| 279801. |
- Shevchenko, Ganna, et al.
(författare)
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Cloud-point extraction and delipidation of porcine brain proteins in combination with bottom-up mass spectrometry approaches for proteome analysis
- 2010
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Ingår i: Journal of Proteome Research. - : ACS. - 1535-3893 .- 1535-3907. ; 9:8, s. 3903-3911
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Tidskriftsartikel (refereegranskat)abstract
- In this study, temperature-induced phase fractionation also known as cloud-point extraction (CPE) with the nonionic surfactant Triton X-114 was used to simultaneously extract hydrophobic and hydrophilic proteins from porcine brain tissue. Various protein precipitation/delipidation procedures were investigated to efficiently remove lipids and detergents while retaining maximum protein recoveries. The best performing delipidation method was then used in combination with CPE to compare three different mass spectrometry (MS) based "bottom-up" proteomic approaches for protein analysis of the porcine brain. In the first approach, the intact proteins were initially separated by one-dimensional (1D) gel electrophoresis. The excised protein bands were digested with trypsin, and the peptides were separated by reversed phase nanoliquid chromatography (RP-nanoLC) followed by electrospray ionization (ESI) tandem mass spectrometry (MS/MS) analysis. The other bottom-up proteomic approaches were based on first enzymatical digestion of the proteins followed by RP-nanoLC separation in combination with matrix assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF MS) or on the combination of in-solution isoelectric focusing (IEF) with ESI-nanoLC-MS/MS of the IEF separated peptides. In total, we found and unambiguously identified 331 unique proteins. The overlap between different techniques was about 10%, showing that the use of multiple proteomic approaches is beneficial to yield a better coverage of the proteome. Furthermore, the overlap between the CPE extracted hydrophilic and hydrophobic proteins was rather small (9-16%), indicating an efficient sample preparation technique to extract and separate hydrophilic and hydrophobic proteins from brain tissue. The percentage of identified membrane proteins was 27%, which is in accordance to the fact that about one-third of all genes in various organisms encode for this class of proteins. The results indicate that cloud point extraction is a promising sample preparation tool, which allows simultaneous in depth studies of brain derived membrane proteins as well as hydrophilic proteins. This technique can be very useful when studying human central nervous system (CNS) tissue or animal models of neurological diseases.
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| 279802. |
- Shevchenko, Ganna, et al.
(författare)
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Comparison of Extraction Methods for the Comprehensive Analysis of Mouse Brain Proteome using Shotgun-based Mass Spectrometry
- 2012
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 11:4, s. 2441-2451
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Tidskriftsartikel (refereegranskat)abstract
- This study compares 16 different extraction methods for the comprehensive extraction of mouse brain proteome in combination with "shotgun"-based mass spectrometry (MS). Membrane proteins (MPs) are responsible for a large part of the regulatory functions of the cell and are therefore of great interest to extract and analyze. Sixteen protein extraction protocols were evaluated in regards to protein yield and number of identified proteins with emphasis on MPs. The extracted proteins were delipidated, on-filter digested, and analyzed by reversed phase nanoliquid chromatography (RP-nanoLC) in combination with electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using a 7 T hybrid LTQ: FT mass spectrometer. Detergent-based lysis buffers showed higher efficiencies and yields in the extraction of proteins from the brain tissue compared to solubilization with organic solvents or organic acids. The detergent octyl-beta-D-glucopyranoside gave the highest number of identified proteins (541) as well as numbers and percentages of identified MPs (29%). Detergent-based protocols are the best sample preparation tools for central nervous system (CNS) tissue and can readily be applied to screen for candidate biomarkers of neurological diseases.
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| 279803. |
- Shevchenko, Ganna, et al.
(författare)
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Neuroproteomics Tools in Clinical Practice
- 2015
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Ingår i: Biochimica et Biophysica Acta - Proteins and Proteomics. - : Elsevier BV. - 1570-9639 .- 1878-1454. ; 1854:7, s. 705-717
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Tidskriftsartikel (refereegranskat)abstract
- Abstract Neurodegenerative disorders such as Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS) are characterized by neuronal impairment that leads to disease-specific changes in the neuronal proteins. The early diagnosis of these disorders is difficult, thus, the need for identifying, developing and using valid clinically applicable biomarkers that meet the criteria of precision, specificity and repeatability is very vital. The application of rapidly emerging technology such as mass spectrometry (MS) in proteomics has opened new avenues to accelerate biomarker discovery, both for diagnostic as well as for prognostic purposes. This review summarizes the most recent advances in the mass spectrometry-based neuroproteomics and analyses the current and future directions in the biomarker discovery for the neurodegenerative diseases.11 This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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| 279804. |
- Shevchenko, Valeriy, et al.
(författare)
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Molecular determinants of the interaction between glioblastoma CD133(+) cancer stem cells and the extracellular matrix
- 2020
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Ingår i: NOVEL THERAPEUTIC ADVANCES IN GLIOBLASTOMA. - LONDON ENGLAND : Elsevier. - 9780128211144 ; , s. 155-169
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Bokkapitel (refereegranskat)abstract
- Glioblastoma multiforme (GBM) is the most common primary tumor of the human brain. It is characterized by invasive growth and strong resistance to treatment, and the median survival time of patients is 15 months. The invasive growth of this tumor type is associated with tumor cells with an aggressive phenotype, while its treatment resistance is attributed to cancer stem cells (CSCs). It remains unclear if CSCs have a more invasive nature than differentiated glioblastoma cells (DGCs), and what contribution CSCs make to the aggressive phenotype of GBM. Interaction with the extracellular matrix (ECM) is a key factor in the development of invasion. The aim of the present study was to compare the expression levels of signaling pathway proteins involved in interaction of receptors with the ECM in CSCs and DGCs. The U-87MG GBM cell line was used in the present study CSCs were extracted from gliomaspheres through magnetic-activated cell sorting based on the expression of cluster of differentiation 133 (CD133); CD133-negative DCGs were used as a control. HPLC and mass spectrometry were also used, and biological and molecular functions, signaling pathways and protein-protein interactions were analyzed using publicly available databases. Increased expression levels of the following 10 proteins involved in interaction with the ECM were identified in CSCs, compared with expression levels in DGCs: COL6A1, COL6A3, FN1, ITGA2, ITGA5, ITGAV, ITGB1, ITGB3, LAMB1 and LAMC1. The proteome of CSCs was observed to have >2-fold higher expression of these key proteins, when compared with the DGC proteome. Increased expression levels of four proteins (FERMT2, LOXL2, HDAC2 and FBN1) involved in activating signaling in response to receptor interaction with the ECM was also observed, indicating that CSCs may have highly invasive nature. LOXL2 expression level was >9-fold higher in CSCs compared to DGCs, suggesting that this protein may have potential as an marker for CSCs and as a target for this cell type in GBM.
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| 279805. |
- Shevchenko, Valery, et al.
(författare)
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Proteins of the Wnt signaling pathway as targets for the regulation of CD133(+) cancer stem cells in glioblastoma
- 2019
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Ingår i: Oncology Reports. - : SPANDIDOS PUBL LTD. - 1021-335X .- 1791-2431. ; 41:5, s. 3080-3088
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Tidskriftsartikel (refereegranskat)abstract
- Glioblastoma multiforme (GBM) is one of the most aggressive types of brain tumor and is highly resistant to therapy. The median survival time for patients with GBM is 15 months. GBM resistance to treatment is associated with cancer stem cells (CSCs). CD133 membrane glycoprotein is the best-known marker of GBM CSCs. The Wnt signaling pathway plays an important role in the proliferation of all stem cells. To the best of our knowledge, the present study was the first to examine the expression levels of proteins associated with the Wnt signaling pathway in CD133(+) CSCs of human GBM. Furthermore, potential targets that may regulate CD133(+) CSCs in human GBM were investigated. The human GBM U-87MG cell line was cultured in neurobasal medium supplemented with B27, fibroblast growth factor, epidermal growth factor and no serum. Immunohistochemical characteristics of glioma spheres were investigated based on the expression of key markers of CSCs. CD133(+) cells were extracted from glioma spheres by cell sorting and then lysed. High-performance liquid chromatography-mass spectrometry was used for proteome analysis. Lysates of CD133(-) cells in GBM were used for comparison. The present study was the first to describe the conceptual proteome differences between GBM and CD133(+) CSCs of the common pool. Major differences were identified in the glycolysis/gluconeogenesis, focal adhesion, tight junction and Wnt signaling pathways. This study aimed to analyze the crucial role that proteins of the Wnt signaling pathway play in stem cell proliferation. The identified proteins were analyzed for their association with the Wnt signaling pathway using the international open databases PubMed, Protein Analysis Through Evolutionary Relationships, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and Search Tool for the Retrieval of Interacting Genes/Proteins. An increased expression of 12 proteins associated with the Wnt signaling pathway were identified in GBM CD133(+) CSCs, which included catenin beta-1, disheveled associated activator of morphogenesis 1, RAC family small GTPase 2 and RAS homolog gene family member A, a number of which are also associated with adherens junctions. The Wnt signaling pathway is not upregulated in CSCs; however, the high expression levels of adenomatous polyposis coli, beta-catenin, C-terminal binding protein (CtBP) and RuvB-like AAA ATPase 1 (RUVBL1 or Pontin52) proteins suggest the possibility of alternative activation of specific genes in the nuclei of these cells. Calcyclin-binding protein, casein kinase II alpha, casein kinase II beta, CtBP1, CtBP2, CUL1 and RUVBL1 proteins may be used as targets for the pharmaceutical regulation of CSCs in complex GBM treatment.
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| 279806. |
- Shevchuk, Olena, et al.
(författare)
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Bio-bibliography of scientists of Ukraine. Mykhailo Mykhailovych Ivanyk.
- 2022
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Annan publikation (refereegranskat)abstract
- Contains a brief outline of scientific, scientific and organizational activities, the main dates of life and a chronological list of the works of the famous Ukrainian geologist, laureate of the Prize named after PAS. Tutkovsky, doctor of geological and mineralogical sciences, professor M.M. Ivanika Highlights the contribution of Ukrainian geologists to the study of the Earth's interior. It is addressed to students, postgraduates, scientists and the general public of readers.
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| 279807. |
- Shevchuk, Olena, et al.
(författare)
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Distinguishing the Hauterivian-Barremian sediments in the Karkinitsko-North-Crimean Trough (Zakhidno-Oktyabrska area) by microfossils
- 2022
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Ingår i: Mineral resources of Ukraine (Мінеральні ресурси України; Mìneralʹnì resursi Ukraïni). - Kyiv, Ukraine : Ukraïnsʹka geologìčna kompanìâ. - 1682-721X .- 2707-8698. ; 2, s. 33-41
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Tidskriftsartikel (refereegranskat)abstract
- According to bio- and lithological methods, we have identified and stratified Lower Cretaceous (Neocomian) deposits from well sections: № 29 and 31, which were drilled on the territory of the Zakhidno-Оktyabrska area of the Karkinitsko-North-Crimean though.Hauterivian deposits are found in the depth range 3131-3142 m (wells № 29 – Zakhidno-Оktyabrska), in the depth range 3218-3228 m (wells № 31 – Zakhidno-Оktyabrska) and Barremian deposits in the depth range 3105-3131 m (wells № 29 – Zakhidno-Оktyabrska) and in the depth range 3196-3218 m (wells № 31 – Zakhidno-Оktyabrska), which were previously dated to the Neocomian.We have supplemented the paleontological characteristics of dinocysts and spore-pollen complexes of the biozonal scheme of Lower Cretaceous sediments of the Plain Crimea, which is being developed in the Department of Stratigraphy and Paleontology of Mesozoic Sediments of the Institute of Geological Sciences of NAS of Ukraine within the budget theme “Biostratigraphy of Meso-Cenozoic deposits of oil and gas regions of Ukraine as a fundamental basic basis for the systematic support of geological works” 2022-2025. Based on the peculiarities of the lithological composition of the rocks and the palynological characteristics of the deposits of the Kalininska suite of the Lower Cretaceous deposits of the Crimean Plain, we suggest that the Mesozoic Commission of the NSC of Ukraine consider the issue of distinguishing within its scope two subsoils: the lower one, represented by gray, red-brown, fine-grained, clayey sandstones, sometimes with gravel, and the characterized the Hauterivian spore-pollen complex, and the upper one, represented by dark gray siltstones with layers of sandy or organogenic-detrital limestones, is characterized by the Barremian spore-pollen complex and dinocyst complex of the Odontochitina operculata zone, dated to the Barremian
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| 279808. |
- Shevchuk, Olena, et al.
(författare)
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Integration of Ukrainian paleobotanists and palynologists into the international community of scientists
- 2023
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Ingår i: Mineral resources of Ukraine. - Kyiv, Ukraine. - 1682-721X. ; 1:1, s. 44-51
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Tidskriftsartikel (refereegranskat)abstract
- Introduction. The European Palaeobotany and Palynology Conference is held every 4 years. At meetings and seminars of the conference, a wide range of scientific problems related to taxonomy of ancient plants, morphology, nomenclature, as well as the latest results of paleobotanical and palynological research are represented, ways of using them for stratigraphic constructions, paleogeographic, including paleoclimatic reconstructions, and the study of archaeological monuments are discussed.Formulation of the problem. A necessary aspect of today’s scientific research in Ukraine is the integration of the research results of Ukrainian scientists into the world scientific space. An important component in the implementation of this direction is the active participation of scientists in international projects and the presentation of research results at international professional conferences. The presented publication is devoted to an overview of one of these forums.Formulation of the purpose of the article. The main purpose of the article is to highlight the latest directions of the modern stage of paleobotanical and palynological research of the world scientific community, which were represented at the 11th European paleobotanical – palynological conference, as well as the characteristics of the scientific results of Ukrainian scientists, which was presented at this forum.Presenting main material. The 11th European Conference on Paleobotany and Palynology was held in Stockholm on June 19-22, 2022. The conference was jointly organized by the Swedish Museum of Natural History and Stockholm University. The head of the organizing committee and event coordinator was Professor Vivi Vaida.The conference gathered more than 240 delegates from 44 countries of the world, which proves the authority of the conference and the exit of EPPC beyond Europe to the international level. More than 180 oral scientific presentations and about 70 poster presentations were presented during the plenary and sectional meetings.The organizers of the conference condemned Russia’s invasion of Ukraine, and the support of the Ukrainian scientific community and the people of Ukraine was felt at all stages of the conference preparation.Main scientific directions of symposia work. Work during the conference took place in 35 scientific symposia of various topics, covering almost all modern aspects of paleobotany and palynology. The article provides a general description of the latest research that was discussed at the conference.Achievements of Ukrainian scientists represented at the conference. In total, scientists from Ukraine presented 2 oral reports – O. A. Shevchuk (The first Cretaceous megaspores from Ukraine) and D. O. Pustovoitova (History of palynological research of Mesozoic deposits in Ukraine) and 6 posters – O. A. Shevchuk (Paleobotanical research in Ukraine); O. A. Sirenko (Changes in the vegetation of Ukraine in the Gelasian time (by palynological data)); A. B. Ivanina, A. О. Myronova (Standardized characteristics of the Geminospora extensa Zone from the Givetian of western Ukraine); V. Р. Grytsenko and O. A. Shevchuk (On the collections of fossil plant and algae in the geological department of the National Museum of Natural History at the National Academy of Sciences of Ukraine); A. I. Martyshyn, O. A. Shevchuk (Taphonomy of tubular fossils (algae) from the deposits of the Late Ediacaran of Ukraine); N. I. Boyarina (The collection of the late Carboniferous plant fossils of the Donets Bassin in the Institute of Geological Sciences of NAS of Ukraine: general review). The scientific reports presented concerned various aspects of paleobotanical and palynological research: historical, taphonomic, stratigraphic, paleogeographic and paleoclimatic reconstructions, review of paleobotanical collections and problems of their storage in modern military conditions. The presented materials covered the results of the study of micro- and macro-plant remains from rocks of all subdivisions of the Phanerozoic (Paleozoic, Mesozoic, Cenozoic), as well as the Neoproterozoic (Ediacaran).Conclusions. At the conference, during the plenary and sectional meetings, considerable attention was paid to the results of research devoted to climate changes and their impact on the biota of high latitudes in the past, as well as reconstructions of the paleogeographic conditions of the formation of deposits of different ages, especially Holocene. Attention is focused on the need to develop new research methods, in particular 3D modeling of paleontological objects, popularization of paleobotany and palynology achievements, preservation of paleontological monuments, interaction of amateur paleontologists with professional paleontologists and scientific institutions and organizations
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| 279809. |
- Shevchuk, Olena
(författare)
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Paleobotanical research in Ukraine
- 2022
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Ingår i: 11<sup>th</sup> European Palaeobotany and Palynology Conference Abstracts, Program and Proceedings. - Stockholm, Sweden : Swedish Museum of Natural History. - 9789152734339 ; , s. 235-236
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Konferensbidrag (refereegranskat)abstract
- Palaeobotanical research in Ukraine has a history of more than one hundred and fifty years, which is calculated from the time of publication (1872) of the work of A.V. Gurov “Fossil organic remains of Donetsk coal deposits”. The research was conducted by scientists from Kyiv, Lviv, Luhansk, Chernihiv, Dnipropetrovsk, Artemivsk. The most numerous was the team of palaeobotanists of the Institute of Geological Sciences of the National Academy of Sciences of Ukraine, headed by the corresponding member E.O. Novik. The stratigraphy of carbonaceous deposits, patterns in the development of the coal flora, and issues of coal accumulation were the areas that were developed under her leadership by experts, such as O.I. Anisimova, T.A. Ishchenko, O.P. Fisunenko and O.K. Shchogolev. Mesozoic and Cenozoic floras were studied by E.E. Mihacheva, F.А. Stanislavsky, Yu.V. Teslenko, N.Ya. Shvaryova and others. The great work of the academician of the USSR, A.M. Kryshtofovych, is the book “Paleobotany”, which includes numerous discoveries of fossil plants from Ukrainian sections. A significant contribution to the development of palaeobotany in Ukraine, its theoretical foundations, and methodology was made by professors O.P. Fisunenko and O.K. Shchogolev. O.P. Fisunenko dealt with the theory and methodology of stratigraphy, analysis of the natural-philosophical problem of time in geology, in seeing the path of detailed development of stratigraphy through the Phanerozoic, taking into account the general laws of evolution of the biota and crust. O.K. Shchogolev initiated a new synthetic biological-geological-geographical scientific direction in palaeobotany–paleophytogeocenology. O.P. Gubskaya studied the plant communities of the Bashkirian and Moscovian (Carboniferous) stages of Donbas. A.A. Ishchenko studied the Silurian algae flora and the Kuksonia flora of Volyn-Podillya. F.A. Stanislavsky’s works on the Triassic leaf flora and middle Jurassic of the north-western outskirts of Donbas have received worldwide recognition. Yu.V. Teslenko studied the flora of the Jurassic and Cenozoic, developed the concept of phased development of the Earth’s vegetation depending on changes in the chemical composition of the atmosphere. He established the vertical botanical and geographical zonation of the eastern regions of the Tethys and Paratethys in the Miocene and Pliocene. The Cenomanian flora near the town of Kaniv (Ukrainian Shield, Central Ukraine) was studied in 1939 by N.V. Pimenova. Later, M.P. Doludenko, E.I. Kostina and I.A. Shilkina attributed this flora to the late Albian. Also, notable are the achievements of Ukrainian paleobotanists L.T. Malyshko and S.O. Molchanov, who studied the Eocene, Oligocene and Neogene floras of the western territory of Ukraine. Today palaeobotanists of the Institute of Geological Sciences of the National Academy of Sciences of Ukraine are working actively. This team includes N.I. Boyarina, who studies the flora of the Palaeozoic and A.I. Martyshyn, who studies the Ediacaran biota. Also, V.P. Hrytsenko has made great achievements in the study of the Ediacarian algae of Podillya (southwestern Ukraine) from the National Science and Natural History Museum of the National Academy of Sciences of Ukraine. Currently, the Paleontological Museum of the Taras Shevchenko National University, namely the Institute of Geology, has a collection of late Albian–Cenomanian plants from the outskirts of Kaniv. This collection is replenished and studied by teachers and students during their annual research internships in this region (Popova, Moroz, 2010). We have recently launched a comprehensive palaeobotanical and palynological research program in Ukraine. Thus, the Bathonian deposits of the north-western outskirts of Donbas (Shevchuk, Slater, Vajda, 2018), the upper Albian-Cenomanian deposits from central part of the Ukrainian Shield (Shevchuk, 2021) were studied.
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| 279810. |
- Shevchuk, Olena, et al.
(författare)
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Palynology of Jurassic (Bathonian) sediments from Donbas, northeast Ukraine
- 2018
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Ingår i: Palaeobiodiversity and Palaeoenvironments. - Berlin : Springer Berlin/Heidelberg. - 1867-1594 .- 1867-1608. ; 98:1, s. 153-164
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Tidskriftsartikel (refereegranskat)abstract
- A palynological and sedimentological study of an outcrop succession adjacent to the village of Kamyanka within the Kharkiv region of northeast Ukraine was carried out. The successions occur within the Dnieper–Donets Basin, which hosts vast successions (> 20 km) of post mid- Devonian strata and is one of the main hydrocarbonproducing basins in Europe. Middle Jurassic sandstones, siltstones and claystones represent the sedimentary successions at the Kamyanska locality. Few palynological studies have been performed on the Jurassic of Ukraine and even fewer presented in the international literature. Thirty spore taxa and 21 pollen taxa were identified, together with taxa kept in open nomenclature (e.g. bisaccate pollen). Two palynological assemblages were identified within the Kamyanska succession (assemblages A and B) dated as Bathonian. Assemblage A is dominated by the fern spores (Cyathidites and Osmundacidites) and gymnosperm pollen produced by Cupressaceae Perinopollenites elatoides), ginkgophytes/Cycadales/Bennettitales (monosulcates) and Cheirolepidiaceae (Classopollis). Assemblage B differs in also comprising high abundances of Gleicheniidites and higher percentages of Pinuspollenites and Araucariacites compared to assemblage A. Another difference between the two units is the high relative abundance of seed fern pollen (Alisporites) in the upper part of assemblage B. The thermal alteration index (TAI) of the palynomorphs is estimated to range from 3 to 3.5, indicating a burial depth corresponding to the mature main phase of liquid petroleum and, to some extent, gas generation. Comparisons between the miospore and macrofloral assemblages show that the palynoflora and macroflora are strongly similar at broad taxonomic levels. Importantly, the miospore assemblages described here compare well with European Middle Jurassic assemblages indicating limited provincialism, with similar vegetation extending from eastern Ukraine and across most of Western Europe.
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