultivated meat to Tesla Roadsters, and researchers at the University of New England have identified the sex of chickens using feather DNA.

In related news, an article in The Ecologist reported that the UK government is contemplating the deregulation of genome-edited organisms in agriculture. The University of Oregon announced the launch of the Plesa lab and DropSynth 2.0, while WIRED published a comprehensive "CRISPR guide". Axios also interviewed Jennifer Doudna regarding CRISPR applications in coronavirus diagnostics.

On the industry front, Carisma has received the go-ahead for a Phase 1 trial of engineered macrophage immunotherapy, Ginkgo introduced their 2020 creative residents, and Genetic Engineering & Biotechnology News featured companies leveraging base editors, exonucleases, and various gene-editing technologies.

In the realm of COVID-19 testing, UC Davis scientists secured a $1.2 million NIH grant to create mice that can contract the COVID-19 virus. Oxford Nanopore rolled out LamPORE, and Ginkgo, Mammoth, and others were awarded a combined $250 million NIH grant to enhance COVID-19 testing capabilities.

This week in research…

Ultrasound-Controlled Engineered T-cells

Recent research from the Shapiro lab at Caltech, published in ACS Synthetic Biology, showcased T-cells with engineered heat shock promoters that can be activated by brief pulses of heat from focused ultrasound, prompting them to release cytokines and target tumor cells.

Automated Genetic Circuit Design for Yeast

The Voigt lab at MIT has successfully constructed nine NOT/NOR gates with a dynamic range of 400-fold in S. cerevisiae. Utilizing Cello 2.0, a software tool for genetic circuit design, they built circuits incorporating up to 11 regulatory proteins. This advancement could greatly simplify circuit design for eukaryotic synthetic biology, as noted in Nature Microbiology.

DIY Automated Cell Culture System

A team from Oxford has developed a cell culture automation system for approximately $300 using off-the-shelf components and printed circuit boards. This device can track and document cell growth, and its seven-color LEDs can simultaneously measure multiple fluorescent proteins or be applied in optogenetics. The Chi.Bio system was discussed in PLoS Biology.

For additional insights on this study, check out my interview with lead author Dr. Harrison Steel.

Designer Disordered Proteins for Phase Separation

The Chilkoti lab at Duke University has engineered a series of artificial, intrinsically disordered proteins (IDPs) that can be used to create intracellular condensates in living cells. Their findings, published in Nature Chemistry, indicate that the behavior of these condensates can be predicted and adjusted by manipulating the mass and structure of the IDPs. Chilkoti emphasized that this research offers straightforward engineering principles for programming intracellular behavior.

Chemical Control of CRISPR Gene Drives

In Seoul, South Korea, the Kim lab at Yonsei University has introduced a chemical approach to regulate CRISPR-based gene drives in Drosophila fruit flies. By employing a site-specific recombinase activated by the chemical RU486, they achieved a gene drive removal rate of 7-12% per generation. This work was also published in ACS Synthetic Biology.

More research…

• A bimodular PKS platform that broadens the biological design space by Zargar, A. et al. in Metabolic Engineering.
• A microgravity-responsive synthetic genetic device in Escherichia coli by Mukhopadhyay, S. and Bagh, S. in Biosensors and Bioelectronics.
• A new method for developing third-generation hybrid rice technology using a cytoplasmic sterility gene and a genic male-sterile gene by Song, S. et al. in Plant Biotechnology Journal. (Open Access)
• A protein-independent fluorescent RNA aptamer reporter for plant genetic engineering by Bai, J. et al. in Nature Communications. (Open Access)
• Bidirectional titration of yeast gene expression using a pooled CRISPR guide RNA method by Bowman, E.K. et al. in PNAS.
• CRISPR-assisted multiplex base editing system in Pseudomonas putida KT2440 by Sun, J. et al. in Frontiers in Bioengineering and Biotechnology. (Open Access)
• Display of lead-binding proteins on the surface of Escherichia coli for bioremediation by Jia, X., Li, Y., Xu, T. and Wu, K. in Biotechnology and Bioengineering.
• DNA targeting and interference by a bacterial Argonaute nuclease by Kuzmenko, A. et al. in Nature.
• Engineering Escherichia coli for the de novo production of flavanones by Dunstan, M.S. et al. in Synthetic Biology. (Open Access)
• Engineering the carotenoid biosynthetic pathway in Rhodothermus marinus for lycopene production by Kristjansdottir, T. et al. in Metabolic Engineering Communications. (Open Access)
• An integrated approach to accelerate the discovery of antiviral antibody therapeutics by Gilchuk, P. et al. in Nature Biomedical Engineering. (Open Access)
• Designing a methanol utilization pathway in E. coli by De Simone, A. et al. in Metabolic Engineering.
• Multimodal recordings of cellular physiology using multiplexed optical sensors in cell arrays by Werley, C.A. et al. in Nature Communications. (Open Access)
• Noise suppression in negatively autoregulated gene expression by Smith, M. and Singh, A. Abstract for the 2020 American Control Conference.
• A rapid method for creating designer algal mitochondrial genomes by Cochrane, R.R. et al. in Algal Research.
• Implementation of a chemically inducible heterotrimerization system by Wu, H.D. et al. in Nature Methods.
• Discovery of molecular glue degraders through scalable chemical profiling by Mayor-Ruiz, C. et al. in Nature Chemical Biology. For more, read the News & Views article on this topic.
• The impact of resource scarcity on the robustness of toggle switches to noise by Gyorgy, A. Abstract for the 2020 American Control Conference.
• Optimizing cyanobacteria for efficient astaxanthin synthesis by Diao, J. et al. in Metabolic Engineering.
• The Synthetic Biology Open Language (SBOL) Version 3: Enhancing data exchange for bioengineering by McLaughlin, J.A. et al. in Frontiers in Bioengineering and Biotechnology.

This week in reviews…

• Innovations in systems metabolic engineering of Bacillus subtilis as a chassis cell by Xiang, M., Kang, Q. and Zhang, D. in Synthetic and Systems Biotechnology. (Open Access)
• Bacterial cellulose: From optimization to new applications by Fernandes, I.A.A. et al. in Macromolecules.
• Utilizing cells for targeted nanoparticle drug delivery in cancer treatment by Singh, B. and Mitragotri, S. in Biotechnology Advances.
• Production of plant natural products via engineered Yarrowia lipolytica by Muhammad, A. et al. in Biotechnology Advances.
• Sequencing that facilitates design and learning in synthetic biology by Gilliot, P. and Gorochowski, T.E. in Current Opinion in Chemical Biology.

This week in preprints…

• A MATLAB toolbox for modeling genetic circuits in cell-free systems by Singhal, V. et al. on bioRxiv.
• An effective vector-based CRISPR/Cas9 system in an Oreochromis mossambicus cell line utilizing endogenous promoters by Hamar, J.C. and Kültz, D. on bioRxiv.
• A novel CRISPR-Cas12a tool for programmable transcriptional control by Schilling, C. et al. on bioRxiv.
• Base-edited CAR T cells for combined therapy against T cell malignancies by Georgiadis, C. et al. on bioRxiv.
• BioCRNpyler: Compiling chemical reaction networks from biomolecular components in various contexts by Poole, W. et al. on bioRxiv.
• Cheetah: A computational toolkit for cybergenetic control by Pedone, E. et al. on bioRxiv.
• CRISPR interference as low-burden logic inverters in synthetic circuits: characterization and tuning by Bellato, M. on bioRxiv.
• CRISPR Turbo Accelerated Knock Out (CRISPy TAKO) for swift in vivo gene function screening by Plasil, S.L. et al. on bioRxiv.
• De novo design of picomolar SARS-CoV-2 miniprotein inhibitors by Cao, L. et al. on bioRxiv.
• Identifying critical, beneficial, neutral, and harmful mutations during directed evolution of a yeast membrane receptor by Adeniran, A. and Tyo, K.E.J. on bioRxiv.
• Efficient population modification gene-drive rescue system in the malaria mosquito Anopheles stephensi by Adolfi, A. et al. on bioRxiv.
• Engineered ACE2 receptor traps effectively neutralize SARS-CoV-2 by Glasgow, A. et al. on bioRxiv.
• Probabilistic models for biological sequence generation accounting for mutational variability by Weinstein, E.N. and Marks, D.S. on bioRxiv.
• Genetically-encoded fluorescent biosensors for rapid protein expression detection by Eason, M.G. et al. on bioRxiv.
• MASSpy: Building, simulating, and visualizing dynamic biological models using mass action kinetics by Haiman, Z.B. et al. on bioRxiv.
• Minicells as a potential platform for engineering lineage-agnostic organisms by Wei, E. et al. on bioRxiv.
• Targeted protein degradation using the Predator method by Liu, C. et al. on bioRxiv.
• SARS-CoV-2 detection utilizing de novo designed synthetic riboregulators by Koksaldi, I.C. et al. on medRxiv.
• Scalable analysis of metabolic pathways by Øyås, O. and Stelling, J. on bioRxiv.
• Swab-Seq: A high-throughput platform for large-scale SARS-CoV-2 testing by Bloom, J.S. et al. on medRxiv.

This Week in Synthetic Biology is published every Friday, highlighting the latest peer-reviewed studies, preprints, and significant news in the field. A version of these newsletters is also available on Medium and hiniko.io.

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