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Son A, Kim W, Park J, Lee W, Lee Y, Choi S, Kim H. Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics. Int J Mol Sci 2024; 25:9725. [PMID: 39273672 PMCID: PMC11395565 DOI: 10.3390/ijms25179725] [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: 08/01/2024] [Revised: 09/06/2024] [Accepted: 09/07/2024] [Indexed: 09/15/2024] Open
Abstract
Protein dynamics play a crucial role in biological function, encompassing motions ranging from atomic vibrations to large-scale conformational changes. Recent advancements in experimental techniques, computational methods, and artificial intelligence have revolutionized our understanding of protein dynamics. Nuclear magnetic resonance spectroscopy provides atomic-resolution insights, while molecular dynamics simulations offer detailed trajectories of protein motions. Computational methods applied to X-ray crystallography and cryo-electron microscopy (cryo-EM) have enabled the exploration of protein dynamics, capturing conformational ensembles that were previously unattainable. The integration of machine learning, exemplified by AlphaFold2, has accelerated structure prediction and dynamics analysis. These approaches have revealed the importance of protein dynamics in allosteric regulation, enzyme catalysis, and intrinsically disordered proteins. The shift towards ensemble representations of protein structures and the application of single-molecule techniques have further enhanced our ability to capture the dynamic nature of proteins. Understanding protein dynamics is essential for elucidating biological mechanisms, designing drugs, and developing novel biocatalysts, marking a significant paradigm shift in structural biology and drug discovery.
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Affiliation(s)
- Ahrum Son
- Department of Molecular Medicine, Scripps Research, San Diego, CA 92037, USA
| | - Woojin Kim
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Jongham Park
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Wonseok Lee
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Yerim Lee
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Seongyun Choi
- Department of Convergent Bioscience and Informatics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Hyunsoo Kim
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
- Department of Convergent Bioscience and Informatics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
- Protein AI Design Institute, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
- SCICS, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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2
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Sheng CQ, Wu SS, Cheng YK, Wu Y, Li YM. Comprehensive review of indicators and techniques for optical mapping of intracellular calcium ions. Cereb Cortex 2024; 34:bhae346. [PMID: 39191664 DOI: 10.1093/cercor/bhae346] [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: 05/01/2024] [Revised: 07/27/2024] [Accepted: 08/09/2024] [Indexed: 08/29/2024] Open
Abstract
Calcium ions (Ca2+) play crucial roles in almost every cellular process, making the detection of changes in intracellular Ca2+ essential to understanding cell function. The fluorescence indicator method has garnered widespread application due to its exceptional sensitivity, rapid analysis, cost-effectiveness, and user-friendly nature. It has successfully delineated the spatial and temporal dynamics of Ca2+ signaling across diverse cell types. However, it is vital to understand that different indicators have varying levels of accuracy, sensitivity, and stability, making choosing the right inspection method crucial. As optical detection technologies advance, they continually broaden the horizons of scientific inquiry. This primer offers a systematic synthesis of the current fluorescence indicators and optical imaging modalities utilized for the detection of intracellular Ca2+. It elucidates their practical applications and inherent limitations, serving as an essential reference for researchers seeking to identify the most suitable detection methodologies for their calcium-centric investigations.
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Affiliation(s)
- Chu-Qiao Sheng
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, No. 2699, Qianjin Street, Changchun, Jilin 130012, China
| | - Shuang-Shuang Wu
- Department of Pediatric Hematology, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yong-Kang Cheng
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yao Wu
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yu-Mei Li
- Department of Pediatric Intensive Care Unit, Children's Medical Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
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Kahali S, Das SK, Kumar R, Gupta K, Kundu R, Bhattacharya B, Nath A, Venkatramani R, Datta A. A water-soluble, cell-permeable Mn(ii) sensor enables visualization of manganese dynamics in live mammalian cells. Chem Sci 2024; 15:10753-10769. [PMID: 39027293 PMCID: PMC11253179 DOI: 10.1039/d4sc00907j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
Central roles of Mn2+ ions in immunity, brain function, and photosynthesis necessitate probes for tracking this essential metal ion in living systems. However, developing a cell-permeable, fluorescent sensor for selective imaging of Mn2+ ions in the aqueous cellular milieu has remained a challenge. This is because Mn2+ is a weak binder to ligand-scaffolds and Mn2+ ions quench fluorescent dyes leading to turn-off sensors that are not applicable for in vivo imaging. Sensors with a unique combination of Mn2+ selectivity, μM sensitivity, and response in aqueous media are necessary for not only visualizing labile cellular Mn2+ ions live, but also for measuring Mn2+ concentrations in living cells. No sensor has achieved this combination thus far. Here we report a novel, completely water-soluble, reversible, fluorescent turn-on, Mn2+ selective sensor, M4, with a K d of 1.4 μM for Mn2+ ions. M4 entered cells within 15 min of direct incubation and was applied to image Mn2+ ions in living mammalian cells in both confocal fluorescence intensity and lifetime-based set-ups. The probe was able to visualize Mn2+ dynamics in live cells revealing differential Mn2+ localization and uptake dynamics under pathophysiological versus physiological conditions. In a key experiment, we generated an in-cell Mn2+ response curve for the sensor which allowed the measurement of the endogenous labile Mn2+ concentration in HeLa cells as 1.14 ± 0.15 μM. Thus, our computationally designed, selective, sensitive, and cell-permeable sensor with a 620 nM limit of detection for Mn2+ in water provides the first estimate of endogenous labile Mn2+ levels in mammalian cells.
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Affiliation(s)
- Smitaroopa Kahali
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Sujit Kumar Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Ravinder Kumar
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Kunika Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Rajasree Kundu
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Baivabi Bhattacharya
- Department of Developmental Biology and Genetics, Indian Institute of Science Bangalore 560012 India
| | - Arnab Nath
- Department of Developmental Biology and Genetics, Indian Institute of Science Bangalore 560012 India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
| | - Ankona Datta
- Department of Chemical Sciences, Tata Institute of Fundamental Research 1 Homi Bhabha Road Mumbai 400005 India
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Molnar N, Miskolci V. Imaging immunometabolism in situ in live animals. IMMUNOMETABOLISM (COBHAM, SURREY) 2024; 6:e00044. [PMID: 39296471 PMCID: PMC11406703 DOI: 10.1097/in9.0000000000000044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Immunometabolism is a rapidly developing field that holds great promise for diagnostic and therapeutic benefits to human diseases. The field has emerged based on seminal findings from in vitro and ex vivo studies that established the fundamental role of metabolism in immune cell effector functions. Currently, the field is acknowledging the necessity of investigating cellular metabolism within the natural context of biological processes. Examining cells in their native microenvironment is essential not only to reveal cell-intrinsic mechanisms but also to understand how cross-talk between neighboring cells regulates metabolism at the tissue level in a local niche. This necessity is driving innovation and advancement in multiple imaging-based technologies to enable analysis of dynamic intracellular metabolism at the single-cell level, with spatial and temporal resolution. In this review, we tally the currently available imaging-based technologies and explore the emerging methods of Raman and autofluorescence lifetime imaging microscopy, which hold significant potential and offer broad applications in the field of immunometabolism.
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Affiliation(s)
- Nicole Molnar
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers Health, Rutgers University, Newark, NJ, USA
- Center for Cell Signaling, Rutgers Health, Rutgers University, Newark, NJ, USA
- Center for Immunity and Inflammation, Rutgers Health, Rutgers University, Newark, NJ, USA
| | - Veronika Miskolci
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers Health, Rutgers University, Newark, NJ, USA
- Center for Cell Signaling, Rutgers Health, Rutgers University, Newark, NJ, USA
- Center for Immunity and Inflammation, Rutgers Health, Rutgers University, Newark, NJ, USA
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Chmykh Y, Nadeau JL. The use of fluorescence lifetime imaging (FLIM) for in situ microbial detection in complex mineral substrates. J Microsc 2024; 294:36-51. [PMID: 38230460 DOI: 10.1111/jmi.13264] [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: 08/01/2023] [Revised: 12/16/2023] [Accepted: 01/09/2024] [Indexed: 01/18/2024]
Abstract
The utility of fluorescence lifetime imaging microscopy (FLIM) for identifying bacteria in complex mineral matrices was investigated. Baseline signals from unlabelled Bacillus subtilis and Euglena gracilis, and Bacillus subtilis labelled with SYTO 9 were obtained using two-photon excitation at 730, 750 and 800 nm, identifying characteristic lifetimes of photosynthetic pigments, unpigmented cellular autofluorescence, and SYTO 9. Labelled and unlabelled B. subtilis were seeded onto marble and gypsum samples containing endolithic photosynthetic cyanobacteria and the ability to distinguish cells from mineral autofluorescence and nonspecific dye staining was examined in parallel with ordinary multichannel confocal imaging. It was found that FLIM enabled discrimination of SYTO 9 labelled cells from background, but that the lifetime of SYTO 9 was shorter in cells on minerals than in pure culture under our conditions. Photosynthetic microorganisms were easily observed using both FLIM and confocal. Unlabelled, nonpigmented bacteria showed weak signals that were difficult to distinguish from background when minerals were present, though cellular autofluorescence consistent with NAD(P)H could be seen in pure cultures, and phasor analysis permitted detection on rocks. Gypsum and marble samples showed similar autofluorescence profiles, with little autofluorescence in the yellow-to-red range. Lifetime or time-gated imaging may prove a useful tool for environmental microbiology. LAY DESCRIPTION: The standard method of bacterial enumeration is to label the cells with a fluorescent dye and count them under high-power fluorescence microscopy. However, this can be difficult when the cells are embedded in soil and rock due to fluorescence from the surrounding minerals and dye binding to ambiguous features of the substrate. The use of fluorescence lifetime imaging (FLIM) can disambiguate these signals and allow for improved detection of bacteria in environmental samples.
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Affiliation(s)
- Yekaterina Chmykh
- Department of Physics, Portland State University, Portland, Oregon, USA
| | - Jay L Nadeau
- Department of Physics, Portland State University, Portland, Oregon, USA
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Gouzou D, Taimori A, Haloubi T, Finlayson N, Wang Q, Hopgood JR, Vallejo M. Applications of machine learning in time-domain fluorescence lifetime imaging: a review. Methods Appl Fluoresc 2024; 12:022001. [PMID: 38055998 PMCID: PMC10851337 DOI: 10.1088/2050-6120/ad12f7] [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: 06/30/2023] [Revised: 09/25/2023] [Accepted: 12/06/2023] [Indexed: 12/08/2023]
Abstract
Many medical imaging modalities have benefited from recent advances in Machine Learning (ML), specifically in deep learning, such as neural networks. Computers can be trained to investigate and enhance medical imaging methods without using valuable human resources. In recent years, Fluorescence Lifetime Imaging (FLIm) has received increasing attention from the ML community. FLIm goes beyond conventional spectral imaging, providing additional lifetime information, and could lead to optical histopathology supporting real-time diagnostics. However, most current studies do not use the full potential of machine/deep learning models. As a developing image modality, FLIm data are not easily obtainable, which, coupled with an absence of standardisation, is pushing back the research to develop models which could advance automated diagnosis and help promote FLIm. In this paper, we describe recent developments that improve FLIm image quality, specifically time-domain systems, and we summarise sensing, signal-to-noise analysis and the advances in registration and low-level tracking. We review the two main applications of ML for FLIm: lifetime estimation and image analysis through classification and segmentation. We suggest a course of action to improve the quality of ML studies applied to FLIm. Our final goal is to promote FLIm and attract more ML practitioners to explore the potential of lifetime imaging.
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Affiliation(s)
- Dorian Gouzou
- Dorian Gouzou and Marta Vallejo are with Institute of Signals, Sensors and Systems, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, EH14 4AS, United Kingdom
| | - Ali Taimori
- Tarek Haloubi, Ali Taimori, and James R. Hopgood are with Institute for Imaging, Data and Communication, School of Engineering, University of Edinburgh, Edinburgh, EH9 3FG, United Kingdom
| | - Tarek Haloubi
- Tarek Haloubi, Ali Taimori, and James R. Hopgood are with Institute for Imaging, Data and Communication, School of Engineering, University of Edinburgh, Edinburgh, EH9 3FG, United Kingdom
| | - Neil Finlayson
- Neil Finlayson is with Institute for Integrated Micro and Nano Systems, School of Engineering, University ofEdinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Qiang Wang
- Qiang Wang is with Centre for Inflammation Research, University of Edinburgh, Edinburgh, EH16 4TJ, United Kingdom
| | - James R Hopgood
- Tarek Haloubi, Ali Taimori, and James R. Hopgood are with Institute for Imaging, Data and Communication, School of Engineering, University of Edinburgh, Edinburgh, EH9 3FG, United Kingdom
| | - Marta Vallejo
- Dorian Gouzou and Marta Vallejo are with Institute of Signals, Sensors and Systems, School of Engineering and Physical Sciences, Heriot Watt University, Edinburgh, EH14 4AS, United Kingdom
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Harel M, Arbiv U, Ankri R. Multiplexed near infrared fluorescence lifetime imaging in turbid media. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:026004. [PMID: 38425720 PMCID: PMC10902792 DOI: 10.1117/1.jbo.29.2.026004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/23/2024] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
Significance Fluorescence lifetime imaging (FLI) plays a pivotal role in enhancing our understanding of biological systems, providing a valuable tool for non-invasive exploration of biomolecular and cellular dynamics, both in vitro and in vivo. Its ability to selectively target and multiplex various entities, alongside heightened sensitivity and specificity, offers rapid and cost-effective insights. Aim Our aim is to investigate the multiplexing capabilities of near-infrared (NIR) FLI within a scattering medium that mimics biological tissues. We strive to develop a comprehensive understanding of FLI's potential for multiplexing diverse targets within a complex, tissue-like environment. Approach We introduce an innovative Monte Carlo (MC) simulation approach that accurately describes the scattering behavior of fluorescent photons within turbid media. Applying phasor analyses, we enable the multiplexing of distinct targets within a single FLI image. Leveraging the state-of-the-art single-photon avalanche diode (SPAD) time-gated camera, SPAD512S, we conduct experimental wide-field FLI in the NIR regime. Results Our study demonstrates the successful multiplexing of dual targets within a single FLI image, reaching a depth of 1 cm within tissue-like phantoms. Through our novel MC simulation approach and phasor analyses, we showcase the effectiveness of our methodology in overcoming the challenges posed by scattering media. Conclusions This research underscores the potential of NIR FLI for multiplexing applications in complex biological environments. By combining advanced simulation techniques with cutting-edge experimental tools, we introduce significant results in the non-invasive exploration of biomolecular dynamics, to advance the field of FLI research.
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Affiliation(s)
- Meital Harel
- Ariel University, Department of Physics, Faculty of Natural Science, Ariel, Israel
| | - Uri Arbiv
- Ariel University, Department of Physics, Faculty of Natural Science, Ariel, Israel
| | - Rinat Ankri
- Ariel University, Department of Physics, Faculty of Natural Science, Ariel, Israel
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Shirmanova MV, Lukina MM, Sirotkina MA, Shimolina LE, Dudenkova VV, Ignatova NI, Tobita S, Shcheslavskiy VI, Zagaynova EV. Effects of Photodynamic Therapy on Tumor Metabolism and Oxygenation Revealed by Fluorescence and Phosphorescence Lifetime Imaging. Int J Mol Sci 2024; 25:1703. [PMID: 38338976 PMCID: PMC10855179 DOI: 10.3390/ijms25031703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
This work was aimed at the complex analysis of the metabolic and oxygen statuses of tumors in vivo after photodynamic therapy (PDT). Studies were conducted on mouse tumor model using two types of photosensitizers-chlorin e6-based drug Photoditazine predominantly targeted to the vasculature and genetically encoded photosensitizer KillerRed targeted to the chromatin. Metabolism of tumor cells was assessed by the fluorescence lifetime of the metabolic redox-cofactor NAD(P)H, using fluorescence lifetime imaging. Oxygen content was assessed using phosphorescence lifetime macro-imaging with an oxygen-sensitive probe. For visualization of the perfused microvasculature, an optical coherence tomography-based angiography was used. It was found that PDT induces different alterations in cellular metabolism, depending on the degree of oxygen depletion. Moderate decrease in oxygen in the case of KillerRed was accompanied by an increase in the fraction of free NAD(P)H, an indicator of glycolytic switch, early after the treatment. Severe hypoxia after PDT with Photoditazine resulted from a vascular shutdown yielded in a persistent increase in protein-bound (mitochondrial) fraction of NAD(P)H. These findings improve our understanding of physiological mechanisms of PDT in cellular and vascular modes and can be useful to develop new approaches to monitoring its efficacy.
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Affiliation(s)
- Marina V. Shirmanova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia
| | - Maria M. Lukina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya, 1a, 119435 Moscow, Russia
| | - Marina A. Sirotkina
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia
| | - Liubov E. Shimolina
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia
| | - Varvara V. Dudenkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia
| | - Nadezhda I. Ignatova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia
| | - Seiji Tobita
- Department of Chemistry and Chemical Biology, Gunma University, Kiryu 376-8515, Gunma, Japan
| | - Vladislav I. Shcheslavskiy
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia
| | - Elena V. Zagaynova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya, 1a, 119435 Moscow, Russia
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Gottlieb D, Asadipour B, Kostina P, Ung TPL, Stringari C. FLUTE: A Python GUI for interactive phasor analysis of FLIM data. BIOLOGICAL IMAGING 2023; 3:e21. [PMID: 38487690 PMCID: PMC10936343 DOI: 10.1017/s2633903x23000211] [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: 04/20/2023] [Revised: 09/16/2023] [Accepted: 10/25/2023] [Indexed: 03/17/2024]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique used to probe the local environment of fluorophores. The fit-free phasor approach to FLIM data is increasingly being used due to its ease of interpretation. To date, no open-source graphical user interface (GUI) for phasor analysis of FLIM data is available in Python, thus limiting the widespread use of phasor analysis in biomedical research. Here, we present Fluorescence Lifetime Ultimate Explorer (FLUTE), a Python GUI that is designed to fill this gap. FLUTE simplifies and automates many aspects of the analysis of FLIM data acquired in the time domain, such as calibrating the FLIM data, performing interactive exploration of the phasor plot, displaying phasor plots and FLIM images with different lifetime contrasts simultaneously, and calculating the distance from known molecular species. After applying desired filters and thresholds, the final edited datasets can be exported for further user-specific analysis. FLUTE has been tested using several FLIM datasets including autofluorescence of zebrafish embryos and in vitro cells. In summary, our user-friendly GUI extends the advantages of phasor plotting by making the data visualization and analysis easy and interactive, allows for analysis of large FLIM datasets, and accelerates FLIM analysis for non-specialized labs.
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Affiliation(s)
- Dale Gottlieb
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Bahar Asadipour
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Polina Kostina
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Thi Phuong Lien Ung
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Chiara Stringari
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
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10
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Campbell JM, Habibalahi A, Handley S, Agha A, Mahbub SB, Anwer AG, Goldys EM. Emerging clinical applications in oncology for non-invasive multi- and hyperspectral imaging of cell and tissue autofluorescence. JOURNAL OF BIOPHOTONICS 2023; 16:e202300105. [PMID: 37272291 DOI: 10.1002/jbio.202300105] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/16/2023] [Indexed: 06/06/2023]
Abstract
Hyperspectral and multispectral imaging of cell and tissue autofluorescence is an emerging technology in which fluorescence imaging is applied to biological materials across multiple spectral channels. This produces a stack of images where each matched pixel contains information about the sample's spectral properties at that location. This allows precise collection of molecularly specific data from a broad range of native fluorophores. Importantly, complex information, directly reflective of biological status, is collected without staining and tissues can be characterised in situ, without biopsy. For oncology, this can spare the collection of biopsies from sensitive regions and enable accurate tumour mapping. For in vivo tumour analysis, the greatest focus has been on oral cancer, whereas for ex vivo assessment head-and-neck cancers along with colon cancer have been the most studied, followed by oral and eye cancer. This review details the scope and progress of research undertaken towards clinical translation in oncology.
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Affiliation(s)
- Jared M Campbell
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, South Australia, Australia
| | - Abbas Habibalahi
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, South Australia, Australia
| | - Shannon Handley
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, South Australia, Australia
| | - Adnan Agha
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, South Australia, Australia
| | - Saabah B Mahbub
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ayad G Anwer
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ewa M Goldys
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, South Australia, Australia
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11
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Zhou X, Bec J, Ehrlich K, Garcia AA, Marcu L. Pulse-sampling fluorescence lifetime imaging: evaluation of photon economy. OPTICS LETTERS 2023; 48:4578-4581. [PMID: 37656559 PMCID: PMC10883700 DOI: 10.1364/ol.490096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/26/2023] [Indexed: 09/03/2023]
Abstract
This Letter presents an experimental study comparing the photon rate and photon economy of pulse sampling fluorescence lifetime imaging (PS-FLIm) with the conventional time-correlated single photon counting (TCSPC) technique. We found that PS-FLIm has a significantly higher photon detection rate (200 MHz) compared with TCSPC (2-8 MHz) but lower photon economy (4-5 versus 1-1.3). The main factor contributing to the lower photon economy in PS-FLIm is laser pulse variability. These results demonstrate that PS-FLIm offers 25× faster imaging speed than TCSPC while maintaining room light rejection in clinical settings. This makes PS-FLIm a robust technique for clinical applications.
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Rodimova S, Mozherov A, Elagin V, Karabut M, Shchechkin I, Kozlov D, Krylov D, Gavrina A, Bobrov N, Zagainov V, Zagaynova E, Kuznetsova D. Effect of Hepatic Pathology on Liver Regeneration: The Main Metabolic Mechanisms Causing Impaired Hepatic Regeneration. Int J Mol Sci 2023; 24:ijms24119112. [PMID: 37298064 DOI: 10.3390/ijms24119112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
Liver regeneration has been studied for many decades, and the mechanisms underlying regeneration of normal liver following resection are well described. However, no less relevant is the study of mechanisms that disrupt the process of liver regeneration. First of all, a violation of liver regeneration can occur in the presence of concomitant hepatic pathology, which is a key factor reducing the liver's regenerative potential. Understanding these mechanisms could enable the rational targeting of specific therapies to either reduce the factors inhibiting regeneration or to directly stimulate liver regeneration. This review describes the known mechanisms of normal liver regeneration and factors that reduce its regenerative potential, primarily at the level of hepatocyte metabolism, in the presence of concomitant hepatic pathology. We also briefly discuss promising strategies for stimulating liver regeneration and those concerning methods for assessing the regenerative potential of the liver, especially intraoperatively.
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Affiliation(s)
- Svetlana Rodimova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603000 Nizhny Novgorod, Russia
| | - Artem Mozherov
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603000 Nizhny Novgorod, Russia
- Laboratory of Molecular Genetic Research, Institute of Clinical Medicine, N.I. Lobachevsky Nizhny Novgorod National Research State University, 23 Gagarina Ave., 603022 Nizhny Novgorod, Russia
| | - Vadim Elagin
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603000 Nizhny Novgorod, Russia
| | - Maria Karabut
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603000 Nizhny Novgorod, Russia
| | - Ilya Shchechkin
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603000 Nizhny Novgorod, Russia
- Laboratory of Molecular Genetic Research, Institute of Clinical Medicine, N.I. Lobachevsky Nizhny Novgorod National Research State University, 23 Gagarina Ave., 603022 Nizhny Novgorod, Russia
| | - Dmitry Kozlov
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603000 Nizhny Novgorod, Russia
- Laboratory of Molecular Genetic Research, Institute of Clinical Medicine, N.I. Lobachevsky Nizhny Novgorod National Research State University, 23 Gagarina Ave., 603022 Nizhny Novgorod, Russia
| | - Dmitry Krylov
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603000 Nizhny Novgorod, Russia
- Laboratory of Molecular Genetic Research, Institute of Clinical Medicine, N.I. Lobachevsky Nizhny Novgorod National Research State University, 23 Gagarina Ave., 603022 Nizhny Novgorod, Russia
| | - Alena Gavrina
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603000 Nizhny Novgorod, Russia
- Laboratory of Molecular Genetic Research, Institute of Clinical Medicine, N.I. Lobachevsky Nizhny Novgorod National Research State University, 23 Gagarina Ave., 603022 Nizhny Novgorod, Russia
| | - Nikolai Bobrov
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603000 Nizhny Novgorod, Russia
- The Volga District Medical Centre of Federal Medical and Biological Agency, 14 Ilinskaya St., 603000 Nizhny Novgorod, Russia
| | - Vladimir Zagainov
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603000 Nizhny Novgorod, Russia
- Nizhny Novgorod Regional Clinical Oncologic Dispensary, Delovaya St., 11/1, 603126 Nizhny Novgorod, Russia
| | - Elena Zagaynova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603000 Nizhny Novgorod, Russia
| | - Daria Kuznetsova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603000 Nizhny Novgorod, Russia
- Laboratory of Molecular Genetic Research, Institute of Clinical Medicine, N.I. Lobachevsky Nizhny Novgorod National Research State University, 23 Gagarina Ave., 603022 Nizhny Novgorod, Russia
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13
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Zimyanin VL, Pielka AM, Glaß H, Japtok J, Großmann D, Martin M, Deussen A, Szewczyk B, Deppmann C, Zunder E, Andersen PM, Boeckers TM, Sterneckert J, Redemann S, Storch A, Hermann A. Live Cell Imaging of ATP Levels Reveals Metabolic Compartmentalization within Motoneurons and Early Metabolic Changes in FUS ALS Motoneurons. Cells 2023; 12:1352. [PMID: 37408187 PMCID: PMC10216752 DOI: 10.3390/cells12101352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/24/2023] [Accepted: 04/30/2023] [Indexed: 07/07/2023] Open
Abstract
Motoneurons are one of the most energy-demanding cell types and a primary target in Amyotrophic lateral sclerosis (ALS), a debilitating and lethal neurodegenerative disorder without currently available effective treatments. Disruption of mitochondrial ultrastructure, transport, and metabolism is a commonly reported phenotype in ALS models and can critically affect survival and the proper function of motor neurons. However, how changes in metabolic rates contribute to ALS progression is not fully understood yet. Here, we utilize hiPCS-derived motoneuron cultures and live imaging quantitative techniques to evaluate metabolic rates in fused in sarcoma (FUS)-ALS model cells. We show that differentiation and maturation of motoneurons are accompanied by an overall upregulation of mitochondrial components and a significant increase in metabolic rates that correspond to their high energy-demanding state. Detailed compartment-specific live measurements using a fluorescent ATP sensor and FLIM imaging show significantly lower levels of ATP in the somas of cells carrying FUS-ALS mutations. These changes lead to the increased vulnerability of diseased motoneurons to further metabolic challenges with mitochondrial inhibitors and could be due to the disruption of mitochondrial inner membrane integrity and an increase in its proton leakage. Furthermore, our measurements demonstrate heterogeneity between axonal and somatic compartments, with lower relative levels of ATP in axons. Our observations strongly support the hypothesis that mutated FUS impacts the metabolic states of motoneurons and makes them more susceptible to further neurodegenerative mechanisms.
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Affiliation(s)
- Vitaly L Zimyanin
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Center for Membrane and Cell Physiology, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Neurology, Technische Universität Dresden, 01307 Dresden, Germany
| | - Anna-Maria Pielka
- Translational Neurodegeneration Section, "Albrecht Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
| | - Hannes Glaß
- Translational Neurodegeneration Section, "Albrecht Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
| | - Julia Japtok
- Department of Neurology, Technische Universität Dresden, 01307 Dresden, Germany
| | - Dajana Großmann
- Translational Neurodegeneration Section, "Albrecht Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
| | - Melanie Martin
- Institute of Physiology, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Deussen
- Institute of Physiology, Technische Universität Dresden, 01307 Dresden, Germany
| | - Barbara Szewczyk
- Translational Neurodegeneration Section, "Albrecht Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
| | - Chris Deppmann
- Department of Biology, Graduate School of Arts and Sciences, University of Virginia, Charlottesville, VA 22902, USA
| | - Eli Zunder
- Department of Biomedical Engineering, School of Medicine, University of Virginia, Charlottesville, VA 22902, USA
| | - Peter M Andersen
- Department of Clinical Sciences, Neurosciences, Umeå University, SE-901 85 Umeå, Sweden
| | - Tobias M Boeckers
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Ulm Site, 89081 Ulm, Germany
- Institute for Anatomy and Cell Biology, Ulm University, 89081 Ulm, Germany
| | - Jared Sterneckert
- Centre for Regenerative Therapie, Technische Universität Dresden, 01307 Dresden, Germany
- Medical Faculty Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Stefanie Redemann
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Center for Membrane and Cell Physiology, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Cell Biology, School of Medicine, University of Virginia, Charlottesville, VA 22902, USA
| | - Alexander Storch
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald, 18147 Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Centre, University of Rostock, 18147 Rostock, Germany
- Department of Neurology, University of Rostock, 18147 Rostock, Germany
| | - Andreas Hermann
- Translational Neurodegeneration Section, "Albrecht Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald, 18147 Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Centre, University of Rostock, 18147 Rostock, Germany
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Campbell JM, Mahbub SB, Habibalahi A, Agha A, Handley S, Anwer AG, Goldys EM. Clinical applications of non-invasive multi and hyperspectral imaging of cell and tissue autofluorescence beyond oncology. JOURNAL OF BIOPHOTONICS 2023; 16:e202200264. [PMID: 36602432 DOI: 10.1002/jbio.202200264] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/20/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Hyperspectral and multispectral imaging of cell and tissue autofluorescence employs fluorescence imaging, without exogenous fluorophores, across multiple excitation/emission combinations (spectral channels). This produces an image stack where each pixel (matched by location) contains unique information about the sample's spectral properties. Analysis of this data enables access to a rich, molecularly specific data set from a broad range of cell-native fluorophores (autofluorophores) directly reflective of biochemical status, without use of fixation or stains. This non-invasive, non-destructive technology has great potential to spare the collection of biopsies from sensitive regions. As both staining and biopsy may be impossible, or undesirable, depending on the context, this technology great diagnostic potential for clinical decision making. The main research focus has been on the identification of neoplastic tissues. However, advances have been made in diverse applications-including ophthalmology, cardiovascular health, neurology, infection, assisted reproduction technology and organ transplantation.
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Affiliation(s)
- Jared M Campbell
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Sydney, Australia
| | - Saabah B Mahbub
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Sydney, Australia
| | - Abbas Habibalahi
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Sydney, Australia
| | - Adnan Agha
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Sydney, Australia
| | - Shannon Handley
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Sydney, Australia
| | - Ayad G Anwer
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Sydney, Australia
| | - Ewa M Goldys
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, Sydney, Australia
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15
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Sun N, Jia Y, Bai S, Li Q, Dai L, Li J. The power of super-resolution microscopy in modern biomedical science. Adv Colloid Interface Sci 2023; 314:102880. [PMID: 36965225 DOI: 10.1016/j.cis.2023.102880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Super-resolution microscopy (SRM) technology that breaks the diffraction limit has revolutionized the field of cell biology since its appearance, which enables researchers to visualize cellular structures with nanometric resolution, multiple colors and single-molecule sensitivity. With the flourishing development of hardware and the availability of novel fluorescent probes, the impact of SRM has already gone beyond cell biology and extended to nanomedicine, material science and nanotechnology, and remarkably boosted important breakthroughs in these fields. In this review, we will mainly highlight the power of SRM in modern biomedical science, discussing how these SRM techniques revolutionize the way we understand cell structures, biomaterials assembly and how assembled biomaterials interact with cellular organelles, and finally their promotion to the clinical pre-diagnosis. Moreover, we also provide an outlook on the current technical challenges and future improvement direction of SRM. We hope this review can provide useful information, inspire new ideas and propel the development both from the perspective of SRM techniques and from the perspective of SRM's applications.
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Affiliation(s)
- Nan Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049
| | - Yi Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Shiwei Bai
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049
| | - Qi Li
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences, Beijing 100190, China
| | - Luru Dai
- Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049.
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16
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Integration of Decay Time Analysis and Radiation Measurement for Quantum-Dot-Based Scintillator’s Characterization. Processes (Basel) 2022. [DOI: 10.3390/pr10101920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this study, we demonstrated the process of an integrated apparatus for decay time analysis and gamma radiation measurement with a liquid-scintillator-based cadmium-doped zinc oxide (CZO) nanomaterial. Generally, time-resolved photon counting is an essential analysis method in the field of precision measurement in the quantum domain. Such photon counting equipment requires a pulse laser that can be repeated quickly while having a sharp pulse width of picoseconds or femtoseconds as a light source. Time-correlated single photon counting (TCSPC) equipment, which is currently a commercial product, is inconvenient for recent development research because the scintillator size and shape are limited. Here, neodymium-doped yttrium aluminum garnet (Nd/YAG) laser TCSPC equipment was constructed to analyze the fluorescence characteristics of scintillators having various sizes and shapes. Then, a liquid scintillator added with CZO nanomaterial was prepared and the Nd/YAG laser TCSPC equipment test was performed. As a result of measuring the scintillator using the manufactured Nd/YAG laser TCSPC equipment, the non-CZO liquid scintillator was analyzed at 2.30 ns and the liquid scintillator equipped with CZO-loaded nanomaterial was analyzed at 11.95 ns. It showed an error within 5% when compared with the result of commercial TCSPC equipment. In addition, it was verified that the Nd/YAG laser TCSPC system can sufficiently measure the decay time in nanoseconds (ns). Moreover, it was presented that the Compton edge energy of Cs−137 is 477.3 keV, which hardly generates a photoelectric effect, and Compton scattering mainly occurs.
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17
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Humayun M, Ayuso JM, Park KY, Martorelli Di Genova B, Skala MC, Kerr SC, Knoll LJ, Beebe DJ. Innate immune cell response to host-parasite interaction in a human intestinal tissue microphysiological system. SCIENCE ADVANCES 2022; 8:eabm8012. [PMID: 35544643 PMCID: PMC9075809 DOI: 10.1126/sciadv.abm8012] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/23/2022] [Indexed: 05/03/2023]
Abstract
Protozoan parasites that infect humans are widespread and lead to varied clinical manifestations, including life-threatening illnesses in immunocompromised individuals. Animal models have provided insight into innate immunity against parasitic infections; however, species-specific differences and complexity of innate immune responses make translation to humans challenging. Thus, there is a need for in vitro systems that can elucidate mechanisms of immune control and parasite dissemination. We have developed a human microphysiological system of intestinal tissue to evaluate parasite-immune-specific interactions during infection, which integrates primary intestinal epithelial cells and immune cells to investigate the role of innate immune cells during epithelial infection by the protozoan parasite, Toxoplasma gondii, which affects billions of people worldwide. Our data indicate that epithelial infection by parasites stimulates a broad range of effector functions in neutrophils and natural killer cell-mediated cytokine production that play immunomodulatory roles, demonstrating the potential of our system for advancing the study of human-parasite interactions.
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Affiliation(s)
- Mouhita Humayun
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Jose M. Ayuso
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, USA
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, USA
| | - Keon Young Park
- Department of Surgery, University of Wisconsin-Madison, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Melissa C. Skala
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Sheena C. Kerr
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Laura J. Knoll
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - David J. Beebe
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
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NAD(P)H fluorescence lifetime imaging of live intestinal nematodes reveals metabolic crosstalk between parasite and host. Sci Rep 2022; 12:7264. [PMID: 35508502 PMCID: PMC9068778 DOI: 10.1038/s41598-022-10705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/11/2022] [Indexed: 11/29/2022] Open
Abstract
Infections with intestinal nematodes have an equivocal impact: they represent a burden for human health and animal husbandry, but, at the same time, may ameliorate auto-immune diseases due to the immunomodulatory effect of the parasites. Thus, it is key to understand how intestinal nematodes arrive and persist in their luminal niche and interact with the host over long periods of time. One basic mechanism governing parasite and host cellular and tissue functions, metabolism, has largely been neglected in the study of intestinal nematode infections. Here we use NADH (nicotinamide adenine dinucleotide) and NADPH (nicotinamide adenine dinucleotide phosphate) fluorescence lifetime imaging of explanted murine duodenum infected with the natural nematode Heligmosomoides polygyrus and define the link between general metabolic activity and possible metabolic pathways in parasite and host tissue, during acute infection. In both healthy and infected host intestine, energy is effectively produced, mainly via metabolic pathways resembling oxidative phosphorylation/aerobic glycolysis features. In contrast, the nematodes shift their energy production from balanced fast anaerobic glycolysis-like and effective oxidative phosphorylation-like metabolic pathways, towards mainly anaerobic glycolysis-like pathways, back to oxidative phosphorylation/aerobic glycolysis-like pathways during their different life cycle phases in the submucosa versus the intestinal lumen. Additionally, we found an increased NADPH oxidase (NOX) enzymes-dependent oxidative burst in infected intestinal host tissue as compared to healthy tissue, which was mirrored by a similar defense reaction in the parasites. We expect that, the here presented application of NAD(P)H-FLIM in live tissues constitutes a unique tool to study possible shifts between metabolic pathways in host-parasite crosstalk, in various parasitic intestinal infections.
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Günther R, Pal A, Williams C, Zimyanin VL, Liehr M, von Neubeck C, Krause M, Parab MG, Petri S, Kalmbach N, Marklund SL, Sterneckert J, Munch Andersen P, Wegner F, Gilthorpe JD, Hermann A. Alteration of Mitochondrial Integrity as Upstream Event in the Pathophysiology of SOD1-ALS. Cells 2022; 11:cells11071246. [PMID: 35406813 PMCID: PMC8997900 DOI: 10.3390/cells11071246] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/06/2023] Open
Abstract
Little is known about the early pathogenic events by which mutant superoxide dismutase 1 (SOD1) causes amyotrophic lateral sclerosis (ALS). This lack of mechanistic understanding is a major barrier to the development and evaluation of efficient therapies. Although protein aggregation is known to be involved, it is not understood how mutant SOD1 causes degeneration of motoneurons (MNs). Previous research has relied heavily on the overexpression of mutant SOD1, but the clinical relevance of SOD1 overexpression models remains questionable. We used a human induced pluripotent stem cell (iPSC) model of spinal MNs and three different endogenous ALS-associated SOD1 mutations (D90Ahom, R115Ghet or A4Vhet) to investigate early cellular disturbances in MNs. Although enhanced misfolding and aggregation of SOD1 was induced by proteasome inhibition, it was not affected by activation of the stress granule pathway. Interestingly, we identified loss of mitochondrial, but not lysosomal, integrity as the earliest common pathological phenotype, which preceded elevated levels of insoluble, aggregated SOD1. A super-elongated mitochondrial morphology with impaired inner mitochondrial membrane potential was a unifying feature in mutant SOD1 iPSC-derived MNs. Impaired mitochondrial integrity was most prominent in mutant D90Ahom MNs, whereas both soluble disordered and detergent-resistant misfolded SOD1 was more prominent in R115Ghet and A4Vhet mutant lines. Taking advantage of patient-specific models of SOD1-ALS in vitro, our data suggest that mitochondrial dysfunction is one of the first crucial steps in the pathogenic cascade that leads to SOD1-ALS and also highlights the need for individualized medical approaches for SOD1-ALS.
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Affiliation(s)
- René Günther
- Department of Neurology, University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany; (R.G.); (A.P.); (V.L.Z.); (M.L.); (M.G.P.)
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 01307 Dresden, Germany
| | - Arun Pal
- Department of Neurology, University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany; (R.G.); (A.P.); (V.L.Z.); (M.L.); (M.G.P.)
- Dresden High Magnetic Field Laboratory (HLD), Helmholtz-Zentrum Dresden-Rossendorf (HZDR), 01328 Dresden, Germany
| | - Chloe Williams
- Department of Integrative Medical Biology, Umeå University, 90187 Umeå, Sweden; (C.W.); (J.D.G.)
| | - Vitaly L. Zimyanin
- Department of Neurology, University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany; (R.G.); (A.P.); (V.L.Z.); (M.L.); (M.G.P.)
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Maria Liehr
- Department of Neurology, University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany; (R.G.); (A.P.); (V.L.Z.); (M.L.); (M.G.P.)
| | - Cläre von Neubeck
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), 69192 Heidelberg, Germany; (C.v.N.); (M.K.)
- OncoRay—National Center for Radiation Research in Oncology, University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany
- Clinic for Particle Therapy, West German Proton Therapy Centre Essen (WPE) gGmbH, University Medical Centre of Essen, 45147 Essen, Germany
| | - Mechthild Krause
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), 69192 Heidelberg, Germany; (C.v.N.); (M.K.)
- OncoRay—National Center for Radiation Research in Oncology, University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany
- Helmholtz-Zentrum Dresden—Rossendorf, Institute of Radiooncology—OncoRay, 01328 Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Mrudula G. Parab
- Department of Neurology, University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany; (R.G.); (A.P.); (V.L.Z.); (M.L.); (M.G.P.)
| | - Susanne Petri
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany; (S.P.); (N.K.); (F.W.)
| | - Norman Kalmbach
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany; (S.P.); (N.K.); (F.W.)
| | - Stefan L. Marklund
- Department of Medical Biosciences, Clinical Chemistry, Umeå University, 90187 Umeå, Sweden;
| | - Jared Sterneckert
- Center for Regenerative Therapies Dresden, Technical University Dresden, 01307 Dresden, Germany;
| | | | - Florian Wegner
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany; (S.P.); (N.K.); (F.W.)
| | - Jonathan D. Gilthorpe
- Department of Integrative Medical Biology, Umeå University, 90187 Umeå, Sweden; (C.W.); (J.D.G.)
| | - Andreas Hermann
- Translational Neurodegeneration Section, “Albrecht Kossel”, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald, 18147 Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
- Correspondence: ; Tel.: +49-381-4949541
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20
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Farina S, Labanca I, Acconcia G, Ghezzi A, Farina A, D'Andrea C, Rech I. Above pile-up fluorescence microscopy with a 32 Mc/s single-channel time-resolved SPAD system. OPTICS LETTERS 2022; 47:82-85. [PMID: 34951886 DOI: 10.1364/ol.444815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
One of the major drawbacks of time-correlated single-photon counting (TCSPC) is generally represented by pile-up distortion, which strongly bounds the maximum acquisition speed to a few percent of the laser excitation rate. Based on a previous theoretical analysis, recently we presented the first, to the best of our knowledge, low-distortion and high-speed TCSPC system capable of overcoming the pile-up limitation by perfectly matching the single-photon avalanche diode (SPAD) dead time to the laser period. In this work, we validate the proposed system in a standard fluorescence measurement by comparing experimental data with the reference theoretical framework. As a result, a count rate of 32 Mc/s was achieved with a single-channel system still observing a negligible lifetime distortion.
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21
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Quantification of protein-protein interactions and activation dynamics: A new path to predictive biomarkers. Biophys Chem 2022; 283:106768. [DOI: 10.1016/j.bpc.2022.106768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/08/2022] [Accepted: 01/24/2022] [Indexed: 12/27/2022]
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22
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Chelushkin PS, Shakirova JR, Kritchenkov IS, Baigildin VA, Tunik SP. Phosphorescent NIR emitters for biomedicine: applications, advances and challenges. Dalton Trans 2021; 51:1257-1280. [PMID: 34878463 DOI: 10.1039/d1dt03077a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Application of NIR (near-infrared) emitting transition metal complexes in biomedicine is a rapidly developing area of research. Emission of this class of compounds in the "optical transparency windows" of biological tissues and the intrinsic sensitivity of their phosphorescence to oxygen resulted in the preparation of several commercial oxygen sensors capable of deep (up to whole-body) and quantitative mapping of oxygen gradients suitable for in vivo experimental studies. In addition to this achievement, the last decade has also witnessed the increased growth of successful alternative applications of NIR phosphors that include (i) site-specific in vitro and in vivo visualization of sophisticated biological models ranging from 3D cell cultures to intact animals; (ii) sensing of various biologically relevant analytes, such as pH, reactive oxygen and nitrogen species, RedOx agents, etc.; (iii) and several therapeutic applications such as photodynamic (PDT), photothermal (PTT), and photoactivated cancer (PACT) therapies as well as their combinations with other therapeutic and imaging modalities to yield new variants of combined therapies and theranostics. Nevertheless, emerging applications of these compounds in experimental biomedicine and their implementation as therapeutic agents practically applicable in PDT, PTT, and PACT face challenges related to a critically important improvement of their photophysical and physico-chemical characteristics. This review outlines the current state of the art and achievements of the last decade and stresses the most promising trends, major development prospects, and challenges in the design of NIR phosphors suitable for biomedical applications.
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Affiliation(s)
- Pavel S Chelushkin
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr., 26, 198504, St. Petersburg, Russia.
| | - Julia R Shakirova
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr., 26, 198504, St. Petersburg, Russia.
| | - Ilya S Kritchenkov
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr., 26, 198504, St. Petersburg, Russia.
| | - Vadim A Baigildin
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr., 26, 198504, St. Petersburg, Russia.
| | - Sergey P Tunik
- Institute of Chemistry, St. Petersburg State University, Universitetskii pr., 26, 198504, St. Petersburg, Russia.
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