Cell Crunch Index (#57)

Synthetic wine yeasts, cheap amplicon sequencing, CAR-T trial updates.

Good morning. A methods paper from Frances Arnold’s group explains how to sequence every variant in a protein library, cheaply, for directed evolution experiments. A new review explains how a synthetic yeast genome could help modern wines compete with the best French vintages.

Thanks for reading.

Notable Papers

( * = open access, † = review article)

Recommended Reads

*Programming cell-free biosensors with DNA strand displacement circuits. Jung J.K. et al. Nature Chemical Biology.

Engineered Wnt ligands enable blood-brain barrier repair in neurological disorders. Martin M. et al. Science.

*evSeq: Cost-Effective Amplicon Sequencing of Every Variant in a Protein Library. Wittmann B.J. et al. ACS Synthetic Biology.

*†Visualising the next frontiers in wine yeast research. Pretorius I.S. FEMS Yeast Research.

Bonus: Gene Therapy / CAR-T Updates

Biologic and Clinical Efficacy of LentiGlobin for Sickle Cell Disease. Kanter J. et al. The New England Journal of Medicine.

Axicabtagene Ciloleucel as Second-Line Therapy for Large B-Cell Lymphoma. Locke F.L. et al. The New England Journal of Medicine.

Second-Line Tisagenlecleucel or Standard Care in Aggressive B-Cell Lymphoma. Bishop M.R. et al. The New England Journal of Medicine.

Basic Research

*Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica. Baisya D. et al. Nature Communications.

*Large-scale analysis of Drosophila core promoter function using synthetic promoters. Qi Z. et al. Molecular Systems Biology.

Experimental evolution of local adaptation under unidimensional and multidimensional selection. White N.J. et al. Current Biology.

*Key sequence features of CRISPR RNA for dual-guide CRISPR-Cas9 ribonucleoprotein complexes assembled with wild-type or HiFi Cas9. Okada K. et al. Nucleic Acids Research.

*Genome-wide RNAi screen identifies novel players in human 60S subunit biogenesis including key enzymes of polyamine metabolism. Dörner K. et al. Nucleic Acids Research.

*Systematic In Vivo Characterization of Fluorescent Protein Maturation in Budding Yeast. Guerra P. et al. ACS Synthetic Biology.

Circuits

*Restoring circadian gene profiles in clock networks using synthetic feedback control. Foo M. et al. npj Systems Biology and Applications.

Meeting Measurement Precision Requirements for Effective Engineering of Genetic Regulatory Networks. Beal J. et al. ACS Synthetic Biology.

*Synthetic robust perfect adaptation achieved by negative feedback coupling with linear weak positive feedback. Sun Z. et al. Nucleic Acids Research.

Computation

*Patient-specific Boolean models of signalling networks guide personalised treatments. Montagud A. et al. eLife.

*Clonally heritable gene expression imparts a layer of diversity within cell types. Mold J.E. et al. bioRxiv (preprint).

Genetic Engineering

*Flexible TALEs for an expanded use in gene activation, virulence and scaffold engineering. Becker S. et al. Nucleic Acids Research.

Medicine & Diagnostics

*Ingestible capsule for detecting labile inflammatory biomarkers in situ. Inda M.E. et al. bioRxiv (preprint).

*Type III CRISPR-based RNA editing for programmable control of SARS-CoV-2 and human coronaviruses. Lin P. et al. Nucleic Acids Research.

*Personalized chordoma organoids for drug discovery studies. Shihabi A.A. et al. Science Advances.

Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants. Sánchez-Rivera F.J. et al. Nature Biotechnology.

Metabolic Engineering

*CRISPR-assisted rational flux-tuning and arrayed CRISPRi screening of an L-proline exporter for L-proline hyperproduction. Liu J. et al. Nature Communications.

*Inducible directed evolution of complex phenotypes in bacteria. Al’Abri I.S. et al. Nucleic Acids Research.

Improving the Robustness of Engineered Bacteria to Nutrient Stress Using Programmed Proteolysis. Szydlo K. et al. ACS Synthetic Biology.

Synthetic metabolic pathways for conversion of CO2 into secreted short-to medium-chain hydrocarbons using cyanobacteria. Yunus I.S. et al. Metabolic Engineering.

Molecular Engineering

*Development and characterization of functional antibodies targeting NMDA receptors. Tajima N. et al. Nature Communications.

*†Engineering tissue morphogenesis: taking it up a Notch. Tiemeijer L.A. et al. Trends in Biotechnology.

A combined cell and gene therapy approach for homotopic reconstruction of midbrain dopamine pathways using human pluripotent stem cells. Moriarty N. et al. Cell Stem Cell.

Tools & Technology

*Protease-controlled secretion and display of intercellular signals. Vlahos A.E. et al. Nature Communications.

RoboMoClo: A Robotics-Assisted Modular Cloning Framework for Multiple Gene Assembly in Biofoundry. Kang D.H. et al. ACS Synthetic Biology.

Preparation and use of wireless reprogrammable multilateral optogenetic devices for behavioral neuroscience. Yang Y. et al. Nature Protocols.

*All-in-one: A Robust Fluorescent Fusion Protein Vector Toolbox for Protein Localization and BiFC Analyses in Plants. Han J. et al. Plant Biotechnology Journal.

Until next time,

— Niko

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