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Robert P Guralnick - One of the best experts on this subject based on the ideXlab platform.
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a recapitulation of the rise and fall of the cell lineage research program the Evolutionary developmental relationship of cleavage to Homology body plans and life history
Journal of the History of Biology, 2002Co-Authors: Robert P GuralnickAbstract:American biologists in the late nineteenthcentury pioneered the descriptive-comparativestudy of all cell divisions from zygote togastrulation – the cell lineage. Data fromcell lineages were crucial to Evolutionary anddevelopmental questions of the day. One of themain questions was the ultimate causation ofdevelopmental patterns – historical ormechanical. E. B. Wilson's groundbreakinglineage work on the polychaete worm Nereis in 1892 set the stage for (1) an attackon Haeckel's phylogenetic-historical notion ofrecapitulation and (2) support for mechanisticexplanations of cleavage patterns. As morelineage work – especially Lillie's work on Unio and Conklin's on Crepidula – becameavailable in the mid-late 1890s, mechanism wastempered with more Evolutionary, Homology-basedviews. However, as I show by focusing on threemajor issues – Homology, body plans and lifehistory – these views were primarily based onthe precocious segregation and prospectivesignificance – what the cell became not what itwas. Even on issues like adaptation, mostlineagists argued teleologically from the adultbackward. Most cell lineage workers, by 1900,were to varying degreesmechanist/experimentalist and recapitulationistsimultaneously. The exception was E. G.Conklin, whose views were more akin to aDarwinian evolutionist than either mechanist orrecapitulationist. Lineage work eventuallydeclined and by 1907 published accounts of newlineages had basically stopped. I argue thatestablished workers and younger researchersstopped wanting to take on cell lineageprojects because the general patterns were thesame for all the spiralians while the specificsshowed too much variation. It was hard totheoretically encompass or analyze the minutiaeof variation in a recapitulationist ormechanist framework. The only establishedworker who continued to do comparative lineagestudies was E. G. Conklin, perhaps because thevariation could best be accommodated byDarwinian evolution.
Guowei Wei - One of the best experts on this subject based on the ideXlab platform.
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Evolutionary Homology on coupled dynamical systems with applications to protein flexibility analysis
Journal of Applied and Computational Topology, 2020Co-Authors: Zixuan Cang, Elizabeth Munch, Guowei WeiAbstract:While the spatial topological persistence is naturally constructed from a radius-based filtration, it has hardly been derived from a temporal filtration. Most topological models are designed for the global topology of a given object as a whole. There is no method reported in the literature for the topology of an individual component in an object to the best of our knowledge. For many problems in science and engineering, the topology of an individual component is important for describing its properties. We propose Evolutionary Homology (EH) constructed via a time evolution-based filtration and topological persistence. Our approach couples a set of dynamical systems or chaotic oscillators by the interactions of a physical system, such as a macromolecule. The interactions are approximated by weighted graph Laplacians. Simplices, simplicial complexes, algebraic groups and topological persistence are defined on the coupled trajectories of the chaotic oscillators. The resulting EH gives rise to time-dependent topological invariants or Evolutionary barcodes for an individual component of the physical system, revealing its topology-function relationship. In conjunction with Wasserstein metrics, the proposed EH is applied to protein flexibility analysis, an important problem in computational biophysics. Numerical results for the B-factor prediction of a benchmark set of 364 proteins indicate that the proposed EH outperforms all the other state-of-the-art methods in the field.
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Evolutionary Homology on coupled dynamical systems
arXiv: Algebraic Topology, 2018Co-Authors: Zixuan Cang, Elizabeth Munch, Guowei WeiAbstract:Time dependence is a universal phenomenon in nature, and a variety of mathematical models in terms of dynamical systems have been developed to understand the time-dependent behavior of real-world problems. Originally constructed to analyze the topological persistence over spatial scales, persistent Homology has rarely been devised for time evolution. We propose the use of a new filtration function for persistent Homology which takes as input the adjacent oscillator trajectories of a dynamical system. We also regulate the dynamical system by a weighted graph Laplacian matrix derived from the network of interest, which embeds the topological connectivity of the network into the dynamical system. The resulting topological signatures, which we call Evolutionary Homology (EH) barcodes, reveal the topology-function relationship of the network and thus give rise to the quantitative analysis of nodal properties. The proposed EH is applied to protein residue networks for protein thermal fluctuation analysis, rendering the most accurate B-factor prediction of a set of 364 proteins. This work extends the utility of dynamical systems to the quantitative modeling and analysis of realistic physical systems.
Wayne A. Hendrickson - One of the best experts on this subject based on the ideXlab platform.
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Structure of human chorionic gonadotropin at 2.6 å resolution from MAD analysis of the selenomethionyl protein
Structure, 1994Co-Authors: Hao Wu, Joyce W. Lustbader, Robert E Canfield, Wayne A. HendricksonAbstract:Abstract Background Human chorionic gonadotropin (hCG) is a placental hormone that stimulates secretion of the pregnancy-sustaining steroid progesterone. It is a member of a family of glycoprotein hormones that are disulfide-rich heterodimers, with a common α - chain and distinctive β -chains specific to their particular G- protein linked receptors. Results We have produced recombinant hCG in mammalian cells as the selenomethionyl protein, and have determined its structure (after partial deglycosylation) at 2.6 a resolution from multiwavelength anomalous diffraction (MAD) measurements. Despite only limited sequence similarity (10 % identity), the α - and β -subunits of hCG have similar tertiary folds. Each subunit has a cystine-knot motif at its core of extended hairpin loops. There is a very extensive subunit interface featuring two inter-chain β -sheets and a unique, disulfide-tethered ‘arm' from the β -subunit which ‘embraces' the α - subunit. The carboxy-terminal peptide of the β -subunit, which is rich in O-linked sugars, is disordered. Conclusions Structural and sequence comparisons indicate an Evolutionary Homology, albeit remote, between the glycoprotein hormone chains and other cystine-knot proteins, notably platelet-derived growth factor. Segments of the α - and β -chains that have been convincingly implicated in receptor binding by hCG are juxtaposed on one side of the molecule. A glycosylation site implicated in signal transduction but not in binding is also close to the presumed binding site suggesting a possible coupling between ligand binding and signaling. This study with selenomethionyl protein produced in mammalian cells extends the realm of MAD phasing.
Jorge Fischbarg - One of the best experts on this subject based on the ideXlab platform.
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predicting the three dimensional structure of the human facilitative glucose transporter glut1 by a novel Evolutionary Homology strategy insights on the molecular mechanism of substrate migration and binding sites for glucose and inhibitory molecules
Biophysical Journal, 2004Co-Authors: Alexis Salasburgos, P Iserovich, Felipe Zuniga, Juan Carlos Vera, Jorge FischbargAbstract:The glucose transporters (GLUT/SLC2A) are members of the major facilitator superfamily. Here, we generated a three-dimensional model for Glut1 using a two-step strategy: 1), GlpT structure as an initial Homology template and 2), Evolutionary Homology using glucose-6-phosphate translocase as a template. The resulting structure (PDB No. 1SUK) exhibits a water-filled passageway communicating the extracellular and intracellular domains, with a funnel-like exofacial vestibule (infundibulum), followed by a 15 A-long × 8 A-wide channel, and a horn-shaped endofacial vestibule. Most residues which, by mutagenesis, are crucial for transport delimit the channel, and putative sugar recognition motifs (QLS, QLG) border both ends of the channel. On the outside of the structure there are two positively charged cavities (one exofacial, one endofacial) delimited by ATP-binding Walker motifs, and an exofacial large side cavity of yet unknown function. Docking sites were found for the glucose substrate and its inhibitors: glucose, forskolin, and phloretin at the exofacial infundibulum; forskolin, and phloretin at an endofacial site next to the channel opening; and cytochalasin B at a positively charged endofacial pocket 3 A away from the channel. Thus, 1SUK accounts for practically all biochemical and mutagenesis evidence, and provides clues for the transport process.
William E. Friedman - One of the best experts on this subject based on the ideXlab platform.
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The evolution of double fertilization and endosperm: an ”historical” perspective
Sexual Plant Reproduction, 1998Co-Authors: William E. FriedmanAbstract:One hundred years ago, the developmental origin of endosperm from double fertilization was discovered independently by Navashin and Guignard. For much of the twentieth century, specific events related to the Evolutionary origin of the endosperm of flowering plants remained a mystery. However, during the past 20 years, advances in phylogenetic reconstruction of seed plants, genetic theory associated with kin selection, and comparative study of the reproductive biology of the closest living relatives of angiosperms (Gnetales) have advanced our understanding of the Evolutionary events associated with the origin of double fertilization and endosperm. Recent developmental analyses of Ephedra and Gnetum (members of Gnetales) indicate that these nonflowering seed plants undergo a regular process of double fertilization that yields two diploid zygotes. Use of explicit genetic and developmental criteria for analysis of Evolutionary Homology demonstrates congruence with the hypothesis that double fertilization processes in Gnetales and angiosperms were inherited from a common ancestor of the two lineages. In its rudimentary form, the second fertilization event in the ancestors of flowering plants yielded a supernumerary diploid embryo that was genetically identical to the normal embryo, a process most similar to what occurs in extant Ephedra. Subsequent to the divergence of the angiosperm stem lineage, the supernumerary embryo derived from double fertilization was developmentally modified into an embryo-nourishing structure, endosperm, that now characterizes angiosperms.
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Double fertilization in Gnetales: implications for understanding reproductive diversification among seed plants
International Journal of Plant Sciences, 1996Co-Authors: William E. Friedman, Jeffrey S. CarmichaelAbstract:The coupled processes of double fertilization and postfertilization endosperm formation have long been viewed as important and synapomorphic features of flowering plants. Recent developmental studies of fertilization in the nonflowering seed plants Ephedra and Gnetum clearly document a regular process of double fertilization. The condition for Welwitschia remains unknown. Unlike angiosperms, the product of the second fertilization event in Ephedra and Gnetum is diploid and expresses the developmental program of an embryo. Explicit criteria for the evaluation of Evolutionary Homology indicate that the processes of double fertilization in Gnetales and angiosperms are homologous, having first evolved in a common ancestor of these two lineages. It is hypothesized that the second fertilization product initially yielded a supernumerary embryo genetically identical to the normal embryo. This rudimentary process is expressed in relatively unmodified form in Ephedra. Other reproductive features of Ephedra that are...
