From a humorous post to a detailed quantum-chemical study: isocyanate synthesis revisited

Isocyanates play an essential role in modern manufacturing processes, especially in polyurethane production. There are numerous synthesis strategies for isocyanates both under industrial and laboratory conditions, which do not prevent searching for alternative highly efficient synthetic protocols. Here, we report a detailed theoretical investigation of the mechanism of sulfur dioxide-catalyzed rearrangement of phenylnitrile oxide into phenyl isocyanate, which was first reported in 1977. The DLPNO-CCSD(T) method and up-to-date DFT protocols were used to perform a highly accurate quantum-chemical study of the rearrangement mechanism. An overview of various organic and inorganic catalysts has revealed other potential catalysts, such as sulfur trioxide and selenium dioxide. Furthermore, the present study elucidated how substituents in phenylnitrile oxide influence reaction kinetics. This study was performed by a self-organized collaboration of scientists initiated by a humorous post on the VK social network.

Development of DNA Aptamers for Visualization of Glial Brain Tumors and Detection of Circulating Tumor Cells

Here, we present DNA aptamers capable of specific binding to glial tumor cells in vitro, ex vivo, and in vivo for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified molecular target proteins of the aptamers by mass spectrometry; the potential binding sites of Gli-233 to the target protein and the role of post-translational modifications were verified by molecular dynamics simulations. The anti-glioma aptamers Gli-233 and Gli-55 were used to detect circulating tumor cells in liquid biopsies. These aptamers were used for in situ, ex vivo tissue staining, histopathological analyses, and fluorescence-guided tumor and PET/CT tumor visualization in mice with xenotransplanted human astrocytoma. The aptamers did not show in vivo toxicity in the preclinical animal study. This study demonstrates the potential applications of aptamers for precise diagnostics and fluorescence-guided surgery of brain tumors.

Advantages and Potential Benefits of Using Organoids in Nanotoxicology

Organoids are microtissues that recapitulate the complex structural organization and functions of tissues and organs. Nanoparticles have several specific properties that must be considered when replacing animal models with in vitro studies, such as the formation of a protein corona, accumulation, ability to overcome tissue barriers, and different severities of toxic effects in different cell types. An increase in the number of articles on toxicology research using organoid models is related to an increase in publications on organoids in general but is not related to toxicology-based publications. We demonstrate how the quantitative assessment of toxic changes in the structure of organoids and the state of their cell collections provide more valuable results for toxicological research and provide examples of research methods. The impact of the tested materials on organoids and their differences are also discussed. In conclusion, we highlight the main challenges, the solution of which will allow researchers to approach the replacement of in vivo research with in vitro research: biobanking and standardization of the structural characterization of organoids, and the development of effective screening imaging techniques for 3D organoid cell organization.

Commercial articulated collaborative in situ 3D bioprinter for skin wound healing

In situ bioprinting is one of the most clinically relevant techniques in the emerging bioprinting technology because it could be performed directly on the human body in the operating room and it does not require bioreactors for post-printing tissue maturation. However, commercial in situ bioprinters are still not available on the market. In this study, we demonstrated the benefit of the originally developed first commercial articulated collaborative in situ bioprinter for the treatment of full-thickness wounds in rat and porcine models. We used an articulated and collaborative robotic arm from company KUKA and developed original printhead and correspondence software enabling in situ bioprinting on curve and moving surfaces. The results of in vitro and in vivo experiments show that in situ bioprinting of bioink induces a strong hydrogel adhesion and enables printing on curved surfaces of wet tissues with a high level of fidelity. The in situ bioprinter was convenient to use in the operating room. Additional in vitro experiments (in vitro collagen contraction assay and in vitro 3D angiogenesis assay) and histological analyses demonstrated that in situ bioprinting improves the quality of wound healing in rat and porcine skin wounds. The absence of interference with the normal process of wound healing and even certain improvement in the dynamics of this process strongly suggests that in situ bioprinting could be used as a novel therapeutic modality in wound healing.

Antitumor activity of photodynamic therapy with tetracationic derivative of synthetic bacteriochlorin in spheroid culture of liver and colon cancer cells

Efficient screening of photosensitizers (PS) as well as studying their photodynamic activity, especially PS excited in the near-infrared region, require informative in vitro models to adequately reflect the architecture, thickness, and intercellular interactions in tumors. In our study, we used spheroids formed from human colon cancer HCT-116 cells and liver cancer Huh7 cells to assess the phototoxicity of a new PS based on tetracationic derivative of synthetic bacteriochlorin (BC4). We optimized conditions for the irradiation regime based on the kinetics of BC4 accumulation in spheroids and kinetics of spheroid growth. Although PS accumulated more efficiently in HCT-116 cells, characterized by more aggressive growth and high proliferative potential, they were less susceptible to the photodynamic therapy (PDT) compared to the slower growing Huh7 cells. We also showed that 3D models of spheroids were less sensitive to BC4 than conventional 2D cultures with relatively identical kinetics of drug accumulation. Our findings suggest that BC4 is a perspective agent for photodynamic therapy against cancer cells.

Design, Fabrication, and Application of Mini-Scaffolds for Cell Components in Tissue Engineering

The concept of "lockyballs" or interlockable mini-scaffolds fabricated by two-photon polymerization from biodegradable polymers for the encagement of tissue spheroids and their delivery into the desired location in the human body has been recently introduced. In order to improve control of delivery, positioning, and assembly of mini-scaffolds with tissue spheroids inside, they must be functionalized. This review describes the design, fabrication, and functionalization of mini-scaffolds as well as perspectives on their application in tissue engineering for precisely controlled cell and mini-tissue delivery and patterning. The development of functionalized mini-scaffolds advances the original concept of "lockyballs" and opens exciting new prospectives for mini-scaffolds' applications in tissue engineering and regenerative medicine and their eventual clinical translation.

Magnetic Patterning of Tissue Spheroids Using Polymer Microcapsules Containing Iron Oxide Nanoparticles

Magnetic tissue engineering is one of the rapidly emerging and promising directions of tissue engineering and biofabrication where the magnetic field is employed as temporal removal support or scaffold. Iron oxide nanoparticles are used to label living cells and provide the desired magnetic properties. Recently, polymer microcapsules loaded with iron oxide nanoparticles have been proposed as a novel approach to designing magnetic materials with high local concentrations. These microcapsules can be readily internalized and retained intracellularly for a long time in various types of cells. The low cytotoxicity of these microcapsules was previously shown in 2D cell culture. This paper has demonstrated that cells containing these nontoxic nanomaterials can form viable 3D tissue spheroids for the first time. The spheroids retained labeled fluorescent microcapsules with magnetic nanoparticles without a detectable cytotoxic effect. The high concentration of packed nanoparticles inside the microcapsules enables the evident magnetic properties of the labeled spheroids to be maintained. Finally, magnetic spheroids can be effectively used for magnetic patterning and biofabrication of tissue-engineering constructs.

Cytoskeleton systems contribute differently to the functional intrinsic properties of chondrospheres

Cytoskeleton systems, actin microfilaments, microtubules (MTs) and intermediate filaments (IFs) provide the biomechanical stability and spatial organization in cells. To understand the specific contributions of each cytoskeleton systems to intrinsic properties of spheroids, we've scrutinized the effects of the cytoskeleton perturbants, cytochalasin D (Cyto D), nocodazole (Noc) and withaferin A (WFA) on fusion, spreading on adhesive surface, morphology and biomechanics of chondrospheres (CSs). We confirmed that treatment with Cyto D but not with Noc or WFA severely affected CSs fusion and spreading dynamics and significantly reduced biomechanical properties of cell aggregates. Noc treatment affected spheroids spreading but not the fusion and surprisingly enhanced their stiffness. Vimentin intermediate filaments (VIFs) reorganization affected CSs spreading only. The analysis of all three cytoskeleton systems contribution to spheroids intrinsic properties was performed for the first time.

Biofabrication of a Functional Tubular Construct from Tissue Spheroids Using Magnetoacoustic Levitational Directed Assembly

In traditional tissue engineering, synthetic or natural scaffolds are usually used as removable temporal support, which involves some biotechnology limitations. The concept of "scaffield" approach utilizing the physical fields instead of biomaterial scaffold has been proposed recently. In particular, a combination of intense magnetic and acoustic fields can enable rapid levitational bioassembly of complex-shaped 3D tissue constructs from tissue spheroids at low concentration of paramagnetic agent (gadolinium salt) in the medium. In the current study, the tissue spheroids from human bladder smooth muscle cells (myospheres) are used as building blocks for assembling the tubular 3D constructs. Levitational assembly is accomplished at low concentrations of gadolinium salts in the high magnetic field at 9.5 T. The biofabricated smooth muscle constructs demonstrate contraction after the addition of vasoconstrictive agent endothelin-1. Thus, hybrid magnetoacoustic levitational bioassembly is considered as a new technology platform in the emerging field of formative biofabrication. This novel technology of scaffold-free, nozzle-free, and label-free bioassembly opens a unique opportunity for rapid biofabrication of 3D tissue and organ constructs with complex geometry.

Organ-specific toxicity of magnetic iron oxide-based nanoparticles

The unique properties of magnetic iron oxide nanoparticles determined their widespread use in medical applications, the food industry, textile industry, which in turn led to environmental pollution. These factors determine the long-term nature of the effect of iron oxide nanoparticles on the body. However, studies in the field of chronic nanotoxicology of magnetic iron particles are insufficient and scattered. Studies show that toxicity may be increased depending on oral and inhalation routes of administration rather than injection. The sensory nerve pathway can produce a number of specific effects not seen with other routes of administration. Organ systems showing potential toxic effects when injected with iron oxide nanoparticles include the nervous system, heart and lungs, the thyroid gland, and organs of the mononuclear phagocytic system (MPS). A special place is occupied by the reproductive system and the effect of nanoparticles on the health of the first and second generations of individuals exposed to the toxic effects of iron oxide nanoparticles. This knowledge should be taken into account for subsequent studies of the toxicity of iron oxide nanoparticles. Particular attention should be paid to tests conducted on animals with pathologies representing human chronic socially significant diseases. This part of preclinical studies is almost in its infancy but of great importance for further medical translation on nanomaterials to practice.

Scaffold-free, Label-free, and Nozzle-free Magnetic Levitational Bioassembler for Rapid Formative Biofabrication of 3D Tissues and Organs

Scaffolding is the conceptual framework of conventional tissue engineering. Over the past decade, scaffold-free approaches as a potential alternative to classic scaffold-based methods have emerged, and scaffold-free magnetic levitational tissue engineering (magnetic force-based tissue engineering [Mag-TE]) is a type of this novel tissue engineering strategy. However, Mag-TE is often based on the use of potentially toxic magnetic nanoparticles. Scaffold-free and label-free magnetic levitational bioassembly do not employ magnetic nanoparticles and thus, the potential toxicity of magnetic nanoparticles can be avoided. In this short review, we describe the conceptual foundation of scaffold-free, label-free, and nozzle-free formative biofabrication using magnetic fields as “scaffields.” The design and implementation of “Organ.Aut,” the first commercial magnetic levitational bioassembler, and the potential applications of magnetic bioassembler are discussed as well.

Extracellular Matrix Determines Biomechanical Properties of Chondrospheres during Their Maturation In Vitro

OBJECTIVE

Chondrospheres represent a variant of tissue spheroids biofabricated from chondrocytes. They are already being used in clinical trials for cartilage repair; however, their biomechanical properties have not been systematically investigated yet. The aim of our study was to characterize chondrospheres in long-term in vitro culture conditions for morphometric changes, biomechanical integrity, and their fusion and spreading kinetics.

RESULTS

It has been demonstrated that the increase in chondrospheres secant modulus of elasticity is strongly associated with the synthesis and accumulation of extracellular matrix. Additionally, significant interplay has been found between biomechanical properties of tissue spheroids and their fusion kinetics in contrast to their spreading kinetics.

CONCLUSIONS

Extracellular matrix is one of the main structural determinants of chondrospheres biomechanical properties during chondrogenic maturation in vitro. The estimation of tissue spheroids' physical behavior in vitro prior to operative treatment can be used to predict and potentially control fusogenic self-assembly process after implantation in vivo.

Scaffold-free and label-free biofabrication technology using levitational assembly in a high magnetic field

The feasibility of magnetic levitational bioassembly of tissue-engineered constructs from living tissue spheroids in the presence of paramagnetic ions (i.e. Gd³⁺) was recently demonstrated. However, Gd³⁺ is relatively toxic at concentrations above 50 mM normally used to enable magnetic levitation with NdFeB-permanent magnets. Using a high magnetic field (a 50 mm-bore, 31 T Bitter magnet) at the High Field Magnet Laboratory at Radboud University in Nijmegen, The Netherlands, we performed magnetic levitational assembly of tissue constructs from living spheroids prepared from the SW1353 chondrosarcoma cell line at 0.8 mM Gd³⁺ containing salt gadobutrol at 19 T magnetic field. The parameters of the levitation process were determined on the basis of polystyrene beads with a 170 μm-diameter. To predict the theoretical possibility of assembly, a zone of stable levitation in the horizontal and vertical areas of cross sections was previously calculated. The construct from tissue spheroids partially fused after 3 h in levitation. The analysis of viability after prolonged exposure (1 h) to strong magnetic fields (up to 30 T) showed the absence of significant cytotoxicity or morphology changes in the tissue spheroids. A high magnetic field works as a temporal and removal support or so-called 'scaffield'. Thus, formative biofabrication of tissue-engineered constructs from tissue spheroids in the high magnetic field is a promising research direction.

Magnetic levitational bioassembly of 3D tissue construct in space

Magnetic levitational bioassembly of three-dimensional (3D) tissue constructs represents a rapidly emerging scaffold- and label-free approach and alternative conceptual advance in tissue engineering. The magnetic bioassembler has been designed, developed, and certified for life space research. To the best of our knowledge, 3D tissue constructs have been biofabricated for the first time in space under microgravity from tissue spheroids consisting of human chondrocytes. Bioassembly and sequential tissue spheroid fusion presented a good agreement with developed predictive mathematical models and computer simulations. Tissue constructs demonstrated good viability and advanced stages of tissue spheroid fusion process. Thus, our data strongly suggest that scaffold-free formative biofabrication using magnetic fields is a feasible alternative to traditional scaffold-based approaches, hinting a new perspective avenue of research that could significantly advance tissue engineering. Magnetic levitational bioassembly in space can also advance space life science and space regenerative medicine.

Fabrication of calcium phosphate 3D scaffolds for bone repair using magnetic levitational assembly

The calcium phosphate particles can be used as building blocks for fabrication of 3D scaffolds intended for bone tissue engineering. This work presents for the first time a rapid creation of 3D scaffolds using magnetic levitation of calcium phosphate particles. Namely, tricalcium phosphate particles of equal size and certain porosity are used, which undergo the process of recrystallization after magnetic levitational assembly of the scaffold to ensure stitching of the scaffold. Label-free levitational assembly is achieved by using a custom-designed magnetic system in the presence of gadolinium salts, which allows the levitation of calcium phosphate particles. Chemical transformation of tricalcium- to octacalcium phosphate under the condition of magnetic levitation in non-homogeneous magnetic field is also demonstrated. This approach allows obtaining rapidly the octacalcium phosphate phase in the final 3D product, which is biocompatible.

Viscoll collagen solution as a novel bioink for direct 3D bioprinting

Collagen is one of the most promising materials for 3D bioprinting because of its distinguished biocompatibility. Cell-laden constructs made of pure collagen with or without incorporated growth supplements support engineered constructs persistence in culture and are perfectly suitable for grafting. The limiting factor for direct 3D collagen printing was poor printability of collagen solutions, especially admixed with cells or tissue spheroids. In our study, we showed that concentrated solutions of native collagen branded Viscoll were effective as bioinks with high fidelity performance. Viscoll containing 20, 30, or 40 mg/ml collagen were used for direct extrusion 3D bioprinting to form scaffolds appropriate to support spatial arrangement of tissue spheroids into rigid patterns with resolution of 0.5 mm in details. Incorporated cells demonstrated sufficient viability. Associated rheological study showed that good printability of the collagen solutions correlates with their increased storage modulus value, notably exceeding the loss modulus value. The proper combination of these physical parameters could become technological criteria for manufacturing various collagen bioinks for 3D bioprinting.

A definition of bioinks and their distinction from biomaterial inks

Biofabrication aims to fabricate biologically functional products through bioprinting or bioassembly (Groll et al 2016 Biofabrication 8 013001). In biofabrication processes, cells are positioned at defined coordinates in three-dimensional space using automated and computer controlled techniques (Moroni et al 2018 Trends Biotechnol. 36 384-402), usually with the aid of biomaterials that are either (i) directly processed with the cells as suspensions/dispersions, (ii) deposited simultaneously in a separate printing process, or (iii) used as a transient support material. Materials that are suited for biofabrication are often referred to as bioinks and have become an important area of research within the field. In view of this special issue on bioinks, we aim herein to briefly summarize the historic evolution of this term within the field of biofabrication. Furthermore, we propose a simple but general definition of bioinks, and clarify its distinction from biomaterial inks.

Scaffold-free, label-free and nozzle-free biofabrication technology using magnetic levitational assembly

Tissue spheroids have been proposed as building blocks in 3D biofabrication. Conventional magnetic force-driven 2D patterning of tissue spheroids requires prior cell labeling by magnetic nanoparticles, meanwhile a label-free approach for 3D magnetic levitational assembly has been introduced. Here we present first time report on rapid assembly of 3D tissue construct using scaffold-free, nozzle-free and label-free magnetic levitation of tissue spheroids. Chondrospheres of standard size, shape and capable to fusion have been biofabricated from primary sheep chondrocytes using non-adhesive technology. Label-free magnetic levitation was performed using a prototype device equipped with permanent magnets in presence of gadolinium (Gd³⁺) in culture media, which enables magnetic levitation. Mathematical modeling and computer simulations were used for prediction of magnetic field and kinetics of tissue spheroids assembly into 3D tissue constructs. First, we used polystyrene beads to simulate the assembly of tissue spheroids and to determine the optimal settings for magnetic levitation in presence of Gd³⁺. Second, we proved the ability of chondrospheres to assemble rapidly into 3D tissue construct in the permanent magnetic field in the presence of Gd³⁺. Thus, scaffold- and label-free magnetic levitation of tissue spheroids is a promising approach for rapid 3D biofabrication and attractive alternative to label-based magnetic force-driven tissue engineering.

Terahertz radiation from bismuth surface induced by femtosecond laser pulses

We report on the first experimental observation of terahertz (THz) wave generation from bismuth mono- and polycrystalline samples irradiated by femtosecond laser pulses. Dependencies of the THz signal on the crystal orientation, optical pulse energy, incidence angle, and polarization are presented and discussed together with features of the sample surfaces. The optical-to-THz conversion efficiency was up to two orders of magnitude higher than for metal at a moderate fluence of ∼1  mJ/cm². We also found nonlinear effects not previously observed using other metal and semiconductor materials: (a) asymmetry of THz response with respect to a half-turn of a sample around its normal, (b) THz polarization control by orientation of the sample surface, and

Why does mutation of Gln61 in Ras by the nitro analog NGln maintain activity of Ras-GAP in hydrolysis of guanosine triphosphate?

Interpretation of the experiments showing that the Ras-GAP protein complex maintains activity in guanosine triphosphate (GTP) hydrolysis upon replacement of Glu61 in Ras with its unnatural nitro analog, NGln, is an important issue for understanding details of chemical transformations at the enzyme active site. By using molecular modeling we demonstrate that both glutamine and its nitro analog in the aci-nitro form participate in the reaction of GTP hydrolysis at the stages of proton transfer and formation of inorganic phosphate. The computed structures and the energy profiles for the complete pathway from the enzyme-substrate to enzyme-product complexes for the wild-type and mutated Ras suggest that the reaction mechanism is not affected by this mutation.

Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras

The free energy profiles for the chemical reaction of the guanosine triphosphate hydrolysis GTP + H2O → GDP + Pi by Ras-GAP for the wild-type and G13V mutated Ras were computed by using molecular dynamics protocols with the QM(ab initio)/MM potentials. The results are consistent with the recent measurements of reaction kinetics in Ras-GAP showing about two-order reduction of the rate constant upon G13V mutation in Ras: the computed activation barrier on the free energy profile is increased by 3 kcal/mol upon the G13V replacement. The major reason for a higher energy barrier is a shift of the "arginine finger" (R789 from GAP) from the favorable position in the active site. The results of simulations provide support for the mechanism of the reference reaction according to which the Q61 side chain directly participates in chemical transformations at the proton transfer stage.

[SPREADING OF TISSUE SPHEROIDS FROM PRIMARY HUMAN FIBROBLASTS ON THE SURFACE OF MICROFIBROUS ELECTROSPUN POLYURETHANE MATRIX (A scanning electron microscopic study)]

Tissue spheroids biofabricated from primary human fibroblasts using non-adhesive agarose forms, were placed by 3D bioprinter on the surface of microfibrous electrospun matrix. It was demonstrated that tissue spheroids attached to the surface of matrix during several hours and then gradually spread for several days which indicates high level of biocompatibiity of electrospun microfibrous polyurethane matrix. During this activity, human fibroblasts used processes of leading cell borders for initial step of attachment to matrix filaments. Tissue constructions formed during spreading of tissue spheroids on the surface of electrospun microfibrous polyurethane matrix seem to be a perspective technology platform for development of new methods of biofabrication and 3D bioprinting.

[PERIPHERAL AUTONOMOUS REGULATION OF SINUS (SINOATRIAL) NODE IN TYPE 1 AND 2 DIABETES MELLITUS]

The aim of this work was to study peripheral vegetative regulation of pacemaker activity of the sinus (sinoatrial) node (SN) by high resolution analysis of cardiac rhythm variability (CRV) in patients with type 1 and 2 diabetes mellitus (DM). All CRV waves in the temporal and spectral regions were shown to be reduced. Regulatory effects of SN were pathologically distributed as appears from the increase of inefficient sympatho-metabolic influence due to the decrease of sympatho-parasympathetic one. Such change and redistribution of effects of regulatory SN factors are the predictors of cardiovascular disorders associated with DM1 and DM2. The low-amplitude CRV fluctuations of certain period and frequency suggest their pathogenetic relationship with DM decompensation. They differed from normal parasympathetic lengthening of a single RR-interval due to the high speed of pulse passage along parasympathetic fibers. It is supposed that these waves with periods 2.33. ± 2.35 and 2.3 ± 2.1 s and spectral density peaks 0.23 ± 0.045 and 0.24 ± 0.16 Hz showing average and moderate correlation with clinical and laboratory data (r = 0.543 ± 0.028 in DM1 and 0.388 ± 0.034 in DM2) are markers of diabetic endotoxicosis.

Modeling the role of G12V and G13V Ras mutations in the Ras-GAP-catalyzed hydrolysis reaction of guanosine triphosphate

Cancer-associated point mutations in Ras, in particular, at glycine 12 and glycine 13, affect the normal cycle between inactive GDP-bound and active GTP-bound states. In this work, the role of G12V and G13V replacements in the GAP-stimulated intrinsic GTP hydrolysis reaction in Ras is studied using molecular dynamics (MD) simulations with quantum mechanics/molecular mechanics (QM/MM) potentials. A model molecular system was constructed by motifs of the relevant crystal structure (Protein Data Bank entry 1WQ1 ). QM/MM optimization of geometry parameters in the Ras-GAP-GTP complex and QM/MM-MD simulations were performed with a quantum subsystem comprising a large fraction of the enzyme active site. For the system with wild-type Ras, the conformations fluctuated near the structure ready to be involved in the efficient chemical reaction leading to the cleavage of the phosphorus-oxygen bond in GTP upon approach of the properly aligned catalytic water molecule. Dynamics of the system with the G13V mutant is characterized by an enhanced flexibility in the area occupied by the γ-phosphate group of GTP, catalytic water, and the side chains of Arg789 and Gln61, which should somewhat hinder fast chemical steps. Conformational dynamics of the system with the G12V mutant shows considerable displacement of the Gln61 side chain and catalytic water from their favorable arrangement in the active site that may lead to a marked reduction in the reaction rate. The obtained computational results correlate well with the recent kinetic measurements of the Ras-GAP-catalyzed hydrolysis of GTP.

Thermal isomerization of the chromoprotein asFP595 and its kindling mutant A143G: QM/MM molecular dynamics simulations

Chromoprotein asFP595 and its A143G variant called kindling fluorescent protein (KFP) are among the chronologically first species for which trans-cis chromophore isomerization has been proposed as a driving force of photoswitching. In spite of long-lasting efforts to characterize the route between protein conformations referring to the trans and cis forms of the chromophore, the molecular mechanism of this transformation is still under debate. We report the results of computational studies of the trans-cis isomerization of the anionic and neutral chromophore inside the protein matrices in the ground electronic state for both variants, asFP595 and KFP. Corresponding free energy profiles (potentials of mean force) were evaluated by using molecular dynamics simulations with the quantum mechanical-molecular mechanical (QM/MM) forces. The computed free energy barrier for the cis-trans ground state (thermal) isomerization reaction is about 2 kcal/mol higher in KFP than that in asFP595. These results provide interpretation of experimental studies on thermal relaxation from the light-induced activation of fluorescence of these proteins and correctly show that the A143G mutation in asFP595 noticeably increases the lifetime of the fluorescence species.

Exploring structural and optical properties of fluorescent proteins by squeezing: modeling high-pressure effects on the mStrawberry and mCherry red fluorescent proteins

Molecular dynamics calculations of pressure effects on mStrawberry and mCherry fluorescent proteins are reported. The simulations reveal that mStrawberry has much floppier structure at atmospheric pressure, as evidenced by larger backbone fluctuations and the coexistence of two conformers that differ by Ser146 orientation. Consequently, pressure increase has a larger effect on mStrawberry, making its structure more rigid and reducing the population of one of the conformers. The most significant effect of pressure increase is in the hydrogen-bonding network between the chromophore and the nearby residues. The quantum-mechanics/molecular mechanics calculations of excitation energies in mStrawberry explain the observed blue shift and identify Lys70 as the residue that has the most pronounced effect on the spectra. The results suggest that pressure increase causes an initial increase of fluorescence yield only for relatively floppy fluorescent proteins, whereas the fluorescent proteins that have more rigid structures have quantum yields close to their maximum. The results suggest that a low quantum yield in fluorescent proteins is dynamic in nature and depends on the range of thermal motions of the chromophore and fluctuations in the H-bonding network rather than on their average structure.

Terahertz emission from a metallic surface induced by a femtosecond optic pulse

Results of experimental and theoretical investigations on generation of terahertz radiation at the interaction of femtosecond laser pulses with a metal surface are presented. Investigations are performed with the laser pulse intensities higher compared with that used in papers [Opt. Lett.29, 2674 (2004); Opt. Lett.30, 1402 (2005)]. The most effective generation is observed for p-polarized optical pulses with incidence angles in the range 5°-10° (from the surface), depending on the kind of metal. For the copper, the exponential growth of terahertz pulse energy with the increase of optical pulse energy was registered. Theoretical interpretation for some of the experimental results is proposed based on the model of free electrons in metal.

[Dysregulation of the sinoatrial node of the heart in patients with coronary heart disease during coronary artery bypass surgery]

Results of estimation of variability of cardiac rhythms in patients with coronary heart disease during coronary artery bypass surgery are presented. The aim of the study was to search for innovative methods for the assessment of the patients' conditions as a criterion for their rational choice for cardiosurgical intervention to enable adequate anesthesiological support and postoperative follow-up. We revealed additional characteristics of cardiac rhythm variability facilitating such choice and predictors of the risk of life-threatening heart arrhythmias. It is shown that high-resolution analysis of cardiac rhythms allows such peculiarities of dynamics of patient's conditions to be revealed that can not be exposed by the existing standard methods.

Anisotropic effects of terahertz emission from laser sparks in air

Strong terahertz (THz) radiation can be generated by intense femtosecond laser pulses propagating in air. The excitation of transient current induced in the wake just behind the laser pulse is studied in detail using numerical simulations on the basis of Maxwell's equations for THz-band fields and hydrodynamic model for the plasma motion. It is shown that the thermal effects, anisotropic in character in the case of linear polarized laser field, can explain observed quadrupole-type THz radiation pattern in the experiment performed by Akhmedzhanov [Radiophys. Quantum Electron. 52, 482 (2009)]. Taking into account the transverse structure of the plasma filament, our numerical code enables us to calculate the spatial distribution and temporal evolution of terahertz electron current, its spectrum, and angular emission pattern. It is shown that an expansion of full fields in terms of azimuthal modes is a useful tool for research of THz generation in many situations of practical interest.

[Analysis of cardiac rhythm variability in patients with sinoatrial node dysfunction]

The study was designed to elucidate the wave structure of heart rhythm variability (HRV) for the assessment of vegetative regulation of pacemaker activity of the sinoatrial node in 362 patients with coronary heart disease. The results were compared with the data of routine cardiologic examination. Sinus node dysfunction and weakness were shown to be accompanied by differential autonomous dysregulations that may be used as additional symptoms for the diagnosis of arrhythmias. Precision analysis of HRV permits to evaluate the arrhythmogenic events behind vegetative regulation of the sinus node, hemodynamic significance of arrhythmic episodes, and dependence of sinoatrial blockade on the degree of autonomous dysregulation. Autonomous cardioneuropathy syndrome is distinguished, its association with necrobiotic changes in the sinus node is demonstrated by electron microscopy.

[Sinus rhythm variability in bronchial asthma]

The subjects, 265 patients with bronchial asthma (BA) patients (mean age: 41.92 +/- 1.36 yr), were examined using spirometry, peak-flowmetry, body plethysmography, EchoCG, and bronchoscopy with biopsy and histologic study. A high-resolution method--rhythmocardiography with temporal statistical and spectral analysis of sinus rhythm variability at rest and at directed testing using hardware and software complex KAP-RK-01-Micor (Chelyabinsk)--was applied. The patients with BA displayed sinus node dysregulation, insufficient vegetative providence, significant depression of peripheral sympathico-parasympathetic regulation in general, intensification of humoral-and-metabolic influence on pacemaker cells in the sinus node, and the forming of a pathophysiological pattern of response to stimuli during tests.

[Calcium as a regulator of intracellular processes in actinomycetes: a review]

Data on the effects of calcium ions (Ca2+) on processes of morphological and physiological differentiation in cultures of actinomycetes have been reviewed, with emphasis on representatives of the genus Streptomyces. Evidence accumulated thus far, of the regulatory role of serine-threonine protein kinases in the differentiation and of the possible involvement of Ca2+-dependent protein kinases in secondary metabolism (including antibiotic biosynthesis) are analyzed. The possibility that regulatory elements of apoptosis (including Ca2+-dependent) function in actinomycetes is discussed. A hypothesis is advanced, according to which determinants of antibiotic resistance play a key role in the network of signal transduction systems of actinomycetes.

[Antioxidant effect on the growth of Saccharopolyspora erythraea and biosynthesis of erythromycins]

Oxidative stress in the mycelium of submerged culture of S. erythraea, an organism producing erythromycins, was observed. The stress could be eliminated by addition of antioxidants, such as butyloxyanisole, alpha-tocopherol, cytochrome C to the culture. In the presence of the antioxidants the mycelium lysis decreased, the level of the decrease being higher in the medium preferably containing carbohydrates vs. the medium mainly containing lipids (soybean oil). The antioxidants had no specific effect on the biosynthesis of erythromycins.

[Biogenesis and regulation of biosynthesis of erythromycins in Saccharopolyspora erythraea: a review]

Data on the structure and stages of biosynthesis of erythromycins, relating to (1) successive addition of L-mycarose and D-desosamine to the lactones erythronolide B and mycarosyl-erythronolide B, respectively, and (2) biotransformation of erythromycin D to erythromycin A, are presented. Pathways of biosynthesis of L-mycarose, D-desosamine, and methylmalonyl-CoA and methylpropionyl-CoA precursors of erythronolide B are reviewed, along with the properties of genes coding the enzymes involved. Possible mechanisms of biochemical and gene regulation of erythromycin biosynthesis in Saccharopolyspora erythraea are discussed, including the role of factors ensuring predominant formation of the target product, erythromycin A.