Biological Imaging Research Articles

Encapsulation engineering of porous crystalline frameworks for delayed luminescence and circularly polarized luminescence.

Delayed luminescence (DF), including phosphorescence and thermally activated delayed fluorescence (TADF), and circularly polarized luminescence (CPL) exhibit common and broad application prospects in optoelectronic displays, biological imaging, and encryption. Thus, the combination of delayed luminescence and circularly polarized luminescence is attracting increasing attention. The encapsulation of guest emitters in various host matrices to form host-guest systems has been demonstrated to be an appealing strategy to further enhance and/or modulate their delayed luminescence and circularly polarized luminescence. Compared with conventional liquid crystals, polymers, and supramolecular matrices, porous crystalline frameworks (PCFs) including metal-organic frameworks (MOFs), covalent-organic frameworks (COFs), zeolites and hydrogen-bonded organic frameworks (HOFs) can not only overcome shortcomings such as flexibility and disorder but also achieve the ordered encapsulation of guests and long-term stability of chiral structures, providing new promising host platforms for the development of DF and CPL. In this review, we provide a comprehensive and critical summary of the recent progress in host-guest photochemistry via the encapsulation engineering of guest emitters in PCFs, particularly focusing on delayed luminescence and circularly polarized luminescence. Initially, the general principle of phosphorescence, TADF and CPL, the combination of DF and CPL, and energy transfer processes between host and guests are introduced. Subsequently, we comprehensively discuss the critical factors affecting the encapsulation engineering of guest emitters in PCFs, such as pore structures, the confinement effect, charge and energy transfer between the host and guest, conformational dynamics, and aggregation model of guest emitters. Thereafter, we summarize the effective methods for the preparation of host-guest systems, especially single-crystal-to-single-crystal (SC-SC) transformation and epitaxial growth, which are distinct from conventional methods based on amorphous materials. Then, the recent advancements in host-guest systems based on PCFs for delayed luminescence and circularly polarized luminescence are highlighted. Finally, we present our personal insights into the challenges and future opportunities in this promising field.

Water-Soluble Luminescent Polymers with Room Temperature Phosphorescence Based on the α-Amino Acids.

Nonconventional luminophores have received increasing attention, owing to their fundamental importance, advantages in outstanding biocompatibility, easy preparation, environmental friendliness and potential applications in sensing, imaging and encryption, etc. Purely organic molecules with outstanding fluorescence and room-temperature phosphorescence (RTP) have emerged as a new library of benign afterglow agents. However, the cost, toxicity, high reactivity and poor stability of materials also limit their practical applications. Therefore, some natural products, synthetic compounds and biomolecules have entered horizons of people. The as-designed exhibits sky blue and green fluorescence emission and green RTP emission (a lifetime of 343ms and phosphorescence quantum of 15.3%) under air condition. This study presents an organic fluorescence for biological imaging and RTP for anti-counterfeiting and encryption based on amino acids, maleic anhydride (MAH) and 4-Vinylbenzenesulfonic acid sodium salt hydrate (SSS). This study provides a strategy for nonconventional luminophores in designing and synthesizing pure organic RTP materials. This article is protected by copyright. All rights reserved.

Predicting Serotonin Detection with DNA-Carbon Nanotube Sensors across Multiple Spectral Wavelengths.

Owing to the value of DNA-wrapped single-walled carbon nanotube (SWNT)-based sensors for chemically specific imaging in biology, we explore machine learning (ML) predictions DNA-SWNT serotonin sensor responsivity as a function of DNA sequence based on the whole SWNT fluorescence spectra. Our analysis reveals the crucial role of DNA sequence in the binding modes of DNA-SWNTs to serotonin, with a smaller influence of SWNT chirality. Regression ML models trained on existing data sets predict the change in the fluorescence emission in response to serotonin, ΔF/F, at over a hundred wavelengths for new DNA-SWNT conjugates, successfully identifying some high- and low-response DNA sequences. Despite successful predictions, we also show that the finite size of the training data set leads to limitations on prediction accuracy. Nevertheless, incorporating entire spectra into ML models enhances prediction robustness and facilitates the discovery of novel DNA-SWNT sensors. Our approaches show promise for identifying new chemical systems with specific sensing response characteristics, marking a valuable advancement in DNA-based system discovery.

WSM-MIL: A Weakly Supervised Segmentation Method with Multiple Instance Learning for C. elegans Image

Abstract Recently, image analysis techniques have been introduced to automate nematode information assessment. In image analysis-based nematode information assessment, the initial step involves detecting and segmenting C. elegans from microscopic images and network-based methods have been investigated. However, training a network for C. elegans image segmentation is typically associated with the labor-intensive process of pixel-level mask labeling. To address this challenge, we introduced a weakly supervised segmentation method using multiple instance learning (WSM-MIL). The proposed multi-instance weakly supervised segmentation method comprises three key components: a backbone network, a detection branch, and a segmentation branch. In contrast to fully supervised pixel-level annotation, we opted for weakly supervised bounding box-level annotation. This approach reduces the labour cost of annotation to some extent. The approach offers several advantages, such as simplicity, an end-to-end architecture, and good scalability. We conducted experiments comparing the proposed network with benchmark methods, and the results showed that the network exhibits competitive performance in the image segmentation task of C. elegans. The results of this study provide an effective method in the field of biological image analysis, as well as new ideas for solving complex segmentation tasks. The method is not only applicable to the study of C. elegans but also has wide applicability in biological image segmentation problems in other fields.

3D Poissonian image deblurring via patch-based tensor logarithmic Schatten-p minimization

In medical and biological image processing, multi-dimensional images are often corrupted by blur and Poisson noise. In this paper, we first propose a new tensor logarithmic Schatten-p (t-log-Sp ) low-rank measure and a tensor iteratively reweighted Schatten-p minimization algorithm for minimizing such measure. Furthermore, we adopt this low-rank measure to regularize the non-local tensors formed by similar 3D image patches and develop a patch-based non-local low-rank model. The data fidelity term of the model characterizes the Poisson noise distribution and blur operator. The optimization model is further solved by an alternating minimization technique combined with variable splitting. Experimental results tested on 3D fluorescence microscope images show that the proposed patch-based tensor logarithmic Schatten-p minimization method outperforms state-of-the-art methods in terms of image evaluation metrics and visual quality.

Green synthesis of fluorescent carbon dots from ascorbic acid and their application in sensing and biological imaging

A simple, highly efficient, and environmentally friendly one-step method has been developed to synthesize fluorescent carbon dots (CDs) with the assistance of hydrogen peroxide (H2O2). Here H2O2 acts as a green accelerator to promote the preparation of CDs, while temperature plays a critical role in controlling the entire synthesis process. The prepared CDs demonstrate monodispersion, with an average diameter of ∼6.8 nm, superior stability, and excitation-dependent photoluminescent (PL) behavior. The PL mechanism of the CDs was investigated using time-resolved PL decay, revealing that the PL originates from both the defect state and the intrinsic state of the CDs. Furthermore, the CDs show significant promise as pH sensors and versatile nanothermometry devices, owing to their remarkable sensitivity to both pH and temperature, as demonstrated by the pronounced dependence of their steady-state fluorescence emission spectra. It’s worth noting that temperature and pH sensors present significant reversibility, sensitivity, and linearity. More importantly, the CDs display low cytotoxicity, good biocompatibility, and the ability to enter human breast cancer Bcap-37 cells, making them highly suitable candidates for cellular imaging and labeling.

Nitrogen and Chlorine Co-Doped Carbon Dots with Yellow-Green Emission as a Ratiometric Fluorescent and Colorimetric Dual-Signal Probe for Quercetin Detection and Cell Imaging

Despite the emergence of numerous carbon dots (CDs)-based sensors, most of them are fluorescent probes. To improve the reliability of the results, using ratiometric fluorescence/UV-vis absorption dual-signal probes is an effective method. Herein, nitrogen and chlorine co-doped carbon dots (N, Cl-CDs) with yellow-green fluorescence were prepared and used as a dual-function probe for ratiometric fluorescence/UV-vis. The detection range of the fluorescence method was 0.05–78[Formula: see text][Formula: see text]M, and the limit of detection (LOD) was 1.2[Formula: see text]nM (3[Formula: see text]/s). For the colorimetric method, the linear range was 0.05–186[Formula: see text][Formula: see text]M with LOD of 10.7[Formula: see text]nM. Importantly, the N, Cl-CDs were successfully used to detect Quercetin (QT) in actual water samples. Besides, due to their good biocompatibility, the N, Cl-CDs were applied to in vivo biological imaging of oocysts and shown the potential for environmental survey and biological assay.

A novel NIR fluorescent probe for enhanced β-galactosidase detection and tumor imaging in ovarian cancer models

The advancement of biological imaging techniques critically depends on the development of novel near-infrared (NIR) fluorescent probes. In this study, we introduce a designed NIR fluorescent probe, NRO-βgal, which exhibits a unique off–on response mechanism to β-galactosidase (β-gal). Emitting a fluorescence peak at a wavelength of 670 nm, NRO-βgal showcases a significant Stokes shift of 85 nm, which is indicative of its efficient energy transfer and minimized background interference. The probe achieves a remarkably low in vitro detection limit of 0.2 U/L and demonstrates a rapid response within 10 min, thereby underscoring its exceptional sensitivity, selectivity, and operational swiftness. Such superior analytical performance broadens the horizon for its application in intricate biological imaging studies. To validate the practical utility of NRO-βgal in bio-imaging, we employed ovarian cancer cell and mouse models, where the probe's efficacy in accurately delineating tumor cells was examined. The results affirm NRO-βgal's capability to provide sharp, high-contrast images of tumor regions, thereby significantly enhancing the precision of surgical tumor resection. Furthermore, the probe's potential for real-time monitoring of enzymatic activity in living tissues underscores its utility as a powerful tool for diagnostics in oncology and beyond.

Non-telecentric photoacoustic microscopy for multi-scale imaging.

Optical-resolution photoacoustic microscopy (OR-PAM) excels in precisely imaging a biological tissue based on absorption contrast. However, existing OR-PAMs are confined by fixed compromises between spatial resolution and field of view (FOV), preventing the integration of large FOV and local high-resolution within one system. Here, we present a non-telecentric OR-PAM (nTC-PAM) that empowers efficient adaptation of FOV and spatial resolution to match the multi-scale requirement of diverse biological imaging. Our method allows for a large-scale transformation in FOV and even surpassing the nominal FOV of the objective with minimal marginal degradation of the lateral resolution. We demonstrate the advantage of nTC-PAM through multi-scale imaging of the leaf phantom, mouse ear, and cortex. The results reveal that nTC-PAM can switch the FOV and spatial resolution to meet the requirements of different biological tissues, such as large-scale imaging of the whole cerebral cortex and high-resolution imaging of microvascular structures in local brain regions.

A novel “Turn-Off-On” fluorescent probe for specific sequential detection of Cu2+ and glyphosate and its application in biological imaging

As common pollutants, Cu2+ and glyphosate pose a serious threat to human health and the ecosystem. Herein, a fluorescent probe (E)-7-(diethylamino)-N'(4-(diethylamino)-2-hydroxybenzyl)-2-oxo-2H chromophore-3-carbazide (DDHC) was designed and synthesised for the sequential recognition of Cu2+ and glyphosate. DDHC has the advantages of a short synthesis path, easy-to-obtain raw materials, good anti-interference ability, and strong stability. The interaction of the DDHC-Cu2+ complexes with glyphosate allows the amino and carboxyl groups in glyphosate molecules to coordinate with Cu2+ strongly, competing for the Cu2+ in the DDHC-Cu2+ complexes and releasing the DDHC, leading to the recovery of fluorescence. The recognition was further validated through Job’s plot, HRMS, and DFT calculations. In addition, the successful recovery of Cu2+ and glyphosate in different environmental water samples fully demonstrates the practical application potential of DDHC. Especially, DDHC has low cytotoxicity and can enter zebrafish and HeLa cells, rapidly reacting with Cu2+ and glyphosate in the body, generating visible fluorescence quenching and recovery phenomena, achieving real-time visual monitoring of exogenous Cu2+ and glyphosate in zebrafish and HeLa cells. The targeting and dual selectivity of DDHC greatly enhance its potential application value in the field of detection, providing important theoretical support for studying the fate of multiple pollutants in the environment.

Build and operation of a custom 3D, multicolor, single-molecule localization microscope.

Single-molecule localization microscopy (SMLM) enables imaging scientists to visualize biological structures with unprecedented resolution. Particularly powerful implementations of SMLM are capable of three-dimensional, multicolor and high-throughput imaging and can yield key biological insights. However, widespread access to these technologies is limited, primarily by the cost of commercial options and complexity of de novo development of custom systems. Here we provide a comprehensive guide for interested researchers who wish to establish a high-end, custom-built SMLM setup in their laboratories. We detail the initial configuration and subsequent assembly of the SMLM, including the instructions for the alignment of all the optical pathways, the software and hardware integration, and the operation of the instrument. We describe the validation steps, including the preparation and imaging of test and biological samples with structures of well-defined geometries, and assist the user in troubleshooting and benchmarking the system's performance. Additionally, we provide a walkthrough of the reconstruction of a super-resolved dataset from acquired raw images using the Super-resolution Microscopy Analysis Platform. Depending on the instrument configuration, the cost of the components is in the range US$95,000-180,000, similar to other open-source advanced SMLMs, and substantially lower than the cost of a commercial instrument. A builder with some experience of optical systems is expected to require 4-8 months from the start of the system construction to attain high-quality three-dimensional and multicolor biological images.

Triple Sensing Modes for Triggered β-Galactosidase Activity Assays Based on Kaempferol-Deduced Silicon Nanoparticles and Biological Imaging of MCF-7 Breast Cancer Cells.

β-Galactosidase (β-Gala) is an essential biomarker enzyme for early detection of breast tumors and cellular senescence. Creating an accurate way to monitor β-Gala activity is critical for biological research and early cancer detection. This work used fluorometric, colorimetric, and paper-based color sensing approaches to determine β-Gala activity effectively. Via the sensing performance, the catalytic activity of β-Gala resulted in silicon nanoparticles (SiNPs), fluorescent indicators obtained via a one-pot hydrothermal process. As a standard enzymatic hydrolysis product of the substrate, kaempferol 3-O-β-d-galactopyranoside (KOβDG) caused the fluorometric signal to be attenuated on kaempferol-silicon nanoparticles (K-SiNPs). The sensing methods demonstrated a satisfactory linear response in sensing β-Gala and a low detection limit. The findings showed the low limit of detection (LOD) as 0.00057 and 0.098 U/mL for fluorometric and colorimetric, respectively. The designed probe was then used to evaluate the catalytic activity of β-Gala in yogurt and human serum, with recoveries ranging from 98.33 to 107.9%. The designed sensing approach was also applied to biological sample analysis. In contrast, breast cancer cells (MCF-7) were used as a model to test the in vitro toxicity and molecular fluorescence imaging potential of K-SiNPs. Hence, our fluorescent K-SiNPs can be used in the clinic to diagnose breast cellular carcinoma, since they can accurately measure the presence of invasive ductal carcinoma in serologic tests.

High‐Efficiency Single‐Photon Upconversion Photoluminescence of Perovskite Quantum Dots via Intragap State Regulation

AbstractLead halide perovskite quantum dots (PQDs) have shown remarkable single‐photon upconversion photoluminescence (SPUC‐PL) bringing them a brilliant perspective as the active media for biological imaging, optiag, and upconversion photovoltaics. However, the mechanism of SPUC in PQDs is still in dispute, and the specific strategy for optimizing PQDs toward a higher SPUC performance has yet to be established, which impedes the application of PQDs‐based SPUC‐PL in practice. In this work it is revealed that the PL quantum yield is declined by surface trap states, while the SPUC efficiency is promoted by Urbach tail states. These two types of intragap states can be chemically manipulated by engineering the surface ligand and the growth kinetics of perovskite nanocrystals, bringing on the improvement of light emission efficiency and the promotion of subgap low‐energy photon absorption, respectively. As a proof of concept, utilizing the synergistic effect of the proposed chemical manipulation method, the SPUC‐PL efficiency of PQDs is boosted by more than 40%, which gives rise to a spectral window of optical refrigeration gain as broad as ≈130 meV.

Near-infrared mechanoluminescence sensor: A new method for on-site infrastructure detection.

Near-infrared mechanoluminescence is a phenomenon that produces high penetrating near-infrared light under external stimulation. Near-infrared light coincides with the biological window, lower optical loss, and the fact that the mechanoluminescence material is a medium that converts mechanical energy into light energy. The near-infrared mechanoluminescence material has potential application prospects in the fields of biological imaging, medical diagnosis, and monitoring of building materials. In this article, we report on a perovskite-type Sr3Sn2O7:Nd3+ near-infrared mechanoluminescence material, and its peaks locate in the first near-infrared window (800-1000 nm) and the second near-infrared window (1080, 1350 nm), respectively. Under the condition of pre-sintering with Li2CO3 as flux, the best sintering conditions are obtained, and the luminescence of material is in perfect agreement with the applied mechanical stress. In addition, a near-infrared mechanoluminescence sensor is proposed to solve the problem of building damage and timely maintenance.

High pH Stability and Ultralong‐Lived Room Temperature Phosphorescence Carbon Dots in Aqueous Environment

AbstractLong‐lived room temperature phosphorescence (RTP) materials have many potential applications in areas such as luminescent lighting, biological imaging, and information security owing to their unique optical properties. However, traditional RTP materials are challenged by the fact that their phosphorescence can be easily quenched by dissolved oxygen and solvent‐assisted relaxation, making it difficult for them to emit phosphorescence in aqueous solutions, particularly in extreme pH environments. In this study, a multicolor RTP carbon dot‐based composite material (u‐CDs) is developed with urea and 3‐aminophenylboronic acid as raw materials. This material exhibits ultra‐long phosphorescence emission lifetime and high pH stability by constructing a rigid hydrogen bond network structure in an aqueous environment. The u‐CDs have an optimal emission of 448 nm, a quantum yield of 21.6%, a phosphorescence lifetime of 2.35 s, and an afterglow time of more than 50 s. With such unique properties, u‐CDs have great potential for applications in anti‐counterfeiting, information encryption, and 3D printing.

The Artistic Characteristics of Biological Art

The new application scenarios and technology applications of biological art provide people with new ideas and ways of expression. In this space, biologists and artists can conduct more levels and richer research from different perspectives and in different ways. Biological art has made great progress in breaking through the rigid "dialogue" between biological artists and organisms to the flexible application of biological materials, the aesthetic paradigm of ecological art, and the bold expression of biological images, so that this complex has a wider tolerance. In this context, art and biotechnology in the traditional sense are converging and merging, and the cross penetration of biotechnology and art industries is spawning a new trend that is redefining design and its future. In their mutual cooperation, they try to find more and deeper cultural problems, so as to obtain more accurate and novel artistic expression.

Development of a polarity-sensitive ratiometric fluorescent probe based on the intramolecular reaction of spiro-oxazolidine and its applications for in situ visualizing the fluctuations of polarity during ER stress

Polarity is a vital element in endoplasmic reticulum (ER) microenvironment, and its variation is closely related to many physiological and pathological activities of ER, so it is necessary to trace fluctuations of polarity in ER. However, most of fluorescent probes for detecting polarity dependent on the changes of single emission, which could be affected by many factors and cause false signals. Ratiometric fluorescent probe with “built-in calibration” can effectively avoid detection errors. Here, we have designed a ratiometric fluorescent probe HM for monitoring the ER polarity based on the intramolecular reaction of spiro-oxazolidine. It forms ring open/closed isomers driven by polarity to afford ratiometric sensing. Probe HM have manifested its ratiometric responses to polarity in spectroscopic results, which could offer much more precise information for the changes of polarity in living cells with the internal built-in correction. It also showed large emission shift ( 133 nm), high selectivity and photo-stability. In biological imaging, HM could selectively accumulate in ER with high photo-stability. Importantly, HM has ability for in situ tracing the changes of ER polarity with ratiometric behavior during the ER stress process with the stimulation of tunicamycin, dithiothreitol and hypoxia, suggesting that HM is an effective molecule tool for monitoring the variations of ER polarity.

Mitophagy and its regulatory mechanisms in the biological effects of nanomaterials.

Mitophagy is a selective cellular process critical for the removal of damaged mitochondria. It is essential in regulating mitochondrial number, ensuring mitochondrial functionality, and maintaining cellular equilibrium, ultimately influencing cell destiny. Numerous pathologies, such as neurodegenerative diseases, cardiovascular disorders, cancers, and various other conditions, are associated with mitochondrial dysfunctions. Thus, a detailed exploration of the regulatory mechanisms of mitophagy is pivotal for enhancing our understanding and for the discovery of novel preventive and therapeutic options for these diseases. Nanomaterials have become integral in biomedicine and various other sectors, offering advanced solutions for medical uses including biological imaging, drug delivery, and disease diagnostics and therapy. Mitophagy is vital in managing the cellular effects elicited by nanomaterials. This review provides a comprehensive analysis of the molecular mechanisms underpinning mitophagy, underscoring its significant influence on the biological responses of cells to nanomaterials. Nanoparticles can initiate mitophagy via various pathways, among which the PINK1-Parkin pathway is critical for cellular defense against nanomaterial-induced damage by promoting mitophagy. The role of mitophagy in biological effects was induced by nanomaterials, which are associated with alterations in Ca2+ levels, the production of reactive oxygen species, endoplasmic reticulum stress, and lysosomal damage.

Encoding biological metaverse: Advancements and challenges in neural fields from macroscopic to microscopic

Neural fields can efficiently encode three-dimensional (3D) scenes, providing a bridge between two-dimensional (2D) images and virtual reality. This method becomes a trendsetter in bringing the metaverse into vivo life. It has initially captured the attention of macroscopic biology, as demonstrated by computed tomography and magnetic resonance imaging, which provide a 3D field of view for diagnostic biological images. Meanwhile, it has also opened up new research opportunities in microscopic imaging, such as achieving clearer de novo protein structure reconstructions. Introducing this method to the field of biology is particularly significant, as it is refining the approach to studying biological images. However, many biologists have yet to fully appreciate the distinctive meaning of neural fields in transforming 2D images into 3D perspectives. This article discusses the application of neural fields in both microscopic and macroscopic biological images and their practical uses in biomedicine, highlighting the broad prospects of neural fields in the future biological metaverse. We stand at the threshold of an exciting new era, where the advancements in neural field technology herald the dawn of exploring the mysteries of life in innovative ways.

Aqueous synthesis of highly luminescent AgInSe2/ZnS core/shell nanocrystals

Ternary I-III-VI chalcopyrite-type nanocrystals (NCs) range among the most important alternative materials to Cd-based NCs. Within this materials family, AgInSe2 (AISe) presents a narrower bandgap than widely studied AgInS2 (AIS), making it more suitable for numerous applications. At present, it remains a long-standing challenge to directly synthesize high-quality AISe core and AISe/ZnS core/shell NCs in aqueous solution at atmospheric pressure. In this work, we describe their synthesis using glutathione and citric acid as dual stabilizers. First, to form AISe core NCs, the Se precursor is injected into a solution containing the Ag and In complexes at 96 °C for 20 min. In the second step, the AISe/ZnS core/shell structure is created by growing the ZnS shell on the AISe NCs surface at 90 °C for 60 min. The synthesized AISe and AISe/ZnS core/shell NCs are characterized using X-ray diffraction, transmission electron microscopy, and UV-Vis absorption and photoluminescence for optical spectroscopies. After the growth of the ZnS shell, AISe/ZnS core/shell NCs exhibit higher photostability and emit intense luminescence at a wavelength of 680 nm with an impressive quantum yield (QY) of 30 %, which represents a threefold higher than the AISe core NCs. These properties make the aqueous soluble AISe/ZnS core/shell NCs favorable candidates for lighting, displays, and biological imaging applications.