005. Факультет природничих наук

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The 2nd Scientific workshop for students "Computational Physics of DNA"
(2024) Perepelytsya, Sergiy; Tetiana, Bubon
The article is devoted to the 2nd Scientific workshop for students “Computational physics of DNA”.
4-(N-Boc-амино)-1Н-1,2,3-триазолкарботиоамиды в синтезе производных новой гетероциклической системы [1,2,3]триазоло[4,5-e][1,4]тиазепина
(2021) Сирота, Наталия; Кемский, Сергей; Больбут, Андрей; Чернобаев, Игорь; Лявинец, Александр; Вовк, Михаил
4-(N-Boc-амино)-1Н-1,2,3-триазолкарботиоамиды, полученные последовательной обработкой 4-(N-Boc-амино)-1Н-1,2,3-три- азолов n-BuLi и алкилизотиоцианатами при –78÷–60°C, при действии этилбромацетата образуют соответствующие 4-(N-Boc- амино)-5-тиоимидаты, которые в насыщенном НCl диоксане подвергаются внутримолекулярной циклоконденсации в 8-(алкил- имино)-4,8-дигидро-1Н-[1,2,3]триазоло[4,5-e][1,4]тиазепин-5(6Н)-оны.
6-gene promoter methylation assay is potentially applicable for prostate cancer clinical staging based on urine collection following prostatic massage
(2019) Nekrasov, Kostyantyn; Vikarchuk, Mark; Rudenko, Evgeniya; Ivanitskiy, Igor; Grygorenko, Viacheslav; Danylets, Rostyslav; Kondratov, A.; Stoliar, Liubov; Sharopov, Bizhan; Kashuba, Volodymyr
The detection of prostate cancer (PCa) biomarkers in bodily fluids, a process known as liquid biopsy, is a promising approach and particularly beneficial when performed in urine samples due to their maximal non‑invasiveness requirement of collection. A number of gene panels proposed for this purpose have allowed discrimination between disease‑free prostate and PCa; however, they bear no significant prognostic value. With the purpose to develop a gene panel for PCa diagnosis and prognosis, the methylation status of 17 cancer‑associated genes were analyzed in urine cell‑free DNA obtained from 31 patients with PCa and 33 control individuals using methylation‑specific polymerase chain reaction (MSP). Among these, 13 genes indicated the increase in methylation frequency in patients with PCa compared with controls. No prior association has been reported between adenomatosis polyposis coli 2 (APC2), homeobox A9, Wnt family member 7A (WNT7A) and N‑Myc downstream‑regulated gene 4 protein genes with PCa. The 6‑gene panel consisting of APC2, cadherin 1, forkhead box P1, leucine rich repeat containing 3B, WNT7A and zinc family protein of the cerebellum 4 was subsequently developed providing PCa detection with 78% sensitivity and 100% specificity. The number of genes methylated (NGM) value introduced for this panel was indicated to rise monotonically from 0.27 in control individuals to 4.6 and 4.25 in patients with highly developed and metastatic T2/T3 stage cancer, respectively. Therefore, the approach of defining the NGM value may not only allow for the detection of PCa, but also provide a rough evaluation of tumor malignancy and metastatic potential by non‑invasive MSP analysis of urine samples.
A new nanocomposite amperometric biosensor for L-lactate determination
(2021) Vorobiienko, А.; Biloivan, O.
The development of nanocomposite biosensor for l-lactate determination in sweat. The investigation included the development of a high-performance nanocomposite sensor.
Ab initio розрахунки борофосфідних кластерів
(2000) Ісаєв, С.; Гребешок, А.; Черногоренко, В.; Корнілов, М.
Методом ab initio (HF, МР2) розраховані величини загальної енергії кластерів . для m = = 4 —12. Знайдені ентальпії перетворення моноелементних кластерів у мішані. З'ясовано, що ймовірне утворення кластерів з приблизно однаковою кількістю атомів бору та фосфору. Вже для т = 12 мішані кластери стають невигідними.
Actual Problems of Health Protection of Ukrainian Youth
(2015) Posudin, Yuriy
Розглядаються основні проблеми зі здоров'ям української молоді, викликані неякісним швидким харчуванням, пивним алкоголізмом, курінням. Внаслідок цих згубних звичок, а також непродуманої державної політики та впливу реклами, молоде покоління страждає від низки небезпечних захворювань, що ведуть у ряді випадків до смертельних наслідків.
Adsorption of proteins on nano-silica modified with antimicrobial drugs
(2019) Gaidai, Alina; Vakuliuk, Polina; Furtat, Iryna; Kunytsia, Natalia; Murlanova, Tatiana; Golub, Alexander
Матеріали конференції "Українська конференція з міжнародною участю "Хімія, фізика та технологія поверхні" та практикум "Біосумісні наночастинки на основі металів: синтез та застосування".
Algae, bryophytes, and vascular plants of calcareous rocks of the Dumka Cave complex (Dniester Regional Landscape Park, Ukraine)
(2025) Mikhailyuk, Tatiana; Vinogradova, Oksana; Nyporko, Svitlana; Vasheniak, Iuliia
Research on chasmophytic communities of the calcareous cliff of the Dumka Cave complex in the Dniester Regional Landscape Park (Ivano-Frankivsk Region) has revealed diverse vegetation dominated by ferns, bryophytes, and algae. The cave complex was examined in three parts: the so-called “karst bridge” (pile of fragments of a cave vault), limestone blocks at the entrance to the cave, and the walls of the front grotto of the cave. In total, fifty-six species of algae (Cyanobacteria — 21 species, Chlorophyta — 23, Charophyta — 2, Heterokontophyta — 9), 25 species of bryophytes (Marchantiophyta — 8, Bryophyta — 17), and 21 species of vascular plants (Pteridophytina — 5, Spermatophytina — 16) were found in the studied habitat. The highest species diversity was recorded on the karst bridge and the walls at the entrance to the cave. In both locations, the algal cover was dominated by cyanobacteria and green algae. Algae and bryophytes on the walls of the front grotto were less diverse, vascular plants were completely absent. Cyanobacteria were absent, and trebuxiophycean green algae and diatoms predominated. A comparison of the species composition of algae and bryophytes using the Sørensen-Chekanovsky index showed a certain resemblance between the karst bridge and the walls at the entrance to the cave and the specificity of the front grotto of the cave. Among the discovered species of algae, two are first reported for Ukraine (Synechococcus sciophilus and Synechocystis primigenia). Several taxa are rare and noteworthy records (Gloeocapsa coracina, Microcoleus vulgaris, Scotinosphaera sp., Pseudostichococcus undulatus, etc.). Fifteen species of bryophytes are listed for the first time for the park; among them, Pedinophyllum interruptum and Fissidens gracifolius are new records for Ivano-Frankivsk Region. For the latter species, this is the second locality in Ukraine. For Timmia bavarica, a rare species in the Ukrainian Carpathians, this is the third locality in Ivano-Frankivsk Region. Vascular plants are characteristic of shaded epilithic habitats. Such communities belong to the biotope H32c "Cabonate rocks of the temperate zone, occurring on the plain and in the lower mountain belt", are characterized syntaxonomically as a group of the Polypodietea class, and belong to the second category of rarity and require protection. The main threat to the existence of this biotope is deforestation, which leads to increased light levels, heating of rocks, and moisture deficiency, as well as eutrophication due to recreational load.
Algorithm for simulating melting polar ice, Earth internal movement and volcano eruption with 3-dimensional inertia tensor
(2023) Matsuki, Yoshio; Bidyuk, Petro
This paper reports the result of an investigation of a hypothesis that the melting polar ice of Earth flowing down to the equatorial region causes volcano eruptions. We assumed a cube inside the spherical body of Earth, formulated a 3-dimensional inertia tensor of the cube, and then simulated the redistribution of the mass that is to be caused by the movement of melted ice on the Earth’s surface. Such mass distribution changes the inertia tensor of the cube. Then, the cube’s rotation inside Earth was simulated by multiplying the Euler angle matrix by the inertia tensor. Then, changes in the energy intensity and the angular momentum of the cube were calculated as coefficients of Hamiltonian equations of motion, which are made of the inertia tensor and sine and cosine curves of the rotation angles. The calculations show that the melted ice increases Earth’s internal energy intensity and angular momentum, possibly increasing volcano eruptions.
Alien flora of Ukraine: structure and dynamics in a historical aspect
(Polskie Towarzystwo Botaniczn, 2025) Shevera, Myroslav; Protopopova, Vira; Budzhak, Vasyl; Kucher, Oksana; Zavialova, Liudmyla; Dvirna, Tetiana
Ukrainian alien flora is the most dynamic and progressing group in the flora. Its influence on the structure, dynamics, and florogenesis has increased significantly over the last centuries. Diversity of analyzed flora is determined by natural conditions of the territory and the geographical location of Ukraine, which provides transcontinental and trans-zonal transport connection. In the southern and southeastern regions of Ukraine, which are characterized by a higher degree of anthropogenic environmental transformation, synanthropization of the flora occurs faster. On the other hand, in the north and northwest, this process is much slower due to the better preservation of the natural vegetation cover.
Allelopathic activity analysis of the invasive grassland species Elaeagnus angustifolia L. by t he method of Neubauer & Schneider
(2016) Norenko, Kateryna
The material of the speech at 13th Eurasian Grassland Conference Management and Conservation of Semi-natural grasslands: from theory to practice (Sighişoara, Romania, 20-24 September 2016).
Alternative routes for HB-EGF mitogenic effects inhibition
(2023) Siromolot, Andriy; Kolybo, Denys
Heparin-binding epidermal growth factor–like growth factor (HB-EGF) is a member of the epidermal growth factor family and has a variety of physiological and pathophysiological functions. Also, HB-EGF plays a pivotal role in distinct tumors progression. HB-EGF is highly expressed in certain cancer cells, such as ovarian and breast cancers, that makes it beneficial for the development of antitumor therapeutic agents. Neutralizing agents against HB-EGF can act on two strategies: sterically blocking the binding of HB-EGF with receptors (monoclonal or polyclonal antibodies, diphtheria toxin derivatives) or capable preventing the formation of soluble HB-EGF from proHB-EGF (ectodomain shedding) with MMPs or ADAMs inhibitors. Recombinant analogs of Corynebacterium diphtheriae toxin fragments (subunit B) and it toxoid CRM197 are able to block the binding of fluorescent derivative HB-EGF (HB-EGF-mCherry) with receptors HER1 and HER4 on the surface of A431 and Vero cell lines. It has been shown that immune serum-containing polyclonal antibodies against HB-EGF is able to inhibit HBEGF binding to surface cellular receptors and block the mitogenic activation with HB-EGF of cells by deactivating Ras-MAPK/ERK1/2. Mitogenic activity of sHB-EGF is significantly enhanced by membrane-associated heparan sulfate proteoglycans (HSPG). Interaction of the N-terminal heparin-binding region of HB-EGF with HSPG leads to stabilization of the EGF-like domain of the molecule in complex with the receptor. The ability of heparin to block proliferation of A431 and Vero cells by exogenous HB-EGF has been demonstrated, probably, due to binding with heparin-binding domain of HB-EGF. Moreover, leupeptin and a broad-spectrum metalloproteinase blocker GM6001, and EDTA significantly decrease paracrine activation of cells by HB-EGF. Thus, searching and development of effective neutralizing agents against sHB-EGF is important and perspective research direction for establishing of a new targeted antitumor therapy.
Analysis and assessment of the environmental situation within Muromets Island (Kyiv)
(2022) Derevska, Kateryna; Nesterovskyi, Victor; Manyuk, Volodymyr; Rudenko, Kseniia; Hurina, Maria
The environmental situation within Muromets floodplain island, which is considered one of the oldest and largest islands of the Kyiv metropolis was studied. This sandy island was formed due to fluvial migration and numerous alluvial deposits since the Holocene. The island is located in the modern Dnipro floodplain, bordering Trukhaniv Island from the south. The environmental state of the island’s plants, landscapes, water bodies, soils and rocks was analyzed. The environmental protection objects of the territory were also characterized. Satellite images of the Earth’s surface over the past 37 years were analyzed to study modern changes in the island outline and hydrography within the Dnipro floodplain near Kyiv. Changes in the shoreline of Muromets Island were assessed. Using our field research data, cartographic schemes, space photographs and scientific publications of various years, we characterized the island’s geological environment, presented the dynamics of shoreline development, analyzed the ecological situation, and identified environmental problems. We found that the island’s environmental condition correlates with the influence of both natural and anthropogenic factors. The degree and severity of impact of the above-mentioned factors on the island’s geological environment was established. It was shown that intense changes in this territory occur due to the geological work of surface water and the work of the wind ,which are intensified by anthropogenic actions. The land shoreline has been migrating for a long time as a result of active water erosion by the Dnipro, Desna and Chartoryi (Desenka) rivers and their tributaries. New straits, peninsulas and individual small islands are formed. The results indicate significant natural dynamics of the Dnipro floodplain development, which occurs against the background of anthropogenic influence, the pressure of which is constantly increasing. The complex of anthropogenic and natural factors lead to the active development of invasive plants, eutrophication of water bodies, shoreline erosion, and significant loss of water and land resources of Muromets Island. The conclusions substantiated in the article are of general geological, ecological and practical significance. They are the beginning of environmental monitoring on this issue, expand knowledge about the peculiarities of the geological structure of Kyiv and the Dnipro floodplain, and update data on the development and ecological situation of this territory. This provides an opportunity to predict and determine the direction of development of negative environmental changes in advance, to make early decisions regarding agents of negative influence and pressure on the geological environment, and to respond in time to their localization or termination. The obtained data can also be used in the arrangement of geological and engineering works related to the preservation of the Dnipro floodplain and the shoreline of the dry land, as well as in the planning of environmental protection measures.
Analysis of Arabidopsis non-reference accessions reveals high diversity of metabolic gene clusters and discovers new candidate cluster members
(2023) Marszalek-Zenczak, Malgorzata; Satyr, Anastasiia; Wojciechowski, Pawel; Zenczak, Michal; Sobieszczanska, Paula; Brzezinski, Krzysztof; Iefimenko, Tetiana; Figlerowicz, Marek; Zmienko, Agnieszka
Metabolic gene clusters (MGCs) are groups of genes involved in a common biosynthetic pathway. They are frequently formed in dynamic chromosomal regions, which may lead to intraspecies variation and cause phenotypic diversity. We examined copy number variations (CNVs) in four Arabidopsis thaliana MGCs in over one thousand accessions with experimental and bioinformatic approaches. Tirucalladienol and marneral gene clusters showed little variation, and the latter was fixed in the population. Thalianol and especially arabidiol/baruol gene clusters displayed substantial diversity. The compact version of the thalianol gene cluster was predominant and more conserved than the noncontiguous version. In the arabidiol/baruol cluster, we found a large genomic insertion containing divergent duplicates of the CYP705A2 and BARS1 genes. The BARS1 paralog, which we named BARS2, encoded a novel oxidosqualene synthase. The expression of the entire arabidiol/baruol gene cluster was altered in the accessions with the duplication. Moreover, they presented different root growth dynamics and were associated with warmer climates compared to the reference-like accessions. In the entire genome, paired genes encoding terpene synthases and cytochrome P450 oxidases were more variable than their nonpaired counterparts. Our study highlights the role of dynamically evolving MGCs in plant adaptation and phenotypic diversity.
Analysis of grassland ANPP dynamics due to changes in climate variables at Ukrainian Biosphere Reserve "Askania-Nova"
(2017) Belyakov, Sergiy; Gofman, Orysia; Vyshenska, Iryna; Zvegintsev, Sergey
The Ukrainian feather-grass steppe ecosystems are highly vulnerable to climate changes. To study the impact of climatic factors on steppe ecosystems’ productivity, the correlation and stepwise regression analysis between ANPP and other variables were provided. The correlation of bioclimatic variables (month precipitation, relative humidity and air and soil temperatures) and aboveground net primary production (ANPP) were investigated for three study plots that represent major steppe microrelief: plain, slope and lowland. The results of multiple regression analysis showed the major components that influenced the ANPP at each of the study plots "Plain", "Slope" and "Lowland". The precipitation and relative humidity in the months before the vegetation peak were most important for ANPP accumulation. Results of this study are important for the prediction of ecosystem changes under the climate changes and also for the development of nature conservation programmes.
Analysis of Moon's gravitational - wave and Earth's global temperature: influence of timetrend and cyclic change of distance from Moon
(2018) Matsuki, Yoshio; Bidyuk, Petro
This research examined the influence of Moon’s gravitational-wave to Earth’s global warming process and the effects of time-trend and cyclic change of the distance between Moon and Earth. In the pervious research, we found that the Moon’s gravitational-wave could influence the process of the Earth’s global warming; and, we also found that Moon’s cyclic movement around Earth needed to be further investigated, because it gave a unique pattern of distribution in the data for the empirical analysis; while both global temperature and global carbon-dioxide increase almost linearly in the time-series. In this research we added dummy binary variables that simulate the trend of time and the cyclic changes. As a result we confirmed that the influence of Moon’s gravitational-wave is significant in the process of rising global temperature on Earth.
Analysis of polyamine levels in blood serum of patients with breast cancer using optical SPR-based immune biosensor
(2019) Prylutskyi, Maksym; Starodub, Nickolaj
The aim of the study was to develop a method for qualitative and quantitative analysis of polyamines as potential tumour markers in blood serum of patients diseased with breast cancer with use of newly created immune biosensor based on effect of surface plasmon resonance.
Analytical approach for calculating the chemotaxis sensitivity function
(2017) Vasilev, Aleksey
We consider the chemotaxis problem for a one-dimensional system. To analyze the interaction of bacteria and an attractant, we use a modified Keller-Segel model, which accounts for the attractant absorption. To describe the system, we use the chemotaxis sensitivity function, which characterizes the nonuniformity of the bacteria distribution. In particular, we investigate how the chemotaxis sensitivity function depends on the concentration of an attractant at the boundary of the system. It is known that, in the system without absorption, the chemotaxis sensitivity function has a bell shape maximum. Here, we show that the attractant absorption and special boundary conditions for bacteria can cause the appearance of an additional maximum in the chemotaxis sensitivity function. The value of this maximum is determined by the intensity of absorption.
Antarctic Hairgrass Rhizosphere Microbiomes: Microscale Effects Shape Diversity, Structure, and Function
(2022) Prekrasna, Ievgeniia; Pavlovska, Mariia; Miryuta, Natalia; Dzhulai, Artem; Dykyi, Evgen; Convey, Peter; Kozeretska, Iryna; Bedernichek, Tymur; Parnikoza, Ivan
The rhizosphere microbiome of the native Antarctic hairgrass Deschampsia antarctica from the central maritime Antarctic was investigated using 16S RNA metagenomics and compared to those of the second native Antarctic plant Colobanthus quitensis and closely related temperate D. cespitosa. The rhizosphere microbial communities of D. antarctica and D. cespitosa had high taxon richness, while that of C. quitensis had markedly lower diversity. The majority of bacteria in the rhizosphere communities of the hairgrass were affiliated to Proteobacteria, Bacteroidetes, and Actinobacteria. The rhizosphere of C. quitensis was dominated by Actinobacteria. All microbial communities included high proportions of unique amplicon sequence variants (ASVs) and there was high heterogeneity between samples at the ASV level. The soil parameters examined did not explain this heterogeneity. Bacteria belonging to Actinobacteria, Bacteroidetes, and Proteobacteria were sensitive to fluctuations in the soil surface temperature. The values of the United Soil Surface Temperature Influence Index (UTII, It i) showed that variations in most microbial communities from Galindez Island were associated with microscale variations in temperature. Metabolic predictions in silico using PICRUSt 2.0, based on the taxonomically affiliated part of the microbiomes, showed similarities with the rhizosphere community of D. antarctica in terms of the predicted functional repertoire. The results obtained indicate that these communities are involved in the primary processes of soil development (particularly the degradation of lignin and lignin-derived compounds) in the central maritime Antarctic and may be beneficial for the growth of Antarctic vascular plants. However, due to the limitations associated with interpreting PICRUSt 2.0 outputs, these predictions need to be verified experimentally.
Anthropogenic impact of the war on the condition of surface waters of the rivers Kazennyi Torets and Kryvyi Torets within the city of Druzhkivka
(2025) Horoshkovа, Lidiia; Menshov, Oleksandr; Nekos, Alla; Korniichuk, Yuliia; Khaduskina, Kateryna
Purpose. To provide a comprehensive ecological assessment of the surface waters state of the Kryviy Torets and Kazenny Torets rivers in the city of Druzhkivka in order to determine the main anthropogenic factors of influence, in particular the consequences of war. Methods. System analysis, statistical processing methods, analysis of retrospective dynamics, and forecasting of future trends. Results. An analysis of water condition indicators was carried out for the monitoring posts – Kryvyi Torets River and Kazennyi Torets River. Organic pollution (BOD₅ and dissolved oxygen) in both rivers throughout the entire observation period there was a systematic excess of BOD₅ over the MPC. The concentration of dissolved oxygen repeatedly dropped below the standard, which indicates a threat to aquatic biota and disruption of selfpurification processes. Nitrites constantly and significantly exceeded the standard, especially in 2005–2008. Periodic significant maxima of phosphate-ion content were recorded, which indicates eutrophication processes and the inflow of phosphates from detergents and fertilizers. Water mineralization (sulfate and chloride ions) is high, especially in 2006–2008 and 2011–2013. Since 2014, stabilization has been observed, but at a high level. Using the Forecast Sheet resource forecasting carried out, which showed good convergence of forecast and actual values. No positive dynamics in water quality were recorded — in 2024–2025 most indicators exceed the MPC. Conclusions. The rivers Kazennyi Torets and Kryvyi Torets are in a state of persistent organic and chemical pollution. The overall ecological condition remains unsatisfactory, and in 2024–2025 the situation has even worsened. Overall, the war has significantly deepened the ecological problems of these rivers. They require a comprehensive approach to restoration: modernization of treatment facilities, rehabilitation of aquatic ecosystems, and restoration of the monitoring system. Without this, there is a threat of further degradation of the region’s water resources, which will have long-term consequences for the environment and human health.

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