Browsing by Author "Goncharov, Nikolay V."
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Item Metadata only An algorithm for deriving new combinatorial biomarkers based on ridge regression(Cifra, 2018-02-22) Terpilowski, M. A.; Korf, E. A.; Jenkins, R. O.; Goncharov, Nikolay V.Motivation: Combinatorial biomarkers are considered more specific and sensitive than single markers in medical diagnostics and prediction, yet even detection of such these combinatorial biomarkers requires deep computational analysis. The principles of analytic combinatorics, linear and kernel ridge regression, and machine learning were applied to derive new combinatorial biomarkers of muscle damage. Results: Lactate, phosphate, and middle-chain fatty acids were most often included into biochemical combinatorial markers, while the following physiological parameters were found to be prevalent: muscle isometric strength, H-reflex length, and contraction tone. Several strongly correlated combinatorial biomarkers of muscle damage with high prediction accuracy scores were identified. The approach — based on computational methods, regression algorithms and machine learning — provides a flexible, platform independent and highly extendable means of discovery and evaluation of combinatorial biomarkers alongside current diagnostic tools. Availability: The developed algorithm was implemented in Python programming language on a quantitative dataset comprising 23 biochemical parameters, 37 physiological parameters and 3,903 observations. The algorithm and our dataset are available free of charge on GitHub. Supplementary information: Supplementary data are available at Journal of Bioinformatics and Genomics online.Item Open Access Anticancer drug cytotoxicity assessed using controllable HELA TET-ON/HCYP1 cell lines(2016-04) Jenkins, R. O.; Li, N-G; Goncharov, Nikolay V.Objective: P450 enzymes have a key role in the metabolism of a many anticancer drugs. Metabolism via CYP1s in a variety of solid tumours is thought to aid tumour avoidance of chemotherapeutic induced cytotoxicity. The objective of the present research was to establish the influence of CYP1 mediated metabolism of three anticancer drugs (baicalein, resveratrol, doxorubicin) on their cytotoxicity, using a series of HeLa Tet-ON/hCYP1 cell lines controllably expressing CYP1 enzymes. Methods: The full length genes coding human CYP1A1, CYP1A2 and CYP1B1 were cloned from human liver cDNA library by PCR into the cloning plasmid pBluescriptKS(+) and expressed in different mammalian vectors, with subsequent DNA sequencing of the cloned CYP1 genes. The cytotoxicity of the anticancer drugs (baicalein, resveratrol, doxorubicin) by CYP1 cells was investigated in the presence and absence of α-naphthoflavone (ANF; potent inhibitor of CYP1 family). Cell survival was assessed by the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. Results: CYP1A1 was found to be the most potent enzyme for conversion of the anticancer drugs to more cytotoxic metabolites. CYP1A1, but not CYP1B1 or CYP1A2, enhanced cytotoxicity of resveratrol. Doxorubicin was found to have highest increase (53-fold) in cytotoxicity mediated by CYP1A1 (Table 1 and Fig. 1). Conclusion: Tumours expressing CYP1A1 would respond more favourably to doxorubicin and could be treated effectively with lower doses of the anticancer agent, thus reducing harm to normal tissue. The double stable cell lines expressing CYP1 enzymes were effective cellular systems for assessing cytotoxicity profiles of candidate anticancer agents.Item Open Access Apoptosis/necrosis ratio in THP-1 cell line (human monocytic leukemia cells) exposed to esters of 2,3-dihydroazete series.(2016-04) Jenkins, R. O.; Kudryavtsev, I.; Serebriakova, M.; Smetanin, I. A.; Agafonova, A. V.; Voitenko, Natalia G.; Trulioff, A.; Goncharov, Nikolay V.Objective: The failure of many anti-cancer chemotherapeutics is due to their inability to induce apoptosis at the cellular level. Many cancers can develop pro-survival adaptations and anti-apoptotic signaling pathways, leading to drug resistance. Development of prodrugs that induce targeted necrosis is one strategy to circumvent apoptosis-resistance. However, we hold the opinion that necrosis should be the natural outcome of primary and fully developed apoptosis, in order to maximally avoid side effects with healthy tissues at the stage of preclinical and clinical studies. Recently we developed two two-step procedures for the synthesis of thermally and hydrolytically stable 2,3-dihydroazete-2,3-di-/2,2,3-tricarboxylates (2,3-dihydroazetes) [in press]. The objective of the present research was to assess their pro-apoptotic and/or pro-necrotic abilities with cell suspension culture of human monocytic leukemia cells (THP-1), along with their general cytotoxic effect. Methods: Cultivation of the THP-1 cell line was in supplemented RPMI-1640 medium. For assessment of cell viability, two DNA binding dyes - YO-PRO-1 and propidium iodide (PI) - were used (‘normal’cells, not stained; cells at early stages of apoptosis, YO-PRO-1 positive; cells at later stages, YO-PRO-1 and PI positive). Results: 2,3-Dihydroazetes tested over the range 10-5 to 2×10-4 M showed significant differences in their ability not only to induce the cell death, but also in the way they do so by inducing predominantly apoptosis or necrosis. To adequately describe and quantitatively assess their apoptotic and/or necrotic potential, on one hand, and their general cytotoxic potential, on the other hand, we took the difference between the two areas under the curves, apoptotic and necrotic, over the concentration range. Dihydroazete 2a exhibited the maximal apoptotic/necrotic difference with the THP-1 cell line (Figs. 1, 2); 2m,n,k showed a lower and non-significant difference due to higher necrotic potential at nearly the same cytotoxicity as 2a; dihydroazetes 2b,e and 8a showed a lower though significant difference due to higher necrotic potential coupled with a lower cytotoxicity; 2h had both a very low difference and a very low cytotoxicity, and dihydroazetes 8g,c exhibited a negative difference due to predominantly necrotic cell death at a moderate to high level of cytotoxicity. Figure 1. The quantitative estimates of the apoptotic/necrotic difference (AND) of the dihydroazetes 2a,b,e,h,k,m,n and 8a,c,g exhibited with the THP-1 cell line. *) Р<0.05 Figure 2. Concentration dependency (C = mole × L-1) of apoptosis and necrosis induction. Percentage of dead cells as determined by DNA binding dyes YO-PRO-1 and PI via flow cytometry after treatment of THP-1 cells for 24 h with different concentrations of 2a. Conclusion: The newly synthesized thermally stable 2,3-dihydroazetes greatly differ in their ability to induce apoptosis and/or necrosis, and could be good candidates for further studies of their anti-cancer activities.Item Metadata only Application of a low-angle light scattering technique to cell volume and cell signaling studies on Ehrlich ascite tumor cells.(ISO Press, 2006) Zinchenko, V. P.; Lee, V. V.; Berezhnov, V. A.; Mindukshev, I. V.; Jenkins, R. O.; Goncharov, Nikolay V.Item Open Access Chemical pretreatment of cells for enhanced discrimination of clinical yeasts isolates by MALDI-TOF-MS(2014) Jenkins, R. O.; Kwok, R. W. L.; Goncharov, Nikolay V.; Haris, P. I. (Parvez I.)Item Open Access Chemical pretreatment of cells for enhanced MALDI-TOF-MS discrimination of clinical staphylococci including MRSA(IOS Press, 2014) Jenkins, R. O.; Kwok, R. W. L.; Goncharov, Nikolay V.; Halliwell, R.; Haris, P. I. (Parvez I.)BACKGROUND: Limited success has been reported for matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) differentiation of staphylococci, including methicillin resistant Staphylococcus aureus (MRSA) strains. Chemical pretreatment of cells prior to MALDI-TOF-MS analysis has not been systematically investigated for enhanced discrimination of S.aureus strains. OBJECTIVES: To evaluate various chemical pretreatment of cells for MALDI-TOF-MS discrimination of clinical staphylococcal isolates, with a focus on differentiation of MRSA from methicillin sensitive S. aureus (MSSA) strains and from other staphylococcal species. METHOD: MALDI-TOF-MS of a well-characterised S. aureus strain(s) was optimised with respect to matrix chemical(s), matrix solvent and target plating method. Various chemical pretreatments (solvents, reductants, detergents) and pretreatment application methods were then evaluated for enhancement of spectral richness. The three most promising pretreatments were applied to MALDI-TOF-MS discrimination of three set of clinical isolates comprising non-S.aureus staphylococci (77 isolates ), MSSA (36) and MRSA (43), with analysis by total or set specific resolved peaks. RESULTS: The optimized MALDI-TOF-MS protocol involved α-cyano-4-hydroxycinnamic acid (CHCA) as matrix chemical (in 1:2 acetonitrile:H2O and 2% trifluoroacetic acid), with application as an overlay onto smeared cells (on-probe). On-probe application of chemical pretreatment was most effective at enhancing MALDI-TOF-MS spectral richness. Use of reductants and detergents as pretreatments were ineffective. The three most effective solvents/acid pretreatments - ethanol:formate, ethanol:acetate and formate:isopropanol - each generated reproducible and distinct spectra over the 2,000 -10,000 m/z range. For the combined sets of clinical isolates (114), all three of these pretreatments increased the total number of resolved peaks in comparison with no pretreatment controls. The ethanol:formate pretreatment gave 100% clustering of non-S. aureus staphylococci, based on total resolved peaks. The formate:isopropanol pretreatment generated the largest increase in number of MRSA set specific peaks (from 18 to 32; 78% increase) and clustered the majority (77%) of the MRSA strains together, although compete discrimination of the MSSA and MRSA was not achieved. CONCLUSION: MALDI-TOF-MS discrimination of clinical isolates of staphylococci is enhanced through chemical pretreatment of cells. Three chemical pretreatments, not previously applied to staphylococci, are highlighted for enhancing spectral richness and offering new opportunities for improved discrimination of staphylococci, including MRSA and MSSA strains.Item Metadata only Determination of fluoroacetic acid in water and biological samples by GC-FID and GC-MS in combination with solid-phase microextraction.(Springer Verlag, 2006-11-01) Jenkins, R. O.; Khlebnikova, N. S.; Koryagina, N. L.; Savelieva, E. I.; Goncharov, Nikolay V.; Radilov, Andrey S.Item Open Access Effects of exposure of rat erythrocytes to a hypogeomagnetic field(IOS Press, 2018-06-19) Nadeev, A.D.; Terpilowski, M.A.; Bogdanov, V.A.; Khmelevskoy, D.A.; Schegolev, B.F.; Surma, S.V.; Stefanov, V.E.; Goncharov, Nikolay V.; Jenkins, R. O.Background:Hypomagnetic fields can disrupts the normal functioning of living organisms by a mechanism thought to involve oxidative stress. In erythrocytes, oxidative stress can inter alia lead to changes to hemoglobin content and to hemolysis. Objective:To study the effects of hypomagnetism on the state of rat erythrocytes in vitro. Methods:Rat erythrocytes were exposed to an attenuated magnetic field (AMF) or Earth’s magnetic field (EMF), in the presence of tert-butyl hydroperoxide (TBHP) as inducer of oxidative stress. Determinations: total hemoglobin (and its three forms – oxyhemoglobin, methemoglobin, and hemichrome) released from erythrocytes, spectral data (500–700 nm); oxygen radical concentrations, electron paramagnetic resonance. Results:AMF and EMF exposed erythrocytes were compared. After 4 h incubation at high TBHP concentrations (>700 μM), AMF exposed erythrocytes released significantly more (p<0.05) hemoglobin (Hb), mostly as methemoglobin (metHb). Conversely, after 24 h incubation at low TBHP concentrations (⩽350 μM), EMF exposed erythrocytes released significantly more (p<0.001) hemoglobin, with metHb as a significant proportion of the total Hb. Erythrocytes exposed to AMF generated more radicals than those exposed to the EMF. Conclusion:Under particular conditions of oxidative stress, hypomagnetic fields can disrupt the functional state of erythrocytes and promote cell death; an additive effect is implicated.Item Metadata only Electrophysiological study of infant and adult rats under acute intoxication with fluoroacetamide.(Wiley, 2007) Kuznetsov, S.; Jenkins, R. O.; Goncharov, Nikolay V.Item Metadata only Flow cytometry and light scattering technique in evaluation of nutraceuticals.(Elsevier, 2016) Goncharov, Nikolay V.; Mindukshev, I. V.; Kudryavtsev, I.; Serebriakova, M.; Trulioff, A.; Gambaryan, S.; Sudnitsyna, J.; Khmelevskoy, D.; Voitenko, Natalia G.; Avdonin, P.; Jenkins, R. O.Item Metadata only Fluroacetate(Elsevier, 2009) Goncharov, Nikolay V.; Glashkina, L.; Savelieva, E. I.; Zinchenko, V.; Teplova, V. V.; Vinokurov, M.; Kuznetsov, S.; Mindukshev, I. V.; Avdonin, P.; Jenkins, R. O.; Radilov, Andrey S.Item Metadata only Fluroacetate.(Elsevier, 2015) Goncharov, Nikolay V.; Savelieva, E. I.; Zinchenko, V.; Kuznetsov, S.; Mindukshev, I. V.; Vinokurov, M.; Avdonin, P.; Voitenko, Natalia G.; Ukolov, A.; Orlova, O. I.; Jenkins, R. O.; Kuznetsov, A.Action of fluoroacetate (FA) becomes apparent after a latent period, even after exposure to lethal doses. The best known representative of FA is its sodium salt. There are also series of fluorinated compounds which metabolism is connected with formation of FA. To reveal intoxications, adequate analytical procedures should be developed, as well as unequivocal biochemical, physiological and clinical signs of intoxication should be described. Also, new approaches to development of an effective therapy for treating acute intoxications by FA are highly important, because after many decades of toxicological studies on FA effective antidotes are not available. These and other points are the subjects of discussion in this chapter. Some old and new data are critically revised, together with presentation of the authors’ experimental results, the main theme of which is development of new and effective therapy for treating acute intoxication by FA.Item Metadata only Fundamental and applied research on fluoroacetate(2007-10) Goncharov, Nikolay V.; Jenkins, R. O.; Radilov, Andrey S.Item Metadata only High-sensitivity determination of 2-chlorovinylarsonous acid in biomedical samples for retrospective detection of exposure to lewisite upon antidotal therapy.(IOS Press, 2011) Koryagina, N. L.; Ukolova, E. S.; Savelieva, E. I.; Voitenko, Natalia G.; Orlova, O. I.; Jenkins, R. O.; Goncharov, Nikolay V.Item Open Access Inhibition of protein tyrosine phosphatases unmasks vasoconstriction and potentiates calcium signalling in rat aorta smooth muscle cells in response to an agonist of 5-HT2B receptors BW723C86(Elsevier, 2016-12-13) Mironova, G. Y.; Avdonin, P. P.; Goncharov, Nikolay V.; Jenkins, R. O.; Avdonin, P. V.In blood vessels, serotonin 5-HT2B receptors mainly mediate relaxation, although their activation by the selective agonist BW723C86 is known to exert contraction of aorta in deoxycorticosterone acetate (DOCA)-salt and N(omega)-nitro-L-arginine (L-NAME) hypertensive rats [Russel et al., 2002; Banes et al., 2003] and in mice with type 2 diabetes [Nelson et al., 2012]. The unmasking effect on vasoconstriction can be caused by a shift in the balance of tyrosine phosphorylation in smooth muscle cells (SMC) due to oxidative stress induced inhibition of protein tyrosine phosphatases (PTP). We have demonstrated that BW723C86 which does not cause contraction of rat aorta and mesenteric artery rings, evoked a vasoconstrictor effect in the presence of PTP inhibitors sodium orthovanadate (Na3VO4) or BVT948. BW723C86 induced a weak rise of [Ca2+]i in the SMC isolated from rat aorta; however, after pre-incubation with Na3VO4 the response to BW723C86 increased more than 5-fold. This effect was diminished by protein tyrosine kinase (PTK) inhibitor genistein, inhibitor of Src-family kinases PP2, inhibitor of NADPH-oxidase VAS2870 and completely suppressed by N-acetylcysteine and 5-HT2B receptor antagonist RS127445. Using fluorescent probe DCFH-DA we have shown that Na3VO4 induces oxidative stress in SMC. In the presence of Na3VO4 BW723C86 considerably increased formation of reactive oxygen species while alone had no appreciable effect on DCFH oxidation. We suggest that oxidative stress causes inhibition of PTP and unmasking of 5-HT2B receptors functional activity.Item Metadata only Low-angle light scattering technique in clinical pathology and experimental toxicology(2007-10) Mindukshev, I. V.; Krivoshlyk, V. V.; Ermolaeva, E. E.; Jenkins, R. O.; Goncharov, Nikolay V.Item Metadata only Markers and Biomarkers of Endothelium: When Something Is Rotten in the State(Hindawi, 2017-11-23) Goncharov, Nikolay V.; Nadeev, A. D.; Jenkins, R. O.; Avdonin, P. V.Endothelium is a community of endothelial cells (ECs), which line the blood and lymphatic vessels, thus forming an interface between the tissues and the blood or lympha. This strategic position of endothelium infers its indispensable functional role in controlling vasoregulation, haemostasis, and inflammation. The state of endothelium is simultaneously the cause and effect of many diseases, and this is coupled with modifications of endothelial phenotype represented by markers and with biochemical profile of blood represented by biomarkers. In this paper, we briefly review data on the functional role of endothelium, give definitions of endothelial markers and biomarkers, touch on the methodological approaches for revealing biomarkers, present an implicit role of endothelium in some toxicological mechanistic studies, and survey the role of reactive oxygen species (ROS) in modulation of endothelial status.Item Metadata only Microplate biochemical determination of Russian VX: influence of admixtures and avoidance of false negative results.(Elsevier, 2012-02) Jenkins, R. O.; Goncharov, Nikolay V.; Prokofieva, Daria S.Two microplate spectroscopic methods for determination of organophosphates, based on inhibition of acetylcholinesterase (AChE) activity, were further improved and evaluated for determination of the chemical weapon agent Russian VX (RVX) in aqueous solutions. The linear range of the Hestrin method (74.8 – 1120 pM) was 3.1-fold wider than that of the Ellman method (37.4 – 374 pM). Limits of detection and quantification of RVX for both methods were below the maximal allowable concentration of RVX in water-soluble washouts. One of the early product of RVX hydrolysis N,N-diethylaminoethanethiol, like GSH, caused false negative results in the Ellman method at concentrations exceeding 10 µM; individual blanks were necessary to eliminate the effect. The Hestrin method showed greater specificity (about three orders of magnitude) for analysis of samples containing mercaptans. A major product of RVX degradation, 2,2'-dithiobis(N,N-diethylethanamine), caused significant inhibition of AChE at concentrations of ≥0.1 mM (p<0,01) and had a false positive effect at higher concentrations (≥2mM). For environmental monitoring of RVX, the method based on Hestrin is preferred over that of Ellman, principally because the former method was less sensitive to interference from major admixtures and did not give rise to potentially dangerous false negative results.Item Metadata only Microplate spectroscopic methods for determination of the organophosphate soman.(The Royal Society of Chemistry, 2010-12) Prokofieva, Daria S.; Voitenko, Natalia G.; Gustyleva, Lyudmila K.; Babakov, Vladimir N.; Savelieva, E. I.; Jenkins, R. O.; Goncharov, Nikolay V.Two microplate spectroscopic methods for determination of organophosphates, based on inhibition of acetylcholinesterase activity, have been elaborated and evaluated for determination of the chemical weapon agent soman. The principal difference between the methods is that one measures reaction substrate concentration (elaborated from Hestrin), while the other measures reaction product (elaborated from Ellman). The linear ranges of the two methods were found to be similar. Although the limit of quantification was lower for the Ellman method (110 pM), the sensitivity coefficient was in favor of the Hestrin method (1.55-fold higher). The effects of the main soman hydrolysis products were consistent for the two methods: both methylphosphonic acid and pinacolyl methylphosphonic acid did not inhibit acetylcholinesterase activity. The main components of decontaminating solutions showed differential effects: while monoethanolamine had no influence upon results obtained by either method, hydrogen peroxide interfered with the Ellman method at far lower concentrations than with the Hestrin method. In practical applications involving samples containing hydrogen peroxide, the method based on Hestrin should be regarded as much more specific for OP determination than the Ellman method.Item Metadata only Necrotic and apoptotic volume changes of red blood cells investigated by low-angle light scattering technique.(Science Group Publisher, 2007-06-01) Jenkins, R. O.; Ermolaeva, E. E.; Krivoshlyk, V. V.; Mindukshev, I. V.; Dobrylko, Irina A.; Senchenkov, Evgeniy V.; Goncharov, Nikolay V.; Krivchenko. Alexander I.