1
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Wang H, Zhang L, Huang J, Yang Z, Fan C, Yuan L, Zhao H, Zhang Z, Liu X. Imaging the intracellular refractive index distribution (IRID) for dynamic label-free living colon cancer cells via circularly depolarization decay model (CDDM). BIOMEDICAL OPTICS EXPRESS 2024; 15:2451-2465. [PMID: 38633098 PMCID: PMC11019712 DOI: 10.1364/boe.518957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 04/19/2024]
Abstract
Label-free detection of intracellular substances for living cancer cells remains a significant hurdle in cancer pathogenesis research. Although the sensitivity of light polarization to intracellular substances has been validated, current studies are predominantly focused on tissue lesions, thus label-free detection of substances within individual living cancer cells is still a challenge. The main difficulty is to find specific detection methods along with corresponding characteristic parameters. With refractive index as an endogenous marker of substances, this study proposes a detection method of intracellular refractive index distribution (IRID) for label-free living colon cancer (LoVo) cells. Utilizing the circular depolarization decay model (CDDM) to calculate the degree of circular polarization (DOCP) modulated by the cell allows for the derivation of the IRID on the focal plane. Experiments on LoVo cells demonstrated the refractive index of single cell can be accurately and precisely measured, with precision of 10-3 refractive index units (RIU). Additionally, chromatin content during the interphases (G1, S, G2) of cell cycle was recorded at 56.5%, 64.4%, and 71.5%, respectively. A significantly finer IRID can be obtained compared to the phase measurement method. This method is promising in providing a dynamic label-free intracellular substances detection method in cancer pathogenesis studies.
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Affiliation(s)
- Huijun Wang
- State Key Laboratory for Manufacturing System Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Lu Zhang
- State Key Laboratory for Manufacturing System Engineering, Xi’an Jiaotong University, Xi’an 710049, China
- School of Instrument Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Jie Huang
- State Key Laboratory for Manufacturing System Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Zewen Yang
- State Key Laboratory for Manufacturing System Engineering, Xi’an Jiaotong University, Xi’an 710049, China
| | - Chen Fan
- State Key Laboratory for Manufacturing System Engineering, Xi’an Jiaotong University, Xi’an 710049, China
- School of Instrument Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Li Yuan
- First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Hong Zhao
- State Key Laboratory for Manufacturing System Engineering, Xi’an Jiaotong University, Xi’an 710049, China
- School of Instrument Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Zhenxi Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi’an Jiaotong University, Xi’an 710049, China
| | - Xiaolong Liu
- Mengchao Hepatobiliary Hospital of Fujian Medical University, The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Provincey, Fuzhou 350025, China
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2
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Litunenko DN, Moskalensky AE. Wireless monitoring of cell cultures based on light scattering: A novel optical scheme and portable prototype. JOURNAL OF BIOPHOTONICS 2024; 17:e202300234. [PMID: 37795552 DOI: 10.1002/jbio.202300234] [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: 06/15/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/06/2023]
Abstract
Cell cultures are widely used in scientific research, biomedicine, and industry. When culturing, it is important to maintain certain conditions, including the concentration of cells. Monitoring of the culture growth and cell counting is an urgent task for the optimization of technological processes. Most existing methods require sampling from a culture flask. This procedure is time-consuming and associated with the risks of contamination. We present a device able to monitor the growth of cells number in a suspension noninvasively. The device uses a laser beam that pass through the culture flask and measures the intensity of scattered light as a function of coordinate along the beam. This optical scheme allows one to obtain accurate results for both high- and low-scattering samples. We constructed the wireless portable prototype for monitoring of cell culture growth directly in the incubator and demonstrated the applicability of the device for Jurkat cells and Escherichia coli bacteria.
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3
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Strokotov DI, Nekrasov VM, Gilev KV, Karpenko AA, Maltsev VP. Ultraviolet light scattering scanning flow cytometry in the characterization of submicron microparticles. Cytometry A 2023; 103:736-743. [PMID: 37306103 DOI: 10.1002/cyto.a.24769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 05/02/2023] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
Ultraviolet lasers are commonly used in flow cytometry to excite fluorochrome molecules with subsequent measurement of the specific fluorescence of individual cells. In this study, the performance of the ultraviolet light scattering (UVLS) in the analysis of individual particles with flow cytometry has been demonstrated for the first time. The main advantage of the UVLS relates to the improvement of the analysis of submicron particles due to the strong dependence of the scattering efficiency on the wavelength of the incident light. In this work, submicron particles were analyzed using a scanning flow cytometer (SFC) that allows measurements of light scattering in an angle-resolved regime. The measured light-scattering profiles of individual particles were utilized in solution of the inverse light-scattering problem to retrieve the particle characteristics using a global optimization. The standard polystyrene microspheres were successfully characterized from the analysis of UVLS which provided the size and refractive index (RI) of individual beads. We believe that the main application of UVLS relates to the analysis of microparticles in a serum, in particular in the analysis of chylomicrons (CMs). We have demonstrated the performance of the UVLS SFC in the analysis of CMs of a donor. The RI versus size scatterplot of CMs was successfully retrieved from the analysis. The current set-up of the SFC has allowed us to characterize individual CMs starting from the size of 160 nm that provides determination of the CM concentration in a serum with flow cytometry. This feature of the UVLS should help with the analysis of lipid metabolism measuring RI and size map evolution after lipase action.
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Affiliation(s)
- Dmitry I Strokotov
- Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation
| | - Vyacheslav M Nekrasov
- Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation
| | - Konstantin V Gilev
- Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation
| | - Andrey A Karpenko
- State Research Institute of Circulation Pathology, Novosibirsk, Russian Federation
| | - Valeri P Maltsev
- Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation
- Biomedical Physics Department, Novosibirsk State University, Novosibirsk, Russian Federation
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4
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Reale R, Peruzzi G, Ghoreishi M, Stabile H, Ruocco G, Leonetti M. A low-cost, label-free microfluidic scanning flow cytometer for high-accuracy quantification of size and refractive index of particles. LAB ON A CHIP 2023; 23:2039-2047. [PMID: 36897350 PMCID: PMC10091359 DOI: 10.1039/d2lc01179d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Flow cytometers and fluorescence activated cells sorters (FCM/FACS) represent the gold standard for high-throughput single-cell analysis, but their usefulness for label-free applications is limited by the unreliability of forward and side scatter measurements. Scanning flow cytometers represent an appealing alternative, as they exploit measurements of the angle-resolved scattered light to provide accurate and quantitative estimates of cellular properties, but the requirements of current setups are unsuitable for integration with other lab-on-chip technologies or for point-of-care applications. Here we present the first microfluidic scanning flow cytometer (μSFC), able to achieve accurate angle-resolved scattering measurements within a standard polydimethylsiloxane microfluidic chip. The system exploits a low cost linearly variable optical density (OD) filter to reduce the dynamic range of the signal and to increase its signal-to-noise ratio. We present a performance comparison between the μSFC and commercial machines for the label free characterization of polymeric beads with different diameters and refractive indices. In contrast to FCM and FACS, the μSFC yields size estimates linearly correlated with nominal particle sizes (R2 = 0.99) and quantitative estimates of particle refractive indices. The feasibility of using the μSFC for the characterization of biological samples is demonstrated by analyzing a population of monocytes identified based on the morphology of a peripheral blood mononuclear cells sample, which yields values in agreement with the literature. The proposed μSFC combines low setup requirements with high performance, and has great potential for integration within other lab-on-chip systems for multi-parametric cell analysis and for next-generation point-of-care diagnostic applications.
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Affiliation(s)
- Riccardo Reale
- Center for Life Nano- & Neuro-Science, Italian Institute of Technology, Rome, Italy.
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science, Italian Institute of Technology, Rome, Italy.
| | - Maryamsadat Ghoreishi
- Center for Life Nano- & Neuro-Science, Italian Institute of Technology, Rome, Italy.
| | - Helena Stabile
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nano- & Neuro-Science, Italian Institute of Technology, Rome, Italy.
| | - Marco Leonetti
- Center for Life Nano- & Neuro-Science, Italian Institute of Technology, Rome, Italy.
- Soft and Living Matter Laboratory, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy
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5
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Biospeckle Analysis and Biofilm Electrostatic Tests, Two Useful Methods in Microbiology. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1030036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The development of more sensitive methodologies, capable of quickly detecting and monitoring a microbial population present in a specific biological matrix, as well as performing to allow for the study of all its metabolic changes (e.g., during the formation of biofilm) to occur, is an essential requirement for both well-being and the food industry. Two techniques, in particular, have gained the attention of scientists: The first is “biospeckle”, an optical technique representing an innovative tool for applications in food quality, food safety, and nutraceuticals. With this technique, we can quickly evaluate and monitor the presence of bacteria (or their proliferation) in a solid or liquid biological matrix. In addition, the technique is helpful in quantifying and optimizing the correct storage time of the pro-biotics, if they are entrapped in matrices such as alginate and follow their survival rate in simulated gastro-intestinal conditions. A second technique with great chances is the “biofilm electrostatic test” (BET). BET undoubtedly represents a fast, simple, and highly reproducible tool suitable for admitting the evaluation of the in vitro bacterial capacity in order to adhere through an electrostatic interaction with a pyro-electrified carrier after only 2 h of incubation. BET could represent the way for a quick and standardized evaluation of bacterial resistance among biofilm-producing microorganisms through a fast evaluation of the potential presence of the biofilm.
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6
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Qiu L, Zhang L, Horowitz GL, Turzhitsky V, Coughlan MF, Glyavina M, Khan U, Zakharov YN, Vitkin E, Itzkan I, Perelman LT. Rapid detection and identification of bacteria directly from whole blood with light scattering spectroscopy based biosensor. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 346:130489. [PMID: 34483482 PMCID: PMC8415441 DOI: 10.1016/j.snb.2021.130489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial infections are one of the major causes of death worldwide. The identification of a bacterial species that is the source of an infection generally takes a long time, and often exceeds the treatment window for seriously ill patients. Many of these deaths are preventable if the bacterial species can be identified quickly. Here we present an optical spectroscopic method for rapid detection and identification of bacteria directly from whole blood using a light scattering spectroscopy technique. This technique was originally developed to detect pre-cancerous changes in epithelial tissues, characterize changes in tissue on the cellular scale, and characterize biological structures comparable to or smaller than a single wavelength. We demonstrate here that not only can an inexpensive light scattering spectroscopy-based biosensor rapidly detect and identify four bacteria species in the blood, responsible for the majority of death causing infections, but that species-level identification can potentially be made based on approximately one thousand bacterial cells per milliliter of blood. Observing entire colonies or performing susceptibility testing is therefore not required.
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Affiliation(s)
- Le Qiu
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Lei Zhang
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Gary L. Horowitz
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University, Boston, Massachusetts 02111 USA
| | - Vladimir Turzhitsky
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Mark F. Coughlan
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Maria Glyavina
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Umar Khan
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Yuri N. Zakharov
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Edward Vitkin
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Irving Itzkan
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Lev T. Perelman
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, Massachusetts 02115 USA
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7
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Güler S, Oruç Ç. Comparison of the behavior of negative electrically charged E. coli and E. faecalis bacteria under electric field effect. Colloids Surf B Biointerfaces 2021; 208:112097. [PMID: 34560441 DOI: 10.1016/j.colsurfb.2021.112097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/11/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
The negative electrical charge of Escherichia coli and Enterococcus faecalis bacteria is an indication that they can be affected by an electric field. To show that the movements of electrically charged bacteria can be controlled, impedance spectroscopy method was used on a porous silicon (PS) structure with 60 % porosity and 7-12 μm pore size. The main purpose of this study is to use the electric charge of these two bacterial species to bring bacteria closer to the sensors with the help of an electric field, and to compare the behavior of these bacterial species in the process. The effect of bacterial contact on porous silicon surface impedance spectra was studied under electrical fields between 0 and 5 kV/cm at a constant bacterial concentration. It was observed that both bacteria can be approximated to the PS surface by the electric field effect. However, the shape and dimensional differences of these two bacterial species caused differences both in their movements in the electric field and in their settlement on the PS surface, and these differences were interpreted. In addition, similar experiments were repeated for dead bacteria and it was determined that the electric field control was not the same as for living bacteria.
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Affiliation(s)
- Sevinç Güler
- Izmir Tinaztepe University, Vocational School of Health Services, Izmir, Turkey.
| | - Çiğdem Oruç
- Yildiz Technical University, Faculty of Science & Art, Department of Physics, 34722 Esenler, Istanbul, Turkey
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8
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Litvinenko AL, Nekrasov VM, Strokotov DI, Moskalensky AE, Chernyshev AV, Shilova AN, Karpenko AA, Maltsev VP. Blood platelet quantification by light scattering: from morphology to activation. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3233-3241. [PMID: 34184022 DOI: 10.1039/d1ay00431j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Analysis of blood platelets encounters a number of different preanalytical issues, which greatly decrease the reliability and accuracy of routine clinical analysis. Modern hematology analyzers determine only four parameters relating to platelets. Platelet shape and dose-dependent activation parameters are outside the scope of commercial instruments. We used the original scanning flow cytometer for measurement of angle-resolved light scattering and the discrete dipole approximation for simulation of light scattering from a platelet optical model, as an oblate spheroid, and global optimization with two algorithms: the DATABASE algorithm to retrieve platelet characteristics from light scattering and the DIRECT algorithm to retrieve dose-dependent activation parameters. We developed the original sampling protocol to decrease spontaneous platelet activation. The new protocol allows us to keep most of the platelets in resting and partially activated states before analysis. The analysis delivers 13 content and morphological parameters of the platelets. To analyze platelet shape change during ADP activation we developed a phenomenological model. This model was applied to the analysis of ADP activation of platelets to give 8 dose-dependent activation parameters. To demonstrate the applicability of the developed protocol and analytical method, we analyzed platelets from five donors. This novel approach to the analysis of platelets allows the determination of 21 parameters relating to their content, morphology and dose-dependent activation.
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Affiliation(s)
- Alena L Litvinenko
- Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation.
| | - Vyacheslav M Nekrasov
- Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation. and Novosibirsk State University, Novosibirsk, Russian Federation
| | - Dmitry I Strokotov
- Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation.
| | - Alexander E Moskalensky
- Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation. and Novosibirsk State University, Novosibirsk, Russian Federation
| | - Andrey V Chernyshev
- Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation. and Novosibirsk State University, Novosibirsk, Russian Federation
| | - Anna N Shilova
- State Research Institute of Circulation Pathology, Novosibirsk, Russian Federation
| | - Andrey A Karpenko
- State Research Institute of Circulation Pathology, Novosibirsk, Russian Federation
| | - Valeri P Maltsev
- Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk, Russian Federation. and Novosibirsk State University, Novosibirsk, Russian Federation
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9
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Seeger M, Stiel AC, Ntziachristos V. In vitro optoacoustic flow cytometry with light scattering referencing. Sci Rep 2021; 11:2181. [PMID: 33500461 PMCID: PMC7838204 DOI: 10.1038/s41598-021-81584-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/08/2021] [Indexed: 11/09/2022] Open
Abstract
Morphological and functional optoacoustic imaging is enhanced by dedicated transgene reporters, in analogy to fluorescence methods. The development of optoacoustic reporters using protein engineering and directed evolution would be accelerated by high-throughput in-flow screening for intracellular, genetically encoded, optoacoustic contrast. However, accurate characterization of such contrast is impeded because the optoacoustic signals depend on the cell's size and position in the flow chamber. We report herein an optoacoustic flow cytometer (OA-FCM) capable of precise measurement of intracellular optoacoustic signals of genetically-encoded chromoproteins in flow. The novel system records light-scattering as a reference for the detected optoacoustic signals in order to account for cell size and position, as well as excitation light flux in the focal volume, which we use to reference the detected optoacoustic signals to enhance the system's precision. The OA-FCM was calibrated using micrometer-sized particles to showcase the ability to assess in-flow objects in the size range of single-cells. We demonstrate the capabilities of our OA-FCM to identify sub-populations in a mixture of two E. coli stocks expressing different reporter-proteins with a precision of over 90%. High-throughput screening of optoacoustic labels could pave the way for identifying genetically encoded optoacoustic reporters by transferring working concepts of the fluorescence field such as directed evolution and activated cell sorting.
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Affiliation(s)
- Markus Seeger
- Chair of Biological Imaging (CBI) and Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Biological and Medical Imaging (IBMI), Helmholtz Zentrum München, Neuherberg, Germany
| | - Andre C Stiel
- Institute of Biological and Medical Imaging (IBMI), Helmholtz Zentrum München, Neuherberg, Germany.
| | - Vasilis Ntziachristos
- Chair of Biological Imaging (CBI) and Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.
- Institute of Biological and Medical Imaging (IBMI), Helmholtz Zentrum München, Neuherberg, Germany.
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10
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Sankova N, Shalaev P, Semeykina V, Dolgushin S, Odintsova E, Parkhomchuk E. Spectrally encoded microspheres for immunofluorescence analysis. J Appl Polym Sci 2020. [DOI: 10.1002/app.49890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Natalya Sankova
- Department of Natural Sciences Novosibirsk State University Novosibirsk Russian Federation
- Boreskov Institute of Catalysis SB RAS, Group of template synthesis Novosibirsk Russian Federation
| | - Pavel Shalaev
- Gamaleya Research Center of Epidemiology and Microbiology, Translational Biomedicine Laboratory Moscow Russian Federation
- Aivok LLC Moscow Russian Federation
- National Research University of Electronic Technology, Institute of Biomedical Systems Moscow Russian Federation
| | - Viktoriya Semeykina
- Department of Natural Sciences Novosibirsk State University Novosibirsk Russian Federation
- Boreskov Institute of Catalysis SB RAS, Group of template synthesis Novosibirsk Russian Federation
| | - Sergey Dolgushin
- Gamaleya Research Center of Epidemiology and Microbiology, Translational Biomedicine Laboratory Moscow Russian Federation
- Aivok LLC Moscow Russian Federation
| | - Elena Odintsova
- Sechenov First Moscow State Medical University Moscow Russian Federation
| | - Ekaterina Parkhomchuk
- Department of Natural Sciences Novosibirsk State University Novosibirsk Russian Federation
- Boreskov Institute of Catalysis SB RAS, Group of template synthesis Novosibirsk Russian Federation
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11
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Yastrebova ES, Konokhova AI, Strokotov DI, Karpenko AA, Maltsev VP, Chernyshev AV. Proposed Dynamics of CDB3 Activation in Human Erythrocytes by Nifedipine Studied with Scanning Flow Cytometry. Cytometry A 2019; 95:1275-1284. [PMID: 31750613 DOI: 10.1002/cyto.a.23918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 12/16/2022]
Abstract
Nifedipine is calcium channels and pumps blocker widely used in medicine. However, mechanisms of nifedipine action in blood are not clear. In particular, the influence of nifedipine on erythrocytes is far from completely understood. In this work, applying scanning flow cytometry, we observed experimentally for the first time the dynamics behind a significant increase of HCO3 - /Cl- transmembrane exchange rate of CDB3 (main anion exchanger, AE1, Band 3, SLC4A1) of human erythrocytes in the presence of nifedipine in blood. It was found that the rate of CDB3 activation is not limited by the rate of nifedipine binding and/or Ca2+ transport. In order to explain the experimental data, we suggested a kinetic model assuming that the rate of CDB3 activation is limited by the dynamics of the balance between two intracellular processes (1) the activation of CDB3 limited by its interaction with intracellular Ca2+ , and (2) the spontaneous deactivation of CDB3. Thus the use of scanning flow cytometry allowed to clarify quantitatively the molecular kinetic mechanism of nifedipine action on human erythrocytes. In particular, the efficiency (~30) and rates of activation (~0.3 min-1 ) and deactivation (~10-3 min-1 ) of CDB3 in human erythrocytes was evaluated for two donors. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- Ekaterina S Yastrebova
- Voevodsky Institute of Chemical Kinetics and Combustion, Institutskaya 3, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova 2, Novosibirsk, 630090, Russia.,Meshalkin National Medical Research Center, Ministry of Health of Russian Federation, Rechkunovskaya 15, 630055, Novosibirsk, Russia
| | - Anastasiya I Konokhova
- Voevodsky Institute of Chemical Kinetics and Combustion, Institutskaya 3, Novosibirsk, 630090, Russia.,Meshalkin National Medical Research Center, Ministry of Health of Russian Federation, Rechkunovskaya 15, 630055, Novosibirsk, Russia
| | - Dmitry I Strokotov
- Voevodsky Institute of Chemical Kinetics and Combustion, Institutskaya 3, Novosibirsk, 630090, Russia.,Novosibirsk State Medical University, Krasny Prospect 52, Novosibirsk, 630091, Russia
| | - Andrei A Karpenko
- Meshalkin National Medical Research Center, Ministry of Health of Russian Federation, Rechkunovskaya 15, 630055, Novosibirsk, Russia
| | - Valeri P Maltsev
- Voevodsky Institute of Chemical Kinetics and Combustion, Institutskaya 3, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova 2, Novosibirsk, 630090, Russia.,Novosibirsk State Medical University, Krasny Prospect 52, Novosibirsk, 630091, Russia
| | - Andrei V Chernyshev
- Voevodsky Institute of Chemical Kinetics and Combustion, Institutskaya 3, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova 2, Novosibirsk, 630090, Russia
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12
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Müller D, Geiger D, Stark J, Kienle A. Angle-resolved light scattering of single human chromosomes: experiments and simulations. Phys Med Biol 2019; 64:045016. [PMID: 30630136 DOI: 10.1088/1361-6560/aafd6f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Angle-resolved light scattering measurements of human metaphase chromosomes were compared to the results of numerical light scattering simulations with geometrical models based on atomic force microscopy (AFM) measurements of the same chromosomes. The simulations were conducted using the discrete dipole approximation method (DDA), which solves Maxwell's equations for induced dipoles, positioned in a discrete lattice. A remarkable agreement between the light scattering simulations and measurements of all 6 studied chromosomes was found. Additionally, the influence of small changes in the orientation of a complex scatterer geometry on its angle-resolved scattering pattern is shown. A method is presented to approximate such variations in the scatterer's orientation by a linear shift of the angular scattering pattern. This method provides an initial guess on the scatterers orientation, reducing the amount of simulations needed considerably. It was validated on simulations of a cuboid and successfully applied in the evaluation of the chromosome measurements.
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Affiliation(s)
- Dennis Müller
- Institute for Lasertechnologies in Medicine and Metrology (ILM), Helmholtzstr. 12, 89081 Ulm, Germany. Author to whom any correspondence should be addressed
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13
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Gilev K, Yastrebova E, Strokotov D, Yurkin M, Karmadonova N, Chernyshev A, Lomivorotov V, Maltsev V. Advanced consumable-free morphological analysis of intact red blood cells by a compact scanning flow cytometer. Cytometry A 2017; 91:867-873. [DOI: 10.1002/cyto.a.23141] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/27/2017] [Accepted: 05/02/2017] [Indexed: 01/14/2023]
Affiliation(s)
- K.V. Gilev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3; Novosibirsk 630090 Russia
- Novosibirsk State University, Pirogova 2; Novosibirsk 630090 Russia
| | - E.S. Yastrebova
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3; Novosibirsk 630090 Russia
- Novosibirsk State University, Pirogova 2; Novosibirsk 630090 Russia
| | - D.I. Strokotov
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3; Novosibirsk 630090 Russia
- Novosibirsk State Medical University, Krasny Prospect 52; Novosibirsk 630091 Russia
| | - M.A. Yurkin
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3; Novosibirsk 630090 Russia
- Novosibirsk State University, Pirogova 2; Novosibirsk 630090 Russia
| | - N.A. Karmadonova
- Siberian Biomedical Research Center, Rechkunovskaya 15; Novosibirsk 630055 Russia
| | - A.V. Chernyshev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3; Novosibirsk 630090 Russia
- Novosibirsk State University, Pirogova 2; Novosibirsk 630090 Russia
| | - V.V. Lomivorotov
- Siberian Biomedical Research Center, Rechkunovskaya 15; Novosibirsk 630055 Russia
| | - V.P. Maltsev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Institutskaya 3; Novosibirsk 630090 Russia
- Novosibirsk State University, Pirogova 2; Novosibirsk 630090 Russia
- Novosibirsk State Medical University, Krasny Prospect 52; Novosibirsk 630091 Russia
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Litvinenko A, Moskalensky A, Karmadonova N, Nekrasov V, Strokotov D, Konokhova A, Yurkin M, Pokushalov E, Chernyshev A, Maltsev V. Fluorescence-free flow cytometry for measurement of shape index distribution of resting, partially activated, and fully activated platelets. Cytometry A 2016; 89:1010-1016. [DOI: 10.1002/cyto.a.23003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 09/01/2016] [Accepted: 10/05/2016] [Indexed: 11/11/2022]
Affiliation(s)
- A.L. Litvinenko
- Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk Russian Federation
- Novosibirsk State University; Novosibirsk Russian Federation
| | - A.E. Moskalensky
- Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk Russian Federation
- Novosibirsk State University; Novosibirsk Russian Federation
| | - N.A. Karmadonova
- State Research Institute of Circulation Pathology; Novosibirsk Russian Federation
| | - V.M. Nekrasov
- Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk Russian Federation
- Novosibirsk State University; Novosibirsk Russian Federation
| | - D.I. Strokotov
- Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk Russian Federation
- Novosibirsk State Medical University; Novosibirsk Russian Federation
| | - A.I. Konokhova
- Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk Russian Federation
| | - M.A. Yurkin
- Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk Russian Federation
- Novosibirsk State University; Novosibirsk Russian Federation
| | - E.A. Pokushalov
- State Research Institute of Circulation Pathology; Novosibirsk Russian Federation
| | - A.V. Chernyshev
- Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk Russian Federation
- Novosibirsk State University; Novosibirsk Russian Federation
| | - V.P. Maltsev
- Voevodsky Institute of Chemical Kinetics and Combustion; Novosibirsk Russian Federation
- Novosibirsk State University; Novosibirsk Russian Federation
- Novosibirsk State Medical University; Novosibirsk Russian Federation
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15
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Schwarz-Linek J, Arlt J, Jepson A, Dawson A, Vissers T, Miroli D, Pilizota T, Martinez VA, Poon WC. Escherichia coli as a model active colloid: A practical introduction. Colloids Surf B Biointerfaces 2016; 137:2-16. [DOI: 10.1016/j.colsurfb.2015.07.048] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/17/2015] [Accepted: 07/19/2015] [Indexed: 10/23/2022]
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16
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Davison M, Hall E, Zare R, Bhaya D. Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity. PHOTOSYNTHESIS RESEARCH 2015; 126:135-146. [PMID: 25515769 DOI: 10.1007/s11120-014-0066-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 12/10/2014] [Indexed: 06/04/2023]
Abstract
Cyanobacteria have played a crucial role in the history of early earth and continue to be instrumental in shaping our planet, yet applications of cutting edge technology have not yet been widely used to explore cyanobacterial diversity. To provide adequate background, we briefly review current sequencing technologies and their innovative uses in genomics and metagenomics. Next, we focus on current cell capture technologies and the challenges of using them with cyanobacteria. We illustrate the utility in coupling breakthroughs in DNA amplification with cell capture platforms, with an example of microfluidic isolation and subsequent targeted amplicon sequencing from individual terrestrial thermophilic cyanobacteria. Single cells of thermophilic, unicellular Synechococcus sp. JA-2-3-B'a(2-13) (Syn OS-B') were sorted in a microfluidic device, lysed, and subjected to whole genome amplification by multiple displacement amplification. We amplified regions from specific CRISPR spacer arrays, which are known to be highly diverse, contain semi-palindromic repeats which form secondary structure, and can be difficult to amplify. Cell capture, lysis, and genome amplification on a microfluidic device have been optimized, setting a stage for further investigations of individual cyanobacterial cells isolated directly from natural populations.
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Affiliation(s)
- Michelle Davison
- Department of Plant Biology, Carnegie Institution of Science, 260 Panama Street, Stanford, CA, 94305, USA.
| | - Eric Hall
- SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA
| | - Richard Zare
- Department of Chemistry, Stanford University, 333 Campus Drive Mudd Building, Room 121, Stanford, CA, 94305-4401, USA
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution of Science, 260 Panama Street, Stanford, CA, 94305, USA
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17
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Essential validation methods for E. coli strains created by chromosome engineering. J Biol Eng 2015; 9:11. [PMID: 26140052 PMCID: PMC4488041 DOI: 10.1186/s13036-015-0008-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/02/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromosome engineering encompasses a collection of homologous recombination-based techniques that are employed to modify the genome of a model organism in a controlled fashion. Such techniques are widely used in both fundamental and industrial research to introduce multiple insertions in the same Escherichia coli strain. To date, λ-Red recombination (also known as recombineering) and P1 phage transduction are the most successfully implemented chromosome engineering techniques in E. coli. However, due to errors that can occur during the strain creation process, reliable validation methods are essential upon alteration of a strain's chromosome. RESULTS AND DISCUSSION Polymerase chain reaction (PCR)-based methods and DNA sequence analysis are rapid and powerful methods to verify successful integration of DNA sequences into a chromosome. Even though these verification methods are necessary, they may not be sufficient in detecting all errors, imposing the requirement of additional validation methods. For example, as extraneous insertions may occur during recombineering, we highlight the use of Southern blotting to detect their presence. These unwanted mutations can be removed via transducing the region of interest into the wild type chromosome using P1 phages. However, in doing so one must verify that both the P1 lysate and the strains utilized are free from contamination with temperate phages, as these can lysogenize inside a cell as a large plasmid. Thus, we illustrate various methods to probe for temperate phage contamination, including cross-streak agar and Evans Blue-Uranine (EBU) plate assays, whereby the latter is a newly reported technique for this purpose in E. coli. Lastly, we discuss methodologies for detecting defects in cell growth and shape characteristics, which should be employed as an additional check. CONCLUSION The simple, yet crucial validation techniques discussed here can be used to reliably verify any chromosomally engineered E. coli strains for errors such as non-specific insertions in the chromosome, temperate phage contamination, and defects in growth and cell shape. While techniques such as PCR and DNA sequence verification should standardly be performed, we illustrate the necessity of performing these additional assays. The discussed techniques are highly generic and can be easily applied to any type of chromosome engineering.
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Bianco V, Marchesano V, Finizio A, Paturzo M, Ferraro P. Self-propelling bacteria mimic coherent light decorrelation. OPTICS EXPRESS 2015; 23:9388-9396. [PMID: 25968769 DOI: 10.1364/oe.23.009388] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We show here that live e-coli bacterial culture, thanks to the self-propelling feature, can significantly reduce the coherent noise. In fact, the typical self-propelled drive of such microorganisms provides enough time diversity in speckle patterns. Optical properties of a bacteria suspension have been investigated and analyzed thus showing that it behaves as a quite good optical speckle decorrelation device. Samples with different bacteria densities have been studied. The decorrelation effect has been demonstrated by probing the imaging performance in through transmission in coherent microscope configuration.
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19
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Konokhova AI, Rodionov AA, Gilev KV, Mikhaelis IM, Strokotov DI, Moskalensky AE, Yurkin MA, Chernyshev AV, Maltsev VP. Enhanced characterisation of milk fat globules by their size, shape and refractive index with scanning flow cytometry. Int Dairy J 2014. [DOI: 10.1016/j.idairyj.2014.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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