Synthetic biology articles within Nature

Featured

  • News & Views |

    In experiments dubbed the Random Genome Project, researchers have integrated DNA strands with random sequences into yeast and mouse cells to find the default transcriptional state of their genomes.

    • Sean R. Eddy

  • Article
    | Open Access

    Introduction of a long synthetic DNA into yeast genomic loci results in high default transcriptional activity in yeast but low activity in mouse, suggesting distinct default levels of genomic activity in these organisms.

    • Brendan R. Camellato
    • , Ran Brosh
    •  & Jef D. Boeke

  • Article
    | Open Access

    tRNA display enables the direct selection of orthogonal aminoacyl-tRNA synthetases that acylate orthogonal tRNAs with non-canonical monomers, enabling in vivo synthesis of proteins that include these monomers and expanding the repertoire of the genetic code.

    • Daniel L. Dunkelmann
    • , Carlos Piedrafita
    •  & Jason W. Chin

  • Article
    | Open Access

    Deep learning models were used to design synthetic cell-type-specific enhancers that work in fruit fly brains and human cell lines, an approach that also provides insights into these gene regulatory elements.

    • Ibrahim I. Taskiran
    • , Katina I. Spanier
    •  & Stein Aerts

  • Article
    | Open Access

    This study describes a method to insert large stretches of exogenous DNA into mammalian genomes, which is used to insert human ACE2 loci into mouse to produce a model of human SARS-CoV-2 infection.

    • Weimin Zhang
    • , Ilona Golynker
    •  & Jef D. Boeke

  • Article |

    A biosensor comprising bacteria engineered to respond to transient inflammatory signals has been packaged with electronic readout and transmission circuits in a small device that could be swallowed to monitor gastrointestinal health.

    • M. E. Inda-Webb
    • , M. Jimenez
    •  & T. K. Lu

  • Research Briefing |

    A deep-learning model called Geneformer has been developed and pretrained using about 30 million single-cell gene-expression profiles to enable it to make predictions about gene-network biology in instances in which gene-expression data are limited. Geneformer can be tuned for many downstream applications to accelerate discovery of key gene-network regulators and candidate therapeutic targets.

  • Research Briefing |

    Creating protein interactions through computational design is a key challenge in the fields of both basic and translational biology. An approach that uses the machine-learned fingerprints of protein-surface features was used to produce synthetic proteins that engage immunotherapeutic or viral targets with binding affinities comparable to those of naturally occurring proteins.

  • Article |

    A high throughput recruitment assay testing the transcriptional activity of more than 100,000 protein fragments tiling across most human chromatin regulators and transcription factors maps the locations and strengths of activation, repression and bifunctional domains, and identifies the sequences necessary for these functions.

    • Nicole DelRosso
    • , Josh Tycko
    •  & Lacramioara Bintu

  • Nature Podcast |

    A streamlined genome makes bacteria immune to viral infection, and designing mini-MRI scanners for low- and middle-income countries.

    • Shamini Bundell
    •  & Nick Petrić Howe

  • Article |

    A study details the creation of an Escherichia coli genetically recoded organism that is resistant to viral infection, and describes a further modification that keeps the organism and its genetic information biocontained.

    • Akos Nyerges
    • , Svenja Vinke
    •  & George M. Church

  • Article |

    Logic gating is used to develop a CAR T cell platform that is highly specific and allows the activity of T cells to be restricted to the encounter of two antigens, thus reducing on-target, off-tumour toxicity.

    • Aidan M. Tousley
    • , Maria Caterina Rotiroti
    •  & Robbie G. Majzner

  • Article
    | Open Access

    Synthetic cell adhesion molecules yield customized cell–cell interactions with adhesion properties that are similar to native interactions, and offer abilities for cell and tissue engineering and for systematically studying multicellular organization.

    • Adam J. Stevens
    • , Andrew R. Harris
    •  & Wendell A. Lim

  • Article |

    The combination of synthetic biology and materials engineering enabled the development of biosensors that produce electrical readouts and real-time detection capabilities.

    • Joshua T. Atkinson
    • , Lin Su
    •  & Caroline M. Ajo-Franklin

  • News & Views |

    Can artificial cells be built from basic components? Systems that have complex architectures and functions evocative of natural cells have been prepared by recycling the contents of bacterial cells in synthetic droplets.

    • N. Amy Yewdall

  • Article |

    A bacteriogenic strategy for constructing membrane-bounded, molecularly crowded, and compositionally, structurally and morphologically complex synthetic cells provides opportunities for the fabrication of new synthetic cell modules and augmented living/synthetic cell constructs.

    • Can Xu
    • , Nicolas Martin
    •  & Stephen Mann

  • News & Views |

    The engineering of cells to express synthetic adhesion molecules creates a simple logic for patterning cell populations with visible boundaries. The approach paves the way for smart living materials and programmable biosensors.

    • Luis Ángel Fernández

  • Article
    | Open Access

    A synthetic cell-cell adhesion logic using swarming E. coli with 4 bits of information is introduced, enabling the programming of interfaces that combine to form universal tessellation patterns over a large scale.

    • Honesty Kim
    • , Dominic J. Skinner
    •  & Ingmar H. Riedel-Kruse

  • Article
    | Open Access

    Synthetic chimeric orthogonal IL-2 receptors that incorporate the intracellular domain of receptors for other γ-chain cytokines such as IL-9 can reroute orthogonal signalling and alter the phenotype of T cells to improve anti-tumour responses.

    • Anusha Kalbasi
    • , Mikko Siurala
    •  & K. Christopher Garcia

  • News & Views |

    Synthetic receptor proteins can enable customized and flexible control of immune cells called T lymphocytes. A defined framework for the proteins’ design now improves their potential for use in cancer immunotherapy.

    • Mohamad Hamieh
    •  & Maria Themeli

  • Article |

    A framework for studying and engineering gene regulatory DNA sequences, based on deep neural sequence-to-expression models trained on large-scale libraries of random DNA, provides insight into the evolution, evolvability and fitness landscapes of regulatory DNA.

    • Eeshit Dhaval Vaishnav
    • , Carl G. de Boer
    •  & Aviv Regev

  • News & Views |

    A sophisticated theory for learning motor skills places emphasis on the need for inferring context — drawing conclusions about the structure of the environment — for efficiently storing and expressing motor memories.

    • Anne G. E. Collins
    •  & Samuel D. McDougle

  • Article |

    A modular de novo designed biosensor platform consisting of a cage and key molecule is developed, and used to create sensors for seven distinct proteins including the spike protein from SARS-CoV-2 and anti-SARS antibodies.

    • Alfredo Quijano-Rubio
    • , Hsien-Wei Yeh
    •  & David Baker

  • News & Views |

    Yeast has been engineered to convert simple sugars and amino acids into drugs that inhibit a neurotransmitter molecule. The work marks a step towards making the production of these drugs more reliable and sustainable.

    • José Montaño López
    •  & José L. Avalos

  • Technology Feature |

    A powerful set of molecular tools helps synthetic biologists to assemble DNA of different sizes, from the gene to the chromosome scale.

    • Michael Eisenstein

  • Obituary |

    Organic chemist whose rules aided the synthesis of natural products.

    • Georgina Ferry

  • Outlook |

    Modified bacteria and carefully formulated microbial communities could form the basis of new living treatments.

    • Claire Ainsworth

  • Article |

    A technique for the de novo design of switchable protein systems controlled by induced conformational change is demonstrated for three functional motifs, in vitro and in yeast and mammalian cells.

    • Robert A. Langan
    • , Scott E. Boyken
    •  & David Baker

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