--- _id: '1892' abstract: - lang: eng text: Behavioural variation among conspecifics is typically contingent on individual state or environmental conditions. Sex-specific genetic polymorphisms are enigmatic because they lack conditionality, and genes causing adaptive trait variation in one sex may reduce Darwinian fitness in the other. One way to avoid such genetic antagonism is to control sex-specific traits by inheritance via sex chromosomes. Here, controlled laboratory crossings suggest that in snail-brooding cichlid fish a single locus, two-allele polymorphism located on a sex-linked chromosome of heterogametic males generates an extreme reproductive dimorphism. Both natural and sexual selection are responsible for exceptionally large body size of bourgeois males, creating a niche for a miniature male phenotype to evolve. This extreme intrasexual dimorphism results from selection on opposite size thresholds caused by a single ecological factor, empty snail shells used as breeding substrate. Paternity analyses reveal that in the field parasitic dwarf males sire the majority of offspring in direct sperm competition with large nest owners exceeding their size more than 40 times. Apparently, use of empty snail shells as breeding substrate and single locus sex-linked inheritance of growth are the major ecological and genetic mechanisms responsible for the extreme intrasexual diversity observed in Lamprologus callipterus. acknowledgement: "This research was supported by grants of the Swiss National Science Foundation to M.T.\r\nWe thank Tetsu Sato for providing field samples, Olivier Goffinet for field assistance, Dolores Schütz for vital help in the field and with the manuscript, David Lank, Barbara Taborsky, Suzanne Alonzo and two anonymous referees for comments on earlier manuscript versions, and the Fisheries Department, Ministry of Agriculture and Livestock of Zambia, for permission and support." article_number: '20140253' article_processing_charge: No article_type: original author: - first_name: Sabine full_name: Ocana, Sabine last_name: Ocana - first_name: Patrick full_name: Meidl, Patrick id: 4709BCE6-F248-11E8-B48F-1D18A9856A87 last_name: Meidl - first_name: Danielle full_name: Bonfils, Danielle last_name: Bonfils - first_name: Michael full_name: Taborsky, Michael last_name: Taborsky citation: ama: Ocana S, Meidl P, Bonfils D, Taborsky M. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. 2014;281(1794). doi:10.1098/rspb.2014.0253 apa: Ocana, S., Meidl, P., Bonfils, D., & Taborsky, M. (2014). Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2014.0253 chicago: Ocana, Sabine, Patrick Meidl, Danielle Bonfils, and Michael Taborsky. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2014. https://doi.org/10.1098/rspb.2014.0253. ieee: S. Ocana, P. Meidl, D. Bonfils, and M. Taborsky, “Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794. The Royal Society, 2014. ista: Ocana S, Meidl P, Bonfils D, Taborsky M. 2014. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20140253. mla: Ocana, Sabine, et al. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794, 20140253, The Royal Society, 2014, doi:10.1098/rspb.2014.0253. short: S. Ocana, P. Meidl, D. Bonfils, M. Taborsky, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014). date_created: 2018-12-11T11:54:34Z date_published: 2014-11-07T00:00:00Z date_updated: 2022-06-07T09:12:32Z day: '07' department: - _id: CampIT doi: 10.1098/rspb.2014.0253 external_id: pmid: - '25232141' intvolume: ' 281' issue: '1794' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211437/ month: '11' oa: 1 oa_version: Submitted Version pmid: 1 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: The Royal Society publist_id: '5203' quality_controlled: '1' scopus_import: '1' status: public title: Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 281 year: '2014' ... --- _id: '1891' abstract: - lang: eng text: We provide theoretical tests of a novel experimental technique to determine mechanostability of proteins based on stretching a mechanically protected protein by single-molecule force spectroscopy. This technique involves stretching a homogeneous or heterogeneous chain of reference proteins (single-molecule markers) in which one of them acts as host to the guest protein under study. The guest protein is grafted into the host through genetic engineering. It is expected that unraveling of the host precedes the unraveling of the guest removing ambiguities in the reading of the force-extension patterns of the guest protein. We study examples of such systems within a coarse-grained structure-based model. We consider systems with various ratios of mechanostability for the host and guest molecules and compare them to experimental results involving cohesin I as the guest molecule. For a comparison, we also study the force-displacement patterns in proteins that are linked in a serial fashion. We find that the mechanostability of the guest is similar to that of the isolated or serially linked protein. We also demonstrate that the ideal configuration of this strategy would be one in which the host is much more mechanostable than the single-molecule markers. We finally show that it is troublesome to use the highly stable cystine knot proteins as a host to graft a guest in stretching studies because this would involve a cleaving procedure. acknowledgement: Grant Nr. 2011/01/N/ST3/02475 author: - first_name: Mateusz full_name: Chwastyk, Mateusz last_name: Chwastyk - first_name: Albert full_name: Galera Prat, Albert last_name: Galera Prat - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora - first_name: Àngel full_name: Gómez Sicilia, Àngel last_name: Gómez Sicilia - first_name: Mariano full_name: Carrión Vázquez, Mariano last_name: Carrión Vázquez - first_name: Marek full_name: Cieplak, Marek last_name: Cieplak citation: ama: 'Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. 2014;82(5):717-726. doi:10.1002/prot.24436' apa: 'Chwastyk, M., Galera Prat, A., Sikora, M. K., Gómez Sicilia, À., Carrión Vázquez, M., & Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.24436' chicago: 'Chwastyk, Mateusz, Albert Galera Prat, Mateusz K Sikora, Àngel Gómez Sicilia, Mariano Carrión Vázquez, and Marek Cieplak. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 2014. https://doi.org/10.1002/prot.24436.' ieee: 'M. Chwastyk, A. Galera Prat, M. K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, and M. Cieplak, “Theoretical tests of the mechanical protection strategy in protein nanomechanics,” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5. Wiley-Blackwell, pp. 717–726, 2014.' ista: 'Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. 2014. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. 82(5), 717–726.' mla: 'Chwastyk, Mateusz, et al. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5, Wiley-Blackwell, 2014, pp. 717–26, doi:10.1002/prot.24436.' short: 'M. Chwastyk, A. Galera Prat, M.K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, M. Cieplak, Proteins: Structure, Function and Bioinformatics 82 (2014) 717–726.' date_created: 2018-12-11T11:54:34Z date_published: 2014-05-01T00:00:00Z date_updated: 2021-01-12T06:53:52Z day: '01' department: - _id: CaHe doi: 10.1002/prot.24436 intvolume: ' 82' issue: '5' language: - iso: eng month: '05' oa_version: None page: 717 - 726 publication: 'Proteins: Structure, Function and Bioinformatics' publication_status: published publisher: Wiley-Blackwell publist_id: '5204' scopus_import: 1 status: public title: Theoretical tests of the mechanical protection strategy in protein nanomechanics type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 82 year: '2014' ... --- _id: '1884' abstract: - lang: eng text: Unbiased high-throughput massively parallel sequencing methods have transformed the process of discovery of novel putative driver gene mutations in cancer. In chronic lymphocytic leukemia (CLL), these methods have yielded several unexpected findings, including the driver genes SF3B1, NOTCH1 and POT1. Recent analysis, utilizing down-sampling of existing datasets, has shown that the discovery process of putative drivers is far from complete across cancer. In CLL, while driver gene mutations affecting >10% of patients were efficiently discovered with previously published CLL cohorts of up to 160 samples subjected to whole exome sequencing (WES), this sample size has only 0.78 power to detect drivers affecting 5% of patients, and only 0.12 power for drivers affecting 2% of patients. These calculations emphasize the need to apply unbiased WES to larger patient cohorts. author: - first_name: Dan full_name: Landau, Dan last_name: Landau - first_name: Chip full_name: Stewart, Chip last_name: Stewart - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Michael full_name: Lawrence, Michael last_name: Lawrence - first_name: Carrie full_name: Sougnez, Carrie last_name: Sougnez - first_name: Jennifer full_name: Brown, Jennifer last_name: Brown - first_name: Armando full_name: Lopez Guillermo, Armando last_name: Lopez Guillermo - first_name: Stacey full_name: Gabriel, Stacey last_name: Gabriel - first_name: Eric full_name: Lander, Eric last_name: Lander - first_name: Donna full_name: Neuberg, Donna last_name: Neuberg - first_name: Carlos full_name: López Otín, Carlos last_name: López Otín - first_name: Elias full_name: Campo, Elias last_name: Campo - first_name: Gad full_name: Getz, Gad last_name: Getz - first_name: Catherine full_name: Wu, Catherine last_name: Wu citation: ama: 'Landau D, Stewart C, Reiter J, et al. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 2014;124(21):1952-1952.' apa: 'Landau, D., Stewart, C., Reiter, J., Lawrence, M., Sougnez, C., Brown, J., … Wu, C. (2014). Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. American Society of Hematology.' chicago: 'Landau, Dan, Chip Stewart, Johannes Reiter, Michael Lawrence, Carrie Sougnez, Jennifer Brown, Armando Lopez Guillermo, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” Blood. American Society of Hematology, 2014.' ieee: 'D. Landau et al., “Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples,” Blood, vol. 124, no. 21. American Society of Hematology, pp. 1952–1952, 2014.' ista: 'Landau D, Stewart C, Reiter J, Lawrence M, Sougnez C, Brown J, Lopez Guillermo A, Gabriel S, Lander E, Neuberg D, López Otín C, Campo E, Getz G, Wu C. 2014. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 124(21), 1952–1952.' mla: 'Landau, Dan, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” Blood, vol. 124, no. 21, American Society of Hematology, 2014, pp. 1952–1952.' short: D. Landau, C. Stewart, J. Reiter, M. Lawrence, C. Sougnez, J. Brown, A. Lopez Guillermo, S. Gabriel, E. Lander, D. Neuberg, C. López Otín, E. Campo, G. Getz, C. Wu, Blood 124 (2014) 1952–1952. date_created: 2018-12-11T11:54:32Z date_published: 2014-12-04T00:00:00Z date_updated: 2021-01-12T06:53:50Z day: '04' department: - _id: KrCh intvolume: ' 124' issue: '21' language: - iso: eng main_file_link: - url: http://www.bloodjournal.org/content/124/21/1952?sso-checked=true month: '12' oa_version: None page: 1952 - 1952 publication: Blood publication_status: published publisher: American Society of Hematology publist_id: '5211' status: public title: 'Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 124 year: '2014' ... --- _id: '1889' abstract: - lang: eng text: We study translation-invariant quasi-free states for a system of fermions with two-particle interactions. The associated energy functional is similar to the BCS functional but also includes direct and exchange energies. We show that for suitable short-range interactions, these latter terms only lead to a renormalization of the chemical potential, with the usual properties of the BCS functional left unchanged. Our analysis thus represents a rigorous justification of part of the BCS approximation. We give bounds on the critical temperature below which the system displays superfluidity. acknowledgement: We would like to thank Max Lein and Andreas Deuchert for valuable suggestions and remarks. Partial financial support by the NSERC (R.S.) is gratefully acknowledged. article_number: '1450012' article_processing_charge: No article_type: original author: - first_name: Gerhard full_name: Bräunlich, Gerhard last_name: Bräunlich - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Bräunlich G, Hainzl C, Seiringer R. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 2014;26(7). doi:10.1142/S0129055X14500123 apa: Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X14500123 chicago: Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X14500123. ieee: G. Bräunlich, C. Hainzl, and R. Seiringer, “Translation-invariant quasi-free states for fermionic systems and the BCS approximation,” Reviews in Mathematical Physics, vol. 26, no. 7. World Scientific Publishing, 2014. ista: Bräunlich G, Hainzl C, Seiringer R. 2014. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 26(7), 1450012. mla: Bräunlich, Gerhard, et al. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics, vol. 26, no. 7, 1450012, World Scientific Publishing, 2014, doi:10.1142/S0129055X14500123. short: G. Bräunlich, C. Hainzl, R. Seiringer, Reviews in Mathematical Physics 26 (2014). date_created: 2018-12-11T11:54:33Z date_published: 2014-08-01T00:00:00Z date_updated: 2022-06-07T09:03:09Z day: '01' department: - _id: RoSe doi: 10.1142/S0129055X14500123 external_id: arxiv: - '1305.5135' intvolume: ' 26' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1305.5135 month: '08' oa: 1 oa_version: Submitted Version publication: Reviews in Mathematical Physics publication_status: published publisher: World Scientific Publishing publist_id: '5206' quality_controlled: '1' scopus_import: '1' status: public title: Translation-invariant quasi-free states for fermionic systems and the BCS approximation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2014' ... --- _id: '1894' abstract: - lang: eng text: 'Background: Bacterial Dsb enzymes are involved in the oxidative folding of many proteins, through the formation of disulfide bonds between their cysteine residues. The Dsb protein network has been well characterized in cells of the model microorganism Escherichia coli. To gain insight into the functioning of the Dsb system in epsilon-Proteobacteria, where it plays an important role in the colonization process, we studied two homologs of the main Escherichia coli Dsb oxidase (EcDsbA) that are present in the cells of the enteric pathogen Campylobacter jejuni, the most frequently reported bacterial cause of human enteritis in the world. Methods and Results: Phylogenetic analysis suggests the horizontal transfer of the epsilon-Proteobacterial DsbAs from a common ancestor to gamma-Proteobacteria, which then gave rise to the DsbL lineage. Phenotype and enzymatic assays suggest that the two C. jejuni DsbAs play different roles in bacterial cells and have divergent substrate spectra. CjDsbA1 is essential for the motility and autoagglutination phenotypes, while CjDsbA2 has no impact on those processes. CjDsbA1 plays a critical role in the oxidative folding that ensures the activity of alkaline phosphatase CjPhoX, whereas CjDsbA2 is crucial for the activity of arylsulfotransferase CjAstA, encoded within the dsbA2-dsbB-astA operon. Conclusions: Our results show that CjDsbA1 is the primary thiol-oxidoreductase affecting life processes associated with bacterial spread and host colonization, as well as ensuring the oxidative folding of particular protein substrates. In contrast, CjDsbA2 activity does not affect the same processes and so far its oxidative folding activity has been demonstrated for one substrate, arylsulfotransferase CjAstA. The results suggest the cooperation between CjDsbA2 and CjDsbB. In the case of the CjDsbA1, this cooperation is not exclusive and there is probably another protein to be identified in C. jejuni cells that acts to re-oxidize CjDsbA1. Altogether the data presented here constitute the considerable insight to the Epsilonproteobacterial Dsb systems, which have been poorly understood so far.' article_number: e106247 author: - first_name: Anna full_name: Grabowska, Anna last_name: Grabowska - first_name: Ewa full_name: Wywiał, Ewa last_name: Wywiał - first_name: Stanislaw full_name: Dunin Horkawicz, Stanislaw last_name: Dunin Horkawicz - first_name: Anna full_name: Łasica, Anna last_name: Łasica - first_name: Marc full_name: Wösten, Marc last_name: Wösten - first_name: Anna A full_name: Nagy-Staron, Anna A id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87 last_name: Nagy-Staron - first_name: Renata full_name: Godlewska, Renata last_name: Godlewska - first_name: Katarzyna full_name: Bocian Ostrzycka, Katarzyna last_name: Bocian Ostrzycka - first_name: Katarzyna full_name: Pieńkowska, Katarzyna last_name: Pieńkowska - first_name: Paweł full_name: Łaniewski, Paweł last_name: Łaniewski - first_name: Janusz full_name: Bujnicki, Janusz last_name: Bujnicki - first_name: Jos full_name: Van Putten, Jos last_name: Van Putten - first_name: Elzbieta full_name: Jagusztyn Krynicka, Elzbieta last_name: Jagusztyn Krynicka citation: ama: Grabowska A, Wywiał E, Dunin Horkawicz S, et al. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0106247 apa: Grabowska, A., Wywiał, E., Dunin Horkawicz, S., Łasica, A., Wösten, M., Nagy-Staron, A. A., … Jagusztyn Krynicka, E. (2014). Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0106247 chicago: Grabowska, Anna, Ewa Wywiał, Stanislaw Dunin Horkawicz, Anna Łasica, Marc Wösten, Anna A Nagy-Staron, Renata Godlewska, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0106247. ieee: A. Grabowska et al., “Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014. ista: Grabowska A, Wywiał E, Dunin Horkawicz S, Łasica A, Wösten M, Nagy-Staron AA, Godlewska R, Bocian Ostrzycka K, Pieńkowska K, Łaniewski P, Bujnicki J, Van Putten J, Jagusztyn Krynicka E. 2014. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 9(9), e106247. mla: Grabowska, Anna, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One, vol. 9, no. 9, e106247, Public Library of Science, 2014, doi:10.1371/journal.pone.0106247. short: A. Grabowska, E. Wywiał, S. Dunin Horkawicz, A. Łasica, M. Wösten, A.A. Nagy-Staron, R. Godlewska, K. Bocian Ostrzycka, K. Pieńkowska, P. Łaniewski, J. Bujnicki, J. Van Putten, E. Jagusztyn Krynicka, PLoS One 9 (2014). date_created: 2018-12-11T11:54:35Z date_published: 2014-09-02T00:00:00Z date_updated: 2021-01-12T06:53:54Z day: '02' ddc: - '570' department: - _id: CaGu doi: 10.1371/journal.pone.0106247 file: - access_level: open_access checksum: 7d02c3da7f72b82bb5d7932d80c3251f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:19Z date_updated: 2020-07-14T12:45:20Z file_id: '5205' file_name: IST-2016-438-v1+1_journal.pone.0106247.pdf file_size: 4248801 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 9' issue: '9' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '09' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '5201' pubrep_id: '438' quality_controlled: '1' scopus_import: 1 status: public title: Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '1895' abstract: - lang: eng text: Major histocompatibility complex class I (MHCI) molecules were recently identified as novel regulators of synaptic plasticity. These molecules are expressed in various brain areas, especially in regions undergoing activity-dependent synaptic plasticity, but their role in the nucleus accumbens (NAc) is unknown. In this study, we investigated the effects of genetic disruption of MHCI function, through deletion of β2-microblobulin, which causes lack of cell surface expression of MHCI. First, we confirmed that MHCI molecules are expressed in the NAc core in wild-type mice. Second, we performed electrophysiological recordings with NAc core slices from wild-type and β2-microglobulin knock-out mice lacking cell surface expression of MHCI. We found that low frequency stimulation induced long-term depression in wild-type but not knock-out mice, whereas high frequency stimulation induced long-term potentiation in both genotypes, with a larger magnitude in knock-out mice. Furthermore, we demonstrated that knock-out mice showed more persistent behavioral sensitization to cocaine, which is a NAc-related behavior. Using this model, we analyzed the density of total AMPA receptors and their subunits GluR1 and GluR2 in the NAc core, by SDS-digested freeze-fracture replica labeling. After repeated cocaine exposure, the density of GluR1 was increased, but there was no change in total AMPA receptors and GluR2 levels in wildtype mice. In contrast, following repeated cocaine exposure, increased densities of total AMPA receptors, GluR1 and GluR2 were observed in knock-out mice. These results indicate that functional deficiency of MHCI enhances synaptic potentiation, induced by electrical and pharmacological stimulation. acknowledgement: This work was supported in part by a Grant-in-Aid for Scientific Research on Innovative Areas (Comprehensive Brain Science Network) and (B) 17330153, from the Ministry of Education, Culture, Sports, Science and Technology of Japan. article_number: e107099 author: - first_name: Mitsuhiro full_name: Edamura, Mitsuhiro last_name: Edamura - first_name: Gen full_name: Murakami, Gen last_name: Murakami - first_name: Hongrui full_name: Meng, Hongrui last_name: Meng - first_name: Makoto full_name: Itakura, Makoto last_name: Itakura - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Atsuo full_name: Fukuda, Atsuo last_name: Fukuda - first_name: Daiichiro full_name: Nakahara, Daiichiro last_name: Nakahara citation: ama: Edamura M, Murakami G, Meng H, et al. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0107099 apa: Edamura, M., Murakami, G., Meng, H., Itakura, M., Shigemoto, R., Fukuda, A., & Nakahara, D. (2014). Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0107099 chicago: Edamura, Mitsuhiro, Gen Murakami, Hongrui Meng, Makoto Itakura, Ryuichi Shigemoto, Atsuo Fukuda, and Daiichiro Nakahara. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0107099. ieee: M. Edamura et al., “Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014. ista: Edamura M, Murakami G, Meng H, Itakura M, Shigemoto R, Fukuda A, Nakahara D. 2014. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 9(9), e107099. mla: Edamura, Mitsuhiro, et al. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One, vol. 9, no. 9, e107099, Public Library of Science, 2014, doi:10.1371/journal.pone.0107099. short: M. Edamura, G. Murakami, H. Meng, M. Itakura, R. Shigemoto, A. Fukuda, D. Nakahara, PLoS One 9 (2014). date_created: 2018-12-11T11:54:35Z date_published: 2014-09-30T00:00:00Z date_updated: 2021-01-12T06:53:54Z day: '30' ddc: - '570' department: - _id: RySh doi: 10.1371/journal.pone.0107099 file: - access_level: open_access checksum: 1f3be936be93114596d61ba44cacee69 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:01Z date_updated: 2020-07-14T12:45:20Z file_id: '4724' file_name: IST-2016-439-v1+1_journal.pone.0107099.pdf file_size: 6262085 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 9' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '5200' pubrep_id: '439' scopus_import: 1 status: public title: Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '1893' abstract: - lang: eng text: Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with PtdIns3P, the presumable product of their activity. In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants. acknowledgement: This work was supported by grants from the Research Foundation-Flanders (Odysseus). author: - first_name: Petra full_name: Nováková, Petra id: 44E59624-F248-11E8-B48F-1D18A9856A87 last_name: Nováková - first_name: Sibylle full_name: Hirsch, Sibylle last_name: Hirsch - first_name: Elena full_name: Feraru, Elena last_name: Feraru - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Ringo full_name: Van Wijk, Ringo last_name: Van Wijk - first_name: Tom full_name: Viaene, Tom last_name: Viaene - first_name: Mareike full_name: Heilmann, Mareike last_name: Heilmann - first_name: Jennifer full_name: Lerche, Jennifer last_name: Lerche - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Mugurel full_name: Feraru, Mugurel last_name: Feraru - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Marc full_name: Van Montagu, Marc last_name: Van Montagu - first_name: Ingo full_name: Heilmann, Ingo last_name: Heilmann - first_name: Teun full_name: Munnik, Teun last_name: Munnik - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Marhavá P, Hirsch S, Feraru E, et al. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 2014;111(7):2818-2823. doi:10.1073/pnas.1324264111 apa: Marhavá, P., Hirsch, S., Feraru, E., Tejos, R., Van Wijk, R., Viaene, T., … Friml, J. (2014). SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1324264111 chicago: Marhavá, Petra, Sibylle Hirsch, Elena Feraru, Ricardo Tejos, Ringo Van Wijk, Tom Viaene, Mareike Heilmann, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1324264111. ieee: P. Marhavá et al., “SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis,” PNAS, vol. 111, no. 7. National Academy of Sciences, pp. 2818–2823, 2014. ista: Marhavá P, Hirsch S, Feraru E, Tejos R, Van Wijk R, Viaene T, Heilmann M, Lerche J, De Rycke R, Feraru M, Grones P, Van Montagu M, Heilmann I, Munnik T, Friml J. 2014. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 111(7), 2818–2823. mla: Marhavá, Petra, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS, vol. 111, no. 7, National Academy of Sciences, 2014, pp. 2818–23, doi:10.1073/pnas.1324264111. short: P. Marhavá, S. Hirsch, E. Feraru, R. Tejos, R. Van Wijk, T. Viaene, M. Heilmann, J. Lerche, R. De Rycke, M. Feraru, P. Grones, M. Van Montagu, I. Heilmann, T. Munnik, J. Friml, PNAS 111 (2014) 2818–2823. date_created: 2018-12-11T11:54:34Z date_published: 2014-02-18T00:00:00Z date_updated: 2021-01-12T06:53:53Z day: '18' department: - _id: JiFr doi: 10.1073/pnas.1324264111 ec_funded: 1 intvolume: ' 111' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932866/ month: '02' oa: 1 oa_version: Submitted Version page: 2818 - 2823 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5202' scopus_import: 1 status: public title: SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '1896' abstract: - lang: eng text: 'Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.' acknowledgement: The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.). article_number: '032701' article_processing_charge: No author: - first_name: Richard full_name: Kollár, Richard last_name: Kollár - first_name: Katarína full_name: Bod'ová, Katarína id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87 last_name: Bod'ová orcid: 0000-0002-7214-0171 - first_name: Jozef full_name: Nosek, Jozef last_name: Nosek - first_name: Ľubomír full_name: Tomáška, Ľubomír last_name: Tomáška citation: ama: Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701 apa: Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.032701 chicago: Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.032701. ieee: R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014. ista: Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701. mla: Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701. short: R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014). date_created: 2018-12-11T11:54:35Z date_published: 2014-03-04T00:00:00Z date_updated: 2022-08-01T10:50:10Z day: '04' department: - _id: NiBa - _id: GaTk doi: 10.1103/PhysRevE.89.032701 intvolume: ' 89' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.0430 month: '03' oa: 1 oa_version: Submitted Version publication: Physical Review E Statistical Nonlinear and Soft Matter Physics publication_status: published publisher: American Institute of Physics publist_id: '5198' scopus_import: '1' status: public title: Mathematical model of alternative mechanism of telomere length maintenance type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 89 year: '2014' ... --- _id: '1897' abstract: - lang: eng text: GNOM is one of the most characterized membrane trafficking regulators in plants, with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor) class to mediate vesicle budding at endomembranes. The crucial role of GNOM in recycling of PIN auxin transporters and other proteins to the plasma membrane was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM, the most prominent regulator of recycling in plants, has been proposed to act and localize at so far elusive recycling endosomes. Here, we report the GNOM localization in context of its cellular function in Arabidopsis thaliana. State-of-the-art imaging, pharmacological interference, and ultrastructure analysis show that GNOM predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus, whereas prolonged exposures results in GNOM translocation to trans-Golgi network (TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role for GNOM in maintaining TGN/EE function. Our results redefine the subcellular action of GNOM and reevaluate the identity and function of recycling endosomes in plants. acknowledgement: This work was supported by the Odysseus Program of the Research Foundation-Flanders (J.F.). author: - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Marisa full_name: Otegui, Marisa last_name: Otegui - first_name: Natsumaro full_name: Kutsuna, Natsumaro last_name: Kutsuna - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Tomoko full_name: Dainobu, Tomoko last_name: Dainobu - first_name: Michael full_name: Karampelias, Michael last_name: Karampelias - first_name: Masaru full_name: Fujimoto, Masaru last_name: Fujimoto - first_name: Elena full_name: Feraru, Elena last_name: Feraru - first_name: Daisuke full_name: Miki, Daisuke last_name: Miki - first_name: Hiroo full_name: Fukuda, Hiroo last_name: Fukuda - first_name: Akihiko full_name: Nakano, Akihiko last_name: Nakano - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Naramoto S, Otegui M, Kutsuna N, et al. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 2014;26(7):3062-3076. doi:10.1105/tpc.114.125880 apa: Naramoto, S., Otegui, M., Kutsuna, N., De Rycke, R., Dainobu, T., Karampelias, M., … Friml, J. (2014). Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.125880 chicago: Naramoto, Satoshi, Marisa Otegui, Natsumaro Kutsuna, Riet De Rycke, Tomoko Dainobu, Michael Karampelias, Masaru Fujimoto, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.125880. ieee: S. Naramoto et al., “Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,” Plant Cell, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076, 2014. ista: Naramoto S, Otegui M, Kutsuna N, De Rycke R, Dainobu T, Karampelias M, Fujimoto M, Feraru E, Miki D, Fukuda H, Nakano A, Friml J. 2014. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 26(7), 3062–3076. mla: Naramoto, Satoshi, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell, vol. 26, no. 7, American Society of Plant Biologists, 2014, pp. 3062–76, doi:10.1105/tpc.114.125880. short: S. Naramoto, M. Otegui, N. Kutsuna, R. De Rycke, T. Dainobu, M. Karampelias, M. Fujimoto, E. Feraru, D. Miki, H. Fukuda, A. Nakano, J. Friml, Plant Cell 26 (2014) 3062–3076. date_created: 2018-12-11T11:54:36Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T06:53:55Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.114.125880 intvolume: ' 26' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/ month: '07' oa: 1 oa_version: Submitted Version page: 3062 - 3076 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '5199' scopus_import: 1 status: public title: Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2014' ... --- _id: '1899' abstract: - lang: eng text: Asymmetric cell divisions allow stem cells to balance proliferation and differentiation. During embryogenesis, murine epidermis expands rapidly from a single layer of unspecified basal layer progenitors to a stratified, differentiated epithelium. Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation protein LGN, but little is known about how the apical localization of LGN is regulated. Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to explore the functions of the LGN-interacting proteins Par3, mInsc and Gα i3. Whereas loss of each gene alone leads to randomized division angles, combined loss of Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of LGN. These findings lend experimental support for the hitherto untested model that Par3-mInsc and Gα i3 act cooperatively to polarize LGN and promote perpendicular divisions. Finally, we uncover a developmental switch between delamination-driven early stratification and spindle-orientation-dependent differentiation that occurs around E15, revealing a two-step mechanism underlying epidermal maturation. article_processing_charge: No article_type: original author: - first_name: Scott full_name: Williams, Scott last_name: Williams - first_name: Lyndsay full_name: Ratliff, Lyndsay last_name: Ratliff - first_name: Maria P full_name: Postiglione, Maria P id: 2C67902A-F248-11E8-B48F-1D18A9856A87 last_name: Postiglione - first_name: Juergen full_name: Knoblich, Juergen last_name: Knoblich - first_name: Elaine full_name: Fuchs, Elaine last_name: Fuchs citation: ama: Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 2014;16(8):758-769. doi:10.1038/ncb3001 apa: Williams, S., Ratliff, L., Postiglione, M. P., Knoblich, J., & Fuchs, E. (2014). Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3001 chicago: Williams, Scott, Lyndsay Ratliff, Maria P Postiglione, Juergen Knoblich, and Elaine Fuchs. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb3001. ieee: S. Williams, L. Ratliff, M. P. Postiglione, J. Knoblich, and E. Fuchs, “Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN,” Nature Cell Biology, vol. 16, no. 8. Nature Publishing Group, pp. 758–769, 2014. ista: Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. 2014. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 16(8), 758–769. mla: Williams, Scott, et al. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” Nature Cell Biology, vol. 16, no. 8, Nature Publishing Group, 2014, pp. 758–69, doi:10.1038/ncb3001. short: S. Williams, L. Ratliff, M.P. Postiglione, J. Knoblich, E. Fuchs, Nature Cell Biology 16 (2014) 758–769. date_created: 2018-12-11T11:54:36Z date_published: 2014-07-13T00:00:00Z date_updated: 2021-01-12T06:53:55Z day: '13' department: - _id: SiHi doi: 10.1038/ncb3001 external_id: pmid: - '25016959' intvolume: ' 16' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159251/ month: '07' oa: 1 oa_version: Submitted Version page: 758 - 769 pmid: 1 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '5196' quality_controlled: '1' scopus_import: 1 status: public title: Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2014' ... --- _id: '1898' abstract: - lang: eng text: Fast synaptic transmission is important for rapid information processing. To explore the maximal rate of neuronal signaling and to analyze the presynaptic mechanisms, we focused on the input layer of the cerebellar cortex, where exceptionally high action potential (AP) frequencies have been reported invivo. With paired recordings between presynaptic cerebellar mossy fiber boutons and postsynaptic granule cells, we demonstrate reliable neurotransmission upto ~1 kHz. Presynaptic APs are ultrafast, with ~100μs half-duration. Both Kv1 and Kv3 potassium channels mediate the fast repolarization, rapidly inactivating sodium channels ensure metabolic efficiency, and little AP broadening occurs during bursts of up to 1.5 kHz. Presynaptic Cav2.1 (P/Q-type) calcium channels open efficiently during ultrafast APs. Furthermore, a subset of synaptic vesicles is tightly coupled to Ca2+ channels, and vesicles are rapidly recruited to the release site. These data reveal mechanisms of presynaptic AP generation and transmitter release underlying neuronal kHz signaling. author: - first_name: Andreas full_name: Ritzau Jost, Andreas last_name: Ritzau Jost - first_name: Igor full_name: Delvendahl, Igor last_name: Delvendahl - first_name: Annika full_name: Rings, Annika last_name: Rings - first_name: Niklas full_name: Byczkowicz, Niklas last_name: Byczkowicz - first_name: Harumi full_name: Harada, Harumi id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87 last_name: Harada orcid: 0000-0001-7429-7896 - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Johannes full_name: Hirrlinger, Johannes last_name: Hirrlinger - first_name: Jens full_name: Eilers, Jens last_name: Eilers - first_name: Stefan full_name: Hallermann, Stefan last_name: Hallermann citation: ama: Ritzau Jost A, Delvendahl I, Rings A, et al. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 2014;84(1):152-163. doi:10.1016/j.neuron.2014.08.036 apa: Ritzau Jost, A., Delvendahl, I., Rings, A., Byczkowicz, N., Harada, H., Shigemoto, R., … Hallermann, S. (2014). Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.08.036 chicago: Ritzau Jost, Andreas, Igor Delvendahl, Annika Rings, Niklas Byczkowicz, Harumi Harada, Ryuichi Shigemoto, Johannes Hirrlinger, Jens Eilers, and Stefan Hallermann. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.08.036. ieee: A. Ritzau Jost et al., “Ultrafast action potentials mediate kilohertz signaling at a central synapse,” Neuron, vol. 84, no. 1. Elsevier, pp. 152–163, 2014. ista: Ritzau Jost A, Delvendahl I, Rings A, Byczkowicz N, Harada H, Shigemoto R, Hirrlinger J, Eilers J, Hallermann S. 2014. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 84(1), 152–163. mla: Ritzau Jost, Andreas, et al. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron, vol. 84, no. 1, Elsevier, 2014, pp. 152–63, doi:10.1016/j.neuron.2014.08.036. short: A. Ritzau Jost, I. Delvendahl, A. Rings, N. Byczkowicz, H. Harada, R. Shigemoto, J. Hirrlinger, J. Eilers, S. Hallermann, Neuron 84 (2014) 152–163. date_created: 2018-12-11T11:54:36Z date_published: 2014-10-01T00:00:00Z date_updated: 2021-01-12T06:53:55Z day: '01' department: - _id: RySh doi: 10.1016/j.neuron.2014.08.036 intvolume: ' 84' issue: '1' language: - iso: eng month: '10' oa_version: None page: 152 - 163 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5197' quality_controlled: '1' scopus_import: 1 status: public title: Ultrafast action potentials mediate kilohertz signaling at a central synapse type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 84 year: '2014' ... --- _id: '1906' abstract: - lang: eng text: In this paper, we introduce a novel scene representation for the visualization of large-scale point clouds accompanied by a set of high-resolution photographs. Many real-world applications deal with very densely sampled point-cloud data, which are augmented with photographs that often reveal lighting variations and inaccuracies in registration. Consequently, the high-quality representation of the captured data, i.e., both point clouds and photographs together, is a challenging and time-consuming task. We propose a two-phase approach, in which the first (preprocessing) phase generates multiple overlapping surface patches and handles the problem of seamless texture generation locally for each patch. The second phase stitches these patches at render-time to produce a high-quality visualization of the data. As a result of the proposed localization of the global texturing problem, our algorithm is more than an order of magnitude faster than equivalent mesh-based texturing techniques. Furthermore, since our preprocessing phase requires only a minor fraction of the whole data set at once, we provide maximum flexibility when dealing with growing data sets. acknowledgement: This research was supported by the Austrian Research Promotion Agency (FFG) project REPLICATE (no. 835948), the EU FP7 project HARVEST4D (no. 323567). author: - first_name: Murat full_name: Arikan, Murat last_name: Arikan - first_name: Reinhold full_name: Preiner, Reinhold last_name: Preiner - first_name: Claus full_name: Scheiblauer, Claus last_name: Scheiblauer - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Michael full_name: Wimmer, Michael last_name: Wimmer citation: ama: Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 2014;20(9):1280-1292. doi:10.1109/TVCG.2014.2312011 apa: Arikan, M., Preiner, R., Scheiblauer, C., Jeschke, S., & Wimmer, M. (2014). Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2014.2312011 chicago: Arikan, Murat, Reinhold Preiner, Claus Scheiblauer, Stefan Jeschke, and Michael Wimmer. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2312011. ieee: M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, and M. Wimmer, “Large-scale point-cloud visualization through localized textured surface reconstruction,” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9. IEEE, pp. 1280–1292, 2014. ista: Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. 2014. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 20(9), 1280–1292. mla: Arikan, Murat, et al. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9, IEEE, 2014, pp. 1280–92, doi:10.1109/TVCG.2014.2312011. short: M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, M. Wimmer, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 1280–1292. date_created: 2018-12-11T11:54:39Z date_published: 2014-09-09T00:00:00Z date_updated: 2021-01-12T06:53:59Z day: '09' ddc: - '000' department: - _id: ChWo doi: 10.1109/TVCG.2014.2312011 file: - access_level: open_access checksum: 5bf58942d2eb20adf03c7f9ea2e68124 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:41Z date_updated: 2020-07-14T12:45:20Z file_id: '5297' file_name: IST-2016-573-v1+1_arikan-2014-pcvis-draft.pdf file_size: 13594598 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 20' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 1280 - 1292 project: - _id: 25357BD2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 24352-N23 name: 'Deep Pictures: Creating Visual and Haptic Vector Images' publication: IEEE Transactions on Visualization and Computer Graphics publication_status: published publisher: IEEE publist_id: '5189' pubrep_id: '573' scopus_import: 1 status: public title: Large-scale point-cloud visualization through localized textured surface reconstruction type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2014' ... --- _id: '1905' abstract: - lang: eng text: The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution). acknowledgement: This study was funded by grants from the National Science Foundation (NSF) to MT (IOS-1121832) and IS (DEB-0743406) and from the German Science Foundation (DFG; PL 470/1-2) and ‘LOEWE − Landesoffensive zur Entwicklung wissenschaftlich-ökonomischer Exzellenz’ of Hesse's Ministry of Higher Education, Research, and the Arts, to MP. article_processing_charge: No article_type: original author: - first_name: Michael full_name: Tobler, Michael last_name: Tobler - first_name: Martin full_name: Plath, Martin last_name: Plath - first_name: Rüdiger full_name: Riesch, Rüdiger last_name: Riesch - first_name: Ingo full_name: Schlupp, Ingo last_name: Schlupp - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Gopi full_name: Munimanda, Gopi last_name: Munimanda - first_name: C full_name: Setzer, C last_name: Setzer - first_name: Dustin full_name: Penn, Dustin last_name: Penn - first_name: Yoshan full_name: Moodley, Yoshan last_name: Moodley citation: ama: Tobler M, Plath M, Riesch R, et al. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 2014;27(5):960-974. doi:10.1111/jeb.12370 apa: Tobler, M., Plath, M., Riesch, R., Schlupp, I., Grasse, A. V., Munimanda, G., … Moodley, Y. (2014). Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.12370 chicago: Tobler, Michael, Martin Plath, Rüdiger Riesch, Ingo Schlupp, Anna V Grasse, Gopi Munimanda, C Setzer, Dustin Penn, and Yoshan Moodley. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology. Wiley, 2014. https://doi.org/10.1111/jeb.12370. ieee: M. Tobler et al., “Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations,” Journal of Evolutionary Biology, vol. 27, no. 5. Wiley, pp. 960–974, 2014. ista: Tobler M, Plath M, Riesch R, Schlupp I, Grasse AV, Munimanda G, Setzer C, Penn D, Moodley Y. 2014. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 27(5), 960–974. mla: Tobler, Michael, et al. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology, vol. 27, no. 5, Wiley, 2014, pp. 960–74, doi:10.1111/jeb.12370. short: M. Tobler, M. Plath, R. Riesch, I. Schlupp, A.V. Grasse, G. Munimanda, C. Setzer, D. Penn, Y. Moodley, Journal of Evolutionary Biology 27 (2014) 960–974. date_created: 2018-12-11T11:54:38Z date_published: 2014-04-12T00:00:00Z date_updated: 2022-06-07T09:22:20Z day: '12' department: - _id: SyCr doi: 10.1111/jeb.12370 external_id: pmid: - '24725091' intvolume: ' 27' issue: '5' language: - iso: eng month: '04' oa_version: None page: 960 - 974 pmid: 1 publication: Journal of Evolutionary Biology publication_identifier: eissn: - 1420-9101 issn: - 1010-061X publication_status: published publisher: Wiley publist_id: '5190' quality_controlled: '1' scopus_import: '1' status: public title: Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2014' ... --- _id: '1902' abstract: - lang: eng text: In the 1960s-1980s, determination of bacterial growth rates was an important tool in microbial genetics, biochemistry, molecular biology, and microbial physiology. The exciting technical developments of the 1990s and the 2000s eclipsed that tool; as a result, many investigators today lack experience with growth rate measurements. Recently, investigators in a number of areas have started to use measurements of bacterial growth rates for a variety of purposes. Those measurements have been greatly facilitated by the availability of microwell plate readers that permit the simultaneous measurements on up to 384 different cultures. Only the exponential (logarithmic) portions of the resulting growth curves are useful for determining growth rates, and manual determination of that portion and calculation of growth rates can be tedious for high-throughput purposes. Here, we introduce the program GrowthRates that uses plate reader output files to automatically determine the exponential portion of the curve and to automatically calculate the growth rate, the maximum culture density, and the duration of the growth lag phase. GrowthRates is freely available for Macintosh, Windows, and Linux.We discuss the effects of culture volume, the classical bacterial growth curve, and the differences between determinations in rich media and minimal (mineral salts) media. This protocol covers calibration of the plate reader, growth of culture inocula for both rich and minimal media, and experimental setup. As a guide to reliability, we report typical day-to-day variation in growth rates and variation within experiments with respect to position of wells within the plates. article_processing_charge: No article_type: original author: - first_name: Barry full_name: Hall, Barry last_name: Hall - first_name: Hande full_name: Acar, Hande id: 2DDF136A-F248-11E8-B48F-1D18A9856A87 last_name: Acar orcid: 0000-0003-1986-9753 - first_name: Anna full_name: Nandipati, Anna last_name: Nandipati - first_name: Miriam full_name: Barlow, Miriam last_name: Barlow citation: ama: Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. Molecular Biology and Evolution. 2014;31(1):232-238. doi:10.1093/molbev/mst187 apa: Hall, B., Acar, H., Nandipati, A., & Barlow, M. (2014). Growth rates made easy. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst187 chicago: Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/mst187. ieee: B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” Molecular Biology and Evolution, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014. ista: Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular Biology and Evolution. 31(1), 232–238. mla: Hall, Barry, et al. “Growth Rates Made Easy.” Molecular Biology and Evolution, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:10.1093/molbev/mst187. short: B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238. date_created: 2018-12-11T11:54:37Z date_published: 2014-01-01T00:00:00Z date_updated: 2022-06-07T11:08:13Z day: '01' department: - _id: JoBo doi: 10.1093/molbev/mst187 external_id: pmid: - '24170494' intvolume: ' 31' issue: '1' language: - iso: eng month: '01' oa_version: None page: 232 - 238 pmid: 1 publication: Molecular Biology and Evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: Oxford University Press publist_id: '5193' quality_controlled: '1' scopus_import: '1' status: public title: Growth rates made easy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2014' ... --- _id: '1901' abstract: - lang: eng text: In plants, the patterning of stem cell-enriched meristems requires a graded auxin response maximum that emerges from the concerted action of polar auxin transport, auxin biosynthesis, auxin metabolism, and cellular auxin response machinery. However, mechanisms underlying this auxin response maximum-mediated root stem cell maintenance are not fully understood. Here, we present unexpected evidence that WUSCHEL-RELATED HOMEOBOX 5 (WOX5) transcription factor modulates expression of auxin biosynthetic genes in the quiescent center (QC) of the root and thus provides a robust mechanism for the maintenance of auxin response maximum in the root tip. This WOX5 action is balanced through the activity of indole-3-acetic acid 17 (IAA17) auxin response repressor. Our combined genetic, cell biology, and computational modeling studies revealed a previously uncharacterized feedback loop linking WOX5-mediated auxin production to IAA17-dependent repression of auxin responses. This WOX5-IAA17 feedback circuit further assures the maintenance of auxin response maximum in the root tip and thereby contributes to the maintenance of distal stem cell (DSC) populations. Our experimental studies and in silico computer simulations both demonstrate that the WOX5-IAA17 feedback circuit is essential for the maintenance of auxin gradient in the root tip and the auxin-mediated root DSC differentiation. acknowledgement: "This work was supported by funding from the projects CZ.1.07/2.3.00/20.0043 and CZ.1.05/1.1.00/02.0068 (to CEITEC, Central European Institute of Technology) and the Odysseus program of the Research Foundation-Flanders to J.F\r\n" author: - first_name: Huiyu full_name: Tian, Huiyu last_name: Tian - first_name: Krzysztof T full_name: Wabnik, Krzysztof T last_name: Wabnik - first_name: Tiantian full_name: Niu, Tiantian last_name: Niu - first_name: Hongjiang full_name: Li, Hongjiang last_name: Li - first_name: Qianqian full_name: Yu, Qianqian last_name: Yu - first_name: Stephan full_name: Pollmann, Stephan last_name: Pollmann - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Willy full_name: Govaerts, Willy last_name: Govaerts - first_name: Jakub full_name: Rolčík, Jakub last_name: Rolčík - first_name: Markus full_name: Geisler, Markus last_name: Geisler - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Zhaojun full_name: Ding, Zhaojun last_name: Ding citation: ama: Tian H, Wabnik KT, Niu T, et al. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 2014;7(2):277-289. doi:10.1093/mp/sst118 apa: Tian, H., Wabnik, K. T., Niu, T., Li, H., Yu, Q., Pollmann, S., … Ding, Z. (2014). WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. Oxford University Press. https://doi.org/10.1093/mp/sst118 chicago: Tian, Huiyu, Krzysztof T Wabnik, Tiantian Niu, Hongjiang Li, Qianqian Yu, Stephan Pollmann, Steffen Vanneste, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant. Oxford University Press, 2014. https://doi.org/10.1093/mp/sst118. ieee: H. Tian et al., “WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis,” Molecular Plant, vol. 7, no. 2. Oxford University Press, pp. 277–289, 2014. ista: Tian H, Wabnik KT, Niu T, Li H, Yu Q, Pollmann S, Vanneste S, Govaerts W, Rolčík J, Geisler M, Friml J, Ding Z. 2014. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 7(2), 277–289. mla: Tian, Huiyu, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant, vol. 7, no. 2, Oxford University Press, 2014, pp. 277–89, doi:10.1093/mp/sst118. short: H. Tian, K.T. Wabnik, T. Niu, H. Li, Q. Yu, S. Pollmann, S. Vanneste, W. Govaerts, J. Rolčík, M. Geisler, J. Friml, Z. Ding, Molecular Plant 7 (2014) 277–289. date_created: 2018-12-11T11:54:37Z date_published: 2014-02-01T00:00:00Z date_updated: 2021-01-12T06:53:57Z day: '01' department: - _id: JiFr doi: 10.1093/mp/sst118 intvolume: ' 7' issue: '2' language: - iso: eng month: '02' oa_version: None page: 277 - 289 publication: Molecular Plant publication_status: published publisher: Oxford University Press publist_id: '5194' scopus_import: 1 status: public title: WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2014' ... --- _id: '1904' abstract: - lang: eng text: We prove a Strichartz inequality for a system of orthonormal functions, with an optimal behavior of the constant in the limit of a large number of functions. The estimate generalizes the usual Strichartz inequality, in the same fashion as the Lieb-Thirring inequality generalizes the Sobolev inequality. As an application, we consider the Schrödinger equation with a time-dependent potential and we show the existence of the wave operator in Schatten spaces. author: - first_name: Rupert full_name: Frank, Rupert last_name: Frank - first_name: Mathieu full_name: Lewin, Mathieu last_name: Lewin - first_name: Élliott full_name: Lieb, Élliott last_name: Lieb - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Frank R, Lewin M, Lieb É, Seiringer R. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 2014;16(7):1507-1526. doi:10.4171/JEMS/467 apa: Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2014). Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/467 chicago: Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “Strichartz Inequality for Orthonormal Functions.” Journal of the European Mathematical Society. European Mathematical Society, 2014. https://doi.org/10.4171/JEMS/467. ieee: R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “Strichartz inequality for orthonormal functions,” Journal of the European Mathematical Society, vol. 16, no. 7. European Mathematical Society, pp. 1507–1526, 2014. ista: Frank R, Lewin M, Lieb É, Seiringer R. 2014. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 16(7), 1507–1526. mla: Frank, Rupert, et al. “Strichartz Inequality for Orthonormal Functions.” Journal of the European Mathematical Society, vol. 16, no. 7, European Mathematical Society, 2014, pp. 1507–26, doi:10.4171/JEMS/467. short: R. Frank, M. Lewin, É. Lieb, R. Seiringer, Journal of the European Mathematical Society 16 (2014) 1507–1526. date_created: 2018-12-11T11:54:38Z date_published: 2014-08-23T00:00:00Z date_updated: 2021-01-12T06:53:58Z day: '23' department: - _id: RoSe doi: 10.4171/JEMS/467 intvolume: ' 16' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1306.1309 month: '08' oa: 1 oa_version: Submitted Version page: 1507 - 1526 project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication: Journal of the European Mathematical Society publication_status: published publisher: European Mathematical Society publist_id: '5191' quality_controlled: '1' scopus_import: 1 status: public title: Strichartz inequality for orthonormal functions type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2014' ... --- _id: '1900' abstract: - lang: eng text: Epithelial cell layers need to be tightly regulated to maintain their integrity and correct function. Cell integration into epithelial sheets is now shown to depend on the N-WASP-regulated stabilization of cortical F-actin, which generates distinct patterns of apical-lateral contractility at E-cadherin-based cell-cell junctions. author: - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt - 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: Behrndt M, Heisenberg C-PJ. Lateral junction dynamics lead the way out. Nature Cell Biology. 2014;16(2):127-129. doi:10.1038/ncb2913 apa: Behrndt, M., & Heisenberg, C.-P. J. (2014). Lateral junction dynamics lead the way out. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2913 chicago: Behrndt, Martin, and Carl-Philipp J Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb2913. ieee: M. Behrndt and C.-P. J. Heisenberg, “Lateral junction dynamics lead the way out,” Nature Cell Biology, vol. 16, no. 2. Nature Publishing Group, pp. 127–129, 2014. ista: Behrndt M, Heisenberg C-PJ. 2014. Lateral junction dynamics lead the way out. Nature Cell Biology. 16(2), 127–129. mla: Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” Nature Cell Biology, vol. 16, no. 2, Nature Publishing Group, 2014, pp. 127–29, doi:10.1038/ncb2913. short: M. Behrndt, C.-P.J. Heisenberg, Nature Cell Biology 16 (2014) 127–129. date_created: 2018-12-11T11:54:37Z date_published: 2014-01-31T00:00:00Z date_updated: 2021-01-12T06:53:56Z day: '31' department: - _id: CaHe doi: 10.1038/ncb2913 intvolume: ' 16' issue: '2' language: - iso: eng month: '01' oa_version: None page: 127 - 129 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '5195' quality_controlled: '1' scopus_import: 1 status: public title: Lateral junction dynamics lead the way out type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2014' ... --- _id: '1909' abstract: - lang: eng text: 'Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution.' acknowledgement: 'Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1' author: - first_name: Thomas full_name: Ezard, Thomas last_name: Ezard - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - first_name: Rebecca full_name: Hoyle, Rebecca last_name: Hoyle citation: ama: Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701. doi:10.1111/1365-2435.12207 apa: Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12207 chicago: Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207. ieee: T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014. ista: Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701. mla: Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207. short: T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701. date_created: 2018-12-11T11:54:40Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T06:54:00Z day: '01' ddc: - '570' department: - _id: NiBa - _id: GaTk doi: 10.1111/1365-2435.12207 file: - access_level: open_access checksum: 3cbe8623174709a8ceec2103246f8fe0 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:45Z date_updated: 2020-07-14T12:45:20Z file_id: '5167' file_name: IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf file_size: 536154 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 28' issue: '3' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 693 - 701 publication: Functional Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '5186' pubrep_id: '419' scopus_import: 1 status: public title: The fitness costs of adaptation via phenotypic plasticity and maternal effects 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2014' ... --- _id: '1910' abstract: - lang: eng text: angerhans cells (LCs) are a unique subset of dendritic cells (DCs) that express epithelial adhesion molecules, allowing them to form contacts with epithelial cells and reside in epidermal/epithelial tissues. The dynamic regulation of epithelial adhesion plays a decisive role in the life cycle of LCs. It controls whether LCs remain immature and sessile within the epidermis or mature and egress to initiate immune responses. So far, the molecular machinery regulating epithelial adhesion molecules during LC maturation remains elusive. Here, we generated pure populations of immature human LCs in vitro to systematically probe for gene-expression changes during LC maturation. LCs down-regulate a set of epithelial genes including E-cadherin, while they upregulate the mesenchymal marker N-cadherin known to facilitate cell migration. In addition, N-cadherin is constitutively expressed by monocyte-derived DCs known to exhibit characteristics of both inflammatory-type and interstitial/dermal DCs. Moreover, the transcription factors ZEB1 and ZEB2 (ZEB is zinc-finger E-box-binding homeobox) are upregulated in migratory LCs. ZEB1 and ZEB2 have been shown to induce epithelial-to-mesenchymal transition (EMT) and invasive behavior in cancer cells undergoing metastasis. Our results provide the first hint that the molecular EMT machinery might facilitate LC mobilization. Moreover, our study suggests that N-cadherin plays a role during DC migration. acknowledgement: 'FWF. Grant Number: P22058-B20' author: - first_name: Sabine full_name: Konradi, Sabine last_name: Konradi - first_name: Nighat full_name: Yasmin, Nighat last_name: Yasmin - first_name: Denise full_name: Haslwanter, Denise last_name: Haslwanter - first_name: Michele full_name: Weber, Michele id: 3A3FC708-F248-11E8-B48F-1D18A9856A87 last_name: Weber - first_name: Bernd full_name: Gesslbauer, Bernd last_name: Gesslbauer - 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: Herbert full_name: Strobl, Herbert last_name: Strobl citation: ama: Konradi S, Yasmin N, Haslwanter D, et al. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 2014;44(2):553-560. doi:10.1002/eji.201343681 apa: Konradi, S., Yasmin, N., Haslwanter, D., Weber, M., Gesslbauer, B., Sixt, M. K., & Strobl, H. (2014). Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201343681 chicago: Konradi, Sabine, Nighat Yasmin, Denise Haslwanter, Michele Weber, Bernd Gesslbauer, Michael K Sixt, and Herbert Strobl. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” European Journal of Immunology. Wiley-Blackwell, 2014. https://doi.org/10.1002/eji.201343681. ieee: S. Konradi et al., “Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2,” European Journal of Immunology, vol. 44, no. 2. Wiley-Blackwell, pp. 553–560, 2014. ista: Konradi S, Yasmin N, Haslwanter D, Weber M, Gesslbauer B, Sixt MK, Strobl H. 2014. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 44(2), 553–560. mla: Konradi, Sabine, et al. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” European Journal of Immunology, vol. 44, no. 2, Wiley-Blackwell, 2014, pp. 553–60, doi:10.1002/eji.201343681. short: S. Konradi, N. Yasmin, D. Haslwanter, M. Weber, B. Gesslbauer, M.K. Sixt, H. Strobl, European Journal of Immunology 44 (2014) 553–560. date_created: 2018-12-11T11:54:40Z date_published: 2014-02-01T00:00:00Z date_updated: 2021-01-12T06:54:01Z day: '01' department: - _id: MiSi doi: 10.1002/eji.201343681 intvolume: ' 44' issue: '2' language: - iso: eng month: '02' oa_version: None page: 553 - 560 publication: European Journal of Immunology publication_status: published publisher: Wiley-Blackwell publist_id: '5185' scopus_import: 1 status: public title: Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2 type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 44 year: '2014' ... --- _id: '1907' abstract: - lang: eng text: 'Most cryptographic security proofs require showing that two systems are indistinguishable. A central tool in such proofs is that of a game, where winning the game means provoking a certain condition, and it is shown that the two systems considered cannot be distinguished unless this condition is provoked. Upper bounding the probability of winning such a game, i.e., provoking this condition, for an arbitrary strategy is usually hard, except in the special case where the best strategy for winning such a game is known to be non-adaptive. A sufficient criterion for ensuring the optimality of non-adaptive strategies is that of conditional equivalence to a system, a notion introduced in [1]. In this paper, we show that this criterion is not necessary to ensure the optimality of non-adaptive strategies by giving two results of independent interest: 1) the optimality of non-adaptive strategies is not preserved under parallel composition; 2) in contrast, conditional equivalence is preserved under parallel composition.' article_number: '6875125' author: - first_name: Grégory full_name: Demay, Grégory last_name: Demay - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Ueli full_name: Maurer, Ueli last_name: Maurer - first_name: Björn full_name: Tackmann, Björn last_name: Tackmann citation: ama: 'Demay G, Gazi P, Maurer U, Tackmann B. Optimality of non-adaptive strategies: The case of parallel games. In: IEEE International Symposium on Information Theory. IEEE; 2014. doi:10.1109/ISIT.2014.6875125' apa: 'Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2014). Optimality of non-adaptive strategies: The case of parallel games. In IEEE International Symposium on Information Theory. Honolulu, USA: IEEE. https://doi.org/10.1109/ISIT.2014.6875125' chicago: 'Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” In IEEE International Symposium on Information Theory. IEEE, 2014. https://doi.org/10.1109/ISIT.2014.6875125.' ieee: 'G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Optimality of non-adaptive strategies: The case of parallel games,” in IEEE International Symposium on Information Theory, Honolulu, USA, 2014.' ista: 'Demay G, Gazi P, Maurer U, Tackmann B. 2014. Optimality of non-adaptive strategies: The case of parallel games. IEEE International Symposium on Information Theory. IEEE International Symposium on Information Theory Proceedings, 6875125.' mla: 'Demay, Grégory, et al. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” IEEE International Symposium on Information Theory, 6875125, IEEE, 2014, doi:10.1109/ISIT.2014.6875125.' short: G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, IEEE International Symposium on Information Theory, IEEE, 2014. conference: end_date: 2014-07-04 location: Honolulu, USA name: IEEE International Symposium on Information Theory Proceedings start_date: 2014-06-29 date_created: 2018-12-11T11:54:39Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:53:59Z day: '01' department: - _id: KrPi doi: 10.1109/ISIT.2014.6875125 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2014/299 month: '01' oa: 1 oa_version: Submitted Version publication: IEEE International Symposium on Information Theory publication_status: published publisher: IEEE publist_id: '5188' quality_controlled: '1' scopus_import: 1 status: public title: 'Optimality of non-adaptive strategies: The case of parallel games' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ...