Featured
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| Open AccessAnalysis and modeling of cancer drug responses using cell cycle phase-specific rate effects
Understanding the impact of anti-cancer therapies on cell cycle progression could contribute to the discovery of effective therapeutic treatments. Here, the authors use genetically engineered breast cancer cell lines and computational models to analyse drug effects on specific cell cycle phases and identify effective combination treatments.
- Sean M. Gross
- , Farnaz Mohammadi
- & Laura M. Heiser
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Article
| Open AccessIntracranial electrophysiological and structural basis of BOLD functional connectivity in human brain white matter
Whether connectivity in white matter detected by functional MRI relates to underlying electrophysiological synchronization is unclear. Here, the authors show that blood-oxygenation-level-dependent (BOLD) functional connectivity and intracranial stereotactic-electroencephalography (SEEG) connectivity are correlated across a wide range of frequency bands.
- Yali Huang
- , Peng-Hu Wei
- & Guoguang Zhao
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Article
| Open AccessTransparent tissue in solid state for solvent-free and antifade 3D imaging
Current liquid-based optical clearing protocols can suffer from solvent evaporation and photobleaching. Here, the authors develop a solid high-refractive-index polymer to embed mouse and human tissues for clearing and antifade high-resolution 3D imaging.
- Fu-Ting Hsiao
- , Hung-Jen Chien
- & Shiue-Cheng Tang
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Article
| Open AccessEvaluation of therapeutic PD-1 antibodies by an advanced single-molecule imaging system detecting human PD-1 microclusters
Immune checkpoint inhibitors are now routinely used in cancer therapy, however, the dosage and integration into conventional cancer therapy is determined via empirical experience rather than mechanistic rationale. Here authors establish an advanced single-molecule imaging method, by with which they are directly monitoring and evaluating the effect of immune checkpoint inhibitors on T cell signaling.
- Wataru Nishi
- , Ei Wakamatsu
- & Tadashi Yokosuka
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Article
| Open AccessHierarchical fluctuation shapes a dynamic flow linked to states of consciousness
The neuroanatomical basis of consciousness is not fully understood. Here the authors show that a global state of consciousness might not depend on a specific brain region or location in Euclidean space; rather, it is linked to a low-dimensional dynamic pattern in topological space, as shown through the analysis of different experimental paradigms, imaging techniques, and species.
- Ang Li
- , Haiyang Liu
- & Bing Liu
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Article
| Open AccessParallel interrogation of the chalcogenide-based micro-ring sensor array for photoacoustic tomography
The authors report a highly sensitive chalcogenide-based micro-ring sensor array for photoacoustic tomography and develops a compatible parallel interrogation means by synthesizing a digital optical frequency comb. Imaging is demonstrated on fast-moving objects, leaf veins, and live zebrafish.
- Jingshun Pan
- , Qiang Li
- & Zhaohui Li
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Article
| Open AccessQuantitative structured illumination microscopy via a physical model-based background filtering algorithm reveals actin dynamics
Quantitative live-cell superresolution imaging that maintains the linearity of fluorescence signals remains difficult. Here, the authors propose a physical model-based background filtering method for 2D-SIM, which allows for quantitative imaging and high signal completeness.
- Yanquan Mo
- , Kunhao Wang
- & Liangyi Chen
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Article
| Open AccessWound infiltrating adipocytes are not myofibroblasts
Adipocyte plasticity during injury repair is debated. Here, the authors find that injury causes temporary adipocyte migration, but without lineage conversion to myofibroblasts. Distinct migration patterns, transcriptomics and ECM depositions indicate that adipocytes, unlike fibroblasts, do not contribute to fibrotic scars.
- Shruthi Kalgudde Gopal
- , Ruoxuan Dai
- & Yuval Rinkevich
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Article
| Open AccessNear-lifespan longitudinal tracking of brain microvascular morphology, topology, and flow in male mice
Brain vascular impairment may occur early in diseases such as Alzheimer’s disease. Here the authors longitudinally study brain vascular dynamics in mice using advanced optical coherence tomography and deep learning algorithms, which enables tracking of slow vascular decline in aging and models of disease.
- Konrad W. Walek
- , Sabina Stefan
- & Jonghwan Lee
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Article
| Open AccessUsing mass spectrometry imaging to map fluxes quantitatively in the tumor ecosystem
Isotopologue spectral analysis was originally designed to assess metabolic fluxes from bulk samples. Here, the authors adapted this approach to infer fluxes from discrete regions in tissue by using mass spectrometry imaging, showing increased fatty acid synthesis flux in brain tumors of mice.
- Michaela Schwaiger-Haber
- , Ethan Stancliffe
- & Gary J. Patti
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Article
| Open AccessSingle-frame deep-learning super-resolution microscopy for intracellular dynamics imaging
Multi-frame super-resolution microscopy is hampered by long acquisition times and phototoxicity, which hinder its use for live-cell imaging. Here, authors propose a deep-learning-based single-frame super-resolution approach to image cellular dynamics with high spatiotemporal resolution.
- Rong Chen
- , Xiao Tang
- & Shuhuai Yao
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Article
| Open AccessA local water molecular-heating strategy for near-infrared long-lifetime imaging-guided photothermal therapy of glioblastoma
Neodymium (Nd)-doped nanoparticles have been described for imaging-guided photothermal therapy. Here the authors design a Nd-Yb co-doped nanomaterial as nearinfrared long-lifetime imaging-guided waterheating probe, showing photothermal ablation in a glioblastoma pre-clinical mode
- Dongkyu Kang
- , Hyung Shik Kim
- & Joonseok Lee
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Article
| Open AccessSpatial metabolomics reveals glycogen as an actionable target for pulmonary fibrosis
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
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Article
| Open AccessIn vivo bioluminescence imaging of natural bacteria within deep tissues via ATP-binding cassette sugar transporter
Bioluminescent imaging of bacteria in vivo generally requires the use of engineered bacteria. Here the authors take advantage of bacteria specific ATP-binding cassette sugar transporters to enable selective delivery of bioluminescent nanoprobes into bacteria for visualisation, including in deep tissues.
- Qian Zhang
- , Bin Song
- & Yao He
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Article
| Open AccessHybrid photoacoustic and fast super-resolution ultrasound imaging
Dual photoacoustic and fast super-resolution ultrasound imaging technique bridges the physiological and structural details in vivo. The authors demonstrated that this interleaved technology allows revealing the transient changes of blood flow and blood oxygenation over time.
- Shensheng Zhao
- , Jonathan Hartanto
- & Yun-Sheng Chen
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Article
| Open AccessFunctional MRI reveals brain-wide actions of thalamically-initiated oscillatory activities on associative memory consolidation
Thalamic spindle activities may support memory consolidation. Here the authors show that optogenetically-evoked somatosensory thalamic spindle-like activity enhances memory performance in male rats.
- Xunda Wang
- , Alex T. L. Leong
- & Ed X. Wu
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Article
| Open AccessInsights into receptor structure and dynamics at the surface of living cells
It is challenging to approach protein structures in living cells. Here the authors investigate Interleukin-4 receptor alpha, which has a noncanonical amino acid incorporated at different locations, and see that evaluating click efficiency with calibrated imaging gives information on structure-related properties.
- Frederik Steiert
- , Peter Schultz
- & Thomas Weidemann
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Article
| Open AccessMultiplex translaminar imaging in the spinal cord of behaving mice
Fluorescence imaging of the spinal cord poses challenges, including depth of imaging. Here the authors describe a custom microscope and chronically implanted microprism that enables multicolor translaminar imaging of sensory and motor evoked activity in behaving mice, and show that spinal astrocytes show sensorimotor program-dependent calcium excitation.
- Pavel Shekhtmeyster
- , Erin M. Carey
- & Axel Nimmerjahn
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Article
| Open AccessThe structural flexibility of MAD1 facilitates the assembly of the Mitotic Checkpoint Complex
The formation of the mitotic checkpoint complex requires an intricate spatial coordination amongst the proteins Bub1, Mad1, Cdc20, and Mad2. Chen et al show that a structural flexibility in Mad1 plays an essential role in achieving this coordination.
- Chu Chen
- , Valentina Piano
- & Ajit P. Joglekar
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Article
| Open AccessSpatial profiling of microbial communities by sequential FISH with error-robust encoding
Spatial analysis of microbiomes at single cell resolution is challenging. Here the authors report a highly multiplexed method for spatial profiling, sequential error-robust fluorescence in situ hybridisation (SEER-FISH), and show that this allows mapping of microbial communities at micron-scale.
- Zhaohui Cao
- , Wenlong Zuo
- & Lei Dai
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Article
| Open Access1,2,4,5-Tetrazine-tethered probes for fluorogenically imaging superoxide in live cells with ultrahigh specificity
Specific detection of cellular superoxide is challenging. Here, the authors designed 1,2,4,5-tetrazine based fluorogenic probes for specific and sensitive imaging of superoxide, and applied them in high throughput screening of modulators of oxidative stress.
- Xuefeng Jiang
- , Min Li
- & Xin Li
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Article
| Open AccessChemogenetic attenuation of cortical seizures in nonhuman primates
Pharmacological and surgical treatments of epilepsy can have unsatisfactory outcomes, so a more targeted and on-demand approach is desirable. Here, the authors demonstrate the usage of inhibitory chemogenetics in male nonhuman primates to attenuate the magnitude and spread of cortical seizures and subsequent body convulsions.
- Naohisa Miyakawa
- , Yuji Nagai
- & Takafumi Minamimoto
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Article
| Open AccessBright Tm3+-based downshifting luminescence nanoprobe operating around 1800 nm for NIR-IIb and c bioimaging
Fluorescence imaging in the near-infrared region yields high-quality images that overcome the current depth limitations. Here, the authors report a Tm3 + -based nanoprobe for NIR-IIb/c imaging, providing references to future bioimaging beyond 1700 nm.
- Yulei Chang
- , Haoren Chen
- & Xianggui Kong
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Article
| Open AccessMolecular imaging of liver inflammation using an anti-VCAM-1 nanobody
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
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Article
| Open AccessVisualizing orthogonal RNAs simultaneously in live mammalian cells by fluorescence lifetime imaging microscopy (FLIM)
No multi-color RNA fluorescent tags are currently available for use in live cells. Here, the authors show that fluorescence lifetime imaging microscopy is advantageous for multiplexed RNA visualization while achieving robust cellular contrast.
- Nadia Sarfraz
- , Emilia Moscoso
- & Esther Braselmann
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Article
| Open AccessIntrinsic macroscale oscillatory modes driving long range functional connectivity in female rat brains detected by ultrafast fMRI
The mechanisms which generate fMRI signal correlations across the brain are not fully understood. Here, the authors record ultrafast fMRI signals in anesthetized female rats to demonstrate intrinsic macroscale oscillatory modes which drive correlated activity between distant regions.
- Joana Cabral
- , Francisca F. Fernandes
- & Noam Shemesh
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Article
| Open AccessA FRET-based respirasome assembly screen identifies spleen tyrosine kinase as a target to improve muscle mitochondrial respiration and exercise performance in mice
Mitochondrial supercomplex assembly may efficiently supply energy, yet its role remains controversial. Here, the authors show that SYK inhibitors increase supercomplex assembly and mitochondrial respiration in cells and can enhance exercise performance in mice.
- Ami Kobayashi
- , Kotaro Azuma
- & Satoshi Inoue
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Article
| Open AccessRevealing the tissue-level complexity of endogenous glucagon-like peptide-1 receptor expression and signaling
Visualizing endogenous GPCRs is challenging. Here the authors generate mice with an enzyme self-label genome-edited into the endogenous glucagon-like peptide-1 receptor locus, design fluorescent dyes for specific labelling in complex tissue, and reveal tissue-level organisation and dynamics of an endogenous class B GPCR.
- Julia Ast
- , Daniela Nasteska
- & David J. Hodson
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Article
| Open AccessAn optofluidic platform for interrogating chemosensory behavior and brainwide neural representation in larval zebrafish
Studying chemosensory processing desires precise chemical cue presentation, behavioral response monitoring, and large-scale neuronal activity recording. Here, the authors report a fluidics-based toolkit for studying chemosensation in larval zebrafish, and used it to reveal the brainwide neural representations of cadaverine sensing and its binasal input-dependent behavioral avoidance.
- Samuel K. H. Sy
- , Danny C. W. Chan
- & Ho Ko
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Article
| Open AccessComputational conjugate adaptive optics microscopy for longitudinal through-skull imaging of cortical myelin
The authors realize longitudinal deep-brain imaging through an intact mouse skull by constructing a high-speed reflection matrix microscope at 1.3 µm wavelength and developing a computational conjugate adaptive optics algorithm eliminating skull aberrations.
- Yongwoo Kwon
- , Jin Hee Hong
- & Wonshik Choi
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Article
| Open AccessFilamin A organizes γ‑aminobutyric acid type B receptors at the plasma membrane
GABAB receptors mediate the effects of the main inhibitory neurotransmitter in the brain. Here, authors identify the cytoskeletal protein filamin A as a key player that controls the exact location and function of GABAB receptors at the cell surface.
- Marie-Lise Jobin
- , Sana Siddig
- & Davide Calebiro
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Article
| Open AccessEngineering inducible biomolecular assemblies for genome imaging and manipulation in living cells
Imaging non-repetitive loci in living cells remains challenging. Here, the authors engineered an inducible system whereby biomolecular assemblies can be guided to specific genomic loci by a nuclease-defective Cas9, allowing the simultaneous imaging and manipulation of the loci.
- Qin Peng
- , Ziliang Huang
- & Yingxiao Wang
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Article
| Open AccessTiltable objective microscope visualizes selectivity for head motion direction and dynamics in zebrafish vestibular system
Signals about head orientation and movement in the vestibular periphery are fundamental to the sense of balance and motion, but difficult to measure systematically during head motion. Here, the authors build a microscope that visualizes neural activity in hair cells and vestibular ganglion cells during 360° head tilt and vibration in zebrafish larvae, and reveal a topographic organization of direction- and static/dynamic stimulus-selective responses.
- Masashi Tanimoto
- , Ikuko Watakabe
- & Shin-ichi Higashijima
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Article
| Open AccessAchieving single nucleotide sensitivity in direct hybridization genome imaging
Visualisation of point mutations in situ is informative for studying genetic diseases. Here the authors report single guide genome oligopaint via local denaturation fluorescence in situ hybridisation, sgGOLDFISH, a direct hybridisation genome imaging method with single-nucleotide sensitivity.
- Yanbo Wang
- , W. Taylor Cottle
- & Taekjip Ha
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Article
| Open AccessIn-depth mapping of protein localizations in whole tissue by micro-scaffold assisted spatial proteomics (MASP)
Accurate protein mapping on whole-tissue levels provides critical insights into diseases/therapies. Here, the authors described a novel spatial proteomics method, based on tissue compartmentalization using a 3D-printed micro-scaffold, generated thousands of protein maps across a whole-tissue slice.
- Min Ma
- , Shihan Huo
- & Jun Qu
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Article
| Open AccessNext generation genetically encoded fluorescent sensors for serotonin
Genetically encoded sensors have been developed and become versatile tools for imaging serotonin dynamics. Here, authors developed a family of serotonin (5-HT) sensors (sDarken), three variants with different affinities for 5-HT enable high spatiotemporal resolution of 5-HT dynamics.
- Martin Kubitschke
- , Monika Müller
- & Olivia Andrea Masseck
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Article
| Open AccessGraph-based autoencoder integrates spatial transcriptomics with chromatin images and identifies joint biomarkers for Alzheimer’s disease
Methods for jointly analysing the different spatial data modalities in 3D are lacking. Here the authors report the computational framework STACI (Spatial Transcriptomic data using over-parameterized graph-based Autoencoders with Chromatin Imaging data) which they apply to an Alzheimer’s disease mouse model.
- Xinyi Zhang
- , Xiao Wang
- & Caroline Uhler
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Article
| Open AccessExtending resolution within a single imaging frame
The presented Mean-Shift Super Resolution (MSSR) algorithm can extend spatial resolution within a single microscopy image. Its applicability extends across a wide range of experimental and instrumental configurations and it is compatible with other super-resolution microscopy approaches.
- Esley Torres-García
- , Raúl Pinto-Cámara
- & Adán Guerrero
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Article
| Open AccessThe BrightEyes-TTM as an open-source time-tagging module for democratising single-photon microscopy
The authors developed an open-source, low-cost, multi-channel time-tagging module for fluorescence lifetime image scanning microscopy and correlation spectroscopy that can tag in parallel multiple single-photon events with 30 ps precision.
- Alessandro Rossetta
- , Eli Slenders
- & Giuseppe Vicidomini
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Article
| Open AccessAcousto-holographic reconstruction of whole-cell stiffness maps
Traditional methods for cell stiffness measurements are limited by long processing times and unsuitability for multiple cell analysis. Here, the authors demonstrate a fast technique based on acoustic stimulation and holographic imaging to reconstruct whole-cell stiffness maps of individual and multiple cells.
- Rahmetullah Varol
- , Zeynep Karavelioglu
- & Huseyin Uvet
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Article
| Open AccessGene activation guided by nascent RNA-bound transcription factors
Gene activation methods are valuable for studying gene functions and may have potential applications in bioengineering and medicine. Here the authors developed Narta technology to achieve gene activation by recruiting artificial transcription factors to transcription sites through nascent RNAs of the target gene.
- Ying Liang
- , Haiyue Xu
- & Baohui Chen
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Article
| Open AccessThe molecular organization of differentially curved caveolae indicates bendable structural units at the plasma membrane
Caveolae can bend and flatten, but how this is regulated is not well understood. Authors use correlative super-resolution light and electron microscopy to map the key proteins that mediate curvature of the caveolar coat.
- Claudia Matthaeus
- , Kem A. Sochacki
- & Justin W. Taraska
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Article
| Open AccessHigh-precision estimation of emitter positions using Bayesian grouping of localizations
Single-molecule localization microscopy relies on stochastic blinking events, treated as independent events without assignment to a particular emitter. Here, BaGoL takes low precision localizations generated from multiple emitter blinkings during DNAPAINT and dSTORM and finds the underlying emitter positions with high precision.
- Mohamadreza Fazel
- , Michael J. Wester
- & Keith A. Lidke
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Article
| Open AccessMultiplexed and reproducible high content screening of live and fixed cells using Dye Drop
It is currently difficult to perform accurate single-cell assays in 384-well plates. Here the authors report Dye Drop which uses sequential density displacement and microscopy for multi-step assays on cells, and use this to collect single-cell dose-response data for small molecules in breast cancer cells.
- Caitlin E. Mills
- , Kartik Subramanian
- & Peter K. Sorger
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Article
| Open AccessSharp-wave ripple doublets induce complex dendritic spikes in parvalbumin interneurons in vivo
The influence of sharp-wave ripples (SPW-Rs) on dendritic computation remains poorly understood. Here, the authors demonstrate the existence of SPW-R associated, branch-specific, dendritic spikes which serve as a temporal and spatial coincidence detectors during SPW-R-doublets in PV+ interneuron dendrites of awake mice.
- Linda Judák
- , Balázs Chiovini
- & Balázs Rózsa
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Article
| Open AccessDiffusion MRI anisotropy in the cerebral cortex is determined by unmyelinated tissue features
In gray matter, the relative contributions of myelinated axons and other tissue features to diffusion MRI (dMRI) are poorly understood. Here the authors combine ex vivo high-resolution dMRI of marmoset brain with histological sections of the same brain, and their findings suggest that in cortex, dMRI does not match the spatial distribution of myelin in the gray matter.
- Colin Reveley
- , Frank Q. Ye
- & David A. Leopold
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Article
| Open AccessLong-term monitoring of intravital biological processes using fluorescent protein-assisted NIR-II imaging
The retention time and toxicity of synthetic NIR-II fluorophores limit long-term application. Here the authors use infrared fluorescent proteins (iRFPs) as NIR-II probes for prolonged continuous imaging in mice, and generate a transgenic mouse model which they use to image liver and pancreas.
- Muxiong Chen
- , Zhe Feng
- & Zhengping Xu
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Article
| Open AccessA genetically encoded fluorescent biosensor for detecting itaconate with subcellular resolution in living macrophages
Itaconate has been identified as an immunomodulatory metabolite produced by activated macrophages, but methods for detecting itaconate in live cells are lacking. Here, the authors develop a fluorescent biosensor named BioITA for detecting itaconate in subcellular compartments of living macrophages.
- Pengkai Sun
- , Zhenxing Zhang
- & Xinjian Li
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Article
| Open AccessOptical gearbox enabled versatile multiscale high-throughput multiphoton functional imaging
The authors develop an optical gearbox to accelerate the laser scanning microscopes, achieving flexible adjustment of imaging frame rate from tens of Hz to 1 kHz. The technology is validated through in vivo functional imaging of mice brains.
- Jianian Lin
- , Zongyue Cheng
- & Meng Cui
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