Biomedical Chemistry: Research and Methods

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EISSN : 2618-7531
Published by: Institute of Biochemistry (10.18097)
Total articles ≅ 96
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A.O. Tokareva, V.V. Chagovets, A.S. Kononikhin, N.L. Starodubtseva, V.E. Frankevich, E.N. Nikolaev
Biomedical Chemistry: Research and Methods, Volume 4; https://doi.org/10.18097/bmcrm00156

Abstract:
A pathology diagnostic using molecular marker is a perspective direction of clinical medicine. Mass-spectrometry (MS) is a one of methods, which are used for obtaining information about molecular profiles. Selection of species, essential for classification “case/control is an important task for data processing. Pipeline of data processing has been proposed using MS data, obtained during analysis of tumor breast tissue samples and health breast tissue samples, with the aim of metastasis marker selection. As a result, selection of lipid markers that belong to classes, related to metastasis and proliferation processes, makes it possible to create high sensitivity diagnostic model, based on logistic regression. The proposed method is applicable for data processing, obtained by MS analysis of other “omics”: metabolome, proteome, glycome.
K.A. Shcherbakov, D.S. Shcherbinin, A.V. Veselovsky
Biomedical Chemistry: Research and Methods, Volume 4; https://doi.org/10.18097/bmcrm00145

Abstract:
Prostate cancer is hormone-dependent and the androgen receptor (AR) is involved in its development. AR is a transcription factor that is activated by ligand binding, result in its translocation into the nucleus, where it initiates gene transcription. In an inactive state in cytoplasm AR exists as a complex with heat shock protein 90 (HSP90) and some other proteins. When the agonist binds, a conformational change in AR occurs, resulting in HSP90 and other chaperones dissociating. Recently it has been shown that for the dissociation of the HSP90-AR complex and the translocation of the latter into the nucleus, phosphorylation of the Thr-90 residue of the N-terminal domain of HSP90 is necessary. In this work, the effect of the HSP90 inhibitor, geldanamycin, interacting with the ATP-binding site, on the Thr90 phosphorylation site was investigated by molecular modeling methods. It has been shown that inhibitor binding slightly affects the size and mobility of cavity around Thr90. It is suggested that inhibitor binding to HSP90 does not result in changing the protein structure and does not influence on protein phosphorylation, and partially explains low effectiveness of such type of drugs in the therapy of prostate cancer.
V.I. Fedchenko, A.A. Kaloshin, S.A. Kaloshina, A.E. Medvedev
Biomedical Chemistry: Research and Methods, Volume 4; https://doi.org/10.18097/bmcrm00158

Abstract:
Renalase (RNLS) is a flavoproteinin which its N-terminal peptide (residues 1-17) has several important functions. In cells, it participates in the formation of the so-called Rossmanfold (residues 2-35), needed for «accommodation» of the FAD cofactor and for performing the catalytic functions of RNLS as a FAD-dependent oxidoreductase (EC 1.6.3.5). RNLS secretion into the extracellular space is accompanied by cleavage of this peptide. The resultant truncated extracellular RNLS cannot bind FAD and therefore performs various noncatalytic functions. In this work, we have performed expression the genetic construct encoding RNLS lacking its N-terminal signal peptide (tRNLS) in E. coli Rosetta (DE3) cells. The recombinant protein was accumulated in inclusion bodies in an insoluble form, which could be solubilized in the presence of a high concentration of urea or guanidine chloride. In contrast to full-length RNLS, which was effectively solubilized in the presence of 8 M urea, tRNLS was preferentially solubilized in the presence of 6 M guanidine chloride.
N.S. Yudina, Ya.N. Barashkova, O.V. Vladimirova, V.A. Myasnikov
Biomedical Chemistry: Research and Methods, Volume 4; https://doi.org/10.18097/bmcrm00152

Abstract:
A comparative evaluation of methods for preparing blood serum samples for determination of the lectin content of the mistletoe Viscum Album, viscumin, by high-performance liquid chromatography in combination with high-resolution mass-spectrometry detection has been carried out. Based on the results of the analysis of the lectin hydrolyzate, a specific peptide fragment with m/z 791.388 suitable for subsequent quantitative determination was selected. Isolation of viscumin from serum components was carried out without the use of specific antibodies. The study used methods employing various spin columns and the method of protein precipitation with 1% TCA (trichloroacetic acid) in IPA (isopropyl alcohol). Testing the methods of depletion of blood serum proteins was based on the determination of the degree of extraction of lectin from model serum samples. As a result of our research, we have developed a technique for the quantitative analysis of viscumin in blood serum by the most efficient method of sample preparation using the ProteoMiner spin columns. The technique allows to determine the protein concentration up to 5·10-4 mg/ml with the extraction degree (2.7 ± 0.6) %.
A.A. Yakovlev, V.D. Antonov, T.A. Druzhkova, A.B. Guekht, N.V. Gulyaeva
Biomedical Chemistry: Research and Methods, Volume 4; https://doi.org/10.18097/bmcrm00148

Abstract:
Exosomes and microvesicles, collectively referred to as small extracellular vesicles (sEV) are vesicles with an average size of about 100-150 nm. Currently, the role of sEV in various aspects of signaling in the body is being actively investigated; in addition, sEV can often serve as markers of various pathologies. The active study of the sEV composition is continuing. In this study we have demonstrated that in sEV it is possible to determine cholesterol and triglycerides concentration by using commercial kits designed for serum. The technique was tested on sEV from the blood of patients diagnosed with depression and on healthy volunteers. No differences were found in the concentration of cholesterol and triglycerides in mEV from the blood serum of depressed patients and the control group. The concentration of cholesterol and triglycerides in the samples is several times higher than the sensitivity threshold of the methods set by the manufacturer of the kits.
E.A. Sorokina, E.S. Zhgun, Yu.V. Kislun, E.A. Denisova, Yu.A. Bespyatykh, E.N. Ilina
Biomedical Chemistry: Research and Methods, Volume 4; https://doi.org/10.18097/bmcrm00151

Abstract:
Fecal microbiota transplantation (FMT) is now considered as an effective tool for the treatment of various GI pathologies. Fecal preparations are delivered both through the lower GIT (enema, colonoscopy) and upper (endoscopy, capsules). A common disadvantage of instrumental methods of administration is their high invasiveness associated with the risk of intestinal perforation and the use of anesthesia. Oral capsules are minimally invasive, comfortable and more aesthetic, so this method of drug delivery is gaining popularity. The main issue with the use of frozen feces (including the lyophilisate used in capsules) is its efficiency compared to the original material. During lyophilization, cells are exposed to stress factors such as low temperatures, water crystallization, osmotic stress, changes in pH, and dehydration. To reduce the likelihood of cell damage during lyophilization, protective media (lyo-protectants) are used. In this work sucrose, gelatin, and their combinations have been used as lyoprotectors. To estimate the number of microorganisms, a bacteriological study was carried out. The number of Bifidobacteria, Lactobacilli, and the total number of E.coli and Enterobacteriaceae was estimated. It was found that the lyophilized stool sample containing 10% sucrose as a protective medium had the highest number of viable cells. Also, the physical properties of the lyophilisate (its flowability) are convenient for preparing capsulated form. The molar ratios of short chain fatty acids (SCFAs) in the original fecal samples and lyophilisates were studied by gas chromatography. The molar ratios of major SCFAs (acetate, propionate and butyrate) were identical in the samples studied. The composition of the protective medium in which the lyophilized biomaterial corresponds to the original feces in terms of the number of "live" microorganisms has been proposed. According to its physical characteristics lyophilisate is convenient for capsules preparation.
D.A. Olisov, V.V Chagovets, N.L. Starodubtseva, A.A. Smetnik, V.V. Rodionov, V.V. Kometova, K.S. Chingin, V.E. Frankevich
Biomedical Chemistry: Research and Methods, Volume 4; https://doi.org/10.18097/bmcrm00147

Abstract:
Although estrogen contribution estrogen to breast cancer development is not fully understood, an effective method of their measurement, in the mammary gland might provide additional insight. In this study, we have developed a LC-MS/MS method of simultaneous quantification of estrone and estradiol in breast tissue samples. Analytes were extracted with methyl tert-butyl ether by sonication and derivatized with dansyl chloride. Estrogens were analyzed by liquid chromatography-tandem mass spectrometry with an electrospray ionization source. Accuracy and precision were better than 20% for most concentrations. Although estrone and estradiol levels in normal and malignant breast tissue samples analyzed using our method insignificantly differed. The method developed may be used in further studies aimed at evaluating a role estrogens in breast cancer risk.
A. Tamadon, M.B. Askarov, U. Zhanbyrbekuly, R.A. Zhankina, D.T. Saipiyeva, A.K. Ibragimov, B.E. Kadirova, A. Yessenuly, R.S. Sherkhanov, M.A. Suleiman
Biomedical Chemistry: Research and Methods, Volume 4; https://doi.org/10.18097/bmcrm00141

Abstract:
Stem cells are considered as new much promising therapeutic agents in treatment of male infertility due to their high differentiation potential and unlimited supply. In this review we summarized current views on application of mesenchymal stem cells in reproductive medicine.
E.N. Ilina, E.M. Mayorova, A.I. Manolov, A.A. Korenkova, V.V. Bahmetjev, K.S. Gorbunov
Biomedical Chemistry: Research and Methods, Volume 4; https://doi.org/10.18097/bmcrm00146

Abstract:
The human physiology textbooks traditionally consider the intestine as a metabolically active organ, with its activity primarily associated with the production of numerous digestive enzymes. The development of molecular analysis technologies has significantly detailized this picture, primarily by decoding the metabolic potential of the intestinal microbiota. Data from numerous metagenomic studies indicate that the number of eukaryotic and bacterial cells in the human body is comparable - about 3.0×1013, while the number of genes in the intestinal metagenome is one hundred times greater than in the human genome. Obviously, the gut microbiota exhibits both direct and indirect effects on the metabolism of drugs and xenobiotics, that can affect their effectiveness and toxicity. Orally administrated xenobiotics have been found to be metabolized by intestinal microbial enzymes before being absorbed from the gastrointestinal tract into the blood flow. The metabolic reactions performed by the gut microbiota greatly differ from the metabolic reactions of the liver, providing modification of drugs by acetylation, deacetylation, decarboxylation, dehydroxylation, demethylation, dehalogenation, etc. Despite the metabolism of xenobiotics by microbial enzymes of the intestine is rather known, information about the specific microflora mediating each metabolic reaction is still limited, mainly by the lack of an adequate model of the intestinal microbial community to allow the accumulation of experimental data for the creation of computational models. Currently, studies of drug metabolism use microfluidic chips, reproducing functions of various organs and tissues, such as the liver, kidney, lungs and intestine, as in vitro models in the form of 2D and 3D cell cultures. Supplementation of such systems with the microbial community will allow to get as close as possible to in vitro modeling of complicated biological processes in the interests of pharmacological research and the accumulation of data for constructing computational models.
K.A. Deinichenko, G.S. Krasnov, S.P. Radko, K.G. Ptitsyn, V.V. Shapovalova, O.S. Timoshenko, S.A. Khmeleva, L.K. Kurbatov, Y.Y. Kiseleva, E.V. Ilgisonis, et al.
Biomedical Chemistry: Research and Methods, Volume 4; https://doi.org/10.18097/bmcrm00144

Abstract:
Missing (MP) and functionally uncharacterized proteins (uPE1) comprise less than 5% of the total number of proteins encoded by human Chr18 genes. Within half a year, since the January 2020 version of NextProt, the number of entries in the MP+uPE1 datasets changed, mainly due to the achievements of antibody-based proteomics. Assuming that the proteome is closely related to the transcriptome scaffold, quantitative PCR, Illumina HiSeq, and Oxford Nanopore Technology were applied to characterize the liver samples of three male donors in comparison with the HepG2 cell line. The data mining of the Expression Atlas (EMBL-EBI) and the profiling of biopsy samples by using orthogonal methods of transcriptome analysis have shown that in HepG2 cells and the liver, the genes encoding functionally uncharacterized proteins (uPE1) are expressed as low as for the missing proteins (less than 1 copy per cell), except the selected cases of HSBP1L1, TMEM241, C18orf21, and KLHL14. The initial expectation that uPE1 genes might be expressed at higher levels than MP genes, was compromised by severe discrepancies in our semi-quantitative gene expression data and in public databanks. Such discrepancy forced us to revisit the transcriptome of Chr18, the target of the Russian C-HPP Consortium. Tanglegram of highly expressed genes and further correlation analysis have shown the severe dependencies on the mRNA extraction method and the analytical platform. Targeted gene expression analysis by quantitative PCR (qPCR) and high-throughput transcriptome profiling (Illumina HiSeq and ONT MinION) for the same set of samples from normal liver tissue and HepG2 cells revealed the detectable expression of 250+ (92%) protein-coding genes of Chr18 (at least one method). The expression of slightly more than 50% protein-coding genes was detected simultaneously by all three methods. Correlation analysis of the gene expression profiles showed that the grouping of the datasets depended almost equally on both the type of biological material and the experimental method, particularly cDNA/mRNA isolation and library preparation.
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