DNA Origami Ratchet: Index #59
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
More soon,
— Niko
Twitter: @NikoMcCarty // Email: niko@newscience.org