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Protein Barrels by Design & Prime Editing Made Easy

Cell Crunch (Issue 2021.02.22)

Credit: Doze Studios | Giphy
Credit: Hiroshi Nishimasu, F. Ann Ran, Patrick D. Hsu, Silvana Konermann, Soraya I. Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang, and Osamu Nureki | Wikimedia.

🧫 Other Studies Published This Week

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  • Oxygen-releasing biomaterials: Current challenges and future applications (Review). Trends in Biotechnology. Link


  • Advances in synthetic biology, biosafety governance and pandemic control strategies (Review). Frontiers in Bioengineering and Biotechnology. Link


  • Bioengineering of genetically encoded gene promoter repressed by flavonoids for constructing intracellular sensor for molecular events. bioRxiv (preprint). Link
  • A de novo strategy to develop NIR precipitating fluorochrome for long-term in situ cell membrane bioimaging. PNAS. Link

Fundamental Discoveries

  • Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science. Link
  • Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement. Science Advances. Open Access. Link
  • Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism. PNAS. Open Access. Link
  • Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies. Cell Systems. Link
  • Genome-wide CRISPR/Cas9-knockout in human induced Pluripotent Stem Cell (iPSC)-derived macrophages. Scientific Reports. Open Access. Link
  • Identification of efficient prokaryotic cell-penetrating peptides with applications in bacterial biotechnology. Communications Biology. Open Access. Link

Genetic Circuits

  • Model-guided design of mammalian genetic programs. Science Advances. Open Access. Link

Genetic Engineering & Control

  • Mitochondrial DNA editing in mice with DddA-TALE fusion deaminases. Nature Communications. Open Access. Link
  • Cas12a-assisted precise targeted cloning using in vivo Cre-lox recombination. Nature Communications. Open Access. Link
  • Cre-Controlled CRISPR mutagenesis provides fast and easy conditional gene inactivation in zebrafish. Nature Communications. Open Access. Link
  • Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights. bioRxiv (preprint). Link
  • Expanding the potential of mammalian genome engineering via targeted DNA integration (Review). ACS Synthetic Biology. Link
  • Rapid genome engineering of Pseudomonas assisted by fluorescent markers and tractable curing of plasmids. Bio-protocol. Open Access. Link
  • Automated rational strain construction based on high-throughput conjugation. ACS Synthetic Biology. Open Access. Link

Medicine and Diagnostics

  • Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody. Science. Open Access. Link
  • An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. Science Advances. Open Access. Link
  • Comparative analysis of assays to measure CAR T-cell-mediated cytotoxicity. Nature Protocols. Link

Metabolic Engineering

  • Re-routing of sugar catabolism provides a better insight into fungal flexibility in using plant biomass-derived monomers as substrates. Frontiers in Bioengineering and Biotechnology. Link
  • Yeast-based bioproduction of disulfide-rich peptides and their cyclization via asparaginyl endopeptidases. Nature Protocols. Link
  • Engineering Saccharomyces cerevisiae for isoprenol production. Metabolic Engineering. Link
  • Production of β‐carotene in Saccharomyces cerevisiae through altering yeast lipid metabolism. Biotechnology and Bioengineering. Link
  • Evolving a new efficient mode of fructose utilization for improved bioproduction in Corynebacterium glutamicum. bioRxiv (preprint). Link
  • Enzyme engineering and in vivo testing of a formate-reduction pathway. bioRxiv (preprint). Link
  • Recent advances in silent gene cluster activation in Streptomyces (Review). Frontiers in Bioengineering and Biotechnology. Link

New Technology

  • Simple and reliable detection of CRISPR-induced on-target effects by qgPCR and SNP genotyping. Nature Protocols. Link
  • SUGAR-seq enables simultaneous detection of glycans, epitopes, and the transcriptome in single cells. Science Advances. Open Access. Link
  • Inference and analysis of cell-cell communication using CellChat. Nature Communications. Open Access. Link
  • Microbial single-cell RNA sequencing by split-pool barcoding. Science. Link
  • Quantitative yeast–yeast two hybrid for the discovery and binding affinity estimation of protein–protein interactions. ACS Synthetic Biology. Link

Protein Engineering

  • Phage-assisted evolution of botulinum neurotoxin proteases with reprogrammed specificity. Science. Link
  • Absolute and arbitrary orientation of single-molecule shapes. Science. Link
  • Ribosome-mediated incorporation of fluorescent amino acids into peptides in vitro. Chemical Communications. Link
  • Self-sufficient class VII cytochromes P450: From full-length structure to synthetic biology applications (Review). Trends in Biotechnology. Link
  • De novo sequence redesign of a functional Ras binding domain globally inverted the surface charge distribution and led to extreme thermostability. Biotechnology and Bioengineering. Link
  • Engineering the immune adaptor protein STING as a biologic. bioRxiv (preprint). Link
  • Engineering nucleosomes for generating diverse chromatin assemblies. Nucleic Acids Research. Open Access. Link


  • A set of active promoters with different activity profiles for superexpressing Rhodococcus strain. ACS Synthetic Biology. Link
  • A programmable toolkit to dynamically signal cells using peptide strand displacement. bioRxiv (preprint). Link

Miscellaneous Topics

  • Million-year-old DNA sheds light on the genomic history of mammoths. Nature. Link
  • Optical control of fast and processive engineered myosins in vitro and in living cells. Nature Chemical Biology. Link



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