Molecular imaging articles within Nature Communications

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  • Article
    | Open Access

    Bioimaging with photocontrol and multiplexing capability is vital for studying cellular interactions and dynamics, but multiplexed stimulated Raman scattering (SRS) imaging with reversible photocontrol is elusive. Here, the authors report SRS microscopy with Carbow-switch enabling multiplexed SRS imaging and tracking in live cells with reversible photocontrol and high spatiotemporal selectivity.

    • Yueli Yang
    • , Xueyang Bai
    •  & Fanghao Hu
  • Article
    | Open Access

    Spatial imaging methods in lipid research can disrupt tissue integrity and can have limited spatial and spectral resolution. Here, the authors present an SRS-based hyperspectral imaging platform to visualise lipids and lipoproteins in a variety of tissues and animal species.

    • Wenxu Zhang
    • , Yajuan Li
    •  & Lingyan Shi
  • Article
    | Open Access

    The integration of single-cell and spatial data can provide a more comprehensive picture of the network of cells within the tumour microenvironment. Here the authors use a combination of single-cell and spatial technologies including 10x Xenium to characterise serial formalin-fixed, paraffin-embedded human breast cancer sections.

    • Amanda Janesick
    • , Robert Shelansky
    •  & Sarah E. B. Taylor
  • Article
    | Open Access

    Oncologic tumour resection is not fully accurate. Here the authors report a label-free virtual histological imaging method based on a non-contact, reflection-mode ultraviolet photoacoustic remote sensing and scattering microscope, combined with unsupervised deep learning using a cycle-consistent GAN.

    • Matthew T. Martell
    • , Nathaniel J. M. Haven
    •  & Roger J. Zemp
  • Article
    | Open Access

    pH alterations are a hallmark of many pathologies including cancer and kidney disease. Here the authors describe [1,5- 13 C2]Z-OMPD as a probe for hyperpolarized 13C-MRI with good pH sensitivity and hyperpolarization properties which combined with tailored MRI protocols allow sub-minute imaging of pH, renal perfusion and filtration simultaneously.

    • Martin Grashei
    • , Pascal Wodtke
    •  & Franz Schilling
  • Article
    | Open Access

    Live-cell RNA imaging with high spatial and temporal resolution remains a major challenge. Here the authors design spirocyclic rhodamine probes that enable a fluorescent light-up aptamer system suitable for visualizing RNAs in live or fixed cells with two different super-resolution microscopy modalities SMLM and STED.

    • Daniel Englert
    • , Eva-Maria Burger
    •  & Murat Sunbul
  • Article
    | Open Access

    Spatial metabolomics are used to describe the location and chemistry of small molecules involved in metabolic phenotypes. Here, Conroy et al. present a bioinformatic pipeline to analyze MALDI data and show that it can be used to identify actionable targets such as glycogen in fibrotic lungs of both human and mice.

    • Lindsey R. Conroy
    • , Harrison A. Clarke
    •  & Ramon C. Sun
  • Article
    | Open Access

    Here, the authors present a noninvasive tool to detect liver inflammation using nuclear imaging, as an alternative to biopsy. The prove the diagnostic power of this tool to detect liver inflammation in preclinical models of chronic liver disease.

    • Maxime Nachit
    • , Christopher Montemagno
    •  & Pascale Perret
  • Article
    | Open Access

    Oxidized phosphatidylcholines (oxPCs) are a structurally diverse class of lipids associated with various diseases. Here, the authors use mass spectrometry to construct a spectral library of 465 oxPCs and subsequently profile oxPCs formed during acetaminophen-induced acute liver failure in mice.

    • Yuta Matsuoka
    • , Masatomo Takahashi
    •  & Ken-ichi Yamada
  • Article
    | Open Access

    Photoacoustic imaging is limited by a lack of contrast agents which can enable combined molecular and physiological imaging at depth. Here the authors address these limitations by developing and validating a contrast agent based on targeted liposomes loaded with J-aggregated indocyanine green dye.

    • Cayla A. Wood
    • , Sangheon Han
    •  & Richard R. Bouchard
  • Article
    | Open Access

    Currently relatively few functional probes for Raman-based live-cell profiling exist. Here the authors build on their previous ultra-bright Raman dots to devise a 14-plexed Raman probe panel to quantify cell surface proteins, endocytosis activities and metabolic dynamics of single live cells.

    • Chen Chen
    • , Zhilun Zhao
    •  & Wei Min
  • Article
    | Open Access

    Probes with reversible fluorescence are useful in super-resolution microscopy, but lack sufficient chemical specificity. Here, the authors engineer alkyne tagged diarylethene to realize photo-switchable stimulated Raman scattering probes with high chemical resolution, for applications in living cells.

    • Jianpeng Ao
    • , Xiaofeng Fang
    •  & Minbiao Ji
  • Article
    | Open Access

    Centrosomes function as microtubule organizing centers where several mRNAs accumulate. By employing high-throughput single molecule FISH screening, the authors discover that 8 human mRNAs localize to centrosomes with unique cell cycle dependent patterns using an active polysome targeting mechanism.

    • Adham Safieddine
    • , Emeline Coleno
    •  & Edouard Bertrand
  • Article
    | Open Access

    Spectroscopic photoacoustic imaging has been limited by wavelength-dependent fluence variations and tissue motion. Here, the authors achieve real-time fluence and motion correction in vivo by using a wavelength-tunable laser, sequential scan of a narrow beam and partial image reconstruction for each pulse.

    • Geng-Shi Jeng
    • , Meng-Lin Li
    •  & Matthew O’Donnell
  • Article
    | Open Access

    Label-free protein characterization at surfaces requires digestion or matrix application prior to mass spectrometry. Here, the authors report the assignment of undigested proteins at surfaces by de novo sequencing and apply the methodology to a protein monolayer biochip and for in situ depth profiling of proteins through human skin.

    • Anna M. Kotowska
    • , Gustavo F. Trindade
    •  & David J. Scurr
  • Article
    | Open Access

    Detection of amyloid beta deposits is often performed with fluorescent compounds that bind plaques. Here the authors develop turn-on chemiluminescent probes that bind amyloid beta plaques in vivo, and amplify the signal via chemiluminescence resonance energy transfer to the plaque-binding fluorescent molecule CRANAD-3.

    • Jing Yang
    • , Wei Yin
    •  & Chongzhao Ran
  • Article
    | Open Access

    α-Syn in CSF is a biomarker of neurodegenerative diseases; however, the detection of clinically relevant species is difficult. Here, the authors create a nanobody biosensor that reveals the presence of α-Syn in cells, which allow the detection of transmittable forms of α-Syn present in human CSF.

    • Christoph Gerdes
    • , Natalia Waal
    •  & Felipe Opazo
  • Article
    | Open Access

    Noninvasive detection of molecular targets in living subjects could provide valuable insights into healthy function and disease. Here, the authors develop vasoactive imaging probes which allow wide-field in vivo mapping of nanomolar-level molecular species in rat brain.

    • Robert Ohlendorf
    • , Agata Wiśniowska
    •  & Alan Jasanoff
  • Article
    | Open Access

    The contribution of central and peripheral channels of nuclear pores to transport of transmembrane proteins is unclear. Here the authors show that most inner nuclear membrane proteins use only peripheral channels, but some extend nuclear localization signals into the central channel for directed nuclear transport.

    • Krishna C. Mudumbi
    • , Rafal Czapiewski
    •  & Weidong Yang
  • Article
    | Open Access

    Adeno-associated viruses (AAVs) can be targeted in a tissue-specific manner, but their tissue accumulation cannot be assessed in a non-invasive manner. Here the authors conjugate a multivalent chelator labelled with Cu-64 to the surface of AAVs and image the brain accumulation of the PHB.eB capsid by PET.

    • Jai Woong Seo
    • , Elizabeth S. Ingham
    •  & Katherine W. Ferrara
  • Article
    | Open Access

    Sensitive diagnostic tools for bacterial infections of wounds and surgical sites are necessary to enable early detection and determine optimal means of treatment. Here, the authors develop a fluorescent and optoacoustic probe based on a maltotriose scaffold, which is selectively taken up by gram-positive and gram-negative bacteria.

    • Aimen Zlitni
    • , Gayatri Gowrishankar
    •  & Sanjiv Sam Gambhir
  • Article
    | Open Access

    Phosphocreatine plays a vital role in cellular energetic homeostasis, but there are no routine diagnostic tests to noninvasively map the distribution with clinically relevant spatial resolution. Here, the authors develop and validate a noninvasive approach for quantifying and imaging phosphocreatine, without contrast agents, on widely available clinical MRI scanners with artificial neural networks.

    • Lin Chen
    • , Michael Schär
    •  & Jiadi Xu
  • Article
    | Open Access

    Taccalonolide microtubule stabilizers covalently bind β-tubulin and overcome taxane resistance mechanisms. Here, the authors synthesized fluorogenic taccalonolide probes and investigated the specificity of taccalonolide binding to β-tubulin and the molecular interactions between drug and target,

    • Lin Du
    • , Samantha S. Yee
    •  & April L. Risinger
  • Article
    | Open Access

    Numerous fluorescent Zn2+ sensors are available but most are unsuitable to detect physiological dynamics of cytosolic Zn2+. In this study, the authors present a genetically encoded sensor with sub-nanomolar sensitivity and show that Zn2 + is released from endolysosomal vesicles via TRPML1 in neurons.

    • Taylor F. Minckley
    • , Chen Zhang
    •  & Yan Qin
  • Article
    | Open Access

    Nanosecond imaging techniques, such as fluorescence lifetime imaging microscopy (FLIM), are limited by low efficiency of current detectors. Here, the authors implement an electro-optic approach using Pockels cells for wide-field image gating and demonstrate high throughput FLIM on standard camera sensors.

    • Adam J. Bowman
    • , Brannon B. Klopfer
    •  & Mark A. Kasevich
  • Article
    | Open Access

    Although quantum biological electron transfer is important in many biological processes, imaging of the events in live cells has remained challenging. Here, the authors demonstrate real-time optical detection of quantum biological electron tunnelling between nanoparticles and cytochrome c inside living cells.

    • Hongbao Xin
    • , Wen Jing Sim
    •  & Luke P. Lee
  • 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

    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
  • Article
    | Open Access

    FRET sensors hardly achieve visualization of spatiotemporal dynamics of protein activity in vivo. Here the authors present intensiometric small GTPase biosensors based on dimerization-dependent fluorescent proteins that enable monitoring of activity of small GTPases in the brains of behaving mice at a single spine resolution.

    • Jihoon Kim
    • , Sangkyu Lee
    •  & Won Do Heo
  • Article
    | Open Access

    Fluorescent tracers are being tested in clinical trials to improve detection of tumor margins, but procedures are not standardised. Here, the authors develop an analytical framework that is compatible with the workflow in the operating theatre, and show that it leads to an 88% increase in intraoperative detection of tumor margins in patients with breast cancer.

    • Marjory Koller
    • , Si-Qi Qiu
    •  & Gooitzen M. van Dam
  • Article
    | Open Access

    MRI contrast agents containing the rare earth metal gadolinium are very effective, yet unstable and thus potentially hazardous. Here, the authors developed complexes between gadolinium and the scaffolding compound DOTA with increased stability, which also lend themselves to radiometal labelling.

    • Lixiong Dai
    • , Chloe M. Jones
    •  & Ga-Lai Law
  • Article
    | Open Access

    Integrin αβ heterodimer cell surface receptors mediate adhesive interactions that provide traction for cell migration. Here the authors show that actin flow can orient cell surface integrins during leukocyte migration, suggesting integrin activation by cytoskeletal force.

    • Pontus Nordenfelt
    • , Travis I. Moore
    •  & Timothy A. Springer
  • Article
    | Open Access

    Local pH alterations can be manifestations of pathologies such as cancer, inflammation and ischaemia. Here Düwelet al. show hyperpolarized 13C-labelled zymonic acid can be used as a non-invasive probe to map and measure pH in vivo, suggesting it as a candidate for clinical imaging and a diagnostic tool.

    • Stephan Düwel
    • , Christian Hundshammer
    •  & Franz Schilling
  • Article
    | Open Access

    Visualizing single genomic loci in living cells remains technically challenging. Here the authors adopt a strategy of labelling a pair of transcription activator-like effectors (TALEs) with differently coloured quantum dots and use them to identify integrated HIV-1 proviral DNA sequences in living cells.

    • Yingxin Ma
    • , Mingxiu Wang
    •  & Zongqiang Cui
  • Article
    | Open Access

    Advances in chemical imaging capability can add to our understanding of complex cellular systems. Here the authors develop a framework for label-free quantitative volumetric Raman spectroscopic imaging and use it to visualize and quantify biomolecules in various 3D cellular systems.

    • Charalambos Kallepitis
    • , Mads S. Bergholt
    •  & Molly M. Stevens
  • Article
    | Open Access

    CRISPR-Cas9 has been used to image repetitive loci in live cells to explore genome organization. Here the authors demonstrate the imaging of low-repeat regions with a single-guide RNA and the imaging of a non-repetitive region, allowing the tracking of transcriptionally active and inactive regions.

    • Peiwu Qin
    • , Mahmut Parlak
    •  & Mazhar Adli
  • Article
    | Open Access

    The vasculature produces strong endogenous contrast in magnetic resonance imaging (MRI). Here Desai et al. report genetically encoded imaging probes derived from the vasodilator, calcitonin gene-related peptide, which allows visualization of molecular events via haemodynamic changes in optical imaging or MRI.

    • Mitul Desai
    • , Adrian L. Slusarczyk
    •  & Alan Jasanoff
  • Article
    | Open Access

    The circadian rhythms of peripheral clocks are difficult to study. Here the authors demonstrate a technique to image clock gene expression simultaneously in various tissues of freely moving mice, and use it to show that a long duration light pulse resets the rhythms in the olfactory bulb faster than other tissues.

    • Toshiyuki Hamada
    • , Kenneth Sutherland
    •  & Ken-ichi Honma
  • Article |

    Mutations in the enzyme superoxide dismutase 1 (SOD1) underlie a form of neurodegenerative disease called amyotrophic lateral sclerosis. Here the authors employ in-cell NMR to show that SOD1 mutants adopt unstructured conformations that are unable to bind zinc and may form toxic SOD1 aggregates.

    • Enrico Luchinat
    • , Letizia Barbieri
    •  & Lucia Banci
  • Article
    | Open Access

    Single molecule fluorescence microscopy is a powerful technique to study protein dynamics in cells, but it has not been applied to adult animals. The authors use complementation-activated light microscopy in C. elegansto discover that dystrophin regulates the diffusion properties of voltage-dependent calcium ion channels at the surface of body-wall muscle cells.

    • Hong Zhan
    • , Ramunas Stanciauskas
    •  & Fabien Pinaud
  • Article
    | Open Access

    Complex molecular interactions occur in the active zone cytomatrix (CAZ) within the presynaptic terminal to regulate synaptic plasticity. Here, the authors use imaging techniques to show that the CAZ is composed of units containing on average 137 Bruchpilot proteins, many of which are arranged into clusters.

    • Nadine Ehmann
    • , Sebastian van de Linde
    •  & Robert J. Kittel