Light Triggers Synthetic Cells to Talk

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Hello. Apologies that this newsletter is one day late. I traveled this weekend, and haven’t quite gotten caught up yet. I hope that this abbreviated form of the newsletter is still useful to you; we’ll be back to regular programming next week.

Papers

(↑ = recommended article, * = open access, † = review article, )

Basic Research

↑Stepwise-edited, human melanoma models reveal mutations’ effect on tumor and microenvironment. Hodis E…Regev A. Science. Link

*Genome-wide screen for enhanced noncanonical amino acid incorporation in yeast. Zackin MT, Stieglitz JT & Van Deventer JA. bioRxiv (preprint). Link

Biomanufacturing

Engineering cofactor supply and recycling to drive phenolic acid biosynthesis in yeast. Chen R…Zhou YJ. Nature Chemical Biology. Link

↑†Genetically encoded tools for measuring and manipulating metabolism. Choe M & Titov DV. Nature Chemical Biology. Link

†Recycling carbon for sustainable protein production using gas fermentation. Marcellin E…Molitor B. Current Opinion in Biotechnology. Link

*†Quality by Design for enabling RNA platform production processes. Daniel S…Shah N. Trends in Biotechnology. Link

*In-situ scalable manufacturing of Epstein–Barr virus-specific T-cells using bioreactor with an expandable culture area (BECA). Chen S…Liu D. Scientific Reports. Link

†Strategies for improving antimicrobial peptide production. Deo S…Wieden H. Biotechnology Advances. Link

Directed evolution as an approach to increase fructose utilisation in synthetic grape juice by wine yeast AWRI 796 Get access Arrow. Walker ME…Jiranek V. FEMS Yeast Research. Link

Increased Production of Riboflavin by Coordinated Expression of Multiple Genes in Operons in Bacillus subtilis. You J…Rao Z. ACS Synthetic Biology. Link

Cell Engineering

↑*Synthetic cells with self-activating optogenetic proteins communicate with natural cells. Adir O…Schroeder A. Nature Communications. Link

*Engineering artificial photosynthetic life-forms through endosymbiosis. Cournoyer JE…Mehta AP. Nature Communications. Link

Computational Tools & Models

*Algorithmic design of 3D wireframe RNA polyhedra. Elonen A…Orponen P. bioRxiv (preprint). Link

CRISPR & Genetic Control

*Targeted A-to-G base editing in human mitochondrial DNA with programmable deaminases. Cho S…Kim J. Cell. Link

*Machine learning-coupled combinatorial mutagenesis enables resource-efficient engineering of CRISPR-Cas9 genome editor activities. Thean DGL…Wong ASL. Nature Communications. Link

Dynamic modulation of enzyme activity by synthetic CRISPR–Cas6 endonucleases. Mitkas AA, Valverde M & Chen W. Nature Chemical Biology. Link

Combining CRISPR–Cpf1 and Recombineering Facilitates Fast and Efficient Genome Editing in Escherichia coli. Zhu X…Liu L. ACS Synthetic Biology. Link

Medicine & Diagnostics

Antigen-bearing outer membrane vesicles as tumour vaccines produced in situ by ingested genetically engineered bacteria. Yue Y…Nie G. Nature Biomedical Engineering. Link

↑*Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants. Zhang JZ…Baker D. Nature Biotechnology. Link

*A Pan-Coronavirus Vaccine Candidate: Nine Amino Acid Substitutions in the ORF1ab Gene Attenuate 99% of 365 Unique Coronaviruses: A Comparative Effectiveness Research Study. Luellen E. bioRxiv (preprint). Link

*Enhanced safety and efficacy of protease-regulated CAR-T cell receptors. Labanieh L…Mackall CL. Cell. Link

*Protective prototype-Beta and Delta-Omicron chimeric RBD-dimer vaccines against SARS-CoV-2. Xu K…Gao GF. Cell. Link

Central and peripheral delivered AAV9-SMN are both efficient but target different pathomechanisms in a mouse model of spinal muscular atrophy. Reilly A…Kothary R. Gene Therapy. Link

Adeno-associated virus serotype 9 antibody titers in patients with SMA pre-screened for treatment with onasemnogene abeparvovec –routine care evidence. Aharoni S…Nevo Y. Gene Therapy. Link

Safety profile of intravenous administration of live Pichia pastoris cells in mice. Becerril-García MÁ…Palma-Nicolás JP. FEMS Yeast Research. Link

Detection of Major SARS-CoV-2 Variants of Concern in Clinical Samples via CRISPR-Cas12a-Mediated Mutation-Specific Assay. Liang Y…Tang S. ACS Synthetic Biology. Link

Plants

*Overexpression of cytoplasmic C4 Flaveria bidentis carbonic anhydrase in C3 Arabidopsis thaliana increases amino acids, photosynthetic potential, and biomass. Kandoi D…Tripathy BC. Plant Biotechnology Journal. Link

Protein & Molecular Engineering

↑Machine learning-aided engineering of hydrolases for PET depolymerization. Lu H…Alper HS. Nature. Link

Computational design of mechanically coupled axle-rotor protein assemblies. Courbet A…Baker D. Science. Link

*A reversibly gated protein-transporting membrane channel made of DNA. Dey S…Yan H. Nature Communications. Link

*An engineered ACE2 decoy neutralizes the SARS-CoV-2 Omicron variant and confers protection against infection in vivo. Ikemura N…Hoshino A. Science Translational Medicine. Link

*Development of broadly neutralizing antibodies targeting the cytomegalovirus subdominant antigen gH. Parsons AJ…Tortorella D. Communication Biology. Link

Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches. Andreasson JOL…Greenleaf WJ. PNAS. Link

Tools & Technology

*Highly Efficient Libraries Design for Saturation Mutagenesis. Pines G, Pines A & Eckert CA. Synthetic Biology. Link

All-optical interrogation of neural circuits in behaving mice. Russell LE…Häusser M. Nature Protocols. Link

*Efficient golden gate assembly of DNA constructs for single molecule force spectroscopy and imaging. Bell NAW & Molloy JE. Nucleic Acids Research. Link

*Development and characterization of new tools for detecting poly(ADP-ribose) in vitro and in vivo. Challa S…Kraus WL. eLife. Link

Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging. Chung KKH…Bewersdorf J. Nature Methods. Link

Miscellaneous

*Comparison of public discussions of gene editing on social media between the United States and China. Ji J…Barnett GA. PLOS ONE. Link

*The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism . Zhang H…Fu X. Nucleic Acids Research. Link


More soon,

— Niko // @NikoMcCarty // niko@codonmag.com