Biophysical methods articles within Nature Communications

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  • Article
    | Open Access

    Here Arndt et al. establish rotating-crystal magneto-optical detection (RMOD) as a near-point-of-care diagnostic tool for malaria detection and report a sensitivity and specificity of 82% and 84%, respectively, as validated by analyzing a clinical population in a high transmission setting in Papua New Guinea.

    • L. Arndt
    • , T. Koleala
    •  & S. Karl

  • Article
    | Open Access

    Patch clamp recording of neurons is slow and labor-intensive. Here the authors present a method for automated deep learning driven label-free image guided patch clamp physiology to perform measurements on hundreds of human and rodent neurons.

    • Krisztian Koos
    • , Gáspár Oláh
    •  & Peter Horvath

  • Article
    | Open Access

    Mechanical strength of in situ assembled nuclear lamin filaments arranged in a 3D meshwork is unclear. Here, using mechanical, structural and simulation tools, the authors report the hierarchical organization of the lamin meshwork that imparts strength and toughness to lamin filaments at par with silk and Kevlar®

    • K. Tanuj Sapra
    • , Zhao Qin
    •  & Ohad Medalia

  • Article
    | Open Access

    Existing tools to study hearing are limited. Here the authors report Bio-OptoAcoustic (BOA) stimulation wherein they use optical forces to generate localised sound and activate the auditory system of zebrafish larvae.

    • Itia A. Favre-Bulle
    • , Michael A. Taylor
    •  & Ethan K. Scott

  • Article
    | Open Access

    Septins are GTP-binding proteins involved in diverse cellular processes including division, polarity maintenance and membrane remodeling. Here authors use high-speed atomic force microscopy to show that assembly of septin filaments is a diffusion-driven process, while septin assembly into higher-order involves septin self-templating

    • Fang Jiao
    • , Kevin S. Cannon
    •  & Simon Scheuring

  • Article
    | Open Access

    Excitatory amino acid transporters (EAATs) are crucial for the removal of excitatory amino acids from the synaptic cleft. Here authors combined high-speed atomic force microscopy line-scanning with automated state assignment for the determination of transport dynamics of GltPh, a prokaryotic EAAT homologue, with millisecond temporal resolution.

    • Tina R. Matin
    • , George R. Heath
    •  & Simon Scheuring

  • Article
    | Open Access

    Single molecule force measurements have shed light on dynamic biological events, but rare events escape notice owing to low throughput of the methods. Here, the authors combine an array of magnetic tweezers with lateral flow to increase throughput 100-fold, and detect rare DNA breaks induced by gyrase.

    • Rohit Agarwal
    •  & Karl E. Duderstadt

  • Article
    | Open Access

    Reported wearable dry electrodes have limited long-term use due to their imperfect skin compliance and high motion artifacts. Here, the authors report an intrinsically conductive, stretchable polymer dry electrode with excellent self-adhesiveness for long-term high-quality biopotential detection.

    • Lei Zhang
    • , Kirthika Senthil Kumar
    •  & Jianyong Ouyang

  • Article
    | Open Access

    Mechanically stable specific heterodimerization formed with reversible bonds are used as a molecular anchorage in single-molecule force spectroscopy studies with unique mechanical properties. Here authors develop a variety of heterodimerization molecular systems with a range of mechanical stability from a set of recently engineered helix-heterotetramers.

    • Miao Yu
    • , Zhihai Zhao
    •  & Jie Yan

  • Article
    | Open Access

    Cystic fibrosis (CF) is a lethal genetic disease that is primarily caused by misfolding of the cystic fibrosis transmembrane conductance regulator (CFTR). Here authors show that disease-causing mutations located within the first nucleotide binding domain of CFTR have distinct effects on nascent polypeptides.

    • Hideki Shishido
    • , Jae Seok Yoon
    •  & William R. Skach

  • Article
    | Open Access

    Membrane proteins are embedded in the lipid bilayer of the plasma membrane and their function in this context is often linked to their specific location and dynamics within the membrane. Here authors report the use of fluorescent magnetic nanoparticles to track membrane molecules and to manipulate their movement and pull membrane components laterally through the membrane with femtonewton-range forces.

    • Jia Hui Li
    • , Paula Santos-Otte
    •  & Helge Ewers

  • Article
    | Open Access

    Label-free trapping of nanoparticles via dielectophoretic forces is traditionally done with electrodes in a horizontal gap layout. Here, the authors present a vertical nanogap architecture, which allows for precise capture and spatiotemporal manipulation of nanoparticles and molecular assemblies.

    • Eui-Sang Yu
    • , Hyojin Lee
    •  & Yong-Sang Ryu

  • Article
    | Open Access

    High-throughput rheological measurements of cells and cell clusters by microfluidics is limited by fixed channel dimensions. Here the authors create virtual fluidic channels inside the cuvette of commercial flow cytometers to dynamically tune channel cross section to enable rheological measurements from cells and cell clusters.

    • Muzaffar H. Panhwar
    • , Fabian Czerwinski
    •  & Oliver Otto

  • Article
    | Open Access

    Annexins are cytoplasmic proteins, which bind to membranes exposing negatively charged phospholipids in a Ca2+-dependent manner. Here the authors use high-speed atomic force microscopy and other techniques to show that annexin-V self-assembles into highly structured lattices that lead to a membrane phase transition on PS-rich membranes.

    • Yi-Chih Lin
    • , Christophe Chipot
    •  & Simon Scheuring

  • Article
    | Open Access

    Many intracellular pathogens mimic extracellular matrix motifs to specifically interact with the host membrane which may influences virus particle uptake. Here authors use single molecule tension sensors to reveal the minimal forces exerted on single virus particles and demonstrate that the uptake forces scale with the adhesion energy.

    • Tina Wiegand
    • , Marta Fratini
    •  & Joachim P. Spatz

  • Article
    | Open Access

    Electrical stimulation of the brain can have variable effects, perhaps because of individual differences in brain structure which produce differences in the electric fields. Here, the authors show that using functional and structural brain imaging along with electric field modeling can predict the effectiveness of stimulation.

    • Florian H. Kasten
    • , Katharina Duecker
    •  & Christoph S. Herrmann

  • Article
    | Open Access

    The endoplasmic reticulum (ER) is an intracellular network characterized by highly dynamic behavior whose control mechanisms are unclear. Here, the authors show that the ER-membrane protein Reticulon (Rtnl1) can constrict ER bilayers and lead to ER fission.

    • Javier Espadas
    • , Diana Pendin
    •  & Andrea Daga

  • Article
    | Open Access

    Fluorescence correlation spectroscopy is widely used for in vivo and in vitro applications, yet extracting information from experiments still requires long acquisition times. Here, the authors exploit Bayesian non-parametrics to directly analyze the output of confocal fluorescence experiments thereby probing physical processes on much faster timescales.

    • Sina Jazani
    • , Ioannis Sgouralis
    •  & Steve Pressé

  • Article
    | Open Access

    The ability to encapsulate living cells could lead to many applications. Here, the authors present a flexible method to graft DNA polymers onto bacteria, yeast and mammalian cells, polymerize them into DNA cocoons and use these to manipulate and select cells based on the encoded polymer sequences on DNA cocoons.

    • Tao Gao
    • , Tianshu Chen
    •  & Genxi Li

  • Article
    | Open Access

    The bacterial protein Cnu together with the transcription repressor H-NS regulate expression of virulence factors in an osmo-sensitive manner. Here authors show that the structure of Cnu swells with decreasing ionic strength driving the oligomerization of H-NS and regulating osmo-sensory response.

    • Abhishek Narayan
    • , Soundhararajan Gopi
    •  & Athi N. Naganathan

  • Article
    | Open Access

    Understanding how forces orchestrate tissue formation requires technologies to map internal tissue stress at cellular length scales. Here, authors develop ultrasoft sensors that visibly deform under cell-generated stress to capture patterns of internal stress development during multicellular spheroid formation.

    • Wontae Lee
    • , Nikita Kalashnikov
    •  & Christopher Moraes

  • Article
    | Open Access

    Myocardial tissue undergoes steady functional decline when cultured in vitro. Here, the authors report a protocol for culture of human cardiac slices that allows maintenance of contractility for up to four months, and show that the model is suitable for evaluation of drug safety, as exemplified for drugs interfering with cardiomyocyte repolarization.

    • Carola Fischer
    • , Hendrik Milting
    •  & Andreas Dendorfer

  • Article
    | Open Access

    Desmosomes are intercellular adhesion complexes that connect the intermediate filament cytoskeletons of neighboring cells but direct evidence for their load-bearing nature is lacking. Here the authors develop FRET-based tension sensors to measure the forces experienced by desmoplakin and infer that desmosomes become mechanically loaded when cells are exposed to external mechanical stresses.

    • Andrew J. Price
    • , Anna-Lena Cost
    •  & Carsten Grashoff

  • Article
    | Open Access

    Sample orientation is crucial to ensure optimal image quality in light microscopy. Here the authors enable multi-axis orientation of fixed mouse embryos and shrimp, and live zebrafish embryos and larvae by introducing magnetic beads and rotating the sample with a magnetic field in a microscope.

    • Frederic Berndt
    • , Gopi Shah
    •  & Jan Huisken

  • Article
    | Open Access

    The dynamics of biomolecules can occur over a wide range of time and length scales. Here the authors develop a high-speed AFM height spectroscopy method to directly detect the motion of unlabeled molecules at Angstrom spatial and microsecond temporal resolution.

    • George R. Heath
    •  & Simon Scheuring

  • Article
    | Open Access

    Red blood cell disorders are often accompanied by increased release of extracellular vesicles (EVs), but their structural and mechanical properties are not fully understood. Here, the authors show that red blood cell EVs show liposome-like mechanical features and are softened in blood disorder patients.

    • Daan Vorselen
    • , Susan M. van Dommelen
    •  & Wouter H. Roos

  • Article
    | Open Access

    The SNARE complex enables the fusion of synaptic vesicles with presynaptic membrane via a zippering process that is modulated by the protein complexin, though the precise mechanism remains unclear. Here, the authors used magnetic tweezers to show how complexin prepares a SNARE complex for fusion under mechanical tension.

    • Min Ju Shon
    • , Haesoo Kim
    •  & Tae-Young Yoon

  • Article
    | Open Access

    Atomic force microscopy is an indispensable method in characterizing soft materials but the complexity of biological samples makes reproducible measurements difficult. Here the authors use a 3-step method to investigate biological specimens in which vertical and lateral heterogeneity hinders a precise quantitative characterization.

    • Massimiliano Galluzzi
    • , Guanlin Tang
    •  & Florian J. Stadler

  • Article
    | Open Access

    The circadian clock proteins KaiA, KaiB, and KaiC reconstitute a circa-24 h oscillation of KaiC phosphorylation in vitro. Here the authors use high-speed atomic force microscopy to visualize in real time and quantify the dynamic interactions of KaiA with KaiC on the sub-second timescale to discover mechanisms of oscillatory resilience.

    • Tetsuya Mori
    • , Shogo Sugiyama
    •  & Toshio Ando

  • Article
    | Open Access

    Supercooled water is susceptible to spontaneous freezing, and preventing this process is a challenge. Here, the authors use surface sealing with immiscible liquids to eliminate primary ice nucleation at the water/air interface, enabling deep supercooling of large volumes of water and red cell suspensions for long time periods.

    • Haishui Huang
    • , Martin L. Yarmush
    •  & O. Berk Usta

  • Article
    | Open Access

    Myosin-5B is an actin-based motor important for endosome recycling, but the molecular mechanism underlying its motility remains unknown. Here authors use single molecule imaging and high-speed laser tweezers to dissect the mechanoenzymatic properties of myosin-5B, which shows processive motility with peculiar mechanosensitivity.

    • Lucia Gardini
    • , Sarah M. Heissler
    •  & Marco Capitanio

  • Article
    | Open Access

    FRAP analysis often relies on simplified assumptions that can affect measurement accuracy. Here the authors present a Python-based FRAP analysis software using simulations instead of simplified theoretical models to fit the data, which accounts for complex sample geometries and bleach conditions.

    • Alexander Bläßle
    • , Gary Soh
    •  & Patrick Müller

  • Article
    | Open Access

    There is growing evidence that the kinetics of interactions between inhibitors and their targets can strongly impact therapeutic efficacy. Here the authors describe an isothermal titration calorimetry-based method that can rapidly quantify inhibition kinetics and measure sub-nM binding affinities.

    • Justin M. Di Trani
    • , Stephane De Cesco
    •  & Anthony K. Mittermaier

  • Article
    | Open Access

    The BRICHOS domain is a chaperone that can act against amyloid-β peptide fibril formation and non-fibrillar protein aggregation. Here the authors use a multidisciplinary approach and show that the Bri2 BRICHOS domain has qualitatively different chaperone activities depending on its quaternary structure.

    • Gefei Chen
    • , Axel Abelein
    •  & Jan Johansson

  • Article
    | Open Access

    Circadian rhythms usually rely on cyclic variations in gene expression. Red blood cells, however, display circadian rhythms while being devoid of nuclear DNA. Here, Henslee and colleagues show that circadian rhythms in isolated human red blood cells are dependent on rhythmic transport of K+ ions.

    • Erin A. Henslee
    • , Priya Crosby
    •  & Fatima H. Labeed

  • Article
    | Open Access

    Large electronics limit low-noise, non-invasive electrophysiological measurements to a thousand simultaneously recording channels. Here the authors build an array of 65k simultaneously recording and stimulating electrodes and use it to sort and classify single neurons across the entire mouse retina.

    • David Tsai
    • , Daniel Sawyer
    •  & Kenneth L. Shepard

  • Article
    | Open Access

    The neural circuits of the vestibular system, which detects gravity and motion, remain incompletely characterised. Here the authors use an optical trap to manipulate otoliths (ear stones) in zebrafish larvae, and elicit corrective tail movements and eye rolling, thus establishing a method for mapping vestibular processing.

    • Itia A. Favre-Bulle
    • , Alexander B. Stilgoe
    •  & Ethan K. Scott

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