Cell Crunch Index (#60)
Lab-grown β cells for diabetes, new CasX proteins
Good morning. An inhibitor called I-BET151 helps pancreatic progenitor cells expand and switch into functional pancreatic β cells that, when transplanted into animals, ameliorate diabetes. The study marks “a substantial step toward unlimited supplies of functional β cells for biomedical research and regenerative medicine.” Elsewhere, two new CasX proteins (compact gene editors, with less than 1,000 amino acids) were developed.
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Notable Papers
( * = open access, † = review article)
Recommended Reads
*Human expandable pancreatic progenitor–derived β cells ameliorate diabetes. Ma X. et al. Science Advances.
Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity. Tsuchida C.A. et al. Molecular Cell.
*Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale. Liew F.E. et al. Nature Biotechnology.
Augmented lipid-nanoparticle-mediated in vivo genome editing in the lungs and spleen by disrupting Cas9 activity in the liver. Sago C.D. et al. Nature Biomedical Engineering. (Read more.)
*A cell-free self-replenishing CO2-fixing system. Luo S. et al. Nature Catalysis.
Genetic circuit design automation with Cello 2.0. Jones T.S. et al. Nature Protocols.
Basic Research
*Investigation of Cas9 antibodies in the human eye. Toral M.A. et al. Nature Communications.
*Discovery of potent and versatile CRISPR–Cas9 inhibitors engineered for chemically controllable genome editing. Song G. et al. Nucleic Acids Research.
*High-throughput metabolomics predicts drug–target relationships for eukaryotic proteins. Holbrook-Smith D. et al. Molecular Systems Biology.
Computation
Using deep learning to annotate the protein universe. Bileschi M.L. et al. Nature Biotechnology.
Genetic Engineering
*CRISPR-iPAS: a novel dCAS13-based method for alternative polyadenylation interference. Tian S. et al. Nucleic Acids Research.
*Ligation-assisted homologous recombination enables precise genome editing by deploying both MMEJ and HDR. Zhao Z. et al. Nucleic Acids Research.
Programmable Synthetic Upstream Activating Sequence Library for Fine-Tuning Gene Expression Levels in Saccharomyces cerevisiae. Li S. et al. ACS Synthetic Biology.
Medicine & Diagnostics
*Rapid manufacturing of non-activated potent CAR T cells. Ghassemi S. et al. Nature Biomedical Engineering.
*3D bioprinting of an implantable xeno-free vascularized human skin graft. Baltazar T. et al. bioRxiv (preprint).
*†Challenges to, and prospects for, reverse engineering the gastrointestinal tract using organoids. Kakni P. et al Trends in Biotechnology.
Metabolic Engineering
*Galaxy-SynBioCAD: Automated Pipeline for Synthetic Biology Design and Engineering. Hérisson J. et al. bioRxiv (preprint).
*†Biotechnological production of chiral acetoin. Meng W. et al. Trends in Biotechnology.
Molecular Engineering
In silico evolution of nucleic acid-binding proteins from a nonfunctional scaffold. Raven S.A. et al. Nature Chemical Biology.
*Switchable assembly and function of antibody complexes in vivo using a small molecule. Martinko A.J. et al. PNAS.
*Deubiquitinase-targeting chimeras for targeted protein stabilization. Henning N.J. et al. Nature Chemical Biology.
Versatile Design of Intracellular Protein-Responsive Translational Regulation System for Synthetic mRNA. Nakanishi H. et al. ACS Synthetic Biology.
Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells. Veling M.T. et al. ACS Synthetic Biology.
Plants
*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.
Tools & Technology
Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons. Wimmer F. et al. Molecular Cell.
*SYMBIOSIS: synthetic manipulable biobricks via orthogonal serine integrase systems. Ba F. et al. Nucleic Acids Research.
*Multichannel optogenetics combined with laminar recordings for ultra-controlled neuronal interrogation. Eriksson D. et al. Nature Communications.
Generation of CRISPR–Cas9-mediated genetic knockout human intestinal tissue–derived enteroid lines by lentivirus transduction and single-cell cloning. Lin S. et al. Nature Protocols.
A bacterial three-hybrid assay for forward and reverse genetic analysis of RNA–protein interactions. Stockert O.M. et al. Nature Protocols.
Combining CRISPRi and metabolomics for functional annotation of compound libraries. Anglada-Girotto M. et al. Nature Chemical Biology.
Miscellaneous
*Real-time tracking of bioluminescent influenza A virus infection in mice. Kim J.H. et al. Scientific Reports.
Until next time,