--- _id: '245' abstract: - lang: eng text: For given non-zero integers a, b, q we investigate the density of solutions (x; y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined over ℚ. author: - first_name: Stephan full_name: Baier, Stephan last_name: Baier - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: Baier S, Browning TD. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. 2013;(680):69-151. doi:10.1515/crelle.2012.039 apa: Baier, S., & Browning, T. D. (2013). Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle.2012.039 chicago: Baier, Stephan, and Timothy D Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, 2013. https://doi.org/10.1515/crelle.2012.039. ieee: S. Baier and T. D. Browning, “Inhomogeneous cubic congruences and rational points on del Pezzo surfaces,” Journal fur die Reine und Angewandte Mathematik, no. 680. Walter de Gruyter, pp. 69–151, 2013. ista: Baier S, Browning TD. 2013. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. (680), 69–151. mla: Baier, Stephan, and Timothy D. Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte Mathematik, no. 680, Walter de Gruyter, 2013, pp. 69–151, doi:10.1515/crelle.2012.039. short: S. Baier, T.D. Browning, Journal Fur Die Reine Und Angewandte Mathematik (2013) 69–151. date_created: 2018-12-11T11:45:24Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T06:57:33Z day: '01' doi: 10.1515/crelle.2012.039 extern: 1 issue: '680' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1011.3434 month: '07' oa: 1 page: 69 - 151 publication: Journal fur die Reine und Angewandte Mathematik publication_status: published publisher: Walter de Gruyter publist_id: '7659' quality_controlled: 0 status: public title: Inhomogeneous cubic congruences and rational points on del Pezzo surfaces type: journal_article year: '2013' ... --- _id: '2457' author: - first_name: Tom full_name: Viaene, Tom last_name: Viaene - first_name: Charles full_name: Delwiche, Charles last_name: Delwiche - first_name: Stefan full_name: Rensing, Stefan last_name: Rensing - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Viaene T, Delwiche C, Rensing S, Friml J. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 2013;18(1):5-10. doi:10.1016/j.tplants.2012.08.009 apa: Viaene, T., Delwiche, C., Rensing, S., & Friml, J. (2013). Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2012.08.009 chicago: Viaene, Tom, Charles Delwiche, Stefan Rensing, and Jiří Friml. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” Trends in Plant Science. Cell Press, 2013. https://doi.org/10.1016/j.tplants.2012.08.009. ieee: T. Viaene, C. Delwiche, S. Rensing, and J. Friml, “Origin and evolution of PIN auxin transporters in the green lineage,” Trends in Plant Science, vol. 18, no. 1. Cell Press, pp. 5–10, 2013. ista: Viaene T, Delwiche C, Rensing S, Friml J. 2013. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 18(1), 5–10. mla: Viaene, Tom, et al. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” Trends in Plant Science, vol. 18, no. 1, Cell Press, 2013, pp. 5–10, doi:10.1016/j.tplants.2012.08.009. short: T. Viaene, C. Delwiche, S. Rensing, J. Friml, Trends in Plant Science 18 (2013) 5–10. date_created: 2018-12-11T11:57:46Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:57:36Z day: '01' doi: 10.1016/j.tplants.2012.08.009 extern: '1' intvolume: ' 18' issue: '1' language: - iso: eng month: '01' oa_version: None page: 5 - 10 publication: Trends in Plant Science publication_status: published publisher: Cell Press publist_id: '4446' quality_controlled: '1' status: public title: Origin and evolution of PIN auxin transporters in the green lineage type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2013' ... --- _id: '246' abstract: - lang: eng text: Given an intersection of two quadrics X Pm1, with m > 9, the quantitative arithmetic of the set X(Q) is investigated under the assumption that the singular locus of X consists of a pair of conjugate singular points defined over Q(i). acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council" author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Ritabrata full_name: Munshi, Ritabrata last_name: Munshi citation: ama: Browning TD, Munshi R. Rational points on singular intersections of quadrics. Compositio Mathematica. 2013;149(9):1457-1494. doi:10.1112/S0010437X13007185 apa: Browning, T. D., & Munshi, R. (2013). Rational points on singular intersections of quadrics. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X13007185 chicago: Browning, Timothy D, and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” Compositio Mathematica. Cambridge University Press, 2013. https://doi.org/10.1112/S0010437X13007185. ieee: T. D. Browning and R. Munshi, “Rational points on singular intersections of quadrics,” Compositio Mathematica, vol. 149, no. 9. Cambridge University Press, pp. 1457–1494, 2013. ista: Browning TD, Munshi R. 2013. Rational points on singular intersections of quadrics. Compositio Mathematica. 149(9), 1457–1494. mla: Browning, Timothy D., and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” Compositio Mathematica, vol. 149, no. 9, Cambridge University Press, 2013, pp. 1457–94, doi:10.1112/S0010437X13007185. short: T.D. Browning, R. Munshi, Compositio Mathematica 149 (2013) 1457–1494. date_created: 2018-12-11T11:45:25Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T06:57:37Z day: '01' doi: 10.1112/S0010437X13007185 extern: 1 intvolume: ' 149' issue: '9' month: '09' page: 1457 - 1494 publication: Compositio Mathematica publication_status: published publisher: Cambridge University Press publist_id: '7658' quality_controlled: 0 status: public title: Rational points on singular intersections of quadrics type: journal_article volume: 149 year: '2013' ... --- _id: '2471' abstract: - lang: eng text: The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation. article_number: e70013 author: - first_name: Inmaculada full_name: Sanchez Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez Romero - first_name: Antonio full_name: Ariza, Antonio last_name: Ariza - first_name: Keith full_name: Wilson, Keith last_name: Wilson - first_name: Michael full_name: Skjøt, Michael last_name: Skjøt - first_name: Jesper full_name: Vind, Jesper last_name: Vind - first_name: Leonardo full_name: De Maria, Leonardo last_name: De Maria - first_name: Lars full_name: Skov, Lars last_name: Skov - first_name: Jose full_name: Sánchez Ruiz, Jose last_name: Sánchez Ruiz citation: ama: Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070013 apa: Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L., … Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070013 chicago: Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt, Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070013. ieee: I. Sanchez-Romero et al., “Mechanism of protein kinetic stabilization by engineered disulfide crosslinks,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013. ista: Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L, Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 8(7), e70013. mla: Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One, vol. 8, no. 7, e70013, Public Library of Science, 2013, doi:10.1371/journal.pone.0070013. short: I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L. Skov, J. Sánchez Ruiz, PLoS One 8 (2013). date_created: 2018-12-11T11:57:51Z date_published: 2013-07-30T00:00:00Z date_updated: 2021-01-12T06:57:41Z day: '30' ddc: - '570' department: - _id: HaJa doi: 10.1371/journal.pone.0070013 file: - access_level: open_access checksum: c0c96cc76ed7ef0d036a31a7e33c9a37 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:07Z date_updated: 2020-07-14T12:45:41Z file_id: '5124' file_name: IST-2016-414-v1+1_journal.pone.0070013.pdf file_size: 1323666 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 8' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4430' pubrep_id: '414' quality_controlled: '1' scopus_import: 1 status: public title: Mechanism of protein kinetic stabilization by engineered disulfide crosslinks 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ... --- _id: '2472' abstract: - lang: eng text: Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development. article_number: e70069 author: - first_name: Christopher full_name: Cazzonelli, Christopher last_name: Cazzonelli - first_name: Marleen full_name: Vanstraelen, Marleen last_name: Vanstraelen - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Kuide full_name: Yin, Kuide last_name: Yin - first_name: Ashley full_name: Carron Arthur, Ashley last_name: Carron Arthur - first_name: Nazia full_name: Nisar, Nazia last_name: Nisar - first_name: Gauri full_name: Tarle, Gauri last_name: Tarle - first_name: Abby full_name: Cuttriss, Abby last_name: Cuttriss - first_name: Iain full_name: Searle, Iain last_name: Searle - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ulrike full_name: Mathesius, Ulrike last_name: Mathesius - first_name: Josette full_name: Masle, Josette last_name: Masle - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Barry full_name: Pogson, Barry last_name: Pogson citation: ama: Cazzonelli C, Vanstraelen M, Simon S, et al. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070069 apa: Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron Arthur, A., Nisar, N., … Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070069 chicago: Cazzonelli, Christopher, Marleen Vanstraelen, Sibu Simon, Kuide Yin, Ashley Carron Arthur, Nazia Nisar, Gauri Tarle, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070069. ieee: C. Cazzonelli et al., “Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013. ista: Cazzonelli C, Vanstraelen M, Simon S, Yin K, Carron Arthur A, Nisar N, Tarle G, Cuttriss A, Searle I, Benková E, Mathesius U, Masle J, Friml J, Pogson B. 2013. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 8(7), e70069. mla: Cazzonelli, Christopher, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One, vol. 8, no. 7, e70069, Public Library of Science, 2013, doi:10.1371/journal.pone.0070069. short: C. Cazzonelli, M. Vanstraelen, S. Simon, K. Yin, A. Carron Arthur, N. Nisar, G. Tarle, A. Cuttriss, I. Searle, E. Benková, U. Mathesius, J. Masle, J. Friml, B. Pogson, PLoS One 8 (2013). date_created: 2018-12-11T11:57:52Z date_published: 2013-07-29T00:00:00Z date_updated: 2021-01-12T06:57:41Z day: '29' ddc: - '580' - '570' department: - _id: JiFr - _id: EvBe doi: 10.1371/journal.pone.0070069 ec_funded: 1 file: - access_level: open_access checksum: 3be71828b6c2ba9c90eb7056e3f7f57a content_type: application/pdf creator: system date_created: 2018-12-12T10:16:34Z date_updated: 2020-07-14T12:45:41Z file_id: '5222' file_name: IST-2015-393-v1+1_journal.pone.0070069.pdf file_size: 9003465 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 8' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4431' pubrep_id: '393' quality_controlled: '1' scopus_import: 1 status: public title: Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ...