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Contract number
Time span of the project

As of 22.05.2020

Number of staff members
scientific publications
Objects of intellectual property
General information

Name of the project: Imaging and engineering of eukaryotic genomes

Goals and objectives

Project objective: Achieving breakthrough results in mapping images of eukaryotic genomes using multimode tomography and multidisciplinary approaches allowing to assess efficiency of work of the CRISPR/Cas9 systems on different biological models: 2D models of mammal cells, spheroids and 3D models, in small laboratory animals

The practical value of the study
We were the first to create lentiviral carrier vectors for doxycycline-regulated expression of chimera proteins based on the catalytically inactive endonuclease Cas9 (dCas9);
The Laboratory has conducted experiments in coexpression and localisation in nuclei of chimera protein cells based on dCas9 orthologues;
Using a non-cryogenic research device for pre-clinical MRI scanning we have conducted a study of the distribution of mixtures illuminating the surface of skin in subdermal tissue.

Education and career development:

  • We have developed and read a lecture course entitled «Basics of molecular visualization in living systems» for the Faculty of Bioengineering and Bioinformatics of the Moscow State University (Russia).
  • We developed and read a course entitled «Tissue optics and optical clearing of tissues and cells» consisting of three lectures (São Paulo School of Advanced Science on Modern Topics in Biophotonics, Brazil, 2019).
  • We organized the third ADFLIM youth school (advanced methods of fluorescent imaging) for academic training of young researchers and professionals (Saratov, Russia, 2018).
  • We organized the «Saratov Fall Meeting 2018» youth school for optics, laser physics and biophotonics (Saratov, Russia, 2018).
  • Participation in the expert committee for the evaluation of works (project teams) of young researchers in the «Medicine and Pharmacology» section at the 3rd International Scientific Conference «Science of the Future» and the 4th All-Russian Forum «Science of the Future – Science of the Youth».

  • We have conducted the 4th International School on Advanced Fluorescent Imaging Methods on the grounds of the Saratov State University from 23 to 27 September 2019 together with the 23rd International School for Students and Young Scientists on Optics, Laser Physics and Biophotonics. Attendees of the schools also participated in the work of the International Symposium «Optics and Biophotonics - VII» that was held by the Saratov State University and the Federal Research Centre for Biotechnologies of the Russian Academy of Sciences from 24 to 27 September 2019.

  • 6 postgraduates and 2 students have participated in work of the Laboratory.

Other results:

In late May 2019 a state-of-the-art М3™ device for pre-clinical MRI imaging was installed in the laboratory room. The device is used for imaging of the anatomy and physiology of experimental animals (critters weighing up to 30 grams).

The М3™ MRI scanner is built on the basis of a compact highly efficient constant magnet with the magnetic field strength of 1 tesla that does not require cryogenic support. This MRI device is, for now, the only system in Russia and one of about 100 pre-clinical MRI systems installed in leading research centres of the world.


Laboratory of Laser Diagnostics of Engineering and Living Systems of the Institute of Precision Mechanics and Control of the Russian Academy of Sciences (Russia), Laboratory of Biophotonics of the Research and Education Institute for Optics and Biophootonics of the Saratov State University: joint research and publications.

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A.A. Bogdanov Jr., N.I. Kazachkina, V.V. Zherdeva, I.G. Meerovich, D.K. Tuchina, I.D. Solovyev, A.P. Savitsky, and V.V. Tuchin
Magnetic resonance imaging study of diamagnetic and paramagnetic agents for optical clearing of tumor-specific fluorescent signal in vivo, in Handbook of Tissue Optical Clearing: New Prospects in Optical Imaging, V.V. Tuchin, D. Zhu, E.A. Genina (Eds.), Taylor & Francis Group LLC, CRC Press, Boca Raton, FL (2022), pp. 459-470. https://www.routledge.com/Handbook-of-Tissue-Optical-Clearing-New-Prospects-in-Optical-Imaging/Tuchin-Zhu-Genina/p/book/9780367895099
N.I. Kazachkina, V.V. Zherdeva, I.G. Meerovich, A.N. Saydasheva, I.D. Solovyev, D.K. Tuchina, A.P. Savitsky, V.V. Tuchin, A.A. Bogdanov Jr.
“MR and fluorescence imaging of gadobutrol-induced optical clearing of red fluorescent protein signal in an in vivo cancer model,” NMR in Biomedicine, e4708-1-13 (2022). doi:10.1002/nbm.4708.
H. F. Silva, I. S. Martins, A. A. Bogdanov Jr, V. V. Tuchin, L. M. Oliveira,
Characterization of optical clearing mechanisms in muscle during treatment with glycerol and gadobutrol solutions, J. Biophotonics 2022, e202200205. https://doi.org/10. 1002/jbio.202200205.
Tuchina, D.K., Meerovich, I.G., Sindeeva, O.A., Zherdeva V.V., Kazachkina N.I., Solov'ev I.D., Savitsky A.P., Bogdanov, A.A., Tuchin, V.V.,
Prospects for multimodal visualisation of biological tissues using fluorescence imaging, Quantum Electronics 51(2), 104–117 (2021).
N.I. Kazachkina, V.V. Zherdeva, A.N. Saydasheva, I.G. Meerovich, V.V. Tuchin, Savitsky A.P., Bogdanov, A.A.
Topical Gadobutrol Application Causes Fluorescence Intensity Change in RFP-expressing Tumor-Bearing Mice, Journal of Biomedical Photonics & Engineering 7 020301(2021).
Bogdanov AA, Solovyev ID, Savitsky AP.
Sensors for Proteolytic Activity Visualization and Their Application in Animal Models of Human Diseases. Biochemistry-Moscow 2019, Vol.84, Supplement1, S1-S18.
Xie Q., Zeng N., Huang Y., Tuchin V. V., Ma H.
Study on the tissue clearing process using different agents by Mueller matrix microscope. Biomed. Opt. Express.2019. 10(7), 3269–3280.
Munkhbat O., Canakci M., Zheng S., Hu W., Osborne B., Bogdanov A.A., Thayumanavan S.
19F MRI of Polymer Nanogels Aided by Improved Segmental Mobility of Embedded Fluorine Moieties. Biomacromolecules 2019, 20(2): 790-800. https://doi.org/10.1021/acs.biomac.8b01383
Rodríguez-Rodríguez A., Shuvaev S., Rotile N., Jones C.M., Probst C.K., Ferreira D.D.S., Graham-O′Regan K., Boros E., Knipe R.S., Griffith J.W., Tager A.M., Bogdanov Jr. A.A., Caravan P.
Peroxidase Sensitive Amplifiable Probe for Molecular Magnetic Resonance Imaging of Pulmonary Inflammation. ACS Sens. 2019, 4(9): 2412-2419, https://doi.org/10.1021/acssensors.9b01010
Metelev VG, Bogdanov AA Jr
Synthesis and applications of theranostic oligonucleotides carrying multiple fluorine atoms. Theranostics 2020, 10 (3), 1391.
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