Cell Crunch Index (#51)

A weekly roundup of notable papers.

Welcome back to Cell Crunch, a newsletter about all things genetic engineering and synthetic biology. I’ve returned from hiatus and intend to keep this newsletter running far into the future.

This is the first edition of Cell Crunch Index. Every Monday, notable papers from the last week are compiled. Research explainers, Q&As and other journalism will be sent out on other weekdays. Thanks for reading.

Notable Papers

( * = open access, † = review article)

Recommended Reads

Decade-long leukaemia remissions with persistence of CD4+ CAR T cells. Melenhorst J.J. et al. Nature.

*Predicting bacterial promoter function and evolution from random sequences. Lagator M. et al. eLife.

*Genetically stable CRISPR-based kill switches for engineered microbes. Rottinghaus A.G. et al. Nature Communications.

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Basic Research

*A pan-CRISPR analysis of mammalian cell specificity identifies ultra-compact sgRNA subsets for genome-scale experiments. Zhao B. et al. Nature Communications.

*Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity. Fu R. et al. Nature Communications.

*DNA-encoded library versus RNA-encoded library selection enables design of an oncogenic noncoding RNA inhibitor. Benhamou R.I. et al. PNAS.

Computational Modeling

*†Genome-scale modeling of yeast metabolism: retrospectives and perspectives. Chen Y. et al. FEMS Yeast Research.

*Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins. Hie B.L. et al. Cell Systems.

Genetic Engineering

Reprogramming the piRNA pathway for multiplexed and transgenerational gene silencing in C. elegans. Priyadarshini M. et al. Nature Methods.

*CRISPR–Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells. Lin-Shiao E. et al. Nucleic Acids Research.

*Supramolecular CRISPR-OFF switches with host–guest chemistry. Xiong W. et al. Nucleic Acids Research.

Reduction of the Bacterial Genome by Transposon-Mediated Random Deletion. Ma S. et al. ACS Synthetic Biology.

Programmable Fusion and Differentiation of Synthetic Minimal Cells. Gaut N.J. et al. ACS Synthetic Biology.

*CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations. Höijer I. et al. Nature Communications.

*Inhibition of base editors with anti-deaminases derived from viruses. Liu Z. et al. Nature Communications.

Medicine & Diagnostics

*†Development of Synthetic Biotics as Treatments for Human Diseases. Brennan A.M. Synthetic Biology.

*Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages. Huang X. et al. Nature Protocols.

Transplantation of intestinal organoids into a mouse model of colitis. Watanabe S. et al. Nature Protocols.

†Bioengineering strategies for restoring vision. Cehajic-Kapetanovic J. et al. Nature Biomedical Engineering.

*Generation of an anticoagulant aptamer that targets factor V/Va and disrupts the FVa-membrane interaction in normal and COVID-19 patient samples. Soule E.E. et al. Cell Chemical Biology.

*Fundamental limits of amplification-free CRISPR-Cas12 and Cas13 diagnostics. Huyke D.A. et al. bioRxiv (preprint).

Betibeglogene Autotemcel Gene Therapy for Non–β0/β0 Genotype β-Thalassemia. Locatelli F. et al. New England Journal of Medicine.

†Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics. Song P. et al. Nature Biomedical Engineering.

Metabolic Engineering

Electrogenetic Signal Transmission and Propagation in Coculture to Guide Production of a Small Molecule, Tyrosine. VanArsdale E. et al. ACS Synthetic Biology.

*Multiplex genome editing of mammalian cells for producing recombinant heparin. Thacker B.E. et al. Metabolic Engineering.

Multilevel metabolic engineering of Bacillus licheniformis for de novo biosynthesis of 2-phenylethanol. Zhan Y. et al. Metabolic Engineering.

*Going beyond the limit: Increasing global translation activity leads to increased productivity of recombinant secreted proteins in Pichia pastoris. Staudacher J. et al. Metabolic Engineering.

Far-Red Light Triggered Production of Bispecific T Cell Engagers (BiTEs) from Engineered Cells for Antitumor Application. Zhang C. et al. ACS Synthetic Biology.

Molecular Engineering

Directed Evolution of Replication-Competent Double-Stranded DNA Bacteriophage toward New Host Specificity. Liang J. et al. ACS Synthetic Biology.

†Targeted protein degradation: Emerging concepts and protein state-specific targeting principles. Tao A.J. et al. Current Opinion in Chemical Biology.

Engineering and functional analysis of yeast with a monotypic 40S ribosome subunit. Hu X. et al. PNAS.

Recovery of Information Stored in Modified DNA with an Evolved Polymerase. Shroff R. et al. ACS Synthetic Biology.

Tools & Technology

*Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking. Gentile F. et al. Nature Protocols.

Harnessing plasmid replication mechanism to enable dynamic control of gene copy in bacteria. Li C. et al. Metabolic Engineering.

Computationally designed dual-color MRI reporters for noninvasive imaging of transgene expression. Allouche-Arnon H. et al. Nature Biotechnology.

†Strategies for developing DNA-encoded libraries beyond binding assays. Huang Y. et al. Nature Chemistry.

*A high-throughput method to deliver targeted optogenetic stimulation to moving C. elegans populations. Liu M. et al. PLOS Biology.

*Programmable allosteric DNA regulations for molecular networks and nanomachines. Zhang C. et al. Science Advances.

*Machine learning-informed and synthetic biology-enabled semi-continuous algal cultivation to unleash renewable fuel productivity. Long B. et al. Nature Communications.

*Chemically modified dsRNA induces RNAi effects in insects in vitro and in vivo: A potential new tool for improving RNA-based plant protection. Howard J.D. et al. bioRxiv (preprint).

*Efficient and error-free fluorescent gene tagging in human organoids without double-strand DNA cleavage. Bollen Y. et al. PLOS Biology.

Miscellaneous

Round Trip: An Automated Pipeline for Experimental Design, Execution, and Analysis. Bryce D. et al. ACS Synthetic Biology.

†Biomimetic 3D living materials powered by microorganisms. Wangpraseurt D. et al. Trends in Biotechnology.

*3D printed bioreactor enabling the physiological culture and the study of pathological processes in large vessels. Matos R.S. et al. bioRxiv (preprint).

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Pending changes to this newsletter:

• A paid option. People who may not be able to afford the cost, especially students, will always be able to get the newsletter for free.

• Cell Crunch Index, sent on Mondays. This is a roundup of notable papers from the last week, and will always be sent to all subscribers, free and paid.

• Brief news stories and paid-only content throughout the week. These will include Q&As, explainers, and highlights of new and notable papers.

Until next time,

— Niko

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