Department of Biomaterials and Bionanotechnology
Groups in the department:
Core-Shell CdSSe Nanoplatelets are New Efficient Quantum Nanoplateles Fluorophores with Two-Photon Excitation for Cell Visualization
Two-photon fluorescence microscopy revealed order of magnitude larger fluorescence response from nanoplatelets which opens the door to use them as highly efficient 2P fluorescent labels in biomedicine.
It was shown, that in spite of much larger lateral size in comparison with QDs, can be efficiently absorbed by cells. Due to their higher efficiency of 1P and 2P excitation of photoluminescence, new fluorophores allow realize detection and visualization at much lower concentration of nanoplateles inside cells as compared to QDs. This is especially important in case of specific targeting of a small amount of proteins in the cells.
- (2020). Emitters with different dimensionality: 2D cadmium chalcogenide nanoplatelets and 0D quantum dots in non-specific cell labeling and two-photon imaging. Nanotechnology 31 (43), 435102
A versatile platform for bioimaging based on colominic acid-decorated upconversion nanoparticles
Nanocrystals with anti-Stokes fluorescence (UCNPs) are a promising platform for the bioreagents formation for in vivo visualization of pathological tissues under the action of near infrared radiation, which can penetrate deep into biological tissues maintaining a high signal-to-noise ratio. The successful implementation of UCNPs is associated with the surface biofunctionalization, which ensures non-toxicity and biocompatibility, along with a long circulation time of UCNPs in the bloodstream and their accumulation in the target tissue. This work demonstrated an approach to the UCNP biofunctionalization using endogenous colominic acid and the reagent preparations that are characterized by a low level both non-specific protein adsorption and uptake by macrophages. This approach made it possible to increase the circulation time in the bloodstream of small animals up to 3 hours, acquire an intense photoluminescent signal in inflammatory tissue, and visualize micro- and macro-blood vessels. The work was carried out jointly with the Federal Research Center "Crystallography and Photonics", the Russian Oncology Center named after N.N. Blokhin and the First Moscow State Medical University named after I.M. Sechenov.
- (2020). A versatile platform for bioimaging based on colominic acid-decorated upconversion nanoparticles. Biomater Sci 8 (16), 4570–4580
Fabrication and evaluation of nanocontainers for lipophilic anticancer drug delivery in 3D in vitro model.
The novel polysaccharide nanocontainers (NC) by one-step ultrasonication technique were fabricated and their accumulation efficacy and cytotoxicity in 2D (monolayer culture) and 3D (tumor spheroids) in vitro models was studied. The developed NC are promising for lipophilic anticancer drug delivery.
- (2020). Fabrication and evaluation of nanocontainers for lipophilic anticancer drug delivery in 3D in vitro model. J Biomed Mater Res B Appl Biomater 109 (4), 527–537
Toxigenic staphylococcus infection is one of the causes of diseases associated with food poisoning. Highly stable enterotoxin of staphylococcus (SE) is need for improved methods of quality control of foods. We developed a highly sensitive method for the simultaneous detection of three staphylococcal enterotoxins (staphylococcal enterotoxin A (SEA), staphylococcal enterotoxin B (SEB), staphylococcal enterotoxin H (SEH)) by flow cytometry. For detection, we used functional beads coupled with monoclonal capture antibodies, biotinylated monoclonal detection antibodies, and streptavidin conjugated to phycoerythrin. The linear ranges of detection of SEA, SEB, and SEH were 0.02–20 ng/mL, 0.2–30 ng/mL, and 0.2–20 ng/mL, respectively. Each toxin was specifically detected without cross-reactions. The components of the detection medium did not affect the specificity and sensitivity of the determination.
- (2020). Development of a Bead-Based Multiplex Assay for the Simultaneous Quantification of Three Staphylococcal Enterotoxins in Food by Flow Cytometry. FOOD ANAL METHOD 13 (5), 1202–1210
Evaluation of aliphatic/aromatic compounds and fluorophores in dissolved organic matter of contrasting natural waters by SEC-HPLC with multi-wavelength absorbance and fluorescence detections
The analytical high performance size exclusion liquid chromatography (SEC-HPLC) with multi-wavelength absorbance and fluorescence detections and fluorescence 3D-excitation/emission matrix (EEM) were used for the analysis of average molecular size (MS), molecular size distribution of aliphatic/aromatic compounds and fluorophores in dissolved organic matter (DOM) from Suwannee River (SRDOM) and two Karelian lakes (Vodoprovodnoe Lake - L1DOM and Onego Lake - L2DOM). The average MS of DOM samples varied in the order SRDOM > L1DOM > L2DOM. The absorbance ratios A250/A365 and A210/A254 have been used for the DOM samples characterization. The absorbance ratio A250/A365 provided significant information about average MS of the bulk aquatic DOMs but was not exactly correlated with the results of SEC-HPLC data. The absorbance ratio A210/A254 in combination with SEC was well correlated with the content of DOM aliphatic/aromatic compounds and could be used as an important water quality index to estimate the level of protein-like material in the aquatic DOM. Regardless of the origin (river or lakes), different geographical locations and different average MS of DOM, several similar types of humic-like SEC-separated fluorophores were found within the samples. In all DOM samples the decrease of the fluorophores emission maxima paralleled the decrease of their relative MS. The combination of SEC-HPLC with multi-wavelength fluorescence and absorbance detection and EEM analyses appears very useful for DOM characterization and for tracking of microbial activity resulting from anthropogenic and/or eutrophic impact in aquatic environments.
On the way to obtaining environmentally friendly photodestructors of organic pollutants based on humic substances
Chernozem humic acid (HA) fractions with nominal molecular sizes (MS) >100, 30–100, 5–30 and <5 kDa were obtained, using a combination of low-pressure preparative size exclusion chromatography with analytical polyacrylamide gel electrophoresis or multistep ultrafiltration. The initial HA and fractions were tested for the ability to destroy model aromatic compounds 2,4,6-trimethylphenol and furfurol in aqueous solution when illuminated with polychromatic light in the range 300–450 nm under laboratory conditions.
It has been found that chernozem HA fractions with MS less than 5 kDa had the maximum ability to decompose the above-mentioned substances, while fractions with MS above 30 kDa practically did not perform this function. The data obtained allow us to explain partially the mechanisms of the photoinduced transformation of many organic pollutants by soil humic substances.
- (2019). Photochemical Degradation of Organic Pollutants in Solutions of Soil Humic Acids. EURASIAN SOIL SCI+ 52 (9), 1075–1080
Cerasomes for doxorubicin delivery
Mostly all known anticancer formulations are poor water soluble and non-selective towards cancer cells. As a result, all formulations have side effects. Loading anticancer drugs into nanocarriers, in particular liposomes allows to overcome these disadvantages. However, presently all liposomal formulations at the market are not stable enough to provide long time circulation of entrapped drugs in the blood stream. Liposomes of new generation, so called cerasomes have been developed and tested in 3D in vitro model at Laboratory of biomedical materials (IBCh) and Moscow Technological University (campus MITHT). Cerasomes are modified cationic liposomes coated with silico-organic membrane which allows prolonged release of anticancer drugs, in particular doxorubicin. The results have been published in Materials Science & Engineering C (IF 5.08).
- (2019). Lipoamino acid-based cerasomes for doxorubicin delivery: Preparation and in vitro evaluation. Mater Sci Eng C Mater Biol Appl 100, 724–734
Anisotropic hydrogels with a system of oriented channels for the directed growth of animal cells
An insistent task of tissue engineering is the search for materials that can be used as an alternative to allotransplants. A method was developed for producing of hydrogels with a biomimetic structure that simulates the perineurium/epineuria of the peripheral nerve. Anisotropic hydrogels are formed as a result of phase separation of chitosan-PVA compositions in the presence of a precipitant, accompanied by the formation of parallel-oriented channels. The obtained hydrogels are characterized by low cytotoxicity and provide directed growth of animal cells (C6 gliomas).
- (2019). Multichannel hydrogel based on a chitosan–poly(vinyl alcohol) composition for directed growth of animal cells. Colloids Surf B Biointerfaces 184, 110495
Whole Genome Characterization of Staphylococcus aureus Virulence Factors Associated with Bovine Mastitis in Russia
In this work, we investigated S. aureus isolates using whole-genome sequence analysis and tried to establish a relationship of these isolates with the development of bovine mastitis in Russia. A set of virulence genes (enterotoxins, cytotoxins, superantigen like proteins, exfoliative toxins and others) was detected. The most prevalence factor associated with bovine mastitis in Russia we identified as cytolytic toxins, hemolysins (100%) and leukocidins (80%).
38% isolates were classified as toxicogenic by enterotoxins (there are seg, sei) which encoded by egc cluster. Furthermore, we detect the possible connection of bovine mastitis problem in Russia with eta positive S. aureus. All S. aureus isolates were identified as MSSA. In addition, it was found that several of isolates have multidrug resistance, which could be confirmed by the presence of antibiotic resistance genes in these isolates. This work was carried out within the framework of grant 15-16-00020 under an agreement with the Russian Science Foundation.
Method for determining 3-D distributions of magnetic nano-objects in a matrix. Definition of "Anatomy" of microbeads for multiplexing diagnostics
A technique has been developed for determining the 3-D distributions of magnetic nano-objects in the matrix. Methods is based on the use of the potential of a unique scientific setup developed previously at the Institute of Bioorganic Chemistry, RAS.
The capabilities of the method are demonstrated by determining the 3-D distribution of magnetic nanoparticles in polymer microbeads (Luminex company) for multiplexing diagnostics, including metabolic diseases, immunology, neurodegenerative diseases, toxicity, cancer, and more, using minimal sample volumes.
- (2017). An instrumental approach to combining confocal microspectroscopy and 3D scanning probe nanotomography. Ultramicroscopy 182, 118–123
Supramers on the base of amphiphillic molecules lipid-oligopeptide-biotin
It was found that oligopeptides with terminal lipid and biotin fragments are able to form micelle-like supramers (globules) in an aqueous solution. Using optical spectroscopy, atomic-force and electron microscopy, as well as small-angle X-ray scattering and computer simulation, it was shown that the globules are very uniform in size (about 14.6 nm). It was found that globules have the core/shell structure. The core contains lipid and part (up to 90%) of the biotin fragments. The polar oligopeptide spacer folds back upon itself and predominantly places the biotin reside inside the globule. But the part ( <10%) of biotin residues is exposed outside, and can be used for the selective attachment of specified molecules. Micelle-like supramers containing compounds that are natural to a living organism can become the basis for new types of carriers for targeted drug delivery.
High-Performance Bio-Photoelectrodes for Quantification and Measurements of Photocurrent Generated by a Single Photosynthetic Reaction Center
A new approach to fabrication of a high-performance biophotoelectrodes consisting of photosynthetic reaction center (RC) proteins immobilized on a conducting surface is developed. The voltammetry measurements at the conductive interface between a single photosynthetic RC and a golden electrode were used as the base of this study. It allowed use not only the quantification of the efficiency of the method of RC immobilization used, but also the measurements of current of the single RC. It was shown that covalent RC immobilization through S-Au bonds is much more efficient (up to ten times) than the use of a spacer. Development of this approach can be very perspective for creation of highly efficient biohybrid photosensing devices.
Investigation of Staphylococcus aureus isolates associated with subclinical cow's mastitis.
The spread and toxigenic properties of S. aureus associated with cow’s mastitis in Central Russia were investigated. Strains contained some pore-forming peptides and protein toxins were detected. The distribution of the genes of pore-forming toxins phenol-soluble modulins was determined: hla – 70%, lucS – 46.6%, psma – 81.6%, psmb – 95% and hld – 78.3%.
About 88% of studied isolates had different genes of exotoxins. The percentage of genes was shown: sea in 53.3%; seb, in 3.3%; sed, 4%; see, 46.6%; seg, 70%; sei, 58.3%; selp, 3.3%; tsst-1 in 1.6% of the cases, while seh gene was not detected. The production of enterotoxins in bacterial culture medium was confirmed and consists from 18 ng/ml in maximal level.
Five S. aureus isolates were analyzed by whole genome sequencing, annotated and registered in GenBank. The presence of various staphylococcal exotoxins was confirmed.
- (2018). Exotoxin diversity of Staphylococcus aureus isolated from milk of cows with subclinical mastitis in Central Russia. J Dairy Sci 101 (5), 4325–4331
- (2018). Immunochemical assay with monoclonal antibodies for detection of staphylococcal enterotoxin H. J Food Drug Anal 26 (2), 741–750
- (2018). Draft genome sequences of five Staphylococcus aureus strains isolated from clinically healthy cows in the Russian Federation. Genome Announc 6 (16),
- (2017). Detection of staphylococcal enterotoxin a by phage display mediated immuno-PCR method. Russ. J. Bioorganic Chem. 43 (5), 540–543
- (2017). Детекция стафилоккокового энтеротоксина А методом фаговой иммуно-ПЦР. 43, 518–522
- (2016). Staphylococcal enterotoxin a detection with phage displayed antibodies. Russ. J. Bioorganic Chem. 42 (3), 294–299
Research on the role of YB-1 protein in innate immunity reactions.
In the framework of the study number 59.8. "Research on the role of YB-1 protein in innate immunity reactions" the following results were obtained:
We confirmed that the bacterial cell-wall derivative GMDP potentiates the B cell response to Y. pestis V antigen'; centrally, we also report that a major binding target for GMDP, the host protein YB-1, itself has in vivo adjuvant properties, and that the combination of YB-1 and GMDP synergistically increased both B cell number and affinity for V antigen. Indeed, YB-1 was able to promote survival in mice receiving lethal challenge injection with E. coli, a model of acute bacterial sepsis, and recombinant protein administration to mice 12 h before lethal challenge with E. coli led to 50% long-term survival. The data obtained by us in an in vitro and in vivo model allow us to propose a scheme of biochemical pathways for the implementation of GMDP signaling in animal cells and the key role of the YB-1 protein.
- (2016). Muramyl peptides activate innate immunity conjointly via YB1 and NOD2. Innate Immun 22 (8), 666–673
Identification of fluorophores in nanoparticles of dissolved organic matter from the Suwanee River (USA)
- (2018). Molecular Size Distribution of Fluorophores in Aquatic Natural Organic Matter: Application of HPSEC with Multi-Wavelength Absorption and Fluorescence Detection Following LPSEC-PAGE Fractionation. Environ Sci Technol 52 (9), 5287–5295
- (2018). Excitation-Dependent Fluorescence Quantum Yield for Freshwater Chromophoric Dissolved Organic Matter from Northern Russian Lakes. J Spectrosc (Hindawi) 2018,
A new method of single-step DNA isolation from the soil samples for PCR diagnostics of phytopathogens.
A new bioseparating element (BE) containing polyaniline-modified silica and polyalginate microspheres, providing one-step DNA isolation from the soil extracts with simultaneous purification of DNA from the fractions of humic acids, was developed for PCR diagnostics of phytopathogens. All sorption-active components of EB are manufactured in the laboratory using original methods.
The corresponding publication was prepared and scheduled for the first quarter of 2019 in Colloids and Surfaces B: Biointerfaces (IF 3.997, Q1).
Authors: Prostyakova A.I., Zybin D.I., Kapustin D.V.
Composite material for radiopaque imaging of non-radiopaque implants.
Biocompatible biodegradable polymer coatings (based on polylactic acid) included glycolane (or lanthanum) for use in a composition of polymer biodegradable vascular stents (and other polymeric implants) were developed. Due to inclusion conditions the coatings ensure an adequate radiopacity not only during the stent installation to the patient, but also after installation, and at the same time provides an additional positive effect due to the therapeutic properties of glycolane. Glycolane is a complex compound of lanthanum nitrate and triethylene glycol [La (NO3) 3 • C6H14O4 • mH2O], which demonstrates an antimicrobial effect.
1. Generalova AN, Prostyakova AI, Pashkin II, Zubov VP, Kapustin DV. Composite material for radiopaque imaging of non-radiopaque implants. Patent RF 2599510 (15.09.2016).
2. Generalova AN, Prostyakova AI, Pashkin II, Zubov VP, Kapustin DV. Composite material for the X-ray contrast imaging of non-X-ray contrast implants. Patent WO/2016209107 A1 (29.12.2016).
3-D fluorescence spectra as a test system for evaluation the efficiency of humic substances preparative fractionation.
In recent years, three-dimensional fluorescence spectroscopy has been widely used to study complex heterogeneous mixtures, including natural humic substances, based on computer analysis of data obtained after removing several tens of emission spectra of the same sample at different excitation wavelengths of a given range. The set of data allows to obtain three-dimensional fluorescent diagrams with identification of all possible fluorescence maxima and their intensities. This method has been mastered and successfully used as a test system for evaluating the efficiency of fractionation of humic substances of various origin for the purpose of isolating and identifying individual fluorophores. The figure shows the three-dimensional fluorescent diagrams of the initial preparation of the dissolved organic matter and its fractions obtained by preparative exclusion chromatography. The three-dimensional fluorescent diagram allows not only to estimate the efficiency of fractionation, but also serve as a direct confirmation of the supramolecular organization of natural humic substances.Publications:Trubetskoi O.A., Trubetskaya O.E. Three-dimensional fluorescence analysis of chernozem humic acids and their electrophoretic fractions. Eurasian Soil Science (2017) 50:1018-1024. (Перевод: Почвоведение 2017, № 9, с.1057-1064). DOI:10.7868/S0032180X17090088Trubetskoi O.A., Trubetskaya O.E. Identification of fluorophores of organic matter of natural water. Water Resources (2017) Accepted for publication.
Unique scientific setup “System for probe-optical 3D correlative microscopy”
Designed, build and included in the register of unique scientific experimental instruments “System for probe-optical 3D correlative microscopy”
The new tool is designed to obtain three-dimensional images of biological and other objects, reconstruction of the 3D distribution of various physicochemical parameters along the volume of the object, including the determination of the chemical composition in the local regions of the object with a resolution of the nanometer scale.
All techniques of SPM are available (contact, semicontact, dynamic contact, and tapping modes, force modulation, magnetic and electrostatic force, Kelvin-probe and scanning spreading resistance microscopy. Also, it has the possibility to use the confocal fluorescence, Raman, surface and tip enhanced Raman scattering spectroscopy (SERS and TERS), and SNOM. Axial resolution of ultramicrotomography – 20 nm. Instrument contains the hard and software for reconstruction 3-D reconstruction of the morphological/optical structure of samples.
The figure shows the appearance of a unique tool, its scheme and principle of action. As the example of application, the "architecture" of the magnetic-fluorescent microbeads for clinical diagnosis and drug delivery, determined using ultramicrotomography, fluorescent microspectroscopy, and magnetic force microscopy was defined.
- (2017). An instrumental approach to combining confocal microspectroscopy and 3D scanning probe nanotomography. Ultramicroscopy 182, 118–123
- (2017). A novel design of a scanning probe microscope integrated with an ultramicrotome for serial block-face nanotomography. Rev Sci Instrum 88 (2), 023701
The composite material for radiopaque visualization radio non-opaque implants.
As a part of R&D (Step 2) under the Agreement between the IBCh RAS and LLC “BIOSTEN” No 08.01.2014 from 28.08.2014 [in pursuance of to the Agreement with the Fund "Skolkovo" grant No 18 from 28 June 2011, assigned in the framework of the Innovation project "Development of multi purpose endovascular implants (stents) with the properties of biodegradation"] a new biocompatible and biodegradable polymer glycolan-containing coatings on the surface of the polymeric biodegradable vascular stents, as well as methods of administration of glycolan into the volume of the stent material were developed. Due to optimized conditions of glycolan inclusion, it provides satisfactory radiopacity not only during the stenting procedure, but also after the installation, and at the same time it provides an additional positive effect by virtue of the therapeutic properties of glycolan.
The multichannel tip for extraction of nucleic acids, proteins and peptides.
A method of modifying the inner surface of the glass multi capillaries (MC) with nano layers of polyaniline, and a method of the manufactured MC-containing tips for mechanical dispensers utilization in DNA extraction procedure from blood for subsequent PCR-analysis were elaborated. According to experts from FGIH Russian Research Anti-Plague Institute "Microbe" the developed systems have been effective in the sample preparation procedure relating to DNA isolation from blood samples, in particular, to detect the strains of Vibrio cholerae and Yersinia pseudotuberculosis.
Jointly with the RDE “Nanostructured Glass Technology", Saratov, Russia, the RF Patent No 2547597 from 12.03.2015 (Skibina Y.S., Beloglazov V.I., Tuchin V.V., Kapustin D.V., Prostyakova A.I. "Multichannel tip for extraction of nucleic acids, proteins and peptides") was obtained.
Submicron polyacrolein particles in situ embedded with upconversion nanoparticles for bioassay
We report a new surface modification approach of upconversion nanoparticles (UCNPs) structured as an inorganic host NaYF4 codoped with Yb3+ and Er3+ based on their encapsulation at a two-stage process of precipitation polymerization of acrolein under alkaline conditions in the presence of UCNPs. The use of tetramethylammonium hydroxide both as an initiator of the acrolein polymerization and agent for the UCNP hydrophilization made it possible to increase the polyacrolein yield up to 90%. This approach enabled facile, lossless embedment of UCNPs into the polymer particles suitable for bioassay. These particles are readily dispersible in aqueous and physiological buffers, exhibiting excellent photoluminescent properties, chemical stability, and allowed control of the particle diameters. The feasibility of as-produced photoluminescent polymer particles mean-sized 260 nm for in vivo optical whole-animal imaging was also demonstrated using a home-built epi-luminescence imaging system.
- (2015). Submicron polyacrolein particles in situ embedded with upconversion nanoparticles for bioassay. Nanoscale 7 (5), 1709–1717
- (2015). Cytotoxicity and non-specific cellular uptake of bare and surface-modified upconversion nanoparticles in human skin cells. Nano Res 8 (5), 1546–1562