Yaroslav Blume - Academia.edu (original) (raw)

Papers by Yaroslav Blume

Springer Proceedings in Physics, 2016

During recent decades there is a growing need in advanced nanotechnology-based gene delivery tech... more During recent decades there is a growing need in advanced nanotechnology-based gene delivery techniques for biology, biotechnology, and biomedicine since conventional genetic transformation techniques are exhausting their potentialities in front of recent major challenges in respective fields. There exists a wide variety of nanostructures of different properties and compositions that are considered suitable for this aim. Among them, carbon nanotubes (CNTs) are viewed to pose promising platform for the development of advanced gene delivery methods due to their acceptable biocompatibility levels, needlelike structure, and high surface area responsible for extensive modification and molecular cargo binding. In this review the background and recent achievements of using CNTs as gene delivery vehicles are discussed. The applicability of covalent and non-covalent CNT functionalization approaches for the design of favorable CNT interfaces useful in biology is elucidated as well as basic mechanisms of these processes are outlined. In contrast to widely exploited covalent functionalization, the potential of non-covalent surface modification of CNTs is considered.

... 1) Petro SMERTENKO, Vitaliy KOSTYLYOV, Ivan KUSHNEROV, Olexandra SHMYRYEVA, Eduard MANOILOV, ... more ... 1) Petro SMERTENKO, Vitaliy KOSTYLYOV, Ivan KUSHNEROV, Olexandra SHMYRYEVA, Eduard MANOILOV, 2) Mykola BRYCHENKO, Valeriy KRUGLOV, Anatoliy MARYENKO, Rostislav STOLYARENKO, 3) Yaroslav BLUME 4) Don J ... Data are displayed on the LCD panel. ...

The Open Agriculture Journal, 2020

Recently, in the greenhouses of Ukraine, a sharp increase in the infestation of tomato plants wit... more Recently, in the greenhouses of Ukraine, a sharp increase in the infestation of tomato plants with soft (wet) rot has been registered. Purpose: To identify the pathogen of the soft rot, study its biological properties and develop practical recommendations for plant protection measures. Methods: The work was performed using classical microbiological and biochemical research methods. The API 20E (Bio Merieux) test system was used to study the physiological and biochemical properties of the bacteria. The study of bacterial fatty acids was carried out by mass-spectrometry. Results: Using a bacteriological analysis of tomato plants selected in greenhouses of the Kyiv region, for the first time, virulent strains from this crop were identified and assigned, according to their physiological, biochemical, morphological and cultural characteristics, to the Pectobacterium carotovorum species. The fatty acid profile of the total cell lipids of the isolated strains was distinguished by the prese...

Journal of Molecular Liquids, 2021

Abstract Silver nanoparticles (SNPs) synthesized extracellularly using extracts of the different ... more Abstract Silver nanoparticles (SNPs) synthesized extracellularly using extracts of the different genus Pleurotus fungi samples, were tested for their potential to serve as the therapeutic agents targeting insulin amyloid formation at physiological conditions in vitro. The relatively monodisperse crystallites of average size ∼ 6 – 20 nm, and ∼ 14 – 38 nm hydrodynamic diameters, stabilized by a fungal protein cap and possessing zeta potential values ∼ – (39 – 55) mV, were obtained, as revealed by dynamic light scattering and X-ray diffraction analysis. Absorption maxima of the SNPs were within the range of 406 – 413 nm, corresponding to the surface plasmon resonance, while weak fluorescence bands centered at 600 – 610 nm were observed both in buffer and in the presence of the insulin amyloid fibrils. The Thioflavin T (ThT) fluorescence intensity at 480 nm in the protein samples incubated with the SNPs, was reduced to ∼ 29 – 42 % of its value in the control, revealing lower amount of the formed fibrillar species. The insulin fibrillar structures of ∼ 17 ± 5 nm in thickness and ∼ 1.4 ± 0.2 µm in length were grown in the control, while the protein spherical assemblies of ∼ 30 – 100 nm in diameter, as well as amorphous aggregates, both containing the SNPs in their structure, were observed in the presence of the SNPs, as revealed by transmission electron microscopy. Of these, the nanoparticles, referred to here as QD1, QD4, synthesized at NaNO3 : biological medium molar ratio ∼ 1 : 1, and possessing the highest agglomeration stability, showed the pronounced anti-amyloid effect at low ratios of the SNPs to insulin ∼ 0.01 and 0.08, respectively. Based on the above results, van der Waals and hydrophobic interactions between the insulin prefibrillar assemblies and the SNPs were suggested to induce partial distortion of their structure followed by inhibition of the amyloid elongation phase and formation of the amorphous precipitates, respectively. Overall, the obtained results may represent a starting point for the application of the most effective SNPs as anti-amyloid agents.

Frontiers in Plant Science, 2019

Molecular Simulation, 2019

Aggregates of amyloid-beta proteins (Aβ) have been recognised to be intimately related to pathoge... more Aggregates of amyloid-beta proteins (Aβ) have been recognised to be intimately related to pathogenesis of Alzheimer's disease (AD). Indeed, Aβ aggregates of various sizes from dimers to fibrils were found in the brains of AD patients, and these aggregates can be self-organised. Since abnormal accumulation of metal ions such as Zn, Cu and Fe was also observed in the brains, the association between Aβ aggregations and these metal ions has been studied widely. In the present study, to elucidate the influence of Zn ions on the stability of Aβ aggregates, we performed molecular dynamics (MD) simulations and ab initio fragment molecular orbital (FMO) calculations on the Aβ nonamers with and without Zn ions and investigated the change in its structure and electronic states induced by Zn ions at atomic and electronic levels. The MD simulations revealed that Aβ nonamer cannot keep its symmetry structure, whereas Aβ nonamer with Zn ions keeps the structure. The FMO results indicated that electrostatic interactions among the charged amino-acid residues of Aβ nonamer are significantly changed by the influence of Zn ions to stabilise Aβ nonamer. These results provide useful information for proposing novel compounds, which binds specifically to Aβ and inhibits the Aβ aggregation.

Current Biotechnology, 2016

Dual-specificity tyrosine phosphorylation-regulated kinases or DYRKs (Dual specificity YAK1-relat... more Dual-specificity tyrosine phosphorylation-regulated kinases or DYRKs (Dual specificity YAK1-related kinases), play a key role in the signaling pathways regulating nuclear functions during cell proliferation and differentiation. It is well known that phosphorylation of tau microtubule-associated proteins by Dyrk1A, related to brain development [PMID: 17906291] and Down syndrome [PMID: 18405873]. The DYRK family kinases are autophosphorylated on tyrosine, serine and threonine residues, but their catalitical activities are strongly associated with serine and threonine phosphorylation [PMID: 8631952]. Previously, we have identified the row of plant homologues of animal microtubule- and cell cycle related serine-threonine PKs [1]. The goal of this study was reconstruction of spatial structure of plant DYRK-homologues and their catalytic functions. Accordingly to PDB-BLAST search we specified template X-ray PDB-structures (2VX3, 3ANQ, 1Z57) for template-based protein structure modeling (M...

International Journal of Molecular Sciences

Ag-based quantum dots (QDs) are semiconductor nanomaterials with exclusive electrooptical propert... more Ag-based quantum dots (QDs) are semiconductor nanomaterials with exclusive electrooptical properties ideally adaptable for various biotechnological, chemical, and medical applications. Silver-based semiconductor nanocrystals have developed rapidly over the past decades. They have become a promising luminescent functional material for in vivo and in vitro fluorescent studies due to their ability to emit at the near-infrared (NIR) wavelength. In this review, we discuss the basic features of Ag-based QDs, the current status of classic (chemical) and novel methods (“green” synthesis) used to produce these QDs. Additionally, the advantages of using such organisms as bacteria, actinomycetes, fungi, algae, and plants for silver-based QDs biosynthesis have been discussed. The application of silver-based QDs as fluorophores for bioimaging application due to their fluorescence intensity, high quantum yield, fluorescent stability, and resistance to photobleaching has also been reviewed.

Linum usitatissimum L. (flax or linseed) is one of the oldest economically important crops used i... more Linum usitatissimum L. (flax or linseed) is one of the oldest economically important crops used in biotechnology as a source for bioactive compounds. Flax fiber and seed have industrial significance as a source of cellulosic fiber for textile and paper industry and seed oil for pharmaceutical, cosmetic and food industry. The elaboration of new effective techniques for in vitro regeneration of Linum usitatissimum L. is very actual problem today. The influence of low molecular weight five and six membered heterocyclic compounds on organogenesis of Linum usitatissimum L. cultivar heavenly in vitro has been studied. It was found that heterocyclic compounds derivatives pyridine, pyrimidine, pyrazole and isoflavones revealed high stimulating effect on direct shoot organogenesis of Linum usitatissimum L. in vitro. The maximal shoot regeneration frequency was obtained on the MS media containing heterocyclic compounds at the concentration 10-8 M/l as compared to lower regeneration frequency obtained on the control MS medium containing 1 mg/l BAP and 0.05 mg/l NAA. The maximal index of explants with regeneration (in %) that exceeded almost twice the same index in control MS medium was obtained on the MS medium containing heterocyclic compound derivative of isoflavones. At the same time, the index of explants with regeneration (in %) that exceeded one and a half times the same index in control MS medium and the maximal index of shoots elongated more than 1 cm (in %) that exceeded almost twice the same index in control MS medium were obtained on the MS media containing heterocyclic compounds derivatives of pyridine, pyrimidine and pyrazole. The current study confirms perspective of using of low molecular weight five and six-membered heterocyclic compounds at the concentration 10-8 М/l of the MS medium as new effective substitutes of traditional growth regulators auxin NAA and cytokinin BAP for regeneration of Linum usitatissimum L. cultivar heavenly in vitro. Keywords: screening of new plant growth regulators, nitrogen-containing heterocyclic compounds, pyridine, pyrimidine, pyrazolotriazinone and isoflavones, Linum usitatissimum L., direct shoot organogenesis in vitro

International Journal of Research, 2016

Impact of new Microbial Plant Resistance/Plant Growth Protection (PR/PGP) Inducers for increasing... more Impact of new Microbial Plant Resistance/Plant Growth Protection (PR/PGP) Inducers for increasing tolerance of Brassica rapa subsp. pekinensis (Chinese cabbage) to parasitic nematode Heterodera schachtii Schmidt was studied. In the greenhouse conditions on the artificial invasive nematode background the accumulation of Chinese cabbage biomass was increased as follows: under impact of Avercom nova-2-up to 94%, Phytovit-up to 55%, Violar-up to 32% and Avercom-up to 17%, accordingly as compared to control. In the laboratory conditions the biomass of affected by nematode and treated by microbial PR/PGP inducers plants was increased up to 26-43 % as compared to biomass of control affected by nematode plants. Influence of Microbial PR/PGP Inducers on molecular-genetic indexes of Chinese cabbage resistance to nematode Heterodera schachtii was investigated. The increase in the difference of Dot-blot hybridization index up to 27-49% between cytoplasmic mRNA and small regulatory RNA (si/miRNA), isolated from control and affected by nematode and treated by microbial PR/PGP inducers plants was shown. Silencing activity of si/miRNA isolated from affected by nematode and treated by microbial PR/PGP inducers plants was increased up to 32-67 % in the wheat embryo cell free system. Obtained data testify that microbial PR/PGP inducers stimulate synthesis in the plant cells of immune-protective si/miRNA. As a result of this, plant tolerance against this parasitic nematode is increased.

Impact of microbial biostimulants: Avercom, Avercom nova-2, Violar and Phytovit on induction of c... more Impact of microbial biostimulants: Avercom, Avercom nova-2, Violar and Phytovit on induction of callus formation and regeneration of plantlets of wheat (Triticum aestivum L.) of cultivar Zimoyarka on the MS nutrient media supplemented with these biostimulants was studied in vitro conditions. The increase of frequency of formation of callus cells (from 43 up to 74 %) was observed on the apical meristem of 4-5-day-old seedlings of wheat placed on the MS media supplemented with microbial biostimulants: Avercom, Avercom nova-2, Violar and Phytovit used at the concentrations ranging from 10 up to 60 μl/l in combination with 1 mg/l auxin 2.4-D (experiment) as compared with lower frequency of formation of callus cells obtained on the MS media supplemented with only auxin 2.4-D used at the concentration 1 mg/l (control). The increase of efficiency of regeneration of wheat shoots (from 35 up to 65 %) was observed on the 3-4-week-old callus tissue grown on the MS media supplemented with micro...

European Journal of Biotechnology and Bioscience, 2016

The Open Agriculture Journal, 2019

Background: By inducing the production of inhibitory allelochemicals and mechanisms of systemic r... more Background: By inducing the production of inhibitory allelochemicals and mechanisms of systemic resistance plant growth promoting bacteria (PGPB) help plants to cope with stresses. Materials and Methods: In this study cell suspensions of Bacillus subtilis, Pseudomonas fluorescens or Azotobacter chroococcum were used to test the efficacy of these PGPB in inducing resistance in tomato (Lycopersicon esculentum Mill) against Clavibacter michiganensis subsp michiganensis, a bacteria known to cause canker disease. To test this hypothesis, seedlings of Chaika variety, characterized by short growing, early-ripening, high productivity and resistance against fusarium and the C. michiganensis strain ІZ-38 isolated in Kyiv were employed. Results and Conclusion: The use of cell suspensions of the PGPB B. subtilis, A. chroococcum or P. fluorescens induced an increment in the resistance of tomato plants against the causative agent of bacterial canker (C. michiganensis subsp. michiganensis) by 42–5...

Antibiotics, 2020

The inhibition of a bacterial cell division protein, filamentous temperature-sensitive Z (FtsZ), ... more The inhibition of a bacterial cell division protein, filamentous temperature-sensitive Z (FtsZ), prevents the reproduction of Mycobacteria. To propose potent inhibitors of FtsZ, the binding properties of FtsZ with various derivatives of Zantrin ZZ3 were investigated at an electronic level, using molecular simulations. We here employed protein–ligand docking, classical molecular mechanics (MM) optimizations, and ab initio fragment molecular orbital (FMO) calculations. Based on the specific interactions between FtsZ and the derivatives, as determined by FMO calculations, we proposed novel ligands, which can strongly bind to FtsZ and inhibit its aggregations. The introduction of a hydroxyl group into ZZ3 was found to enhance its binding affinity to FtsZ.

Impact of microbial biostimulants on the increase (up to 75-87%) of resistance of wheat plants of... more Impact of microbial biostimulants on the increase (up to 75-87%) of resistance of wheat plants of two varieties Yatran 60 and Zimoyarka to the cereal cyst nematode Heterodera avenae was found. The increase of difference in the index of Dot-blot hybridization (up to 37-65%) between cytoplasmic mRNA and si/miRNA isolated from control and experimental (affected by nematode and treated with biostimulants) plants was observed. In the wheat-embryo cell-free system the increase of silencing activity (up to 52-78%) of si/miRNA isolated from experimental as compared to control wheat plants was revealed. These data indicate that microbial biostimulants cause reprogramming wheat genome by inducing synthesis si/miRNA with immune-protective properties against nematode; as a result the wheat resistance to nematode invasion is increased. To obtain new lines of wheat cells resistant to nematode. H. avenae the microbial biostimulants were used for preparing of MS media for cultivation of isolated wheat tissues in vitro. The indirect and direct shoot organogenesis was observed on the apical meristem of shoot and root on the MS media supplemented with each microbial biostimulant at the concentrations 10-50 μl/l in combination with either 1-2 mg/l axing 2.4-D or 1-2 mg/l cytokinin BAP. The obtained wheat plants will be further tested on the resistance to nematode H. avenae in greenhouse conditions. Keywords: bioregulators of microbiological origin, Triticum aestivum L., shoot organogenesis in vitro

Cytology and Genetics, 2016

Literature data and results of the studies carried out us concerning the involvement of plant cel... more Literature data and results of the studies carried out us concerning the involvement of plant cell cytoskeleton in cellular mechanisms of metal toxicity are summarized. Characteristics of cytotoxic effect of metals on plant cytoskeleton and, in particular, on microtubules and actin filaments are reviewed. Particular attention is paid to cellular and molecular mechanisms of metal impact on cytoskeleton. The most probable binding sites of heavy metals, as well as alternative mechanisms of their impact on cytoskeleton, are discussed.

Cytology and Genetics, Aug 1, 2009

Characteristics of the interaction of dinitroaniline compounds with tubulin molecules have an ext... more Characteristics of the interaction of dinitroaniline compounds with tubulin molecules have an extremely high selectivity: these substances efficiently bind to the tubulins of both plant and protozoan origins and practically do not interact with any animal and fungal tubulins despite a very high similarity between the corresponding sequences. This work summarizes and comprehensively analyzes the specific structural features and mechanisms

Springer Proceedings in Physics, 2016

The Open Agriculture Journal, 2020

Journal of Molecular Liquids, 2021

Frontiers in Plant Science, 2019

Molecular Simulation, 2019

Current Biotechnology, 2016

International Journal of Molecular Sciences

International Journal of Research, 2016

European Journal of Biotechnology and Bioscience, 2016

The Open Agriculture Journal, 2019

Antibiotics, 2020

Cytology and Genetics, 2016

Cytology and Genetics, Aug 1, 2009

The Monograph “ Research Advances in Plant Biotechnology”. Series: Plant Science Research and Practices / Ed. Yaroslav B. Blume. Nova Science Publishers, Inc. USA. 2020. 375 p. ISBN: 978-1-53616-432-9., 2020

Chapter 6 of the Monograph“ Research Advances in Plant Biotechnology” presents the results of sys... more Chapter 6 of the Monograph“ Research Advances in Plant Biotechnology” presents the results of systematic studies of the effects of new ecologically friendly polycomponent biostimulants of microbiological origin (developed in Ukraine on the basis of either 2,6-dimethylpyridine-N-oxide, or metabolic products of root endophyte fungus from the roots of ginseng, or metabolites of several strains of soil Streptomyces) on improving commercially useful traits in important agricultural crops, including improved growth, productivity and increased resistance to pathogenic fungi, parasitic nematodes and insects. Special attention is paid to the analysis of molecular-genetic mechanisms of the effect of microbial biostimulants at organismal, cellular, and molecular levels. The results of these studies proved that the mechanism of bioprotective effect of microbial biostimulants involves the delivery of RNA interference (RNAi) into plant cells, i.e. induction of synthesis of endogenous small regulatory si/miRNAs with immuno-protective, antipathogenic and antiparasitic properties.

Although various plant microtubule-associated proteins (MAPs) have been described because of thei... more Although various plant microtubule-associated proteins (MAPs)
have been described because of their role in modulating microtubule functions, the full complement of these important sequences has not yet been described. Taking into account the high level of homology between animal and plant tubulins, and the potential conservation of their MAP binding domains, we carried out a bioinformatic investigation of the MAP1, MAP2, tau protein, and MAP4 families from animals and humans. The
gene-identification strategy, utilizing site-based and comparative methods, allowed us to identify amino acid motifs that are conserved within each MAP family. According to these amino acid motifs we designed corresponding nucleotide motifs in IUPAC code, accommodating potential codon polymorphism by applying the universal symbols representing all possible substitutions. Scanning the complete sequences of all five Arabidopsis thaliana chromosomes, we identified candidate coding sequences for plant homologues of animal structural MAPs. Furthermore, we identified 200 loci (i.e., 178 of MAP1 and 22 of MAP2 and tau) that are of interest as potential chromosomal regions for plant structural MAPs.
Interestingly, consensus regions for MAP4 were not identified in
A. thaliana. Chromosomal locations for three previously known plant homologues of MAP1 (i.e., AtEB1a, AtEB1b and AtEB1c) were also identified in the A. thaliana genome.

Conference Presentation

Impact of microbial biostimulants on the increase (up to 75-87%) of resistance of wheat plants of... more Impact of microbial biostimulants on the increase (up to 75-87%) of resistance of wheat plants of two varieties Yatran 60 and Zimoyarka to the cereal cyst nematode Heterodera avenae was found. The increase of difference in the index of Dot-blot hybridization (up to 37-65%) between cytoplasmic mRNA and si/miRNA isolated from control and experimental (affected by nematode and treated with biostimulants) plants was observed. In the wheat-embryo cell-free system the increase of silencing activity (up to 52-78%) of si/miRNA isolated from experimental as compared to control wheat plants was revealed. These data indicate that microbial biostimulants cause reprogramming wheat genome by inducing synthesis si/miRNA with immune-protective properties against nematode; as a result the wheat resistance to nematode invasion is increased. To obtain new lines of wheat cells resistant to nematode. H. avenae the microbial biostimulants were used for preparing of MS media for cultivation of isolated wheat tissues in vitro. The indirect and direct shoot organogenesis was observed on the apical meristem of shoot and root on the MS media supplemented with each microbial biostimulant at the concentrations 10-50 μl/l in combination with either 1-2 mg/l axing 2.4-D or 1-2 mg/l cytokinin BAP. The obtained wheat plants will be further tested on the resistance to nematode H. avenae in greenhouse conditions.
Keywords: bioregulators of microbiological origin, Triticum aestivum L., shoot organogenesis in vitro

Linum usitatissimum L. (flax or linseed) is one of the oldest economically important crops used i... more Linum usitatissimum L. (flax or linseed) is one of the oldest economically important crops used in biotechnology as a source for bioactive compounds. Flax fiber and seed have industrial significance as a source of cellulosic fiber for textile and paper industry and seed oil for pharmaceutical, cosmetic and food industry. The elaboration of new effective techniques for in vitro regeneration of Linum usitatissimum L. is very actual problem today. The influence of low molecular weight five and six membered heterocyclic compounds on organogenesis of Linum usitatissimum L. cultivar heavenly in vitro has been studied. It was found that heterocyclic compounds derivatives pyridine, pyrimidine, pyrazole and isoflavones revealed high stimulating effect on direct shoot organogenesis of Linum usitatissimum L. in vitro. The maximal shoot regeneration frequency was obtained on the MS media containing heterocyclic compounds at the concentration 10-8 M/l as compared to lower regeneration frequency obtained on the control MS medium containing 1 mg/l BAP and 0.05 mg/l NAA. The maximal index of explants with regeneration (in %) that exceeded almost twice the same index in control MS medium was obtained on the MS medium containing heterocyclic compound derivative of isoflavones. At the same time, the index of explants with regeneration (in %) that exceeded one and a half times the same index in control MS medium and the maximal index of shoots elongated more than 1 cm (in %) that exceeded almost twice the same index in control MS medium were obtained on the MS media containing heterocyclic compounds derivatives of pyridine, pyrimidine and pyrazole. The current study confirms perspective of using of low molecular weight five and six-membered heterocyclic compounds at the concentration 10-8 М/l of the MS medium as new effective substitutes of traditional growth regulators auxin NAA and cytokinin BAP for regeneration of Linum usitatissimum L. cultivar heavenly in vitro.
Keywords: screening of new plant growth regulators, nitrogen-containing heterocyclic compounds, pyridine, pyrimidine, pyrazolotriazinone and isoflavones, Linum usitatissimum L., direct shoot organogenesis in vitro