Biomedical Chemistry: Research and Methods最新文献

{"title":"Optimization of Conditions for Human Bacterial Preparation for Biological Correction of Intestinal Microflora","authors":"E. Sorokina, E. S. Zhgun, Y. Kislun, E. A. Denisova, Yu. A. Bespyatykh, E. Ilina","doi":"10.18097/bmcrm00151","DOIUrl":"https://doi.org/10.18097/bmcrm00151","url":null,"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.","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132082551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Determination of Cholesterol and Triglyceride Concentrations in Serum Extracellular Vesicles Using Commercial Kits","authors":"A. A. Yakovlev, V. D. Antonov, T. Druzhkova, A. Guekht, N. Gulyaeva","doi":"10.18097/bmcrm00148","DOIUrl":"https://doi.org/10.18097/bmcrm00148","url":null,"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.","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"76 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131401917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Measurement of Breast Tissue Estrogens by Liquid Chromatography-tandem Mass Spectrometry","authors":"D. A. Olisov, V. Chagovets, N. Starodubtseva, A. Smetnik, V. V. Rodionov, V. Kometova, K. Chingin, V. Frankevich","doi":"10.18097/bmcrm00147","DOIUrl":"https://doi.org/10.18097/bmcrm00147","url":null,"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.","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124047672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteoliposomes as a Method of Membrane Protein Immobilization for SPR-analysis with the Human CYP3A4 and CYB5A Interaction as an Example","authors":"L. Kaluzhskiy, E. Yablokov, M. Kisel, A. M. Tumilovich, S. Usanov, T. Shkel, O. Gnedenko, A. Ivanov","doi":"10.18097/bmcrm00160","DOIUrl":"https://doi.org/10.18097/bmcrm00160","url":null,"abstract":"Microsomal systems of human cytochrome P450 consist of three components, which are membrane proteins: cytochrome P450 hemoprotein (CYP), NADPH-dependent cytochrome P450 reductase (CPR), and a small regulatory heme-containing protein cytochrome b5 (CYB5A). In the study of the cytochrome P450 system functioning the study of intermolecular interactions both with partner proteins and with possible drug prototypes is of great importance. Surface plasmon resonance (SPR) is a powerful and reliable tool for studying intermolecular interactions. However, there is a problem of immobilization of membrane proteins on the optical chip of the SPR biosensor. It is important to immobilize such proteins in native conditions with respect to the correct orientation of the protein globule to the surface of sensor. Previously, we have developed and described a method involving direct native immobilization of membrane proteins into a planar bilayer lipid membrane on the surface of a biosensor chip. At the same time, one of the commonly used approaches to working with membrane proteins using various methods is the construction of proteoliposomes containing membrane proteins. In this work, using CYP3A4 and CYB5A as protein partners, we evaluated two approaches to the creation of proteoliposomes: incorporation of a membrane protein into liposomes saturated with detergents and incorporation of a membrane protein into the forming proteoliposomes by the mechanism of micellar coalescence. The interaction of CYP3A4 with proteoliposomes obtained by incorporating CYB5A into detergent-saturated liposomes was shown. On the contrary, interaction between CYP3A4 and proteoliposomes containing CYB5A, obtained by the method of micellar coalescence, was not detected. Thus, it was shown that the incorporation of the membrane protein into liposomes saturated with a detergent was a more preferable method for working with an SPR biosensor as compared to the method of proteoliposomes formation by micellar coalescence. Detailed protocols for the creation of proteoliposomes and SPR-analysis can be useful to a wide range of researchers.","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123994582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a Method for the Extraction of the Total Proteome of Bacillus anthracis Spores","authors":"E. Koteneva, O. Tsygankova, A. Kalinin, V. Shcherbakova, I. S. Rodionov, V. Serdyukov, A. V. Abramovich","doi":"10.18097/bmcrm00154","DOIUrl":"https://doi.org/10.18097/bmcrm00154","url":null,"abstract":"We have developed a method for obtaining the total proteome of Bacillus anthracis spores, which combines efficient protein extraction with reliable disinfection of samples. We used 7 strains of B. anthracis: 4 plasmid-free, 3 diplasmid, one of which with an atypical type of capsule formation in air. The schemes for isolating the total spore proteome were tested using various lysis solutions in the presence of bacterial protease inhibitors, with the inclusion of the stages of treatment of spores with trichloroacetic acid and mechanical disintegration and with their exclusion. The quality and completeness of the extraction of the total proteome of the spores of the samples was assessed in one-dimensional (1D) and twodimensional (2D) electrophoresis. Treatment of spores with trichloroacetic acid increased the reliability of material disinfection and reduces the loss of the final product. Mechanical disintegration after treatment of spores with lysing solutions increases the completeness of extraction of spore proteins in a wide range of molecular weights and facilitated the process of sterilizing filtration. Final filtration of the lysate through a PVDF filter with a pore size of 0.22 μm provided additional decontamination of samples without reducing their quality. Thus, the use of the proposed sample preparation scheme makes it possible to obtain complete protein extracts of spores of B. anthracis strains, suitable for comparative analysis of the proteome and search for a possible correlation with the features phenotypic properties and mechanisms that ensure the preservation of the pathogen anthrax in environmental objects, including soil","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129535632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Prediction of the Isoelectric Point Value of Peptides and Proteins with a Wide Range of Chemical Modifications","authors":"Vladlen S. Skvortsov, A. Voronina, Y. Ivanova, A. Rybina","doi":"10.18097/bmcrm00161","DOIUrl":"https://doi.org/10.18097/bmcrm00161","url":null,"abstract":"The scale of virtual pKa values for calculating the isoelectric point of peptides and proteins with chemical and post-translational modifications (PTM) is presented. The learning set of pKa values is based on data from 25 experiments of isoelectric focusing of peptides with subsequent mass spectrometric identification (ProteomeXchange accession codes: PXD000065, PXD005410, PXD006291, PXD010006 and PXD017201). In order to enrich the resulting sets with peptides containing modifications the identification of peptides was repeated using raw mass spectrometry data of all datasets. In the final learning set have included peptides satisfying the following conditions: the peptide was found in the fraction with scoring function maximum and maximum peptide abundance; the peptide was found in more than one experiment, and differences of the pI value between experiments was less than 0.15 pH unit. Two variants of the scales were created. In the first variant, pKa values depended only on the residue position relative to the ends of the sequence (N- or C-terminal residue or inside the chain). In the second variant, the effect of neighboring residues was also taken into account. The prediction accuracy of the second variant was higher. The comparison with other methods of pI prediction was carried out. Although the scale was calculated from set containing only peptides, it would be applicable for pI prediction of proteins with and without PTM. The software for prediction of pI values using the resulting pKa scales is available at http://pIPredict3.ibmc.msk.ru.","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"53 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132965089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Processing Oxford Nanopore Long Reads Using Amazon Web Services","authors":"V. Shapovalova, S. Radko, K. Ptitsyn, G. Krasnov, K. V. Nakhod, O. S. Konash, M. Vinogradina, E. Ponomarenko, D. Druzhilovskiy, A. Lisitsa","doi":"10.18097/bmcrm00131","DOIUrl":"https://doi.org/10.18097/bmcrm00131","url":null,"abstract":"Studies of genomes and transcriptomes are performed using sequencers that read the sequence of nucleotide residues of genomic DNA, RNA, or complementary DNA (cDNA). The analysis consists of an experimental part (obtaining primary data) and bioinformatic processing of primary data. The bioinformatics part is performed with different sets of input parameters. The selection of the optimal values of the parameters, as a rule, requires significant computing power. The article describes a protocol for processing transcriptome data by virtual computers provided by the cloud platform Amazon Web Services (AWS) using the example of the recently emerging technology of long DNA and RNA sequences (Oxford Nanopore Technology). As a result, a virtual machine and instructions for its use have been developed, thus allowing a wide range of molecular biologists to independently process the results obtained using the \"Oxford nanopore\".","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"106 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128148282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Construction of a chimeric human gene encoding renalase with a modified N-terminus","authors":"V. Fedchenko, A. Kaloshin, N. I. Kozlova, A. Kopylov, A. E. Medvedev","doi":"10.18097/bmcrm00137","DOIUrl":"https://doi.org/10.18097/bmcrm00137","url":null,"abstract":"Renalase (RNLS) is a recently discovered protein that plays different roles inside and outside cells. Extracellular RNLS exhibits protective effects on the cell, acting on its receptor proteins, while intracellular RNLS acts as FAD-dependent oxidoreductase (EC 1.6.3.5). The ratio of the intracellular and extracellular forms of this protein, as well as the mechanisms and factors responsible for its transport from the cell, remain unknown. One of the approaches to studying these issues can be the creation of chimeric forms of this protein with modified fragments of its amino acid sequences. This work describes a method for constructing a chimeric human RNLS gene encoding RNLS without its N-terminal peptid","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129190309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antituberculosis, antimicrobic and antioxidant properties of Persica vulgaris L. extracts","authors":"I. Mamatova, I. Askarov, M. Mamarakhmonov","doi":"10.18097/bmcrm00125","DOIUrl":"https://doi.org/10.18097/bmcrm00125","url":null,"abstract":"Peach is a medicinal plant which has many traditional applications uses against various diseases. In this study we have evaluated differences in tannins and flavonoids in the composition of flowers and peach leaves and their antioxidant properties. Antibacterial activity of the peach flower and leaf extract was investigated using Mycobacterium tuberculosis and E. coli by the disk diffusion method. Total fractions of flavonoids and tannins were obtained using ethanol and aqueous extraction, respectively. The antioxidant activity was evaluated using the adrenaline autooxidation test. The results have shown that the peach flower extract contains many flavonoids, tannins that probably account for better antimicrobial effects as compared with the peach leaf extract. This shows perspectives for the use of peach flowers for the treatment of many diseases, especially for tuberculosis, and other diseases associated with overproduction of free radicals.","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128942377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Prediction of the Ion Fraction of the Peptide with Selected Charge in Mass Spectrometry with Positive Electrospray Ionization","authors":"Vladlen S. Skvortsov, N. Alekseychuk, Yu. V. Miroshnichenko, A. Rybina","doi":"10.18097/bmcrm00100","DOIUrl":"https://doi.org/10.18097/bmcrm00100","url":null,"abstract":"The possibility of prediction of selected ion fraction in the total peptide fraction obtained during mass spectrometry with positive ionization\u0000by electrospray was investigated on the basis of the amino acid sequence. The data obtained in the MS / MS experiment [Ramus et al., 2015] using\u0000the standardized UPS1 kit (48 highly purified human proteins) and deposited in ProteomeXchange (identifier PXD001819) were used as the initial\u0000data set. For each of the identified peptides belonging to one of the proteins of the UPS kit, a list of detected ions of different charge was formed.\u0000The sum of the peak intensities detected for the primary ion was used as a measure of quantity. Since the ratio of the peptide fractions of ions with\u0000different charges does not depend on the concentration in the experimental sample, the total sample was assembled by combining the data obtained\u0000for different dilutions of UPS1. A set of equations of prediction of the fraction of 1+, 2+, and 3+ ions has been constructed. This computational\u0000analysis has shown applicability of the proposed for prediction of the ion fraction of the peptide with selected charge in mass spectrometry with\u0000positive electrospray ionization.","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121757504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}