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  • 1
    Online Resource
    Online Resource
    Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
    Oxford University Press (OUP) ; 2021
    In:  Systematic Biology Vol. 70, No. 1 ( 2021-01-01), p. 49-66
    Details
    In: Systematic Biology, Oxford University Press (OUP), Vol. 70, No. 1 ( 2021-01-01), p. 49-66
    Abstract: Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree–species tree discordance; genomics; information theory.]
    Type of Medium: Online Resource
    ISSN: 1063-5157 , 1076-836X
    URL: Article
    DOI: 10.1093/sysbio/syaa034
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
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    SSG: 12
    Location Call Number Limitation Availability
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  • 2
    Online Resource
    Online Resource
    Aromatic amino‐acid residues at the active and peripheral anionic sites control the binding of E2020 (Aricept®) to cholinesterases
    Wiley ; 2003
    In:  European Journal of Biochemistry Vol. 270, No. 22 ( 2003-11), p. 4447-4458
    Details
    In: European Journal of Biochemistry, Wiley, Vol. 270, No. 22 ( 2003-11), p. 4447-4458
    Abstract: E2020 ( R , S )‐1‐benzyl‐4‐[(5,6‐dimethoxy‐1‐indanon)‐2‐yl]methyl)piperidine hydrochloride is a piperidine‐based acetylcholinesterase (AChE) inhibitor that was approved for the treatment of Alzheimer's disease in the United States. Structure‐activity studies of this class of inhibitors have indicated that both the benzoyl containing functionality and the N ‐benzylpiperidine moiety are the key features for binding and inhibition of AChE. In the present study, the interaction of E2020 with cholinesterases (ChEs) with known sequence differences, was examined in more detail by measuring the inhibition constants with Torpedo AChE, fetal bovine serum AChE, human butyrylcholinesterase (BChE), and equine BChE. The basis for particular residues conferring selectivity was then confirmed by using site‐specific mutants of the implicated residue in two template enzymes. Differences in the reactivity of E2020 toward AChE and BChE (200‐ to 400‐fold) show that residues at the peripheral anionic site such as Asp74( 72 ), Tyr72( 70 ), Tyr124( 121 ), and Trp286( 279 ) in mammalian AChE may be important in the binding of E2020 to AChE. Site‐directed mutagenesis studies using mouse AChE showed that these residues contribute to the stabilization energy for the AChE–E2020 complex. However, replacement of Ala277(Trp279) with Trp in human BChE does not affect the binding of E2020 to BChE. Molecular modeling studies suggest that E2020 interacts with the active‐site and the peripheral anionic site in AChE, but in the case of BChE, as the gorge is larger, E2020 cannot simultaneously interact at both sites. The observation that the K I value for mutant AChE in which Ala replaced Trp286 is similar to that for wild‐type BChE, further confirms our hypothesis.
    Type of Medium: Online Resource
    ISSN: 0014-2956 , 1432-1033
    URL: Article
    DOI: 10.1046/j.1432-1033.2003.03837.x
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2003
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    detail.hit.zdb_id: 1464377-7
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Reconsideration of the catalytic center and mechanism of mammalian paraoxonase/arylesterase.
    Proceedings of the National Academy of Sciences ; 1995
    In:  Proceedings of the National Academy of Sciences Vol. 92, No. 16 ( 1995-08), p. 7187-7191
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 92, No. 16 ( 1995-08), p. 7187-7191
    Abstract: For three decades, mammalian paraoxonase (A-esterase, aromatic esterase, arylesterase; PON, EC 3.1.8.1) has been thought to be a cysteine esterase demonstrating structural and mechanistic homologies with the serine esterases (cholinesterases and carboxyesterases). Human, mouse, and rabbit PONs each contain only three cysteine residues, and their positions within PON have been conserved. In purified human PON, residues Cys-41 and Cys-352 form an intramolecular disulfide bond and neither could function as an active-center cysteine. Highly purified, enzymatically active PON contains a single titratable sulfhydryl group. Thus, Cys-283 is the only probable candidate for an active-center cysteine. Through site-directed mutagenesis of the human cDNA, Cys-283 was replaced with either serine (C283S) or alanine (C283A). The expressed C283 (wild-type) enzyme was inactivated by para-hydroxymercuribenzoate, but the C283S and C283A mutant enzymes were not inactivated. C283A and C283S mutant enzymes retained both paraoxonase and arylesterase activities, and the Km values for paraoxon and phenyl acetate were similar to those of the wild type. Clearly, residue Cys-283 is free in active PON, but a free sulfhydryl group is not required for either paraoxonase or arylesterase activities. Consequently, it is necessary to examine other models for the active-site structure and catalytic mechanism of PON.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.92.16.7187
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 1995
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    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Genome size drives morphological evolution in organ‐specific ways
    Wiley ; 2022
    In:  Evolution Vol. 76, No. 7 ( 2022-07), p. 1453-1468
    Details
    In: Evolution, Wiley, Vol. 76, No. 7 ( 2022-07), p. 1453-1468
    Type of Medium: Online Resource
    ISSN: 0014-3820 , 1558-5646
    URL: Issue
    URL: Article
    DOI: 10.1111/evo.v76.7
    DOI: 10.1111/evo.14519
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2036375-8
    detail.hit.zdb_id: 127650-5
    SSG: 12
    Location Call Number Limitation Availability
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