bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetically modified yeasts in studies of human amyloidosis
Authors: Kulichikhin Konstantin Yu. , Zelinsky Andrew A. , Gorsheneva Natalia A. , Ryabinina Marina V. , Grizel Alexey V. , Azarov Vladimir V. , Rubel Aleksandr A. 
Published: December 2022

Amyloid protein aggregation is a key factor in the development of a variety of serious diseases in humans, commonly named as amyloidoses (Alzheimers and Parkinsons diseases, type II diabetes, etc.), and a determinant of protein-based inheritance in lower eukaryotes. In yeast, translation termination factor Sup35 is one of the most extensively studied amyloidogenic proteins. Aggregation of Sup35 (induction of [PSI+] prion) decreases its functional activity and leads to the suppression of nonsense-mutation as stop-codons become recognized as meaningful more frequently. This phenomenon is the basis of phenotypic detection of Sup35 aggregation in yeast strains possessing nonsense mutation ade1-14 in ADE1 gene.
Yeast is convenient model for genetic, biochemical and molecular biology studies. Yeast genome can be easily edited and plasmids can be used for induction of gene expression. Yeast is suitable for analysis of mammalian genes and proteins and thus can be applied for the analysis of amyloidogenic properties of proteins associated with human diseases. Phenotyping detection of [PSI+] prion can be modified for the analysis of amyloid aggregation of mammalian proteins in yeast.
We use genetically modified yeasts Saccharomyces cerevisiae adopted for amyloid biology research. The mutations leading to auxotrophy toward certain amino acids (leucine, lysine, tryptophane, histidine) and nucleobases (adenine, uracil) were implemented into yeast genome allowing phenotyping detection of [PSI+] and the usage of plasmids for the investigation of mammalian protein in yeast.
Application of yeast-based experimental system for studies of different aspects of human amyloidoses is discussed.
This study was supported by Saint Petersburg State University (project 93025998).
Overexpression of the <i>Ib-rolB/C</i> gene perturbs biosynthesis of caffeoylquinic acid derivatives in transgenic calli of sweet potato
Authors: Vasyutkina Elena A. , Yugay Yulia A. , Grigorchuk Valeria P. , Grishchenko Olga V. , Stepochkina Varvara D. , Shkryl Yury N. 
Published: December 2022

Ipomoea batatas is a root crop widely cultivated in South America, Africa, and Asia. This is also a source of caffeoylquinic acid derivatives (CQAs) with potential health-promoting benefits. Sweet potato genome carries two separate cellular T-DNA (cT-DNA) regions (IbT-DNA1 and IbT-DNA2). Especially, IbT-DNA2 contains five ORFs homologous to the Agrobacterium rhizogenes T-DNA, namely ORF13, ORF14, ORF17n, ORF18/ORF17n, and RolB/RolC proteins [1]. Unfortunately, presently there is insufficient information on IbT-DNA2 genes function in the physiological processes of sweet potatoes.
In this study, expressional levels of the IbT-DNA2 genes and the effect of Ib-rolB/C overexpression were examined using I. batatas cell culture. We discovered that I. batatas cT-DNA genes were not expressed in callus, and abiotic stresses and chemical elicitors affected their transcriptional levels weakly. Additionally, two Ib-rolBC-transgenic cell lines have been established though Agrobacterium-mediated transformation of I. batatas callus cells. Overexpression of Ib-rolB/C gene reduced biomass accumulation of transgenic cell lines by 1.21.6 times and increased the CQAs content by 1.51.9-fold. To justify the metabolic fluctuations, the study also looked into the expression patterns of the major biosynthetic genes, namely bPAL, IbC4H, Ib4CL, IbHCT, and IbHQT. The obtained data demonstrated that the overexpression of the Ib-rolB/C reduced the IbPAL transcript but considerable increase in the transcript levels of the IbHQT. We propose that this result was obtained through as-yet-uncharacterized signaling pathways activated by RolB/RolC.
Homologues of octopine/vitopine synthase genes in natural GMOs
Authors: Shaposhnikov Anton D. , Matveeva Tatiana V. 
Published: December 2022

The process of horizontal gene transfer causes the appearance of natural genetically modified organisms. At the moment, it is known that over 7% of dicotyledonous plant species are naturally transgenic, i.e. nGMO [1]. These plants contain the genes of agrobacteria, which are integrated in the nuclear genome during infection. In some species of naturally transgenic plants, agrobacterial genes have been preserved for millions of years of evolution. Among these genes, genes encoding octopine/vitopine synthase (ocs/vis) can be distinguished [2].
The study of homologues of octopin/vitopin synthase genes in naturally transgenic plants: their structures and diversity, products of encoded enzymes will allow us to establish the functions and evolutionary role of homologues in nGMO. Currently, bioinformatic and genetic engineering methods are used to solve these problems.
ocs\vis-like were found in 7 species: Albizia julibrissin Durazz., Cenostigma pyramidale (Tul.) Gagnon G.P.Lewis, Paulownia fortunei (Seem.) Hemsl., Pterocarya stenoptera C.DC., Rehmannia glutinosa Steud., Santalum album L., Viscum album L. In total twenty one ocs/vis sequences are known in 17 nGMO species. Twenty sequences are intact. This may indicate the functional significance of these genes for nGMO.
Phylogenetic analysis of currently known ocs/vis-like genes of Agrobacterium, Rhizobium and natural GMOs suggests that diversity of studied genes is wider, than it was estimated based on agrobacterial sequences. On the phylogenetic tree constructed by the neighbor-joining method, 6 clusters for ocs/vis can be distinguished. Three clusters contain nGMOs and agrobacteria, showing the relationship of the T-DNA sequences of nGMO with those of currently known strains of of Agrobacterium/Rhizobium. Three clusters contain only nGMOs. One of them consists of species that belong to the Cannabaceae family. Other clusters are heterogeneous. No significant ecological similarities were found among the studied species.
The obtained results can be used to study the diversity of ancient and modern strains of agrobacteria, their host specificity and the possible role of their genes in plant evolution.
The work was supported by the RSF, grant 21-14-00050 and Research Resource Center for molecular and cellular technologies of Saint Petersburg State University.
Application of genetically modified microorganisms for potential human amyloids search
Authors: Ryabinina Marina V. , Zelinsky Andrew A. , Rubel Aleksandr A. 
Published: December 2022

Amyloids are fibrous protein structures often found in patients with severe diseases, such as Alzheimers, Parkinsons diseases etc. A number of studies have shown that the production of heterologous amyloidogenic proteins in Saccharomyces cerevisiae strains results in formation of amyloid aggregates with properties similar to those found in mammals.
Amyloid aggregates formed in yeasts usually do not have their own phenotypic manifestation. To assess amyloidogenic potential of individual proteins a yeast test-system was developed under supervision of Prof. Y.O. Chernoff. The system is based on usage of genetically modified S. cerevisiae cells auxotrophic for certain growth factors, allowing effective phenotypic selection to search for amyloidogenic proteins within proteomes of various organisms [1]. Using this test-system, our laboratory evaluated amyloid potential of a spectrum of human proteins, the amyloidogenicity of which was previously predicted by bioinformatics algorithms. The proteins that have shown amyloidogenic potential in yeast-based model are being currently tested in vitro and in vivo. Some mutant Escherichia coli strains can be applied for studying propensity of heterologous proteins to form amyloids in vitro. Thus, application of genetically modified microorganisms makes it possible to identify new human amyloidogenic proteins and to improve predictive ability of bioinformatics algorithms.
The research is supported by RSF grant №20-14-00148 and by St. Petersburg State University (project No. 93025998). Authors acknowledge SPbSU Resource Centers Chromas, Molecular and Cell Technologies and Biobank.
<i>MtWOX2</i> gene in somatic embryogenesis of <i>Medicago truncatula</i>
Authors: Krasnoperova Elizaveta Y. , Tvorogova Varvara E. , Lutova Ludmila A. 
Published: December 2022

Somatic embryogenesis (SE) is one of the plant regeneration pathways. This process is very similar to zygotic embryogenesis, but embryos develop not from zygote, but from vegetative tissues. This process is widely used in biotechnology for plant transformation and propagation. Somatic embryos can derive directly from the vegetative tissues or through the formation of callus. The search for SE stimulators is very important for plant biotechnology.
Several genes were reported to be the regulators of this process, among them the WOX (WUSCHEL-RELATED HOMEOBOX) family members are presented. These genes encode homeodomain-containing transcription factors, participating in different developmental processes. WOX2 is known for its participation in zygotic embryogenesis. It is expressed in the zygote and later in the apical domain of the embryo. We study the role of this gene in the somatic embryogenesis. Overexpression of MtWOX2 in some cases leads to the development of embryogenic calli with increased size. We performed transcriptome analysis of Medicago truncatula calli with overexpression of this gene compared to the calli overexpressing GUS.
It was shown that MtWOX2 overexpression led to the changes in expression levels of genes, enriched with several GO pathways, including groups related to oxidative stress and ROS formation, response to toxic substance and auxin-activated signaling pathway. Among differentially expressed genes there are members of several TF families, e.g. MADS-box, BHLH, MYB, bZIP and others. These genes may regulate embryogenic callus development. Together, these results can be used for the search of new morphogenic regulators applicable for plant transformation.
The research was supported by RFBR grant 20-016-00124.
New cellular T-DNAs in naturally transgenic plants
Authors: Lipatov Pavel Yu. , Bogomaz Fedor D. , Gosudarev Konstantin D. , Kondrashova Sofya A. , Kuchevsky Maxim V. , Malyuga Nikita L. , Myagkiy Egor V. , Sergeenkova Marta V. , Tverdokhlebova Valeria R. , Shtina Anna D. , Matveeva Tatiana V. , Khafizova Galina V. 
Published: December 2022

Naturally transgenic plants represent the result of Agrobacterium-mediated gene transfer. T-DNA of soil bacteria Agrobacterium integrated into plants genome is called cellular T-DNA (cT-DNA) [1]. Today, more than 50 species of naturally transgenic plants, or natural GMO (nGMO) are known [2, 3]. The function of cT-DNA in plants remains unknown. It is assumed that the fixation of transgenes could give plants different selective advantages depending on which genes had been integrated into the plant [4]. In order to clarify this issue, it is necessary to study more naturally transgenic plants. Until recently, the list of nGM plants contained less than 2 dozen species, but a search through genomic and transriptomic sequencing data made it possible to more than double this list [2]. In this work, we used the same approach, looking for cT-DNA genes in whole genome sequencing data that have appeared in the NCBI WGS since 2021. We found 14 new species of naturally transgenic plants, among which the most extended cT-DNAs were found in Triadica sebifera, Lonicera japonica, and Lonicera maackii. The cT-DNAs in these species are organized as imperfect inverted repeats. In the genomes of the species Paulownia fortunei, Apocynum venetum, Elaeagnus angustifolia, Erythroxylum havanense, E. densum, E. daphnites, E. cataractarum, Ceriops decandra, Camellia oleifera, Silene uniflora, short cT-DNAs containing only opine synthesis genes were found. We also estimated the approximate age of the cT-DNAs. The first described examples date back to the Late Paleogene, and the process continues to the present. Thus, we can conclude that natural GMOs are a widespread phenomenon, many aspects of which remain unclear, requiring additional research on the topic.
The article was made with support of the Ministry of Science and Higher Education of the Russian Federation in accordance with agreement No. 075-15-2022-322 dated 22.04.2022 on providing a grant in the form of subsidies from the federal budget of the Russian Federation. The grant was provided for state support for the creation and development of a world-class scientific center, Agrotechnologies for the Future.
Search and analysis of mutations affecting the aggregation of amyloid beta peptides
Authors: Malikova Oksana A. , Zobnina Anastasia E. , Kachkin Daniel V. , Aksenova Anna Yu. , Chernoff Yury O. , Rubel Aleksandr A. 
Published: December 2022

Alzheimers disease (AD) is a fatal neurodegenerative disorder and the most common form of dementia in late life. According to the generally accepted hypothesis, the main cause of AD is the aggregation of the amyloid beta (A) peptide which leads to the formation and accumulation of plaques around a brain cells. A isoform that prevails in plaques consists of 42 amino acid residues and is termed A42. Here, we apply the yeast-based assay for searching mutations that affecting human A42 peptide aggregation. This assay is based on phenotypic detection of amyloid aggregation, nucleated by the attachment of A to prion domain of the yeast protein Sup35 in yeast S. cerevisiae (Chandramowlishwaran et al. 2018 J. Biol. Chem. 293:3436). As a result of screening, 70 derivatives with single or multiple mutations, altering amyloid nucleation were identified. Effects of most interesting mutations on biochemical and cytological parameters of A aggregates, as well on the A amyloid structure have been investigated. Results of these experiments shed light on modes and pathways of A aggregation.
This study was supported by grant 20-14-00148 from Russian Science Foundation and by St. Petersburg State University (project 93025998). Authors acknowledge SPbSU Resource Centers Chromas, Molecular and Cell Technologies, and Biobank.
The development of approaches to create new symbiotic systems
Authors: Dolgikh Elena  A. , Kantsurova Elizaveta S. , Dymo Alina M. 
Published: December 2022

Plants interact with a wide range of soil microorganisms, while interactions with symbiotic microorganisms are the most important for them. Symbiosis with nitrogen-fixing nodule bacteria provides a significant advantage in the existence of plants in nitrogen-poor soils. Since only plants from the Fabales and Rosales (a single representative Parasponia) enter into symbiosis with nodule bacteria, an idea about expanding the number of plants entering into such interactions became popular. To solve the problem of constructing new symbiotic systems, it is necessary to provide recognition of the symbiont (by transferring receptor genes into non-legume plants), morphogenesis of the nodule, and its infection.
We have managed to introduce the genes encoding receptors to surface components of rhizobia into the non-legume plants, and it provided increased colonization by nodule bacteria. It may improve the growth and development of non-legume plants and ensure their greater resistance to phytopathogens. Genome analysis of non-legume plant hop Humulus lupulus showed the existence of genes involved in symbiosis regulation, but some important regulators such as gene encoding NIN transcription factor were lost. Using genetic engineering approaches, the hop plants carrying the gene encoding NIN transcription factor were created. Analysis of these plants may provide important information about regulation of organogenesis in non-legume plants.
The work was financially supported by RSF 21-16-00106.
WAVE GENERATOR BASED ON A HYDRAULIC SYSTEM
Authors: Komarov Timofei D. , Sverbilov V. Ya. 
Published: December 2022

Renewable energy is the production of energy from resources that are inexhaustible on a human scale. The main principle is the use of energy from processes occurring in the environment.
Alternative energy is a set of promising methods for obtaining, transferring and using energy, which are less common than traditional ones, but are of interest due to the low risk of causing harm to the environment.
Currently, the generation of electricity through the use of wave energy is not common and is experimental. Nevertheless, it is one of the most promising renewable energy sources, and also has the potential to become one of the main components of the world's energy production.
In this work, a wave generator based on a hydraulic system has been designed. Various versions of this installation are considered, and the existing designs of such devices are analyzed. Based on this, the most efficient design was selected.
The following stages have been completed: the design of the wave generator, the design of the hydraulic system, the calculation of the system elements according the technical requirements, the selection of standard components and units, the calculation of efficiency and mathematical modeling of the system operation.
SYSTEM OF MECHATRONIC CONTROL MODULES FOR ADAPTIVE BRAKING
Authors: Solyatov Artyom А. , Sidorenko Valentin S. 
Published: December 2022

The purpose of the work is to increase the stability of the process of movement and braking, as well as to increase the wear resistance of the equipment of the locomotive and the rail track, by developing and improving adaptive systems that maintain optimal adhesion of the wheel to the working surface of the rail.
The theoretical conclusions obtained and the results of model studies show the effectiveness of the proposed adaptive control method for adaptive systems and the possibility of building a simple microprocessor control system for the brake and sand feeding, supplementing the regular system of the locomotive, aimed at eliminating the loss of adhesion.
Does culture influence online customer engagement of university stakeholders: pandemic perspective
Authors: Voropai Olga , Pichyk Kateryna , Chala Nina 
Published: December 2022

The COVID-19 pandemic has significantly increased the role of social media in the communication policy of educational institutions. Ensuring the effective use of social networks to communicate with target audiences requires universities to understand, among other things, the importance of cultural context for the audience’s engagement.We analyzed the engagement rates (ER) in Facebook and Instagram for the most influential universities in the Eastern Partnership (EaP) countries to determine the influence of the country’s cultural characteristics.The study examines two hypotheses. H1: Stakeholders in collectivist cultures with a high level of power distance are more likely to increase online engagement when limited in offline communication. H2: High uncertainty avoidance countries with long-term orientation will demonstrate broader social media engagement.The results showed that the dynamics of stakeholder activity in the social networks Facebook and Instagram for the most influential universities in the Eastern Partnership countries do not depend on the country’s cultural profile.Thus, we can conclude that universities can expand their presence in the digital communication space while addressing representatives of their target audiences from different countries without differentiating their communication messages. The study results also indicate the prospects for expanding remote students’ mobility programs as they will not require different approaches to effective digital communication.
JEL classіfіcatіon: M30, M39, I20, I29
Main characteristics of the image of the higher school teacher and the factors of influence on it
Authors: Galytska Eleonora , Donkohlova Natalia 
Published: December 2022

The article highlights the essence of the concept of image and the image of a teacher of a higher education institution, analyzes scientific works devoted to this issue, highlights the results of a questionnaire survey and interviews, which made it possible to determine the respondents’ vision of those qualities and traits that should be inherent in teachers of higher education institutions.In order to assess the closeness of the connection between the specified features, the correlation coefficient of Spearman’s ranks was calculated and its value was checked for the significance of the connection. In particular, it was determined how important it is for students that the teacher has a scientific degree and title; own scientific articles, manuals and textbooks; and how important it is for the teacher to be a practitioner. It was found out whether students pay attention to how the teacher communicates with other teachers and students, how the teacher answers students’ questions and whether it is important for them when there is contact with the teacher on social networks and the latest technologies are used in the educational process; do students pay attention to how the teacher reacts to the opposite opinion, what are his manners in the process of interaction in the environment of colleagues and students, what appearance of the teacher impresses students more, etc.The importance (on the basis of a rank scale) of image characteristics indicated personally (answers to open questions) by both male and female respondents was determined. The following main characteristics of the image of a teacher of a higher education institution were noted: self-confident professional; has a love and flair for teaching; is able to convey information, interest, capture the attention of students; is able to clearly explain tasks and their evaluation criteria; objective and impartial; punctual, responsible in fulfilling commitments and keeping one’s word; friendly and open in communication; sociable, with a sense of humor; able to consider the psychological characteristics of students; has a suitable appearance.
JEL classіfіcatіon: A22, Z00
Kyiv School of Political Economy as a subject of scientific studies
Authors: Kurbet Oleksandra 
Published: December 2022

The main purpose of this paper was the historical and economic analysis of the Kyiv School of Political Economy representation in the modern scientific literature and the systematization of approaches to determining this community of Kyiv economists. Analysis showed that in the Soviet period the scientific heritage of this community of scholars had been critical, and the school itself had been defined as bourgeois. At the end of the 20th century researchers began to show a creative perception of scientific achievements of the 19th – early 20th century economists, including Kyiv scholars’ achievements. The number of historical and economic studies were increased and the issues diversified. The author of this paper systematized approaches to studying the Kyiv School based on the complex analysis of modern scientific literature. These approaches are legal, financial, managerial and political-economic. Within these approaches, researchers study Kyiv University School of Police Law, Kyiv School of Financial Law, Kyiv Financial School, School of Ukrainian Management Scientific Thought, Kyiv Psychological School of Political Economy, Kyiv School of Economics, Kyiv School of Political Economy, etc. The most common one is the political-economic approach, within which researchers study the methodology and scientific achievements of the Kyiv school and some of its representatives in the field of economic research. The author emphasized that such a variety of different approaches is generated by the multifaceted Kyiv School’ scientific achievements that give food for research to modern specialists in various fields of economics and law. It was concluded that an attempt to reduce the community of Kyiv scholars to one scientific school, focusing on the only research area, would be artificial as it would cut off other areas that don’t meet the requirements of the chosen peculiarity.
JEL classification: B19