--- _id: '3933' abstract: - lang: eng text: Resident dendritic cells (DC) within the T cell area of the lymph node take up soluble antigens that enter via the afferent lymphatics before antigen carrying DC arrive from the periphery. The reticular network within the lymph node is a conduit system forming the infrastructure for the fast delivery of soluble substances from the afferent lymph to the lumen of high endothelial venules (HEVs). Using high-resolution light microscopy and 3D reconstruction, we show here that these conduits are unique basement membrane-like structures ensheathed by fibroblastic reticular cells with occasional resident DC embedded within this cell layer. Conduit-associated DC are capable of taking up and processing soluble antigens transported within the conduits, whereas immigrated mature DC occur remote from the reticular fibers. The conduit system is, therefore, not a closed compartment that shuttles substances through the lymph node but represents the morphological equivalent to the filtering function of the lymph node. author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Nobuo full_name: Kanazawa, Nobuo last_name: Kanazawa - first_name: Manuel full_name: Selg, Manuel last_name: Selg - first_name: Thomas full_name: Samson, Thomas last_name: Samson - first_name: Gunnel full_name: Roos, Gunnel last_name: Roos - first_name: Dieter full_name: Reinhardt, Dieter last_name: Reinhardt - first_name: Reinhard full_name: Pabst, Reinhard last_name: Pabst - first_name: Manfred full_name: Lutz, Manfred last_name: Lutz - first_name: Lydia full_name: Sorokin, Lydia last_name: Sorokin citation: ama: Sixt MK, Kanazawa N, Selg M, et al. The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node. Immunity. 2005;22(1):19-29. doi:10.1016/j.immuni.2004.11.013 apa: Sixt, M. K., Kanazawa, N., Selg, M., Samson, T., Roos, G., Reinhardt, D., … Sorokin, L. (2005). The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2004.11.013 chicago: Sixt, Michael K, Nobuo Kanazawa, Manuel Selg, Thomas Samson, Gunnel Roos, Dieter Reinhardt, Reinhard Pabst, Manfred Lutz, and Lydia Sorokin. “The Conduit System Transports Soluble Antigens from the Afferent Lymph to Resident Dendritic Cells in the T Cell Area of the Lymph Node.” Immunity. Cell Press, 2005. https://doi.org/10.1016/j.immuni.2004.11.013. ieee: M. K. Sixt et al., “The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node,” Immunity, vol. 22, no. 1. Cell Press, pp. 19–29, 2005. ista: Sixt MK, Kanazawa N, Selg M, Samson T, Roos G, Reinhardt D, Pabst R, Lutz M, Sorokin L. 2005. The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node. Immunity. 22(1), 19–29. mla: Sixt, Michael K., et al. “The Conduit System Transports Soluble Antigens from the Afferent Lymph to Resident Dendritic Cells in the T Cell Area of the Lymph Node.” Immunity, vol. 22, no. 1, Cell Press, 2005, pp. 19–29, doi:10.1016/j.immuni.2004.11.013. short: M.K. Sixt, N. Kanazawa, M. Selg, T. Samson, G. Roos, D. Reinhardt, R. Pabst, M. Lutz, L. Sorokin, Immunity 22 (2005) 19–29. date_created: 2018-12-11T12:05:58Z date_published: 2005-01-25T00:00:00Z date_updated: 2021-01-12T07:53:18Z day: '25' doi: 10.1016/j.immuni.2004.11.013 extern: '1' intvolume: ' 22' issue: '1' language: - iso: eng month: '01' oa_version: None page: 19 - 29 publication: Immunity publication_status: published publisher: Cell Press publist_id: '2195' status: public title: The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2005' ... --- _id: '3983' abstract: - lang: eng text: Cdc25 phosphatases are key activators of the eukaryotic cell cycle and compelling anticancer targets because their overexpression has been associated with numerous cancers. However, drug discovery targeting these phosphatases has been hampered by the lack of structural information about how Cdc25s interact with their native protein substrates, the cyclin-dependent kinases. Herein, we predict a docked orientation for Cdc25B with its Cdk2-pTpY-CycA protein substrate by a rigid-body docking method and refine the docked models with full-scale molecular dynamics simulations and minimization. We validate the stable ensemble structure experimentally by a variety of in vitro and in vivo techniques. Specifically, we compare our model with a crystal structure of the substrate-trapping mutant of Cdc25B. We identify and validate in vivo a novel hot-spot residue on Cdc25B (Arg492) that plays a central role in protein substrate recognition. We identify a hot-spot residue on the Substrate Cdk2 (Asp206) and confirm its interaction with hot-spot residues on Cdc25 using hot-spot swapping and double mutant cycles to derive interaction energies. Our experimentally validated model is consistent with previous studies of Cdk2 and its interaction partners and initiates the opportunity for drug discovery of inhibitors that target the remote binding sites of this protein-protein interaction. author: - first_name: Jungsan full_name: Sohn, Jungsan last_name: Sohn - first_name: Jerry full_name: Parks, Jerry M last_name: Parks - first_name: Gregory full_name: Buhrman, Gregory last_name: Buhrman - first_name: Paul full_name: Brown, Paul last_name: Brown - first_name: Kolbrun full_name: Kristjánsdóttir, Kolbrun last_name: Kristjánsdóttir - first_name: Alexias full_name: Safi, Alexias last_name: Safi - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Weitao full_name: Yang, Weitao T last_name: Yang - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph citation: ama: Sohn J, Parks J, Buhrman G, et al. Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry. 2005;44(50):16563-16573. doi:10.1021/bi0516879 apa: Sohn, J., Parks, J., Buhrman, G., Brown, P., Kristjánsdóttir, K., Safi, A., … Rudolph, J. (2005). Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry. ACS. https://doi.org/10.1021/bi0516879 chicago: Sohn, Jungsan, Jerry Parks, Gregory Buhrman, Paul Brown, Kolbrun Kristjánsdóttir, Alexias Safi, Herbert Edelsbrunner, Weitao Yang, and Johannes Rudolph. “Experimental Validation of the Docking Orientation of Cdc25 with Its Cdk2-CycA Protein Substrate.” Biochemistry. ACS, 2005. https://doi.org/10.1021/bi0516879. ieee: J. Sohn et al., “Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate,” Biochemistry, vol. 44, no. 50. ACS, pp. 16563–16573, 2005. ista: Sohn J, Parks J, Buhrman G, Brown P, Kristjánsdóttir K, Safi A, Edelsbrunner H, Yang W, Rudolph J. 2005. Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry. 44(50), 16563–16573. mla: Sohn, Jungsan, et al. “Experimental Validation of the Docking Orientation of Cdc25 with Its Cdk2-CycA Protein Substrate.” Biochemistry, vol. 44, no. 50, ACS, 2005, pp. 16563–73, doi:10.1021/bi0516879. short: J. Sohn, J. Parks, G. Buhrman, P. Brown, K. Kristjánsdóttir, A. Safi, H. Edelsbrunner, W. Yang, J. Rudolph, Biochemistry 44 (2005) 16563–16573. date_created: 2018-12-11T12:06:16Z date_published: 2005-11-24T00:00:00Z date_updated: 2021-01-12T07:53:39Z day: '24' doi: 10.1021/bi0516879 extern: 1 intvolume: ' 44' issue: '50' month: '11' page: 16563 - 16573 publication: Biochemistry publication_status: published publisher: ACS publist_id: '2144' quality_controlled: 0 status: public title: Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate type: journal_article volume: 44 year: '2005' ... --- _id: '3982' abstract: - lang: eng text: We present an efficient algorithm for generating a small set of coarse alignments between interacting proteins using meaningful features on their surfaces. The proteins are treated as rigid bodies, but the results are more generally useful as the produced configurations can serve as input to local improvement algorithms that allow for protein flexibility. We apply our algorithm to a diverse set of protein complexes from the Protein Data Bank, demonstrating the effectivity of our algorithm, both for bound and for unbound protein docking problems. author: - first_name: Yusu full_name: Wang, Yusu last_name: Wang - first_name: Pankaj full_name: Agarwal, Pankaj K last_name: Agarwal - first_name: Paul full_name: Brown, Paul last_name: Brown - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph citation: ama: 'Wang Y, Agarwal P, Brown P, Edelsbrunner H, Rudolph J. Coarse and reliable geometric alignment for protein docking. In: World Scientific Publishing; 2005:64-75. doi:10.1142/9789812702456_0007' apa: 'Wang, Y., Agarwal, P., Brown, P., Edelsbrunner, H., & Rudolph, J. (2005). Coarse and reliable geometric alignment for protein docking (pp. 64–75). Presented at the PSB: Pacific Symposium on Biocomputing, World Scientific Publishing. https://doi.org/10.1142/9789812702456_0007' chicago: Wang, Yusu, Pankaj Agarwal, Paul Brown, Herbert Edelsbrunner, and Johannes Rudolph. “Coarse and Reliable Geometric Alignment for Protein Docking,” 64–75. World Scientific Publishing, 2005. https://doi.org/10.1142/9789812702456_0007. ieee: 'Y. Wang, P. Agarwal, P. Brown, H. Edelsbrunner, and J. Rudolph, “Coarse and reliable geometric alignment for protein docking,” presented at the PSB: Pacific Symposium on Biocomputing, 2005, pp. 64–75.' ista: 'Wang Y, Agarwal P, Brown P, Edelsbrunner H, Rudolph J. 2005. Coarse and reliable geometric alignment for protein docking. PSB: Pacific Symposium on Biocomputing, 64–75.' mla: Wang, Yusu, et al. Coarse and Reliable Geometric Alignment for Protein Docking. World Scientific Publishing, 2005, pp. 64–75, doi:10.1142/9789812702456_0007. short: Y. Wang, P. Agarwal, P. Brown, H. Edelsbrunner, J. Rudolph, in:, World Scientific Publishing, 2005, pp. 64–75. conference: name: 'PSB: Pacific Symposium on Biocomputing' date_created: 2018-12-11T12:06:16Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:53:38Z day: '01' doi: 10.1142/9789812702456_0007 extern: 1 month: '01' page: 64 - 75 publication_status: published publisher: World Scientific Publishing publist_id: '2143' quality_controlled: 0 status: public title: Coarse and reliable geometric alignment for protein docking type: conference year: '2005' ... --- _id: '4144' abstract: - lang: eng text: Wnt11 plays a central role in tissue morphogenesis during vertebrate gastrulation, but the molecular and cellular mechanisms by which Wnt11 exerts its effects remain poorly understood. Here, we show that Wnt11 functions during zebrafish gastrulation by regulating the cohesion of mesodermal and endodermal (mesendodermal) progenitor cells. Importantly, we demonstrate that Wnt11 activity in this process is mediated by the GTPase Rab5, a key regulator of early endocytosis, as blocking Rab5c activity in wild-type embryos phenocopies slb/wnt11 mutants, and enhancing Rab5c activity in slb/wnt11 mutant embryos rescues the mutant phenotype. In addition, we find that Wnt11 and Rab5c control the endocytosis of E-cadherin and are required in mesendodermal cells for E-cadherin-mediated cell cohesion. Together, our results suggest that Wnt11 controls tissue morphogenesis by modulating E-cadherin-mediated cell cohesion through Rab5c, a novel mechanism of Wnt signaling in gastrulation. article_processing_charge: No author: - first_name: Florian full_name: Ulrich, Florian last_name: Ulrich - first_name: Michael full_name: Krieg, Michael last_name: Krieg - first_name: Eva full_name: Schötz, Eva last_name: Schötz - first_name: Vinzenz full_name: Link, Vinzenz last_name: Link - first_name: Irinka full_name: Castanon, Irinka last_name: Castanon - first_name: Viktor full_name: Schnabel, Viktor last_name: Schnabel - first_name: Anna full_name: Taubenberger, Anna last_name: Taubenberger - first_name: Daniel full_name: Müller, Daniel last_name: Müller - first_name: Pierre full_name: Puech, Pierre last_name: Puech - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Ulrich F, Krieg M, Schötz E, et al. Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin. Developmental Cell. 2005;9(4):555-564. doi:10.1016/j.devcel.2005.08.011 apa: Ulrich, F., Krieg, M., Schötz, E., Link, V., Castanon, I., Schnabel, V., … Heisenberg, C.-P. J. (2005). Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2005.08.011 chicago: Ulrich, Florian, Michael Krieg, Eva Schötz, Vinzenz Link, Irinka Castanon, Viktor Schnabel, Anna Taubenberger, Daniel Müller, Pierre Puech, and Carl-Philipp J Heisenberg. “Wnt11 Functions in Gastrulation by Controlling Cell Cohesion through Rab5c and E-Cadherin.” Developmental Cell. Cell Press, 2005. https://doi.org/10.1016/j.devcel.2005.08.011. ieee: F. Ulrich et al., “Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin,” Developmental Cell, vol. 9, no. 4. Cell Press, pp. 555–564, 2005. ista: Ulrich F, Krieg M, Schötz E, Link V, Castanon I, Schnabel V, Taubenberger A, Müller D, Puech P, Heisenberg C-PJ. 2005. Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin. Developmental Cell. 9(4), 555–564. mla: Ulrich, Florian, et al. “Wnt11 Functions in Gastrulation by Controlling Cell Cohesion through Rab5c and E-Cadherin.” Developmental Cell, vol. 9, no. 4, Cell Press, 2005, pp. 555–64, doi:10.1016/j.devcel.2005.08.011. short: F. Ulrich, M. Krieg, E. Schötz, V. Link, I. Castanon, V. Schnabel, A. Taubenberger, D. Müller, P. Puech, C.-P.J. Heisenberg, Developmental Cell 9 (2005) 555–564. date_created: 2018-12-11T12:07:12Z date_published: 2005-10-01T00:00:00Z date_updated: 2021-01-12T07:54:50Z day: '01' doi: 10.1016/j.devcel.2005.08.011 extern: '1' intvolume: ' 9' issue: '4' language: - iso: eng month: '10' oa_version: None page: 555 - 564 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '1977' status: public title: Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2005' ... --- _id: '4138' abstract: - lang: eng text: |- Adaptive dynamics describes the evolution of an asexual population through the successive substitution of mutations of small effect. Waxman & Gavrilets (2005) give an excellent overview of the method and its applications. In this note, we focus on the plausibility of the key assumption that mutations have small effects, and the consequences of relaxing that assumption. We argue that: (i) successful mutations often have large effects; (ii) such mutations generate a qualitatively different evolutionary pattern, which is inherently stochastic; and (iii) in models of competition for a continuous resource, selection becomes very weak once several phenotypes are established. This makes the effects of introducing new mutations unpredictable using the methods of adaptive dynamics. We should make clear at the outset that our criticism is of methods that rely on local analysis of fitness gradients (eqn 2 of Waxman & Gavrilets, 2005), and not of the broader idea that evolution can be understood by examining the invasion of successive mutations. We use the term ‘adaptive dynamics’ to refer to the former technique, and contrast it with a more general population genetic analysis of probabilities of invasion. author: - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jitka full_name: Jitka Polechova id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 citation: ama: Barton NH, Polechova J. The limitations of adaptive dynamics as a model of evolution. Journal of Evolutionary Biology. 2005;18(5):1186-1190. doi:10.1111/j.1420-9101.2005.00943.x apa: Barton, N. H., & Polechova, J. (2005). The limitations of adaptive dynamics as a model of evolution. Journal of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/j.1420-9101.2005.00943.x chicago: Barton, Nicholas H, and Jitka Polechova. “The Limitations of Adaptive Dynamics as a Model of Evolution.” Journal of Evolutionary Biology. Wiley-Blackwell, 2005. https://doi.org/10.1111/j.1420-9101.2005.00943.x. ieee: N. H. Barton and J. Polechova, “The limitations of adaptive dynamics as a model of evolution,” Journal of Evolutionary Biology, vol. 18, no. 5. Wiley-Blackwell, pp. 1186–1190, 2005. ista: Barton NH, Polechova J. 2005. The limitations of adaptive dynamics as a model of evolution. Journal of Evolutionary Biology. 18(5), 1186–1190. mla: Barton, Nicholas H., and Jitka Polechova. “The Limitations of Adaptive Dynamics as a Model of Evolution.” Journal of Evolutionary Biology, vol. 18, no. 5, Wiley-Blackwell, 2005, pp. 1186–90, doi:10.1111/j.1420-9101.2005.00943.x. short: N.H. Barton, J. Polechova, Journal of Evolutionary Biology 18 (2005) 1186–1190. date_created: 2018-12-11T12:07:10Z date_published: 2005-09-01T00:00:00Z date_updated: 2021-01-12T07:54:47Z day: '01' doi: 10.1111/j.1420-9101.2005.00943.x extern: 1 intvolume: ' 18' issue: '5' month: '09' page: 1186 - 1190 publication: Journal of Evolutionary Biology publication_status: published publisher: Wiley-Blackwell publist_id: '1982' quality_controlled: 0 status: public title: The limitations of adaptive dynamics as a model of evolution type: journal_article volume: 18 year: '2005' ...