Biological techniques

  • Article
    | Open Access

    Multifocal imaging suffers from a number of limitations. Here the authors report an open-source 3D reconstruction algorithm to enable label-free tracking of spherical and filamentous structures which they use to characterise fluid flow and flagellar beating of human and sea urchin sperm.

    • Jan N. Hansen
    • , An Gong
    •  & Luis Alvarez
  • Article
    | Open Access

    Many current immunoassays require multiple washing, incubation and optimization steps. Here the authors present Ratiometric Plug-and-Play Immunodiagnostics (RAPPID), a generic assay platform that uses ratiometric bioluminescent detection to allow sandwich immunoassays to be performed directly in solution.

    • Yan Ni
    • , Bas J. H. M. Rosier
    •  & Maarten Merkx
  • Article
    | Open Access

    Mitochondrial transport toward both the plus- and minus-ends of microtubules is mediated by motor proteins linked to mitochondria by TRAK adaptor proteins. Here the authors investigate the role of TRAK2 as a bidirectional motor adaptor, and propose a model where TRAK2 coordinates the activities of opposing kinesin-1 and cytoplasmic dynein motors as a single interdependent motor complex.

    • Adam R. Fenton
    • , Thomas A. Jongens
    •  & Erika L. F. Holzbaur
  • Article
    | Open Access

    Differentiation of hPSCs to cardiomyocytes suffers from high variability. Here the authors report a label-free live cell imaging platform based on autofluorescence imaging to enable the prediction of cardiomyocyte differentiation efficiency from hPSCs.

    • Tongcheng Qian
    • , Tiffany M. Heaster
    •  & Melissa C. Skala
  • Article
    | Open Access

    Imaging rates in single-pixel imaging has been limited by the dependence on configurable spatial light modulators. Here, the authors use cyclic Hadamard patterns coded onto a spinning mask to demonstrate dynamic imaging with rates up to 72 frames per second and real time reconstruction capabilities.

    • Evgeny Hahamovich
    • , Sagi Monin
    •  & Amir Rosenthal
  • Article
    | Open Access

    The authors develop a method to build Manhattan Raman Scattering (MARS) probes based on different core atoms, conjugation ring numbers, and stable isotope substitutions. A quantitative model predicts vibrational frequencies of MARS dyes from structures, which are used in supermultiplexed vibrational imaging.

    • Yupeng Miao
    • , Naixin Qian
    •  & Wei Min
  • Article
    | Open Access

    Currently, bidirectional control of activity in the same neurons in the same experiment is difficult. Here the authors report a Bidirectional Pair of Opsins for Light-induced Excitation and Silencing, BiPOLES, which they use in a range of organisms including worms, fruit flies, mice and ferrets.

    • Johannes Vierock
    • , Silvia Rodriguez-Rozada
    •  & J. Simon Wiegert
  • Article
    | Open Access

    Quantitative methods to assess the quality of hPSC-derived organoids have not been developed. Here they present a prediction algorithm to assess the transcriptomic similarity between hPSC-derived organoids and the corresponding human target organs and perform validation on lung bud organoids, antral gastric organoids, and cardiomyocytes.

    • Mi-Ok Lee
    • , Su-gi Lee
    •  & Hyun-Soo Cho
  • Article
    | Open Access

    Existing long-read de novo assembly methods can partially, but not completely, separate strains. Here, the authors develop Strainberry, a metagenome assembly bioinformatic pipeline that exclusively uses longread data to accurately separate and reconstruct strain genomes from single-sample low-complexity microbiomes.

    • Riccardo Vicedomini
    • , Christopher Quince
    •  & Rayan Chikhi
  • Article
    | Open Access

    Pannexin 1 (PANX1) is a membrane channel mediating release of signaling molecules to the extracellular space. PANX1 can be activated by GPCRs. Here, the authors elucidate a non-canonical channel activation pathway by α1-adrenergic receptor that involves HDAC6- mediated lysine deacetylation of PANX1.

    • Yu-Hsin Chiu
    • , Christopher B. Medina
    •  & Douglas A. Bayliss
  • Article
    | Open Access

    Scintillators emit visible luminescence when irradiated with X-rays and may enable remote optogenetic control of neurons deep in the brain. The authors inject an inorganic scintillator to activate and inhibit midbrain dopamine neurons in freely moving mice by X-ray irradiation to modulate place preference behavior.

    • Takanori Matsubara
    • , Takayuki Yanagida
    •  & Takayuki Yamashita
  • Article
    | Open Access

    Currently many of the time resolved serial femtosecond (SFX) crystallography experiments are done with light driven protein systems, whereas the reaction initiation for non-light triggered enzymes remains a major bottle neck. Here, the authors present an expanded Drop-on-Tape system, where picoliter-sized droplets of a substrate or inhibitor are turbulently mixed with nanoliter sized droplets of microcrystal slurries, and they use it for time-resolved SFX measurements of inhibitor binding to lysozyme and secondly, binding of a β-lactam antibiotic to a bacterial serine β-lactamase.

    • Agata Butryn
    • , Philipp S. Simon
    •  & Allen M. Orville
  • Article
    | Open Access

    Spatial analysis of RNAseq data is important. Here the authors report a method for transcriptome profiling combined with photo-isolation chemistry to allow determination of expression profiles specifically from photo-irradiated regions of interest which they use in mouse brains and embryonic tissues.

    • Mizuki Honda
    • , Shinya Oki
    •  & Yasuyuki Ohkawa
  • Article
    | Open Access

    High-speed atomic force microscopy height spectroscopy and single channel electrophysiology recordings are used to correlate conformational and functional dynamics of the model membrane protein, outer membrane protein G (OmpG). These techniques show that both states coexist and rapidly interchange in all conditions supported by molecular dynamics simulations.

    • Raghavendar Reddy Sanganna Gari
    • , Joel José Montalvo‐Acosta
    •  & Simon Scheuring
  • Article
    | Open Access

    Wavefront shaping is used to overcome scattering in biological tissues during imaging, but determining the compensation is slow. Here, the authors use holographic phase stepping interferometry, where new phase information is updated after each measurement, enabling fast improvement of the wavefront correction.

    • Molly A. May
    • , Nicolas Barré
    •  & Alexander Jesacher
  • Article
    | Open Access

    Pleckstrin homology (PH) domains are presumed to bind phosphoinositides (PIPs) but only few specific interactions are known. Using TIRF microscopy based assays, functional studies and an experimentally validated prediction algorithm, the authors show that specific PIP binding is widespread among human PH domains.

    • Nilmani Singh
    • , Adriana Reyes-Ordoñez
    •  & Jie Chen
  • Article
    | Open Access

    Current methods to estimate energy expenditure are either infeasible for everyday use or associated with significant errors. Here the authors present a Wearable System using inertial measurement units worn on the shank and thigh that estimates metabolic energy expenditure in real-time during common steady-state and time-varying activities.

    • Patrick Slade
    • , Mykel J. Kochenderfer
    •  & Steven H. Collins
  • Article
    | Open Access

    Single-cell RNA-seq reveals the cellular heterogeneity in development and disease. Here the authors present a single-nucleus RNA-seq2 that allows deep characterization of nuclei isolated from frozen archived tissues, apply it for transcriptional profiling of individual hepatocytes, and determine a functional crosstalk between liver zonation and ploidy.

    • M. L. Richter
    • , I. K. Deligiannis
    •  & C. P. Martinez-Jimenez
  • Article
    | Open Access

    The epithelial-mesenchymal transition (EMT) has been implicated in stem cell properties and therapeutic resistance in cancer. Here, the authors show organoids derived from mesenchymal breast cancers exhibit a spikey structure which can be reverted and exploited for screening drugs that reverse EMT.

    • Na Zhao
    • , Reid T. Powell
    •  & Jeffrey M. Rosen
  • Article
    | Open Access

    The transcriptional regulators underlying the induction and differentiation of dense connective tissues remain largely unknown. Here the authors generate tendon and fibrocartilage cells from mouse embryonic stem cells and apply scRNA-seq to identify molecular regulation of the cell fate switch between these lineages.

    • Deepak A. Kaji
    • , Angela M. Montero
    •  & Alice H. Huang
  • Article
    | Open Access

    It remains unclear how spatial information controls endothelial cell identity and behavior in the developing heart. Here the authors perform single cell RNA sequencing at key developmental timepoints in mice to interrogate cellular contributions to coronary vessel patterning and maturation in the epicardium.

    • Pearl Quijada
    • , Michael A. Trembley
    •  & Eric M. Small
  • Article
    | Open Access

    Limited understanding of the interactions between nanoparticle drug carriers and the blood-brain barrier underlies many translational failures in treatments of brain disorders. Here the authors use two-photon microscopy in mice to characterize the receptor-mediated transcytosis of nanoparticles at all steps of delivery from the blood to the brain in vivo.

    • Krzysztof Kucharz
    • , Kasper Kristensen
    •  & Martin Johannes Lauritzen
  • Article
    | Open Access

    Mucins play critical roles in maintaining the human microbiome, with their O-glycosylated tandem repeats (TRs) providing important cues for microbiota. Here, the authors develop a cellular platform for producing TRs with defined O-glycan structures to dissect the functions of TR O-glycosylation.

    • Rebecca Nason
    • , Christian Büll
    •  & Yoshiki Narimatsu
  • Article
    | Open Access

    Schinzel-Giedion syndrome (SGS) is a fatal developmental syndrome characterized by severe intellectual and physical deficits due, at least in part, to early neurodegeneration. Here the authors introduce a human SGS model that displays disease-relevant phenotypes to demonstrate that neuronal death in SGS originates from developmental alterations mainly in safeguarding cell identity and homeostasis.

    • Federica Banfi
    • , Alicia Rubio
    •  & Alessandro Sessa
  • Article
    | Open Access

    STAT1a is required for pro-inflammatory responses in macrophages. Here the authors reveal that post-translational modification of STAT1a, ADPribosylation, plays a critical role in enhancer formation and activation, thus modulating IFNγ-stimulated inflammatory responses in macrophages.

    • Rebecca Gupte
    • , Tulip Nandu
    •  & W. Lee Kraus
  • Article
    | Open Access

    Pyrrolysine (Pyl) exists in nature as the 22nd proteinogenic amino acid, but studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, the authors developed an improved PANCE approach to evolve the pylBCD pathway for increased production of Pyl proteins in E. coli.

    • Joanne M. L. Ho
    • , Corwin A. Miller
    •  & Matthew R. Bennett
  • Article
    | Open Access

    Secondary structures and long-range RNA interactions of the SARS-CoV-2 genome have been investigated by various sequencing methods. Here the authors use an RNA-RNA hybrid sequencing method to predict the secondary and tertiary structure of the SRAS-CoV-2 RNA genome in the virion.

    • Changchang Cao
    • , Zhaokui Cai
    •  & Yuanchao Xue
  • Article
    | Open Access

    The current biorefineries yield lignin with inadequate fractionation for bioconversion, yet substantial changes of these biorefinery designs could jeopardize carbohydrate efficiency and increase capital costs. Here the authors resolve the dilemma by designing ‘plug-in processes of lignin’ to enable economic waste valorization.

    • Zhi-Hua Liu
    • , Naijia Hao
    •  & Joshua S. Yuan
  • Article
    | Open Access

    Human Treg cells are central to immune tolerance, yet their heterogeneity and differentiation remain incompletely understood. Here the authors perform single-cell RNA and T cell receptor sequencing to resolve Treg cells from healthy individuals and patients with or without acute graft-versus-host disease revealing Treg complexity in health and disease.

    • Yuechen Luo
    • , Changlu Xu
    •  & Xiaoming Feng
  • Article
    | Open Access

    Current near-IR optogenetic systems to regulate transcription consist of a number of large protein components. Here the authors report a smaller single-component near-IR system, iLight, developed from a bacterial phytochrome that they use to control gene transcription in bacterial and mammalian cells.

    • Andrii A. Kaberniuk
    • , Mikhail Baloban
    •  & Vladislav V. Verkhusha
  • Article
    | Open Access

    The electron-withdrawing target (EWT)-induced fluorescence quenching is an unsolved issue in intramolecular charge transfer (ICT) fluorophores that limits their applicability. Here, the authors report a simple and generalizable strategy to reverse the EWT-induced quenching mode into light-up mode, by introducing an indazole building block between the π-bridge and the donor in the ICT scaffold.

    • Chenxu Yan
    • , Zhiqian Guo
    •  & Wei-Hong Zhu
  • Review Article
    | Open Access

    This review presents an overview of scenarios where van der Waals (vdW) materials provide unique advantages for nanophotonic biosensing applications. The authors discuss basic sensing principles based on vdW materials, advantages of the reduced dimensionality as well as technological challenges.

    • Sang-Hyun Oh
    • , Hatice Altug
    •  & Michael S. Strano
  • Article
    | Open Access

    Precise and dynamic manipulation of nano-objects on a large scale has been challenging. Here, the authors introduce acoustoelectronic nanotweezers, combining precision of electronic tweezers with large-field dynamic control of acoustic tweezers, demonstrating complex patterning of sub-100 nm objects.

    • Peiran Zhang
    • , Joseph Rufo
    •  & Tony Jun Huang