@article{4255, abstract = {Humans and their closest evolutionary relatives, the chimpanzees, differ in ∼1.24% of their genomic DNA sequences. The fraction of these changes accumulated during the speciation processes that have separated the two lineages may be of special relevance in understanding the basis of their differences. We analyzed human and chimpanzee sequence data to search for the patterns of divergence and polymorphism predicted by a theoretical model of speciation. According to the model, positively selected changes should accumulate in chromosomes that present fixed structural differences, such as inversions, between the two species. Protein evolution was more than 2.2 times faster in chromosomes that had undergone structural rearrangements compared with colinear chromosomes. Also, nucleotide variability is slightly lower in rearranged chromosomes. These patterns of divergence and polymorphism may be, at least in part, the molecular footprint of speciation events in the human and chimpanzee lineages. }, author = {Navarro, Arcadio and Barton, Nicholas H}, issn = {0036-8075}, journal = {Science}, number = {5617}, pages = {321 -- 324}, publisher = {American Association for the Advancement of Science}, title = {{Chromosomal speciation and molecular divergence -- Accelerated evolution in rearranged chromosomes}}, doi = {10.1126/science.1080600 }, volume = {300}, year = {2003}, } @article{4146, abstract = {During vertebrate gastrulation, highly coordinated cellular rearrangements lead to the formation of the three germ layers, ectoderm, mesoderm and endoderm. In zebrafish, silberblick (slb)/wnt11 regulates normal gastrulation movements by activating a signalling pathway similar to the Frizzled-signalling pathway, which establishes epithelial planar cell polarity (PCP) in Drosophila. However, the cellular mechanisms by which slb/wnt11 functions during zebrafish gastrulation are still unclear. Using high-resolution two-photon confocal imaging followed by computer-assisted reconstruction and motion analysis, we have analysed the movement and morphology of individual cells in three dimensions during the course of gastrulation. We show that in slb-mutant embryos, hypoblast cells within the forming germ ring have slower, less directed migratory movements at the onset of gastrulation. These aberrant cell movements are accompanied by defects in the orientation of cellular processes along the individual movement directions of these cells. We conclude that slb/wnt11-mediated orientation of cellular processes plays a role in facilitating and stabilising movements of hypoblast cells in the germ ring, thereby pointing at a novel function of the slb/wnt11 signalling pathway for the regulation of migratory cell movements at early stages of gastrulation.}, author = {Ulrich, Florian and Concha, Miguel and Heid, Paul and Voss, Ed and Witzel, Sabine and Roehl, Henry and Tada, Masazumi and Wilson, Stephen and Adams, Richard and Soll, David and Heisenberg, Carl-Philipp J}, issn = {1011-6370}, journal = {Development}, number = {22}, pages = {5375 -- 5384}, publisher = {Company of Biologists}, title = {{Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset of zebrafish gastrulation}}, doi = {10.1242/dev.00758}, volume = {130}, year = {2003}, } @article{4169, abstract = {Background: During vertebrate gastrulation, cell polarization and migration are core components in the cellular rearrangements that lead to the formation of the three germ layers, ectoderm, mesoderm, and endoderm. Previous studies have implicated the Wnt/planar cell polarity (PCP) signaling pathway in controlling cell morphology and movement during gastrulation. However, cell polarization and directed cell migration are reduced but not completely abolished in the absence of Wnt/PCP signals; this observation indicates that other signaling pathways must be involved. Results: We show that Phosphoinositide 3-Kinases (PI3Ks) are required at the onset of zebrafish gastrulation in mesendodermal cells for process formation and cell polarization. Platelet Derived Growth Factor (PDGF) functions upstream of PI3K, while Protein Kinase B (PKB), a downstream effector of PI3K activity, localizes to the leading edge of migrating mesendodermal cells. In the absence of PI3K activity, PKB localization and cell polarization are strongly reduced in mesendodermal cells and are followed by slower but still highly coordinated and directed movements of these cells. Conclusions: We have identified a novel role of a signaling pathway comprised of PDGF, PI3K, and PKB in the control of morphogenetic cell movements during gastrulation. Furthermore, our findings provide insight into the relationship between cell polarization and directed cell migration at the onset of zebrafish gastrulation.}, author = {Montero, Juan and Kilian, Beate and Chan, Joanne and Bayliss, Peter and Heisenberg, Carl-Philipp J}, issn = {1879-0445}, journal = {Current Biology}, number = {15}, pages = {1279 -- 1289}, publisher = {Cell Press}, title = {{Phosphoinositide 3-kinase is required for process outgrowth and cell polarization of gastrulating mesendodermal cells}}, doi = {10.1016/S0960-9822(03)00505-0}, volume = {13}, year = {2003}, } @article{4185, abstract = {Wnt genes play important roles in regulating patterning and morphogenesis during vertebrate gastrulation. In zebrafish, slb/wnt11 is required for convergence and extension movements, but not cell fate specification during gastrulation. To determine if other Wnt genes functionally interact with slb/wnt11, we analysed the role of ppt/wnt5 during zebrafish gastrulation. ppt/wnt5 is maternally provided and zygotically expressed at all stages during gastrulation. The analysis of ppt mutant embryos reveals that Ppt/Wnt5 regulates cell elongation and convergent extension movements in posterior regions of the gastrula, while its function in more anterior regions is largely redundant to that of Slb/Wnt11. Frizzled-2 functions downstream of ppt/wnt5, indicating that it might act as a receptor for Ppt/Wnt5 in this process. The characterisation of the role of Ppt/Wnt5 provides insight into the functional diversity of Wnt genes in regulating vertebrate gastrulation movements. (C) 2003 Elsevier Science Ireland Ltd. All rights reserved.}, author = {Kilian, Beate and Mansukoski, Hannu and Barbosa, Filipa and Ulrich, Florian and Tada, Masazumi and Heisenberg, Carl-Philipp J}, issn = {0925-4773}, journal = {Mechanisms of Development}, number = {4}, pages = {467 -- 476}, publisher = {Elsevier}, title = {{The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation}}, doi = {10.1016/S0925-4773(03)00004-2}, volume = {120}, year = {2003}, } @article{3992, abstract = {Computing the volume occupied by individual atoms in macromolecular structures has been the subject of research for several decades. This interest has grown in the recent years, because weighted volumes are widely used in implicit solvent models. Applications of the latter in molecular mechanics simulations require that the derivatives of these weighted volumes be known. In this article, we give a formula for the volume derivative of a molecule modeled as a space-filling diagram made up of balls in motion. The formula is given in terms of the weights, radii, and distances between the centers as well as the sizes of the facets of the power diagram restricted to the space-filling diagram. Special attention is given to the detection and treatment of singularities as well as discontinuities of the derivative.}, author = {Edelsbrunner, Herbert and Koehl, Patrice}, issn = {0027-8424}, journal = {PNAS}, number = {5}, pages = {2203 -- 2208}, publisher = {National Academy of Sciences}, title = {{The weighted-volume derivative of a space-filling diagram}}, doi = {10.1073/pnas.0537830100}, volume = {100}, year = {2003}, } @inproceedings{3999, abstract = {We introduce relaxed scheduling as a paradigm for mesh maintenance and demonstrate its applicability to triangulating a skin surface in R-3.}, author = {Edelsbrunner, Herbert and Üngör, Alper}, booktitle = {Proceedings of the Japanese Conference on Discrete and Computational Geometry }, isbn = {9783540207764}, location = {Tokyo, Japan}, pages = {135 -- 151}, publisher = {Springer}, title = {{Relaxed scheduling in dynamic skin triangulation}}, doi = {10.1007/978-3-540-44400-8_14}, volume = {2866}, year = {2003}, } @inproceedings{3997, abstract = {We combine topological and geometric methods to construct a multi-resolution data structure for functions over two-dimensional domains. Starting with the Morse-Smale complex, we construct a topological hierarchy by progressively canceling critical points in pairs. Concurrently, we create a geometric hierarchy by adapting the geometry to the changes in topology. The data structure supports mesh traversal operations similarly to traditional multi-resolution representations.}, author = {Bremer, Peer and Edelsbrunner, Herbert and Hamann, Bernd and Pascucci, Valerio}, booktitle = {Proceedings of the 14th IEEE Conference on Visualization }, isbn = {0780381203}, location = {Seattle, WA, USA }, pages = {139 -- 146}, publisher = {IEEE}, title = {{A multi-resolution data structure for two-dimensional Morse-Smale functions}}, doi = {10.1109/VISUAL.2003.1250365}, year = {2003}, } @article{4168, abstract = {Recent studies show that signaling through integrin receptors is required for normal cell movements during Xenopus gastrulation. Integrins function in this process by modulating the activity of cadherin adhesion molecules within tissues undergoing convergence and extension movements.}, author = {Montero, Juan and Heisenberg, Carl-Philipp J}, issn = {1878-1551}, journal = {Developmental Cell}, number = {2}, pages = {190 -- 191}, publisher = {Cell Press}, title = {{Adhesive crosstalk in gastrulation}}, doi = {10.1016/S1534-5807(03)00235-1}, volume = {5}, year = {2003}, } @inbook{3991, abstract = {We give analytic inclusion-exclusion formulas for the area and perimeter derivatives of a union of finitely many disks in the plane.}, author = {Cheng, Ho and Edelsbrunner, Herbert}, booktitle = {Computer Science in Perspective: Essays Dedicated to Thomas Ottmann}, isbn = {9783540005797}, pages = {88 -- 97}, publisher = {Springer}, title = {{Area and perimeter derivatives of a union of disks}}, doi = {10.1007/3-540-36477-3_7}, volume = {2598}, year = {2003}, }