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Maloshenok LG, Abushinova GA, Ryazanova AY, Bruskin SA, Zherdeva VV. Visualizing the Nucleome Using the CRISPR–Cas9 System: From in vitro to in vivo. BIOCHEMISTRY (MOSCOW) 2023; 88:S123-S149. [PMID: 37069118 PMCID: PMC9940691 DOI: 10.1134/s0006297923140080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
One of the latest methods in modern molecular biology is labeling genomic loci in living cells using fluorescently labeled Cas protein. The NIH Foundation has made the mapping of the 4D nucleome (the three-dimensional nucleome on a timescale) a priority in the studies aimed to improve our understanding of chromatin organization. Fluorescent methods based on CRISPR-Cas are a significant step forward in visualization of genomic loci in living cells. This approach can be used for studying epigenetics, cell cycle, cellular response to external stimuli, rearrangements during malignant cell transformation, such as chromosomal translocations or damage, as well as for genome editing. In this review, we focused on the application of CRISPR-Cas fluorescence technologies as components of multimodal imaging methods for in vivo mapping of chromosomal loci, in particular, attribution of fluorescence signal to morphological and anatomical structures in a living organism. The review discusses the approaches to the highly sensitive, high-precision labeling of CRISPR-Cas components, delivery of genetically engineered constructs into cells and tissues, and promising methods for molecular imaging.
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Affiliation(s)
- Liliya G Maloshenok
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Gerel A Abushinova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexandra Yu Ryazanova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Sergey A Bruskin
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Victoria V Zherdeva
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
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Oliveira LR, Ferreira RM, Pinheiro MR, Silva HF, Tuchin VV, Oliveira LM. Broadband spectral verification of optical clearing reversibility in lung tissue. JOURNAL OF BIOPHOTONICS 2023; 16:e202200185. [PMID: 36054631 DOI: 10.1002/jbio.202200185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/23/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
The increase of tissue transparency through sequential optical immersion clearing treatments and treatment reversibility have high interest for clinical applications. To evaluate the clearing reversibility in a broad spectral range and the magnitude of the transparency created by a second treatment, the present study consisted on measuring the spectral collimated transmittance of lung tissues during a sequence of two treatments with electronic cigarette (e-cig) fluid, which was intercalated with an immersion in saline. The saline immersion clearly reverted the clearing effect in the lung tissue in the spectral range between 220 and 1000 nm. By a later application of a second treatment with the e-cig fluid, the magnitude of the optical clearing effect was observed to be about the double as the one observed in the first treatment, showing that the molecules of the optical clearing agent might have converted some bound water into mobile water during the first treatment.
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Affiliation(s)
- Luís R Oliveira
- Centre of Innovation in Engineering and Industrial Technology (CIETI), School of Engineering, Polytechnic of Porto, Porto, Portugal
| | - Ricardo M Ferreira
- Physics Department-Polytechnic of Porto, School of Engineering, Porto, Portugal
| | - Maria R Pinheiro
- Physics Department-Polytechnic of Porto, School of Engineering, Porto, Portugal
| | - Hugo F Silva
- Centre of Innovation in Engineering and Industrial Technology (CIETI), School of Engineering, Polytechnic of Porto, Porto, Portugal
| | - Valery V Tuchin
- Science Medical Center, Saratov State University, Saratov, Russian Federation
- Laboratory of Laser Molecular Imaging and Machine Learning, Tomsk State University, Tomsk, Russian Federation
- Laboratory of Laser Diagnostics of Technical and Living Systems, Institute of Precision Mechanics and Control, FRC "Saratov Research Centre of Russian Academy of Sciences", Saratov, Russian Federation
| | - Luís M Oliveira
- Centre of Innovation in Engineering and Industrial Technology (CIETI), School of Engineering, Polytechnic of Porto, Porto, Portugal
- Physics Department-Polytechnic of Porto, School of Engineering, Porto, Portugal
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Martins IS, Silva HF, Lazareva EN, Chernomyrdin NV, Zaytsev KI, Oliveira LM, Tuchin VV. Measurement of tissue optical properties in a wide spectral range: a review [Invited]. BIOMEDICAL OPTICS EXPRESS 2023; 14:249-298. [PMID: 36698664 PMCID: PMC9841994 DOI: 10.1364/boe.479320] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
A distinctive feature of this review is a critical analysis of methods and results of measurements of the optical properties of tissues in a wide spectral range from deep UV to terahertz waves. Much attention is paid to measurements of the refractive index of biological tissues and liquids, the knowledge of which is necessary for the effective application of many methods of optical imaging and diagnostics. The optical parameters of healthy and pathological tissues are presented, and the reasons for their differences are discussed, which is important for the discrimination of pathologies and the demarcation of their boundaries. When considering the interaction of terahertz radiation with tissues, the concept of an effective medium is discussed, and relaxation models of the effective optical properties of tissues are presented. Attention is drawn to the manifestation of the scattering properties of tissues in the THz range and the problems of measuring the optical properties of tissues in this range are discussed. In conclusion, a method for the dynamic analysis of the optical properties of tissues under optical clearing using an application of immersion agents is presented. The main mechanisms and technologies of optical clearing, as well as examples of the successful application for differentiation of healthy and pathological tissues, are analyzed.
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Affiliation(s)
- Inês S. Martins
- Center for Innovation in Engineering and Industrial Technology, ISEP, Porto, Portugal
| | - Hugo F. Silva
- Porto University, School of Engineering, Porto, Portugal
| | - Ekaterina N. Lazareva
- Science Medical Center, Saratov State University, Saratov, Russia
- Laboratory of Laser Molecular Imaging and Machine Learning, Tomsk State University, Tomsk, Russia
| | | | - Kirill I. Zaytsev
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow, Russia
| | - Luís M. Oliveira
- Physics Department, Polytechnic of Porto – School of Engineering (ISEP), Porto, Portugal
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal
| | - Valery V. Tuchin
- Science Medical Center, Saratov State University, Saratov, Russia
- Laboratory of Laser Molecular Imaging and Machine Learning, Tomsk State University, Tomsk, Russia
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Naumova EV, Vladimirov YA, Tuchin VV, Namiot VA, Volodyaev IV. Methods of Studying Ultraweak Photon Emission from Biological Objects: III. Physical Methods. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Tuchin VV, Genina EA, Tuchina ES, Svetlakova AV, Svenskaya YI. Optical clearing of tissues: Issues of antimicrobial phototherapy and drug delivery. Adv Drug Deliv Rev 2022; 180:114037. [PMID: 34752842 DOI: 10.1016/j.addr.2021.114037] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/23/2021] [Accepted: 10/28/2021] [Indexed: 02/08/2023]
Abstract
This review presents principles and novelties in the field of tissue optical clearing (TOC) technology, as well as application for optical monitoring of drug delivery and effective antimicrobial phototherapy. TOC is based on altering the optical properties of tissue through the introduction of immersion optical cleaning agents (OCA), which impregnate the tissue of interest. We also analyze various methods and kinetics of delivery of photodynamic agents, nanoantibiotics and their mixtures with OCAs into the tissue depth in the context of antimicrobial and antifungal phototherapy. In vitro and in vivo studies of antimicrobial phototherapies, such as photodynamic, photothermal plasmonic and photocatalytic, are summarized, and the prospects of a new TOC technology for effective killing of pathogens are discussed.
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Fernandes L, Carvalho S, Carneiro I, Henrique R, Tuchin VV, Oliveira HP, Oliveira LM. Diffuse reflectance and machine learning techniques to differentiate colorectal cancer ex vivo. CHAOS (WOODBURY, N.Y.) 2021; 31:053118. [PMID: 34240956 DOI: 10.1063/5.0052088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/20/2021] [Indexed: 06/13/2023]
Abstract
In this study, we used machine learning techniques to reconstruct the wavelength dependence of the absorption coefficient of human normal and pathological colorectal mucosa tissues. Using only diffuse reflectance spectra from the ex vivo mucosa tissues as input to algorithms, several approaches were tried before obtaining good matching between the generated absorption coefficients and the ones previously calculated for the mucosa tissues from invasive experimental spectral measurements. Considering the optimized match for the results generated with the multilayer perceptron regression method, we were able to identify differentiated accumulation of lipofuscin in the absorption coefficient spectra of both mucosa tissues as we have done before with the corresponding results calculated directly from invasive measurements. Considering the random forest regressor algorithm, the estimated absorption coefficient spectra almost matched the ones previously calculated. By subtracting the absorption of lipofuscin from these spectra, we obtained similar hemoglobin ratios at 410/550 nm: 18.9-fold/9.3-fold for the healthy mucosa and 46.6-fold/24.2-fold for the pathological mucosa, while from direct calculations, those ratios were 19.7-fold/10.1-fold for the healthy mucosa and 33.1-fold/17.3-fold for the pathological mucosa. The higher values obtained in this study indicate a higher blood content in the pathological samples used to measure the diffuse reflectance spectra. In light of such accuracy and sensibility to the presence of hidden absorbers, with a different accumulation between healthy and pathological tissues, good perspectives become available to develop minimally invasive spectroscopy methods for in vivo early detection and monitoring of colorectal cancer.
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Affiliation(s)
- Luís Fernandes
- Center for Innovation in Engineering and Industrial Technology, Polytechnic of Porto-School of Engineering, 4249-015 Porto, Portugal
| | - Sónia Carvalho
- Department of Pathology and Cancer Biology and Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
| | - Isa Carneiro
- Department of Pathology and Cancer Biology and Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
| | - Rui Henrique
- Department of Pathology and Cancer Biology and Epigenetics Group-Research Center, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
| | - Valery V Tuchin
- Science Medical Center, Saratov State University, Saratov 410012, Russia
| | - Hélder P Oliveira
- Institute for Systems and Computer Engineering, Technology and Science, INESC TEC, 4200-465 Porto, Portugal
| | - Luís M Oliveira
- Center for Innovation in Engineering and Industrial Technology, Polytechnic of Porto-School of Engineering, 4249-015 Porto, Portugal
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Abstract
The study of the optical properties of biological tissues for a wide spectral range is necessary for the development and planning of noninvasive optical methods to be used in clinical practice. In this study, we propose a new method to calculate almost all optical properties of tissues as a function of wavelength directly from spectral measurements. Using this method, and with the exception of the reduced scattering coefficient, which was obtained by traditional simulation methods, all the other optical properties were calculated in a simple and fast manner for human and pathological colorectal tissues. The obtained results are in good agreement with previous published data, both in magnitude and in wavelength dependence. Since this method is based on spectral measurements and not on discrete-wavelength experimental data, the calculated optical properties contain spectral signatures that correspond to major tissue chromophores such as DNA and hemoglobin. Analysis of the absorption bands of hemoglobin in the wavelength dependence of the absorption spectra of normal and pathological colorectal mucosa allowed to identify differentiated accumulation of a pigment in these tissues. The increased content of this pigment in the pathological mucosa may be used for the future development of noninvasive diagnostic methods for colorectal cancer detection.
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