Innovative Biosystems and Bioengineering http://ibb.kpi.ua/ <p>The international scientific journal Innovative Biosystems and Bioengineering was founded in 2017. IBB introduces a systems approach to life sciences problems.</p> <p>IBB is a quarterly peer-reviewed Open Access e-journal in which readers, immediately upon online publication, can access articles free of costs and subscription charges.</p> <p>e-ISSN 2616-177X</p> <p>Founder: National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute”.</p> <p>Frequency: 4 issues a year.</p> <p>We accept papers in following languages: English, Ukrainian.</p> <p>Cite the title as: Innov Biosyst Bioeng.</p> <p>Readership: Biotechnologists, Biologists, Biophysicists, Bioinformaticists, Biomedical researchers and engineers, Medical, biochemical, and pharmaceutical scientists.</p> <p>Keywords: Applied biology, Biotechnology, Bioengineering, Biophysics, Bioinformatics, Bioorganic chemistry, Biomedicine, Biochemical engineering, Biomaterials, Bioprocess engineering.</p> <p>Indexing: DOAJ; ROAD; HINARI; Chemical Abstracts Service; CNKI Scholar; Norwegian Register for Scientific Journals, Series and Publishers; J-Gate; Public Knowledge Project Index; ICMJE; JournalTOCs; WCOSJ; Vifabio; EZB; Federation of Finnish Learned Societies; Zeitschriftendatenbank; Polska Bibliografia Naukowa; Scilit; Bielefeld Academic Search Engine; OpenAir; WorldCat.</p> Igor Sikorsky Kyiv Polytechnic Institute en-US Innovative Biosystems and Bioengineering 2616-177X <p><span>The ownership of copyright remains with the Authors.</span></p><p>Authors may use their own material in other publications provided that the Journal is acknowledged as the original place of publication and National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute” as the Publisher.</p><p>Authors are reminded that it is their responsibility to comply with copyright laws. It is essential to ensure that no part of the text or illustrations have appeared or are due to appear in other publications, without prior permission from the copyright holder.</p>IBB articles are published under Creative Commons licence:<br /><ol type="a"><li>Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under <a href="https://creativecommons.org/licenses/by/4.0/">CC BY 4.0</a> that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.<br /><br /></li><li>Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.<br /><br /></li><li>Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work.</li></ol> Aspects of Lyophilization of Cardiac Bioimplant http://ibb.kpi.ua/article/view/239725 <p>The use of implants of biological origin in clinical practice has led to the search for methods of long-term storage of tissues without damaging their functional and structural characteristics. Xenografts (extracted from pericardium of pigs, horses, bulls) are drawing more and more interest. The bovine pericardium is exposed to chemical and physical factors providing complete purification of tissue from cells and their components. Such scaffolds are protein (collagen) complexes that fully replicate the microstructure of the pericardial tissue. Lyophilisation ensures long-term preservation of the extracellular matrix properties. The principle of the method is in drying pre-frozen tissue, in which water is sublimated. The method is intended for storage, transportation, and the subsequent use of the bioimplant in clinical practice. However, the lyophilization process may be accompanied by various undesirable factors that can lead to denaturation of the matrix protein or loss of its functionality and structure. To preserve the natural microstructure, stabilizers or various modifications (slow/fast freezing, reducing the degree of supercooling, etc.) of the lyophilization process are applied to biological prostheses. In this review, the main processes of lyophilization of biological tissue are described, which can affect the operation of a cardiac implant. A deep understanding of the parameters of the lyophilization process is crucial for creation of stable tissue grafts and their subsequent long-term storage.</p> Nataliia Shchotkina Copyright (c) 2021 The autror(s) http://creativecommons.org/licenses/by/4.0 2021-12-23 2021-12-23 5 4 200 206 10.20535/ibb.2021.5.4.239725 Human Gut Microbiome as an Indicator of Human Health http://ibb.kpi.ua/article/view/244375 <p>The undeniable achievement in the study of the gut microbiome as an association of different microorganisms, including viruses, that colonize various organs and systems of the body, is the establishment of the fact that some diseases that were consmicrobiotaidered as non-infectious can also be transmitted through microorganisms. This resulted in the gut microbiome being called a forgotten organ that could serve as an additional and kind of missing link for a more objective and better diagnosis and treatment of many diseases that were not considered infectious. The rapid development of gut microbiome research in recent years not only is connected with better understanding of the functioning of the microbiome by the scientific community, but also inseparable from the strategic support of each country. Global investment in researches, related to the human microbiome, has exceeded $1.7 billion over the past decade. These researches contribute to the development of new diagnostic methods and therapeutic interventions. Our review is dedicated to the analysis of the possibilities of application of the human gut microbiome for the diagnosis of diseases, and the role of the intestines in the provocation and causing of certain diseases. Significant differences in the composition and diversity of the human microbiome are shown depending on geographical location and the change of socio-economic formations towards a gradual decrease in the diversity of the gut microbiome due to three stages of human population’s existence: food production, agriculture and industrial urban life. We analyze the influence of dietary patterns, various diseases (including malignant neoplasms) and viral infections (in particular, coronavirus) on the gut microbiome. And vice versa – the influence of the gut microbiome on the drugs effect and their metabolism, which affects the host's immune response and course of the disease.</p> Anasnasiia Ivanova Olena Yalovenko Alexey Dugan Copyright (c) 2021 The Author(s) http://creativecommons.org/licenses/by/4.0 2021-12-23 2021-12-23 5 4 207 219 10.20535/ibb.2021.5.4.244375 Antimicrobial Activity of Fomitopsis Officinalis (Vill.) Bondartsev & Singer in Pure Culture http://ibb.kpi.ua/article/view/246668 <p><strong>Background. </strong>According to the World Health Organization antibiotic resistance is among the top ten threats to human health, food safety and development. Today antibiotic resistance has reached alarmingly high levels all over the world. Meanwhile, the increase in the synthetic drugs' production has led to the pathogenic mycobiota's rapid adaptation to the created chemicals, which have a narrow focus of application. That is why in modern biotechnology and pharmacology much attention is paid to natural producers of biologically active compounds, in particular – to xylotrophic fungi. It has been experimentally proven that the xylotrophic macromycete <em>Fomitopsis officinalis</em> or tinder fungus can be considered to be a promising producer of pharmacological substances with a broad spectrum of action. Studies of active metabolites, contained in the mycelial mass, culture fluid of the medicinal xylotrophic macromycete <em>F.</em><em> </em><em>officinalis,</em> and determination of their biological action remain relevant.</p> <p><strong>Objective. </strong>The objective was to determine the antimicrobial activity of culture fluid and mycelial mass of <em>F.</em><em> </em><em>officinalis</em> different strains from the mushrooms collection (<em>IBK</em> Mushroom Culture Collection of the M.G. Kholodny Institute of Botany, NAS of Ukraine) against gram-negative and gram-positive bacteria species.</p> <p><strong>Methods.</strong> An <em>in vitro</em> study of the antimicrobial activity of ethyl acetate extracts of culture fluid and aqueous-ethyl extracts of mycelial mass for <em>F.</em><em> </em><em>officinalis </em>strains <em>IBK</em>-5004, <em>IBK</em>-2497, <em>IBK</em>-2498 against gram-positive <em>Staphylococcus aureus</em> (B-918), <em>Bacillus subtilis </em>(В-901) and gram-negative <em>Escherichia coli</em> (B-906), <em>Bacillus subtilis </em>(B-900), <em>Klebsiella pneumoniae </em>(M-123) bacteria by disc-diffusion method was conducted.</p> <p><strong>Results. </strong>High antimicrobial activity of tinder fungus culture fluid and mycelial mass extracts against <em>Staphylococcus aureus</em> was established after the 21<sup>st</sup> day of cultivation, while on the 28<sup>th </sup>day the zone of growth retardation was maximal (15–25 mm). The highest indices were recorded in <em>F.</em><em> </em><em>officinalis</em> <em>IBK-</em>5004 (20–25 mm) and <em>IBK</em>-2498 (20–24 mm) strains. Antimicrobial activity against <em>Klebsiella pneumoniae</em> in culture fluid extracts was manifested on the 21<sup>st</sup> and 28<sup>th</sup> days of cultivation. The highest antimicrobial activity against <em>Klebsiella pneumoniae</em> was observed in the culture fluid of the strain <em>F.</em><em> </em><em>officinalis IBK</em>-5004, the diameter of the growth retardation zone was 18 mm on the 28<sup>th</sup> day of cultivation. Mycelial mass's extracts showed moderate activity on the 14<sup>th</sup> day of cultivation (7-8 mm); maximal activity was recorded on the 28<sup>th</sup> day (12–22 mm). The most active strain was <em>Fomitopsis officinalis IBK</em>-2498. No antimicrobial activity against test organisms was detected in the following studied strains: <em>Escherichia coli, Pseudomonas aeruginosa</em>,<em> Bacillus subtilis.</em></p> <p><strong>Conclusions. </strong>It has been established that the mycelial mass and culture fluid extracts of <em>F.</em><em> officinalis IBK</em>-5004, <em>IBK</em>-2497, <em>IBK</em>-2498 strains have high antimicrobial activity against <em>Staphylococcus aureus</em> and moderate antimicrobial activity against <em>Klebsiella pneumoniae</em> on the 21<sup>st </sup>and 28<sup>th</sup> day of cultivation.</p> Oksana Mykchaylova Nataliia Poyedіnok Copyright (c) 2021 The autror(s) http://creativecommons.org/licenses/by/4.0 2021-12-27 2021-12-27 5 4 220 227 10.20535/ibb.2021.5.4.246668 Biological Evaluation of Medical Devices in the Form of Suppositories for Rectal and Vaginal Use http://ibb.kpi.ua/article/view/249082 <p><strong>Background.</strong> Programs of preclinical safety studies of the health care products depend on the regulatory status of the investigated products. The classification of such products, in particular suppositories for rectal and vaginal use, is a critical step of developing tactics for their biological evaluation. Adaptation of biological evaluation methods for the medical devices based on the combination of biologically active substances, as well as evaluation of the results of such studies is urgent task of biomedicine.</p> <p><strong>Objective. </strong>To substantiate the regulatory status and to carry out a biological evaluation of medical devices in the form of vaginal suppositories based on octenidine dihydrochloride ("Prodexyn") and in the form of rectal suppositories based on <em>Saw palmetto</em>, <em>Levisticum officinale</em> and <em>Calendula officinalis</em> extracts ("Pravenor").</p> <p><strong>Methods. </strong>Biological evaluation was conducted according to the requirements of ISO 10993 standards using <em>in vitro</em> and <em>in vivo</em> biological test systems (cytotoxicity in cell culture and the MTT test, sensitizing and irritating effect in guinea pigs).</p> <p><strong>Results. </strong>The cytotoxicity (СС<sub>50</sub>) of the medical device "Prodexyn" extract in Vero cell culture was 8.35 μg/ml calculated as octenidine dihydrochloride and 416.65 μg/ml calculated as dexpanthenol. "Pravenor" medical device was found to be non-toxic in Vero cell culture. According to the results of MMT assay CC<sub>50 </sub>for octenidine dihydrochloride was 1.67 μg/ml, and 83.33 μg/ml – for dexpanthenol. CC<sub>50</sub> indicators calculated for the different active ingredients of the medical device "Pravenor" were the following: 50 mg/ml for the dwarf palm berries extract (<em>Saw palmetto</em>), 16.67 mg/ml for the lovage roots extract (<em>Levisticum officinale</em>), and 16.67 mg/ml for the calendula flowers extract (<em>Calendula officinalis</em>). No sensitizing or skin irritating effects were observed in guinea pigs.</p> <p><strong>Conclusions.</strong> Biological evaluation of medical devices in the form of rectal suppositories "Pravenor" and vaginal suppositories "Prodexyn" performed using <em>in vitro</em> and <em>in vivo</em> biological systems. It was demonstrated an acceptable level of safety of the products. The MTT test was 5 times more sensitive than the Vero cell culture method in determination of cytotoxicity.</p> Oleksandra Dmytrenko Maryna Arkhypova Darya Starosyla Svitlana Rybalko Michael Gevorkyan Alexander Galkin Copyright (c) 2021 The autror(s) http://creativecommons.org/licenses/by/4.0 2021-12-26 2021-12-26 5 4 228 237 10.20535/ibb.2021.5.4.249082 QSAR Analysis of the Effect of Metal Ions on the Peptidase Bacillus thuringiensis var. israelensis IMV B-7465 Activity http://ibb.kpi.ua/article/view/243373 <p><strong>Background. </strong>The catalytic activity of enzymes, which is their most important characteristic, can change significantly under the influence of effectors, for example, metal ions, and is the subject of special studies that are important for biochemistry, biotechnology, medicine, and other branches of science. Usually, the activity of enzymes in the presence of metals is assessed by the change in the rate of the enzymatic reaction. However, conducting such experimental studies, especially for new enzymes, as in the case of peptidase <em>Bacillus thuringiensis </em>var. <em>israelensis</em> IMV B-7465, requires significant resources and extensive kinetic studies. Therefore, it is advisable to use the methods of computational chemistry, the basic task of which is to search for the structure–property relationship, to build a model that can assess the effect of metal ions on peptidase activity with a high degree of probability.</p> <p><strong>Objective. </strong>We are aimed to develop QSAR models for analysis and prediction of the effect of metal ions on the activity of peptidase <em>Bacillus thuringiensis </em>var. <em>israelensis </em>IMV B-7465.</p> <p><strong>Methods.</strong> The effect of metal ions was studied by determining the proteolytic activity of peptidase after co-incubation for 30 min in 0.0167 M Tris-HCl buffer solution (pH 7.5, 37 °C). The final concentration of metal chlorides Li<sup>+</sup>; Na<sup>+</sup>; K<sup>+</sup>; Cs<sup>+</sup>; Cu<sup>2+</sup>; Be<sup>2+</sup>; Mg<sup>2+</sup>; Ca<sup>2+</sup>; Sr<sup>2+</sup>; Ba<sup>2+</sup>; Zn<sup>2+</sup>; Cd<sup>2+</sup>; Hg<sup>2+</sup>; Cr<sup>3+</sup>; Mn<sup>2+</sup>; Co<sup>2+</sup>; Ni<sup>2+</sup> in the buffer solution was 4 mmol/dm<sup>3</sup>. To search for the quantitative structure–property relationship, we used the reference data on the properties of metal ions, as well as trend vector and random forest methods.</p> <p><strong>Results.</strong> A study of the effect of metal ions on the proteolytic activity of peptidase <em>Bacillus thuringiensis </em>var. <em>israelensis</em> IMV B-7465 showed that some metal ions (Li<sup>+</sup>, Mn<sup>2+</sup> и Co<sup>2+</sup>) activated peptidase, while others (Cu<sup>2+</sup>, Be<sup>2+</sup>, Cd<sup>2+</sup>, Hg<sup>2+</sup>, Cr<sup>3</sup>) inhibited the enzyme activity. Adequate statistical models without classification errors and activity class prediction errors for the test set were constructed by nonlinear trend vector and random forest methods. Both models show that the most important characteristics of metal ions affecting enzyme activity are electronegativity (<em>EN</em><sub>Pol</sub>), the first ionization potential (<em>IP</em><sub>1</sub>), the entropy of ions in aqueous solution (<em>S</em>), and the electron affinity energy (<em>E</em><sub>ae</sub>).</p> <p><strong>Conclusions.</strong> QSAR analysis methods in combination with nonlinear trend vector and random forest methods allow adequately describing the effect of metal ions on the peptidase <em>Bacillus thuringiensis </em>var. <em>israelensis </em>IMV B-7465 activity due to descriptors reflecting a certain balance of their electron-donating and electron-accepting properties (electronegativity, the first ionization potential, the electron affinity energy) and thermodynamic properties in aqueous solution (entropy of solvation). Both statistical methods give similar values of the importance of descriptors, but only the trend vector method allows us to analyze the direction of influence of specific characteristics of ions.</p> Anatoly Artemenko Svetlana Dekina Irina Romanovska Victor Kuz'min Copyright (c) 2021 The Author(s) http://creativecommons.org/licenses/by/4.0 2021-12-29 2021-12-29 5 4 238 246 10.20535/ibb.2021.5.4.243373