Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy

An AIE-active near-infrared molecular probe for migrasome labeling

Migrasomes, newly identified organelles, play crucial roles in various physiological and pathological activities, including embryogenesis, immune responses, wound healing, and metastasis of cancer cells. Migrasome visualization is essential for the deep exploration of migrasome biology. Despite the reported labeling methods based on migrasome marker proteins, a simple and convenient method for migrasome labeling is more desirable compared to the complicated transfection technique. Here, an aggregation-induced emission (AIE) based near-infrared (NIR) molecular probe named TTCPy was presented, which can bind to the phospholipid on migrasomes and light up migrasomes with a turn-on NIR fluorescence. TTCPy allows for high-performance imaging of migrasomes in both live cells and living chorioallantoic membranes via simple and rapid staining. Moreover, TTCPy achieves live-cell super-resolution imaging of migrasomes, affording remarkedly improved spatial resolution and signal-to-background ratio. This work offers a simple yet powerful tool for migrasome visualization and will contribute to the booming hotspot of migrasome biology.

Advancing biosensing through super-resolution fluorescence microscopy

Advancement of super-resolution fluorescence microscopy (SRM) has recently allowed applications to the biosensing by offering significant advantages over conventional methods. Its nanoscale spatial resolution and single-molecule sensitivity allow visualization and quantification of biomolecular targets without the need of signal amplification steps typically required in traditional biosensing methods. Moreover, recent innovations in probe design and imaging protocols have expanded SRM capabilities to enable dynamic biosensing in living cells, revealing molecular processes in their native cellular contexts. In this review, we discuss these applications of various SRM techniques to biosensing by highlighting their unique capabilities in providing spatial distribution information and high molecular sensitivity. We address several challenges that must be overcome for the broader application of SRM-based biosensing. Finally, we discuss perspectives on future directions for advancing this field towards practical applications.

Super-resolution imaging informed scRNA sequencing analysis reveals the critical role of GDF15 in rejuvenating aged hematopoietic stem cells

Although changes in mitochondrial morphology consistently associated with the aging of hematopoietic stem cells (HSCs), the specific molecular and cellular mechanisms involved are partially unclear. Live-cell super-resolution (SR) microscopy has been used to identify distinct HSC subsets that characterized by mitochondria unique morphologies and spatial distributions. The integration of SR microscopy with single-cell RNA sequencing enabled the classification of approximately 200 HSCs from young and aged mice into 5 discrete clusters. These clusters displayed molecular profiles that corresponded to the observed mitochondria states. An integrated approach combining RNA biomarker analysis and potential regulon assessment revealed previously unrecognized roles of GDF15 in mediating mitochondrial signals and morphologies that influence HSC fate. Thus, combining SR imaging with a bioinformatics pipeline provides an effective method for identifying key molecular players in specific phases of cellular transition, even with a relatively small dataset.

Dark-based optical sectioning assists background removal in fluorescence microscopy

In fluorescence microscopy, a persistent challenge is the defocused background that obscures cellular details and introduces artifacts. Here, we introduce Dark sectioning, a method inspired by natural image dehazing for removing backgrounds that leverages dark channel prior and dual frequency separation to provide single-frame optical sectioning. Unlike denoising or deconvolution, Dark sectioning specifically targets and removes out-of-focus backgrounds, stably improving the signal-to-background ratio by nearly 10 dB and structural similarity index measure of images by approximately tenfold. Dark sectioning was validated using wide-field, confocal, two/three-dimensional structured illumination and one/two-photon microscopy with high-fidelity reconstruction. We further demonstrate its potential to improve the segmentation accuracy in deep tissues, resulting in better recognition of neurons in the mouse brain and accurate assessment of nuclei in prostate lesions or mouse brain sections. Dark sectioning is compatible with many other microscopy modalities, including light-sheet and light-field microscopy, as well as processing algorithms, including deconvolution and super-resolution optical fluctuation imaging.

Physics-driven self-supervised learning for fast high-resolution robust 3D reconstruction of light-field microscopy

Light-field microscopy (LFM) and its variants have significantly advanced intravital high-speed 3D imaging. However, their practical applications remain limited due to trade-offs among processing speed, fidelity, and generalization in existing reconstruction methods. Here we propose a physics-driven self-supervised reconstruction network (SeReNet) for unscanned LFM and scanning LFM (sLFM) to achieve near-diffraction-limited resolution at millisecond-level processing speed. SeReNet leverages 4D information priors to not only achieve better generalization than existing deep-learning methods, especially under challenging conditions such as strong noise, optical aberration, and sample motion, but also improve processing speed by 700 times over iterative tomography. Axial performance can be further enhanced via fine-tuning as an optional add-on with compromised generalization. We demonstrate these advantages by imaging living cells, zebrafish embryos and larvae, Caenorhabditis elegans, and mice. Equipped with SeReNet, sLFM now enables continuous day-long high-speed 3D subcellular imaging with over 300,000 volumes of large-scale intercellular dynamics, such as immune responses and neural activities, leading to widespread practical biological applications.

Targeting the Galectin-7/TRPM2/Zn2+/DRP-1 Signaling Pathway: A Potential Therapeutic Intervention in the Pathogenesis of SJS/TEN

BACKGROUND

Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) represent a spectrum of severe drug-induced cutaneous reactions. These conditions are characterized by widespread and confluent keratinocyte apoptosis, which differentiates them from erythema multiforme (EM). Mounting evidence has implicated the mitochondrial-dependent apoptosis pathway in the pathogenesis of SJS/TEN, but the potential roles and specific mechanisms of these pathways in SJS/TEN remain largely unexplored.

METHODS

Proteomic analyses were conducted to investigate differential protein expression in blister fluid (BF)-derived exosomes from suction surgery in healthy individuals (Con Exo) or patients with EM (EM Exo) or SJS/TEN (TEN Exo). Further analysis involved glutathione S-transferase (GST) pull-down assay, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, and validation of MS results through proximity ligation assay (PLA) and coimmunoprecipitation (co-IP). Phenotypic and mechanistic analyses were performed using immunohistochemistry (IHC) staining, enzyme-linked immunosorbent assay (ELISA), western blotting, reverse transcription-polymerase chain reaction (RT-PCR), co-IP, CCK-8 assay, adenosine triphosphate (ATP) level measurements, and flow cytometry.

RESULTS

Galectin-7 was markedly upregulated in BF-derived exosomes from SJS/TEN patients and showed a correlation with disease severity. Further analysis confirmed the interaction between galectin-7 and transient receptor potential (melastatin) 2 (TRPM2). BF-derived exosomes from SJS/TEN patients induced an imbalance in mitochondrial dynamics via galectin-7/TRPM2 upregulation. Activation of TRPM2 led to an elevation in mitochondrial Zn2+, which facilitated the recruitment of the fission factor dynamin-related protein-1 (DRP-1) to mitochondria to trigger mitochondrial fission in the keratinocyte. In addition, the recruitment of DRP-1-dependent mitochondrial fission via the voltage-dependent anion channel 1 (VDAC1)/hexokinase 2 (HK2)-mediated opening of the mitochondrial permeability transition pore (mPTP)-triggered cytochrome c release. These effects ultimately induce activation of the intrinsic mitochondrial apoptotic pathway and contribute to the pathogenesis of SJS/TEN.

CONCLUSIONS

Targeting the galectin-7/TRPM2/Zn2+/DRP-1 signaling pathway in keratinocytes presents a prospective therapeutic strategy for mitigating SJS/TEN in the future.

Recent Advances in Structured Illumination Microscopy: From Fundamental Principles to AI-Enhanced Imaging

Structured illumination microscopy (SIM) has emerged as a pivotal super-resolution technique in biological imaging. This review aims to introduce the fundamental principles of SIM, primarily focuses on the latest developments in super-resolution SIM imaging, such as the light illumination and modulation devices, and the image reconstruction algorithms. Additionally, the application of deep learning (DL) technology in SIM imaging is explored, which is employed to enhance image quality, accelerate imaging and reconstruction speed or replace the current image reconstruction method. Furthermore, the key evaluation metrics are proposed and discussed for assessment of deep-learning neural networks, especially for their employment in SIM. Finally, the future integration of artificial intelligence (AI) with SIM system and the perspective of smart microscope are also discussed.

Recruitment of Atg1 to the phagophore by Atg8 orchestrates autophagy machineries

Autophagy-related (Atg) proteins catalyze autophagosome formation at the phagophore assembly site (PAS). The assembly of Atg proteins at the PAS follows a semihierarchical order, in which Atg8 is thought to be quite downstream but still able to control the size of autophagosomes. Yet, how Atg8 coordinates multiple branches of autophagy machinery to regulate autophagosomal size is not clear. Here, we show that, in yeast, Atg8 positively regulates the autophagy-specific phosphatidylinositol 3-OH kinase complex and the retrograde trafficking of Atg9 vesicles through interaction with Atg1. Mechanistically, Atg8 does not enhance the kinase activity of Atg1; instead, it recruits Atg1 to the surface of the phagophore likely to orient Atg1's activity toward select substrates, leading to efficient phagophore expansion. Artificial tethering of Atg1 kinase domains to Atg8s enhanced autophagy in yeast, human and plant cells and improved muscle performance in worms. We propose that Atg8-mediated relocation of Atg1 from the PAS scaffold to the phagophore is a critical step in positive autophagy regulation.

Highly dynamic and sensitive NEMOer calcium indicators for imaging ER calcium signals in excitable cells

The Endoplasmic/sarcoplasmic reticulum (ER/SR) is central to calcium (Ca2+) signaling, yet current genetically encoded Ca2+ indicators (GECIs) cannot detect elementary Ca2+ release events from ER/SR, particularly in muscle cells. Here, we report NEMOer, a set of organellar GECIs, to efficiently capture ER Ca2+ dynamics with increased sensitivity and responsiveness. NEMOer indicators exhibit dynamic ranges an order of magnitude larger than G-CEPIA1er, enabling 2.7-fold more sensitive detection of Ca2+ transients in both non-excitable and excitable cells. The ratiometric version further allows super-resolution monitoring of local ER Ca2+ homeostasis and dynamics. Notably, NEMOer-f enabled the inaugural detection of Ca2+ blinks, elementary Ca2+ releasing signals from the SR of cardiomyocytes, as well as in vivo spontaneous SR Ca2+ releases in zebrafish. In summary, the highly dynamic NEMOer sensors expand the repertoire of organellar Ca2+ sensors that allow real-time monitoring of intricate Ca2+ dynamics and homeostasis in live cells with high spatiotemporal resolution.

A Multi-Modal Light Sheet Microscope for High-Resolution 3D Tomographic Imaging with Enhanced Raman Scattering and Computational Denoising

Three-dimensional (3D) cellular models, such as spheroids, serve as pivotal systems for understanding complex biological phenomena in histology, oncology, and tissue engineering. In response to the growing need for advanced imaging capabilities, we present a novel multi-modal Raman light sheet microscope designed to capture elastic (Rayleigh) and inelastic (Raman) scattering, along with fluorescence signals, in a single platform. By leveraging a shorter excitation wavelength (532 nm) to boost Raman scattering efficiency and incorporating robust fluorescence suppression, the system achieves label-free, high-resolution tomographic imaging without the drawbacks commonly associated with near-infrared modalities. An accompanying Deep Image Prior (DIP) seamlessly integrates with the microscope to provide unsupervised denoising and resolution enhancement, preserving critical molecular details and minimizing extraneous artifacts. Altogether, this synergy of optical and computational strategies underscores the potential for in-depth, 3D imaging of biomolecular and structural features in complex specimens and sets the stage for future advancements in biomedical research, diagnostics, and therapeutics.

Bright and photostable yellow fluorescent proteins for extended imaging

Fluorescent proteins are indispensable molecular tools for visualizing biological structures and processes, but their limited photostability restricts the duration of dynamic imaging experiments. Yellow fluorescent proteins (YFPs), in particular, photobleach rapidly. Here, we introduce mGold2s and mGold2t, YFPs with up to 25-fold greater photostability than mVenus and mCitrine, two commonly used YFPs, while maintaining comparable brightness. These variants were identified using a high-throughput pooled single-cell platform, simultaneously screening for high brightness and photostability. Compared with our previous benchmark, mGold, the mGold2 variants display a ~4-fold increase in photostability without sacrificing brightness. mGold2s and mGold2t extend imaging durations across diverse modalities, including widefield, total internal reflection fluorescence (TIRF), super-resolution, single-molecule, and laser-scanning confocal microscopy. When incorporated into fluorescence resonance energy transfer (FRET)-based biosensors, the proposed YFPs enable more reliable, prolonged imaging of dynamic cellular processes. Overall, the enhanced photostability of mGold2s and mGold2t enables high-sensitivity imaging of subcellular structures and cellular activity over extended periods, broadening the scope and precision of biological imaging.

Mapping Dynamic Protein Clustering with AIEgen-Active Chemigenetic Probe

Protein clustering/disassembling is a fundamental process in biomolecular condensates, playing a crucial role in cell fate decision and cellular homeostasis. However, the inherent features of protein clustering, especially for its reversible behavior and subtle microenvironment variation, present significant hurdles in probe chemistry for tracking protein clustering dynamics. Herein, we report a bilateral-tailored chemigenetic probe, in which an "amphiphilic" aggregate-induced emission luminogen (AIEgen) QMSO3Cl is covalently conjugated to a protein tag that is genetically fused to protein-of-interest (POI). Prior to target POI, the "amphiphilic" AIE-active QMSO3Cl achieves a completely dark state in both aqueous biological environment and lipophilic organelles, thereby ensuring an ultra-low intrinsic background interference. Upon reaching POI, the combination of synthetic molecule and genetically encoded protein allows for protein clustering-dependent ultra-sensitive response, with a substantial lighting-up fluorescence (67.5-fold) as protein transitions from disassembling to clustering state. Such ultra-high signal-to-noise ratio enables to monitor the dynamic and fate of inositol requiring enzyme 1 (IRE1) clustering/disassembling under both acute and chronic endoplasmic reticulum (ER) stress in living cells. For the first time, we have demonstrated the use of chemigenetic probe to reveal therapy-induced ER stress and screen drugs in a three-dimensional scenario: microviscosity change, clustering dynamic, and cluster morphology. This chemigenetic probe design strategy would greatly facilitate the advancement of mapping protein dynamics in cell homeostasis and medicine research.

Hyperspectral Metachip-Based 3D Spatial Map for Cancer Cell Screening and Quantification

In this paper, compact terahertz (THz) metachips for hyperspectral screening and quantitative evaluation of human cancer cells is reported. This pixelated resonant metachips feature the resonance channel from 1 and 3 THz frequency with a record-high quality factor (up to 230). Through the interactions of various cancer cells of different concentrations, high-dimensional spectral signatures are obtained, which are further transformed into a spatial map for labelling and quantification purposes. The screening of up to 15 cancer cells is experimentally reported, with very high detecting accuracy of 93.33% and with attractive quantitative concentration sensitivity up to 1320 kHz cell mL-1. This hyperspectral metachips are low-cost, highly compact, and label-free for fast, high-throughput and high-sensitivity detections and evaluation of human cancer cells. This technology does not require clinical experience, representing an accessible technology for early diagnosis of cancer.

Highly spatial-temporal electrochemical profiling of molecules trafficking at a single mitochondrion in one living cell

Simultaneous profiling of multiple molecules trafficking at a single organelle and the surrounding cytosol within a living cell is crucial for elucidating their functions, necessitating advanced techniques that provide high spatial-temporal resolution and molecule specificity. In this study, we present an electrochemical nanodevice based on a θ-nanopipette designed to coanalyze calcium ions (Ca2+) and reactive oxygen species (ROS) at a single mitochondrion and its surrounding cytosol, thereby enhancing our understanding of their trafficking within the signaling pathways of cellular autophagy. Two independent nanosensors integrated within the channels of the θ-nanopipette spatially isolate a single target mitochondrion from the cytosol and simultaneously measure the release of Ca2+ and ROS with high spatial-temporal resolution. Dynamic tracking reveals the direct trafficking of lysosomal Ca2+ to the mitochondrion rather than to the cytosol, which triggers ROS-induced ROS release within the mitochondria. Furthermore, highly temporal and concurrent observations revealed a second burst of Ca2+ in both the mitochondrion and the cytosol, which is not consistent with the change in ROS. These dynamic data elucidate the potential role of a beneficial feedback loop between the Ca2+ signaling pathway and the subsequent generation of mitochondrial ROS in ML-SA-induced autophagy. More importantly, this innovative platform facilitates detailed profiling of the molecular interactions between trafficking molecules within the mitochondria and the adjacent cytosolic environment, which is hardly realized using the current superresolution optical microscopy.

Asgard Arf GTPases can act as membrane-associating molecular switches with the potential to function in organelle biogenesis

Inward membrane budding, i.e., the bending of membrane towards the cytosol, is essential for forming and maintaining eukaryotic organelles. In eukaryotes, Arf GTPases initiate this inward budding. Our research shows that Asgard archaea genomes encode putative Arf proteins (AArfs). AArfs possess structural elements characteristic of their eukaryotic counterparts. When expressed in yeast and mammalian cells, some AArfs displayed GTP-dependent membrane targeting. In vitro, AArf associated with both eukaryotic and archaeal membranes. In yeast, AArfs interacted with and were regulated by key organelle biogenesis players. Expressing an AArf led to a massive proliferation of endomembrane organelles including the endoplasmic reticulum and Golgi. This AArf interacted with Sec23, a COPII vesicle coat component, in a GTP-dependent manner. These findings suggest certain AArfs are membrane-associating molecular switches with the functional potential to initiate organelle biogenesis, and the evolution of a functional coat could be the next critical step towards establishing eukaryotic cell architecture.

Advancing Super-Resolution Microscopy: Recent Innovations in Commercial Instruments

Super-resolution microscopy techniques have accelerated scientific progress, enabling researchers to explore cellular structures and dynamics with unprecedented detail. This review highlights the most recent developments in commercially available super-resolution microscopes, focusing on the most widely used techniques: confocal laser scanning systems, structured illumination microscopy (SIM), stimulated emission depletion (STED) microscopy, and single-molecule localization microscopy (SMLM). We detail the technological advancements of Confocal.NL's GAIA, Nikon's NSPARC, CSR Biotech's MI-SIM, Zeiss's Lattice SIM 5, Leica's STELLARIS STED, and abberior's STED and MINFLUX systems, as well as Abbelight's SAFe MN360 and Bruker's Vutara VXL SMLM platforms. These advancements address the need for enhanced resolution, reduced phototoxicity, and improved imaging capabilities in a range of sample types, while also aiming to enhance user friendliness.

CRSP8-driven fatty acid metabolism reprogramming enhances hepatocellular carcinoma progression by inhibiting RAN-mediated PPARα nucleus-cytoplasm shuttling

BACKGROUND

In-depth exploration into the dysregulation of lipid metabolism in hepatocellular carcinoma (HCC) has contributed to the development of advanced antitumor strategies. CRSP8 is a critical component of mediator multiprotein complex involved in transcriptional recruiting. However, the regulatory mechanisms of CRSP8 on fatty acid metabolism reprogramming and HCC progression remain unclear.

METHODS

In-silico/house dataset analysis, lipid droplets (LDs) formation, HCC mouse models and targeted lipidomic analysis were performed to determine the function of CRSP8 on regulating lipid metabolism in HCC. The subcellular colocalization and live cell imaging of LDs, transmission electron microscopy, co-immunoprecipitation and luciferase reporter assay were employed to investigate their potential mechanism.

RESULTS

CRSP8 was identified as a highly expressed oncogene essential for the proliferation and aggressiveness of HCC in vitro and in vivo. The tumor promotion of CRSP8 was accompanied by LDs accumulation and increased de novo fatty acids (FAs) synthesis. Moreover, CRSP8 diminished the colocalization between LC3 and LDs to impair lipophagy in a nuclear-localized PPARα-dependent manner, which decreased the mobilization of FAs from LDs degradation and hindered mitochondrial fatty acid oxidation. Mechanistically, the small ras family GTPase RAN was transcriptionally activated by CRSP8, leading to the reinforcement of RAN/CRM1-mediated nuclear export. CRSP8-induced enhanced formation of RAN/CRM1/PPARα nucleus-cytoplasm shuttling heterotrimer orchestrated cytoplasmic translocation of PPARα, attenuated nPPARα-mediated lipophagy and fatty acid catabolism, subsequently exacerbated HCC progression. In CRSP8-enriched HCC, lipid synthesis inhibitor Orlistat effectively reshaped the immunosuppressive tumor microenvironment (TME) and improved the efficacy of anti-PD-L1 therapy in vivo.

CONCLUSION

Our study establishes that CRSP8-driven fatty acid metabolism reprogramming facilitates HCC progression via the RAN/CRM1/PPARα nucleus-cytoplasm shuttling heterotrimer and impaired lipophagy-derived catabolism. Targeting the energy supply sourced from lipids could represent a promising therapeutic strategy for treating CRSP8-sufficient HCC.

BOOST: a robust ten-fold expansion method on hour-scale

Expansion microscopy enhances the microscopy resolution by physically expanding biological specimens and improves the visualization of structural and molecular details. Numerous expansion microscopy techniques and labeling methods have been developed over the past decade to cater to specific research needs. Nonetheless, a shared limitation among current protocols is the extensive sample processing time, particularly for challenging-to-expand biological specimens (e.g., formalin-fixed paraffin-embedded (FFPE) sections and large three-dimensional specimens). Here we present BOOST, a rapid and robust expansion microscopy workflow that leverages a series of microwave-accelerated expansion microscopy chemistry. Specifically, BOOST enables a single-step 10-fold expansion of cultured cells, tissue sections, and even the challenging-to-expand FFPE sections under 90 minutes. Notably, BOOST pioneers a 10-fold expansion of large millimeter-sized three-dimensional specimens, previously unattainable to the best of our knowledge. The workflow is also easily adaptable based on stable and common reagents, thus boosting the potential adoption of expansion microscopy for applications.

Chromatin assembly factor 1 subunit A promotes TLS pathway by recruiting E3 ubiquitin ligase RAD18 in cancer cells

The translesion DNA synthesis (TLS) pathway mediated by proliferating cell nuclear antigen (PCNA) monoubiquitination is an essential mechanism by which cancer cells bypass DNA damage caused by DNA damage to maintain genomic stability and cell survival. Chromatin assembly factor 1 subunit A (CHAF1A) traditionally promotes histone assembly during DNA replication. Here, we revealed that CHAF1A is a novel regulator of the TLS pathway in cancer cells. CHAF1A promotes restart and elongation of the replication fork under DNA replication stress. Mechanistically, the C-terminal domain of CHAF1A directly interacts with E3 ubiquitin ligase RAD18, enhancing RAD18 binding on the stalled replication fork. CHAF1A facilitates PCNA K164 monoubiquitination mediated by RAD18, thereby promoting the recruitment of Y-family DNA polymerases and enhancing cancer cell resistance to DNA damage. In addition, CHAF1A-mediated RAD18 recruitment and PCNA monoubiquitination are independent of the CHAF1A-PCNA interaction and its histone assembly function. Taken together, these findings improve our understanding of the mechanisms that regulate the TLS pathway and provide insights into the relationship between CHAF1A and DNA replication stress in cancer cells.

AKAP1/PKA-mediated GRP75 phosphorylation at mitochondria-associated endoplasmic reticulum membranes protects cancer cells against ferroptosis

Emerging evidence suggests that signaling pathways can be spatially regulated to ensure rapid and efficient responses to dynamically changing local cues. Ferroptosis is a recently defined form of lipid peroxidation-driven cell death. Although the molecular mechanisms underlying ferroptosis are emerging, spatial aspects of its signaling remain largely unexplored. By analyzing a public database, we found that a mitochondrial chaperone protein, glucose-regulated protein 75 (GRP75), may have a previously undefined role in regulating ferroptosis. This was subsequently validated. Interestingly, under ferroptotic conditions, GRP75 translocated from mitochondria to mitochondria-associated endoplasmic reticulum (ER) membranes (MAMs) and the cytosol. Further mechanistic studies revealed a highly spatial regulation of GRP75-mediated antiferroptotic signaling. Under ferroptotic conditions, lipid peroxidation predominantly accumulated at the ER, which activated protein kinase A (PKA) in a cAMP-dependent manner. In particular, a signaling microdomain, the outer mitochondrial membrane protein A-kinase anchor protein 1 (AKAP1)-anchored PKA, phosphorylated GRP75 at S148 in MAMs. This caused GRP75 to be sequestered outside the mitochondria, where it competed with Nrf2 for Keap1 binding through a conserved high-affinity RGD-binding motif, ETGE. Nrf2 was then stabilized and activated, leading to the transcriptional activation of a panel of antiferroptotic genes. Blockade of the PKA/GRP75 axis dramatically increased the responses of cancer cells to ferroptosis both in vivo and in vitro. Our identification a localized signaling cascade involved in protecting cancer cells from ferroptosis broadens our understanding of cellular defense mechanisms against ferroptosis and also provides a new target axis (AKAP1/PKA/GRP75) to improve the responses of cancer cells to ferroptosis.

Deep learning-driven automated high-content dSTORM imaging with a scalable open-source toolkit

Super-resolution microscopy offers the ability to visualize molecular structures in biological samples with unprecedented detail. However, the full potential of these techniques is often hindered by a lack of automated, user-independent workflows. Here, we present an open-source toolkit that automates dSTORM super-resolution microscopy using deep learning for segmentation and object detection. This standalone program enables reliable segmentation of diverse biomedical images, even in low-contrast samples, surpassing existing solutions. Integrated into the imaging pipeline, it rapidly processes high-content data in minutes, reducing manual labor. Demonstrated by biological examples, such as microtubules in cell culture and the βII-spectrin in nerve fibers, our approach makes super-resolution imaging faster, more robust, and easy to use, even by nonexperts. This broadens its potential applications in biomedicine, including high-throughput experimentation.

Host cytoskeleton and membrane network remodeling in the regulation of viral replication

Viral epidemics pose major threats to global health and economies. A hallmark of viral infection is the reshaping of host cell membranes and cytoskeletons to form organelle-like structures, known as viral factories, which support viral genome replication. Viral infection in many cases induces the cytoskeletal network to form cage-like structures around viral factories, including actin rings, microtubule cages, and intermediate filament cages. Viruses hijack various organelles to create these replication factories, such as viroplasms, spherules, double-membrane vesicles, tubes, and nuclear viral factories. This review specifically examines the roles of cytoskeletal elements and the endomembrane system in material transport, structural support, and biochemical regulation during viral factory formation. Furthermore, we discuss the broader implications of these interactions for viral replication and highlight potential future research directions.

DeepCristae, a CNN for the restoration of mitochondria cristae in live microscopy images

Mitochondria play an essential role in the life cycle of eukaryotic cells. However, we still don't know how their ultrastructure, like the cristae of the inner membrane, dynamically evolves to regulate these fundamental functions, in response to external conditions or during interaction with other cell components. Although high-resolution fluorescent microscopy coupled with recently developed innovative probes can reveal this structural organization, their long-term, fast and live 3D imaging remains challenging. To address this problem, we have developed a CNN, called DeepCristae, to restore mitochondria cristae in low spatial resolution microscopy images. Our network is trained from 2D STED images using a novel loss specifically designed for cristae restoration. To efficiently increase the size of the training set, we also developed a random image patch sampling centered on mitochondrial areas. To evaluate DeepCristae, quantitative assessments are carried out using metrics we derived by focusing on the mitochondria and cristae pixels rather than on the whole image as usual. Depending on the conditions of use indicated, DeepCristae works well on broad microscopy modalities (Stimulated Emission Depletion (STED), Live-SR, AiryScan and LLSM). It is ultimately applied in the context of mitochondrial network dynamics during interaction with endo/lysosome membranes.

Neuronal FAM171A2 mediates α-synuclein fibril uptake and drives Parkinson's disease

Neuronal accumulation and spread of pathological α-synuclein (α-syn) fibrils are key events in Parkinson's disease (PD) pathophysiology. However, the neuronal mechanisms underlying the uptake of α-syn fibrils remain unclear. In this work, we identified FAM171A2 as a PD risk gene that affects α-syn aggregation. Overexpressing FAM171A2 promotes α-syn fibril endocytosis and exacerbates the spread and neurotoxicity of α-syn pathology. Neuronal-specific knockdown of FAM171A2 expression shows protective effects. Mechanistically, the FAM171A2 extracellular domain 1 interacts with the α-syn C terminus through electrostatic forces, with >1000 times more selective for fibrils. Furthermore, we identified bemcentinib as an effective blocker of FAM171A2-α-syn fibril interaction with an in vitro binding assay, in cellular models, and in mice. Our findings identified FAM171A2 as a potential receptor for the neuronal uptake of α-syn fibrils and, thus, as a therapeutic target against PD.

The spatial choreography of mRNA biosynthesis

Properly timed gene expression is essential for all aspects of organismal physiology. Despite significant progress, our understanding of the complex mechanisms governing the dynamics of gene regulation in response to internal and external signals remains incomplete. Over the past decade, advances in technologies like light and cryo-electron microscopy (Cryo-EM), cryo-electron tomography (Cryo-ET) and high-throughput sequencing have spurred new insights into traditional paradigms of gene expression. In this Review, we delve into recent concepts addressing 'where' and 'when' gene transcription and RNA splicing occur within cells, emphasizing the dynamic spatial and temporal organization of the cell nucleus.

Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues

Lipid membranes are key to the nanoscale compartmentalization of biological systems, but fluorescent visualization of them in intact tissues, with nanoscale precision, is challenging to do with high labeling density. Here, we report ultrastructural membrane expansion microscopy (umExM), which combines an innovative membrane label and optimized expansion microscopy protocol, to support dense labeling of membranes in tissues for nanoscale visualization. We validate the high signal-to-background ratio, and uniformity and continuity, of umExM membrane labeling in brain slices, which supports the imaging of membranes and proteins at a resolution of ~60 nm on a confocal microscope. We demonstrate the utility of umExM for the segmentation and tracing of neuronal processes, such as axons, in mouse brain tissue. Combining umExM with optical fluctuation imaging, or iterating the expansion process, yields ~35 nm resolution imaging, pointing towards the potential for electron microscopy resolution visualization of brain membranes on ordinary light microscopes.

Fast reconstruction and optical-sectioning three-dimensional structured illumination microscopy

Three-dimensional structured illumination microscopy (3DSIM) is a popular method for observing subcellular/cellular structures or animal/plant tissues with gentle phototoxicity and 3D super-resolution. However, its time-consuming reconstruction process poses challenges for high-throughput imaging and real-time observation. Moreover, traditional 3DSIM typically requires more than six z layers for successful reconstruction and is susceptible to defocused backgrounds. This poses a great gap between single-layer 2DSIM and 6-layer 3DSIM, and limits the observation of thicker samples. To address these limitations, we developed FO-3DSIM, a novel method that integrates spatial-domain reconstruction with optical-sectioning SIM. FO-3DSIM enhances reconstruction speed by up to 855.7 times with superior performance with limited z layers and under high defocused backgrounds. It retains the high-fidelity, low-photon reconstruction capabilities of our previously proposed Open-3DSIM. Utilizing fast reconstruction and optical sectioning, we achieved large field-of-view (FOV) 3D super-resolution imaging of mouse kidney actin, covering a region of 0.453 mm × 0.453 mm × 2.75 μm within 23 min of acquisition and 13 min of reconstruction. Near real-time performance was demonstrated in live actin imaging with FO-3DSIM. Our approach reduces photodamage through limited z layer reconstruction, allowing the observation of ER tubes with just three layers. We anticipate that FO-3DSIM will pave the way for near real-time, large FOV 6D imaging, encompassing xyz super-resolution, multi-color, long-term, and polarization imaging with less photodamage, removed defocused backgrounds, and reduced reconstruction time.

Nuclear ANLN regulates transcription initiation related Pol II clustering and target gene expression

Anillin (ANLN), a mitotic protein that regulates contractile ring assembly, has been reported as an oncoprotein. However, the function of ANLN in cancer cells, especially in the nucleus, has not been fully understood. Here, we report a role of nuclear ANLN in gene transcriptional regulation. We find that nuclear ANLN directly interacts with the RNA polymerase II (Pol II) large subunit to form transcriptional condensates. ANLN enhances initiated Pol II clustering and promotes Pol II CTD phase separation. Short-term depletion of ANLN alters the chromatin binding and enhancer-mediated transcriptional activity of Pol II. The target genes of ANLN-Pol II axis are involved in oxidoreductase activity, Wnt signaling and cell differentiation. THZ1, a super-enhancer inhibitor, specifically inhibits ANLN-Pol II clustering, target gene expression and esophageal squamous cell carcinoma (ESCC) cell proliferation. Our results reveal the function of nuclear ANLN in transcriptional regulation, providing a theoretical basis for ESCC treatment.

Matrix stiffness regulates mitochondria-lysosome contacts to modulate the mitochondrial network, alleviate the senescence of MSCs

The extracellular microenvironment encompasses the extracellular matrix, neighbouring cells, cytokines, and fluid components. Anomalies in the microenvironment can trigger aging and a decreased differentiation capacity in mesenchymal stem cells (MSCs). MSCs can perceive variations in the firmness of the extracellular matrix and respond by regulating mitochondrial function. Diminished mitochondrial function is intricately linked to cellular aging, and studies have shown that mitochondria-lysosome contacts (M-L contacts) can regulate mitochondrial function to sustain cellular equilibrium. Nonetheless, the influence of M-L contacts on MSC aging under varying matrix stiffness remains unclear. In this study, utilizing single-cell RNA sequencing and atomic force microscopy, we further demonstrate that reduced matrix stiffness in older individuals leads to MSC aging and subsequent decline in osteogenic ability. Mechanistically, augmented M-L contacts under low matrix stiffness exacerbate MSC aging by escalating mitochondrial oxidative stress and peripheral division. Moreover, under soft matrix stiffness, cytoskeleton reorganization facilitates rapid movement of lysosomes. The M-L contacts inhibitor ML282 ameliorates MSC aging by reinstating mitochondrial network and function. Overall, our findings confirm that MSC aging is instigated by disruption of the mitochondrial network and function induced by matrix stiffness, while also elucidating the potential mechanism by which M-L Contact regulates mitochondrial homeostasis. Crucially, this presents promise for cellular anti-aging strategies centred on mitochondria, particularly in the realm of stem cell therapy.

Elucidating subcellular architecture and dynamics at isotropic 100-nm resolution with 4Pi-SIM

Three-dimensional structured illumination microscopy (3D-SIM) provides excellent optical sectioning and doubles the resolution in all dimensions compared with wide-field microscopy. However, its much lower axial resolution results in blurred fine details in that direction and overall image distortion. Here we present 4Pi-SIM, a substantial revamp of I5S that synergizes 3D-SIM with interferometric microscopy to achieve isotropic optical resolution through interference in both the illumination and detection wavefronts. We evaluate the performance of 4Pi-SIM by imaging various subcellular structures across different cell types with high fidelity. Furthermore, we demonstrate its capability by conducting time-lapse volumetric imaging over hundreds of time points, achieving a 3D resolution of approximately 100 nm. Additionally, we illustrate its ability to simultaneously image in two colors and capture the rapid interactions between closely positioned organelles in three dimensions. These results underscore the great potential of 4Pi-SIM for elucidating subcellular architecture and revealing dynamic behaviors at the nanoscale.

Polyphenol Mediated Assembly: Tailored Nano-Dredger Unblocks Axonal Autophagosomes Retrograde Transport Traffic Jam for Accelerated Alzheimer's Waste Clearance

Clear-cut evidence has linked defective autophagy to Alzheimer's disease (AD). Recent studies underscore a unique hurdle in AD neuronal autophagy: impaired retrograde axonal transport of autophagosomes, potent enough to induce autophagic stress and neurodegeneration. Nonetheless, pertinent therapy is unavailable. Here, a novel combinational therapy composed of siROCK2 and lithospermic acid B (LA) is introduced, tailored to dredge blocked axonal autophagy by multi-mitigating microtubule disruption, ATP depletion, oxidative stress, and autophagy initiation impediments in AD. Leveraging the recent discovery of multi-interactions between polyphenol LA and siRNA, ε-Poly-L-lysine, and anionic lipid nanovacuoles, LA and siROCK2 are successfully co-loaded into a fresh nano-drug delivery system, LIP@PL-LA/siRC, via a ratio-flexible and straightforward fabrication process. Further modification with the TPL peptide onto LIP@PL-LA/siRC creates a brain-neuron targeted, biocompatible, and pluripotent nanomedicine, named "Nano-dredger" (T-LIP@PL-LA/siRC). Nano-dredger efficiently accelerates axonal retrograde transport and lysosomal degradation of autophagosomes, thereby facilitating the clearance of neurotoxic proteins, improving neuronal complexity, and alleviating memory defects in 3×Tg-AD transgenic mice. This study provides a fresh and flexible polyphenol/siRNA co-delivery paradigm and furnishes conceptual proof that dredging axonal autophagy represents a promising AD therapeutic avenue.

Approaching maximum resolution in structured illumination microscopy via accurate noise modeling

Biological images captured by microscopes are characterized by heterogeneous signal-to-noise ratios (SNRs) due to spatially varying photon emission across the field of view convoluted with camera noise. State-of-the-art unsupervised structured illumination microscopy (SIM) reconstruction methods, commonly implemented in the Fourier domain, often do not accurately model this noise. Such methods therefore suffer from high-frequency artifacts, user-dependent choices of smoothness constraints making assumptions on biological features, and unphysical negative values in the recovered fluorescence intensity map. On the other hand, supervised algorithms rely on large datasets for training, and often require retraining for new sample structures. Consequently, achieving high contrast near the maximum theoretical resolution in an unsupervised, physically principled manner remains an open problem. Here, we propose Bayesian-SIM (B-SIM), a Bayesian framework to quantitatively reconstruct SIM data, rectifying these shortcomings by accurately incorporating known noise sources in the spatial domain. To accelerate the reconstruction process, we use the finite extent of the point-spread-function to devise a parallelized Monte Carlo strategy involving chunking and restitching of the inferred fluorescence intensity. We benchmark our framework on both simulated and experimental images, and demonstrate improved contrast permitting feature recovery at up to 25% shorter length scales over state-of-the-art methods at both high- and low SNR. B-SIM enables unsupervised, quantitative, physically accurate reconstruction without the need for labeled training data, democratizing high-quality SIM reconstruction and expands the capabilities of live-cell SIM to lower SNR, potentially revealing biological features in previously inaccessible regimes.

C1orf115 interacts with clathrin adaptors to undergo endocytosis and induces ABCA1 to promote enteric cholesterol efflux

C1orf115 has been identified in high-throughput screens as a regulator of multidrug resistance possibly mediated through an interaction with ATP-dependent membrane transporter ABCB1. Here we show that C1orf115 not only shares structural similarities with FACI/C11orf86 to interact with clathrin adaptors to undergo endocytosis, but also induces ABCA1 transcription to promote cholesterol efflux. C1orf115 consists of an N-terminal intrinsically disordered region and a C-terminal α-helix. Its α-helix binds to phosphoinositides, and mediates C1orf115 localization to the plasma membrane, nucleolus and nuclear speckles. An acidic dileucine-like motif "ExxxIL" within C1orf115 binds with the AP2 complex and mediates its localization to clathrin-coating pits. The positively charged amphipathic α-helix undergoes acetylation, which redistributes C1orf115 from the plasma membrane and nucleolus to nuclear speckles. C1orf115 is widely expressed and most abundant in the small intestine. The ability of C1orf115 in clathrin-mediated endocytosis is required for its regulation of drug resistance, which is modulated by acetylation. RNA-seq analysis reveals that C1orf115 induces intestinal transcription of another ATP-dependent transporter ABCA1 and consequently promotes ABCA1-mediated cholesterol efflux in enterocytes. Our study provides mechanistic insight into how C1orf115 modulates drug resistance and cholesterol efflux through clathrin-mediated endocytosis and ABCA1 expression.

Multi-resolution analysis for high-fidelity deconvolution microscopy

A fidelity-ensured multi-resolution analysis deconvolution algorithm significantly enhances fluorescence microscopy's resolution and noise control, enabling more accurate and detailed imaging for advanced biological research applications.

Identification of Nicotinic Acetylcholine Receptor for N-Acetylcysteine to Rescue Nicotine-induced Injury Using Beating Cilia in Primary Tissue Derived Airway Organoids

Smoking is one of the major contributors to airway injuries. N-acetylcysteine (NAC) has been proposed as a treatment or preventive measure for such injuries. However, the exact nature of the smoking-induced injury and the protective mechanism of NAC are not yet fully understood. Here, patient tissue-derived airway organoids for modeling smoking-induced injury, therapeutic investigation, and mechanism studies are developed. Airway organoids consist mainly of ciliated cells, together with basal cells, goblet cells, and myofibroblast-like cells. The organoids display apical-out and basal-in polarity and are enriched in beating cilia, which are sensitive to smoking challenge and NAC treatment. An algorithm is developed to measure ciliary beating activity by analyzing the altered beating pattern of cilia in response to nicotine challenge and NAC treatment. Nicotinic acetylcholine receptors (nAChRs) expressed by airway organoids are involved in the mechanisms of nicotine-induced injury through the nicotine-nAChR pathway. In contrast to the common understanding that NAC has an antioxidative effect that mitigates airway damage, it is elucidated that NAC binding to nicotine can abolish the binding capacity of nicotine to nAChRs and thus prevent nicotine-induced injury. This study focuses on the advances and potential of humanized organoids in understanding biological processes, mechanisms, and identifying therapeutic targets.

Optical sectioning methods in three-dimensional bioimaging

In recent advancements in life sciences, optical microscopy has played a crucial role in acquiring high-quality three-dimensional structural and functional information. However, the quality of 3D images is often compromised due to the intense scattering effect in biological tissues, compounded by several issues such as limited spatiotemporal resolution, low signal-to-noise ratio, inadequate depth of penetration, and high phototoxicity. Although various optical sectioning techniques have been developed to address these challenges, each method adheres to distinct imaging principles for specific applications. As a result, the effective selection of suitable optical sectioning techniques across diverse imaging scenarios has become crucial yet challenging. This paper comprehensively overviews existing optical sectioning techniques and selection guidance under different imaging scenarios. Specifically, we categorize the microscope design based on the spatial relationship between the illumination and detection axis, i.e., on-axis and off-axis. This classification provides a unique perspective to compare the implementation and performances of various optical sectioning approaches. Lastly, we integrate selected optical sectioning methods on a custom-built off-axis imaging system and present a unique perspective for the future development of optical sectioning techniques.

Deep Learning-Based Image Restoration and Super-Resolution for Fluorescence Microscopy: Overview and Resources

Fluorescence microscopy is a key method for the visualization of cellular, subcellular, and molecular live-cell dynamics, enabling access to novel insights into mechanisms of health and disease. However, effects like phototoxicity, the fugitive nature of signals, photo bleaching, and method-inherent noise can degrade the achievable signal-to-noise ratio and image resolution. In recent years, deep learning (DL) approaches have been increasingly applied to remove these degradations. In this review, we give a brief overview over existing classical and DL approaches for denoising, deconvolution, and computational super-resolution of fluorescence microscopy data. We summarize existing open-source databases within these fields as well as code repositories related to corresponding publications and further contribute an example project for DL-based image denoising, which provides a low barrier entry into DL coding and respective applications. In summary, we supply interested researchers with tools to apply or develop DL applications in live-cell imaging and foster research participation in this field.

Two Hundred Nanometer Thin Multifocal Graphene Oxide Metalens for Varying Magnification Broadband Imaging

Conventional microscopes, which rely on multiple objective lenses for varying magnifications, are bulky, complex, and costly, making them difficult to integrate into compact devices. They require frequent manual adjustments, complicating the imaging process and increasing maintenance burdens. This paper explores the potential of single ultrathin graphene metalens to address this issue. We propose and demonstrate a 200 nm thin multiaxial focus graphene metalens with high-quality focusing, designed using spatial multiplexing and fabricated by one-step laser nanoprinting. A five-focal graphene metalens has been created, achieving clear imaging with varying magnifications across a broadband covering the entire visible wavelength. The graphene metalens has significantly reduced the size of the imaging system by orders of magnitude and holds profound potential for facilitating the integration and miniaturization of optical microscopic systems.

Automatic Optical Path Alignment Method for Optical Biological Microscope

A high-quality optical path alignment is essential for achieving superior image quality in optical biological microscope (OBM) systems. The traditional automatic alignment methods for OBMs rely heavily on complex masker-detection techniques. This paper introduces an innovative, image-sensor-based optical path alignment approach designed for low-power objective (specifically 4×) automatic OBMs. The proposed method encompasses reference objective (RO) identification and alignment processes. For identification, a model depicting spot movement with objective rotation near the optical axis is developed, elucidating the influence of optical path parameters on spot characteristics. This insight leads to the proposal of an RO identification method utilizing an edge gradient and edge position probability. In the alignment phase, a symmetry-based weight distribution scheme for concentric arcs is introduced. A significant observation is that the received energy stabilizes with improved alignment precision, prompting the design of an advanced alignment evaluation method that surpasses conventional energy-based assessments. The experimental results confirm that the proposed RO identification method can effectively differentiate between 4× and 10× objectives across diverse light intensities and exposure levels, with a significant numerical difference of up to 100. The error-radius ratio of the weighted circular fitting method is maintained below 1.16%, and the fine alignment stage's evaluation curve is notably sharper. Moreover, tests under various imaging conditions in artificially saturated environments indicate that the alignment estimation method, predicated on critical saturation positions, achieves an average error of 0.875 pixels.

lncRNAs maintain the functional phase state of nucleolar prion-like protein to facilitate rRNA processing

Liquid-to-solid phase transition of proteins with prion-like domains (PLDs) has been associated with neurodegenerative diseases and aging. High protein concentration is one important aspect triggering the transition; however, several prion-like proteins, including fibrillarin (FBL), an important phase-separated protein in the nucleolus for pre-rRNA processing, show relatively high expression levels in certain cells, especially cancer cells, without obvious phase transitions and growth arrest. How cells maintain prion-like protein proteostasis is still unknown. Here, we attempt to answer the question, with FBL as an example. We find that lncRNA DNAJC3-AS1 can buffer the behavior of FBL condensation and maintain the state and function of fibrillar component/dense fibrillar component (FC/DFC) units in human cell lines through two mechanisms, not only facilitating FBL condensation but also inhibiting excessive aggregation by binding multiple PLDs and partially blocking their interactions. We propose that lncRNAs could supply buffered systems to sustain functional phase states of prion-like proteins.

Mitochondrial dysfunction of Astrocyte induces cell activation under high salt condition

Excess dietary sodium can accumulate in brain and adversely affect human health. We have confirmed in previous studies that high salt can induce activation of astrocyte manifested by the secretion of various inflammatory factors. In order to further explore the effect of high salt on the internal cell metabolism of astrocytes, RNA sequencing was performed on astrocytes under high salt environment, which indicated the oxidative phosphorylation and glycolysis pathways of astrocytes were downregulated. Next, we found that high salt concentrations elicited astrocyte mitochondrial morphology change, as evidenced by swelling from a short rod to a round shape through a High Intelligent and Sensitive Structured Illumination Microscope (HIS-SIM). Furthermore, we found that high salt concentrations reduced astrocyte mitochondrial oxygen consumption and membrane potential. Treatment with 18-kDa translocator protein (TSPO) ligands FGIN-1-27 improved mitochondrial networks and reversed astrocyte activation under high-salt circumstances. Our study shows that high salt can directly disrupt astrocytic mitochondrial homeostasis and function. Targeting translocator protein signaling may have therapeutic potential against high-salt neurotoxicity.

Mitochondrial dynamics govern whole-body regeneration through stem cell pluripotency and mitonuclear balance

Tissue regeneration is a complex process involving large changes in cell proliferation, fate determination, and differentiation. Mitochondrial dynamics and metabolism play a crucial role in development and wound repair, but their function in large-scale regeneration remains poorly understood. Planarians offer an excellent model to investigate this process due to their remarkable regenerative abilities. In this study, we examine mitochondrial dynamics during planarian regeneration. We find that knockdown of the mitochondrial fusion gene, opa1, impairs both tissue regeneration and stem cell pluripotency. Interestingly, the regeneration defects caused by opa1 knockdown are rescued by simultaneous knockdown of the mitochondrial fission gene, drp1, which partially restores mitochondrial dynamics. Furthermore, we discover that Mitolow stem cells exhibit an enrichment of pluripotency due to their fate choices at earlier stages. Transcriptomic analysis reveals the delicate mitonuclear balance in metabolism and mitochondrial proteins in regeneration, controlled by mitochondrial dynamics. These findings highlight the importance of maintaining mitochondrial dynamics in large-scale tissue regeneration and suggest the potential for manipulating these dynamics to enhance stem cell functionality and regenerative processes.

Metabolic nanoscopy enhanced by experimental and computational approaches

The advances in microscopy techniques have led to new findings in biology. The recent advances in super-resolution microscopy technologies revealed precise molecular distribution. The techniques to visualize the distributions of multiple molecules in biological samples from experimental techniques to computational approaches are reviewed. By summarizing the techniques, the future direction of collaborative research of the techniques is highlighted to show the nanoscopic chemical details of biological samples.

Structured illumination microscopy based on Kramers-Kronig relations for quantitative phase reconstruction

Structured illumination microscopy (SIM) is a widely applied fluorescence super-resolution imaging technique. It can also serve as high-throughput imaging in coherent imaging systems. However, coherent SIM requires additional qualitative/quantitative phase imaging methods to acquire phase information. This paper proposes a structured illumination microscopy technique based on the Kramers-Kronig relations (KK-SIM) that achieves quantitative phase imaging without the need for extra technical assistance and relies solely on the spatial-domain intensity images reconstructed through conventional SIM. KK-SIM utilizes a non-iterative approach to recover intensity into amplitude and phase, maintaining SIM's high acquisition speed and reconstruction efficiency. Our work enables high-throughput quantitative phase imaging using conventional SIM experimental setups and data post-processing, making SIM suitable for label-free, noninvasive dynamic observation.

A novel GAN-based three-axis mutually supervised super-resolution reconstruction method for rectal cancer MR image

BACKGROUND AND OBJECTIVE

This study aims to enhance the resolution in the axial direction of rectal cancer magnetic resonance (MR) imaging scans to improve the accuracy of visual interpretation and quantitative analysis. MR imaging is a critical technique for the diagnosis and treatment planning of rectal cancer. However, obtaining high-resolution MR images is both time-consuming and costly. As a result, many hospitals store only a limited number of slices, often leading to low-resolution MR images, particularly in the axial plane. Given the importance of image resolution in accurate assessment, these low-resolution images frequently lack the necessary detail, posing substantial challenges for both human experts and computer-aided diagnostic systems. Image super-resolution (SR), a technique developed to enhance image resolution, was originally applied to natural images. Its success has since led to its application in various other tasks, especially in the reconstruction of low-resolution MR images. However, most existing SR methods fail to account for all anatomical planes during reconstruction, leading to unsatisfactory results when applied to rectal cancer MR images.

METHODS

In this paper, we propose a GAN-based three-axis mutually supervised super-resolution reconstruction method tailored for low-resolution rectal cancer MR images. Our approach involves performing one-dimensional (1D) intra-slice SR reconstruction along the axial direction for both the sagittal and coronal planes, coupled with inter-slice SR reconstruction based on slice synthesis in the axial direction. To further enhance the accuracy of super-resolution reconstruction, we introduce a consistency supervision mechanism across the reconstruction results of different axes, promoting mutual learning between each axis. A key innovation of our method is the introduction of Depth-GAN for synthesize intermediate slices in the axial plane, incorporating depth information and leveraging Generative Adversarial Networks (GANs) for this purpose. Additionally, we enhance the accuracy of intermediate slice synthesis by employing a combination of supervised and unsupervised interactive learning techniques throughout the process.

RESULTS

We conducted extensive ablation studies and comparative analyses with existing methods to validate the effectiveness of our approach. On the test set from Shanxi Cancer Hospital, our method achieved a Peak Signal-to-Noise Ratio (PSNR) of 34.62 and a Structural Similarity Index (SSIM) of 96.34 %. These promising results demonstrate the superiority of our method.

Advanced Imaging Integration: Multi-Modal Raman Light Sheet Microscopy Combined with Zero-Shot Learning for Denoising and Super-Resolution

This study presents an advanced integration of Multi-modal Raman Light Sheet Microscopy with zero-shot learning-based computational methods to significantly enhance the resolution and analysis of complex three-dimensional biological structures, such as 3D cell cultures and spheroids. The Multi-modal Raman Light Sheet Microscopy system incorporates Rayleigh scattering, Raman scattering, and fluorescence detection, enabling comprehensive, marker-free imaging of cellular architecture. These diverse modalities offer detailed spatial and molecular insights into cellular organization and interactions, critical for applications in biomedical research, drug discovery, and histological studies. To improve image quality without altering or introducing new biological information, we apply Zero-Shot Deconvolution Networks (ZS-DeconvNet), a deep-learning-based method that enhances resolution in an unsupervised manner. ZS-DeconvNet significantly refines image clarity and sharpness across multiple microscopy modalities without requiring large, labeled datasets, or introducing artifacts. By combining the strengths of multi-modal light sheet microscopy and ZS-DeconvNet, we achieve improved visualization of subcellular structures, offering clearer and more detailed representations of existing data. This approach holds significant potential for advancing high-resolution imaging in biomedical research and other related fields.

Visualizing highly bright and uniform cellular ultrastructure by expansion-microscopy with tetrahedral DNA nanostructures

Expansion Microscopy (ExM) is a widely used super-resolution technique that enables imaging of structures beyond the diffraction limit of light. However, ExM suffers from weak labeling signals and expansion distortions, limiting its applicability. Here, we present an innovative approach called Tetrahedral DNA nanostructure Expansion Microscopy (TDN-ExM), addressing these limitations by using tetrahedral DNA nanostructures (TDNs) for fluorescence labeling. Our approach demonstrates a 3- to 10-fold signal amplification due to the multivertex nature of TDNs, allowing the modification of multiple dyes. Previous studies have confirmed minimal distortion on a large scale, and our strategy can reduce the distortion at the ultrastructural level in samples because it does not rely on anchoring agents and is not affected by digestion. This results in a brighter fluorescence, better uniformity, and compatibility with different labeling strategies and optical super-resolution technologies. We validated the utility of TDN-ExM by imaging various biological structures with improved resolutions and signal-to-noise ratios.

Visualizing DNA/RNA, Proteins, and Small Molecule Metabolites within Live Cells

Live cell imaging is essential for obtaining spatial and temporal insights into dynamic molecular events within heterogeneous individual cells, in situ intracellular networks, and in vivo organisms. Molecular tracking in live cells is also a critical and general requirement for studying dynamic physiological processes in cell biology, cancer, developmental biology, and neuroscience. Alongside this context, this review provides a comprehensive overview of recent research progress in live-cell imaging of RNAs, DNAs, proteins, and small-molecule metabolites, as well as their applications in molecular diagnosis, immunodiagnosis, and biochemical diagnosis. A series of advanced live-cell imaging techniques have been introduced and summarized, including high-precision live-cell imaging, high-resolution imaging, low-abundance imaging, multidimensional imaging, multipath imaging, rapid imaging, and computationally driven live-cell imaging methods, all of which offer valuable insights for disease prevention, diagnosis, and treatment. This review article also addresses the current challenges, potential solutions, and future development prospects in this field.

Suppression of non-muscle myosin II boosts T cell cytotoxicity against tumors

Increasing evidence highlights the importance of immune mechanoregulation in establishing and sustaining tumor-specific cytotoxicity required for desirable immunotherapeutic outcomes. However, the molecular connections between mechanobiological inputs and outputs and the designated immune activities remain largely unclear. Here, we show that partial inhibition of non-muscle myosin II (NM II) augmented the traction force exerted by T cells and potentiated T cell cytotoxicity against tumors. By using T cells from mice and patients with cancer, we found that NM II is required for the activity of NKX3-2 in maintaining the expression of ADGRB3, which shapes the filamentous actin (F-actin) organization and ultimately attributes to the reduced traction force of T cells in the tumor microenvironment. In animal models, suppressing the NM II-NKX3-2-ADGRB3 pathway in T cells effectively suppressed tumor growth and improved the efficacy of the checkpoint-specific immunotherapy. Overall, this work provides insights into the biomechanical regulation of T cell cytotoxicity that can be exploited to optimize clinical immunotherapies.