Acharya A.,University of Southern California |
Bogdanov A.M.,Nizhny Novgorod State Medical Academy |
Grigorenko B.L.,RAS Emanuel Institute of Biochemical Physics |
Bravaya K.B.,Boston University |
And 3 more authors.
Chemical Reviews | Year: 2017
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed. © 2016 American Chemical Society.
Senkov O.,Molecular Neuroplasticity Group |
Mironov A.,Nizhny Novgorod State Medical Academy |
Dityatev A.,Molecular Neuroplasticity Group |
Dityatev A.,Otto Von Guericke University of Magdeburg
Frontiers in Neuroscience | Year: 2015
To characterize information transfer in defined brain circuits involving multiple brain regions and to evaluate underlying molecular mechanisms and their dysregulation in major brain diseases, a simple and reliable system is ultimately required for electrophysiological recording of local field potentials (LFPs, or local EEG) in combination with local delivery of drugs, enzymes and gene expression-controlling viruses near the place of recording. Here we provide a new design of a versatile reusable hybrid infusion-recording (HIME) system which can be utilized in freely moving mice performing cognitive tasks. The HIME system allows monitoring neuronal activity in multiple layers in several brain structures. Here, we provide examples of bilateral injection and recordings of full spectrum of learning and memory related oscillations, i.e., theta (4-12 Hz), gamma (40-100) and ripple activity (130-150 Hz), in five hippocampal layers as well as in the CA1 and CA2 regions. Furthermore, the system is designed to be used for parallel recordings in the amygdala, cortex and other brain areas, before and after infusion of reagents of interest, either in or offa cognitive test. We anticipate that the HIME system can be particularly convenient to advance functional neuroglycobiological studies and molecular deciphering of mechanisms governing long-term memory consolidation. © 2015 Senkov, Mironov and Dityatev.
Vakhlamov V.A.,Nizhny Novgorod State Medical Academy
Sovremennye Tehnologii v Medicine | Year: 2017
The aim of the investigation was to demonstrate the feasibilities of using up-to-date methods of examination for assessing the effect of smoking on the course of bronchial asthma (BA) and development of comorbid metabolic pathology. Materials and Methods. 201 patients with noncontrolled BA were investigated. Group 1 comprised 152 nonsmoking patients, group 2 included 18 smokers, group 3 consisted of 31 heavy smokers. Along with the general clinical methods of examination, external respiration function with evaluation of forced life capacity, forced expiratory volume in 1 second, and Tiffeneau index were investigated. To diagnose obesity, a bioelectrical impedance analysis was used, body mass index was determined, and waist measurements were performed. To study the carbohydrate metabolism, the level of glycated hemoglobin (HbA1c), immunoreactive insulin, and C-peptide were estimated. Results. Waist measurements, bioelectrical impedance analysis, determination HbA1c, immunoreactive insulin, and C-peptide levels are established to play a great role in the diagnosis of comorbid endocrine pathology in BA. The severity of the disease in BA patients is aggravated by visceral obesity and diabetes mellitus, and cigarette smoking is an essential risk factor of their development. Longterm heavy smokers with BA are characterized by the addition of chronic obstructive pulmonary disease and the development of overlap syndrome with an extremely severe course. © 2017, Nizhny Novgorod State Medical Academy. All rights reserved.
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: email@example.com. Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email: firstname.lastname@example.org.
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.