The Experts below are selected from a list of 306 Experts worldwide ranked by ideXlab platform
Oxana V. Galzitskaya - One of the best experts on this subject based on the ideXlab platform.
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Functionally Significant Amino Acid Motifs of Heat Shock Proteins: Structural and Bioinformatics Analyses of Hsp60/Hsp10 in Five Classes of Chordata
Molecular Biology, 2018Co-Authors: T. S. Tikhomirova, Oxana V. GalzitskayaAbstract:The Hsp60/Hsp10 chaperonin system is one of the most studied systems of cell emergency responses to stresses associated with changes in environmental conditions. In this regard, we have performed a bioinformatics analysis of 164 amino acid sequences of Hsp60 and 125 amino acid sequences of Hsp10 in five classes of Chordata. This enabled uncovering the relationship between the identity of the amino acid composition of Hsp60/Hsp10 and the evolutionary distance between classes of Chordata. In the course of the study of the chaperonin crystal structure, potentially significant amino acid motifs responsible for the oligomerization of Hsp60 and Hsp10 monomers and the association/dissociation of the Hsp60 and Hsp10 hetero-dimer have been identified. In addition, we have established that Hsp60 and Hsp10 can form amyloid fibrils due to structural features through the alternative using of the oligomerization sites of monomers as well as association/dissociation sites.
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functionally significant amino acid motifs of heat shock proteins structural and bioinformatics analyses of hsp60 hsp10 in five classes of Chordata
Molecular Biology, 2018Co-Authors: T. S. Tikhomirova, Oxana V. GalzitskayaAbstract:The Hsp60/Hsp10 chaperonin system is one of the most studied systems of cell emergency responses to stresses associated with changes in environmental conditions. In this regard, we have performed a bioinformatics analysis of 164 amino acid sequences of Hsp60 and 125 amino acid sequences of Hsp10 in five classes of Chordata. This enabled uncovering the relationship between the identity of the amino acid composition of Hsp60/Hsp10 and the evolutionary distance between classes of Chordata. In the course of the study of the chaperonin crystal structure, potentially significant amino acid motifs responsible for the oligomerization of Hsp60 and Hsp10 monomers and the association/dissociation of the Hsp60 and Hsp10 heterodimer have been identified. In addition, we have established that Hsp60 and Hsp10 can form amyloid fibrils due to structural features through the alternative using of the oligomerization sites of monomers as well as association/dissociation sites.
Çinar M.e. - One of the best experts on this subject based on the ideXlab platform.
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Checklist of the phyla platyhelminthes, Xenacoelomorpha, Nematoda, Acanthocephala, Myxozoa, Tardigrada, Cephalorhyncha, Nemertea, Echiura, Brachiopoda, Phoronida, Chaetognatha, and Chordata (Tunicata, CephaloChordata, and hemiChordata) from the coast
'The Scientific and Technological Research Council of Turkey', 2014Co-Authors: Çinar M.e.Abstract:In this paper, the current status of the species diversity of 13 phyla, namely Platyhelminthes, Xenacoelomorpha, Nematoda, Acanthocephala, Myxozoa, Tardigrada, Cephalorhyncha, Nemertea, Echiura, Brachiopoda, Phoronida, Chaetognatha, and Chordata (invertebrates, only Tunicata, CephaloChordata, and HemiChordata) along the coasts of Turkey is reviewed. Platyhelminthes was represented by 186 species, Chordata by 64 species, Nemertea by 26 species, Nematoda by 20 species, Xenacoelomorpha by 11 species, Chaetognatha by 10 species, Acanthocephala by 9 species, Brachiopoda and Phoronida by 4 species, Myxozoa and Tradigrada by 2 species, and Cephalorhyncha and Echiura by 1 species. Two platyhelminth (Planocera cf. graf and Prostheceraeus vittatus), 2 nemertean (Drepanogigas albolineatus and Tubulanus superbus), 1 phoronid (Phoronis australis), and 2 ascidian (Polyclinella azemai and Ciona roulei) species are being newly reported for the first time from the coasts of Turkey. Four tunicate (Symplegma brakenhielmi, Microcosmus exasperatus, Herdmania momus, and Phallusia nigra) and 1 chaetognath (Ferosagitta galerita) species were classifed as alien species in the region. © 2014 Turkiye Klinikleri Journal of Medical Sciences. All rights reserved
Melih Ertan Cinar - One of the best experts on this subject based on the ideXlab platform.
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checklist of the phyla platyhelminthes xenacoelomorpha nematoda acanthocephala myxozoa tardigrada cephalorhyncha nemertea echiura brachiopoda phoronida chaetognatha and Chordata tunicata cephaloChordata and hemiChordata from the coasts of turkey
Turkish Journal of Zoology, 2014Co-Authors: Melih Ertan CinarAbstract:In this paper, the current status of the species diversity of 13 phyla, namely Platyhelminthes, Xenacoelomorpha, Nematoda, Acanthocephala, Myxozoa, Tardigrada, Cephalorhyncha, Nemertea, Echiura, Brachiopoda, Phoronida, Chaetognatha, and Chordata (invertebrates, only Tunicata, CephaloChordata, and HemiChordata) along the coasts of Turkey is reviewed. Platyhelminthes was represented by 186 species, Chordata by 64 species, Nemertea by 26 species, Nematoda by 20 species, Xenacoelomorpha by 11 species, Chaetognatha by 10 species, Acanthocephala by 9 species, Brachiopoda and Phoronida by 4 species, Myxozoa and Tradigrada by 2 species, and Cephalorhyncha and Echiura by 1 species. Two platyhelminth (Planocera cf. graffi and Prostheceraeus vittatus), 2 nemertean (Drepanogigas albolineatus and Tubulanus superbus), 1 phoronid (Phoronis australis), and 2 ascidian (Polyclinella azemai and Ciona roulei) species are being newly reported for the first time from the coasts of Turkey. Four tunicate (Symplegma brakenhielmi, Microcosmus exasperatus, Herdmania momus, and Phallusia nigra) and 1 chaetognath (Ferosagitta galerita) species were classified as alien species in the region.
Noriyuki Satoh - One of the best experts on this subject based on the ideXlab platform.
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The phylum Vertebrata: a case for zoological recognition
Zoological Letters, 2018Co-Authors: Naoki Irie, Noriyuki Satoh, Shigeru KurataniAbstract:The group Vertebrata is currently placed as a subphylum in the phylum Chordata, together with two other subphyla, CephaloChordata (lancelets) and UroChordata (ascidians). The past three decades, have seen extraordinary advances in zoological taxonomy and the time is now ripe for reassessing whether the subphylum position is truly appropriate for vertebrates, particularly in light of recent advances in molecular phylogeny, comparative genomics, and evolutionary developmental biology. Four lines of current research are discussed here. First, molecular phylogeny has demonstrated that Deuterostomia comprises Ambulacraria (Echinodermata and HemiChordata) and Chordata (CephaloChordata, UroChordata, and Vertebrata), each clade being recognized as a mutually comparable phylum. Second, comparative genomic studies show that vertebrates alone have experienced two rounds of whole-genome duplication, which makes the composition of their gene family unique. Third, comparative gene-expression profiling of vertebrate embryos favors an hourglass pattern of development, the most conserved stage of which is recognized as a phylotypic period characterized by the establishment of a body plan definitively associated with a phylum. This mid-embryonic conservation is supported robustly in vertebrates, but only weakly in chordates. Fourth, certain complex patterns of body plan formation (especially of the head, pharynx, and somites) are recognized throughout the vertebrates, but not in any other animal groups. For these reasons, we suggest that it is more appropriate to recognize vertebrates as an independent phylum, not as a subphylum of the phylum Chordata.
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Chordate evolution and the three-phylum system.
Proceedings of The Royal Society B: Biological Sciences, 2014Co-Authors: Noriyuki Satoh, Daniel S Rokhsar, Teruaki NishikawaAbstract:Traditional metazoan phylogeny classifies the Vertebrata as a subphylum of the phylum Chordata, together with two other subphyla, the UroChordata (Tunicata) and the CephaloChordata. The Chordata, together with the phyla Echinodermata and HemiChordata, comprise a major group, the Deuterostomia. Chordates invariably possess a notochord and a dorsal neural tube. Although the origin and evolution of chordates has been studied for more than a century, few authors have intimately discussed taxonomic ranking of the three chordate groups themselves. Accumulating evidence shows that echinoderms and hemichordates form a clade (the Ambulacraria), and that within the Chordata, cephalochordates diverged first, with tunicates and vertebrates forming a sister group. Chordates share tadpole-type larvae containing a notochord and hollow nerve cord, whereas ambulacrarians have dipleurula-type larvae containing a hydrocoel. We propose that an evolutionary occurrence of tadpole-type larvae is fundamental to understanding mechanisms of chordate origin. Protostomes have now been reclassified into two major taxa, the Ecdysozoa and Lophotrochozoa, whose developmental pathways are characterized by ecdysis and trochophore larvae, respectively. Consistent with this classification, the profound dipleurula versus tadpole larval differences merit a category higher than the phylum. Thus, it is recommended that the Ecdysozoa, Lophotrochozoa, Ambulacraria and Chordata be classified at the superphylum level, with the Chordata further subdivided into three phyla, on the basis of their distinctive characteristics.
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a cdna resource for the cephalochordate amphioxus branchiostoma floridae
Development Genes and Evolution, 2008Co-Authors: Jr-kai Yu, Linda Z. Holland, Yuji Kohara, Mingchih Wang, Tadasu Shini, Noriyuki Satoh, Yutaka SatouAbstract:Cephalochordates are the basal invertebrate chordates within the phylum Chordata. They are widely used as a model system for research in evolutionary developmental biology (EvoDevo) to understand the basic patterning mechanisms for the chordate body plan and the origin of vertebrates. Recently, the genome of the cephalochordate Branchiostoma floridae was sequenced, which further brings this organism to the front for comparative genomic studies. In this paper, we report the generation of large-scale 5′- and 3′-expressed sequence tags (ESTs) from B. floridae and the complementary deoxyribonucleic acid (cDNA) resource for this species. Both 5′- and 3′-ESTs were sequenced for approximately 140,000 cDNA clones derived from five developmental stages, and the cDNA clones were subsequently grouped into independent clusters using 3′-EST sequences. We identified 21,229 cDNA clusters, and each corresponds to a unique transcript species from B. floridae. We then chose 24,020 cDNA clones representing all of these 21,229 clusters to generate the “Branchiostoma floridae Gene Collection Release 1.” We also constructed a database with a searchable interface for this EST dataset and the related information on “Branchiostoma floridae Gene Collection Release 1.” This set of cDNA clones along with our cDNA database will serve as an important resource for future research in this basal chordate. This Gene Collection and the original 140,000 individual cDNA clones are available to the research community upon request.
Loren Dean Williams - One of the best experts on this subject based on the ideXlab platform.
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G-Quadruplexes in Human Ribosomal RNA.
Journal of molecular biology, 2019Co-Authors: Santi Mestre-fos, Petar I. Penev, Suttipong Suttapitugsakul, Chieri Ito, Anton S. Petrov, Roger M. Wartell, Loren Dean WilliamsAbstract:rRNA is the single most abundant polymer in most cells. Mammalian rRNAs are nearly twice as large as those of prokaryotes. Differences in rRNA size are due to expansion segments, which contain extended tentacles in metazoans. Here we show that the terminus of an rRNA tentacle of Homo sapiens contains 10 tandem G-tracts that form highly stable G-quadruplexes in vitro. We characterized rRNA of the H. sapiens large ribosomal subunit by computation, circular dichroism, UV melting, fluorescent probes, nuclease accessibility, electrophoretic mobility shifts, and blotting. We investigated Expansion Segment 7 (ES7), oligomers derived from ES7, intact 28S rRNA, 80S ribosomes, and polysomes. We used mass spectrometry to identify proteins that bind to rRNA G-quadruplexes in cell lysates. These proteins include helicases (DDX3, CNBP, DDX21, DDX17) and heterogeneous nuclear ribonucleoproteins. Finally, by multiple sequence alignments, we observe that G-quadruplex-forming sequences are a general feature of LSU rRNA of Chordata but not, as far as we can tell, of other species. Chordata ribosomes present polymorphic tentacles with the potential to switch between inter- and intramolecular G-quadruplexes. To our knowledge, G-quadruplexes have not been reported previously in ribosomes.