Кафедра біології

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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.
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.
Antifungal activity of new quinolone and acridone-derivatives
(2019) Voloshchuk, N.; Vasylchenko, O.; Kosovska, N.; Bashta, O.; Sorokin, O.; Shyrina, T.; Palchykovska, L.
Meeting abstract of the he APS Northeastern Division meeting in State College, Pennsylvania, April 3–5, 2019.
Beta-amylase gene variability in introgressive wheat lines: [preprint]
(2016) Antonyuk, Maksym; Navalikhina, Anastasiia; Ternovska, Tamara
Variability of the beta-amylase gene in bread wheat, artificial amphidiploids, and derived introgression wheat lines was analyzed. Variation in homeologous beta-amylase sequences caused by the presence of MITE (Miniature Inverted-Repeat Transposable Element) and its footprint has been identified in bread wheat. The previously unknown location of MITE in Triticum urartu and T. aestivum L. beta-amylase gene has been found. These species have a MITE sequence in the third intron of beta-amylase, as opposed to Aegilops comosa and a number of other Triticeae species, which have it in the fourth intron. These two MITEs from Ae. comosa and T. aestivum were shown to have low identity scores. Miosa, an artificial amphidiploid, which has the M genome from Ae. comosa was shown to lose the MITE sequences. This loss might be caused by genomic shock due to allopolyploidization.
Concept of Teaching Academic Biosecurity and Biosafety Disciplines as a Countermeasure to the Main Challenges Under the Conditions of Disinformation War Against Ukraine
(2022) Furtat, Iryna
Disinformation spreading as part of the hybrid war concept is one of the characteristic features of the modern Russia-Ukraine war. Its peculiarity is that the aggressor country uses various actors and information technologies to defeat its opponents both in the absence of direct armed conflict and during active actions.
Cytogenetical characteristic of the introgressive common wheat lines including and lacking the 4Sl chromosome
(2009) Antonyuk, Maksym; Bodylyova, Mariya; Ternovska, Tamara
Diverse Pathway to Obtain Antibacterial and Antifungal Agents Based on Silica Particles Functionalized by Amino and Phenyl Groups with Cu(II) Ion Complexes
(2020) Tomina, Veronika; Furtat, Iryna; Lebed, Anastasia; Kotsyuda, Sofiya; Kolev, Hristo; Kanuchova, Maria; Behunova, Dominika; Vaclavikova, Miroslava; Melnyk, Inna
Production of environmentally friendly multitasking materials is among the urgent challenges of chemistry and ecotechnology. The current research paper describes the synthesis of amino−/silica and amino−/phenyl−/silica particles using a one-pot sol−gel technique. CHNS analysis and titration demonstrated a high content of functional groups, while scanning electron microscopy revealed their spherical form and ∼200 nm in size. X-ray photoelectron spectroscopy data testified that hydrophobic groups reduced the number of water molecules and protonated amino groups on the surface, increasing the portion of free amino groups. The complexation with Cu(II) cations was used to analyze the sorption capacity and reactivity of the aminopropyl groups and to enhance the antimicrobial action of the samples. Antibacterial activities of suspensions of aminosilica particles and their derivative forms containing adsorbed copper(II) ions were assayed against Gram-positive (Staphylococcus aureus ATCC 25923) and Gram-negative bacteria (Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853). Meanwhile, antifungal activity was tested against fungi (Candida albicans UCM Y-690). According to zeta potential measurements, its value could be depended on the suspension concentration, and it was demonstrated that the positively charged suspension had higher antibacterial efficiency. SiO2/−C6H5/−NH2 + Cu(II) sample’s water suspension (1%) showed complete growth inhibition of the bacterial culture on the solid medium. The antimicrobial activity could be due to occurrence of multiple and nonspecific interactions between the particle surfaces and the surface layers of bacteria or fungi.
Effect of Synthesis Conditions on the Formation of Spherical Silica Particles with Amino Groups and their Investigation in Sorption and as Antibacterial Agents
(2018) Melnyk, I.; Tomina, V.; Stoliarchuk, Nataliya; Lebed, A.; Furtat, Iryna; Kanuchova, Maria; Vaclavikova, M.
The research is financed from the SASPRO Programme No. 1298/03/01. Spherical silica particles with amino groups are simple and unique, as well as convenient materials for application in catalysis, nanomedicine, separation processes, adsorption, or energy-storage technology. Usually, the procedure of producing aminosilica particles includes two stages: (1) production of pure silica particles and (2) their post-synthetic grafting using aminopropyltriethoxysilane (APTES)...
Fetal Tissues Tested for Microbial Sterility by Culture- and PCR-Based Methods Can be Safely Used in Clinics
(2017) Vitrenko, Yakov; Kostenko, Iryna; Kulebyakina, Kateryna; Duda, Alla; Klunnyk, Mariya; Sorochynska, Khrystyna
Cell preparations to be used in elinieal practice must be free of infectious agents. Safety concerns are especially elevated upon the use of human fetal tissues, which are otherwise highly advantageous in eell therapy. We demonstrate that treating fetal samples with antibiotie, extensive washing, and homogenization prior to cryoconservation efficiently removes microbes in general. Screening a large collection by an automatic culture system showed that 89.2% fetal tissue samples were sterile, while contamination was detected in 10.8% samples. Liver and ehorion were contaminated more than the brain, kidney, lung, and soft tissues. Broad- range PCR from the bacterial 16s rRNA gene was adopted as a confirmatory assay; however, the eoneordanee between the eulture-based and PCR assays was weak. Taxonomic identification was done for contaminated samples by bacteriological methods and sequencing 16s rRNA PCR products. The two approaches revealed different spectra of taxonomic groups sharing only Lactobacillus, the most frequently found genus. In addition, other representatives of vaginal microbiota were detected by culture-based identification, while PCR product sequencing has also revealed a subset of nosocomial microorganisms. Importantly, species known to cause sepsis were identified by both techniques, arguing for their indispensability and mutual complementarity. We suggest that most contaminations are taken up during collection of fetal material rather than originating from an in utero infection. In conclusion, a rigorous microbiological control by culture and PCR is a prerequisite for safe elinieal use of fetal tissue suspensions.
First Report of Potato Viruses Infecting Lamium purpureum in Ukraine
(2021) Kyrychenko, A.; Bohdan, M.; Snihur, H.; Shcherbatenko, I.; Antipov, I.
Weeds as reservoirs for destructive plant pathogens have a significant impact on the viral epidemiology, ecology and, as a result, on local economy, and are therefore being investigated in many parts of the world. Thus, the aim of this study was to investigate virus occurrence in red dead-nettle plants (Lamium purpureum L.) widespread in urban and field conditions throughout the in the Kyiv region of Ukraine. Methods. Field crop observations, visual diagnosis, biological testing of the virus, immunoassay (ELISA), polymerase chain reaction with reverse transcription (RT-PCR), sanger sequencing of partial genome sequences of PVX, PVY, PVS, PVM. Results. The results obtained in the study indicate that Lamium plants could be alternative weed hosts of number important viral diseases including potatoes and other vegetables. Serological and molecular test results evidence plants were infected by Potato virus X, Potato virus Y, Potato virus M, Potato virus S and therefore Lamium L. species can serve as a potential source of inoculum for wide range of vegetables and ornamentals. This study is the first report of Lamium plants being naturally infected with Potato virus M and Potato virus S in central Europe. Conclusions. These plants are alternative host of mixed infection with viruses belonging to different families: Alphaflexiviridae, Betaflexiviridae and Potyviridae.
Genetic basis of awnednessin grasses
(2015) Navalikhina, Anastasiia; Antonyuk, Maksym; Ternovska, Tamara
Some representatives of grasses, such as rice, barley, oats, and wheat, have long needle-like elongations of lemma – awns. Genetic mechanisms of awns development control remain poorly understood. This article give a literature review on the awnedness control in rice, barley, and wheat. Due to these species relationship and evolutionary conservatism of developmental mechanisms, it is possible to apply principle of synteny to transfer existing data on rice and barley to a wheat. Thus, it is possible to find out the mechanisms of awns development and discovery the corresponding genes in wheat, which is important and necessary task.
The genetic control of the α-amylase isozymes of the durum wheat (Triticum durum Desf.)
(2009) Prokopyk, Daria; Antonyuk, Maksym; Ternovska, Tamara
The hybridoiogical analysis was provided on several durum wheat genotypes with utilizing three F2 populations developed from the crossing between parental forms that differed in the invariable malt-zone triplet on elecirophoretic spectrum of α-amylase. Three components of this zone are controlled by three genes with an independent way of inheritance: one of them is located on the 6B or 5B chromosome, and two genes are located on the chromosomes of A subgenome.
Genome Structure of Intro-Gressive Lines Triticum Aes-Tivum/Aegilops Sharonensis
(2009) Antonyuk, Maksym; Bodylyova, Mariya; Ternovska, Tamara
The lines Triticum aestivum/Aegifops sharonensis were explored in regard to the presence of introgressions in the line genomes, their amount and belonging to deﬁnite homoeologic group. The results of studying of chromosome associations in M1 of PMC in the hybrids between the lines with each other and with recurrent common wheat genotype Avrora were compared with the data of the line assessmentfor the chromosomal biochemical and morphological markers. 26 lines were distinguished, between six groups with speciﬁc genome rearrangement regard to recurrent genotype.
The impact of silica functionalized microspheres on the ability of microorganisms to adhesion and biofilms formation
(2017) Furtat, Iryna; Lebed, A.; Kotsyuda, S.; Tomina, V.; Vaclavikova, M.; Melnyk, I. V.
Теза доповіді на ХV з’їзді Товариства мікробіологів України ім. С. М. Виноградського, 11-15 вересня 2017 р.
Methylation pattern of tumor-suppressor gene promoters as putative noninvasive diagnostic markers for prostate cancer
(2021) Mankovska, Oksana; Korsakova, A.; Cherniavskyi, K.; Kononenko, O.; Stakhovskyy, E.; Bondarenko, Yu.; Kashuba, Volodymyr; Gerashchenko, G.
Aim. To assess the rate of promoter methylation of putative TSGs for PCa in tumor tissue and in urine of PCa patients for better understanding of regulation of gene expression upon the PCa development and to evaluate the possibility to use the data on TSGs’ methylation for the development of noninvasive PCa markers. Methods. A quantitative methyl-specific PCR (qMSP) was used for the analysis of a methylation rate in prostate tissues and cell lines, and an ordinary MSP was performed for the study of urine samples. Results. We found that the RASSF1A promoter demonstrated a higher methylation rate in the TMPRSS2:ERG fusion positive PCa. The methylation of NKX3.1, PTEN and RASSF1A in DNA from urine was more common for cancer patients than for healthy donors. The promoters of CDH1 and GDF15 were methylated more frequently in PCa patients, than in patients with inflammatory disease. Conclusions. The abovementioned five genes can form a panel for early non-invasive detection of PCa. This set can be combined with the detection of the TMPRSS2:ERG fusion transcript. More work should be done to understand the molecular mechanisms explaining the functional role of promoter methylation of the selected genes.
Nanocomposite materials: perspectives on the use as inhibitors of staphylococcal adhesion
(2018) Lupatsii, M.; Lebed, A.; Furtat, Iryna; Murlanova, T.; Vakuliuk, Polina; Melnyk, I.; Tomina, V.
Abstract of the speech at XIV International Scientific Conference for Students and PhD Students "Youth and Progress of Biology", dedicated to the 185th anniversary from the birthday of B. Dybowski (Lviv, April 10–12, 2018).
Nanocomposites with ornidazole-antibacterial and antiadhesive agents against Gram-positive and Gram-negative bacteria
(2020) Furtat, Iryna; Lupatsii, M.; Murlanova, Tatiana; Vakuliuk, Polina; Gaidai, Alina; Biliayeva, O.; Sobczuk, Henryk; Golub, Alexander
Antimicrobial resistance of many microbial species can cause to thousands of deaths worldwide, in this regard new therapeutic strategies have to be invented. To address the question, we have prepared nanocomposites on the basis of pyrogenic silicon dioxide with ornidazole immobilized on the surface (ornidasil) and studied their antimicrobial properties and the therapeutic potential. It has also been shown, that in comparison with pure ornidazole the addition of ornidazole to nanocomposite composition can enhance the antimicrobial spectrum, including Gram-positive and Gram-negative bacteria. The most signifcant bactericidal efect has been reached after more than 24-h treatment with the nanocomposite. Antiadhesive properties of nanocomposite materials were studied using blood types OO+, AO+, BO+, AB+, the degree of bacterial adhesion was estimated using three indexes: average adhesion index, index of erythrocytes involvement, index of microbial adhesion. The efectiveness of the treatment with the nanocomposites obtained was studied on complicated wounds of various etiologies, in particular the wounds caused by diabetic foot syndrome.
One-pot synthesis of advanced aminosilicas for environmental remediation
(2019) Melnyk, I.; Tomina, V.; Stolyarchuk, N.; Vaclavikova, M.; Lebed, A.; Furtat, Iryna; Seisenbaeva, G.; Kessler, V.
Conference abstract of 4th International Scientific Conference NANOAPP 2019 - Nanomaterials & Applications thematically focused on "Nano4Circularity" - Nanomaterials for Circular Economy"
The oxidative status in patients with chronic kidney disease
(2020) Vasylchenko, V.; Korol, L.; Kuchmenko, Olena; Stepanova, N.
An excess of free radicals accompanies the development of renal pathologies and causes numerous concomitant complications and syndromes. The most common of these are cardiometabolic syndromes in patients with chronic kidney disease. Therefore, the purpose of the study was to determine the activity of paraoxonase-1 and myeloperoxidase, which are associated with indicators of high-density lipoproteins content and oxidative stress in the blood of patients with the chronic stage of kidney disease. The activity of the enzymes, thiobarbiturate-active products concentration and transferrin, ceruloplasmin, thiol compounds content were determined in the blood of patients with chronic kidney disease. The oxidative status was shown to be changed. Thus, myeloperoxidase activity, the content of oxidized proteins and the concentration of thiobarbiturate-positive components were increased, while the activity of the antioxidant enzyme paraoxonase-1, the content of transferrin, ceruloplasmin and thiol compounds were decreased. The ratio of myeloperoxidase / paraoxonase-1 activities was progressively increased up to 9-fold, indicating the presence of cardiovascular complications in patients. The data obtained allowed to extend the range of indicators for monitoring the development of cardiometabolic disorders in the progression of chronic kidney disease.

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