Biological techniques

  • Article |

    A combination of multiview imaging, structured illumination, reconstruction algorithms and deep-learning predictions realizes spatial- and temporal-resolution improvements in fluorescence microscopy to produce super-resolution images from diffraction-limited input images.

    • Yicong Wu
    • , Xiaofei Han
    •  & Hari Shroff
  • Article
    | Open Access

    Whole-genome sequencing of 3,171 cultivated and 195 wild chickpea accessions is used to construct a chickpea pan-genome, providing insight into chickpea evolution and enabling breeding strategies that could improve crop productivity.

    • Rajeev K. Varshney
    • , Manish Roorkiwal
    •  & Xin Liu
  • Article
    | Open Access

    Structure of human nuclear pore complex in its cellular environment reveals a substantially dilated central channel and shows that its nucleoplasmic and cytoplasmic rings restrict channel dimensions and create membrane asymmetry at the inner ring.

    • Anthony P. Schuller
    • , Matthias Wojtynek
    •  & Thomas U. Schwartz
  • Article
    | Open Access

    Cryo-electron microscopy structures of the voltage-gated potassium channel Kv4.2 alone and in complex with auxiliary subunits (DPP6S and/or KChIP1) reveal the distinct mechanisms of these two different subunits in modulating channel activity.

    • Yoshiaki Kise
    • , Go Kasuya
    •  & Osamu Nureki
  • Article
    | Open Access

    Observations of rapid repair of double-stranded DNA breaks in sister choromosomes in Escherichia coli are consistent with a reduced-dimensionality-search model of RecA-mediated repair.

    • Jakub Wiktor
    • , Arvid H. Gynnå
    •  & Johan Elf
  • Article
    | Open Access

    AlphaFold is used to predict the structures of almost all of the proteins in the human proteome—the availability of high-confidence predicted structures could enable new avenues of investigation from a structural perspective.

    • Kathryn Tunyasuvunakool
    • , Jonas Adler
    •  & Demis Hassabis
  • Article |

    Single-nucleus transcriptomes of frontal cortex and choroid plexus samples from patients with COVID-19 reveal pathological cell states that are similar to those associated with human neurodegenerative diseases and chronic brain disorders.

    • Andrew C. Yang
    • , Fabian Kern
    •  & Tony Wyss-Coray
  • Article |

    A localization algorithm is applied to datasets obtained with conventional and high-speed atomic force microscopy to increase image resolution beyond the limits set by the radius of the tip used.

    • George R. Heath
    • , Ekaterina Kots
    •  & Simon Scheuring
  • Article |

    A custom adenine base editor can edit the variant of the β-globin gene that causes sickle cell disease into a non-pathogenic variant in human and mouse cells, and transplantation of the edited cells rescues sickle cell disease in mice.

    • Gregory A. Newby
    • , Jonathan S. Yen
    •  & David R. Liu
  • Article |

    In a cynomolgus macaque model, CRISPR base editors delivered in lipid nanoparticles are shown to efficiently and stably knock down PCSK9 in the liver to reduce levels of PCSK9 and low-density lipoprotein cholesterol in the blood.

    • Kiran Musunuru
    • , Alexandra C. Chadwick
    •  & Sekar Kathiresan
  • Article
    | Open Access

    A genetically encoded sensor for the quantitative visualization of auxin distribution in plants enables real-time monitoring of its uptake and clearance by individual cells and within cellular compartments.

    • Ole Herud-Sikimić
    • , Andre C. Stiel
    •  & Gerd Jürgens
  • Article |

    HLA peptidomic analysis identifies recurrent intracellular bacteria-derived peptides presented on HLA-I and HLA-II molecules in melanoma tumours, revealing how bacteria can modulate immune functions and responses to cancer therapies.

    • Shelly Kalaora
    • , Adi Nagler
    •  & Yardena Samuels
  • Article |

    Time-resolved RNA–protein cross-linking with a pulsed femtosecond ultraviolet laser, followed by immunoprecipitation and high-throughput sequencing, enables the determination of binding and dissociation kinetics of the RNA-binding protein DAZL within cells.

    • Deepak Sharma
    • , Leah L. Zagore
    •  & Eckhard Jankowsky
  • Article |

    The net PKA activities in each class of spiny projection neuron in the nucleus accumbens of the mouse are dichotomously modulated by asynchronous positive and negative dopamine signals during different phases of learning.

    • Suk Joon Lee
    • , Bart Lodder
    •  & Bernardo L. Sabatini
  • Article |

    High-phylogenetic-resolution microbiome mapping by fluorescence in situ hybridization (HiPR-FISH) enables the spatial mapping of hundreds of species of microorganisms and shows how microbial networks in the mouse gut are affected by antibiotic treatment.

    • Hao Shi
    • , Qiaojuan Shi
    •  & Iwijn De Vlaminck
  • Article |

    Inhibition of YBX1, a downstream target of the Janus kinase JAK2, sensitizes myeloproliferative neoplasm cells to JAK and could provide a means to eradicate such cells in human haematopoietic cancers.

    • Ashok Kumar Jayavelu
    • , Tina M. Schnöder
    •  & Florian H. Heidel
  • Article |

    The neuronal diversity of the Drosophila optic lobe is described throughout pupal development by single-cell sequencing, leading to the discovery of transient extrinsic neurons and a dorsoventral asymmetry of the visual circuits.

    • Mehmet Neset Özel
    • , Félix Simon
    •  & Claude Desplan
  • Article |

    A genome-wide association study shows that myocardial trabeculae are an important determinant of cardiac performance in the adult heart, identifies conserved pathways that regulate structural complexity and reveals the influence of trabeculae on the susceptibility to cardiovascular disease.

    • Hannah V. Meyer
    • , Timothy J. W. Dawes
    •  & Declan P. O’Regan
  • Article |

    Structural studies of the dimerization quality control E3 ubiquitin ligase SCF–FBXL17 indicate that its selectivity for aberrant complex formation is based on recognizing both shape and complementarity of interacting domains.

    • Elijah L. Mena
    • , Predrag Jevtić
    •  & Michael Rape
  • Article
    | Open Access

    A map of cohesin-mediated chromatin loops in 24 types of human cells identifies loops that show cell-type-specific variation, indicating that chromatin loops may help to specify cell-specific gene expression programs and functions.

    • Fabian Grubert
    • , Rohith Srivas
    •  & Michael Snyder
  • Article |

    Bulk RNA sequencing of organs and plasma proteomics at different ages across the mouse lifespan is integrated with data from the Tabula Muris Senis, a transcriptomic atlas of ageing mouse tissues, to describe organ-specific changes in gene expression during ageing.

    • Nicholas Schaum
    • , Benoit Lehallier
    •  & Tony Wyss-Coray
  • Article |

    A method termed ac4C-seq is introduced for the transcriptome-wide mapping of the RNA modification N4-acetylcytidine, revealing widespread temperature-dependent acetylation that facilitates thermoadaptation in hyperthermophilic archaea.

    • Aldema Sas-Chen
    • , Justin M. Thomas
    •  & Schraga Schwartz
  • Article |

    Neurons in the canary premotor cortex homologue encode past song phrases and transitions, carrying information relevant to future choice of phrases as ‘hidden states’ during song.

    • Yarden Cohen
    • , Jun Shen
    •  & Timothy J. Gardner
  • Article |

    An advanced proteomics workflow is used to identify 340,000 proteins from 100 taxonomically diverse species, providing a comparative view of proteomes across the evolutionary range.

    • Johannes B. Müller
    • , Philipp E. Geyer
    •  & Matthias Mann