Biological techniques articles within Nature Communications

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  • Article
    | Open Access

    Methods to track molecular motion in eukaryotic cells mostly rely on fluorescent labels, transfection or photobleaching. Here the authors use multimodal partial wave spectroscopy to perform label-free live cell measurements of nanoscale structure and macromolecular motion with millisecond temporal resolution.

    • Scott Gladstein
    • , Luay M. Almassalha
    •  & Vadim Backman

  • Article
    | Open Access

    Multicolour images are difficult to acquire with large-scale microscopy approaches. Here the authors present a microtome-assisted microscope capable of trichromatic two-photon excitation and label-free nonlinear modalities based on wavelength mixing, and use it to analyze astrocyte morphology and neuronal projections in thick brain samples.

    • Lamiae Abdeladim
    • , Katherine S. Matho
    •  & Emmanuel Beaurepaire

  • Article
    | Open Access

    Gene-drives use CRISPR-Cas9 to be transmitted in a super-Mendelian fashion. Here the authors develop an allelic-drive for selective inheritance of a desired allele.

    • Annabel Guichard
    • , Tisha Haque
    •  & Ethan Bier

  • Article
    | Open Access

    Gene correction in hematopoietic stem cells could be a powerful way to treat monogenic diseases of the blood and immune system. Here the authors develop a strategy using CRISPR-Cas9 and an aAdeno-Associated vVirus(AAV)-delivered IL2RG cDNA to correct X-linked sSevere Ccombined iImmunodeficiency (SCID-X1) with a high success rate.

    • Mara Pavel-Dinu
    • , Volker Wiebking
    •  & Matthew H. Porteus

  • Article
    | Open Access

    Designing effective genome engineering strategies requires an understanding of the impact that genomic locus has on CRISPR-Cas9 activity. Here the authors use TRIP integrations to profile editing outcomes genome-wide and observe that gRNA sequence influences the structure of the double strand break.

    • Santiago Gisler
    • , Joana P. Gonçalves
    •  & Maarten van Lohuizen

  • Article
    | Open Access

    Affinity purification-mass spectrometry (AP-MS) can identify endogenous protein interactions but the need for high amounts of input material still limits its applicability. Here, the authors present a microfluidic-based AP-MS workflow that can capture protein interactions from 50─100-fold less input material than conventional approaches.

    • Cristina Furlan
    • , René A. M. Dirks
    •  & Michiel Vermeulen

  • Article
    | Open Access

    Autophagic degradation of mitochondria (mitophagy) is a key quality control mechanism in cellular homeostasis, and its misregulation is involved in neurodegenerative diseases. Here the authors develop an optogenetic system for reversible induction of mitophagy and validate its use in cell culture and zebrafish embryos.

    • Pasquale D’Acunzo
    • , Flavie Strappazzon
    •  & Francesco Cecconi

  • Article
    | Open Access

    The spatial organization of the genome plays an important but unclearly defined role in gene regulation. Here, the authors integrate Hi-C, RNA-seq and ATAC-seq data to map cardiogenesis from pluripotent stem cells and describe an RBM20-dependent splicing factory assembling the TTN locus with other RBM20 targets.

    • Alessandro Bertero
    • , Paul A. Fields
    •  & Charles E. Murry

  • Article
    | Open Access

    Untargeted metabolomics detects large numbers of metabolites but their annotation remains challenging. Here, the authors develop a metabolic reaction network-based recursive algorithm that expands metabolite annotation by taking advantage of the mass spectral similarity of reaction-paired neighbor metabolites.

    • Xiaotao Shen
    • , Ruohong Wang
    •  & Zheng-Jiang Zhu

  • Article
    | Open Access

    The hippocampus is involved both in episodic memory recall and scene processing. Here, the authors show that hippocampal neurons first process scene cues before coordinating memory-guided pattern completion in adjacent entorhinal cortex.

    • Bernhard P. Staresina
    • , Thomas P. Reber
    •  & Florian Mormann

  • Article
    | Open Access

    Imaging the mouse brain using glass cranial windows has limitations in terms of flexibility and long-term imaging. Here the authors engineer transparent polymer skulls that can fit various skull morphologies and can be implanted for over 300 days, enabling simultaneous high resolution brain imaging and electrophysiology across large cortical areas.

    • Leila Ghanbari
    • , Russell E. Carter
    •  & Suhasa B. Kodandaramaiah

  • Article
    | Open Access

    D-lactic acidosis typically occurs in the context of short bowel syndrome; excess D-lactate is produced by intestinal bacteria. Here, the authors identify two point mutations in the human lactate dehydrogenase D (LDHD) gene that cause enzymatic loss of function and are associated with elevated plasma D-lactate.

    • Glen R. Monroe
    • , Albertien M. van Eerde
    •  & Judith J. Jans

  • Article
    | Open Access

    Many functions of the human brain are lateralised i.e. associated more strongly with either the left or the right hemisphere of the brain. Here, the authors report the first complete map of functional asymmetries in the human brain, and its relationship with structural inter-hemispheric connectivity.

    • Vyacheslav R. Karolis
    • , Maurizio Corbetta
    •  & Michel Thiebaut de Schotten

  • Article
    | Open Access

    Curli are bacterial functional amyloids that have gained interest as self-assembling biomaterial for biotechnology applications. Here, the authors show that DNA origami decorated with CsgB nucleator proteins induced the site-specific nucleation and subsequent fibrillization of CsgA proteins.

    • Xiuhai Mao
    • , Ke Li
    •  & Chao Zhong

  • Article
    | Open Access

    Rapid and accurate detection of fusion genes is important in cancer diagnostics. Here, the authors demonstrate that targeted RNA sequencing provides fast, sensitive and quantitative gene fusion detection and overcomes the limitations of approaches currently in clinical use.

    • Erin E. Heyer
    • , Ira W. Deveson
    •  & James Blackburn

  • Article
    | Open Access

    A desired product cannot be obtained at higher concentration than its equilibrium concentration when isomerases are used for biotransformation. Here, the authors engineer in vivo oxidoreductive reactions in yeast to overcome the equilibrium limitation of in vitro isomerases-based tagatose production.

    • Jing-Jing Liu
    • , Guo-Chang Zhang
    •  & Yong-Su Jin

  • Article
    | Open Access

    Mass spectrometry facilitates large-scale glycosylation profiling but in-depth analysis of intact glycopeptides is still challenging. Here, the authors show that activated ion electron transfer dissociation is suitable for glycopeptide fragmentation and improves glycoproteome coverage.

    • Nicholas M. Riley
    • , Alexander S. Hebert
    •  & Joshua J. Coon

  • Article
    | Open Access

    Attachment of human noroviruses to histo blood group antigens (HBGAs) is essential for infection. Here the authors report that an asparagine residue located near the HBGA-attachment site can convert into an iso-aspartate residue through spontaneous deamidation and influence HBGA recognition.

    • Alvaro Mallagaray
    • , Robert Creutznacher
    •  & Thomas Peters

  • Article
    | Open Access

    There has been recent controversy over the validity of commonly-used software packages for functional MRI (fMRI) data analysis. Here, the authors compare the performance of three leading packages (AFNI, FSL, SPM) in terms of temporal autocorrelation modeling, a key statistical step in fMRI analysis.

    • Wiktor Olszowy
    • , John Aston
    •  & Guy B. Williams

  • Article
    | Open Access

    The use of TIRF microscopy for DNA-PAINT experiments is limited by inhomogeneous illumination. Here the authors show that quantitative analysis of single-molecule TIRF experiments can be improved by using a segment-wise analysis approach and overcome by using a beam-shaping device to give a flat-top illumination profile.

    • Florian Stehr
    • , Johannes Stein
    •  & Ralf Jungmann

  • Article
    | Open Access

    TIRF imaging is limited by the size and uniformity of the illumination. Here the authors present a waveguide solution to create a large area of uniform evanescent illumination suitable for single molecule imaging coupled with a customised sample holder containing a reservoir for DNA-PAINT solutions.

    • Anna Archetti
    • , Evgenii Glushkov
    •  & Suliana Manley

  • Article
    | Open Access

    Sample processing for biological imaging experiments involves elaborate protocols with low reproducibility and throughput. Here the authors develop an open-source system called NanoJ-Fluidics, composed of off-the-shelf Lego components and an ImageJ-based controller to achieve automated fixation, labelling and imaging of cells.

    • Pedro Almada
    • , Pedro M. Pereira
    •  & Ricardo Henriques

  • Article
    | Open Access

    Current optoacoustic probes for cancer imaging have limitations including background noise, long-term toxicity and scarce imaging depth in living tissue. Here the authors use Rhodobacter, purple bacteria rich in bacteriochlorophyll a, as an optoacoustic reporter to image tumor-associated macrophages in mice in vivo.

    • Lena Peters
    • , Ina Weidenfeld
    •  & Andre C. Stiel

  • Article
    | Open Access

    Platelet aggregates generate contractile forces that contribute to their cohesion and adhesion. Here, Ting et al. develop a microfluidic device to measure contractile forces generated by platelet aggregates, and find it can detect the response of platelets to pharmacological agents and predict bleeding risk in trauma patients.

    • Lucas H. Ting
    • , Shirin Feghhi
    •  & Nathan J. Sniadecki

  • Article
    | Open Access

    Simultaneous quantification of DNA, RNA and protein at the single cell level has not yet been possible. Here the authors introduce a molecular labelling and detection strategy to quantify synthesis of these biomolecules and couple it to transient cell states through parallel quantification of state-dependent biomolecules.

    • Samuel C. Kimmey
    • , Luciene Borges
    •  & Sean C. Bendall

  • Article
    | Open Access

    The first week of life impacts health for all of life, but the mechanisms are little-understood. Here the authors extract multi-omic data from small volumes of blood to study the dynamic molecular changes during the first week of life, revealing a robust developmental trajectory common to different populations.

    • Amy H. Lee
    • , Casey P. Shannon
    •  & Tobias R. Kollmann

  • Article
    | Open Access

    Studying protein kinetics and stability in living organisms is challenging and most studies are performed in cell culture. Here the authors combine meganuclease-mediated transformation and fluorescence-detected temperature-jump microscopy to quantify protein stability in different tissues of living zebrafish.

    • Ruopei Feng
    • , Martin Gruebele
    •  & Caitlin M. Davis

  • Article
    | Open Access

    Stimulation of peripheral nerve activity may be used to treat metabolic and inflammatory disorders, but current approaches need implanted devices. Here, the authors present a non-invasive approach, and show that ultrasound-mediated stimulation can be targeted to specific sub-organ locations in preclinical models and alter the response of metabolic and inflammatory neural pathways.

    • Victoria Cotero
    • , Ying Fan
    •  & Christopher Puleo

  • Article
    | Open Access

    Upon photoactivation the Orange Carotenoid Protein (OCP) binds to the phycobilisome and prevents damage by thermally dissipating excess energy. Here authors use an Anti-Brownian ELectrokinetic trap to determine the photophysics of single OCP-quenched phycobilisomes and observe two distinct OCP-quenched states with either one or two OCPs bound.

    • Allison H. Squires
    • , Peter D. Dahlberg
    •  & W. E. Moerner

  • Article
    | Open Access

    Modulation of the cholinergic pathway and spleen function can reduce inflammation with invasive implants. Here, the authors show that non-invasive ultrasound stimulation of the spleen reduces disease severity in a mouse model of inflammatory arthritis, partly via altering B and T cell function.

    • Daniel P. Zachs
    • , Sarah J. Offutt
    •  & Hubert H. Lim

  • Article
    | Open Access

    Optical control over receptor tyrosine kinase (RTK) activity can find application in both basic biology and synthetic biology. Here the authors combine the photosensory module of DrBphP bacterial phytochrome with the Trk family of RTKs to obtain Trks that are reversibly switchable with near-infrared and far-red light.

    • Anna V. Leopold
    • , Konstantin G. Chernov
    •  & Vladislav V. Verkhusha

  • Article
    | Open Access

    Inferring direct protein−protein interactions (PPIs) and modules in PPI networks remains a challenge. Here, the authors introduce an algorithm to infer potential direct PPIs from quantitative proteomic AP-MS data by identifying enriched interactions of each bait relative to the other baits.

    • Mihaela E. Sardiu
    • , Joshua M. Gilmore
    •  & Michael P. Washburn

  • Article
    | Open Access

    Genome editing often requires cleavage within a narrow sequence window. Here the authors develop an expanded set of zinc finger nuclease architectures that increase the available configurations by a factor of 64 and can target almost every base at loci of therapeutic significance.

    • David E. Paschon
    • , Stephanie Lussier
    •  & Edward J. Rebar

  • Article
    | Open Access

    Bacterial outer membrane vesicles (OMVs) are increasingly used as carriers for drug delivery. Here the authors encapsulate biopolymer melanin into OMVs, extending their use to optoacoustic imaging both in vitro and in vivo, and demonstrate the potential of this tool for photothermal therapy applications.

    • Vipul Gujrati
    • , Jaya Prakash
    •  & Vasilis Ntziachristos

  • Article
    | Open Access

    Attempts to image activated macrophages in vivo have been hampered by selectivity and delivery problems. Here the authors develop a small molecule fluorescent probe specific to activated M1 and M2 macrophages, identify the orphan receptor Slc18b1/SLC18B1 as the mechanism of uptake, and use it to image atherosclerosis in mice.

    • Sung-Jin Park
    • , Beomsue Kim
    •  & Young-Tae Chang

  • Article
    | Open Access

    Neuronal activity leads to a local increase in blood flow and volume, a process termed hyperaemia. Here, the authors employ multiple imaging approaches of neuronal and vascular activity at varying resolution to delineate the spatiotemporal dynamics of neurovascular coupling evoked by odours in the olfactory bulb.

    • Davide Boido
    • , Ravi L. Rungta
    •  & Serge Charpak

  • Article
    | Open Access

    Many human proteins are regulated by lysine acetylation, but the degree of acetylation at individual sites is poorly characterized. Here, the authors measure acetylation stoichiometry in the HeLa cell proteome, providing a resource to assess mechanistic constraints on acetylation-mediated protein regulation.

    • Bogi Karbech Hansen
    • , Rajat Gupta
    •  & Brian T. Weinert

  • Article
    | Open Access

    Despite many recent advances in cryo-EM, imaging smaller macromolecules (below 100 kDa) has remained a challenge. Here the authors show that biological specimens amassing <100 kDa can be resolved to better than 3 Å resolution using conventional defocus-based single-particle analysis methods.

    • Mark A. Herzik Jr.
    • , Mengyu Wu
    •  & Gabriel C. Lander

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