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Sbrana F, Chellini F, Tani A, Parigi M, Garella R, Palmieri F, Zecchi-Orlandini S, Squecco R, Sassoli C. Label-free three-dimensional imaging and quantitative analysis of living fibroblasts and myofibroblasts by holotomographic microscopy. Microsc Res Tech 2024. [PMID: 38984377 DOI: 10.1002/jemt.24648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
Holotomography (HT) is a cutting-edge fast live-cell quantitative label-free imaging technique. Based on the principle of quantitative phase imaging, it combines holography and tomography to record a three-dimensional map of the refractive index, used as intrinsic optical and quantitative imaging contrast parameter of biological samples, at a sub-micrometer spatial resolution. In this study HT has been employed for the first time to analyze the changes of fibroblasts differentiating towards myofibroblasts - recognized as the main cell player of fibrosis - when cultured in vitro with the pro-fibrotic factor, namely transforming growth factor-β1. In parallel, F-actin, vinculin, α-smooth muscle actin, phospho-myosin light chain 2, type-1 collagen, peroxisome proliferator-activated receptor-gamma coactivator-1α expression and mitochondria were evaluated by confocal laser scanning microscopy. Plasmamembrane passive properties and transient receptor potential canonical channels' currents were also recorded by whole-cell patch-clamp. The fluorescence images and electrophysiological results have been compared to the data obtained by HT and their congruence has been discussed. HT turned out to be a valid approach to morphologically distinguish fibroblasts from well differentiated myofibroblasts while obtaining objective measures concerning volume, surface area, projection area, surface index and dry mass (i.e., the mass of the non-aqueous content inside the cell including proteins and subcellular organelles) of the entire cell, nuclei and nucleoli with the major advantage to monitor outer and inner features in living cells in a non-invasive, rapid and label-free approach. HT might open up new research opportunities in the field of fibrotic diseases. RESEARCH HIGHLIGHTS: Holotomography (HT) is a label-free laser interferometric imaging technology exploiting the intrinsic optical property of cells namely refractive index (RI) to enable a direct imaging and analysis of whole cells or intracellular organelles. HT turned out a valid approach to distinguish morphological features of living unlabeled fibroblasts from differentiated myofibroblasts. HT provided quantitative information concerning volume, surface area, projection area, surface index and dry mass of the entire fibroblasts/myofibroblasts, nuclei and nucleoli.
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Affiliation(s)
| | - Flaminia Chellini
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
| | - Alessia Tani
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
| | - Martina Parigi
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
| | - Rachele Garella
- Department of Experimental and Clinical Medicine, Section of Physiological Sciences, University of Florence, Florence, Italy
| | - Francesco Palmieri
- Department of Experimental and Clinical Medicine, Section of Physiological Sciences, University of Florence, Florence, Italy
| | - Sandra Zecchi-Orlandini
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
| | - Roberta Squecco
- Department of Experimental and Clinical Medicine, Section of Physiological Sciences, University of Florence, Florence, Italy
| | - Chiara Sassoli
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
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Vasista AB, Ciraulo B, Schmidt F, Arroyo JO, Quidant R. Non-steady state thermometry with optical diffraction tomography. SCIENCE ADVANCES 2024; 10:eadk5440. [PMID: 38517963 PMCID: PMC10959403 DOI: 10.1126/sciadv.adk5440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/15/2024] [Indexed: 03/24/2024]
Abstract
Label-free thermometry is a pivotal tool for many disciplines. However, most current approaches are only suitable for planar heat sources in steady state, thereby restricting the range of systems that can be reliably studied. Here, we introduce pump probe-based optical diffraction tomography (ODT) as a method to map temperature precisely and accurately in three dimensions (3D) at the single-particle level. To do so, we first systematically characterize the thermal landscape in a model system consisting of gold nanorods in a microchamber and then benchmark the results against simulations and quantitative phase imaging thermometry. We then apply ODT thermometry to resolve thermal landscapes inaccessible to other label-free approaches in the form of nonplanar heat sources embedded in complex environments and freely diffusing gold nanorods in a microchamber. Last, we foresee that our approach will find many applications where routine thermal characterization of heterogeneous nanoparticles samples in 3D or in non-steady state is required.
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Affiliation(s)
- Adarsh B. Vasista
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH-Zürich, 8092 Zürich, Switzerland
| | - Bernard Ciraulo
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH-Zürich, 8092 Zürich, Switzerland
- Pediatric Molecular Neuro-Oncology Research, University Children’s Hospital Zürich, Balgrist Campus, 8008 Zürich, Switzerland
| | - Falko Schmidt
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH-Zürich, 8092 Zürich, Switzerland
| | - Jaime Ortega Arroyo
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH-Zürich, 8092 Zürich, Switzerland
| | - Romain Quidant
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH-Zürich, 8092 Zürich, Switzerland
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3
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Paul PK, Wu W, Srichana T. Monitoring the Interaction Between Solid Lipid Nanoparticles and Alveolar Macrophages Via the Label-Free Technique. J Pharm Sci 2024:S0022-3549(24)00090-X. [PMID: 38492846 DOI: 10.1016/j.xphs.2024.03.006] [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: 01/18/2024] [Revised: 03/09/2024] [Accepted: 03/09/2024] [Indexed: 03/18/2024]
Abstract
Macrophages are employed as targets for delivering genes, drugs, or lipid nanoparticles into tumors or other specific sites. Studying the interaction between solid lipid nanoparticles (SLNs) and macrophages is essential for assessing nanotoxicity and advancing the development of nanomedicines. However, limited data are currently available on the membrane microstructure and biochemical changes that occur when macrophages interact with SLNs. We conducted a label-free morphological and biochemical investigation of NR8383 macrophages using optical diffraction tomography (ODT), which validated the efficiency of the SLNs as a drug delivery system. ODT provided intracellular holotomography to characterize the macrophages and fluorescence imaging to analyze delivery efficiency. ODT analysis revealed the responses of phagocytic macrophages. Additionally, a quantitative analysis of lipid droplets using refractive indices revealed that, compared with incubation with normal cells, incubation with SLNs significantly increased the lipid droplet volume and surface area. The uptake of SLNs into macrophages resulted in increased cell volume, surface area, and concentration, which indicated greater morphological and biochemical variability in the treated cells than in the control cells. The results suggest that ODT imaging is promising for understanding the intracellular distribution of SLNs and useful for validating the efficacy of delivery of SLNs to macrophages.
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Affiliation(s)
- Pijush Kumar Paul
- Drug Delivery System Excellence Center, Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Department of Pharmacy, Gono Bishwabidyalay (University), Dhaka 1344, Bangladesh
| | - Wei Wu
- Key Laboratory of Smart Drug Delivery of MOE, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Teerapol Srichana
- Drug Delivery System Excellence Center, Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand.
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4
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Liu R, Wen K, Li J, Ma Y, Zheng J, An S, Min J, Zalevsky Z, Yao B, Gao P. Multi-harmonic structured illumination-based optical diffraction tomography. APPLIED OPTICS 2023; 62:9199-9206. [PMID: 38108690 DOI: 10.1364/ao.508138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/08/2023] [Indexed: 12/19/2023]
Abstract
Imaging speed and spatial resolution are key factors in optical diffraction tomography (ODT), while they are mutually exclusive in 3D refractive index imaging. This paper presents a multi-harmonic structured illumination-based optical diffraction tomography (MHSI-ODT) to acquire 3D refractive index (RI) maps of transparent samples. MHSI-ODT utilizes a digital micromirror device (DMD) to generate structured illumination containing multiple harmonics. For each structured illumination orientation, four spherical spectral crowns are solved from five phase-shifted holograms, meaning that the acquisition of each spectral crown costs 1.25 raw images. Compared to conventional SI-ODT, which retrieves two spectral crowns from three phase-shifted raw images, MHSI-ODT enhances the imaging speed by 16.7% in 3D RI imaging. Meanwhile, MHSI-ODT exploits both the 1st-order and the 2nd-order harmonics; therefore, it has a better intensity utilization of structured illumination. We demonstrated the performance of MHSI-ODT by rendering the 3D RI distributions of 5 µm polystyrene (PS) microspheres and biological samples.
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Kolb J, Tsata V, John N, Kim K, Möckel C, Rosso G, Kurbel V, Parmar A, Sharma G, Karandasheva K, Abuhattum S, Lyraki O, Beck T, Müller P, Schlüßler R, Frischknecht R, Wehner A, Krombholz N, Steigenberger B, Beis D, Takeoka A, Blümcke I, Möllmert S, Singh K, Guck J, Kobow K, Wehner D. Small leucine-rich proteoglycans inhibit CNS regeneration by modifying the structural and mechanical properties of the lesion environment. Nat Commun 2023; 14:6814. [PMID: 37884489 PMCID: PMC10603094 DOI: 10.1038/s41467-023-42339-7] [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: 02/22/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023] Open
Abstract
Extracellular matrix (ECM) deposition after central nervous system (CNS) injury leads to inhibitory scarring in humans and other mammals, whereas it facilitates axon regeneration in the zebrafish. However, the molecular basis of these different fates is not understood. Here, we identify small leucine-rich proteoglycans (SLRPs) as a contributing factor to regeneration failure in mammals. We demonstrate that the SLRPs chondroadherin, fibromodulin, lumican, and prolargin are enriched in rodent and human but not zebrafish CNS lesions. Targeting SLRPs to the zebrafish injury ECM inhibits axon regeneration and functional recovery. Mechanistically, we find that SLRPs confer mechano-structural properties to the lesion environment that are adverse to axon growth. Our study reveals SLRPs as inhibitory ECM factors that impair axon regeneration by modifying tissue mechanics and structure, and identifies their enrichment as a feature of human brain and spinal cord lesions. These findings imply that SLRPs may be targets for therapeutic strategies to promote CNS regeneration.
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Affiliation(s)
- Julia Kolb
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Biology, Animal Physiology, Friedrich-Alexander-University Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Vasiliki Tsata
- Experimental Surgery, Clinical and Translational Research Center, Biomedical Research Foundation Academy of Athens, 11527, Athens, Greece
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527, Athens, Greece
| | - Nora John
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Biology, Animal Physiology, Friedrich-Alexander-University Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Kyoohyun Kim
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Conrad Möckel
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-University Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Gonzalo Rosso
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Veronika Kurbel
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Asha Parmar
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-University Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Gargi Sharma
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Kristina Karandasheva
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Shada Abuhattum
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Olga Lyraki
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Biology, Animal Physiology, Friedrich-Alexander-University Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Timon Beck
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Paul Müller
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Raimund Schlüßler
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | - Renato Frischknecht
- Department of Biology, Animal Physiology, Friedrich-Alexander-University Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Anja Wehner
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Nicole Krombholz
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Dimitris Beis
- Experimental Surgery, Clinical and Translational Research Center, Biomedical Research Foundation Academy of Athens, 11527, Athens, Greece
- Laboratory of Biological Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Aya Takeoka
- VIB-Neuroelectronics Research Flanders, 3001, Leuven, Belgium
- Department of Neuroscience and Leuven Brain Institute, KU Leuven, 3000, Leuven, Belgium
| | - Ingmar Blümcke
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Stephanie Möllmert
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Kanwarpal Singh
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-University Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Jochen Guck
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-University Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Katja Kobow
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Daniel Wehner
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany.
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany.
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Amini S, Zhu T, Biswas A, Charsooghi MA, Kim K, Reber S, Dauphin Y, Fratzl P. Calcitic Prisms of The Giant Seashell Pinna Nobilis Form Light Guide Arrays. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2304166. [PMID: 37450944 DOI: 10.1002/adma.202304166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
The shells of the Pinnidae family are based on a double layer of single-crystal-like calcitic prisms and inner aragonitic nacre, a structure known for its outstanding mechanical performance. However, on the posterior side, shells are missing the nacreous layer, which raises the question of whether there can be any functional role in giving up this mechanical performance. Here, it is demonstrated that the prismatic part of the Pinna nobilis shell exhibits unusual optical properties, whereby each prism acts as an individual optical fiber guiding the ambient light to the inner shell cavity by total internal reflection. This pixelated light channeling enhances both spatial resolution and contrast while reducing angular blurring, an apt combination for acute tracking of a moving object. These findings offer insights into the evolutionary aspects of light-sensing and imaging and demonstrate how an architectured optical system for efficient light-tracking can be based on birefringent ceramics.
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Affiliation(s)
- Shahrouz Amini
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
| | - Tingting Zhu
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
| | - Abin Biswas
- Max Planck Institute for Infection Biology, 10117, Berlin, Germany
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
| | | | - Kyoohyun Kim
- Max Planck Institute for the Science of Light, 91058, Erlangen, Germany
| | - Simone Reber
- Max Planck Institute for Infection Biology, 10117, Berlin, Germany
| | - Yannicke Dauphin
- UMR 7205 ISYEB, Museum National d'histoire Naturelle, CNRS UPMC EPHE, 57 rue Cuvier, Paris, 75005, France
| | - Peter Fratzl
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
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7
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Kim T, Yoo J, Do S, Hwang DS, Park Y, Shin Y. RNA-mediated demixing transition of low-density condensates. Nat Commun 2023; 14:2425. [PMID: 37105967 PMCID: PMC10140143 DOI: 10.1038/s41467-023-38118-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Biomolecular condensates play a key role in organizing cellular reactions by concentrating a specific set of biomolecules. However, whether condensate formation is accompanied by an increase in the total mass concentration within condensates or by the demixing of already highly crowded intracellular components remains elusive. Here, using refractive index imaging, we quantify the mass density of several condensates, including nucleoli, heterochromatin, nuclear speckles, and stress granules. Surprisingly, the latter two condensates exhibit low densities with a total mass concentration similar to the surrounding cyto- or nucleoplasm. Low-density condensates display higher permeability to cellular protein probes. We find that RNA tunes the biomolecular density of condensates. Moreover, intracellular structures such as mitochondria heavily influence the way phase separation proceeds, impacting the localization, morphology, and growth of condensates. These findings favor a model where segregative phase separation driven by non-associative or repulsive molecular interactions together with RNA-mediated selective association of specific components can give rise to low-density condensates in the crowded cellular environment.
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Affiliation(s)
- Taehyun Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jaeyoon Yoo
- Department of Mechanical Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sungho Do
- Department of Mechanical Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dong Soo Hwang
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, Daejeon, 34141, Republic of Korea
- Tomocube Inc, Daejeon, 34109, South Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Korea.
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Rajora S, Butola M, Khare K. 3D reconstruction of unstained weakly scattering cells from a single defocused hologram. APPLIED OPTICS 2023; 62:D146-D156. [PMID: 37132780 DOI: 10.1364/ao.478351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We investigate the problem of 3D complex field reconstruction corresponding to unstained red blood cells (RBCs) with a single defocused off-axis digital hologram. The main challenge in this problem is the localization of cells to the correct axial range. While investigating the volume recovery problem for a continuous phase object like the RBC, we observe an interesting feature of the backpropagated field that it does not show a clear focusing effect. Therefore, sparsity enforcement within the iterative optimization framework using a single hologram data frame cannot effectively restrict the reconstruction to the true object volume. For phase objects, it is known that the amplitude contrast of the backpropagated object field at the focus plane is minimum. We use this information available in the recovered object field in the hologram plane to device depth-dependent weights that are proportional to the inverse of amplitude contrast. This weight function is employed in the iterative steps of the optimization algorithm to assist the object volume localization. The overall reconstruction process is performed using the mean gradient descent (MGD) framework. Experimental illustrations of 3D volume reconstruction of the healthy as well as malaria-infected RBCs are presented. A test sample of polystyrene microsphere bead is also used to validate the axial localization capability of the proposed iterative technique. The proposed methodology is simple to implement experimentally and provides an approximate tomographic solution, which is axially restricted and consistent with the object field data.
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Liang F, Zhu J, Chai H, Feng Y, Zhao P, Liu S, Yang Y, Lin L, Cao L, Wang W. Non-Invasive and Minute-Frequency 3D Tomographic Imaging Enabling Long-Term Spatiotemporal Observation of Single Cell Fate. SMALL METHODS 2023:e2201492. [PMID: 36950762 DOI: 10.1002/smtd.202201492] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Non-invasive and rapid imaging technique at subcellular resolution is significantly important for multiple biological applications such as cell fate study. Label-free refractive-index (RI)-based 3D tomographic imaging constitutes an excellent candidate for 3D imaging of cellular structures, but its full potential in long-term spatiotemporal cell fate observation is locked due to the lack of an efficient integrated system. Here, a long-term 3D RI imaging system incorporating a cutting-edge white light diffraction phase microscopy module with spatiotemporal stability, and an acoustofluidic device to roll and culture single cells in a customized live cell culture chamber is reported. Using this system, 3D RI imaging experiments are conducted for 250 cells and demonstrate efficient cell identification with high accuracy. Importantly, long-term and frequency-on-demand 3D RI imaging of K562 and MCF-7 cancer cells reveal different characteristics during normal cell growth, drug-induced cell apoptosis, and necrosis of drug-treated cells. Overall, it is believed that the proposed 3D tomographic imaging technique opens up a new avenue for visualizing intracellular structures and will find many applications such as disease diagnosis and nanomedicine.
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Affiliation(s)
- Fei Liang
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Junwen Zhu
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Huichao Chai
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Yongxiang Feng
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Peng Zhao
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Shaofeng Liu
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Yuanmu Yang
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Linhan Lin
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Liangcai Cao
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Wenhui Wang
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
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Ong JJY, Oh J, Yong Ang X, Naidu R, Chu TTT, Hyoung Im J, Manzoor U, Kha Nguyen T, Na SW, Han ET, Davis C, Sun Park W, Chun W, Jun H, Jin Lee S, Na S, Chan JKY, Park Y, Russell B, Chandramohanadas R, Han JH. Optical diffraction tomography and image reconstruction to measure host cell alterations caused by divergent Plasmodium species. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 286:122026. [PMID: 36395614 DOI: 10.1016/j.saa.2022.122026] [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: 08/12/2022] [Revised: 09/29/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Malaria is a life-threatening infectious disease caused by parasites of the genus Plasmodium. Understanding the biological features of various parasite forms is important for the optical diagnosis and defining pathological states, which are often constrained by the lack of ambient visualization approaches. Here, we employ a label-free tomographic technique to visualize the host red blood cell (RBC) remodeling process and quantify changes in biochemical properties arising from parasitization. Through this, we provide a quantitative body of information pertaining to the influence of host cell environment on growth, survival, and replication of P. falciparum and P. vivax in their respective host cells: mature erythrocytes and young reticulocytes. These exquisite three-dimensional measurements of infected red cells demonstrats the potential of evolving 3D imaging to advance our understanding of Plasmodium biology and host-parasite interactions.
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Affiliation(s)
- Jessica J Y Ong
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Jeonghun Oh
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Xiang Yong Ang
- Department of Microbiology and Immunology, National University of Singapore, Singapore
| | - Renugah Naidu
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, Singapore
| | - Trang T T Chu
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, Singapore
| | - Jae Hyoung Im
- Department of Infectious Disease, Inha University School of Medicine, Incheon 22212, Republic of Korea
| | - Umar Manzoor
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Tuyet Kha Nguyen
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Seok-Won Na
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Christeen Davis
- DBT Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Won Sun Park
- Department of Physiology, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Wanjoo Chun
- Department of Pharmacology, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hojong Jun
- Department of Tropical Medicine, Inha University College of Medicine, Incheon 22212, Republic of Korea
| | - Se Jin Lee
- Department of Obstetrics and Gynecology, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon 24341, South Korea
| | - Sunghun Na
- Department of Obstetrics and Gynecology, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon 24341, South Korea
| | - Jerry K Y Chan
- KK Womens' and Childrens' Hospital, Singapore; Academic Clinical Program in Obstetrics and Gynaecology, Duke-NUS Medical School, 169857, Singapore
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea; Tomocube Inc, Daejeon 34109, Republic of Korea
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Rajesh Chandramohanadas
- Department of Microbiology and Immunology, National University of Singapore, Singapore; Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, Singapore; DBT Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
| | - Jin-Hee Han
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand; Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Republic of Korea.
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11
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Shin J, Kim G, Park J, Lee M, Park Y. Long-term label-free assessments of individual bacteria using three-dimensional quantitative phase imaging and hydrogel-based immobilization. Sci Rep 2023; 13:46. [PMID: 36593327 PMCID: PMC9806822 DOI: 10.1038/s41598-022-27158-y] [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: 09/13/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Three-dimensional (3D) quantitative phase imaging (QPI) enables long-term label-free tomographic imaging and quantitative analysis of live individual bacteria. However, the Brownian motion or motility of bacteria in a liquid medium produces motion artifacts during 3D measurements and hinders precise cell imaging and analysis. Meanwhile, existing cell immobilization methods produce noisy backgrounds and even alter cellular physiology. Here, we introduce a protocol that utilizes hydrogels for high-quality 3D QPI of live bacteria maintaining bacterial physiology. We demonstrate long-term high-resolution quantitative imaging and analysis of individual bacteria, including measuring the biophysical parameters of bacteria and responses to antibiotic treatments.
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Affiliation(s)
- Jeongwon Shin
- grid.37172.300000 0001 2292 0500Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea
| | - Geon Kim
- grid.37172.300000 0001 2292 0500Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea ,grid.37172.300000 0001 2292 0500KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea
| | - Jinho Park
- grid.37172.300000 0001 2292 0500Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea
| | - Moosung Lee
- grid.37172.300000 0001 2292 0500Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea ,grid.37172.300000 0001 2292 0500KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea
| | - YongKeun Park
- grid.37172.300000 0001 2292 0500Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea ,grid.37172.300000 0001 2292 0500KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea ,Tomocube Inc., Daejeon, 34051 South Korea
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12
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Lee D, Lee M, Kwak H, Kim YS, Shim J, Jung JH, Park WS, Park JH, Lee S, Park Y. High-fidelity optical diffraction tomography of live organisms using iodixanol refractive index matching. BIOMEDICAL OPTICS EXPRESS 2022; 13:6404-6415. [PMID: 36589574 PMCID: PMC9774853 DOI: 10.1364/boe.465066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Optical diffraction tomography (ODT) enables the three-dimensional (3D) refractive index (RI) reconstruction. However, when the RI difference between a sample and a medium increases, the effects of light scattering become significant, preventing the acquisition of high-quality and accurate RI reconstructions. Herein, we present a method for high-fidelity ODT by introducing non-toxic RI matching media. Optimally reducing the RI contrast enhances the fidelity and accuracy of 3D RI reconstruction, enabling visualization of the morphology and intra-organization of live biological samples without producing toxic effects. We validate our method using various biological organisms, including C. albicans and C. elegans.
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Affiliation(s)
- Dohyeon Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Moosung Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Haechan Kwak
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Young Seo Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Jaehyu Shim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Jik Han Jung
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Wei-sun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Ji-Ho Park
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Sumin Lee
- Tomocube Inc., Daejeon 34109, Republic of Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Tomocube Inc., Daejeon 34109, Republic of Korea
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13
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Stępień P, Ziemczonok M, Kujawińska M, Baczewska M, Valenti L, Cherubini A, Casirati E, Krauze W. Numerical refractive index correction for the stitching procedure in tomographic quantitative phase imaging. BIOMEDICAL OPTICS EXPRESS 2022; 13:5709-5720. [PMID: 36733760 PMCID: PMC9872904 DOI: 10.1364/boe.466403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/16/2022] [Accepted: 08/24/2022] [Indexed: 06/18/2023]
Abstract
Tomographic quantitative phase imaging (QPI) lacks an absolute refractive index value baseline, which poses a problem when large dense objects extending over multiple fields of view are measured volume by volume and stitched together. Some of the measurements lack the natural baseline value that is provided by the mounting medium with a known refractive index. In this work, we discuss the problem of the refractive index (RI) baseline of individual reconstructed volumes that are deprived of access to mounting medium due to the extent of the object. The solution of this problem is provided by establishing the RI offsets based on the overlapping regions. We have proven that the process of finding the offset RI values may be justifiably reduced to the analogous procedure in the 2D baseline correction (2D-BC). Finally, we proposed the enhancement of the state-of-the-art 2D-BC procedure previously introduced in the context of 2D QPI. The processing is validated at the examples of a synthetic dataset and a liver organoid.
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Affiliation(s)
- Piotr Stępień
- Warsaw University of Technology, Institute of Micromechanics and Photonics, ul. Sw. A. Boboli 8, Warsaw, 02-525, Poland
| | - Michał Ziemczonok
- Warsaw University of Technology, Institute of Micromechanics and Photonics, ul. Sw. A. Boboli 8, Warsaw, 02-525, Poland
| | - Małgorzata Kujawińska
- Warsaw University of Technology, Institute of Micromechanics and Photonics, ul. Sw. A. Boboli 8, Warsaw, 02-525, Poland
| | - Maria Baczewska
- Warsaw University of Technology, Institute of Micromechanics and Photonics, ul. Sw. A. Boboli 8, Warsaw, 02-525, Poland
| | - Luca Valenti
- Università degli Studi di Milano, Department of Pathophysiology and Transplantation, Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Department of Transfusion Medicine and Hematology, Milan, Italy
| | - Alessandro Cherubini
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Department of Transfusion Medicine and Hematology, Milan, Italy
| | - Elia Casirati
- Università degli Studi di Milano, Department of Pathophysiology and Transplantation, Milan, Italy
| | - Wojciech Krauze
- Warsaw University of Technology, Institute of Micromechanics and Photonics, ul. Sw. A. Boboli 8, Warsaw, 02-525, Poland
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14
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Běhal J, Borrelli F, Mugnano M, Bianco V, Capozzoli A, Curcio C, Liseno A, Miccio L, Memmolo P, Ferraro P. Developing a Reliable Holographic Flow Cyto-Tomography Apparatus by Optimizing the Experimental Layout and Computational Processing. Cells 2022; 11:cells11162591. [PMID: 36010667 PMCID: PMC9406712 DOI: 10.3390/cells11162591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
Digital Holographic Tomography (DHT) has recently been established as a means of retrieving the 3D refractive index mapping of single cells. To make DHT a viable system, it is necessary to develop a reliable and robust holographic apparatus in order that such technology can be utilized outside of specialized optics laboratories and operated in the in-flow modality. In this paper, we propose a quasi-common-path lateral-shearing holographic optical set-up to be used, for the first time, for DHT in a flow-cytometer modality. The proposed solution is able to withstand environmental vibrations that can severely affect the interference process. Furthermore, we have scaled down the system while ensuring that a full 360° rotation of the cells occurs in the field-of-view, in order to retrieve 3D phase-contrast tomograms of single cells flowing along a microfluidic channel. This was achieved by setting the camera sensor at 45° with respect to the microfluidic direction. Additional optimizations were made to the computational elements to ensure the reliable retrieval of 3D refractive index distributions by demonstrating an effective method of tomographic reconstruction, based on high-order total variation. The results were first demonstrated using realistic 3D numerical phantom cells to assess the performance of the proposed high-order total variation method in comparison with the gold-standard algorithm for tomographic reconstructions: namely, filtered back projection. Then, the proposed DHT system and the processing pipeline were experimentally validated for monocytes and mouse embryonic fibroblast NIH-3T3 cells lines. Moreover, the repeatability of these tomographic measurements was also investigated by recording the same cell multiple times and quantifying the ability to provide reliable and comparable tomographic reconstructions, as confirmed by a correlation coefficient greater than 95%. The reported results represent various steps forward in several key aspects of in-flow DHT, thus paving the way for its use in real-world applications.
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Affiliation(s)
- Jaromír Běhal
- Institute of Applied Sciences and Intelligent Systems, Italian National Research Council (CNR-ISASI), 80078 Pozzuoli, Italy
| | - Francesca Borrelli
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell’Informazione, Università di Napoli Federico II, 80125 Napoli, Italy
| | - Martina Mugnano
- Institute of Applied Sciences and Intelligent Systems, Italian National Research Council (CNR-ISASI), 80078 Pozzuoli, Italy
| | - Vittorio Bianco
- Institute of Applied Sciences and Intelligent Systems, Italian National Research Council (CNR-ISASI), 80078 Pozzuoli, Italy
| | - Amedeo Capozzoli
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell’Informazione, Università di Napoli Federico II, 80125 Napoli, Italy
| | - Claudio Curcio
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell’Informazione, Università di Napoli Federico II, 80125 Napoli, Italy
| | - Angelo Liseno
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell’Informazione, Università di Napoli Federico II, 80125 Napoli, Italy
| | - Lisa Miccio
- Institute of Applied Sciences and Intelligent Systems, Italian National Research Council (CNR-ISASI), 80078 Pozzuoli, Italy
| | - Pasquale Memmolo
- Institute of Applied Sciences and Intelligent Systems, Italian National Research Council (CNR-ISASI), 80078 Pozzuoli, Italy
- Correspondence:
| | - Pietro Ferraro
- Institute of Applied Sciences and Intelligent Systems, Italian National Research Council (CNR-ISASI), 80078 Pozzuoli, Italy
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15
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Tang M, He H, Yu L. Real-time 3D imaging of ocean algae with crosstalk suppressed single-shot digital holographic microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:4455-4467. [PMID: 36032587 PMCID: PMC9408253 DOI: 10.1364/boe.463678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Digital holographic microscopy (DHM) has the potential to reconstruct the 3D shape of volumetric samples from a single-shot hologram in a label-free and noninvasive manner. However, the holographic reconstruction is significantly compromised by the out-of-focus image resulting from the crosstalk between refocused planes, leading to the low fidelity of the results. In this paper, we propose a crosstalk suppression algorithm-assisted 3D imaging method combined with a home built DHM system to achieve accurate 3D imaging of ocean algae using only a single hologram. As a key step in the algorithm, a hybrid edge detection strategy using gradient-based and deep learning-based methods is proposed to offer accurate boundary information for the downstream processing. With this information, the crosstalk of each refocused plane can be estimated with adjacent refocused planes. Empowered by this method, we demonstrated successful 3D imaging of six kinds of ocean algae that agree well with the ground truth; we further demonstrated that this method could achieve real-time 3D imaging of the quick swimming ocean algae in the water environment. To our knowledge, this is the first time single-shot DHM is reported in 3D imaging of ocean algae, paving the way for on-site monitoring of the ocean algae.
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Affiliation(s)
- Ming Tang
- School of Advanced Manufacturing, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Hao He
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Longkun Yu
- School of Advanced Manufacturing, Nanchang University, Nanchang, Jiangxi 330031, China
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16
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Kim G, Ahn D, Kang M, Park J, Ryu D, Jo Y, Song J, Ryu JS, Choi G, Chung HJ, Kim K, Chung DR, Yoo IY, Huh HJ, Min HS, Lee NY, Park Y. Rapid species identification of pathogenic bacteria from a minute quantity exploiting three-dimensional quantitative phase imaging and artificial neural network. LIGHT, SCIENCE & APPLICATIONS 2022; 11:190. [PMID: 35739098 PMCID: PMC9226356 DOI: 10.1038/s41377-022-00881-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 05/14/2023]
Abstract
The healthcare industry is in dire need of rapid microbial identification techniques for treating microbial infections. Microbial infections are a major healthcare issue worldwide, as these widespread diseases often develop into deadly symptoms. While studies have shown that an early appropriate antibiotic treatment significantly reduces the mortality of an infection, this effective treatment is difficult to practice. The main obstacle to early appropriate antibiotic treatments is the long turnaround time of the routine microbial identification, which includes time-consuming sample growth. Here, we propose a microscopy-based framework that identifies the pathogen from single to few cells. Our framework obtains and exploits the morphology of the limited sample by incorporating three-dimensional quantitative phase imaging and an artificial neural network. We demonstrate the identification of 19 bacterial species that cause bloodstream infections, achieving an accuracy of 82.5% from an individual bacterial cell or cluster. This performance, comparable to that of the gold standard mass spectroscopy under a sufficient amount of sample, underpins the effectiveness of our framework in clinical applications. Furthermore, our accuracy increases with multiple measurements, reaching 99.9% with seven different measurements of cells or clusters. We believe that our framework can serve as a beneficial advisory tool for clinicians during the initial treatment of infections.
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Affiliation(s)
- Geon Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - Daewoong Ahn
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | - Minhee Kang
- Smart Healthcare & Device Research Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Jinho Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - DongHun Ryu
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - YoungJu Jo
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Tomocube Inc., Daejeon, 34109, Republic of Korea
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Jinyeop Song
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jea Sung Ryu
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Gunho Choi
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | - Hyun Jung Chung
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Kyuseok Kim
- Department of Emergency Medicine, Bundang CHA Hospital, Seongnam-si, Gyeonggi-Do, 13496, Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - In Young Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | | | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea.
- Tomocube Inc., Daejeon, 34109, Republic of Korea.
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17
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Label-Free Morpho-Molecular Imaging for Studying the Differential Interaction of Black Phosphorus with Tumor Cells. NANOMATERIALS 2022; 12:nano12121994. [PMID: 35745333 PMCID: PMC9227604 DOI: 10.3390/nano12121994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/05/2022] [Accepted: 06/07/2022] [Indexed: 12/02/2022]
Abstract
Black phosphorus nanosheets (2D BP) are emerging as very promising, highly selective chemotherapeutic agents due to their fast degradation in the intracellular matrix of cancer cells. Here, optical diffraction tomography (ODT) and Raman spectroscopy were exploited as a powerful label-free approach to achieve integrated insights into the processes accompanying the administration of exfoliated 2D BP flakes in human prostatic adenocarcinoma and normal human prostate epithelial cells. Our ODT experiments provided unambiguous visualization of the 2D BP internalization in cancer cells and the morphological modifications of those cells in the apoptotic phase. The cellular internalization and damaging occurred, respectively, 18 h and 36–48 h after the 2D BP administration. Changes in the chemical properties of the internalized 2D BP flakes were monitored by Raman spectroscopy. Interestingly, a fast oxidation process of the 2D BP flakes was activated in the intracellular matrix of the cancer cells after 24 h of incubation. This was in sharp contrast to the low 2D BP uptake and minimal chemical changes observed in the normal cells. Along with the understanding of the 2D BP fate in the cancer cells, the proposed label-free morpho-molecular approach offers a powerful, rapid tool to study the pharmacokinetic properties of engineered nanomaterials in preclinical research.
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18
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Mirsky SK, Barnea I, Shaked NT. Dynamic Tomographic Phase Microscopy by Double Six-Pack Holography. ACS PHOTONICS 2022; 9:1295-1303. [PMID: 35480489 PMCID: PMC9026267 DOI: 10.1021/acsphotonics.1c01804] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Indexed: 05/25/2023]
Affiliation(s)
- Simcha K. Mirsky
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - Itay Barnea
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - Natan T. Shaked
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
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19
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He Y, He S, Kandel ME, Lee YJ, Hu C, Sobh N, Anastasio MA, Popescu G. Cell Cycle Stage Classification Using Phase Imaging with Computational Specificity. ACS PHOTONICS 2022; 9:1264-1273. [PMID: 35480491 PMCID: PMC9026251 DOI: 10.1021/acsphotonics.1c01779] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Indexed: 06/01/2023]
Abstract
Traditional methods for cell cycle stage classification rely heavily on fluorescence microscopy to monitor nuclear dynamics. These methods inevitably face the typical phototoxicity and photobleaching limitations of fluorescence imaging. Here, we present a cell cycle detection workflow using the principle of phase imaging with computational specificity (PICS). The proposed method uses neural networks to extract cell cycle-dependent features from quantitative phase imaging (QPI) measurements directly. Our results indicate that this approach attains very good accuracy in classifying live cells into G1, S, and G2/M stages, respectively. We also demonstrate that the proposed method can be applied to study single-cell dynamics within the cell cycle as well as cell population distribution across different stages of the cell cycle. We envision that the proposed method can become a nondestructive tool to analyze cell cycle progression in fields ranging from cell biology to biopharma applications.
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Affiliation(s)
- Yuchen
R. He
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Shenghua He
- Department
of Computer Science & Engineering, Washington
University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mikhail E. Kandel
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Young Jae Lee
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Chenfei Hu
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Nahil Sobh
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- NCSA
Center for Artificial Intelligence Innovation, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Mark A. Anastasio
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Gabriel Popescu
- Department
of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
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20
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Muhamad RK, Stępień P, Kujawińska M, Schelkens P. Off-axis image plane hologram compression in holographic tomography - metrological assessment. OPTICS EXPRESS 2022; 30:4261-4273. [PMID: 35209666 DOI: 10.1364/oe.449932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
In this paper, we present a novel study on the impact of lossy data compression on the metrological properties of holographic tomography reconstruction of the refractive index (RI). We use a spatial bandwidth-optimized compression procedure that leverages the properties of image plane off-axis holograms and standardized compression codecs, both widely applied in research and industry. The compression procedure is tested at multiple bitrates, for four different objects and against three reconstruction algorithms. The metrological evaluation is primarily done by comparison to the reconstruction from original data using the root-mean-squared error (RMSE). We show that due to differences between objects and different noise sensitivities of the reconstruction algorithms, the rate-distortion behaviour varies, but in most cases allows for the compression below 1 bit per pixel, while maintaining an RI RMSE less than 10-4.
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21
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Interactions of Nanoparticles with Macrophages and Feasibility of Drug Delivery for Asthma. Int J Mol Sci 2022; 23:ijms23031622. [PMID: 35163544 PMCID: PMC8835984 DOI: 10.3390/ijms23031622] [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: 12/13/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/10/2022] Open
Abstract
Understanding the interaction between nanoparticles and immune cells is essential for the evaluation of nanotoxicity and development of nanomedicines. However, to date, there is little data on the membrane microstructure and biochemical changes in nanoparticle-loaded immune cells. In this study, we observed the microstructure of nanoparticle-loaded macrophages and changes in lipid droplets using holotomography analysis. Quantitatively analyzing the refractive index distribution of nanoparticle-loaded macrophages, we identified the interactions between nanoparticles and macrophages. The results showed that, when nanoparticles were phagocytized by macrophages, the number of lipid droplets and cell volume increased. The volume and mass of the lipid droplets slightly increased, owing to the absorption of nanoparticles. Meanwhile, the number of lipid droplets increased more conspicuously than the other factors. Furthermore, alveolar macrophages are involved in the development and progression of asthma. Studies have shown that macrophages play an essential role in the maintenance of asthma-related inflammation and tissue damage, suggesting that macrophage cells may be applied to asthma target delivery strategies. Therefore, we investigated the target delivery efficiency of gold nanoparticle-loaded macrophages at the biodistribution level, using an ovalbumin-induced asthma mouse model. Normal and severe asthma models were selected to determine the difference in the level of inflammation in the lung. Consequently, macrophages had increased mobility in models of severe asthma, compared to those of normal asthma disease. In this regard, the detection of observable differences in nanoparticle-loaded macrophages may be of primary interest, as an essential endpoint analysis for investigating nanomedical applications and immunotheragnostic strategies.
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22
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Schlüßler R, Kim K, Nötzel M, Taubenberger A, Abuhattum S, Beck T, Müller P, Maharana S, Cojoc G, Girardo S, Hermann A, Alberti S, Guck J. Correlative all-optical quantification of mass density and mechanics of subcellular compartments with fluorescence specificity. eLife 2022; 11:e68490. [PMID: 35001870 PMCID: PMC8816383 DOI: 10.7554/elife.68490] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 01/08/2022] [Indexed: 01/06/2023] Open
Abstract
Quantitative measurements of physical parameters become increasingly important for understanding biological processes. Brillouin microscopy (BM) has recently emerged as one technique providing the 3D distribution of viscoelastic properties inside biological samples - so far relying on the implicit assumption that refractive index (RI) and density can be neglected. Here, we present a novel method (FOB microscopy) combining BM with optical diffraction tomography and epifluorescence imaging for explicitly measuring the Brillouin shift, RI, and absolute density with specificity to fluorescently labeled structures. We show that neglecting the RI and density might lead to erroneous conclusions. Investigating the nucleoplasm of wild-type HeLa cells, we find that it has lower density but higher longitudinal modulus than the cytoplasm. Thus, the longitudinal modulus is not merely sensitive to the water content of the sample - a postulate vividly discussed in the field. We demonstrate the further utility of FOB on various biological systems including adipocytes and intracellular membraneless compartments. FOB microscopy can provide unexpected scientific discoveries and shed quantitative light on processes such as phase separation and transition inside living cells.
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Affiliation(s)
- Raimund Schlüßler
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
| | - Kyoohyun Kim
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und MedizinErlangenGermany
| | - Martin Nötzel
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
| | - Anna Taubenberger
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
| | - Shada Abuhattum
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und MedizinErlangenGermany
| | - Timon Beck
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und MedizinErlangenGermany
| | - Paul Müller
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und MedizinErlangenGermany
| | - Shovamaye Maharana
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Department of Microbiology and Cell Biology, Indian Institute of ScienceBengaluruIndia
| | - Gheorghe Cojoc
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
| | - Salvatore Girardo
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und MedizinErlangenGermany
| | - Andreas Hermann
- Translational Neurodegeneration Section "Albrecht Kossel", University Rostock, and German Center for Neurodegenerative Diseases (DZNE)Rostock/GreifswaldGermany
| | - Simon Alberti
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Physics of Life, Technische Universität DresdenDresdenGermany
| | - Jochen Guck
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische UniversitätDresdenGermany
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und MedizinErlangenGermany
- Physics of Life, Technische Universität DresdenDresdenGermany
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23
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Hu C, Kandel ME, Lee YJ, Popescu G. Synthetic aperture interference light (SAIL) microscopy for high-throughput label-free imaging. APPLIED PHYSICS LETTERS 2021; 119:233701. [PMID: 34924588 PMCID: PMC8660142 DOI: 10.1063/5.0065628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/29/2021] [Indexed: 05/07/2023]
Abstract
Quantitative phase imaging (QPI) is a valuable label-free modality that has gained significant interest due to its wide potentials, from basic biology to clinical applications. Most existing QPI systems measure microscopic objects via interferometry or nonlinear iterative phase reconstructions from intensity measurements. However, all imaging systems compromise spatial resolution for the field of view and vice versa, i.e., suffer from a limited space bandwidth product. Current solutions to this problem involve computational phase retrieval algorithms, which are time-consuming and often suffer from convergence problems. In this article, we presented synthetic aperture interference light (SAIL) microscopy as a solution for high-resolution, wide field of view QPI. The proposed approach employs low-coherence interferometry to directly measure the optical phase delay under different illumination angles and produces large space-bandwidth product label-free imaging. We validate the performance of SAIL on standard samples and illustrate the biomedical applications on various specimens: pathology slides, entire insects, and dynamic live cells in large cultures. The reconstructed images have a synthetic numeric aperture of 0.45 and a field of view of 2.6 × 2.6 mm2. Due to its direct measurement of the phase information, SAIL microscopy does not require long computational time, eliminates data redundancy, and always converges.
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Lee AJ, Yoon D, Han S, Hugonnet H, Park W, Park JK, Nam Y, Park Y. Label-free monitoring of 3D cortical neuronal growth in vitro using optical diffraction tomography. BIOMEDICAL OPTICS EXPRESS 2021; 12:6928-6939. [PMID: 34858689 PMCID: PMC8606138 DOI: 10.1364/boe.439404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 05/10/2023]
Abstract
The highly complex central nervous systems of mammals are often studied using three-dimensional (3D) in vitro primary neuronal cultures. A coupled confocal microscopy and immunofluorescence labeling are widely utilized for visualizing the 3D structures of neurons. However, this requires fixation of the neurons and is not suitable for monitoring an identical sample at multiple time points. Thus, we propose a label-free monitoring method for 3D neuronal growth based on refractive index tomograms obtained by optical diffraction tomography. The 3D morphology of the neurons was clearly visualized, and the developmental processes of neurite outgrowth in 3D spaces were analyzed for individual neurons.
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Affiliation(s)
- Ariel J Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Current Affiliation: Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Contributed equally
| | - DongJo Yoon
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
- Contributed equally
| | - SeungYun Han
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Current Affiliation: Department of Applied Physics, Yale University, New Haven, CT 06520, USA
- Contributed equally
| | - Herve Hugonnet
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - WeiSun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - YoonKey Nam
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
- Tomocube Inc., Daejeon, Republic of Korea
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25
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Wang Z, Bianco V, Pirone D, Memmolo P, Villone MM, Maffettone PL, Ferraro P. Dehydration of plant cells shoves nuclei rotation allowing for 3D phase-contrast tomography. LIGHT, SCIENCE & APPLICATIONS 2021; 10:187. [PMID: 34526484 PMCID: PMC8443563 DOI: 10.1038/s41377-021-00626-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/15/2021] [Accepted: 08/27/2021] [Indexed: 05/07/2023]
Abstract
Single-cell phase-contrast tomography promises to become decisive for studying 3D intracellular structures in biology. It involves probing cells with light at wide angles, which unfortunately requires complex systems. Here we show an intriguing concept based on an inherent natural process for plants biology, i.e., dehydration, allowing us to easily obtain 3D-tomography of onion-epidermal cells' nuclei. In fact, the loss of water reduces the turgor pressure and we recognize it induces significant rotation of cells' nuclei. Thanks to the holographic focusing flexibility and an ad-hoc angles' tracking algorithm, we combine different phase-contrast views of the nuclei to retrieve their 3D refractive index distribution. Nucleolus identification capability and a strategy for measuring morphology, dry mass, biovolume, and refractive index statistics are reported and discussed. This new concept could revolutionize the investigation in plant biology by enabling dynamic 3D quantitative and label-free analysis at sub-nuclear level using a conventional holographic setup.
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Affiliation(s)
- Zhe Wang
- Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Vittorio Bianco
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Daniele Pirone
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell'Informazione, Università degli Studi di Napoli "Federico II", via Claudio 21, 80125, Napoli, Italy
| | - Pasquale Memmolo
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy.
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
| | - Massimiliano Maria Villone
- Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Pier Luca Maffettone
- Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125, Napoli, Italy
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Pietro Ferraro
- NEAPoLIS, Numerical and Experimental Advanced Program on Liquids and Interface Systems, Joint Research Center CNR - Università degli Studi di Napoli "Federico II", Napoli, Italy.
- CNR-ISASI, Institute of Applied Sciences and Intelligent Systems "E. Caianiello", Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.
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26
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Taddese AM, Verrier N, Debailleul M, Courbot JB, Haeberlé O. Optimizing sample illumination scanning for reflection and 4Pi tomographic diffractive microscopy. APPLIED OPTICS 2021; 60:7745-7753. [PMID: 34613246 DOI: 10.1364/ao.435721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Tomographic diffractive microscopy (TDM) is increasingly gaining attention, owing to its high-resolution, label-free imaging capability. Fast acquisitions necessitate limiting the number of holograms to be recorded. Reconstructions then rely on optimal Fourier space filling to retain image quality and resolution, that is, they rely on optimal scanning of the tomographic illuminations. In this work, we theoretically study reflection TDM, and then the 4Pi TDM, a combination of transmission and reflection systems. Image simulations are conducted to determine optimal angular sweeping. We found that three-dimensional uniform scanning fills Fourier space the best for both reflection and 4Pi configurations, providing a better refractive index estimation for the observed sample.
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27
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Huang J, Bao Y, Gaylord TK. Analytical phase optical transfer function for Gaussian illumination and the optimized illumination profiles. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2021; 38:750-764. [PMID: 33983281 DOI: 10.1364/josaa.417407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
The imaging performance of tomographic deconvolution phase microscopy can be described in terms of the phase optical transfer function (POTF) which, in turn, depends on the illumination profile. To facilitate the optimization of the illumination profile, an analytical calculation method based on polynomial fitting is developed to describe the POTF for general nonuniform axially symmetric illumination. This is then applied to Gaussian and related profiles. Compared to numerical integration methods that integrate over a series of annuli, the present analytical method is much faster and is equally accurate. Further, a "balanced distribution" criterion for the POTF and a least-squares minimization are presented to optimize the uniformity of the POTF. An optimum general profile is found analytically by relaxed optimal search, and an optimum Gaussian profile is found through a tree search. Numerical simulations confirm the performance of these optimum profiles and support the balanced distribution criterion introduced.
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28
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Creative interior design by Plasmodium falciparum: Lipid metabolism and the parasite's secret chamber. Parasitol Int 2021; 83:102369. [PMID: 33905815 DOI: 10.1016/j.parint.2021.102369] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/06/2021] [Accepted: 04/20/2021] [Indexed: 11/21/2022]
Abstract
Malaria parasites conceal themselves within host erythrocytes and establish a necessary logistics system through the three-membrane layered structures of these cells. To establish this system, lipid metabolism is needed for the de novo synthesis of lipids and the recycling of extracellular lipids and erythrocyte lipid components. Cholesterol supply depends on its uptake from the extracellular environment and erythrocyte cytoplasm, but phospholipids can be synthesized on their own. This differential production of lipid species creates unique modifications in the lipid profile of parasitized erythrocytes, which in turn may influence the biophysical and/or mechanical properties of organelles and vesicles and communication among them. Variations in local membrane properties possibly influence the transportation of various molecules such as parasite-derived proteins, because efficiencies in secretion, vesicle fusion and budding are partly determined by the lipid profiles. Comprehensive understanding of the parasite's lipid metabolism and the biophysics of lipid membranes provides fundamental knowledge about these pathogenic organisms and could lead to new anti-malarials.
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Chemotherapy confers a conserved secondary tolerance to EGFR inhibition via AXL-mediated signaling bypass. Sci Rep 2021; 11:8016. [PMID: 33850249 PMCID: PMC8044124 DOI: 10.1038/s41598-021-87599-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/31/2021] [Indexed: 02/01/2023] Open
Abstract
Drug resistance remains the major culprit of therapy failure in disseminated cancers. Simultaneous resistance to multiple, chemically different drugs feeds this failure resulting in cancer relapse. Here, we investigate co-resistance signatures shared between antimitotic drugs (AMDs) and inhibitors of receptor tyrosine kinases (RTKs) to probe mechanisms of secondary resistance. We map co-resistance ranks in multiple drug pairs and identified a more widespread occurrence of co-resistance to the EGFR-tyrosine kinase inhibitor (TKI) gefitinib in hundreds of cancer cell lines resistant to at least 11 AMDs. By surveying different parameters of genomic alterations, we find that the two RTKs EGFR and AXL displayed similar alteration and expression signatures. Using acquired paclitaxel and epothilone B resistance as first-line AMD failure models, we show that a stable collateral resistance to gefitinib can be relayed by entering a dynamic, drug-tolerant persister state where AXL acts as bypass signal. Delayed AXL degradation rendered this persistence to become stably resistant. We probed this degradation process using a new EGFR-TKI candidate YD and demonstrated that AXL bypass-driven collateral resistance can be suppressed pharmacologically. The findings emphasize that AXL bypass track is employed by chemoresistant cancer cells upon EGFR inhibition to enter a persister state and evolve resistance to EGFR-TKIs.
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30
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Guo R, Barnea I, Shaked NT. Limited-angle tomographic phase microscopy utilizing confocal scanning fluorescence microscopy. BIOMEDICAL OPTICS EXPRESS 2021; 12:1869-1881. [PMID: 33996204 PMCID: PMC8086471 DOI: 10.1364/boe.419598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/12/2021] [Accepted: 02/16/2021] [Indexed: 05/03/2023]
Abstract
We present a multimodal imaging technique, combining tomographic phase microscopy with limited angular projection range and number, and two-channel spinning-disk confocal scanning fluorescence microscopy. This technique allows high-accuracy 3D refractive index (RI) profiling of live cells in spite of the missing projections. The cellular outer shape and its interior organelles measured by the confocal fluorescence imaging not only specify the cell in molecular levels, but also provide the 3D distributions of the whole cell as well as its organelles. We take these additional 3D morphological details as constraints in Gerchberg-Papoulis-based optical diffraction tomography algorithm. We then obtain an accurate 3D RI tomogram, even with a sparse angular range having a small number of perspective projections, otherwise providing low-accuracy RI reconstruction. Then, we obtain both cellular molecular specificity and inner RI values of the cell and its organelles. We compare the reconstructed 3D RI profiles of various samples, demonstrating the superiority of the proposed technique.
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31
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Jiao Y, He YR, Kandel ME, Liu X, Lu W, Popescu G. Computational interference microscopy enabled by deep learning. APL PHOTONICS 2021; 6:046103. [PMID: 35308602 PMCID: PMC8931864 DOI: 10.1063/5.0041901] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Quantitative phase imaging (QPI) has been widely applied in characterizing cells and tissues. Spatial light interference microscopy (SLIM) is a highly sensitive QPI method due to its partially coherent illumination and common path interferometry geometry. However, SLIM's acquisition rate is limited because of the four-frame phase-shifting scheme. On the other hand, off-axis methods such as diffraction phase microscopy (DPM) allow for single-shot QPI. However, the laser-based DPM system is plagued by spatial noise due to speckles and multiple reflections. In a parallel development, deep learning was proven valuable in the field of bioimaging, especially due to its ability to translate one form of contrast into another. Here, we propose using deep learning to produce synthetic, SLIM-quality, and high-sensitivity phase maps from DPM using single-shot images as the input. We used an inverted microscope with its two ports connected to the DPM and SLIM modules such that we have access to the two types of images on the same field of view. We constructed a deep learning model based on U-net and trained on over 1000 pairs of DPM and SLIM images. The model learned to remove the speckles in laser DPM and overcame the background phase noise in both the test set and new data. The average peak signal-to-noise ratio, Pearson correlation coefficient, and structural similarity index measure were 29.97, 0.79, and 0.82 for the test dataset. Furthermore, we implemented the neural network inference into the live acquisition software, which now allows a DPM user to observe in real-time an extremely low-noise phase image. We demonstrated this principle of computational interference microscopy imaging using blood smears, as they contain both erythrocytes and leukocytes, under static and dynamic conditions.
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Affiliation(s)
- Yuheng Jiao
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yuchen R. He
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Mikhail E. Kandel
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Xiaojun Liu
- State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wenlong Lu
- State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Gabriel Popescu
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Author to whom correspondence should be addressed:
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32
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Baczewska M, Eder K, Ketelhut S, Kemper B, Kujawińska M. Refractive Index Changes of Cells and Cellular Compartments Upon Paraformaldehyde Fixation Acquired by Tomographic Phase Microscopy. Cytometry A 2021; 99:388-398. [PMID: 32959478 PMCID: PMC8048569 DOI: 10.1002/cyto.a.24229] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/28/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022]
Abstract
Three-dimensional quantitative phase imaging is an emerging method, which provides the 3D distribution of the refractive index (RI) and the dry mass in live and fixed cells as well as in tissues. However, an insufficiently answered question is the influence of chemical cell fixation procedures on the results of RI reconstructions. Therefore, this work is devoted to systematic investigations on the RI in cellular organelles of live and fixed cells including nucleus, nucleolus, nucleoplasm, and cytoplasm. The research was carried out on four different cell lines using a common paraformaldehyde (PFA)-based fixation protocol. The selected cell types represent the diversity of mammalian cells and therefore the results presented provide a picture of fixation caused RI changes in a broader context. A commercial Tomocube HT-1S device was used for 3D RI acquisition. The changes in the RI values after the fixation process are detected in the reconstructed phase distributions and amount to the order of 10-3 . The RI values decrease and the observed RI changes are found to be different between various cell lines; however, all of them show the most significant loss in the nucleolus. In conclusion, our study demonstrates the evident need for standardized preparation procedures in phase tomographic measurements. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Maria Baczewska
- Warsaw University of Technology, Institute of Micromechanics and Photonics, Sw. Boboli 8 St.Warsaw02‐525Poland
| | - Kai Eder
- Biomedical Technology Center of the Medical Faculty, University of Muenster Mendelstr 17MuensterD‐48149Germany
| | - Steffi Ketelhut
- Biomedical Technology Center of the Medical Faculty, University of Muenster Mendelstr 17MuensterD‐48149Germany
| | - Björn Kemper
- Biomedical Technology Center of the Medical Faculty, University of Muenster Mendelstr 17MuensterD‐48149Germany
| | - Małgorzata Kujawińska
- Warsaw University of Technology, Institute of Micromechanics and Photonics, Sw. Boboli 8 St.Warsaw02‐525Poland
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33
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Paidi SK, Shah V, Raj P, Glunde K, Pandey R, Barman I. Coarse Raman and optical diffraction tomographic imaging enable label-free phenotyping of isogenic breast cancer cells of varying metastatic potential. Biosens Bioelectron 2021; 175:112863. [PMID: 33272866 PMCID: PMC7847362 DOI: 10.1016/j.bios.2020.112863] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022]
Abstract
Identification of the metastatic potential represents one of the most important tasks for molecular imaging of cancer. While molecular imaging of metastases has witnessed substantial progress as an area of clinical inquiry, determining precisely what differentiates the metastatic phenotype has proven to be more elusive. In this study, we utilize both the morphological and molecular information provided by 3D optical diffraction tomography and Raman spectroscopy, respectively, to propose a label-free route for optical phenotyping of cancer cells at single-cell resolution. By using an isogenic panel of cell lines derived from MDA-MB-231 breast cancer cells that vary in their metastatic potential, we show that 3D refractive index tomograms can capture subtle morphological differences among the parental, circulating tumor cells, and lung metastatic cells. By leveraging its molecular specificity, we demonstrate that coarse Raman microscopy is capable of rapidly mapping a sufficient number of cells for training a random forest classifier that can accurately predict the metastatic potential of cells at a single-cell level. We also perform multivariate curve resolution alternating least squares decomposition of the spectral dataset to demarcate spectra from cytoplasm and nucleus, and test the feasibility of identifying metastatic phenotypes using the spectra only from the cytoplasmic and nuclear regions. Overall, our study provides a rationale for employing coarse Raman mapping to substantially reduce measurement time thereby enabling the acquisition of reasonably large training datasets that hold the key for label-free single-cell analysis and, consequently, for differentiation of indolent from aggressive phenotypes.
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Affiliation(s)
- Santosh Kumar Paidi
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Vaani Shah
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Piyush Raj
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kristine Glunde
- The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Rishikesh Pandey
- CytoVeris Inc, Farmington, CT, 06032, USA; Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA; The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Department of Oncology, Johns Hopkins University, Baltimore, MD, 21287, USA.
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Taddese AM, Verrier N, Debailleul M, Courbot JB, Haeberlé O. Optimizing sample illumination scanning in transmission tomographic diffractive microscopy. APPLIED OPTICS 2021; 60:1694-1704. [PMID: 33690516 DOI: 10.1364/ao.417061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
Due to the sequential nature of data acquisition, it is preferable to limit the number of illuminations to be used in tomographic diffractive microscopy experiments, especially if fast imaging is foreseen. On the other hand, for high-quality, high-resolution imaging, the Fourier space has to be optimally filled. Up to now, the problem of optimal Fourier space filling has not been investigated in itself. In this paper, we perform a comparative study to analyze the effect of sample scanning patterns on Fourier space filling for a transmission setup. Optical transfer functions for several illumination patterns are studied. Simulation as well as experiments are conducted to compare associated image reconstructions. We found that 3D uniform angular sweeping best fills the Fourier space, leading to better quality images.
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35
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Bakhshandeh S, Taïeb HM, Schlüßler R, Kim K, Beck T, Taubenberger A, Guck J, Cipitria A. Optical quantification of intracellular mass density and cell mechanics in 3D mechanical confinement. SOFT MATTER 2021; 17:853-862. [PMID: 33232425 DOI: 10.1039/d0sm01556c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biophysical properties of cells such as intracellular mass density and cell mechanics are known to be involved in a wide range of homeostatic functions and pathological alterations. An optical readout that can be used to quantify such properties is the refractive index (RI) distribution. It has been recently reported that the nucleus, initially presumed to be the organelle with the highest dry mass density (ρ) within the cell, has in fact a lower RI and ρ than its surrounding cytoplasm. These studies have either been conducted in suspended cells, or cells adhered on 2D substrates, neither of which reflects the situation in vivo where cells are surrounded by the extracellular matrix (ECM). To better approximate the 3D situation, we encapsulated cells in 3D covalently-crosslinked alginate hydrogels with varying stiffness, and imaged the 3D RI distribution of cells, using a combined optical diffraction tomography (ODT)-epifluorescence microscope. Unexpectedly, the nuclei of cells in 3D displayed a higher ρ than the cytoplasm, in contrast to 2D cultures. Using a Brillouin-epifluorescence microscope we subsequently showed that in addition to higher ρ, the nuclei also had a higher longitudinal modulus (M) and viscosity (η) compared to the cytoplasm. Furthermore, increasing the stiffness of the hydrogel resulted in higher M for both the nuclei and cytoplasm of cells in stiff 3D alginate compared to cells in compliant 3D alginate. The ability to quantify intracellular biophysical properties with non-invasive techniques will improve our understanding of biological processes such as dormancy, apoptosis, cell growth or stem cell differentiation.
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Affiliation(s)
- Sadra Bakhshandeh
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
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36
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Kim D, Lee S, Lee M, Oh J, Yang SA, Park Y. Holotomography: Refractive Index as an Intrinsic Imaging Contrast for 3-D Label-Free Live Cell Imaging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1310:211-238. [PMID: 33834439 DOI: 10.1007/978-981-33-6064-8_10] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Live cell imaging provides essential information in the investigation of cell biology and related pathophysiology. Refractive index (RI) can serve as intrinsic optical imaging contrast for 3-D label-free and quantitative live cell imaging, and provide invaluable information to understand various dynamics of cells and tissues for the study of numerous fields. Recently significant advances have been made in imaging methods and analysis approaches utilizing RI, which are now being transferred to biological and medical research fields, providing novel approaches to investigate the pathophysiology of cells. To provide insight into how RI can be used as an imaging contrast for imaging of biological specimens, here we provide the basic principle of RI-based imaging techniques and summarize recent progress on applications, ranging from microbiology, hematology, infectious diseases, hematology, and histopathology.
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Affiliation(s)
- Doyeon Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Sangyun Lee
- Department of Physics, KAIST, Daejeon, South Korea
| | - Moosung Lee
- Department of Physics, KAIST, Daejeon, South Korea
| | - Juntaek Oh
- Department of Physics, KAIST, Daejeon, South Korea
| | - Su-A Yang
- Department of Biological Sciences, KAIST, Daejeon, South Korea
| | - YongKeun Park
- Department of Physics, KAIST, Daejeon, South Korea. .,KAIST Institute Health Science and Technology, Daejeon, South Korea. .,Tomocube Inc., Daejeon, South Korea.
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37
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Fan S, Smith-Dryden S, Li G, Saleh B. Iterative optical diffraction tomography for illumination scanning configuration. OPTICS EXPRESS 2020; 28:39904-39915. [PMID: 33379529 DOI: 10.1364/oe.413230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Optical diffraction tomography (ODT) is used to reconstruct refractive-index distributions from multiple measurements in the object rotating configuration (ORC) or the illumination scanning configuration (ISC). Because of its fast data acquisition and stability, ISC-based ODT has been widely used for biological imaging. ODT typically fails to reconstruct multiply-scattering samples. The previously developed iterative ODT (iODT) was for the multiply-scattering objects in ORC, and could not be directly applied to ISC. To resolve this mismatch, we developed an ISC update and numerically demonstrated its accuracy. With the same prior knowledge, iODT-ISC outperforms conventional ODT in resolving the missing-angle problem.
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Guillén-Boixet J, Kopach A, Holehouse AS, Wittmann S, Jahnel M, Schlüßler R, Kim K, Trussina IREA, Wang J, Mateju D, Poser I, Maharana S, Ruer-Gruß M, Richter D, Zhang X, Chang YT, Guck J, Honigmann A, Mahamid J, Hyman AA, Pappu RV, Alberti S, Franzmann TM. RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation. Cell 2020; 181:346-361.e17. [PMID: 32302572 PMCID: PMC7181197 DOI: 10.1016/j.cell.2020.03.049] [Citation(s) in RCA: 444] [Impact Index Per Article: 111.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 10/23/2019] [Accepted: 03/20/2020] [Indexed: 12/14/2022]
Abstract
Stressed cells shut down translation, release mRNA molecules from polysomes, and form stress granules (SGs) via a network of interactions that involve G3BP. Here we focus on the mechanistic underpinnings of SG assembly. We show that, under non-stress conditions, G3BP adopts a compact auto-inhibited state stabilized by electrostatic intramolecular interactions between the intrinsically disordered acidic tracts and the positively charged arginine-rich region. Upon release from polysomes, unfolded mRNAs outcompete G3BP auto-inhibitory interactions, engendering a conformational transition that facilitates clustering of G3BP through protein-RNA interactions. Subsequent physical crosslinking of G3BP clusters drives RNA molecules into networked RNA/protein condensates. We show that G3BP condensates impede RNA entanglement and recruit additional client proteins that promote SG maturation or induce a liquid-to-solid transition that may underlie disease. We propose that condensation coupled to conformational rearrangements and heterotypic multivalent interactions may be a general principle underlying RNP granule assembly. Under non-stressed conditions, G3BP adopts a compact auto-inhibited state Conformational expansion of G3BP increases the interaction valences G3BP clusters crosslink RNA to assemble stress granules upon cellular stress G3BP condensates prevent RNA entanglement
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Affiliation(s)
- Jordina Guillén-Boixet
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Andrii Kopach
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Alex S Holehouse
- Department of Biomedical Engineering and Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Sina Wittmann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Marcus Jahnel
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Raimund Schlüßler
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Kyoohyun Kim
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Irmela R E A Trussina
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Jie Wang
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Daniel Mateju
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Shovamayee Maharana
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Martine Ruer-Gruß
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Doris Richter
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Xiaojie Zhang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Young-Tae Chang
- Center for Self-Assembly and Complexity, Institute for Basic Science, Pohang 37673, Republic of Korea; Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Jochen Guck
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Simon Alberti
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Titus M Franzmann
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
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Kim K, Guck J. The Relative Densities of Cytoplasm and Nuclear Compartments Are Robust against Strong Perturbation. Biophys J 2020; 119:1946-1957. [PMID: 33091376 PMCID: PMC7732746 DOI: 10.1016/j.bpj.2020.08.044] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/22/2020] [Accepted: 08/04/2020] [Indexed: 12/23/2022] Open
Abstract
The cell nucleus is a compartment in which essential processes such as gene transcription and DNA replication occur. Although the large amount of chromatin confined in the finite nuclear space could install the picture of a particularly dense organelle surrounded by less dense cytoplasm, recent studies have begun to report the opposite. However, the generality of this newly emerging, opposite picture has so far not been tested. Here, we used combined optical diffraction tomography and epi-fluorescence microscopy to systematically quantify the mass densities of cytoplasm, nucleoplasm, and nucleoli of human cell lines, challenged by various perturbations. We found that the nucleoplasm maintains a lower mass density than cytoplasm during cell cycle progression by scaling its volume to match the increase of dry mass during cell growth. At the same time, nucleoli exhibited a significantly higher mass density than the cytoplasm. Moreover, actin and microtubule depolymerization and changing chromatin condensation altered volume, shape, and dry mass of those compartments, whereas the relative distribution of mass densities was generally unchanged. Our findings suggest that the relative mass densities across membrane-bound and membraneless compartments are robustly conserved, likely by different as-of-yet unknown mechanisms, which hints at an underlying functional relevance. This surprising robustness of mass densities contributes to an increasing recognition of the importance of physico-chemical properties in determining cellular characteristics and compartments.
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Affiliation(s)
- Kyoohyun Kim
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany; Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Jochen Guck
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany; Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.
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40
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Lin YH, Liao KYK, Sung KB. Automatic detection and characterization of quantitative phase images of thalassemic red blood cells using a mask region-based convolutional neural network. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:JBO-200187R. [PMID: 33188571 PMCID: PMC7665881 DOI: 10.1117/1.jbo.25.11.116502] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/26/2020] [Indexed: 05/07/2023]
Abstract
SIGNIFICANCE Label-free quantitative phase imaging is a promising technique for the automatic detection of abnormal red blood cells (RBCs) in real time. Although deep-learning techniques can accurately detect abnormal RBCs from quantitative phase images efficiently, their applications in diagnostic testing are limited by the lack of transparency. More interpretable results such as morphological and biochemical characteristics of individual RBCs are highly desirable. AIM An end-to-end deep-learning model was developed to efficiently discriminate thalassemic RBCs (tRBCs) from healthy RBCs (hRBCs) in quantitative phase images and segment RBCs for single-cell characterization. APPROACH Two-dimensional quantitative phase images of hRBCs and tRBCs were acquired using digital holographic microscopy. A mask region-based convolutional neural network (Mask R-CNN) model was trained to discriminate tRBCs and segment individual RBCs. Characterization of tRBCs was achieved utilizing SHapley Additive exPlanation analysis and canonical correlation analysis on automatically segmented RBC phase images. RESULTS The implemented model achieved 97.8% accuracy in detecting tRBCs. Phase-shift statistics showed the highest influence on the correct classification of tRBCs. Associations between the phase-shift features and three-dimensional morphological features were revealed. CONCLUSIONS The implemented Mask R-CNN model accurately identified tRBCs and segmented RBCs to provide single-RBC characterization, which has the potential to aid clinical decision-making.
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Affiliation(s)
- Yang-Hsien Lin
- National Taiwan University, Graduate Institute of Biomedical Electronics and Bioinformatics, Taipei, Taiwan
| | - Ken Y.-K. Liao
- Feng Chia University, College of Information and Electrical Engineering, Taichung, Taiwan
| | - Kung-Bin Sung
- National Taiwan University, Graduate Institute of Biomedical Electronics and Bioinformatics, Taipei, Taiwan
- National Taiwan University, Department of Electrical Engineering, Taipei, Taiwan
- National Taiwan University, Molecular Imaging Center, Taipei, Taiwan
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41
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Stanly TA, Suman R, Rani GF, O’Toole PJ, Kaye PM, Hitchcock IS. Quantitative Optical Diffraction Tomography Imaging of Mouse Platelets. Front Physiol 2020; 11:568087. [PMID: 33041864 PMCID: PMC7526686 DOI: 10.3389/fphys.2020.568087] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/25/2020] [Indexed: 11/13/2022] Open
Abstract
Platelets are specialized anucleate cells that play a major role in hemostasis following vessel injury. More recently, platelets have also been implicated in innate immunity and inflammation by directly interacting with immune cells and releasing proinflammatory signals. It is likely therefore that in certain pathologies, such as chronic parasitic infections and myeloid malignancies, platelets can act as mediators for hemostatic and proinflammatory responses. Fortunately, murine platelet function ex vivo is highly analogous to human, providing a robust model for functional comparison. However, traditional methods of studying platelet phenotype, function and activation status often rely on using large numbers of whole isolated platelet populations, which severely limits the number and type of assays that can be performed with mouse blood. Here, using cutting edge 3D quantitative phase imaging, holotomography, that uses optical diffraction tomography (ODT), we were able to identify and quantify differences in single unlabeled, live platelets with minimal experimental interference. We analyzed platelets directly isolated from whole blood of mice with either a JAK2V617F-positive myeloproliferative neoplasm (MPN) or Leishmania donovani infection. Image analysis of the platelets indicates previously uncharacterized differences in platelet morphology, including altered cell volume and sphericity, as well as changes in biophysical parameters such as refractive index (RI) and dry mass. Together, these data indicate that, by using holotomography, we were able to identify clear disparities in activation status and potential functional ability in disease states compared to control at the level of single platelets.
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Affiliation(s)
- Tess A. Stanly
- York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom
| | - Rakesh Suman
- Technology Facility, Department of Biology, University of York, York, United Kingdom
| | - Gulab Fatima Rani
- York Biomedical Research Institute, Hull York Medical School, University of York, York, United Kingdom
| | - Peter J. O’Toole
- Technology Facility, Department of Biology, University of York, York, United Kingdom
| | - Paul M. Kaye
- York Biomedical Research Institute, Hull York Medical School, University of York, York, United Kingdom
| | - Ian S. Hitchcock
- York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom
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42
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Luo Z, Yurt A, Stahl R, Carlon MS, Ramalho AS, Vermeulen F, Lambrechts A, Braeken D, Lagae L. Fast compressive lens-free tomography for 3D biological cell culture imaging. OPTICS EXPRESS 2020; 28:26935-26952. [PMID: 32906958 DOI: 10.1364/oe.393492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
We present a compressive lens-free technique that performs tomographic imaging across a cubic millimeter-scale volume from highly sparse data. Compared with existing lens-free 3D microscopy systems, our method requires an order of magnitude fewer multi-angle illuminations for tomographic reconstruction, leading to a compact, cost-effective and scanning-free setup with a reduced data acquisition time to enable high-throughput 3D imaging of dynamic biological processes. We apply a fast proximal gradient algorithm with composite regularization to address the ill-posed tomographic inverse problem. Using simulated data, we show that the proposed method can achieve a reconstruction speed ∼10× faster than the state-of-the-art inverse problem approach in 3D lens-free microscopy. We experimentally validate the effectiveness of our method by imaging a resolution test chart and polystyrene beads, demonstrating its capability to resolve micron-size features in both lateral and axial directions. Furthermore, tomographic reconstruction results of neuronspheres and intestinal organoids reveal the potential of this 3D imaging technique for high-resolution and high-throughput biological applications.
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43
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Firdaus ER, Park JH, Lee SK, Park Y, Cha GH, Han ET. 3D morphological and biophysical changes in a single tachyzoite and its infected cells using three-dimensional quantitative phase imaging. JOURNAL OF BIOPHOTONICS 2020; 13:e202000055. [PMID: 32441392 DOI: 10.1002/jbio.202000055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Toxoplasma gondii is an apicomplexan parasite that causes toxoplasmosis in the human body and commonly infects warm-blooded organisms. Pathophysiology of its diseases is still an interesting issue to be studied since T gondii can infect nearly all nucleated cells. Imaging techniques are crucial for studying its pathophysiology. In T gondii-infected cells structural and biochemical alterations occurred. To study that modification, we use digital holotomography to investigate the structure and biochemical alteration of single tachyzoite and its infected cells in a label-free and quantitative manner. Quantification analysis was done by measuring the refractive index distribution, which provides information about the concentration and dry mass of individual cells. This study showed that holotomography could be effectively used to identify the structural and biochemical alteration in tremendously different cells in supporting pathophysiological research in particular for T gondii-caused diseases.
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Affiliation(s)
- Egy Rahman Firdaus
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Ji-Hoon Park
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Seong-Kyun Lee
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Guang-Ho Cha
- Department of Medical Science & Infection Biology, Chungnam National University, School of Medicine, Daejeon, Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
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O’Connor T, Anand A, Andemariam B, Javidi B. Deep learning-based cell identification and disease diagnosis using spatio-temporal cellular dynamics in compact digital holographic microscopy. BIOMEDICAL OPTICS EXPRESS 2020; 11:4491-4508. [PMID: 32923059 PMCID: PMC7449709 DOI: 10.1364/boe.399020] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/01/2020] [Accepted: 07/12/2020] [Indexed: 05/14/2023]
Abstract
We demonstrate a successful deep learning strategy for cell identification and disease diagnosis using spatio-temporal cell information recorded by a digital holographic microscopy system. Shearing digital holographic microscopy is employed using a low-cost, compact, field-portable and 3D-printed microscopy system to record video-rate data of live biological cells with nanometer sensitivity in terms of axial membrane fluctuations, then features are extracted from the reconstructed phase profiles of segmented cells at each time instance for classification. The time-varying data of each extracted feature is input into a recurrent bi-directional long short-term memory (Bi-LSTM) network which learns to classify cells based on their time-varying behavior. Our approach is presented for cell identification between the morphologically similar cases of cow and horse red blood cells. Furthermore, the proposed deep learning strategy is demonstrated as having improved performance over conventional machine learning approaches on a clinically relevant dataset of human red blood cells from healthy individuals and those with sickle cell disease. The results are presented at both the cell and patient levels. To the best of our knowledge, this is the first report of deep learning for spatio-temporal-based cell identification and disease detection using a digital holographic microscopy system.
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Affiliation(s)
- Timothy O’Connor
- Biomedical Engineering Department, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Arun Anand
- Applied Physics Department, Faculty of Tech. & Engineering, M.S. University of Baroda, Vadodara 390001, India
| | - Biree Andemariam
- New England Sickle Cell Institute, University of Connecticut Health, Farmington, Connecticut 06030, USA
| | - Bahram Javidi
- Electrical and Computer Engineering Department, University of Connecticut, Storrs, Connecticut 06269, USA
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45
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Jo Y, Kim HM, Lee J, Lee C, Hugonnet H, Park Y, Liu X, Chang YT, Kim H, Kim P. Fluid–Matrix Interface Triggers a Heterogeneous Activation of Macrophages. ACS APPLIED BIO MATERIALS 2020; 3:4294-4301. [DOI: 10.1021/acsabm.0c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Youngmin Jo
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Hyo Min Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jongbeom Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Chungha Lee
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
- Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Hervé Hugonnet
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
- Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
- Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
- Tomocube, Inc., Daejeon 34051, Republic of Korea
| | - Xiao Liu
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), South Korea & Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Young-Tae Chang
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), South Korea & Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Hyoungsoo Kim
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Pilnam Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
- Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
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46
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Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase. Nat Commun 2020; 11:1970. [PMID: 32327663 PMCID: PMC7181634 DOI: 10.1038/s41467-020-15839-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
Succinic acid (SA), a dicarboxylic acid of industrial importance, can be efficiently produced by metabolically engineered Mannheimia succiniciproducens. Malate dehydrogenase (MDH) is one of the key enzymes for SA production, but has not been well characterized. Here we report biochemical and structural analyses of various MDHs and development of hyper-SA producing M. succiniciproducens by introducing the best MDH. Corynebacterium glutamicum MDH (CgMDH) shows the highest specific activity and least substrate inhibition, whereas M. succiniciproducens MDH (MsMDH) shows low specific activity at physiological pH and strong uncompetitive inhibition toward oxaloacetate (ki of 67.4 and 588.9 μM for MsMDH and CgMDH, respectively). Structural comparison of the two MDHs reveals a key residue influencing the specific activity and susceptibility to substrate inhibition. A high-inoculum fed-batch fermentation of the final strain expressing cgmdh produces 134.25 g L-1 of SA with the maximum productivity of 21.3 g L-1 h-1, demonstrating the importance of enzyme optimization in strain development.
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47
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Fan S, Smith-Dryden S, Li G, Saleh B. Reconstructing complex refractive-index of multiply-scattering media by use of iterative optical diffraction tomography. OPTICS EXPRESS 2020; 28:6846-6858. [PMID: 32225923 DOI: 10.1364/oe.380309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/19/2019] [Indexed: 05/27/2023]
Abstract
Conventional optical diffraction tomography (ODT) techniques fail in the presence of multiple scattering, and the problem becomes even more challenging when the medium is also lossy. Iterative ODT (iODT), which was shown recently to be more tolerant to multiple scattering than conventional ODT, is here augmented with an error-subtraction (ES) module. Numerical results demonstrate the accuracy and efficiency of iODT with ES for reconstructing multiply-scattering objects with complex refractive index.
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48
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Oh J, Ryu JS, Lee M, Jung J, Han S, Chung HJ, Park Y. Three-dimensional label-free observation of individual bacteria upon antibiotic treatment using optical diffraction tomography. BIOMEDICAL OPTICS EXPRESS 2020; 11:1257-1267. [PMID: 32206407 PMCID: PMC7075604 DOI: 10.1364/boe.377740] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/13/2020] [Accepted: 01/27/2020] [Indexed: 05/20/2023]
Abstract
Measuring alterations in bacteria upon antibiotic application is important for basic studies in microbiology, drug discovery, clinical diagnosis, and disease treatment. However, imaging and 3D time-lapse response analysis of individual bacteria upon antibiotic application remain largely unexplored mainly due to limitations in imaging techniques. Here, we present a method to systematically investigate the alterations in individual bacteria in 3D and quantitatively analyze the effects of antibiotics. Using optical diffraction tomography, in-situ responses of Escherichia coli and Bacillus subtilis to various concentrations of ampicillin were investigated in a label-free and quantitative manner. The presented method reconstructs the dynamic changes in the 3D refractive-index distributions of living bacteria in response to antibiotics at sub-micrometer spatial resolution.
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Affiliation(s)
- Jeonghun Oh
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, South Korea
| | - Jea Sung Ryu
- Graduate School of Nanoscience and Technology, KAIST, Daejeon 34141, South Korea
| | - Moosung Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, South Korea
| | - Jaehwang Jung
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, South Korea
- Current Affiliation: Mechatronics R&D Center, Samsung Electronics, Hwasung 18448, South Korea
| | - SeungYun Han
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, South Korea
| | - Hyun Jung Chung
- Graduate School of Nanoscience and Technology, KAIST, Daejeon 34141, South Korea
- Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
| | - Yongkeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, South Korea
- Tomocube Inc., Daejeon 34051, South Korea
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49
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Real-time cholesterol sorting in Plasmodium falciparum-erythrocytes as revealed by 3D label-free imaging. Sci Rep 2020; 10:2794. [PMID: 32066816 PMCID: PMC7026401 DOI: 10.1038/s41598-020-59552-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/28/2020] [Indexed: 12/18/2022] Open
Abstract
Cholesterol, a necessary component of animal cell membranes, is also needed by the lethal human malaria parasite Plasmodium falciparum. Because P. falciparum lacks a cholesterol synthesis pathway and malaria patients have low blood cholesterol, we speculated that it scavenges cholesterol from them in some way. We used time-lapse holotomographic microscopy to observe cholesterol transport in live P. falciparum parasites and structurally investigate erythrocyte membranes, both during and after P. falciparum invasion of human erythrocytes. After P. falciparum initially acquired free cholesterol or inner erythrocytic membrane-derived cholesterol, we observed budding lipid membranes elongating into the cytosol and/or membrane segments migrating there and eventually fusing with the parasite membranes, presumably at the parasitophorous vacuole membrane (PVM). Finally, the cholesterol-containing segments were seen to surround the parasite nucleus. Our imaging data suggest that a novel membrane transport system operates in the cytosol of P. falciparum-infected erythrocytes as a cholesterol import system, likely between the PVM and the erythrocyte membrane, and that this transportation process occurs during the live erythrocyte stages of P. falciparum.
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50
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Zhang HC, Zhang LP, He PH, Xu J, Qian C, Garcia-Vidal FJ, Cui TJ. A plasmonic route for the integrated wireless communication of subdiffraction-limited signals. LIGHT, SCIENCE & APPLICATIONS 2020; 9:113. [PMID: 32637080 PMCID: PMC7329838 DOI: 10.1038/s41377-020-00355-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 05/09/2023]
Abstract
Perfect lenses, superlenses and time-reversal mirrors can support and spatially separate evanescent waves, which is the basis for detecting subwavelength information in the far field. However, the inherent limitations of these methods have prevented the development of systems to dynamically distinguish subdiffraction-limited signals. Utilizing the physical merits of spoof surface plasmon polaritons (SPPs), we demonstrate that subdiffraction-limited signals can be transmitted on planar integrated SPP channels with low loss, low channel interference, and high gain and can be radiated with a very low environmental sensitivity. Furthermore, we show how deep subdiffraction-limited signals that are spatially coupled can be distinguished after line-of-sight wireless transmission. For a visualized demonstration, we realize the high-quality wireless communication of two movies on subwavelength channels over the line of sight in real time using our plasmonic scheme, showing significant advantages over the conventional methods.
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Affiliation(s)
- Hao Chi Zhang
- State Key Laboratory of Millimeter Waves, Southeast University, 210096 Nanjing, China
| | - Le Peng Zhang
- State Key Laboratory of Millimeter Waves, Southeast University, 210096 Nanjing, China
| | - Pei Hang He
- State Key Laboratory of Millimeter Waves, Southeast University, 210096 Nanjing, China
| | - Jie Xu
- State Key Laboratory of Millimeter Waves, Southeast University, 210096 Nanjing, China
| | - Cheng Qian
- State Key Laboratory of Millimeter Waves, Southeast University, 210096 Nanjing, China
| | - Francisco J. Garcia-Vidal
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain
- Donostia International Physics Center (DIPC), Donostia/San Sebastian, Spain
| | - Tie Jun Cui
- State Key Laboratory of Millimeter Waves, Southeast University, 210096 Nanjing, China
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