Biological techniques articles within Nature Communications

Featured

  • Article
    | Open Access

    Chlamydomonas reinhardtii produces a glycoprotein-rich cell wall. Using nuclear magnetic resonance and mass spectrometry approaches, this study reveals unprecedented details on its protein and carbohydrate content, and provide an atomic-level architecture model.

    • Alexandre Poulhazan
    • , Alexandre A. Arnold
    •  & Isabelle Marcotte

  • Article
    | Open Access

    In this study, the authors evaluated the protective capacity of a mucosal, live-attenuated SARS-CoV-2 vaccine and show that it induces systemic and mucosal humoral immunity, protects from clinical disease symptoms, and prevents virus transmission in hamsters more efficiently than an intramuscular mRNA vaccine.

    • Julia M. Adler
    • , Ricardo Martin Vidal
    •  & Jakob Trimpert

  • Article
    | Open Access

    Conventional CRISPR-based approaches to monitor genomic loci can be hampered by high background and nonspecific nucleolar signal. Here, the authors propose a fluorogenic CRISPR (fCRISPR) tool that allows for high-contrast and sensitive imaging of genomic DNA.

    • Zhongxuan Zhang
    • , Xiaoxiao Rong
    •  & Xing Li

  • Article
    | Open Access

    High-throughput electron microscopy demands minimal human intervention and high image quality. Here, authors introduce DeepFocus, a data-driven method for aberration correction in electron microscopy, robust for low SNR images, fast and easily adaptable to microscopes and samples. Peer Review Information: Nature Communications thanks Yang Zhang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available.

    • P. J. Schubert
    • , R. Saxena
    •  & J. Kornfeld

  • Article
    | Open Access

    RNA base-editors are often used in methods for RNA binding protein (RBP) target discovery. Here the authors present a new RBP target discovery method, PRINTER, and suggest optimal RNA base-editors for dual-RBP studies, emphasizing the importance of matching rBEs’ editing biases with RBPs’ binding preferences.

    • Hugo C. Medina-Munoz
    • , Eric Kofman
    •  & Gene W. Yeo

  • Article
    | Open Access

    Cyclic AMP modulation of HCN channels underlies beta adrenergic stimulation of heart rate. Here, authors describe an intramolecular mechanism that controls cAMP affinity of the cyclic nucleotide binding domain of these channels.

    • Alessandro Porro
    • , Andrea Saponaro
    •  & Anna Moroni

  • Article
    | Open Access

    Prime editing in bacteria is currently inefficient. Here the authors report BacPE, a versatile prime editing platform in Escherichia coli that works by inhibiting 3′→5′ DNA exonucleases, highlighting the intrinsic genetic factors that are adverse to efficient prime editing.

    • Hongyuan Zhang
    • , Jiacheng Ma
    •  & Quanjiang Ji

  • Article
    | Open Access

    Longitudinal monitoring of liver function in vivo is hindered by the lack of high-resolution non-invasive imaging techniques. Here, the authors show a crucial and unique tool for longitudinal in vivo imaging of liver spheroids at cellular resolution to study liver physiology and disease.

    • Francesca Lazzeri-Barcelo
    • , Nuria Oliva-Vilarnau
    •  & Per-Olof Berggren

  • Article
    | Open Access

    Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements. Here the authors present an engineered yeast strain with 83 sparsely distributed loxPsym sites across the genome can genrerate large-scale genomic rearrangements, which benefits cell fitness under stress and boosts the SCRaMbLE system when combined with synthetic chromosomes.

    • Li Cheng
    • , Shijun Zhao
    •  & Junbiao Dai

  • Article
    | Open Access

    The origin of SARS-CoV-2 cross-reactive T cells in unexposed humans is unclear. Here, the authors use HLA transgenic mouse models of sequential infections with human coronavirus OC43 and SARSCoV-2 and show that OC43 elicits cross-protective immunity against SARS-CoV-2, which partially depends on CD4 + T cells.

    • Rúbens Prince dos Santos Alves
    • , Julia Timis
    •  & Sujan Shresta

  • Article
    | Open Access

    Varroa and Tropilaelaps mites threaten honeybee health. This study finds that mites alter feeding habits depends on their own, and hosts’, life history stage. Mites feed on the host hemolymph when parasitizing pupae during their reproductive stage but consume fat body during their dispersal stage.

    • Bin Han
    • , Jiangli Wu
    •  & Shufa Xu

  • Article
    | Open Access

    The rapid identification of drug-resistant bacteria is vital for effective treatment and to avoid antibiotic misuse. Here authors report a paper-based sensor which utilises chromogenic carbapenem and cephalosporin substrates for the identification and discrimination of β-lactamase subtypes.

    • Wenshuai Li
    • , Jingqi Li
    •  & Dingbin Liu

  • Article
    | Open Access

    Toxic amyloid-beta plaque and harmful inflammation are two leading hallmarks of Alzheimer’s disease (AD), and precise AD therapy is elusive due to the lack of dual-targeting therapy function, limited blood-brain barrier penetration, and low imaging sensitivity. Here, the authors address these issues by designing a near-infrared-II aggregation-induced emission nanotheranostic for precise AD therapy.

    • Jiefei Wang
    • , Ping Shangguan
    •  & Ben Zhong Tang

  • Article
    | Open Access

    Here, using single molecule FRET, the unfolding and folding of a discontinuous two-domain protein was studied. The authors find that a dynamic, intermediate population entropically limits the rate of folding while the order of domain folding is kept in a slow-folding mutant.

    • Ganesh Agam
    • , Anders Barth
    •  & Don C. Lamb

  • Article
    | Open Access

    Cas13 systems suffer from a lack of spatiotemporal control. Here the authors report paCas13, a light-inducible Cas13 system created by fusing Magnet with fragment pairs; they also report padCas13, a light-inducible base-editing system by fusing ADAR2 to catalytically inactive paCas13 fragments.

    • Jeonghye Yu
    • , Jongpil Shin
    •  & Won Do Heo

  • Article
    | Open Access

    Here the authors screen different lipid nanoparticle (LNP) formulations for intramuscular delivery of plasmid DNA and uptake by antigen-presenting cells. The lead LNP exhibits immunogenicity and protection in small animal models that is comparable to approved SARS-CoV-2 mRNA vaccine formulations.

    • Lays Cordeiro Guimaraes
    • , Pedro Augusto Carvalho Costa
    •  & Pedro Pires Goulart Guimaraes

  • Article
    | Open Access

    The recent emergence of monoclonal antibodies able to neutralize snake toxins have revolutionized the approach of developing novel therapies to treat snakebite envenoming, at least in animal models. Here, the authors show antibody-dependent enhancement of toxicity (ADET) for a toxin derived from snake venom and highlight the importance of this phenomenon when testing therapeutic antibodies against snake venoms in animal models.

    • Christoffer V. Sørensen
    • , Julián Fernández
    •  & Andreas H. Laustsen

  • Article
    | Open Access

    Topologically associating domains (TADs) are critical structural units in 3D genome organization, and their reorganization between health and disease states is associated with essential genome functions. However, computational methods for identifying reorganized TADs are still in the early stages of development. Here, the authors present an algorithm leveraging random matrix theory to identify reorganized TADs.

    • Dunming Hua
    • , Ming Gu
    •  & Dechao Tian

  • Article
    | Open Access

    Systematic understanding of CRISPR enzyme RNA binding specificity and cleavage is lacking. Here the authors report RNA chip-hybridised association-mapping platform (RNA-CHAMP), a workflow that repurposes next generation DNA sequencing chips to measure the binding affinity for RNA targets.

    • Hung-Che Kuo
    • , Joshua Prupes
    •  & Ilya J. Finkelstein

  • Article
    | Open Access

    Magnetic resonance imaging is a useful clinical tool, but its widespread use is constrained by size, cost, and time. Here, the authors report the development of a magnetic resonance sensor for the clinical detection of muscle tissue, allowing for new point-of-care quantitative diagnostic measurements

    • Sydney E. Sherman
    • , Alexa S. Zammit
    •  & Michael J. Cima

  • Article
    | Open Access

    Nanoscale optoelectrodes hold the potential to optically stimulate individual neuron. Here, the authors form nanoscale capacitive optoelectrodes by incorporating zinc porphyrin into nanorods, coated by TiO2, a design that allows for far-field optical modulation of neurons with efficiency and negligible side effects.

    • Jian Chen
    • , Yanyan Liu
    •  & Wenbo Bu

  • Article
    | Open Access

    DNA sequencing methods for characterizing microbial communities are well developed for bacteria, archaea and fungi, but less so for eukaryotic parasites and commensals. Here, the authors present an optimized and validated metabarcoding protocol for host-associated eukaryotic communities.

    • Leah A. Owens
    • , Sagan Friant
    •  & Tony L. Goldberg

  • Editorial
    | Open Access

    Orphan crops hold the potential to diversify our food systems. Considering their unique characteristics, our deep understanding of major crops, and the availability of modern genomic tools, taking a different research path from what major crops have gone through could accelerate the genetic improvement of orphan crops.

  • Article
    | Open Access

    Tripartite ATP-independent periplasmic (TRAP) transporters use an extra substrate binding protein to transport a variety of substrates in bacteria and archaea. Here the authors use a disulfide engineering approach to lock the TRAP transporter HiSiaPQM from H. influenzae in different conformational states for characterisation.

    • Martin F. Peter
    • , Jan A. Ruland
    •  & Gregor Hagelueken

  • Article
    | Open Access

    Homing-based gene drives are novel interventions promising the area-wide, species-specific genetic control of harmful insect populations. Here the authors demonstrate the feasibility of a gene drive approach for the genetic control of the agricultural pest, the medfly, based on complete female-to-male sex conversion.

    • Angela Meccariello
    • , Shibo Hou
    •  & Nikolai Windbichler

  • Article
    | Open Access

    In this longitudinal, case-controlled, cohort design study, authors show that post-exertional malaise is associated with severe exercise-induced myopathy, local and systemic metabolic disturbances and infiltration of amyloid-containing deposits in skeletal muscles of patients with long COVID.

    • Brent Appelman
    • , Braeden T. Charlton
    •  & Rob C. I. Wüst

  • Article
    | Open Access

    While activins are critical regulators of early development, their role in maintaining adult tissue homeostasis remains obscure. Here the authors explore the role of activins in promoting intestinal regeneration and nutrient-dependent gut resizing in Drosophila.

    • Christian F. Christensen
    • , Quentin Laurichesse
    •  & Ditte S. Andersen

  • Article
    | Open Access

    The functional heterogeneity of autophagy in endothelial cells during angiogenesis remains incompletely understood. Here, the authors apply a 3D angiogenesis-on-a-chip coupled with single-cell RNA sequencing to find distinct autophagy functions in two different endothelial cell populations during angiogenic sprouting.

    • Somin Lee
    • , Hyunkyung Kim
    •  & Noo Li Jeon

  • Comment
    | Open Access

    Wearable devices can provide personalised medicine at the point of need, potentially increasing access to health services and therefore improving health equity. Here the authors discuss their experiences developing wearable devices for vulnerable patient populations, including neonates and pregnant individuals.

    • Jessica R. Walter
    • , Shuai Xu
    •  & John A. Rogers

  • Article
    | Open Access

    Copy number variants (CNV) are shown to contribute to the etiology of various genetic disorders. Here, authors present ECOLE, a deep learning-based somatic and germline CNV caller for WES data. Utilising a variant of the transformer architecture, the model is trained to call CNVs per exon.

    • Berk Mandiracioglu
    • , Furkan Ozden
    •  & A. Ercument Cicek

  • Article
    | Open Access

    Newly synthesized tail-anchored membrane proteins (TAs) are relayed in a chaperone triad, Hsp70, Sgt2, and Get3, for delivery to the endoplasmic reticulum. Here, the authors show how the conformational dynamics of the cochaperone Sgt2 generates a decision point to enable efficient and selective TA targeting.

    • Hyunju Cho
    • , Yumeng Liu
    •  & Shu-ou Shan

  • Article
    | Open Access

    Rhodopsins are ubiquitous light-driven membrane proteins that have diverse functions in nature, and value as optogenetics tools. Here the authors characterise type 1 viral channelrhodopsins, showing that they regulate intracellular calcium and can be used for the photocontrol of muscle contraction in vivo.

    • Ana-Sofia Eria-Oliveira
    • , Mathilde Folacci
    •  & Michel Vivaudou

  • Article
    | Open Access

    The cereal endosperm constitutes most of the grain by volume. Here the authors use single-cell analysis of maize developing endosperm to decode gene regulatory networks that likely control endosperm growth and offer a framework for crop improvement.

    • Yue Yuan
    • , Qiang Huo
    •  & Zeyang Ma

  • Article
    | Open Access

    Microbial communities are the siege of complex metabolic interactions including cooperation and competition. Here, the authors report the utilization of optogenetics and spatial light-patterning to activate the expression of the invertase SUC2 at selected locations and selectively switch cooperation and competition roles of the yeast cells.

    • Matthias Le Bec
    • , Sylvain Pouzet
    •  & Pascal Hersen

Browse broader subjects

Browse narrower subjects

Browse Biological techniques across other nature.com journals