DNA Origami Ratchet: Index #59

A momentous leap in engineered motors.

This newsletter is bloated. I want the top section — the news piece — to stand on its own. From here on, Index newsletters will be only paper links. I’ll send long-form news pieces, essays, or industry highlights each week, too, starting next week. I just got married so things have been busy! Thanks for reading.

The Biotech Index

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

Assembly, Synthesis & Sequencing

*A metagenomic DNA sequencing assay that is robust against environmental DNA contamination. Mzava O…De Vlaminck I. Nature Communications. Link

*CMDB: the comprehensive population genome variation database of China. Li Z…Jin X. Nucleic Acids Research. Link

↑↑*The sequences of 150,119 genomes in the UK Biobank. Halldorsson BV…Stefansson K. Nature. Link

Basic Research

*Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer–promoter interactions. Wang K…Hilton IB. Nucleic Acids Research. Link

Deciphering the Rules of Ribosome Binding Site Differentiation in Context Dependence. Duan Y…Xu Z. ACS Synthetic Biology. Link

*Genome-wide CRISPR screen for HSV-1 host factors reveals PAPSS1 contributes to heparan sulfate synthesis. Suzuki T…Kimura H. Communications Biology. Link

*Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories. Fait A…Ingmer H. PNAS. Link

Biomanufacturing & Metabolic Engineering

↑*Genome-scale modeling drives 70-fold improvement of intracellular heme production in Saccharomyces cerevisiae. Ishchuk OP…Petranovic D. PNAS. Link

*Engineering circular RNA for enhanced protein production. Chen R…Chang HY. Nature Biotechnology. Link

*Characterizing a New Fluorescent Protein for a Low Limit of Detection Sensing in the Cell-Free System. Copeland CE…Kwon Y-C. ACS Synthetic Biology. Link

Engineering Metabolic Pathways for Cofactor Self-Sufficiency and Serotonin Production in Escherichia coli. Shen P…Qi F. ACS Synthetic Biology. Link

Stress-Tolerant, Recyclable, and Renewable Biocatalyst Platform Enabled by Engineered Bacterial Spores. Hui Y, Cui Z & Sim S. ACS Synthetic Biology. Link

*†Toward Methanol-Based Biomanufacturing: Emerging Strategies for Engineering Synthetic Methylotrophy in Saccharomyces cerevisiae. Kelso PA…Williams TC. ACS Synthetic Biology. Link

*A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes. Wirth NT…Nikel PI. bioRxiv (preprint). Link

*High-yield production of coenzyme F420 in Escherichia coli by fluorescence-based screening of multi-dimensional gene expression space. Last D…Lackner G. Metabolic Engineering. Link

Computational Tools & Models

*Phenotypic response of yeast metabolic network to availability of proteinogenic amino acids. Simensen V, Seif Y & Almaas E. bioRxiv (preprint). Link

*Language models of protein sequences at the scale of evolution enable accurate structure prediction. Lin Z…Rives A. bioRxiv (preprint). Link

*GroovDB: A database of ligand-inducible transcription factors. d’Oelsnitz S & Ellington AD. bioRxiv (preprint). Link

BMSS2: A Unified Database-Driven Modeling Tool for Systematic Biomodel Selection. Kai Ngo RJ…Poh CL. ACS Synthetic Biology. Link

CRISPR & Gene Editing

*Model-guided engineering of DNA sequences with predictable site-specific recombination rates. Zhang Q…Sarkar CA. Nature Communications. Link

*Biallelic and gene-wide genomic substitution for endogenous intron and retroelement mutagenesis in human cells. Ohno T…Aizawa Y. Nature Communications. Link

*Efficient spatially targeted gene editing using a near-infrared activatable protein-conjugated nanoparticle for brain applications. Rebelo C…Ferreira L. Nature Communications. Link

*CRI-SPA – a mating based CRISPR-Cas9 assisted method for high-throughput genetic modification of yeast strain libraries. Olsson H…Mortensen UH. bioRxiv (preprint). Link

Genomic and epigenetic landscapes drive CRISPR-based genome editing in Bifidobacterium. Pan M…Barrangou R. PNAS. Link

*CRISPR-Cas12a nucleases function with structurally engineered crRNAs: SynThetic trAcrRNA. Jedrzejczyk DJ…Gill RT. Scientific Reports. Link

Medicine & Diagnostics

Phase 1–2 Trial of AAVS3 Gene Therapy in Patients with Hemophilia B. Chowdary P…Nathwani A. The New England Journal of Medicine. Link

*Cloning and base editing of GFP transgenic rhesus monkey and off-target analysis. Kang Y…Niu Y. Science Advances. Link

*A recombinant VSV-vectored vaccine rapidly protects nonhuman primates against heterologous lethal Lassa fever. Cross RW…Geisbert TW. Cell Reports. Link

*Uncovering the mode of action of engineered T cells in patient cancer organoids. Dekkers JF…Rios AC. Nature Biotechnology. Link

*Engineered immunomodulatory accessory cells improve experimental allogeneic islet transplantation without immunosuppression. Wang X…Ma M. Science Advances. Link

*Personalized bacteriophage therapy to treat pandrug-resistant spinal Pseudomonas aeruginosa infection. Ferry T…Resch G. Nature Communications. Link

*Engineering chimeric antigen receptor neutrophils from human pluripotent stem cells for targeted cancer immunotherapy. Chang Y…Bao X. Cell Reports. Link

*Nanocarriers based on bacterial membrane materials for cancer vaccine delivery. Zhao X, Zhao R & Nie G. Nature Protocols. Link

Rescue of autosomal dominant hearing loss by in vivo delivery of mini dCas13X-derived RNA base editor. Xiao Q…Shu Y. Science Translational Medicine. Link

*Cas13d knockdown of lung protease Ctsl prevents and treats SARS-CoV-2 infection. Cui Z…Wang Q. Nature Chemical Biology. Link

Malarial Antibody Detection with an Engineered Yeast Agglutination Assay. Cruz CJG…McMillen DR. ACS Synthetic Biology. Link

Plants

A transcriptional regulator that boosts grain yields and shortens the growth duration of rice. Wei S…Zhou W. Science. Link

*Incorporating male sterility increases hybrid maize yield in low input African farming systems. Collinson S…Olsen MS. Communications Biology. Link

*Genetic modification of flavone biosynthesis in rice enhances biofilm formation of soil diazotrophic bacteria and biological nitrogen fixation. Yan D…Blumwald E. Plant Biotechnology Journal. Link

Protein & Molecular Engineering

↑↑↑*A DNA origami rotary ratchet motor. Pumm A-K…Dietz H. Nature. Link

*Enhancing glycosylase base-editor activity by fusion to transactivation modules. Dong X…Bi C. Cell Reports. Link

Directed evolution of adeno-associated virus for efficient gene delivery to microglia. Lin R…Luo M. Nature Methods. Link

*Logic-gated antibody pairs that selectively act on cells co-expressing two antigens. Oostindie SC…de Jong RN. Nature Biotechnology. Link

Scaffolding protein functional sites using deep learning. Wang J…Baker D. Science. Link

↑*Modulating co-translational protein folding by rational design and ribosome engineering. Ahn M…Christodoulou J. Nature Communications. Link

*De novo design of protein homodimers containing tunable symmetric protein pockets. Hicks DR…Baker D. PNAS. Link

Tools & Technology

↑*Large-scale multiplexed mosaic CRISPR perturbation in the whole organism. Liu B…Chi T. Cell. Link

*A versatile, high-efficiency platform for CRISPR-based gene activation. Heideserbach AJ…Haley B. bioRxiv (preprint). Link

*Light-up split Broccoli aptamer as a versatile tool for RNA assembly monitoring in cell-free TX-TL system, hybrid RNA/DNA origami tagging and DNA biosensing. Torelli E…Krasnogor N. bioRxiv (preprint). Link

*†End-to-end design of wearable sensors. Ceren Ates H…Dincer C. Nature Reviews Materials. Link

*Developing cyanobacterial quorum sensing toolkits: towards interspecies coordination in mixed autotroph/heterotroph communities. Kokarakis EJ…Sakkos JK. bioRxiv (preprint). Link

*Multiplexed high-throughput localized electroporation workflow with deep learning–based analysis for cell engineering. Patino CA…Espinosa HD. Science Advances. Link

*Light-activated mitochondrial fission through optogenetic control of mitochondria-lysosome contacts. Qiu K…Diao J. Nature Communications. Link

†Emerging platforms for high-throughput enzymatic bioassays. Shao F…Wang T-H. Trends in Biotechnology. Link

Miscellaneous

*†Gene drive in species complexes: defining target organisms. Connolly JB…Coulibaly MB. Trends in Biotechnology. Link

*Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete. Neumann GU…Stockhammer PW. Current Biology. Link

Why it is important to study human–monkey embryonic chimeras in a dish. De Los Angeles A…Zambidis ET. Nature Methods. Link

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More soon,

— Niko

Twitter: @NikoMcCarty // Email: niko@newscience.org