The Experts below are selected from a list of 140067 Experts worldwide ranked by ideXlab platform
Eugenia V Zybina - One of the best experts on this subject based on the ideXlab platform.
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Genome Variation in the trophoblast cell lifespan diploidy polyteny depolytenization Genome segregation
World Journal of Medical Genetics, 2014Co-Authors: T G Zybina, Eugenia V ZybinaAbstract:Genome Variation in the trophoblast cell lifespan: Diploidy, polyteny, depolytenization, Genome segregation
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Genome Variation in the trophoblast of different mammalian species diploidy polyteny depolytenization Genome segregation
Placenta, 2014Co-Authors: T G Zybina, G I Stein, Pozharisski Kazimir, Eugenia V ZybinaAbstract:s / Placenta 35 (2014) A1eA112 A66 Factor (PIF) is a peptide secreted by viable mammalian embryos. Moreover, it is detected in pregnant women circulation. Recently, it was shown that PIF, in vitro, promotes invasion in trophoblast cell lines. Objectives: The present study was undertaken to assess the presence of PIF in human placenta during gestation and to characterize its effects on primary human trophoblast invasion. Methods: PIF distribution in implantation site was characterized by immunohistochemistry. Human EVT derived from first trimester placenta were cultured in mediumwith 50 or 100 nM of PIF. Proteolytic activity was detected by zymography and invasiveness was assessed by Matrigel invasion assay. We also investigated the signalling pathways involved in PIF activation in human trophoblasts by using specific inhibitors. Results: At the fetomaternal interface, intense PIF labelling was detected during early gestation in trophoblastic cells. However, a decrease of PIF labelling was observed at term. Furthermore, PIF (50nM) significantly promoted invasion of human EVT. This pro-invasive effect of PIF in EVTwas associatedwith (i) increasedmatrix metalloproteinase MMP-9 activity and (ii) reduced tissue inhibitor of metalloproteinase-1 (TIMP-1) mRNA expression. PIF also regulated av and a1 integrin mRNA expressions. Last, the pro-invasive effect of PIF appeared to be mediated by the mitogenactivated protein kinase (MAPK), phosphoinositide-3-kinase (PI3K), and the Janus-kinase signal transducer and activator of transcription (JAKSTAT) signalling pathways. Conclusion: This work describes the direct positive effect of PIF on the control of human trophoblastic cell invasion by modulating MMP/TIMP balance and integrin expressions. Moreover, these results provide insight into the possible role of PIF in pathological conditions characterized by insufficient or excessive trophoblast invasion. P2.14. Genome Variation IN THE TROPHOBLAST OF DIFFERENT MAMMALIAN SPECIES: DIPLOIDY, POLYTENY, DEPOLYTENIZATION, Genome SEGREGATION Tatiana Zybina , Grigory Stein , Pozharisski Kazimir , Eugenia Zybina a a Institute of Cytology RAS, St.-Petersburg, Russia, Russia; Russian Research Centre for Radiology and Surgical Technologies, St.-Petersburg,
T G Zybina - One of the best experts on this subject based on the ideXlab platform.
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Genome Variation in the trophoblast cell lifespan diploidy polyteny depolytenization Genome segregation
World Journal of Medical Genetics, 2014Co-Authors: T G Zybina, Eugenia V ZybinaAbstract:Genome Variation in the trophoblast cell lifespan: Diploidy, polyteny, depolytenization, Genome segregation
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Genome Variation in the trophoblast of different mammalian species diploidy polyteny depolytenization Genome segregation
Placenta, 2014Co-Authors: T G Zybina, G I Stein, Pozharisski Kazimir, Eugenia V ZybinaAbstract:s / Placenta 35 (2014) A1eA112 A66 Factor (PIF) is a peptide secreted by viable mammalian embryos. Moreover, it is detected in pregnant women circulation. Recently, it was shown that PIF, in vitro, promotes invasion in trophoblast cell lines. Objectives: The present study was undertaken to assess the presence of PIF in human placenta during gestation and to characterize its effects on primary human trophoblast invasion. Methods: PIF distribution in implantation site was characterized by immunohistochemistry. Human EVT derived from first trimester placenta were cultured in mediumwith 50 or 100 nM of PIF. Proteolytic activity was detected by zymography and invasiveness was assessed by Matrigel invasion assay. We also investigated the signalling pathways involved in PIF activation in human trophoblasts by using specific inhibitors. Results: At the fetomaternal interface, intense PIF labelling was detected during early gestation in trophoblastic cells. However, a decrease of PIF labelling was observed at term. Furthermore, PIF (50nM) significantly promoted invasion of human EVT. This pro-invasive effect of PIF in EVTwas associatedwith (i) increasedmatrix metalloproteinase MMP-9 activity and (ii) reduced tissue inhibitor of metalloproteinase-1 (TIMP-1) mRNA expression. PIF also regulated av and a1 integrin mRNA expressions. Last, the pro-invasive effect of PIF appeared to be mediated by the mitogenactivated protein kinase (MAPK), phosphoinositide-3-kinase (PI3K), and the Janus-kinase signal transducer and activator of transcription (JAKSTAT) signalling pathways. Conclusion: This work describes the direct positive effect of PIF on the control of human trophoblastic cell invasion by modulating MMP/TIMP balance and integrin expressions. Moreover, these results provide insight into the possible role of PIF in pathological conditions characterized by insufficient or excessive trophoblast invasion. P2.14. Genome Variation IN THE TROPHOBLAST OF DIFFERENT MAMMALIAN SPECIES: DIPLOIDY, POLYTENY, DEPOLYTENIZATION, Genome SEGREGATION Tatiana Zybina , Grigory Stein , Pozharisski Kazimir , Eugenia Zybina a a Institute of Cytology RAS, St.-Petersburg, Russia, Russia; Russian Research Centre for Radiology and Surgical Technologies, St.-Petersburg,
Martin C J Maiden - One of the best experts on this subject based on the ideXlab platform.
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bigsdb scalable analysis of bacterial Genome Variation at the population level
BMC Bioinformatics, 2010Co-Authors: Keith A Jolley, Martin C J MaidenAbstract:Background The opportunities for bacterial population genomics that are being realised by the application of parallel nucleotide sequencing require novel bioinformatics platforms. These must be capable of the storage, retrieval, and analysis of linked phenotypic and genotypic information in an accessible, scalable and computationally efficient manner.
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bigsdb scalable analysis of bacterial Genome Variation at the population level
BMC Bioinformatics, 2010Co-Authors: Keith A Jolley, Martin C J MaidenAbstract:The opportunities for bacterial population genomics that are being realised by the application of parallel nucleotide sequencing require novel bioinformatics platforms. These must be capable of the storage, retrieval, and analysis of linked phenotypic and genotypic information in an accessible, scalable and computationally efficient manner. The Bacterial Isolate Genome Sequence Database (BIGSDB) is a scalable, open source, web-accessible database system that meets these needs, enabling phenotype and sequence data, which can range from a single sequence read to whole Genome data, to be efficiently linked for a limitless number of bacterial specimens. The system builds on the widely used mlstdbNet software, developed for the storage and distribution of multilocus sequence typing (MLST) data, and incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. These loci can be further organised into 'schemes' for isolate characterisation or for evolutionary or functional analyses. Isolates and loci can be indexed by multiple names and any number of alternative schemes can be accommodated, enabling cross-referencing of different studies and approaches. LIMS functionality of the software enables linkage to and organisation of laboratory samples. The data are easily linked to external databases and fine-grained authentication of access permits multiple users to participate in community annotation by setting up or contributing to different schemes within the database. Some of the applications of BIGSDB are illustrated with the genera Neisseria and Streptococcus. The BIGSDB source code and documentation are available at http://pubmlst.org/software/database/bigsdb/ . Genomic data can be used to characterise bacterial isolates in many different ways but it can also be efficiently exploited for evolutionary or functional studies. BIGSDB represents a freely available resource that will assist the broader community in the elucidation of the structure and function of bacteria by means of a population genomics approach.
Peter Em Taschner - One of the best experts on this subject based on the ideXlab platform.
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pathogenicity interpretation in the age of precision medicine the 2015 annual scientific meeting of the human Genome Variation society
Human Mutation, 2016Co-Authors: William S Oetting, Anthony J Brookes, Shamil R Sunyaev, Marc S Greenblatt, Steven E Brenner, Reece K Hart, Rachel Karchin, Peter Em TaschnerAbstract:There is now a convergence of two modes of genetic testing, that of testing a few candidate genes at a time based on suspicion of a specific genetic disease, and that of genomic testing, especially when a candidate gene(s) is not suspected or known. Both aim to interpret pathogenicity of identified genetic variants. The 2015 annual scientific meeting of the Human Genome Variation Society (HGVS; http://www.hgvs.org) was held on the 6th of October in Baltimore, MD, with the theme of “Pathogenicity Interpretation in the Age of Precision Medicine.” The HGVS is focusing attention on advancing the field of variant interpretation. Progress will require both new developments in analytical methods (in vitro, in silico, statistical, and other methods) and cooperation among scientific, clinical, and regulatory participants in developing and maintaining standards for all areas of pathogenicity assessment, variant nomenclature, and annotation. This year's meeting covered all of these areas.
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Open Access A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
2013Co-Authors: Jeroen Fj Laros, Johan Den T Dunnen, André Blavier, Peter Em Taschner, Ghent BelgiumAbstract:Background: The use of a standard human sequence variant nomenclature is advocated by the Human Genome Variation Society in order to unambiguously describe genetic variants in databases and literature. There is a clear need for tools that allow the mining of data about human sequence variants and their functional consequences from databases and literature. Existing text mining focuses on the recognition of protein variants and their effects. The recognition of variants at the DNA and RNA levels is essential for dissemination of variant data for diagnostic purposes. Development of new tools is hampered by the complexity of the current nomenclature, which requires processing at the character level to recognize the specific syntactic constructs used in variant descriptions. Results: We approached the gene variant nomenclature as a scientific sublanguage and created two formal descriptions of the syntax in Extended Backus-Naur Form: one at the DNA-RNA level and one at the protein level. To ensure compatibility to older versions of the human sequence variant nomenclature, previously recommended variant description formats have been included. The first grammar versions were designed to help build variant description handling in the Alamut mutation interpretation software. The DNA and RNA level descriptions were then updated and used to construct the context-free parser of the Mutalyzer 2 sequence variant nomenclature checker, which has already been used to check more than one million variant descriptions. Conclusions: The Extended Backus-Naur Form provided an overview of the full complexity of the syntax of the sequence variant nomenclature, which remained hidden in the textual format and the division of the recommendations across the DNA, RNA and protein sections of the Human Genome Variation Society nomenclature websit
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A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
BMC Bioinformatics, 2011Co-Authors: Jeroen Fj Laros, André Blavier, Johan T Den Dunnen, Peter Em TaschnerAbstract:Background The use of a standard human sequence variant nomenclature is advocated by the Human Genome Variation Society in order to unambiguously describe genetic variants in databases and literature. There is a clear need for tools that allow the mining of data about human sequence variants and their functional consequences from databases and literature. Existing text mining focuses on the recognition of protein variants and their effects. The recognition of variants at the DNA and RNA levels is essential for dissemination of variant data for diagnostic purposes. Development of new tools is hampered by the complexity of the current nomenclature, which requires processing at the character level to recognize the specific syntactic constructs used in variant descriptions. Results We approached the gene variant nomenclature as a scientific sublanguage and created two formal descriptions of the syntax in Extended Backus-Naur Form: one at the DNA-RNA level and one at the protein level. To ensure compatibility to older versions of the human sequence variant nomenclature, previously recommended variant description formats have been included. The first grammar versions were designed to help build variant description handling in the Alamut mutation interpretation software. The DNA and RNA level descriptions were then updated and used to construct the context-free parser of the Mutalyzer 2 sequence variant nomenclature checker, which has already been used to check more than one million variant descriptions. Conclusions The Extended Backus-Naur Form provided an overview of the full complexity of the syntax of the sequence variant nomenclature, which remained hidden in the textual format and the division of the recommendations across the DNA, RNA and protein sections of the Human Genome Variation Society nomenclature website ( http://www.hgvs.org/mutnomen/ ). This insight into the syntax of the nomenclature could be used to design detailed and clear rules for software development. The Mutalyzer 2 parser demonstrated that it facilitated decomposition of complex variant descriptions into their individual parts. The Extended Backus-Naur Form or parts of it can be used or modified by adding rules, allowing the development of specific sequence variant text mining tools and other programs, which can generate or handle sequence variant descriptions.
S. Yu. Morozov-leonov - One of the best experts on this subject based on the ideXlab platform.
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Hemiclone Diversity in the Hybrid Form Pelophylax esculentus-ridibundus (Amphibia, Ranidae) from the Prypyat, Dnestr, and Southern Boug River Basins
Cytology and Genetics, 2019Co-Authors: S. Yu. Morozov-leonovAbstract:The hemiclonal structure of the Pelophylax esculentus-ridibundus hybrid form from the Pripyat, Dniester, and Southern Boug river basins is analyzed. The interbasin and interpopulation differences in the inherited Genome Variation level are demonstrated. The genetic diversity level of the P. esculentus-ridibundus inherited Genome in the Pripyat basin is significantly lower than in the other two basins. Monoclonal populations of this hybrid form have been identified only in the Pripyat basin. There were no significant differences in the genetic variability level of this hybrid form between the populations of the Dniester and Southern Boug basins. The relationship between the variability level of the inherited Genome of the hybrid form and the potentially possible multiple hybridization of parental species is analyzed.
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Hemiclone diversity in the hybrid form Pelophylax esculentus-ridibundus (Amphibia, Ranidae) from the Tisa river drainage
Cytology and Genetics, 2017Co-Authors: S. Yu. Morozov-leonovAbstract:The hemiclonal structure of a hybrid form of Pelophylax esculentus-ridibundus (Amphibia, Ranidae) from the Tisa river drainage has been analyzed. The interpopulation differences of the inherited Genome Variation level have been demonstrated. The peculiarities of the waterfrogs reproduction system are discussed.