--- OA_type: closed access _id: '4145' abstract: - lang: eng text: The detection of microRNAs (miRNAs) at single-cell resolution is important for studying the role of these posttranscriptional regulators. Here, we use a dual-fluorescent green fluorescent protein (GFP)-reporter/monomeric red fluorescent protein (mRFP)-sensor (DFRS) plasmid, injected into zebrafish blastomeres or electroporated into defined tissues of mouse embryos in utero or ex utero, to monitor the dynamics of specific miRNAs in individual live cells. This approach reveals, for example, that in the developing mouse central nervous system,, miR-124a is expressed not only in postmitotic neurons but also in neuronal progenitor cells. Collectively, our results demonstrate that acute administration of DFRS plasmids.offers an alternative to previous in situ hybridization and transgenic approaches and allows the monitoring of miRNA appearance and disappearance in defined cell lineages during vertebrate development. article_processing_charge: No article_type: original author: - first_name: Davide full_name: Tonelli, Davide last_name: Tonelli - first_name: Frederico full_name: Calegari, Frederico last_name: Calegari - first_name: Ji full_name: Fei, Ji last_name: Fei - first_name: Tadashi full_name: Nomura, Tadashi last_name: Nomura - first_name: Noriko full_name: Osumi, Noriko last_name: Osumi - 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 - first_name: Wieland full_name: Huttner, Wieland last_name: Huttner citation: ama: Tonelli D, Calegari F, Fei J, et al. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. 2006;41(6):727-732. doi:10.2144/000112296 apa: Tonelli, D., Calegari, F., Fei, J., Nomura, T., Osumi, N., Heisenberg, C.-P. J., & Huttner, W. (2006). Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. Informa Healthcare. https://doi.org/10.2144/000112296 chicago: Tonelli, Davide, Frederico Calegari, Ji Fei, Tadashi Nomura, Noriko Osumi, Carl-Philipp J Heisenberg, and Wieland Huttner. “Single-Cell Detection of MicroRNAs in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.” Biotechniques. Informa Healthcare, 2006. https://doi.org/10.2144/000112296. ieee: D. Tonelli et al., “Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid,” Biotechniques, vol. 41, no. 6. Informa Healthcare, pp. 727–732, 2006. ista: Tonelli D, Calegari F, Fei J, Nomura T, Osumi N, Heisenberg C-PJ, Huttner W. 2006. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. 41(6), 727–732. mla: Tonelli, Davide, et al. “Single-Cell Detection of MicroRNAs in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.” Biotechniques, vol. 41, no. 6, Informa Healthcare, 2006, pp. 727–32, doi:10.2144/000112296. short: D. Tonelli, F. Calegari, J. Fei, T. Nomura, N. Osumi, C.-P.J. Heisenberg, W. Huttner, Biotechniques 41 (2006) 727–732. date_created: 2018-12-11T12:07:12Z date_published: 2006-12-01T00:00:00Z date_updated: 2026-08-26T09:09:45Z day: '01' doi: 10.2144/000112296 extern: '1' external_id: pmid: - '17191618 ' fulldoi: https://doi.org/10.2144/000112296 intvolume: ' 41' issue: '6' language: - iso: eng month: '12' oa_version: None page: 727 - 732 pmid: 1 publication: Biotechniques publication_identifier: eissn: - 1940-9818 issn: - 0736-6205 publication_status: published publisher: Informa Healthcare publist_id: '1974' status: public title: Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 41 year: '2006' ... --- OA_place: publisher OA_type: gold _id: '4173' abstract: - lang: eng text: 'Background: Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and proteomics have yet to be developed. Results: As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion: The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis.' article_processing_charge: No article_type: original author: - first_name: Vinzenz full_name: Link, Vinzenz last_name: Link - first_name: Andrej full_name: Shevchenko, Andrej last_name: Shevchenko - 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: Link V, Shevchenko A, Heisenberg C-PJ. Proteomics of early zebrafish embryos. BMC Developmental Biology. 2006;6:1-9. doi:10.1186/1471-213X-6-1 apa: Link, V., Shevchenko, A., & Heisenberg, C.-P. J. (2006). Proteomics of early zebrafish embryos. BMC Developmental Biology. BioMed Central. https://doi.org/10.1186/1471-213X-6-1 chicago: Link, Vinzenz, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Proteomics of Early Zebrafish Embryos.” BMC Developmental Biology. BioMed Central, 2006. https://doi.org/10.1186/1471-213X-6-1. ieee: V. Link, A. Shevchenko, and C.-P. J. Heisenberg, “Proteomics of early zebrafish embryos,” BMC Developmental Biology, vol. 6. BioMed Central, pp. 1–9, 2006. ista: Link V, Shevchenko A, Heisenberg C-PJ. 2006. Proteomics of early zebrafish embryos. BMC Developmental Biology. 6, 1–9. mla: Link, Vinzenz, et al. “Proteomics of Early Zebrafish Embryos.” BMC Developmental Biology, vol. 6, BioMed Central, 2006, pp. 1–9, doi:10.1186/1471-213X-6-1. short: V. Link, A. Shevchenko, C.-P.J. Heisenberg, BMC Developmental Biology 6 (2006) 1–9. date_created: 2018-12-11T12:07:23Z date_published: 2006-01-13T00:00:00Z date_updated: 2026-08-26T09:05:03Z day: '13' doi: 10.1186/1471-213X-6-1 extern: '1' external_id: pmid: - '16412219' fulldoi: https://doi.org/10.1186/1471-213X-6-1 intvolume: ' 6' language: - iso: eng main_file_link: - open_access: '1' url: http://www.biomedcentral.com/1471-213X/6/1 month: '01' oa: 1 oa_version: None page: 1 - 9 pmid: 1 publication: BMC Developmental Biology publication_status: published publisher: BioMed Central publist_id: '1945' status: public title: Proteomics of early zebrafish embryos tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 6 year: '2006' ... --- OA_type: closed access _id: '3978' abstract: - lang: eng text: Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. article_processing_charge: No article_type: original author: - first_name: Yih full_name: Ban, Yih last_name: Ban - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph - first_name: Pei full_name: Zhou, Pei last_name: Zhou - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. 2006;62(4):852-864. doi:10.1002/prot.20811' apa: 'Ban, Y., Rudolph, J., Zhou, P., & Edelsbrunner, H. (2006). Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.20811' chicago: 'Ban, Yih, Johannes Rudolph, Pei Zhou, and Herbert Edelsbrunner. “Evaluating the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 2006. https://doi.org/10.1002/prot.20811.' ieee: 'Y. Ban, J. Rudolph, P. Zhou, and H. Edelsbrunner, “Evaluating the quality of NMR structures by local density of protons,” Proteins: Structure, Function and Bioinformatics, vol. 62, no. 4. Wiley-Blackwell, pp. 852–864, 2006.' ista: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. 2006. Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. 62(4), 852–864.' mla: 'Ban, Yih, et al. “Evaluating the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure, Function and Bioinformatics, vol. 62, no. 4, Wiley-Blackwell, 2006, pp. 852–64, doi:10.1002/prot.20811.' short: 'Y. Ban, J. Rudolph, P. Zhou, H. Edelsbrunner, Proteins: Structure, Function and Bioinformatics 62 (2006) 852–864.' date_created: 2018-12-11T12:06:14Z date_published: 2006-03-01T00:00:00Z date_updated: 2026-08-26T10:56:49Z day: '01' doi: 10.1002/prot.20811 extern: '1' external_id: pmid: - '16342274 ' fulldoi: https://doi.org/10.1002/prot.20811 intvolume: ' 62' issue: '4' language: - iso: eng month: '03' oa_version: None page: 852 - 864 pmid: 1 publication: 'Proteins: Structure, Function and Bioinformatics' publication_identifier: eissn: - 1097-0134 issn: - 0887-3585 publication_status: published publisher: Wiley-Blackwell publist_id: '2146' status: public title: Evaluating the quality of NMR structures by local density of protons type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 62 year: '2006' ... --- OA_type: closed access _id: '3979' abstract: - lang: eng text: Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface surface formed by two or more proteins as a subset of their Voronoi diagram. The definition deals with the difficult and important problem of specifying interface boundaries by invoking methods used in the alpha shape representation of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct surfaces, and the assessment of the importance of topological features. We present an algorithm to construct the surface and define a hierarchy that distinguishes core and peripheral regions. This hierarchy is shown to have correlation with hot-spots in protein-protein interactions. Finally, we study the geometric and topological properties of interface surfaces and show their high degree of contortion. article_processing_charge: No article_type: original author: - first_name: Yih full_name: Ban, Yih last_name: Ban - first_name: Herbert full_name: Edelsbrunner, Herbert 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: Ban Y, Edelsbrunner H, Rudolph J. Interface surfaces for protein-protein complexes. Journal of the ACM. 2006;53(3):361-378. doi:10.1145/1147954.1147957 apa: Ban, Y., Edelsbrunner, H., & Rudolph, J. (2006). Interface surfaces for protein-protein complexes. Journal of the ACM. ACM. https://doi.org/10.1145/1147954.1147957 chicago: Ban, Yih, Herbert Edelsbrunner, and Johannes Rudolph. “Interface Surfaces for Protein-Protein Complexes.” Journal of the ACM. ACM, 2006. https://doi.org/10.1145/1147954.1147957. ieee: Y. Ban, H. Edelsbrunner, and J. Rudolph, “Interface surfaces for protein-protein complexes,” Journal of the ACM, vol. 53, no. 3. ACM, pp. 361–378, 2006. ista: Ban Y, Edelsbrunner H, Rudolph J. 2006. Interface surfaces for protein-protein complexes. Journal of the ACM. 53(3), 361–378. mla: Ban, Yih, et al. “Interface Surfaces for Protein-Protein Complexes.” Journal of the ACM, vol. 53, no. 3, ACM, 2006, pp. 361–78, doi:10.1145/1147954.1147957. short: Y. Ban, H. Edelsbrunner, J. Rudolph, Journal of the ACM 53 (2006) 361–378. date_created: 2018-12-11T12:06:14Z date_published: 2006-05-01T00:00:00Z date_updated: 2026-08-26T11:21:19Z day: '01' doi: 10.1145/1147954.1147957 extern: '1' fulldoi: https://doi.org/10.1145/1147954.1147957 intvolume: ' 53' issue: '3' language: - iso: eng month: '05' oa_version: None page: 361 - 378 publication: Journal of the ACM publication_identifier: eissn: - 1557-735X issn: - 0004-5411 publication_status: published publisher: ACM publist_id: '2147' status: public title: Interface surfaces for protein-protein complexes type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 53 year: '2006' ... --- OA_type: closed access _id: '3980' abstract: - lang: eng text: Given a smoothly embedded 2-manifold in R-3, we define the elevation of a point as the height difference to a canonically defined second point on the same manifold. Our definition is invariant under rigid motions and can be used to define features such as lines of discontinuous or continuous but non-smooth elevation. We give an algorithm for finding points of locally maximum elevation, which we suggest mark cavities and protrusions and are useful in matching shapes as for example in protein docking. article_processing_charge: No article_type: original author: - first_name: Pankaj full_name: Agarwal, Pankaj last_name: Agarwal - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer - first_name: Yusu full_name: Wang, Yusu last_name: Wang citation: ama: Agarwal P, Edelsbrunner H, Harer J, Wang Y. Extreme elevation on a 2-manifold. Discrete & Computational Geometry. 2006;36(4):553-572. doi:10.1007/s00454-006-1265-8 apa: Agarwal, P., Edelsbrunner, H., Harer, J., & Wang, Y. (2006). Extreme elevation on a 2-manifold. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-006-1265-8 chicago: Agarwal, Pankaj, Herbert Edelsbrunner, John Harer, and Yusu Wang. “Extreme Elevation on a 2-Manifold.” Discrete & Computational Geometry. Springer Nature, 2006. https://doi.org/10.1007/s00454-006-1265-8. ieee: P. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang, “Extreme elevation on a 2-manifold,” Discrete & Computational Geometry, vol. 36, no. 4. Springer Nature, pp. 553–572, 2006. ista: Agarwal P, Edelsbrunner H, Harer J, Wang Y. 2006. Extreme elevation on a 2-manifold. Discrete & Computational Geometry. 36(4), 553–572. mla: Agarwal, Pankaj, et al. “Extreme Elevation on a 2-Manifold.” Discrete & Computational Geometry, vol. 36, no. 4, Springer Nature, 2006, pp. 553–72, doi:10.1007/s00454-006-1265-8. short: P. Agarwal, H. Edelsbrunner, J. Harer, Y. Wang, Discrete & Computational Geometry 36 (2006) 553–572. date_created: 2018-12-11T12:06:15Z date_published: 2006-12-01T00:00:00Z date_updated: 2026-08-26T11:28:26Z day: '01' doi: 10.1007/s00454-006-1265-8 extern: '1' fulldoi: https://doi.org/10.1007/s00454-006-1265-8 intvolume: ' 36' issue: '4' language: - iso: eng month: '12' oa_version: None page: 553 - 572 publication: Discrete & Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature publist_id: '2148' status: public title: Extreme elevation on a 2-manifold type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 36 year: '2006' ... --- OA_type: closed access _id: '3934' abstract: - lang: eng text: T cells develop in the thymus in a highly specialized cellular and extracellular microenvironment. The basement membrane molecule, laminin-5 (LN-5), is predominantly found in the medulla of the human thymic lobules. Using high-resolution light microscopy, we show here that LN-5 is localized in a bi-membranous conduit-like structure, together with other typical basement membrane components including collagen type IV, nidogen and perlecan. Other interstitial matrix components, such as fibrillin-1 or -2, tenascin-C or fibrillar collagen types, were also associated with these structures. Three-dimensional (3D) confocal microscopy suggested a tubular structure, whereas immunoelectron and transmission electron microscopy showed that the core of these tubes contained fibrillar collagens enwrapped by the LN-5-containing membrane. These medullary conduits are surrounded by thymic epithelial cells, which in vitro were found to bind LN-5, but also fibrillin and tenascin-C. Dendritic cells were also detected in close vicinity to the conduits. Both of these stromal cell types express major histocompatibility complex (MHC) class II molecules capable of antigen presentation. The conduits are connected to blood vessels but, with an average diameter of 2 mum, they are too small to transport cells. However, evidence is provided that smaller molecules such as a 10 kDa dextran, but not large molecules (>500 kDa), can be transported in the conduits. These results clearly demonstrate that a conduit system, which is also known from secondary lymphatic organs such as lymph nodes and spleen, is present in the medulla of the human thymus, and that it might serve to transport small blood-borne molecules or chemokines to defined locations within the medulla. article_processing_charge: No article_type: original author: - first_name: Mihaela full_name: Drumea Mirancea, Mihaela last_name: Drumea Mirancea - first_name: Johannes full_name: Wessels, Johannes last_name: Wessels - first_name: Claudia full_name: Müller, Claudia last_name: Müller - first_name: Mike full_name: Essl, Mike last_name: Essl - first_name: Johannes full_name: Eble, Johannes last_name: Eble - first_name: Eva full_name: Tolosa, Eva last_name: Tolosa - first_name: Manuel full_name: Koch, Manuel last_name: Koch - first_name: Dieter full_name: Reinhardt, Dieter last_name: Reinhardt - 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: Lydia full_name: Sorokin, Lydia last_name: Sorokin - first_name: York full_name: Stierhof, York last_name: Stierhof - first_name: Heinz full_name: Schwarz, Heinz last_name: Schwarz - first_name: Gerd full_name: Klein, Gerd last_name: Klein citation: ama: 'Drumea Mirancea M, Wessels J, Müller C, et al. Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. 2006;119(Pt 7):1396-1405. doi:10.1242/​jcs.02840' apa: 'Drumea Mirancea, M., Wessels, J., Müller, C., Essl, M., Eble, J., Tolosa, E., … Klein, G. (2006). Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/​jcs.02840' chicago: 'Drumea Mirancea, Mihaela, Johannes Wessels, Claudia Müller, Mike Essl, Johannes Eble, Eva Tolosa, Manuel Koch, et al. “Characterization of a Conduit System Containing Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/​jcs.02840.' ieee: 'M. Drumea Mirancea et al., “Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules,” Journal of Cell Science, vol. 119, no. Pt 7. Company of Biologists, pp. 1396–1405, 2006.' ista: 'Drumea Mirancea M, Wessels J, Müller C, Essl M, Eble J, Tolosa E, Koch M, Reinhardt D, Sixt MK, Sorokin L, Stierhof Y, Schwarz H, Klein G. 2006. Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. 119(Pt 7), 1396–1405.' mla: 'Drumea Mirancea, Mihaela, et al. “Characterization of a Conduit System Containing Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.” Journal of Cell Science, vol. 119, no. Pt 7, Company of Biologists, 2006, pp. 1396–405, doi:10.1242/​jcs.02840.' short: M. Drumea Mirancea, J. Wessels, C. Müller, M. Essl, J. Eble, E. Tolosa, M. Koch, D. Reinhardt, M.K. Sixt, L. Sorokin, Y. Stierhof, H. Schwarz, G. Klein, Journal of Cell Science 119 (2006) 1396–1405. date_created: 2018-12-11T12:05:58Z date_published: 2006-04-01T00:00:00Z date_updated: 2026-08-26T12:39:44Z day: '01' doi: 10.1242/​jcs.02840 extern: '1' external_id: pmid: - '16537647' fulldoi: https://doi.org/10.1242/​jcs.02840 intvolume: ' 119' issue: Pt 7 language: - iso: eng month: '04' oa_version: None page: 1396 - 1405 pmid: 1 publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: Company of Biologists publist_id: '2192' status: public title: 'Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 119 year: '2006' ... --- OA_type: closed access _id: '3935' abstract: - lang: eng text: Integrins regulate cell behavior through the assembly of multiprotein complexes at the site of cell adhesion. Parvins are components of such a multiprotein complex. They consist of three members (alpha-, beta-, and gamma-parvin), form a functional complex with integrin-linked kinase (ILK) and PINCH, and link integrins to the actin cytoskeleton. Whereas alpha- and beta-parvins are widely expressed, gamma-parvin has been reported to be expressed in hematopoietic organs. In the present study, we report the expression pattern of the parvins in hematopoietic cells and the phenotypic analysis of gamma-parvin-deficient mice. Whereas alpha-parvin is not expressed in hematopoietic cells, beta-parvin is only found in myeloid cells and gamma-parvin is present in both cells of the myeloid and lymphoid lineages, where it binds ILK. Surprisingly, loss of gamma-parvin expression had no effect on blood cell differentiation, proliferation, and survival and no consequence for the T-cell-dependent antibody response and lymphocyte and dendritic cell migration. These data indicate that despite the high expression of gamma-parvin in hematopoietic cells it must play a more subtle role for blood cell homeostasis. article_processing_charge: No article_type: original author: - first_name: Haiyan full_name: Chu, Haiyan last_name: Chu - first_name: Ingo full_name: Thievessen, Ingo last_name: Thievessen - 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: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Ari full_name: Waisman, Ari last_name: Waisman - first_name: Attila full_name: Braun, Attila last_name: Braun - first_name: Angelika full_name: Noegel, Angelika last_name: Noegel - first_name: Reinhard full_name: Fässler, Reinhard last_name: Fässler citation: ama: Chu H, Thievessen I, Sixt MK, et al. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. 2006;26(5):1817-1825. doi:10.1128/MCB.26.5.1817-1825.2006 apa: Chu, H., Thievessen, I., Sixt, M. K., Lämmermann, T., Waisman, A., Braun, A., … Fässler, R. (2006). γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. American Society for Microbiology. https://doi.org/10.1128/MCB.26.5.1817-1825.2006 chicago: Chu, Haiyan, Ingo Thievessen, Michael K Sixt, Tim Lämmermann, Ari Waisman, Attila Braun, Angelika Noegel, and Reinhard Fässler. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology. American Society for Microbiology, 2006. https://doi.org/10.1128/MCB.26.5.1817-1825.2006. ieee: H. Chu et al., “γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response,” Molecular and Cellular Biology, vol. 26, no. 5. American Society for Microbiology, pp. 1817–1825, 2006. ista: Chu H, Thievessen I, Sixt MK, Lämmermann T, Waisman A, Braun A, Noegel A, Fässler R. 2006. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. 26(5), 1817–1825. mla: Chu, Haiyan, et al. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology, vol. 26, no. 5, American Society for Microbiology, 2006, pp. 1817–25, doi:10.1128/MCB.26.5.1817-1825.2006. short: H. Chu, I. Thievessen, M.K. Sixt, T. Lämmermann, A. Waisman, A. Braun, A. Noegel, R. Fässler, Molecular and Cellular Biology 26 (2006) 1817–1825. date_created: 2018-12-11T12:05:58Z date_published: 2006-03-01T00:00:00Z date_updated: 2026-08-26T12:58:22Z day: '01' doi: 10.1128/MCB.26.5.1817-1825.2006 extern: '1' external_id: pmid: - '16479001' fulldoi: https://doi.org/10.1128/MCB.26.5.1817-1825.2006 intvolume: ' 26' issue: '5' language: - iso: eng month: '03' oa_version: None page: 1817 - 1825 pmid: 1 publication: Molecular and Cellular Biology publication_identifier: eissn: - 1098-5549 issn: - 0270-7306 publication_status: published publisher: American Society for Microbiology publist_id: '2193' status: public title: γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 26 year: '2006' ... --- OA_type: closed access _id: '3936' abstract: - lang: eng text: At least eight of the twelve known members of the beta1 integrin family are expressed on hematopoietic cells. Among these, the VCAM-1 receptor alpha4beta1 has received most attention as a main factor mediating firm adhesion to the endothelium during blood cell extravasation. Therapeutic trials are ongoing into the use of antibodies and small molecule inhibitors to target this interaction and hence obtain anti-inflammatory effects. However, extravasation is only one possible process that is mediated by beta1 integrins and there is evidence that they also mediate leukocyte retention and positioning in the tissue, lymphocyte activation and possibly migration within the interstitium. Genetic mouse models where integrins are selectively deleted on blood cells have been used to investigate these functions and further studies will be invaluable to critically evaluate therapeutic trials. article_processing_charge: No article_type: original 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: Martina full_name: Bauer, Martina last_name: Bauer - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Reinhard full_name: Fässler, Reinhard last_name: Fässler citation: ama: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. 2006;18(5):482-490. doi:10.1016/j.ceb.2006.08.007' apa: 'Sixt, M. K., Bauer, M., Lämmermann, T., & Fässler, R. (2006). β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2006.08.007' chicago: 'Sixt, Michael K, Martina Bauer, Tim Lämmermann, and Reinhard Fässler. “Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion in Cell Biology. Elsevier, 2006. https://doi.org/10.1016/j.ceb.2006.08.007.' ieee: 'M. K. Sixt, M. Bauer, T. Lämmermann, and R. Fässler, “β1 integrins: zip codes and signaling relay for blood cells,” Current Opinion in Cell Biology, vol. 18, no. 5. Elsevier, pp. 482–490, 2006.' ista: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. 2006. β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. 18(5), 482–490.' mla: 'Sixt, Michael K., et al. “Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion in Cell Biology, vol. 18, no. 5, Elsevier, 2006, pp. 482–90, doi:10.1016/j.ceb.2006.08.007.' short: M.K. Sixt, M. Bauer, T. Lämmermann, R. Fässler, Current Opinion in Cell Biology 18 (2006) 482–490. date_created: 2018-12-11T12:05:59Z date_published: 2006-10-01T00:00:00Z date_updated: 2026-08-26T12:26:38Z day: '01' doi: 10.1016/j.ceb.2006.08.007 extern: '1' external_id: pmid: - '16919433' fulldoi: https://doi.org/10.1016/j.ceb.2006.08.007 intvolume: ' 18' issue: '5' language: - iso: eng month: '10' oa_version: None page: 482 - 490 pmid: 1 publication: Current Opinion in Cell Biology publication_identifier: eissn: - 1879-0410 issn: - 0955-0674 publication_status: published publisher: Elsevier publist_id: '2191' status: public title: 'β1 integrins: zip codes and signaling relay for blood cells' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 18 year: '2006' ... --- OA_type: closed access _id: '3932' abstract: - lang: eng text: 'OBJECTIVES: The EGFR is expressed in malignant ovarian tumor tissue, and tissue content of EGFR has been directly associated with poor prognosis in patients with ovarian cancer. The uPA system plays a role in pericellular proteolysis, cell migration, invasion, and is over-expressed in ovarian cancer. This study explored the effects of EGF on uPAR expression in the ovarian cancer cell line OVCAR-3. METHODS: We used OVCAR-3 cells and the following methods: cell migration assay, time-lapse video microscopy, real-time PCR, assays for cellular binding of 125I-uPA and cellular degradation of 125I-uPA:PAI-1 complex, biosynthetic labeling using 35S-methionin, Western blot, Northern blot, and ELISAs for uPA, PAI-1, and uPAR. RESULTS: EGF up-regulates both protein and mRNA not only for uPAR, but also for the ligand uPA and its inhibitor PAI-1. Cell surface uPAR, in control as well as EGF-stimulated cells, is present only in the intact, not the cleaved, form. Ligand binding experiments showed an increase of endogenously occupied uPAR, whereas non-occupied receptor sites were not increased. In addition, EGF treatment resulted in decreased degradation of radiolabeled uPA:PAI-1 complex. This suggests decreased internalization of uPAR, since the complex is internalized together with uPAR. Like EGF, colchicine, which inhibits endocytosis, increased cell surface expression of uPAR. In addition, we found an immediate increase of uPAR after exposing the cells to EGF and this was accompanied by a transient increase of cell migration. The increase of cell surface uPAR in response to EGF is accompanied by increased release of the soluble form of uPAR (suPAR) to the medium as well as by increased cell migration. Both uPAR and suPAR increased in cells treated with the endocytosis inhibitor colchicine even though cell migration was inhibited, suggesting that the mechanism of uPAR shedding is not related to cell migration. CONCLUSION: Increased cell surface uPAR in response to EGF stimulation results from mobilization of uPAR from detergent-resistant domains, increased expression of uPAR mRNA, and decreased internalization and degradation of uPAR. Both the anti-uPAR antibody R3, which inhibits binding of uPA, and the EGFR phosphorylation inhibitor Iressa inhibited cell migration in response to uPA as well as to EGF, suggesting that EGFR and uPAR are engaged in the same multiprotein assembly on the cell surface.' article_processing_charge: No article_type: original author: - first_name: Emir full_name: Henic, Emir last_name: Henic - 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: Stefan full_name: Hansson, Stefan last_name: Hansson - first_name: Gunilla full_name: Høyer Hansen, Gunilla last_name: Høyer Hansen - first_name: Bertil full_name: Casslén, Bertil last_name: Casslén citation: ama: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. 2006;101(1):28-39. doi:10.1016/j.ygyno.2005.09.038 apa: Henic, E., Sixt, M. K., Hansson, S., Høyer Hansen, G., & Casslén, B. (2006). EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. Elsevier. https://doi.org/10.1016/j.ygyno.2005.09.038 chicago: Henic, Emir, Michael K Sixt, Stefan Hansson, Gunilla Høyer Hansen, and Bertil Casslén. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated with Decreased Internalization, Increased Surface Expression, and Increased Shedding of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology. Elsevier, 2006. https://doi.org/10.1016/j.ygyno.2005.09.038. ieee: E. Henic, M. K. Sixt, S. Hansson, G. Høyer Hansen, and B. Casslén, “EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor,” Gynecologic Oncology, vol. 101, no. 1. Elsevier, pp. 28–39, 2006. ista: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. 2006. EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. 101(1), 28–39. mla: Henic, Emir, et al. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated with Decreased Internalization, Increased Surface Expression, and Increased Shedding of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology, vol. 101, no. 1, Elsevier, 2006, pp. 28–39, doi:10.1016/j.ygyno.2005.09.038. short: E. Henic, M.K. Sixt, S. Hansson, G. Høyer Hansen, B. Casslén, Gynecologic Oncology 101 (2006) 28–39. date_created: 2018-12-11T12:05:57Z date_published: 2006-04-01T00:00:00Z date_updated: 2026-08-26T13:04:22Z day: '01' doi: 10.1016/j.ygyno.2005.09.038 extern: '1' fulldoi: https://doi.org/10.1016/j.ygyno.2005.09.038 intvolume: ' 101' issue: '1' language: - iso: eng month: '04' oa_version: None page: 28 - 39 publication: Gynecologic Oncology publication_identifier: issn: - 0090-8258 publication_status: published publisher: Elsevier publist_id: '2194' status: public title: EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 101 year: '2006' ... --- OA_type: closed access _id: '3912' abstract: - lang: eng text: Invasive species often dramatically change native species communities by directly and indirectly out-competing native species. We studied the direct interference abilities of the invasive garden ant, Lasius neglectus VAN LOON, BOOMSMA & ANDRÁSFALVY, 1990, by performing one-to-one aggression tests of L. neglectus workers towards three native Lasius ant species that occur at the edge of a L. neglectus supercolony in Seva, Spain. Our results show that L. neglectus is highly aggressive against all three native Lasius species tested (L. grandis FOREL, 1909, L. emarginatus (OLIVIER, 1792), and L. cinereus SEIFERT, 1992), expressed as a higher attack rate of L. neglectus and behavioural dominance throughout the aggressive encounters. Attacks of L. neglectus were performed fastest and most frequent against L. grandis, and also the highest antennation frequencies were observed in encounters between these two species. This could be due to the largest difference in body size, or due to a greater overlap in ecological niche between L. neglectus and L. grandis compared to the other two native species. There was only weak support for L. neglectus workers from the periphery of the supercolony to be more aggressive relative to workers from the centre, even though the former encounter native ant species on a daily basis at the edge of the supercolony. article_processing_charge: No article_type: original author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Suzanne full_name: Lommen, Suzanne last_name: Lommen - first_name: Klaus full_name: Petersen, Klaus last_name: Petersen - first_name: Jes full_name: Pedersen, Jes last_name: Pedersen citation: ama: 'Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain. Myrmecological News. 2006;9:13-19.' apa: 'Cremer, S., Ugelvig, L. V., Lommen, S., Petersen, K., & Pedersen, J. (2006). Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain. Myrmecological News. Österreichische Gesellschaft für Entomofaunistik.' chicago: 'Cremer, Sylvia, Line V Ugelvig, Suzanne Lommen, Klaus Petersen, and Jes Pedersen. “Attack of the Invasive Garden Ant: Aggression Behaviour of Lasius Neglectus (Hymenoptera: Formicidae) against Native Lasius Species in Spain.” Myrmecological News. Österreichische Gesellschaft für Entomofaunistik, 2006.' ieee: 'S. Cremer, L. V. Ugelvig, S. Lommen, K. Petersen, and J. Pedersen, “Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain,” Myrmecological News, vol. 9. Österreichische Gesellschaft für Entomofaunistik, pp. 13–19, 2006.' ista: 'Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. 2006. Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain. Myrmecological News. 9, 13–19.' mla: 'Cremer, Sylvia, et al. “Attack of the Invasive Garden Ant: Aggression Behaviour of Lasius Neglectus (Hymenoptera: Formicidae) against Native Lasius Species in Spain.” Myrmecological News, vol. 9, Österreichische Gesellschaft für Entomofaunistik, 2006, pp. 13–19.' short: S. Cremer, L.V. Ugelvig, S. Lommen, K. Petersen, J. Pedersen, Myrmecological News 9 (2006) 13–19. date_created: 2018-12-11T12:05:51Z date_published: 2006-12-01T00:00:00Z date_updated: 2026-08-26T13:06:38Z day: '01' extern: '1' intvolume: ' 9' language: - iso: eng month: '12' oa_version: None page: 13 - 19 publication: Myrmecological News publication_status: published publisher: Österreichische Gesellschaft für Entomofaunistik publist_id: '2239' status: public title: 'Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 9 year: '2006' ... --- OA_type: closed access _id: '3913' abstract: - lang: eng text: Many invasive ant species, such as the Argentine ant or the red imported fire ant, have huge colonies with thousands of mass-foraging workers, which quickly monopolise resources and therefore represent a considerable threat to the native ant fauna. Cardiocondyla obscurior and several other species of this myrmicine genus have similarly been transferred throughout the tropics by human activities. However, because their colonies are tiny and workers forage solitarily, Cardiocondyla are often not recognized as successful invaders. Here, we document that the life history of Cardiocondyla closely resembles that of the more conspicuous tramp species, with polygyny, intranidal mating, budding, worker sterility, low genetic variability, and possibly also unicoloniality. Given that introduced Cardiocondyla may locally reach a very high population density, the effects of these stealthy invaders on the native arthropod fauna should receive more attention. article_processing_charge: No article_type: original author: - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Norbert full_name: Eckl, Norbert last_name: Eckl - first_name: Alexandra full_name: Schrempf, Alexandra last_name: Schrempf citation: ama: 'Heinze J, Cremer S, Eckl N, Schrempf A. Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. 2006;53(1):1-7. doi:10.1007/s00040-005-0847-4' apa: 'Heinze, J., Cremer, S., Eckl, N., & Schrempf, A. (2006). Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. Springer Nature. https://doi.org/10.1007/s00040-005-0847-4' chicago: 'Heinze, Jürgen, Sylvia Cremer, Norbert Eckl, and Alexandra Schrempf. “Stealthy Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux. Springer Nature, 2006. https://doi.org/10.1007/s00040-005-0847-4.' ieee: 'J. Heinze, S. Cremer, N. Eckl, and A. Schrempf, “Stealthy invaders: the biology of Cardiocondyla tramp ants,” Insectes Sociaux, vol. 53, no. 1. Springer Nature, pp. 1–7, 2006.' ista: 'Heinze J, Cremer S, Eckl N, Schrempf A. 2006. Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. 53(1), 1–7.' mla: 'Heinze, Jürgen, et al. “Stealthy Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux, vol. 53, no. 1, Springer Nature, 2006, pp. 1–7, doi:10.1007/s00040-005-0847-4.' short: J. Heinze, S. Cremer, N. Eckl, A. Schrempf, Insectes Sociaux 53 (2006) 1–7. date_created: 2018-12-11T12:05:51Z date_published: 2006-02-01T00:00:00Z date_updated: 2026-08-26T13:15:26Z day: '01' doi: 10.1007/s00040-005-0847-4 extern: '1' fulldoi: https://doi.org/10.1007/s00040-005-0847-4 intvolume: ' 53' issue: '1' language: - iso: eng month: '02' oa_version: None page: 1 - 7 publication: Insectes Sociaux publication_identifier: eissn: - 1420-9098 issn: - 0020-1812 publication_status: published publisher: Springer Nature publist_id: '2240' status: public title: 'Stealthy invaders: the biology of Cardiocondyla tramp ants' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 53 year: '2006' ... --- OA_type: closed access _id: '3890' abstract: - lang: eng text: We consider two-player infinite games played on graphs. The games are concurrent, in that at each state the players choose their moves simultaneously and independently, and stochastic, in that the moves determine a probability distribution for the successor state. The value of a game is the maximal probability with which a player can guarantee the satisfaction of her objective. We show that the values of concurrent games with w-regular objectives expressed as parity conditions can be decided in NP boolean AND coNP. This result substantially improves the best known previous bound of 3EXPTIME. It also shows that the full class of concurrent parity games is no harder than the special case of turn-based stochastic reachability games, for which NP boolean AND coNP is the best known bound. While the previous, more restricted NP boolean AND coNP results for graph games relied on the existence of particularly simple (pure memoryless) optimal strategies, in concurrent games with parity objectives optimal strategies may not exist, and epsilon-optimal strategies (which achieve the value of the game within a parameter epsilon > 0) require in general both randomization and infinite memory. Hence our proof must rely on a more detailed analysis of strategies and, in addition to the main result, yields two results that are interesting on their own. First, we show that there exist epsilon-optimal strategies that in the limit coincide with memoryless strategies; this parallels the celebrated result of Mertens-Neyman for concurrent games with limit-average objectives. Second, we complete the characterization of the memory requirements for epsilon-optimal strategies for concurrent games with parity conditions, by showing that memoryless strategies suffice for epsilon-optimality for coBachi conditions. acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF ITR grant CCR-0225610. article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: De Alfaro, Luca last_name: De Alfaro - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, De Alfaro L, Henzinger TA. The complexity of quantitative concurrent parity games. In: Proceedings of the Seventeenth Annual ACM-SIAM Symposium on Discrete Algorithm. SIAM; 2006:678-687. doi:10.1145/1109557.1109631' apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2006). The complexity of quantitative concurrent parity games. In Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm (pp. 678–687). Miami, FL, United States: SIAM. https://doi.org/10.1145/1109557.1109631' chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “The Complexity of Quantitative Concurrent Parity Games.” In Proceedings of the Seventeenth Annual ACM-SIAM Symposium on Discrete Algorithm, 678–87. SIAM, 2006. https://doi.org/10.1145/1109557.1109631. ieee: K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “The complexity of quantitative concurrent parity games,” in Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm, Miami, FL, United States, 2006, pp. 678–687. ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2006. The complexity of quantitative concurrent parity games. Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm. SODA: Symposium on Discrete Algorithms, 678–687.' mla: Chatterjee, Krishnendu, et al. “The Complexity of Quantitative Concurrent Parity Games.” Proceedings of the Seventeenth Annual ACM-SIAM Symposium on Discrete Algorithm, SIAM, 2006, pp. 678–87, doi:10.1145/1109557.1109631. short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, Proceedings of the Seventeenth Annual ACM-SIAM Symposium on Discrete Algorithm, SIAM, 2006, pp. 678–687. conference: end_date: 2006-01-26 location: Miami, FL, United States name: 'SODA: Symposium on Discrete Algorithms' start_date: 2006-01-22 date_created: 2018-12-11T12:05:43Z date_published: 2006-01-01T00:00:00Z date_updated: 2026-08-27T07:53:44Z day: '01' doi: 10.1145/1109557.1109631 extern: '1' fulldoi: https://doi.org/10.1145/1109557.1109631 language: - iso: eng month: '01' oa_version: None page: 678 - 687 publication: Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm publication_identifier: isbn: - '9780898716054' publication_status: published publisher: SIAM publist_id: '2273' status: public title: The complexity of quantitative concurrent parity games type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2006' ... --- OA_type: closed access _id: '3891' abstract: - lang: eng text: 'We study infinite stochastic games played by two-players over a finite state space, with objectives specified by sets of infinite traces. The games are concurrent (players make moves simultaneously and independently), stochastic (the next state is determined by a probability distribution that depends on the current state and chosen moves of the players) and infinite (proceeds for infinite number of rounds). The analysis of concurrent stochastic games can be classified into: quantitative analysis, analyzing the optimum value of the game; and qualitative analysis, analyzing the set of states with optimum value 1. We consider concurrent games with tail objectives, i.e., objectives that are independent of the finite-prefix of traces, and show that the class of tail objectives are strictly richer than the omega-regular objectives. We develop new proof techniques to extend several properties of concurrent games with omega-regular objectives to concurrent games with tail objectives. We prove the positive limit-one property for tail objectives, that states for all concurrent games if the optimum value for a player is positive for a tail objective Phi at some state, then there is a state where the optimum value is 1 for Phi, for the player. We also show that the optimum values of zero-sum (strictly conflicting objectives) games with tail objectives can be related to equilibrium values of nonzero-sum (not strictly conflicting objectives) games with simpler reachability objectives. A consequence of our analysis presents a polynomial time reduction of the quantitative analysis of tail objectives to the qualitative analysis for the sub-class of one-player stochastic games (Markov decision processes).' alternative_title: - 'LNCS ' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Chatterjee K. Concurrent games with tail objectives. In: Proceedings of the 20th International Conference on Computer Science Logic. Vol 4207. Springer Nature; 2006:256-270. doi:10.1007/11874683_17' apa: 'Chatterjee, K. (2006). Concurrent games with tail objectives. In Proceedings of the 20th international conference on Computer Science Logic (Vol. 4207, pp. 256–270). Szeged, Hungary: Springer Nature. https://doi.org/10.1007/11874683_17' chicago: Chatterjee, Krishnendu. “Concurrent Games with Tail Objectives.” In Proceedings of the 20th International Conference on Computer Science Logic, 4207:256–70. Springer Nature, 2006. https://doi.org/10.1007/11874683_17. ieee: K. Chatterjee, “Concurrent games with tail objectives,” in Proceedings of the 20th international conference on Computer Science Logic, Szeged, Hungary, 2006, vol. 4207, pp. 256–270. ista: 'Chatterjee K. 2006. Concurrent games with tail objectives. Proceedings of the 20th international conference on Computer Science Logic. CSL: Computer Science Logic, LNCS , vol. 4207, 256–270.' mla: Chatterjee, Krishnendu. “Concurrent Games with Tail Objectives.” Proceedings of the 20th International Conference on Computer Science Logic, vol. 4207, Springer Nature, 2006, pp. 256–70, doi:10.1007/11874683_17. short: K. Chatterjee, in:, Proceedings of the 20th International Conference on Computer Science Logic, Springer Nature, 2006, pp. 256–270. conference: end_date: 2006-09-29 location: Szeged, Hungary name: 'CSL: Computer Science Logic' start_date: 2006-09-25 date_created: 2018-12-11T12:05:44Z date_published: 2006-09-28T00:00:00Z date_updated: 2026-08-27T07:36:31Z day: '28' doi: 10.1007/11874683_17 extern: '1' fulldoi: https://doi.org/10.1007/11874683_17 intvolume: ' 4207' language: - iso: eng month: '09' oa_version: None page: 256 - 270 publication: Proceedings of the 20th international conference on Computer Science Logic publication_identifier: eisbn: - '9783540454595' isbn: - '9783540454588' publication_status: published publisher: Springer Nature publist_id: '2272' status: public title: Concurrent games with tail objectives type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 4207 year: '2006' ... --- OA_type: closed access _id: '3908' abstract: - lang: eng text: 'It is commonly believed that both the average length and the frequency of microsatellites correlate with genome size. We have estimated the frequency and the average length for 69 perfect dinucleotide microsatellites in an insect with an exceptionally large genome: Chorthippus biguttulus (Orthoptera, Acrididae). Dinucleotide microsatellites are not more frequent in C. biguttulus, but repeat arrays are 1.4 to 2 times longer than in other insect species. The average repeat number in C. biguttulus lies in the range of higher vertebrates. Natural populations are highly variable. At least 30 alleles per locus were found and the expected heterozygosity is above 0.95 at all three loci studied. In contrast, the observed heterozygosity is much lower (≤0.51), which could be caused by long null alleles.' article_processing_charge: No article_type: original author: - first_name: Jana full_name: Ustinova, Jana last_name: Ustinova - first_name: Roland full_name: Achmann, Roland last_name: Achmann - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Frieder full_name: Mayer, Frieder last_name: Mayer citation: ama: 'Ustinova J, Achmann R, Cremer S, Mayer F. Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution. 2006;62(2):158-167. doi:10.1007/s00239-005-0022-6' apa: 'Ustinova, J., Achmann, R., Cremer, S., & Mayer, F. (2006). Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution. Springer Nature. https://doi.org/10.1007/s00239-005-0022-6' chicago: 'Ustinova, Jana, Roland Achmann, Sylvia Cremer, and Frieder Mayer. “Long Repeats in a Huge Gemome: Microsatellite Loci in the Grasshopper Chorthippus Biguttulus.” Journal of Molecular Evolution. Springer Nature, 2006. https://doi.org/10.1007/s00239-005-0022-6.' ieee: 'J. Ustinova, R. Achmann, S. Cremer, and F. Mayer, “Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus,” Journal of Molecular Evolution, vol. 62, no. 2. Springer Nature, pp. 158–167, 2006.' ista: 'Ustinova J, Achmann R, Cremer S, Mayer F. 2006. Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution. 62(2), 158–167.' mla: 'Ustinova, Jana, et al. “Long Repeats in a Huge Gemome: Microsatellite Loci in the Grasshopper Chorthippus Biguttulus.” Journal of Molecular Evolution, vol. 62, no. 2, Springer Nature, 2006, pp. 158–67, doi:10.1007/s00239-005-0022-6.' short: J. Ustinova, R. Achmann, S. Cremer, F. Mayer, Journal of Molecular Evolution 62 (2006) 158–167. date_created: 2018-12-11T12:05:49Z date_published: 2006-02-01T00:00:00Z date_updated: 2026-08-27T07:31:36Z day: '01' doi: 10.1007/s00239-005-0022-6 extern: '1' external_id: pmid: - '16474983 ' fulldoi: https://doi.org/10.1007/s00239-005-0022-6 intvolume: ' 62' issue: '2' language: - iso: eng month: '02' oa_version: None page: 158 - 167 pmid: 1 publication: Journal of Molecular Evolution publication_identifier: eissn: - 1432-1432 issn: - 0022-2844 publication_status: published publisher: Springer Nature publist_id: '2242' status: public title: 'Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 62 year: '2006' ... --- OA_type: closed access _id: '3914' abstract: - lang: eng text: We compare the performances of established means of character selection for discriminant analysis in species distinction with a combination procedure for finding the optimal character combination (minimum classification error, minimum number of required characters), using morphometric data sets from the ant genera Cardiocondyla, Lasius and Tetramorium. The established methods are empirical character selection as well as forward selection, backward elimination and stepwise selection of discriminant analysis. The combination procedure is clearly superior to the established methods of character selection, and is widely applicable. article_processing_charge: No article_type: original author: - first_name: Karl full_name: Moder, Karl last_name: Moder - first_name: Birgit full_name: Schlick Steiner, Birgit last_name: Schlick Steiner - first_name: Florian full_name: Steiner, Florian last_name: Steiner - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Erhard full_name: Christian, Erhard last_name: Christian - first_name: Bernhard full_name: Seifert, Bernhard last_name: Seifert citation: ama: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. 2006;45(1):82-87. doi:10.1111/j.1439-0469.2006.00372.x' apa: 'Moder, K., Schlick Steiner, B., Steiner, F., Cremer, S., Christian, E., & Seifert, B. (2006). Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell. https://doi.org/10.1111/j.1439-0469.2006.00372.x' chicago: 'Moder, Karl, Birgit Schlick Steiner, Florian Steiner, Sylvia Cremer, Erhard Christian, and Bernhard Seifert. “Optimal Species Distinction by Discriminant Analysis: Comparing Established Methods of Character Selection with a Combination Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.1439-0469.2006.00372.x.' ieee: 'K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, and B. Seifert, “Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study,” Journal of Zoological Systematics and Evolutionary Research, vol. 45, no. 1. Wiley-Blackwell, pp. 82–87, 2006.' ista: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. 2006. Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. 45(1), 82–87.' mla: 'Moder, Karl, et al. “Optimal Species Distinction by Discriminant Analysis: Comparing Established Methods of Character Selection with a Combination Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics and Evolutionary Research, vol. 45, no. 1, Wiley-Blackwell, 2006, pp. 82–87, doi:10.1111/j.1439-0469.2006.00372.x.' short: K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, B. Seifert, Journal of Zoological Systematics and Evolutionary Research 45 (2006) 82–87. date_created: 2018-12-11T12:05:52Z date_published: 2006-08-29T00:00:00Z date_updated: 2026-08-27T07:26:09Z day: '29' doi: 10.1111/j.1439-0469.2006.00372.x extern: '1' fulldoi: https://doi.org/10.1111/j.1439-0469.2006.00372.x intvolume: ' 45' issue: '1' language: - iso: eng month: '08' oa_version: None page: 82 - 87 publication: Journal of Zoological Systematics and Evolutionary Research publication_identifier: eissn: - 1439-0469 issn: - 0947-5745 publication_status: published publisher: Wiley-Blackwell publist_id: '2241' status: public title: 'Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 45 year: '2006' ... --- OA_type: closed access _id: '3889' abstract: - lang: eng text: We study observation-based strategies for two-player turn-based games on graphs with omega-regular objectives. An observation-based strategy relies on imperfect information about the history of a play, namely, on the past sequence of observations. Such games occur in the synthesis of a controller that does not see the private state of the plant. Our main results are twofold. First, we give a fixed-point algorithm for computing the set of states from which a player can win with a deterministic observation-based strategy for any omega-regular objective. The fixed point is computed in the lattice of antichains of state sets. This algorithm has the advantages of being directed by the objective and of avoiding an explicit subset construction on the game graph. Second, we give an algorithm for computing the set of states from which a player can win with probability 1 with a randomized observation-based strategy for a Buchi objective. This set is of interest because in the absence of perfect information, randomized strategies are more powerful than deterministic ones. We show that our algorithms are optimal by proving matching lower bounds. acknowledgement: This research was supported in part by the NSF grants CCR-0225610 and CCR-0234690, by the SNSF under the Indo-Swiss Joint Research Programme, and by the FRFC project “Centre Fédéré en Vérification” funded by the FNRS under grant 2.4530.02. alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jean full_name: Raskin, Jean last_name: Raskin citation: ama: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. Algorithms for omega-regular games with imperfect information. In: Proceedings of the 20th International Conference on Computer Science Logic. Vol 4207. Springer Nature; 2006:287-302. doi:10.1007/11874683_19' apa: 'Chatterjee, K., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Algorithms for omega-regular games with imperfect information. In Proceedings of the 20th international conference on Computer Science Logic (Vol. 4207, pp. 287–302). Szeged, Hungary: Springer Nature. https://doi.org/10.1007/11874683_19' chicago: Chatterjee, Krishnendu, Laurent Doyen, Thomas A Henzinger, and Jean Raskin. “Algorithms for Omega-Regular Games with Imperfect Information.” In Proceedings of the 20th International Conference on Computer Science Logic, 4207:287–302. Springer Nature, 2006. https://doi.org/10.1007/11874683_19. ieee: K. Chatterjee, L. Doyen, T. A. Henzinger, and J. Raskin, “Algorithms for omega-regular games with imperfect information,” in Proceedings of the 20th international conference on Computer Science Logic, Szeged, Hungary, 2006, vol. 4207, pp. 287–302. ista: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. 2006. Algorithms for omega-regular games with imperfect information. Proceedings of the 20th international conference on Computer Science Logic. CSL: Computer Science Logic, LNCS, vol. 4207, 287–302.' mla: Chatterjee, Krishnendu, et al. “Algorithms for Omega-Regular Games with Imperfect Information.” Proceedings of the 20th International Conference on Computer Science Logic, vol. 4207, Springer Nature, 2006, pp. 287–302, doi:10.1007/11874683_19. short: K. Chatterjee, L. Doyen, T.A. Henzinger, J. Raskin, in:, Proceedings of the 20th International Conference on Computer Science Logic, Springer Nature, 2006, pp. 287–302. conference: end_date: 2006-09-29 location: Szeged, Hungary name: 'CSL: Computer Science Logic' start_date: 2006-09-25 date_created: 2018-12-11T12:05:43Z date_published: 2006-11-13T00:00:00Z date_updated: 2026-08-27T08:04:08Z day: '13' doi: 10.1007/11874683_19 extern: '1' fulldoi: https://doi.org/10.1007/11874683_19 intvolume: ' 4207' language: - iso: eng month: '11' oa_version: None page: 287 - 302 publication: Proceedings of the 20th international conference on Computer Science Logic publication_identifier: eisbn: - '9783540454595' eissn: - 1611-3349 isbn: - '9783540454588' issn: - 0302-9743 publication_status: published publisher: Springer Nature publist_id: '2276' status: public title: Algorithms for omega-regular games with imperfect information type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 4207 year: '2006' ... --- OA_type: closed access _id: '3888' abstract: - lang: eng text: A stochastic graph game is played by two players on a game graph with probabilistic transitions. We consider stochastic graph games with omega-regular winning conditions specified as Rabin or Streett objectives. These games are NP-complete and coNP-complete, respectively. The value of the game for a player at a state s given an objective Phi is the maximal probability with which the player can guarantee the satisfaction of Phi from s. We present a strategy-improvement algorithm to compute values in stochastic Rabin games, where an improvement step involves solving Markov decision processes (MDPs) and nonstochastic Rabin games. The algorithm also computes values for stochastic Streett games but does not directly yield an optimal strategy for Streett objectives. We then show how to obtain an optimal strategy for Streett objectives by solving certain nonstochastic Streett games. acknowledgement: This research was supported in part by the NSF grants CCR-0225610 and CCR-0234690, and by the SNSF under the Indo-Swiss Joint Research Programme. alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Henzinger TA. Strategy improvement for stochastic Rabin and Streett games. In: Proceedings of the 17th International Conference on Concurrency Theory. Vol 4137. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2006:375-389. doi:10.1007/11817949_25' apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Strategy improvement for stochastic Rabin and Streett games. In Proceedings of the 17th international conference on Concurrency Theory (Vol. 4137, pp. 375–389). Bonn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/11817949_25' chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Strategy Improvement for Stochastic Rabin and Streett Games.” In Proceedings of the 17th International Conference on Concurrency Theory, 4137:375–89. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006. https://doi.org/10.1007/11817949_25. ieee: K. Chatterjee and T. A. Henzinger, “Strategy improvement for stochastic Rabin and Streett games,” in Proceedings of the 17th international conference on Concurrency Theory, Bonn, Germany, 2006, vol. 4137, pp. 375–389. ista: 'Chatterjee K, Henzinger TA. 2006. Strategy improvement for stochastic Rabin and Streett games. Proceedings of the 17th international conference on Concurrency Theory. CONCUR: Concurrency Theory, LNCS, vol. 4137, 375–389.' mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. “Strategy Improvement for Stochastic Rabin and Streett Games.” Proceedings of the 17th International Conference on Concurrency Theory, vol. 4137, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006, pp. 375–89, doi:10.1007/11817949_25. short: K. Chatterjee, T.A. Henzinger, in:, Proceedings of the 17th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2006, pp. 375–389. conference: end_date: 2006-08-30 location: Bonn, Germany name: 'CONCUR: Concurrency Theory' start_date: 2006-08-27 date_created: 2018-12-11T12:05:43Z date_published: 2006-08-10T00:00:00Z date_updated: 2026-08-27T08:28:45Z day: '10' doi: 10.1007/11817949_25 extern: '1' fulldoi: https://doi.org/10.1007/11817949_25 intvolume: ' 4137' language: - iso: eng month: '08' oa_version: None page: 375 - 389 publication: Proceedings of the 17th international conference on Concurrency Theory publication_identifier: eisbn: - '9783540373773' isbn: - '9783540373766' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '2278' status: public title: Strategy improvement for stochastic Rabin and Streett games type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 4137 year: '2006' ... --- OA_type: closed access _id: '3818' abstract: - lang: eng text: Rigorous analysis of synaptic transmission in the central nervous system requires access to presynaptic terminals. However, cortical terminals have been largely inaccessible to presynaptic patch-clamp recording, due to their small size. Using improved patch-clamp techniques in brain slices, we recorded from mossy fiber terminals in the CA3 region of the hippocampus, which have a diameter of 2-5 microm. The major steps of improvement were the enhanced visibility provided by high-numerical aperture objectives and infrared illumination, the development of vibratomes with minimal vertical blade vibrations and the use of sucrose-based solutions for storage and cutting. Based on these improvements, we describe a protocol that allows us to routinely record from hippocampal mossy fiber boutons. Presynaptic recordings can be obtained in slices from both rats and mice. Presynaptic recordings can be also obtained in slices from transgenic mice in which terminals are labeled with enhanced green fluorescent protein. article_processing_charge: No article_type: original author: - first_name: Josef full_name: Bischofberger, Josef last_name: Bischofberger - first_name: Dominique full_name: Engel, Dominique last_name: Engel - first_name: Liyi full_name: Li, Liyi last_name: Li - first_name: Jörg full_name: Geiger, Jörg last_name: Geiger - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature Protocols. 2006;1(4):2075-2081. doi:10.1038/nprot.2006.312 apa: Bischofberger, J., Engel, D., Li, L., Geiger, J., & Jonas, P. M. (2006). Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.312 chicago: Bischofberger, Josef, Dominique Engel, Liyi Li, Jörg Geiger, and Peter M Jonas. “Patch-Clamp Recording from Mossy Fiber Terminals in Hippocampal Slices.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.312 . ieee: J. Bischofberger, D. Engel, L. Li, J. Geiger, and P. M. Jonas, “Patch-clamp recording from mossy fiber terminals in hippocampal slices,” Nature Protocols, vol. 1, no. 4. Nature Publishing Group, pp. 2075–81, 2006. ista: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. 2006. Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature Protocols. 1(4), 2075–81. mla: Bischofberger, Josef, et al. “Patch-Clamp Recording from Mossy Fiber Terminals in Hippocampal Slices.” Nature Protocols, vol. 1, no. 4, Nature Publishing Group, 2006, pp. 2075–81, doi:10.1038/nprot.2006.312 . short: J. Bischofberger, D. Engel, L. Li, J. Geiger, P.M. Jonas, Nature Protocols 1 (2006) 2075–81. date_created: 2018-12-11T12:05:20Z date_published: 2006-01-01T00:00:00Z date_updated: 2026-08-27T08:31:06Z day: '01' doi: '10.1038/nprot.2006.312 ' extern: '1' external_id: pmid: - '17487197' fulldoi: 'https://doi.org/10.1038/nprot.2006.312 ' intvolume: ' 1' issue: '4' language: - iso: eng month: '01' oa_version: None page: 2075 - 81 pmid: 1 publication: Nature Protocols publication_identifier: eissn: - 1750-2799 issn: - 1754-2189 publication_status: published publisher: Nature Publishing Group publist_id: '2392' status: public title: Patch-clamp recording from mossy fiber terminals in hippocampal slices type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 1 year: '2006' ... --- OA_type: closed access _id: '3813' abstract: - lang: eng text: Hyperpolarization-activated channels (Ih or HCN channels) are widely expressed in principal neurons in the central nervous system. However, Ih in inhibitory GABAergic interneurons is less well characterized. We examined the functional properties of Ih in fast-spiking basket cells (BCs) of the dentate gyrus, using hippocampal slices from 17- to 21-day-old rats. Bath application of the Ih channel blocker ZD 7288 at a concentration of 30 microm induced a hyperpolarization of 5.7 +/- 1.5 mV, an increase in input resistance and a correlated increase in apparent membrane time constant. ZD 7288 blocked a hyperpolarization-activated current in a concentration-dependent manner (IC50, 1.4 microm). The effects of ZD 7288 were mimicked by external Cs+. The reversal potential of Ih was -27.4 mV, corresponding to a Na+ to K+ permeability ratio (PNa/PK) of 0.36. The midpoint potential of the activation curve of Ih was -83.9 mV, and the activation time constant at -120 mV was 190 ms. Single-cell expression analysis using reverse transcription followed by quantitative polymerase chain reaction revealed that BCs coexpress HCN1 and HCN2 subunit mRNA, suggesting the formation of heteromeric HCN1/2 channels. ZD 7288 increased the current threshold for evoking antidromic action potentials by extracellular stimulation, consistent with the expression of Ih in BC axons. Finally, ZD 7288 decreased the frequency of miniature inhibitory postsynaptic currents (mIPSCs) in hippocampal granule cells, the main target cells of BCs, to 70 +/- 4% of the control value. In contrast, the amplitude of mIPSCs was unchanged, consistent with the presence of Ih in inhibitory terminals. In conclusion, our results suggest that Ih channels are expressed in the somatodendritic region, axon and presynaptic elements of fast-spiking BCs in the hippocampus. article_processing_charge: No article_type: original author: - first_name: Yexica full_name: Aponte, Yexica last_name: Aponte - first_name: Cheng full_name: Lien, Cheng last_name: Lien - first_name: Ellen full_name: Reisinger, Ellen last_name: Reisinger - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Aponte Y, Lien C, Reisinger E, Jonas PM. Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology. 2006;574(Pt 1):229-243. doi:10.1113/jphysiol.2005.104042 apa: Aponte, Y., Lien, C., Reisinger, E., & Jonas, P. M. (2006). Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2005.104042 chicago: Aponte, Yexica, Cheng Lien, Ellen Reisinger, and Peter M Jonas. “Hyperpolarization-Activated Cation Channels in Fast-Spiking Interneurons of Rat Hippocampus.” Journal of Physiology. Wiley-Blackwell, 2006. https://doi.org/10.1113/jphysiol.2005.104042. ieee: Y. Aponte, C. Lien, E. Reisinger, and P. M. Jonas, “Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus,” Journal of Physiology, vol. 574, no. Pt 1. Wiley-Blackwell, pp. 229–43, 2006. ista: Aponte Y, Lien C, Reisinger E, Jonas PM. 2006. Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology. 574(Pt 1), 229–43. mla: Aponte, Yexica, et al. “Hyperpolarization-Activated Cation Channels in Fast-Spiking Interneurons of Rat Hippocampus.” Journal of Physiology, vol. 574, no. Pt 1, Wiley-Blackwell, 2006, pp. 229–43, doi:10.1113/jphysiol.2005.104042. short: Y. Aponte, C. Lien, E. Reisinger, P.M. Jonas, Journal of Physiology 574 (2006) 229–43. date_created: 2018-12-11T12:05:19Z date_published: 2006-01-01T00:00:00Z date_updated: 2026-08-27T09:04:43Z day: '01' doi: 10.1113/jphysiol.2005.104042 extern: '1' external_id: pmid: - '16690716' fulldoi: https://doi.org/10.1113/jphysiol.2005.104042 intvolume: ' 574' issue: Pt 1 language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1817792/ month: '01' oa: 1 oa_version: None page: 229 - 43 pmid: 1 publication: Journal of Physiology publication_identifier: eissn: - 1469-7793 issn: - 0022-3751 publication_status: published publisher: Wiley-Blackwell publist_id: '2397' status: public title: Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 574 year: '2006' ... --- OA_type: closed access _id: '3755' abstract: - lang: eng text: A primitive example of adaptation in gene expression is the balance between the rate of synthesis and degradation of cellular RNA, which allows rapid responses to environmental signals. Here, we investigate how multidrug efflux pump systems mediate the dynamics of a simple drug-inducible system in response to a steady level of inducer. Using fluorescence correlation spectroscopy, we measured in real time within a single bacterium the transcription activity at the RNA level of the acrAB-TolC multidrug efflux pump system. When cells are exposed to constant level of anhydrotetracycline inducer and are adsorbed onto a poly-L-lysine-coated surface, we found that the acrAB-TolC promoter is steadily active. We also monitored the activity of the tet promoter to characterize the effect of this efflux system on the dynamics of drug-inducible transcription. We found that the transcriptional response of the tet promoter to a steady level of aTc rises and then falls back to its preinduction level. The rate of RNA degradation was constant throughout the transcriptional pulse, indicating that the modulation of intracellular inducer concentration alone can produce this pulsating response. Single-cell experiments together with numerical simulations suggest that such pulsating response in drug-inducible genetic systems is a property emerging from the dependence of drug-inducible transcription on multidrug efflux systems. article_processing_charge: No article_type: original author: - first_name: Thuc full_name: Le, Thuc last_name: Le - first_name: Thierry full_name: Emonet, Thierry last_name: Emonet - first_name: Sébastien full_name: Harlepp, Sébastien last_name: Harlepp - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Philippe full_name: Cluzel, Philippe last_name: Cluzel citation: ama: Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. 2006;90(9):3315-3321. doi:10.1529/biophysj.105.073353 apa: Le, T., Emonet, T., Harlepp, S., Guet, C. C., & Cluzel, P. (2006). Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. Biophysical Society. https://doi.org/10.1529/biophysj.105.073353 chicago: Le, Thuc, Thierry Emonet, Sébastien Harlepp, Calin C Guet, and Philippe Cluzel. “Dynamical Determinants of Drug-Inducible Gene Expression in a Single Bacterium.” Biophysical Journal. Biophysical Society, 2006. https://doi.org/10.1529/biophysj.105.073353. ieee: T. Le, T. Emonet, S. Harlepp, C. C. Guet, and P. Cluzel, “Dynamical determinants of drug-inducible gene expression in a single bacterium,” Biophysical Journal, vol. 90, no. 9. Biophysical Society, pp. 3315–3321, 2006. ista: Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. 2006. Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. 90(9), 3315–3321. mla: Le, Thuc, et al. “Dynamical Determinants of Drug-Inducible Gene Expression in a Single Bacterium.” Biophysical Journal, vol. 90, no. 9, Biophysical Society, 2006, pp. 3315–21, doi:10.1529/biophysj.105.073353. short: T. Le, T. Emonet, S. Harlepp, C.C. Guet, P. Cluzel, Biophysical Journal 90 (2006) 3315–3321. date_created: 2018-12-11T12:04:59Z date_published: 2006-01-01T00:00:00Z date_updated: 2026-08-27T10:00:40Z day: '01' doi: 10.1529/biophysj.105.073353 extern: '1' external_id: pmid: - '16461398' fulldoi: https://doi.org/10.1529/biophysj.105.073353 intvolume: ' 90' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1432126/ month: '01' oa: 1 oa_version: None page: 3315 - 3321 pmid: 1 publication: Biophysical Journal publication_identifier: eissn: - 1542-0086 issn: - 0006-3495 publication_status: published publisher: Biophysical Society publist_id: '2472' status: public title: Dynamical determinants of drug-inducible gene expression in a single bacterium type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 90 year: '2006' ...