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Guo X, Tian B, Li X, Lei Y, Sun M, Miao Q, Li H, Ma R, Liang H. Aptamer-Loop DNA Nanoflower Recognition and Multicolor Fluorescent Carbon Quantum Dots Labeling System for Multitarget Living Cell Imaging. ACS APPLIED MATERIALS & INTERFACES 2024; 16:45327-45336. [PMID: 39161311 DOI: 10.1021/acsami.4c09358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Visualization of multiple targets in living cells is important for understanding complex biological processes, but it still faces difficulties, such as complex operation, difficulty in multiplexing, and expensive equipment. Here, we developed a nanoplatform integrating a nucleic acid aptamer and DNA nanotechnology for living cell imaging. Aptamer-based recognition probes (RPs) were synthesized through rolling circle amplification, which were further self-assembled into DNA nanoflowers encapsulated by an aptamer loop. The signal probes (SPs) were obtained by conjugation of multicolor emission carbon quantum dots with oligonucleotides complementary to RPs. Through base pairing, RPs and SPs were hybridized to generate aptamer sgc8-, AS1411-, and Apt-based imaging systems. They were used for individual/simultaneous imaging of cellular membrane protein PTK7, nucleolin, and adenosine triphosphate (ATP) molecules. Fluorescence imaging and intensity analysis showed that the living cell imaging system can not only specifically recognize and efficiently bind their respective targets but also provide a 5-10-fold signal amplification. Cell-cycle-dependent distribution of nucleolin and concentration-dependent fluorescence intensity of ATP demonstrated the utility of the system for tracking changes in cellular status. Overall, this system shows the potential to be a simple, low-cost, highly selective, and sensitive living cell imaging platform.
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Affiliation(s)
- Xilin Guo
- College of Biomedical Engineering, Taiyuan University of Technology, 209 University Street, Jinzhong, Shanxi 030600, People's Republic of China
| | - Baohua Tian
- College of Ecology, Taiyuan University of Technology, 79 West Street Yingze, Taiyuan, Shanxi 030024, People's Republic of China
| | - Xinxin Li
- College of Ecology, Taiyuan University of Technology, 79 West Street Yingze, Taiyuan, Shanxi 030024, People's Republic of China
| | - Yu Lei
- College of Biomedical Engineering, Taiyuan University of Technology, 209 University Street, Jinzhong, Shanxi 030600, People's Republic of China
| | - Mingyuan Sun
- College of Biomedical Engineering, Taiyuan University of Technology, 209 University Street, Jinzhong, Shanxi 030600, People's Republic of China
| | - Qiang Miao
- College of Biomedical Engineering, Taiyuan University of Technology, 209 University Street, Jinzhong, Shanxi 030600, People's Republic of China
| | - Hao Li
- College of Biomedical Engineering, Taiyuan University of Technology, 209 University Street, Jinzhong, Shanxi 030600, People's Republic of China
| | - Risheng Ma
- College of Biomedical Engineering, Taiyuan University of Technology, 209 University Street, Jinzhong, Shanxi 030600, People's Republic of China
| | - Haixia Liang
- College of Biomedical Engineering, Taiyuan University of Technology, 209 University Street, Jinzhong, Shanxi 030600, People's Republic of China
- College of Ecology, Taiyuan University of Technology, 79 West Street Yingze, Taiyuan, Shanxi 030024, People's Republic of China
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Wang Q, Akram AR, Dorward DA, Talas S, Monks B, Thum C, Hopgood JR, Javidi M, Vallejo M. Deep learning-based virtual H& E staining from label-free autofluorescence lifetime images. NPJ IMAGING 2024; 2:17. [PMID: 38948152 PMCID: PMC11213708 DOI: 10.1038/s44303-024-00021-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/11/2024] [Indexed: 07/02/2024]
Abstract
Label-free autofluorescence lifetime is a unique feature of the inherent fluorescence signals emitted by natural fluorophores in biological samples. Fluorescence lifetime imaging microscopy (FLIM) can capture these signals enabling comprehensive analyses of biological samples. Despite the fundamental importance and wide application of FLIM in biomedical and clinical sciences, existing methods for analysing FLIM images often struggle to provide rapid and precise interpretations without reliable references, such as histology images, which are usually unavailable alongside FLIM images. To address this issue, we propose a deep learning (DL)-based approach for generating virtual Hematoxylin and Eosin (H&E) staining. By combining an advanced DL model with a contemporary image quality metric, we can generate clinical-grade virtual H&E-stained images from label-free FLIM images acquired on unstained tissue samples. Our experiments also show that the inclusion of lifetime information, an extra dimension beyond intensity, results in more accurate reconstructions of virtual staining when compared to using intensity-only images. This advancement allows for the instant and accurate interpretation of FLIM images at the cellular level without the complexities associated with co-registering FLIM and histology images. Consequently, we are able to identify distinct lifetime signatures of seven different cell types commonly found in the tumour microenvironment, opening up new opportunities towards biomarker-free tissue histology using FLIM across multiple cancer types.
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Affiliation(s)
- Qiang Wang
- Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Ahsan R. Akram
- Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
- Translational Healthcare Technologies Group, Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - David A. Dorward
- Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Sophie Talas
- Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Basil Monks
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Chee Thum
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - James R. Hopgood
- School of Engineering, The University of Edinburgh, Edinburgh, UK
| | - Malihe Javidi
- School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK
- Department of Computer Engineering, Quchan University of Technology, Quchan, Iran
| | - Marta Vallejo
- School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK
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Wu W, Shi Y, Liu J, Liu X, Liu H, Wang T, Zhang G, Xu Z. Carbon dots derived from expired drugs based ratiometric fluorescent sensor for horseradish peroxidase in fruits and vegetables and screening inhibitors. Mikrochim Acta 2024; 191:109. [PMID: 38246895 DOI: 10.1007/s00604-023-06160-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/16/2023] [Indexed: 01/23/2024]
Abstract
Household storage of pharmaceuticals to extract raw materials synthesized from carbon points facilitates the utilization of solid waste resources. A novel ratiometric fluorescence sensing technique was developed to ascertain the presence of horseradish peroxidase (HRP) in fruits and vegetables. The method employed a fluorescent probe, synthesized from expired amoxicillin (referred to as carbon dots, or A-CDs), serving as a reference fluorophore. Additionally, 2,3-diaminophenazine (DAP) was utilized as a specific response signal. DAP resulted from a catalytic reaction system involving phenylenediamine and hydrogen peroxide under the catalysis of HRP. The fluorescence intensity corresponding to DAP at 562 nm exhibited a substantial increase, simultaneous with the fluorescence quenching of A-CDs at 450 nm. The ratiometric fluorescence nanosensors displayed a broad linear range and high sensitivity for the detection of HRP. Across the concentration range 0.01 to 6 U L-1, the fluorescence intensity ratio between DAP and A-CDs demonstrated a proportional increase with rising HRP concentration, achieving an impressive detection limit of 0.002 U L-1. The recovery of HRP in fruit and vegetable samples ranged from 96.1 to 103%, with an RSD value of less than 3.8%. The proposed method facilitated the screening of inhibitors of HRP enzyme activity, contributing to the preservation of freshness in fruits and vegetables.
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Affiliation(s)
- Wei Wu
- Department of Chemistry, School of Science, Xihua University, Chengdu, 610039, People's Republic of China
| | - Yuhan Shi
- Department of Chemistry, School of Science, Xihua University, Chengdu, 610039, People's Republic of China
| | - Jingya Liu
- Department of Chemistry, School of Science, Xihua University, Chengdu, 610039, People's Republic of China
| | - Xiaoyu Liu
- Department of Chemistry, School of Science, Xihua University, Chengdu, 610039, People's Republic of China
| | - Hao Liu
- Department of Chemistry, School of Science, Xihua University, Chengdu, 610039, People's Republic of China
| | - Tao Wang
- Department of Chemistry, School of Science, Xihua University, Chengdu, 610039, People's Republic of China
| | - Guoqi Zhang
- Department of Chemistry, School of Science, Xihua University, Chengdu, 610039, People's Republic of China.
- Food Microbiology Key Laboratory of Sichuan Province, School of Food and Bioengineering, Xihua University, Chengdu, 610039, People's Republic of China.
| | - Zhihong Xu
- Department of Chemistry, School of Science, Xihua University, Chengdu, 610039, People's Republic of China.
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Kaushik V, Dąbrowski M, Gessa L, Kumar N, Fernandes H. Two-photon excitation fluorescence in ophthalmology: safety and improved imaging for functional diagnostics. Front Med (Lausanne) 2024; 10:1293640. [PMID: 38235268 PMCID: PMC10791900 DOI: 10.3389/fmed.2023.1293640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Two-photon excitation fluorescence (TPEF) is emerging as a powerful imaging technique with superior penetration power in scattering media, allowing for functional imaging of biological tissues at a subcellular level. TPEF is commonly used in cancer diagnostics, as it enables the direct observation of metabolism within living cells. The technique is now widely used in various medical fields, including ophthalmology. The eye is a complex and delicate organ with multiple layers of different cell types and tissues. Although this structure is ideal for visual perception, it generates aberrations in TPEF eye imaging. However, adaptive optics can now compensate for these aberrations, allowing for improved imaging of the eyes of animal models for human diseases. The eye is naturally built to filter out harmful wavelengths, but these wavelengths can be mimicked and thereby utilized in diagnostics via two-photon (2Ph) excitation. Recent advances in laser-source manufacturing have made it possible to minimize the exposure of in vivo measurements within safety, while achieving sufficient signals to detect for functional images, making TPEF a viable option for human application. This review explores recent advances in wavefront-distortion correction in animal models and the safety of use of TPEF on human subjects, both of which make TPEF a potentially powerful tool for ophthalmological diagnostics.
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Affiliation(s)
- Vineeta Kaushik
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Dąbrowski
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Luca Gessa
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Nelam Kumar
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Humberto Fernandes
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
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Coucke Q, Parveen N, Fernández GS, Qian C, Hofkens J, Debyser Z, Hendrix J. Particle-based phasor-FLIM-FRET resolves protein-protein interactions inside single viral particles. BIOPHYSICAL REPORTS 2023; 3:100122. [PMID: 37649577 PMCID: PMC10463199 DOI: 10.1016/j.bpr.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a popular modality to create additional contrast in fluorescence images. By carefully analyzing pixel-based nanosecond lifetime patterns, FLIM allows studying complex molecular populations. At the single-molecule or single-particle level, however, image series often suffer from low signal intensities per pixel, rendering it difficult to quantitatively disentangle different lifetime species, such as during Förster resonance energy transfer (FRET) analysis in the presence of a significant donor-only fraction. In this article we investigate whether an object localization strategy and the phasor approach to FLIM have beneficial effects when carrying out FRET analyses of single particles. Using simulations, we first showed that an average of ∼300 photons, spread over the different pixels encompassing single fluorescing particles and without background, is enough to determine a correct phasor signature (SD < 5% for a 4-ns lifetime). For immobilized single- or double-labeled dsDNA molecules, we next validated that particle-based phasor-FLIM-FRET readily allows estimating fluorescence lifetimes and FRET from single molecules. Thirdly, we applied particle-based phasor-FLIM-FRET to investigate protein-protein interactions in subdiffraction HIV-1 viral particles. To do this, we first quantitatively compared the fluorescence brightness, lifetime, and photostability of different popular fluorescent protein-based FRET probes when genetically fused to the HIV-1 integrase enzyme in viral particles, and conclude that eGFP, mTurquoise2, and mScarlet perform best. Finally, for viral particles coexpressing FRET-donor/acceptor-labeled IN, we determined the absolute FRET efficiency of IN oligomers. Available in a convenient open-source graphical user interface, we believe that particle-based phasor-FLIM-FRET is a promising tool to provide detailed insights in samples suffering from low overall signal intensities.
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Affiliation(s)
- Quinten Coucke
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Nagma Parveen
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Guillermo Solís Fernández
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- UFIEC, National Institute of Health Carlos III, Madrid, Spain
| | - Chen Qian
- Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science Munich (CIPSM), and Nanosystems Initiative Munich (NIM), Ludwig Maximilians-Universität München, Munich, Germany
| | - Johan Hofkens
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Hasselt, Belgium
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Palczewska G, Wojtkowski M, Palczewski K. From mouse to human: Accessing the biochemistry of vision in vivo by two-photon excitation. Prog Retin Eye Res 2023; 93:101170. [PMID: 36787681 PMCID: PMC10463242 DOI: 10.1016/j.preteyeres.2023.101170] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/13/2023]
Abstract
The eye is an ideal organ for imaging by a multi-photon excitation approach, because ocular tissues such as the sclera, cornea, lens and neurosensory retina, are highly transparent to infrared (IR) light. The interface between the retina and the retinal pigment epithelium (RPE) is especially informative, because it reflects the health of the visual (retinoid) cycle and its changes in response to external stress, genetic manipulations, and drug treatments. Vitamin A-derived retinoids, like retinyl esters, are natural fluorophores that respond to multi-photon excitation with near IR light, bypassing the filter-like properties of the cornea, lens, and macular pigments. Also, during natural aging some retinoids form bisretinoids, like diretinoid-pyridiniumethanolamine (A2E), that are highly fluorescent. These bisretinoids appear to be elevated concurrently with aging. Vitamin A-derived retinoids and bisretinoidss are detected by two-photon ophthalmoscopy (2PO), using a new class of light sources with adjustable spatial, temporal, and spectral properties. Furthermore, the two-photon (2P) absorption of IR light by the visual pigments in rod and cone photoreceptors can initiate visual transduction by cis-trans isomerization of retinal, enabling parallel functional studies. Recently we overcame concerns about safety, data interpretation and complexity of the 2P-based instrumentation, the major roadblocks toward advancing this modality to the clinic. These imaging and retina-function assessment advancements have enabled us to conduct the first 2P studies with humans.
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Affiliation(s)
- Grazyna Palczewska
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA; International Center for Translational Eye Research, Polish Academy of Sciences, Warsaw, Poland; Polgenix, Inc., Department of Medical Devices, Cleveland, OH, USA; Department of Physical Chemistry of Biological Systems, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| | - Maciej Wojtkowski
- International Center for Translational Eye Research, Polish Academy of Sciences, Warsaw, Poland; Department of Physical Chemistry of Biological Systems, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland; Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Torun, Poland.
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA; Department of Physiology & Biophysics, School of Medicine, And Chemistry, Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
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