Aghayeva U.F.,New York Academy of Sciences |
Nikitin M.P.,RAS A.M. Prokhorov General Physics Institute |
Lukash S.V.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry |
Deyev S.M.,Nizhny Novgorod State Medical Academy
ACS Nano | Year: 2013
To date, a number of biomolecule-mediated nanoparticle self-assembly systems have been developed that are amenable to controllable disassembly under relatively gentle conditions. However, for some applications such as design of self-assembled multifunctional theragnostic agents, high stability of the assembled structures can be of primary importance. Here, we report extraordinarily high durability of protein-assisted nanoparticle self-assembly systems yielding bifunctional colloidal superstructures resistant to extreme denaturing conditions intolerable for most proteins (e.g., high concentrations of chaotropic agents, high temperature). Among the tested systems (barnase-barstar (BBS), streptavidin-biotin, antibody-antigen, and protein A-immunoglobulin), the BBS is notable due to the combination of its high resistance to severe chemical perturbation and unique advantages offered by genetic engineering of this entirely protein-based system. Comparison of the self-assembly systems shows that whereas in all cases the preassembled structures proved essentially resistant to extreme conditions, the ability of the complementary biomolecular pairs to mediate assembly of the initial biomolecule-particle conjugates differs substantially in these conditions. © 2013 American Chemical Society.
News Article | November 14, 2016
Dendra2 is a photo-activated fluorescent protein that was developed 10 years ago by researchers at the M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, based on the Dendra protein from a particular kind of coral, the Dendronephthya sp. octocorals. These proteins are capable of undergoing significant change in their fluorescent properties when irradiated with a certain amount of light of a specific wavelength. Today, they are among the most popular tools for monitoring and tracking proteins, cells and tissues, and are particularly suitable for ultrahigh-resolution fluorescence microscopy. Studies done on the mechanisms through which this protein are light-activated, in particular switching from green to red form under violet or blue light, had long been considered exhaustive. However, a year ago, researchers discovered that the weak photoactivation of the protein under blue light could be repeatedly strengthened by simultaneous irradiation via laser in the near infrared range (700 to 780 nm). This renders unnecessary the use of violet light, which can harm living tissue. However, the process itself involves using costly infrared lasers. In the new study, researchers from the Institute of Bioorganic Chemistry of the Russian Academy of Sciences and the Nizhny Novgorod State Medical Academy discovered that even light sources with a substantially shorter wavelength in the red region of the visible spectrum (630-650 nm) are able to induce the same effect. "During the study, we were able to demonstrate a significant increase in photoactivation efficiency when living cells are simultaneously irradiated with blue and red light under ultrahigh-resolution fluorescence microscopy," notes Alexander Mishin, Ph.D., one of the researchers from the IBCh RAS Laboratory of Biophotonics. "The cheap red lasers that are a standard part of many microscopes have made the new photoactivation method available to a wider range of researchers." The data obtained from this collaborative research is of particular interest for understanding the photoactivation mechanism itself. As the scientists noted, this process is still riddled with many other unknowns, and even the nature of the unusual intermediate state of the fluorescent protein that absorbs light in a wide spectral range is still a mystery to this day. Modern science implements several ways of using light to activate these proteins. The most common method involves transforming them from a green to a red fluorescent state. The first such protein was described by Japanese scientists in 2003, who managed to isolate it from madrepore. They named it Kaede, which means 'maple leaf'. However, this is not the only protein capable of changing its fluorescent properties in this way. More information: N. V. Klementieva et al. Green-to-red primed conversion of Dendra2 using blue and red lasers, Chem. Commun. (2016). DOI: 10.1039/C6CC05599K Nadya G Gurskaya et al. Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light, Nature Biotechnology (2006). DOI: 10.1038/nbt1191 William P Dempsey et al. In vivo single-cell labeling by confined primed conversion, Nature Methods (2015). DOI: 10.1038/nmeth.3405
Kleshnin M.S.,RAS Institute of Applied Physics |
Turchin I.V.,Nizhny Novgorod State Medical Academy
Laser Physics Letters | Year: 2013
The dispersion of biotissue optical properties results in distortion of the spectrum of radiation during propagation through biotissues. This phenomenon can be used for solving the inverse problem in fluorescence diffuse tomography. We have developed the spectrally resolved fluorescence diffuse tomography (SFDT) technique, which allows reconstruction of the spatial distribution of the fluorophore in biotissue even in the presence of unknown autofluorescence. The experimental setup combining epi-illumination and trans-illumination imaging geometries with spectral resolution has been created. Experimental studies on tissue phantoms and small animals in vivo with the proposed SFDT technique have been conducted. The obtained results have shown high accuracy of the inverse problem solution for spatial distribution of fluorophore concentration. © 2013 Astro Ltd.
Luker K.E.,University of Michigan |
Mihalko L.A.,University of Michigan |
Schmidt B.T.,University of Michigan |
Lewin S.A.,University of Michigan |
And 4 more authors.
Nature Medicine | Year: 2012
Studies of ligand-receptor binding and the development of receptor antagonists would benefit greatly from imaging techniques that translate directly from cell-based assays to living animals. We used Gaussia luciferase protein fragment complementation to quantify the binding of chemokine (C-X-C motif) ligand 12 (CXCL12) to chemokine (C-X-C motif) receptor 4 (CXCR4) and CXCR7. Studies established that small-molecule inhibitors of CXCR4 or CXCR7 specifically blocked CXCL12 binding in cell-based assays and revealed differences in kinetics of inhibiting chemokine binding to each receptor. Bioluminescence imaging showed CXCL12-CXCR7 binding in primary and metastatic tumors in a mouse model of breast cancer. We used this imaging technique to quantify drug-mediated inhibition of CXCL12-CXCR4 binding in living mice. We expect this imaging technology to advance research in areas such as ligand-receptor interactions and the development of new therapeutic agents in cell-based assays and small animals. © 2012 Nature America, Inc. All rights reserved.
Prakhov N.D.,Nizhny Novgorod State Medical Academy |
Chernorudskiy A.L.,Nizhny Novgorod State Medical Academy |
Gainullin M.R.,Nizhny Novgorod State Medical Academy
Bioinformatics | Year: 2010
Summary: VSDocker is an original program that allows using AutoDock4 for optimized virtual ligand screening on computer clusters or multiprocessor workstations. This tool is the first implementation of parallel high-performance virtual screening of ligands for MS Windows-based computer systems. Availability: VSDocker 2.0 is freely available for non-commercial use at http://www.bio.nnov.ru/projects/vsdocker2/. Contact: firstname.lastname@example.org. Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email: email@example.com.
Gordetsov A.S.,Nizhny Novgorod State Medical Academy
Sovremennye Tehnologii v Medicine | Year: 2010
Now there is a great interest in experimental and clinical medicine to the new methods of diagnosis, treatment and prophylaxis of different diseases. It is particularly stipulated by appearance of multiple electronic devices, permitting to investigate the qualitative and quantitative characteristics of biological fluids and tissues at the nanotechnology level, making possible a revealing of the molecular transformation mechanisms, causing the pathologic changes in the human organism. The scientific works of the Nizhny Novgorod state medical academy collaborators and other scientists on investigation of the disease diagnosis new methods (including oncologic ones) on a basis of the biological material study by a method of infrared spectroscopy are analyzed. The question history is regarded. The methods of the biological fluid and tissue treatment and the IR-spectrum receipt are described; the examples of the IR-spectrum characteristic mathematical analysis are presented. A conclusion is made of the different disease treatment quality diagnosis and control new IR-spectroscopic method reliability.
Ivanov E.G.,Nizhny Novgorod State Medical Academy
Engineering for Rural Development | Year: 2016
Acoustic-cavitation effect on soaked seeds is created by generating sound waves of certain intensity in water. Passing the vacuum phase of the wave, water is torn forming cavities. Passing the manometric phase of the wave, these cavities collapse with a total speed of the counter walls of 3000 m·s-1. At the point of collapse high energy density is created. This increases the temperature of the treated water, shock waves are created, their interference occurs, and so on. As a result, this causes deformation and mixing of water, as well as changing its properties. When low-quality seeds are soaked in this water their germination increases (up to 90 %), the germination time decreases (in 3 times) compared with the control germination. Seed processing in the passive zone of the cavitator and then their soaking in treated water increases germination up to 97 %, or reduces germination time from 3 days to 6 hours compared to the original (control) process. A series of devices for various methods of cavitator seed treatment are created, both for crop growing and for preparation of highly enriched feed in animal husbandry: liquid whistle of vortex type (vortex cavitator), liquid whistle of vortex type with the resonator placed in an external holder, liquid whistle of vortex type with the rotating resonator, liquid whistle of vortex type with the correcting device and several resonators, liquid whistle of multiple-jet type, the liquid siren combined with the network pump.
Chernorudskiy A.L.,Nizhny Novgorod State Medical Academy |
Gainullin M.R.,Nizhny Novgorod State Medical Academy
Science Signaling | Year: 2013
Ubiquitylation, a widespread and important posttranslational modifi cation of eukaryotic proteins, regulates a multitude of critical cellular processes, both in normal and pathological conditions. A classical view of how ubiquitylation regulates protein function involves recognition of ubiquitin-encoded signals by specifi c ubiquitin-binding domains. However, evidence suggests the existence of direct effects of ubiquitylation, which occur through its impact on protein-protein interactions that do not involve specifi c ubiquitin receptors. Ubiquitin attachment may cause steric limitations that infl uence interaction of the modifi ed protein with other proteins. Here, we present examples of this direct effect of ubiquitylation and propose how a two-level ubiquitin-mediated regulatory mechanism may provide fl exibility.
Bugrova M.L.,Nizhny Novgorod State Medical Academy
Cell and Tissue Biology | Year: 2016
We have studied the accumulation and excretion of atrial (ANP) and brain (BNP) natriuretic peptides in the early and late postreperfusion period (60 min and 60 days) in the myocardium of the right atrium in rats. The model of total ischemia proposed by Korpachev et al. (1982) was used. Immunocytochemical localization of peptides in cardiomyocytes was performed on ultrathin sections using the polyclonal antibodies. The intensities of accumulation (excretion) of ANP and BNP were analyzed by counting the immunolabeled granules (types A and B) with a transmission electron microscope. At 60 min and 60 days of the postreperfusion period, an increase in the synthesis and release of ANP and BNP was found. A more pronounced BNP reaction could be explained by the fact that, under normal conditions, the main hormone of the natriuretic peptide system regulating blood pressure is ANP, while BNP regulates blood pressure in cardiovascular pathology. © 2016, Pleiades Publishing, Ltd.
Shakhov E.B.,Nizhny Novgorod State Medical Academy
Sovremennye Tehnologii v Medicine | Year: 2016
Selective coronary angiography may reveal slightly affected coronary arteries with less than 50% of stenotic areas in 10–15% of patients with clinical and ECG picture of acute coronary syndrome. The aim of the investigation is to evaluate the efficacy of the novel technique of endocardial and epicardial coronary bloodstream correction — intermittent percutaneous coronary sinus occlusion (PCSO) — in patients with acute coronary syndrome without hemodynamically significant atherosclerotic coronary lesions by studying the main functional parameters of the left ventricular myocardium in the medium terms (12 months later). Materials and Methods. The results of treating 8 patients with acute coronary syndrome and ST-segment depression without hemodynamically significant coronary stenoses and initial diastolic dysfunction have been analyzed. Four patients underwent PCSO with subsequent medication, other four patients received only therapeutic treatment. Results. In group 1 the myocardium function was observed to normalize completely in 2 individuals 12 months after the surgery (medium term). In group 2 complete normalization of diastolic myocardial function was not observed in any patient. Patients after PCSO showed statistically significantly better parameters of diastolic function 1 year after the operation compared to the results of only therapeutic treatment. Conclusion. PCSO procedure combined with subsequent adequate therapeutic support in patients with acute coronary syndrome has significantly better effect on restoration completeness of left ventricular diastolic function compared to isolated therapeutic treatment. © 2016, Nizhny Novgorod State Medical Academy. All rights reserved.