Federal Research and Clinical Center of Physical-Chemical Medicine named after Y.M. Lopukhin

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles ("MISEV") guidelines for the field in 2014. We now update these "MISEV2014" guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.

There is a growing need to be able to accurately and efficiently search visual data sets, and in particular, 3D shape data sets. This paper proposes a novel technique, called Topology Matching, in which similarity between polyhedral models is quickly, accurately, and automatically calculated by comparing Multiresolutional Reeb Graphs (MRGs). The MRG thus operates well as a search key for 3D shape data sets. In particular, the MRG represents the skeletal and topological structure of a 3D shape at various levels of resolution. The MRG is constructed using a continuous function on the 3D shape, which may preferably be a function of geodesic distance because this function is invariant to translation and rotation and is also robust against changes in connectivities caused by a mesh simplification or subdivision. The similarity calculation between 3D shapes is processed using a coarse-to-fine strategy while preserving the consistency of the graph structures, which results in establishing a correspondence between the parts of objects. The similarity calculation is fast and efficient because it is not necessary to determine the particular pose of a 3D shape, such as a rotation, in advance. Topology Matching is particularly useful for interactively searching for a 3D object because the results of the search fit human intuition well.

BACKGROUND: Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction. In order to differentiate the effects of these two factors, we conducted a comparative "shotgun" metagenomic survey of 99 patients with the alcohol dependence syndrome represented by two cohorts-with and without liver cirrhosis. The taxonomic and functional composition of the gut microbiota was subjected to a multifactor analysis including comparison with the external control group. RESULTS: Alcoholic dependence and liver cirrhosis were associated with profound shifts in gut community structures and metabolic potential across the patients. The specific effects on species-level community composition were remarkably different between cohorts with and without liver cirrhosis. In both cases, the commensal microbiota was found to be depleted. Alcoholic dependence was inversely associated with the levels of butyrate-producing species from the Clostridiales order, while the cirrhosis-with multiple members of the Bacteroidales order. The opportunist pathogens linked to alcoholic dependence included pro-inflammatory Enterobacteriaceae, while the hallmarks of cirrhosis included an increase of oral microbes in the gut and more frequent occurrence of abnormal community structures. Interestingly, each of the two factors was associated with the expressed enrichment in many Bifidobacterium and Lactobacillus-but the exact set of the species was different between alcoholic dependence and liver cirrhosis. At the level of functional potential, the patients showed different patterns of increase in functions related to alcohol metabolism and virulence factors, as well as pathways related to inflammation. CONCLUSIONS: Multiple shifts in the community structure and metabolic potential suggest strong negative influence of alcohol dependence and associated liver dysfunction on gut microbiota. The identified differences in patterns of impact between these two factors are important for planning of personalized treatment and prevention of these pathologies via microbiota modulation. Particularly, the expansion of Bifidobacterium and Lactobacillus suggests that probiotic interventions for patients with alcohol-related disorders using representatives of the same taxa should be considered with caution. Taxonomic and functional analysis shows an increased propensity of the gut microbiota to synthesis of the toxic acetaldehyde, suggesting higher risk of colorectal cancer and other pathologies in alcoholics.

Water-soluble iron(III) porphyrin and ferrihemoproteins (methemoglobin, metmyoglobin, oxidized cytochrome c, and catalase) associate with NO to yield the nitric oxide adducts. The equilibrium constants for association of ferrihemoproteins and NO are 1 order of magnitude larger than that of the water-soluble iron(III) porphyrin which is free from protein, suggesting that the proteins offset the forward and backward reaction rates in the equilibrium reactions. Nanosecond laser photolysis studies of the nitric oxide adducts of metmyoglobin, oxidized cytochrome c, and catalase, (NO)MbIII, (NO)CytIII, and (NO)CatIII, have been carried out. The transient detected after laser flash photolysis of (NO)CatIIIis identified as CatIII. However, the transients observed for (NO)MbIIIand (NO)CytIIIat 50 ns after laser pulsing are ascribed to MbIIItrand CytIIItr, respectively, with the absorption spectra different from those of uncomplexed MbIIIand CytIII. In particular, the absorption spectrum of CytIIItrmarkedly differs from that of the uncomplexed CytIII. The species MbIIItrand CytIIItrare found to change to MbIIIand CytIII, respectively, within a few microseconds. The quantum yields for the photodissociation of NO from nitric oxide adducts of ferrihemoproteins are 1 order of magnitude less than that from the NO adduct of the water-soluble iron(III) porphyrin, probably due to fast geminate recombination reaction of NO and ferrihemoprotein in a heme pocket. The photochemistry of the nitric oxide adducts of hemoproteins and water-soluble iron(II) porphyrin is also described on the basis of laser phosolysis studies. © 1993, American Chemical Society. All rights reserved.

The importance of curvature as a structural feature of biological membranes has been recognized for many years and has fascinated scientists from a wide range of different backgrounds.On the one hand, changes in membrane morphology are involved in a plethora of phenomena involving the plasma membrane of eukaryotic cells, including endo-and exocytosis, phagocytosis and filopodia formation.On the other hand, a multitude of intracellular processes at the level of organelles rely on generation, modulation, and maintenance of membrane curvature to maintain the organelle shape and functionality.The contribution of biophysicists and biologists is essential for shedding light on the mechanistic understanding and quantification of these processes.Given the vast complexity of phenomena and mechanisms involved in the coupling between membrane shape and function, it is not always clear in what direction to advance to eventually arrive at an exhaustive understanding of this important research area.The 2018 Biomembrane Curvature and Remodeling Roadmap of Journal of Physics D: Applied Physics addresses this need for clarity and is intended to provide guidance both for students who have just entered the field as well as established scientists who would like to improve their orientation within this fascinating area.

SUMMARY: Phigaro is a standalone command-line application that is able to detect prophage regions taking raw genome and metagenome assemblies as an input. It also produces dynamic annotated 'prophage genome maps' and marks possible transposon insertion spots inside prophages. It is applicable for mining prophage regions from large metagenomic datasets. AVAILABILITY AND IMPLEMENTATION: Source code for Phigaro is freely available for download at https://github.com/bobeobibo/phigaro along with test data. The code is written in Python. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The linear and nonlinear dielectrical and depolarization processes of the copolymer of vinylidene fluoride and trifluoroethylene have been measured. The D vs. E hysteresis loop below room temperature indicates the ferroelectricity of this copolymer. The dielectric anomaly and the disappearance of remnant polarization at T 0 =70°C suggest that T 0 is the phase transition temperature from the ferroelectricity to the paraelectricity phase. Results are analyzed on the basis of Weiss-type semimolecular theory.

Abstract External magnetic field and magnetic isotope effects on the dynamic behavior of radical pairs in solutions have been studied theoretically, where the relaxation of their electron spins was taken into account. The decay observed with some radical pairs in micellar solutions under high magnetic fields is successfully interpreted in terms of the relaxation mechanism, and the magnetic field dependence of the relaxation rates is calculated for a model system.

Significance Biocompatible microfluidic double water-in-oil-in-water emulsion (MDE) enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography-mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions. The MDE–FACS platform we developed enabled highly sensitive single-cell selection of predesigned activity and exploration of pairwise interactions between target and effector cells without interference from other microbiota species.

The complex dielectric, elastic and piezoelectric constants were measured for the composites of epoxy resin and ferroelectric PZT ceramics at 10 Hz as a function of temperature, and the magnitudes and loss tangents of these constants were compared with the theoretical predictions. The piezoelectric constants for a two phase system with piezoelectric spherical inclusions were expressed in terms of the properties of the constituents by use of the known expressions of the dielectric and elastic constants. The observed values of the d -constant (electric displacement/stress) were about 3/4 of the predicted. In the local mode dispersion region of epoxy resin near -30°C, the g -constant (electric field/stress) showed a larger temperature variation than the theoretical prediction.

BACKGROUND: Urbanization is the most prevailing cause of habitat transformation worldwide, differing from others by its intense levels of human activity. Despite its obvious impact on wildlife, it is still unclear why and how some species are able to adapt to urban settings. One possibility is that fear of humans and vehicles could preclude most species from invading cities. Species entering urban environments might be those that are more tolerant of human disturbance (i.e., tame species). Alternatively or in addition, urban invaders could be a fraction of variable species, with "tame" individuals invading urban habitats and other individuals remaining in rural areas. METHODOLOGY: Using the contemporary urban invasion by birds in a recently established South American city, we tested both hypotheses by relating interspecific differences in invasiveness to their flight initiation distances (i.e., the distances at which birds flee from approaching cars, FID), as well as to their relative brain size (RBS), a correlate of measures of behavioral flexibility. PRINCIPAL FINDINGS: Urban invasiveness was not significantly related to species' average rural FIDs but positively related to their RBS and inter-individual variability in FID. Moreover, FIDs were consistently lower in urban than in rural conspecifics, and the FIDs of urban individuals were within the lower-range distribution of their rural conspecifics. RBS indirectly influenced urban invasion through its positive effect on inter-individual variability in FID. CONCLUSIONS/SIGNIFICANCE: Urban invaders do not appear to be individuals from apparently tame species, but rather tame individuals from species with a variable response regarding fear of people. Given the positive relationship between RBS and inter-individual variability in FID, our results suggest that behavioural flexibility should be regarded as a specific trait encompassing variability among individuals. Further research is needed to ascertain the neurophysiological mechanisms underlying the relationship between brain size and inter-individual variability in behavioural traits.

Electric-field-induced changes in thickness have been measured interferometrically for thin films of ferroelectric VDF/TrFE copolymers. For sinusoidal fields high enough to induce ferroelectric switching, the strain x in the thickness direction draws a hysteresis loop of butterfly shape while the electric displacement D draws a conventional square D – E hysteresis loop. The x is shown to be proportional to D 2 . Their ratio gives the electrostriction constant κ 33 ranging from -2.1 to -2.5 m 4 /C 2 . Low-field measurements for poled samples with remnant polarization P r yield a linear relationship between x and D . The piezoelectric constant given by the ratio x / D coincides with 2κ 33 P r , implying that the piezoelectric activity of VDF copolymers originates from electrostrictive coupling as does that of traditional ferroelectrics. The role of the dimensional effect in both piezoelectricity and electrostriction is discussed.

Chk1 is a serine-threonine kinase that plays an important role in the DNA damage response, including G(2)/M cell cycle control. UCN-01 (7-hydroxystaurosporine), currently in clinical trials, has recently been shown to be a potent Chk1 inhibitor that abrogates the G(2)/M checkpoint induced by DNA-damaging agents. To understand the structural basis of Chk1 inhibition by UCN-01, we determined the crystal structure of the Chk1 kinase domain in complex with UCN-01. Chk1 structures with staurosporine and its analog SB-218078 were also determined. All three compounds bind in the ATP-binding pocket of Chk1, producing only slight changes in the protein conformation. Selectivity of UCN-01 toward Chk1 over cyclin-dependent kinases can be explained by the presence of a hydroxyl group in the lactam moiety interacting with the ATP-binding pocket. Hydrophobic interactions and hydrogen-bonding interactions were observed in the structures between UCN-01 and the Chk1 kinase domain. The high structural complementarity of these interactions is consistent with the potency and selectivity of UCN-01.

BACKGROUND AND AIM: Advanced glycation end products (AGE), senescent macroprotein derivatives formed at an accelerated rate in diabetes, play important roles in the pathogenesis of diabetic vascular complications. Recently, AGE have also been found to be involved in insulin resistance. Although non-alcoholic steatohepatitis (NASH) is generally considered a hepatic manifestation of insulin resistance, there are no reports showing the link of AGE to NASH. The aim of this study was to evaluate the clinical significance of AGE in patients with NASH. METHODS: Glyceraldehyde-derived AGE levels were assayed from serum obtained from 106 patients: 66 with NASH, 10 with simple steatosis, and 30 controls. RESULTS: Serum glyceraldehyde-derived AGE levels (U/mL) were significantly elevated in NASH patients (9.78 +/- 3.73) compared with simple steatosis (7.17 +/- 2.28, P = 0.018) or healthy controls (6.96 +/- 2.36, P = 0.003). Moreover, these were inversely correlated with adiponectin, an adipocytokine with insulin-sensitizing and anti-inflammatory properties. In addition, immunohistochemistry of glyceraldehyde-derived AGE showed intense staining in the livers of NASH patients. CONCLUSION: The present data suggest that the sustained increase of glyceraldehyde-derived AGE could at least in part contribute to the pathogenesis of NASH. The serum glyceraldehyde-derived AGE level may be a useful biomarker for discriminating NASH from simple steatosis.

Type 2 diabetes (T2D) is a serious disease. The gut microbiota (GM) has recently been identified as a new potential risk factor in addition to well-known diabetes risk factors. To investigate the GM composition in association with the dietary patterns in patients with different glucose tolerance, we analyzed 92 patients: with normal glucose tolerance (n=48), prediabetes (preD, n=24), and T2D (n=20). Metagenomic analysis was performed using 16S rRNA sequencing. The diet has been studied by a frequency method with a quantitative evaluation of food intake using a computer program. Microbiota in the samples was predominantly represented by Firmicutes, in a less degree by Bacteroidetes. Blautia was a dominant genus in all samples. The representation of Blautia, Serratia was lower in preD than in T2D patients, and even lower in those with normal glucose tolerance. After the clustering of the samples into groups according to the percentage of protein, fat, carbohydrates in the diet, the representation of the Bacteroides turned to be lower and Prevotella abundance turned to be higher in carbohydrate cluster. There were more patients with insulin resistance, T2D in the fat-protein cluster. Using the Calinski-Harabasz index identified the samples with more similar diets. It was discovered that half of the patients with a high-fat diet had normal tolerance, the others had T2D. The regression analysis showed that these T2D patients also had a higher representation of Blautia. Our study provides the further evidence concerning the structural modulation of the GM in the T2DM pathogenesis depending on the dietary patterns.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry has emerged as a rapid, cost-effective alternative for bacterial species identification. Identifying 60 blind-coded nonfermenting bacteria samples, this international study (using eight laboratories) achieved 98.75% interlaboratory reproducibility. Only 6 of the 480 samples were misidentified due to interchanges (4 samples) or contamination (1 sample) or not identified because of insufficient signal intensity (1 sample).

There are strong genetic components to cardiorespiratory fitness and its response to exercise training. It would be useful to understand the differences in the genomic profile of highly trained endurance athletes of world class caliber and sedentary controls. An international consortium (GAMES) was established in order to compare elite endurance athletes and ethnicity-matched controls in a case-control study design. Genome-wide association studies were undertaken on two cohorts of elite endurance athletes and controls (GENATHLETE and Japanese endurance runners), from which a panel of 45 promising markers was identified. These markers were tested for replication in seven additional cohorts of endurance athletes and controls: from Australia, Ethiopia, Japan, Kenya, Poland, Russia and Spain. The study is based on a total of 1520 endurance athletes (835 who took part in endurance events in World Championships and/or Olympic Games) and 2760 controls. We hypothesized that world-class athletes are likely to be characterized by an even higher concentration of endurance performance alleles and we performed separate analyses on this subsample. The meta-analysis of all available studies revealed one statistically significant marker (rs558129 at GALNTL6 locus, p = 0.0002), even after correcting for multiple testing. As shown by the low heterogeneity index (I2 = 0), all eight cohorts showed the same direction of association with rs558129, even though p-values varied across the individual studies. In summary, this study did not identify a panel of genomic variants common to these elite endurance athlete groups. Since GAMES was underpowered to identify alleles with small effect sizes, some of the suggestive leads identified should be explored in expanded comparisons of world-class endurance athletes and sedentary controls and in tightly controlled exercise training studies. Such studies have the potential to illuminate the biology not only of world class endurance performance but also of compromised cardiac functions and cardiometabolic diseases.

INTRODUCTION: This study was aimed at deciphering the secretome of adipose-derived mesenchymal stromal cells (ADSCs) cultured in standard and hypoxic conditions to reveal proteins, which may be responsible for regenerative action of these cells. METHODS: Human ADSCs were isolated from 10 healthy donors and cultured for 3-4 passages. Cells were serum deprived and cell purity was assessed using multiple cell surface markers. Conditioned media was collected and analyzed using LC-MS with a focus on characterizing secreted proteins. RESULTS: Purity of the ADSC assessed as CD90+/CD73+/CD105+/CD45-/CD31- cells was greater than 99 % and viability was greater than 97 %. More than 600 secreted proteins were detected in conditioned media of ADSCs. Of these 100 proteins were common to all cultures and included key molecules involved in tissue regeneration such as collagens and collagen maturation enzymes, matrix metalloproteases, matricellular proteins, macrophage-colony stimulating factor and pigment epithelium derived factor. Common set of proteins also included molecules, which contribute to regenerative processes but were not previously associated with ADSCs. These included olfactomedin-like 3, follistatin-like 1 and prosaposin. In addition, ADSCs from the different subjects secreted proteins, which were variable between different cultures. These included proteins with neurotrophic activities, which were not previously associated with ADSCs, such as mesencephalic astrocyte-derived neurotrophic factor, meteorin and neuron derived neurotrophic factor. Hypoxia resulted in secretion of 6 proteins, the most prominent included EGF-like repeats and discoidin I-like domains 3, adrenomedullin and ribonuclease 4 of RNase A family. It also caused the disappearance of 8 proteins, including regulator of osteogenic differentiation cartilage-associated protein. CONCLUSIONS: Human ADSCs with CD90+/CD73+/CD105+/CD45-/CD31-/PDGFRβ+/NG2+/CD146+(-) immunophenotype secrete a large array of proteins, the most represented group is comprised of extracellular matrix components. Number of secreted proteins is largely unaffected by prolonged hypoxia. Variability in the secretion of several proteins from cultured ADSCs of individual subjects suggests that these cells exist as a heterogeneous population containing functionally distinct subtypes, which differ in numbers between donors.

Yoko Katayama-Fujimura, Yoko Komatsu, Hiroshi Kuraishi, Takichi Kaneko; Estimation of DNA Base Composition by High Performance Liquid Chromatography of Its Nucl

Illumina's Infinium HumanMethylation450 BeadChip arrays were used to examine genome-wide DNA methylation profiles in 22 sample pairs from colorectal cancer (CRC) and adjacent tissues and 19 colon tissue samples from cancer-free donors. We show that the methylation profiles of tumors and healthy tissue samples can be clearly distinguished from one another and that the main source of methylation variability is associated with disease status. We used different statistical approaches to evaluate the methylation data. In general, at the CpG-site level, we found that common CRC-specific methylation patterns consist of at least 15,667 CpG sites that were significantly different from either adjacent healthy tissue or tissue from cancer-free subjects. Of these sites, 10,342 were hypermethylated in CRC, and 5,325 were hypomethylated. Hypermethylated sites were common in the maximum number of sample pairs and were mostly located in CpG islands, where they were significantly enriched for differentially methylated regions known to be cancer-specific. In contrast, hypomethylated sites were mostly located in CpG shores and were generally sample-specific. Despite the considerable variability in methylation data, we selected a panel of 14 highly robust candidates showing methylation marks in genes SND1, ADHFE1, OPLAH, TLX2, C1orf70, ZFP64, NR5A2, and COL4A. This set was successfully cross-validated using methylation data from 209 CRC samples and 38 healthy tissue samples from The Cancer Genome Atlas consortium (AUC = 0.981 [95% CI: 0.9677-0.9939], sensitivity = 100% and specificity = 82%). In summary, this study reports a large number of loci with novel differential methylation statuses, some of which may serve as candidate markers for diagnostic purposes.