[{"quality_controlled":0,"date_published":"2015-01-01T00:00:00Z","page":"157 - 167","publisher":"Wiley-Blackwell","extern":1,"author":[{"first_name":"Mahnaz","full_name":"Mansouri, Mahnaz","last_name":"Mansouri"},{"last_name":"Kasugai","full_name":"Kasugai, Yu","first_name":"Yu"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"first_name":"Federica","full_name":"Bertaso, Federica","last_name":"Bertaso"},{"last_name":"Raynaud","first_name":"Fabrice","full_name":"Raynaud, Fabrice"},{"last_name":"Perroy","full_name":"Perroy, Julie","first_name":"Julie"},{"first_name":"Laurent","full_name":"Fagni, Laurent","last_name":"Fagni"},{"first_name":"Walter","full_name":"Walter Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"first_name":"Ryuichi","full_name":"Ryuichi Shigemoto","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ferraguti","full_name":"Ferraguti, Francesco","first_name":"Francesco"}],"volume":41,"citation":{"ista":"Mansouri M, Kasugai Y, Fukazawa Y, Bertaso F, Raynaud F, Perroy J, Fagni L, Kaufmann W, Watanabe M, Shigemoto R, Ferraguti F. 2015. Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex. European Journal of Neuroscience. 41(2), 157–167.","mla":"Mansouri, Mahnaz, et al. “Distinct Subsynaptic Localization of Type 1 Metabotropic Glutamate Receptors at Glutamatergic and GABAergic Synapses in the Rodent Cerebellar Cortex.” <i>European Journal of Neuroscience</i>, vol. 41, no. 2, Wiley-Blackwell, 2015, pp. 157–67, doi:<a href=\"https://doi.org/10.1111/ejn.12779\">10.1111/ejn.12779</a>.","chicago":"Mansouri, Mahnaz, Yu Kasugai, Yugo Fukazawa, Federica Bertaso, Fabrice Raynaud, Julie Perroy, Laurent Fagni, et al. “Distinct Subsynaptic Localization of Type 1 Metabotropic Glutamate Receptors at Glutamatergic and GABAergic Synapses in the Rodent Cerebellar Cortex.” <i>European Journal of Neuroscience</i>. Wiley-Blackwell, 2015. <a href=\"https://doi.org/10.1111/ejn.12779\">https://doi.org/10.1111/ejn.12779</a>.","apa":"Mansouri, M., Kasugai, Y., Fukazawa, Y., Bertaso, F., Raynaud, F., Perroy, J., … Ferraguti, F. (2015). Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex. <i>European Journal of Neuroscience</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/ejn.12779\">https://doi.org/10.1111/ejn.12779</a>","ieee":"M. Mansouri <i>et al.</i>, “Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex,” <i>European Journal of Neuroscience</i>, vol. 41, no. 2. Wiley-Blackwell, pp. 157–167, 2015.","ama":"Mansouri M, Kasugai Y, Fukazawa Y, et al. Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex. <i>European Journal of Neuroscience</i>. 2015;41(2):157-167. doi:<a href=\"https://doi.org/10.1111/ejn.12779\">10.1111/ejn.12779</a>","short":"M. Mansouri, Y. Kasugai, Y. Fukazawa, F. Bertaso, F. Raynaud, J. Perroy, L. Fagni, W. Kaufmann, M. Watanabe, R. Shigemoto, F. Ferraguti, European Journal of Neuroscience 41 (2015) 157–167."},"issue":"2","date_updated":"2023-02-23T10:02:24Z","title":"Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex","date_created":"2018-12-11T11:52:28Z","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) (project W012060-10 to F.F.), The Japan Society for the Promotion of Science (JSPS) (to R.S.) and Agence Nationale de la Recherche (ANR-11-BSV4-018-03, DELTAPLAN), Région Languedoc-Roussillon (Chercheur d’Avenir) (to J.P.). The authors thank S. Schönherr for excellent technical support and Dr Furuichi for kindly providing anti-Homer3 antibodies.","year":"2015","day":"01","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication":"European Journal of Neuroscience","doi":"10.1111/ejn.12779","publist_id":"5662","_id":"1515","type":"journal_article","abstract":[{"lang":"eng","text":"Type 1 metabotropic glutamate (mGlu1) receptors play a pivotal role in different forms of synaptic plasticity in the cerebellar cortex, e.g. long-term depression at glutamatergic synapses and rebound potentiation at GABAergic synapses. These various forms of plasticity might depend on the subsynaptic arrangement of the receptor in Purkinje cells that can be regulated by protein-protein interactions. This study investigated, by means of the freeze-fracture replica immunogold labelling method, the subcellular localization of mGlu1 receptors in the rodent cerebellum and whether Homer proteins regulate their subsynaptic distribution. We observed a widespread extrasynaptic localization of mGlu1 receptors and confirmed their peri-synaptic enrichment at glutamatergic synapses. Conversely, we detected mGlu1 receptors within the main body of GABAergic synapses onto Purkinje cell dendrites. Although Homer proteins are known to interact with the mGlu1 receptor C-terminus, we could not detect Homer3, the most abundant Homer protein in the cerebellar cortex, at GABAergic synapses by pre-embedding and post-embedding immunoelectron microscopy. We then hypothesized a critical role for Homer proteins in the peri-junctional localization of mGlu1 receptors at glutamatergic synapses. To disrupt Homer-associated protein complexes, mice were tail-vein injected with the membrane-permeable dominant-negative TAT-Homer1a. Freeze-fracture replica immunogold labelling analysis showed no significant alteration in the mGlu1 receptor distribution pattern at parallel fibre-Purkinje cell synapses, suggesting that other scaffolding proteins are involved in the peri-synaptic confinement. The identification of interactors that regulate the subsynaptic localization of the mGlu1 receptor at neurochemically distinct synapses may offer new insight into its trafficking and intracellular signalling."}],"intvolume":"        41","status":"public","month":"01"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.tibs.2015.07.006","oa_version":"None","publication_status":"published","month":"09","status":"public","intvolume":"        40","keyword":["Molecular Biology","Biochemistry"],"type":"journal_article","abstract":[{"lang":"eng","text":"It is widely recognized that BMAL1 is an essential subunit of the primary transcription factor that drives rhythmic circadian transcription in the nucleus. In a surprising turn, Lipton et al. now show that BMAL1 rhythmically interacts with translational machinery in the cytosol to stimulate protein synthesis in response to mTOR signaling."}],"scopus_import":"1","author":[{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","full_name":"Michael, Alicia Kathleen","first_name":"Alicia Kathleen"},{"last_name":"Asimgil","first_name":"Hande","full_name":"Asimgil, Hande"},{"last_name":"Partch","full_name":"Partch, Carrie L.","first_name":"Carrie L."}],"extern":"1","date_published":"2015-09-01T00:00:00Z","day":"01","article_type":"original","date_updated":"2024-03-25T11:53:58Z","title":"Cytosolic BMAL1 moonlights as a translation factor","publication":"Trends in Biochemical Sciences","_id":"15159","issue":"9","citation":{"apa":"Michael, A. K., Asimgil, H., &#38; Partch, C. L. (2015). Cytosolic BMAL1 moonlights as a translation factor. <i>Trends in Biochemical Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tibs.2015.07.006\">https://doi.org/10.1016/j.tibs.2015.07.006</a>","ieee":"A. K. Michael, H. Asimgil, and C. L. Partch, “Cytosolic BMAL1 moonlights as a translation factor,” <i>Trends in Biochemical Sciences</i>, vol. 40, no. 9. Elsevier, pp. 489–490, 2015.","ama":"Michael AK, Asimgil H, Partch CL. Cytosolic BMAL1 moonlights as a translation factor. <i>Trends in Biochemical Sciences</i>. 2015;40(9):489-490. doi:<a href=\"https://doi.org/10.1016/j.tibs.2015.07.006\">10.1016/j.tibs.2015.07.006</a>","short":"A.K. Michael, H. Asimgil, C.L. Partch, Trends in Biochemical Sciences 40 (2015) 489–490.","ista":"Michael AK, Asimgil H, Partch CL. 2015. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 40(9), 489–490.","chicago":"Michael, Alicia K., Hande Asimgil, and Carrie L. Partch. “Cytosolic BMAL1 Moonlights as a Translation Factor.” <i>Trends in Biochemical Sciences</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.tibs.2015.07.006\">https://doi.org/10.1016/j.tibs.2015.07.006</a>.","mla":"Michael, Alicia K., et al. “Cytosolic BMAL1 Moonlights as a Translation Factor.” <i>Trends in Biochemical Sciences</i>, vol. 40, no. 9, Elsevier, 2015, pp. 489–90, doi:<a href=\"https://doi.org/10.1016/j.tibs.2015.07.006\">10.1016/j.tibs.2015.07.006</a>."},"volume":40,"publisher":"Elsevier","page":"489-490","quality_controlled":"1","article_processing_charge":"No","year":"2015","publication_identifier":{"issn":["0968-0004"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-03-21T07:57:44Z"},{"language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.1016/j.molcel.2015.03.031","publication_status":"published","status":"public","month":"06","intvolume":"        58","keyword":["Cell Biology","Molecular Biology"],"type":"journal_article","abstract":[{"lang":"eng","text":"The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms."}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2015.03.031"}],"author":[{"last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia Kathleen","full_name":"Michael, Alicia Kathleen"},{"first_name":"Stacy L.","full_name":"Harvey, Stacy L.","last_name":"Harvey"},{"last_name":"Sammons","full_name":"Sammons, Patrick J.","first_name":"Patrick J."},{"full_name":"Anderson, Amanda P.","first_name":"Amanda P.","last_name":"Anderson"},{"last_name":"Kopalle","full_name":"Kopalle, Hema M.","first_name":"Hema M."},{"last_name":"Banham","first_name":"Alison H.","full_name":"Banham, Alison H."},{"full_name":"Partch, Carrie L.","first_name":"Carrie L.","last_name":"Partch"}],"extern":"1","date_published":"2015-06-04T00:00:00Z","day":"04","title":"Cancer/Testis antigen PASD1 silences the circadian clock","date_updated":"2024-03-25T11:52:26Z","article_type":"original","publication":"Molecular Cell","_id":"15160","issue":"5","oa":1,"volume":58,"citation":{"ama":"Michael AK, Harvey SL, Sammons PJ, et al. Cancer/Testis antigen PASD1 silences the circadian clock. <i>Molecular Cell</i>. 2015;58(5):743-754. doi:<a href=\"https://doi.org/10.1016/j.molcel.2015.03.031\">10.1016/j.molcel.2015.03.031</a>","short":"A.K. Michael, S.L. Harvey, P.J. Sammons, A.P. Anderson, H.M. Kopalle, A.H. Banham, C.L. Partch, Molecular Cell 58 (2015) 743–754.","ieee":"A. K. Michael <i>et al.</i>, “Cancer/Testis antigen PASD1 silences the circadian clock,” <i>Molecular Cell</i>, vol. 58, no. 5. Elsevier, pp. 743–754, 2015.","apa":"Michael, A. K., Harvey, S. L., Sammons, P. J., Anderson, A. P., Kopalle, H. M., Banham, A. H., &#38; Partch, C. L. (2015). Cancer/Testis antigen PASD1 silences the circadian clock. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2015.03.031\">https://doi.org/10.1016/j.molcel.2015.03.031</a>","chicago":"Michael, Alicia K., Stacy L. Harvey, Patrick J. Sammons, Amanda P. Anderson, Hema M. Kopalle, Alison H. Banham, and Carrie L. Partch. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” <i>Molecular Cell</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.molcel.2015.03.031\">https://doi.org/10.1016/j.molcel.2015.03.031</a>.","mla":"Michael, Alicia K., et al. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” <i>Molecular Cell</i>, vol. 58, no. 5, Elsevier, 2015, pp. 743–54, doi:<a href=\"https://doi.org/10.1016/j.molcel.2015.03.031\">10.1016/j.molcel.2015.03.031</a>.","ista":"Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch CL. 2015. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 58(5), 743–754."},"publisher":"Elsevier","page":"743-754","article_processing_charge":"No","quality_controlled":"1","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1097-2765"]},"date_created":"2024-03-21T07:58:08Z"},{"pubrep_id":"494","has_accepted_license":"1","scopus_import":"1","file_date_updated":"2020-07-14T12:45:00Z","date_published":"2015-11-29T00:00:00Z","author":[{"first_name":"Matthias","full_name":"Erbar, Matthias","last_name":"Erbar"},{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Renger","first_name":"Michiel","full_name":"Renger, Michiel"}],"day":"29","title":"From large deviations to Wasserstein gradient flows in multiple dimensions","date_updated":"2025-09-23T08:53:14Z","language":[{"iso":"eng"}],"publist_id":"5660","publication_status":"published","oa_version":"Published Version","doi":"10.1214/ECP.v20-4315","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"        20","status":"public","isi":1,"month":"11","abstract":[{"lang":"eng","text":"We study the large deviation rate functional for the empirical distribution of independent Brownian particles with drift. In one dimension, it has been shown by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent (in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher dimensions, part of this statement (the lower bound) has been recently proved by Duong, Laschos and Renger, but the upper bound remained open, since the proof of Duong et al relies on regularity properties of optimal transport maps that are restricted to one dimension. In this note we present a new proof of the upper bound, thereby generalising the result of Adams et al to arbitrary dimensions.\r\n"}],"type":"journal_article","volume":20,"oa":1,"citation":{"apa":"Erbar, M., Maas, J., &#38; Renger, M. (2015). From large deviations to Wasserstein gradient flows in multiple dimensions. <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/ECP.v20-4315\">https://doi.org/10.1214/ECP.v20-4315</a>","ieee":"M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient flows in multiple dimensions,” <i>Electronic Communications in Probability</i>, vol. 20. Institute of Mathematical Statistics, 2015.","short":"M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20 (2015).","ama":"Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows in multiple dimensions. <i>Electronic Communications in Probability</i>. 2015;20. doi:<a href=\"https://doi.org/10.1214/ECP.v20-4315\">10.1214/ECP.v20-4315</a>","ista":"Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 20, 89.","chicago":"Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics, 2015. <a href=\"https://doi.org/10.1214/ECP.v20-4315\">https://doi.org/10.1214/ECP.v20-4315</a>.","mla":"Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” <i>Electronic Communications in Probability</i>, vol. 20, 89, Institute of Mathematical Statistics, 2015, doi:<a href=\"https://doi.org/10.1214/ECP.v20-4315\">10.1214/ECP.v20-4315</a>."},"article_processing_charge":"No","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","file":[{"relation":"main_file","file_id":"4828","access_level":"open_access","content_type":"application/pdf","creator":"system","file_name":"IST-2016-494-v1+1_4315-23820-1-PB.pdf","date_created":"2018-12-12T10:10:39Z","checksum":"135741c17d3e1547ca696b6fbdcd559c","date_updated":"2020-07-14T12:45:00Z","file_size":230525}],"department":[{"_id":"JaMa"}],"year":"2015","external_id":{"isi":["000365470700001"]},"date_created":"2018-12-11T11:52:29Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["519"],"publication":"Electronic Communications in Probability","article_number":"89","_id":"1517"},{"issue":"5","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152"}],"citation":{"chicago":"Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” <i>Evolution</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/evo.12641\">https://doi.org/10.1111/evo.12641</a>.","mla":"Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” <i>Evolution</i>, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:<a href=\"https://doi.org/10.1111/evo.12641\">10.1111/evo.12641</a>.","ista":"Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112.","ama":"Barton NH, Servedio M. The interpretation of selection coefficients. <i>Evolution</i>. 2015;69(5):1101-1112. doi:<a href=\"https://doi.org/10.1111/evo.12641\">10.1111/evo.12641</a>","short":"N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.","apa":"Barton, N. H., &#38; Servedio, M. (2015). The interpretation of selection coefficients. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12641\">https://doi.org/10.1111/evo.12641</a>","ieee":"N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” <i>Evolution</i>, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015."},"volume":69,"oa":1,"page":"1101 - 1112","file":[{"creator":"system","file_id":"4822","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:10:34Z","checksum":"fd8d23f476bc194419929b72ca265c02","date_updated":"2020-07-14T12:45:00Z","file_size":188872,"file_name":"IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf"},{"file_name":"IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf","file_size":577415,"date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:10:35Z","checksum":"b774911e70044641d556e258efcb52ef","relation":"main_file","creator":"system","access_level":"open_access","content_type":"application/pdf","file_id":"4823"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","quality_controlled":"1","article_processing_charge":"No","external_id":{"isi":["000354561600001"]},"year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:29Z","ddc":["570"],"publication":"Evolution","corr_author":"1","_id":"1519","scopus_import":"1","has_accepted_license":"1","ec_funded":1,"pubrep_id":"560","author":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"Servedio, Maria","first_name":"Maria","last_name":"Servedio"}],"date_published":"2015-03-19T00:00:00Z","file_date_updated":"2020-07-14T12:45:00Z","day":"19","title":"The interpretation of selection coefficients","date_updated":"2025-09-23T13:53:01Z","publist_id":"5656","language":[{"iso":"eng"}],"doi":"10.1111/evo.12641","oa_version":"Submitted Version","publication_status":"published","month":"03","isi":1,"status":"public","intvolume":"        69","type":"journal_article","abstract":[{"lang":"eng","text":"Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under &quot;direct&quot; versus &quot;indirect&quot; selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so."}]},{"year":"2015","day":"01","date_created":"2018-12-11T11:52:30Z","title":"Computational design of walking automata","date_updated":"2021-01-12T06:51:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["978-1-4503-3496-9"]},"citation":{"mla":"Bharaj, Gaurav, et al. <i>Computational Design of Walking Automata</i>. ACM, 2015, pp. 93–100, doi:<a href=\"https://doi.org/10.1145/2786784.2786803\">10.1145/2786784.2786803</a>.","chicago":"Bharaj, Gaurav, Stelian Coros, Bernhard Thomaszewski, James Tompkin, Bernd Bickel, and Hanspeter Pfister. “Computational Design of Walking Automata,” 93–100. ACM, 2015. <a href=\"https://doi.org/10.1145/2786784.2786803\">https://doi.org/10.1145/2786784.2786803</a>.","ista":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. 2015. Computational design of walking automata. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 93–100.","ama":"Bharaj G, Coros S, Thomaszewski B, Tompkin J, Bickel B, Pfister H. Computational design of walking automata. In: ACM; 2015:93-100. doi:<a href=\"https://doi.org/10.1145/2786784.2786803\">10.1145/2786784.2786803</a>","short":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, H. Pfister, in:, ACM, 2015, pp. 93–100.","ieee":"G. Bharaj, S. Coros, B. Thomaszewski, J. Tompkin, B. Bickel, and H. Pfister, “Computational design of walking automata,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States, 2015, pp. 93–100.","apa":"Bharaj, G., Coros, S., Thomaszewski, B., Tompkin, J., Bickel, B., &#38; Pfister, H. (2015). Computational design of walking automata (pp. 93–100). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2786784.2786803\">https://doi.org/10.1145/2786784.2786803</a>"},"scopus_import":1,"date_published":"2015-08-01T00:00:00Z","quality_controlled":"1","author":[{"full_name":"Bharaj, Gaurav","first_name":"Gaurav","last_name":"Bharaj"},{"first_name":"Stelian","full_name":"Coros, Stelian","last_name":"Coros"},{"full_name":"Thomaszewski, Bernhard","first_name":"Bernhard","last_name":"Thomaszewski"},{"first_name":"James","full_name":"Tompkin, James","last_name":"Tompkin"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"},{"first_name":"Hanspeter","full_name":"Pfister, Hanspeter","last_name":"Pfister"}],"page":"93 - 100","publisher":"ACM","department":[{"_id":"BeBi"}],"month":"08","status":"public","_id":"1520","type":"conference","abstract":[{"text":"Creating mechanical automata that can walk in stable and pleasing manners is a challenging task that requires both skill and expertise. We propose to use computational design to offset the technical difficulties of this process. A simple drag-and-drop interface allows casual users to create personalized walking toys from a library of pre-defined template mechanisms. Provided with this input, our method leverages physical simulation and evolutionary optimization to refine the mechanical designs such that the resulting toys are able to walk. The optimization process is guided by an intuitive set of objectives that measure the quality of the walking motions. We demonstrate our approach on a set of simulated mechanical toys with different numbers of legs and various distinct gaits. Two fabricated prototypes showcase the feasibility of our designs.","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"5655","publication_status":"published","doi":"10.1145/2786784.2786803","conference":{"start_date":"2015-08-07","end_date":"2015-08-09","location":"Los Angeles, CA, United States","name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation"},"oa_version":"None"},{"type":"journal_article","abstract":[{"text":"In growing cells, protein synthesis and cell growth are typically not synchronous, and, thus, protein concentrations vary over the cell division cycle. We have developed a theoretical description of genetic regulatory systems in bacteria that explicitly considers the cell division cycle to investigate its impact on gene expression. We calculate the cell-to-cell variations arising from cells being at different stages in the division cycle for unregulated genes and for basic regulatory mechanisms. These variations contribute to the extrinsic noise observed in single-cell experiments, and are most significant for proteins with short lifetimes. Negative autoregulation buffers against variation of protein concentration over the division cycle, but the effect is found to be relatively weak. Stronger buffering is achieved by an increased protein lifetime. Positive autoregulation can strongly amplify such variation if the parameters are set to values that lead to resonance-like behaviour. For cooperative positive autoregulation, the concentration variation over the division cycle diminishes the parameter region of bistability and modulates the switching times between the two stable states. The same effects are seen for a two-gene mutual-repression toggle switch. By contrast, an oscillatory circuit, the repressilator, is only weakly affected by the division cycle.","lang":"eng"}],"intvolume":"        12","status":"public","isi":1,"month":"09","publication_status":"published","oa_version":"None","doi":"10.1088/1478-3975/12/6/066003","language":[{"iso":"eng"}],"publist_id":"5641","title":"Impact of the cell division cycle on gene circuits","date_updated":"2025-09-23T09:19:53Z","day":"25","date_published":"2015-09-25T00:00:00Z","author":[{"last_name":"Bierbaum","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","first_name":"Veronika","full_name":"Bierbaum, Veronika"},{"first_name":"Stefan","full_name":"Klumpp, Stefan","last_name":"Klumpp"}],"scopus_import":"1","_id":"1530","article_number":"066003","corr_author":"1","publication":"Physical Biology","date_created":"2018-12-11T11:52:33Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","external_id":{"isi":["000368186300009"]},"article_processing_charge":"No","quality_controlled":"1","department":[{"_id":"MiSi"}],"publisher":"IOP Publishing","volume":12,"citation":{"ieee":"V. Bierbaum and S. Klumpp, “Impact of the cell division cycle on gene circuits,” <i>Physical Biology</i>, vol. 12, no. 6. IOP Publishing, 2015.","apa":"Bierbaum, V., &#38; Klumpp, S. (2015). Impact of the cell division cycle on gene circuits. <i>Physical Biology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">https://doi.org/10.1088/1478-3975/12/6/066003</a>","ama":"Bierbaum V, Klumpp S. Impact of the cell division cycle on gene circuits. <i>Physical Biology</i>. 2015;12(6). doi:<a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">10.1088/1478-3975/12/6/066003</a>","short":"V. Bierbaum, S. Klumpp, Physical Biology 12 (2015).","ista":"Bierbaum V, Klumpp S. 2015. Impact of the cell division cycle on gene circuits. Physical Biology. 12(6), 066003.","mla":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” <i>Physical Biology</i>, vol. 12, no. 6, 066003, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">10.1088/1478-3975/12/6/066003</a>.","chicago":"Bierbaum, Veronika, and Stefan Klumpp. “Impact of the Cell Division Cycle on Gene Circuits.” <i>Physical Biology</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/1478-3975/12/6/066003\">https://doi.org/10.1088/1478-3975/12/6/066003</a>."},"issue":"6"},{"date_updated":"2022-06-10T09:50:14Z","title":"Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature","day":"01","date_published":"2015-01-01T00:00:00Z","author":[{"last_name":"Zobel","full_name":"Zobel, Valentin","first_name":"Valentin"},{"full_name":"Reininghaus, Jan","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus"},{"last_name":"Hotz","full_name":"Hotz, Ingrid","first_name":"Ingrid"}],"edition":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"The Heat Kernel Signature (HKS) is a scalar quantity which is derived from the heat kernel of a given shape. Due to its robustness, isometry invariance, and multiscale nature, it has been successfully applied in many geometric applications. From a more general point of view, the HKS can be considered as a descriptor of the metric of a Riemannian manifold. Given a symmetric positive definite tensor field we may interpret it as the metric of some Riemannian manifold and thereby apply the HKS to visualize and analyze the given tensor data. In this paper, we propose a generalization of this approach that enables the treatment of indefinite tensor fields, like the stress tensor, by interpreting them as a generator of a positive definite tensor field. To investigate the usefulness of this approach we consider the stress tensor from the two-point-load model example and from a mechanical work piece."}],"type":"book_chapter","intvolume":"        40","status":"public","month":"01","publication_status":"published","oa_version":"None","doi":"10.1007/978-3-319-15090-1_13","language":[{"iso":"eng"}],"editor":[{"full_name":"Hotz, Ingrid","first_name":"Ingrid","last_name":"Hotz"},{"last_name":"Schultz","first_name":"Thomas","full_name":"Schultz, Thomas"}],"publist_id":"5640","date_created":"2018-12-11T11:52:33Z","alternative_title":["Mathematics and Visualization"],"publication_identifier":{"isbn":["978-3-319-15089-5"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","article_processing_charge":"No","quality_controlled":"1","page":"257 - 267","publisher":"Springer","department":[{"_id":"HeEd"}],"volume":40,"citation":{"ista":"Zobel V, Reininghaus J, Hotz I. 2015.Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Mathematics and Visualization, vol. 40, 257–267.","chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” In <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, edited by Ingrid Hotz and Thomas Schultz, 1st ed., 40:257–67. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">https://doi.org/10.1007/978-3-319-15090-1_13</a>.","mla":"Zobel, Valentin, et al. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, edited by Ingrid Hotz and Thomas Schultz, 1st ed., vol. 40, Springer, 2015, pp. 257–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">10.1007/978-3-319-15090-1_13</a>.","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature,” in <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, 1st ed., vol. 40, I. Hotz and T. Schultz, Eds. Springer, 2015, pp. 257–267.","apa":"Zobel, V., Reininghaus, J., &#38; Hotz, I. (2015). Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In I. Hotz &#38; T. Schultz (Eds.), <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i> (1st ed., Vol. 40, pp. 257–267). Springer. <a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">https://doi.org/10.1007/978-3-319-15090-1_13</a>","ama":"Zobel V, Reininghaus J, Hotz I. Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Hotz I, Schultz T, eds. <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>. Vol 40. 1st ed. Springer; 2015:257-267. doi:<a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">10.1007/978-3-319-15090-1_13</a>","short":"V. Zobel, J. Reininghaus, I. Hotz, in:, I. Hotz, T. Schultz (Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., Springer, 2015, pp. 257–267."},"_id":"1531","publication":"Visualization and Processing of Higher Order Descriptors for Multi-Valued Data"},{"publication":"Functional Plant Biology","_id":"1532","volume":42,"citation":{"ista":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251.","mla":"Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” <i>Functional Plant Biology</i>, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:<a href=\"https://doi.org/10.1071/FP14171\">10.1071/FP14171</a>.","chicago":"Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann, Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” <i>Functional Plant Biology</i>. CSIRO, 2015. <a href=\"https://doi.org/10.1071/FP14171\">https://doi.org/10.1071/FP14171</a>.","ieee":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source,” <i>Functional Plant Biology</i>, vol. 42, no. 3. CSIRO, pp. 239–251, 2015.","apa":"Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser, B., &#38; Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. <i>Functional Plant Biology</i>. CSIRO. <a href=\"https://doi.org/10.1071/FP14171\">https://doi.org/10.1071/FP14171</a>","short":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251.","ama":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. <i>Functional Plant Biology</i>. 2015;42(3):239-251. doi:<a href=\"https://doi.org/10.1071/FP14171\">10.1071/FP14171</a>"},"issue":"3","article_processing_charge":"No","quality_controlled":"1","publisher":"CSIRO","page":"239 - 251","department":[{"_id":"JiFr"}],"year":"2015","external_id":{"pmid":["32480670"],"isi":["000349635900003"]},"pmid":1,"date_created":"2018-12-11T11:52:34Z","publication_identifier":{"issn":["1445-4408"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"publist_id":"5639","publication_status":"published","oa_version":"None","doi":"10.1071/FP14171","intvolume":"        42","status":"public","isi":1,"month":"03","type":"journal_article","abstract":[{"lang":"eng","text":"Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels."}],"scopus_import":"1","date_published":"2015-03-01T00:00:00Z","author":[{"full_name":"Yang, Huaiyu","first_name":"Huaiyu","last_name":"Yang"},{"full_name":"Von Der Fecht Bartenbach, Jenny","first_name":"Jenny","last_name":"Von Der Fecht Bartenbach"},{"full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lohmann, Jan","first_name":"Jan","last_name":"Lohmann"},{"first_name":"Benjamin","full_name":"Neuhäuser, Benjamin","last_name":"Neuhäuser"},{"last_name":"Ludewig","first_name":"Uwe","full_name":"Ludewig, Uwe"}],"day":"01","title":"Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source","date_updated":"2025-09-23T07:59:44Z","article_type":"original"},{"intvolume":"        25","status":"public","month":"08","isi":1,"type":"journal_article","abstract":[{"lang":"eng","text":"This paper addresses the problem of semantic segmentation, where the possible class labels are from a predefined set. We exploit top-down guidance, i.e., the coarse localization of the objects and their class labels provided by object detectors. For each detected bounding box, figure-ground segmentation is performed and the final result is achieved by merging the figure-ground segmentations. The main idea of the proposed approach, which is presented in our preliminary work, is to reformulate the figure-ground segmentation problem as sparse reconstruction pursuing the object mask in a nonparametric manner. The latent segmentation mask should be coherent subject to sparse error caused by intra-category diversity; thus, the object mask is inferred by making use of sparse representations over the training set. To handle local spatial deformations, local patch-level masks are also considered and inferred by sparse representations over the spatially nearby patches. The sparse reconstruction coefficients and the latent mask are alternately optimized by applying the Lasso algorithm and the accelerated proximal gradient method. The proposed formulation results in a convex optimization problem; thus, the global optimal solution is achieved. In this paper, we provide theoretical analysis of the convergence and optimality. We also give an extended numerical analysis of the proposed algorithm and a comprehensive comparison with the related semantic segmentation methods on the challenging PASCAL visual object class object segmentation datasets and the Weizmann horse dataset. The experimental results demonstrate that the proposed algorithm achieves a competitive performance when compared with the state of the arts."}],"language":[{"iso":"eng"}],"publist_id":"5638","publication_status":"published","oa_version":"None","doi":"10.1109/TCSVT.2014.2379972","day":"01","title":"Segmentation over detection via optimal sparse reconstructions","date_updated":"2025-09-23T10:44:22Z","scopus_import":"1","date_published":"2015-08-01T00:00:00Z","author":[{"first_name":"Wei","full_name":"Xia, Wei","last_name":"Xia"},{"last_name":"Domokos","id":"492DACF8-F248-11E8-B48F-1D18A9856A87","full_name":"Domokos, Csaba","first_name":"Csaba"},{"last_name":"Xiong","first_name":"Junjun","full_name":"Xiong, Junjun"},{"full_name":"Cheong, Loongfah","first_name":"Loongfah","last_name":"Cheong"},{"full_name":"Yan, Shuicheng","first_name":"Shuicheng","last_name":"Yan"}],"_id":"1533","publication":"IEEE Transactions on Circuits and Systems for Video Technology","year":"2015","external_id":{"isi":["000359213400004"]},"date_created":"2018-12-11T11:52:34Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":25,"citation":{"ama":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. Segmentation over detection via optimal sparse reconstructions. <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. 2015;25(8):1295-1308. doi:<a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">10.1109/TCSVT.2014.2379972</a>","short":"W. Xia, C. Domokos, J. Xiong, L. Cheong, S. Yan, IEEE Transactions on Circuits and Systems for Video Technology 25 (2015) 1295–1308.","ieee":"W. Xia, C. Domokos, J. Xiong, L. Cheong, and S. Yan, “Segmentation over detection via optimal sparse reconstructions,” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>, vol. 25, no. 8. IEEE, pp. 1295–1308, 2015.","apa":"Xia, W., Domokos, C., Xiong, J., Cheong, L., &#38; Yan, S. (2015). Segmentation over detection via optimal sparse reconstructions. <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. IEEE. <a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">https://doi.org/10.1109/TCSVT.2014.2379972</a>","chicago":"Xia, Wei, Csaba Domokos, Junjun Xiong, Loongfah Cheong, and Shuicheng Yan. “Segmentation over Detection via Optimal Sparse Reconstructions.” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">https://doi.org/10.1109/TCSVT.2014.2379972</a>.","mla":"Xia, Wei, et al. “Segmentation over Detection via Optimal Sparse Reconstructions.” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>, vol. 25, no. 8, IEEE, 2015, pp. 1295–308, doi:<a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">10.1109/TCSVT.2014.2379972</a>.","ista":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. 2015. Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. 25(8), 1295–1308."},"issue":"8","article_processing_charge":"No","quality_controlled":"1","page":"1295 - 1308","department":[{"_id":"ChLa"}],"publisher":"IEEE"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1038/ncomms9822","oa_version":"Published Version","publication_status":"published","publist_id":"5637","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity.","lang":"eng"}],"isi":1,"month":"11","status":"public","intvolume":"         6","author":[{"first_name":"Hongzhe","full_name":"Wang, Hongzhe","last_name":"Wang"},{"last_name":"Yang","full_name":"Yang, Kezhen","first_name":"Kezhen"},{"full_name":"Zou, Junjie","first_name":"Junjie","last_name":"Zou"},{"first_name":"Lingling","full_name":"Zhu, Lingling","last_name":"Zhu"},{"full_name":"Xie, Zidian","first_name":"Zidian","last_name":"Xie"},{"last_name":"Morita","first_name":"Miyoterao","full_name":"Morita, Miyoterao"},{"last_name":"Tasaka","first_name":"Masao","full_name":"Tasaka, Masao"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Grotewold","full_name":"Grotewold, Erich","first_name":"Erich"},{"first_name":"Tom","full_name":"Beeckman, Tom","last_name":"Beeckman"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"last_name":"Sack","full_name":"Sack, Fred","first_name":"Fred"},{"last_name":"Le","first_name":"Jie","full_name":"Le, Jie"}],"date_published":"2015-11-18T00:00:00Z","file_date_updated":"2020-07-14T12:45:01Z","scopus_import":"1","ec_funded":1,"has_accepted_license":"1","pubrep_id":"485","date_updated":"2025-09-23T14:55:59Z","title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","day":"18","publication":"Nature Communications","ddc":["570"],"_id":"1534","article_number":"8822","department":[{"_id":"JiFr"}],"file":[{"file_name":"IST-2016-485-v1+1_ncomms9822.pdf","date_updated":"2020-07-14T12:45:01Z","file_size":1852268,"checksum":"3c06735fc7cd7e482ca830cbd26001bf","date_created":"2018-12-12T10:17:07Z","relation":"main_file","creator":"system","access_level":"open_access","content_type":"application/pdf","file_id":"5259"}],"publisher":"Nature Publishing Group","quality_controlled":"1","article_processing_charge":"No","project":[{"grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms9822\">https://doi.org/10.1038/ncomms9822</a>.","mla":"Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” <i>Nature Communications</i>, vol. 6, 8822, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms9822\">10.1038/ncomms9822</a>.","ista":"Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 6, 8822.","short":"H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml, E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications 6 (2015).","ama":"Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms9822\">10.1038/ncomms9822</a>","apa":"Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015). Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms9822\">https://doi.org/10.1038/ncomms9822</a>","ieee":"H. Wang <i>et al.</i>, “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015."},"volume":6,"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:34Z","external_id":{"isi":["000366295500008"]},"year":"2015"},{"abstract":[{"text":"Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open readily at relatively low membrane potentials and allow Ca2+ to enter the cells near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation, hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the pacemaking current that sustains action potential (AP) firings and part of the catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating BK channels and drives the resting SK currents. These latter set the inter-spike interval duration between consecutive spikes during spontaneous firing and the rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a primary role in the switch from “tonic” to “burst” firing that occurs in mouse CCs when either the availability of voltage-gated Na channels (Nav) is reduced or the β2 subunit featuring the fast inactivating BK channels is deleted. Here, we discuss the functional role of these “neuronlike” firing modes in CCs and how Cav1.3 contributes to them. The open issue is to understand how these novel firing patterns are adapted to regulate the quantity of circulating catecholamines during resting condition or in response to acute and chronic stress.","lang":"eng"}],"type":"journal_article","intvolume":"         8","isi":1,"month":"10","status":"public","publication_status":"published","doi":"10.2174/1874467208666150507105443","oa_version":"Submitted Version","language":[{"iso":"eng"}],"publist_id":"5636","article_type":"original","date_updated":"2025-09-23T08:12:18Z","title":"Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells","day":"01","date_published":"2015-10-01T00:00:00Z","author":[{"orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","first_name":"David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea","full_name":"Marcantoni, Andrea","last_name":"Marcantoni"},{"last_name":"Carbone","full_name":"Carbone, Emilio","first_name":"Emilio"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/"}],"scopus_import":"1","_id":"1535","publication":"Current Molecular Pharmacology","date_created":"2018-12-11T11:52:35Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","acknowledgement":"This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino.","pmid":1,"external_id":{"isi":["000217186100005"],"pmid":["25966692"]},"quality_controlled":"1","article_processing_charge":"No","publisher":"Bentham Science Publishers","department":[{"_id":"PeJo"}],"page":"149 - 161","citation":{"ista":"Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 8(2), 149–161.","mla":"Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” <i>Current Molecular Pharmacology</i>, vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:<a href=\"https://doi.org/10.2174/1874467208666150507105443\">10.2174/1874467208666150507105443</a>.","chicago":"Vandael, David H, Andrea Marcantoni, and Emilio Carbone. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” <i>Current Molecular Pharmacology</i>. Bentham Science Publishers, 2015. <a href=\"https://doi.org/10.2174/1874467208666150507105443\">https://doi.org/10.2174/1874467208666150507105443</a>.","apa":"Vandael, D. H., Marcantoni, A., &#38; Carbone, E. (2015). Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. <i>Current Molecular Pharmacology</i>. Bentham Science Publishers. <a href=\"https://doi.org/10.2174/1874467208666150507105443\">https://doi.org/10.2174/1874467208666150507105443</a>","ieee":"D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells,” <i>Current Molecular Pharmacology</i>, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161, 2015.","short":"D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8 (2015) 149–161.","ama":"Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. <i>Current Molecular Pharmacology</i>. 2015;8(2):149-161. doi:<a href=\"https://doi.org/10.2174/1874467208666150507105443\">10.2174/1874467208666150507105443</a>"},"volume":8,"oa":1,"issue":"2"},{"_id":"1536","publication":"Current Biology","external_id":{"isi":["000350708800029"]},"acknowledgement":"This work was funded by a grant of the Swiss National Foundation to E.M.\r\nWe thank Dr. José María Mateos (University of Zurich) for providing us with the vibratome, Prof. Dolf Weijers (Wageningen University, the Netherlands) for shipping us his set of ligation-independent cloning vectors, Prof. Bruno Humbel (University of Lausanne) for suggestions on GFP-PDR1 detection, and Dr. Undine Krügel (University of Zurich) and Prof. Michal Jasinski (Polish Academy of Science) for hints on protein quantification.","year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:35Z","issue":"5","volume":25,"citation":{"apa":"Sasse, J., Simon, S., Gübeli, C., Liu, G., Cheng, X., Friml, J., … Borghi, L. (2015). Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2015.01.015\">https://doi.org/10.1016/j.cub.2015.01.015</a>","ieee":"J. Sasse <i>et al.</i>, “Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport,” <i>Current Biology</i>, vol. 25, no. 5. Cell Press, pp. 647–655, 2015.","ama":"Sasse J, Simon S, Gübeli C, et al. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. <i>Current Biology</i>. 2015;25(5):647-655. doi:<a href=\"https://doi.org/10.1016/j.cub.2015.01.015\">10.1016/j.cub.2015.01.015</a>","short":"J. Sasse, S. Simon, C. Gübeli, G. Liu, X. Cheng, J. Friml, H. Bouwmeester, E. Martinoia, L. Borghi, Current Biology 25 (2015) 647–655.","ista":"Sasse J, Simon S, Gübeli C, Liu G, Cheng X, Friml J, Bouwmeester H, Martinoia E, Borghi L. 2015. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 25(5), 647–655.","mla":"Sasse, Joëlle, et al. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” <i>Current Biology</i>, vol. 25, no. 5, Cell Press, 2015, pp. 647–55, doi:<a href=\"https://doi.org/10.1016/j.cub.2015.01.015\">10.1016/j.cub.2015.01.015</a>.","chicago":"Sasse, Joëlle, Sibu Simon, Christian Gübeli, Guowei Liu, Xi Cheng, Jiří Friml, Harro Bouwmeester, Enrico Martinoia, and Lorenzo Borghi. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” <i>Current Biology</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cub.2015.01.015\">https://doi.org/10.1016/j.cub.2015.01.015</a>."},"department":[{"_id":"JiFr"}],"page":"647 - 655","publisher":"Cell Press","article_processing_charge":"No","quality_controlled":"1","status":"public","isi":1,"month":"02","intvolume":"        25","type":"journal_article","abstract":[{"text":"Strigolactones, first discovered as germination stimulants for parasitic weeds [1], are carotenoid-derived phytohormones that play major roles in inhibiting lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore, strigolactones are involved in the regulation of lateral and adventitious root development, root cell division [5, 6], secondary growth [7], and leaf senescence [8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the apical membrane of root hypodermal cells, presumably mediating the shootward transport of strigolactone. Above the root tip, in the hypodermal passage cells that form gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral membrane, compatible with its postulated function as strigolactone exporter from root to soil. Transport studies are in line with our localization studies since (1) a papdr1 mutant displays impaired transport of strigolactones out of the root tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2 levels change in plants deregulated for PDR1 expression, suggestive of variations in endogenous strigolactone contents. In conclusion, our results indicate that the polar localizations of PaPDR1 mediate directional shootward strigolactone transport as well as localized exudation into the soil.","lang":"eng"}],"publist_id":"5635","language":[{"iso":"eng"}],"oa_version":"None","doi":"10.1016/j.cub.2015.01.015","publication_status":"published","day":"12","date_updated":"2025-09-23T07:57:02Z","title":"Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport","scopus_import":"1","author":[{"last_name":"Sasse","first_name":"Joëlle","full_name":"Sasse, Joëlle"},{"orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon"},{"full_name":"Gübeli, Christian","first_name":"Christian","last_name":"Gübeli"},{"first_name":"Guowei","full_name":"Liu, Guowei","last_name":"Liu"},{"full_name":"Cheng, Xi","first_name":"Xi","last_name":"Cheng"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"},{"last_name":"Bouwmeester","full_name":"Bouwmeester, Harro","first_name":"Harro"},{"first_name":"Enrico","full_name":"Martinoia, Enrico","last_name":"Martinoia"},{"last_name":"Borghi","first_name":"Lorenzo","full_name":"Borghi, Lorenzo"}],"date_published":"2015-02-12T00:00:00Z"},{"_id":"1538","publication":"PNAS","pmid":1,"external_id":{"isi":["000357079400070"],"pmid":["26085136"]},"year":"2015","acknowledgement":"J.R., F.P., and J.L. acknowledge support from the European Commission under the Network of Excellence HYCON2 (highly-complex and networked control systems) and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). ","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:36Z","issue":"26","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"citation":{"chicago":"Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1423947112\">https://doi.org/10.1073/pnas.1423947112</a>.","mla":"Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” <i>PNAS</i>, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi:<a href=\"https://doi.org/10.1073/pnas.1423947112\">10.1073/pnas.1423947112</a>.","ista":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153.","ama":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. <i>PNAS</i>. 2015;112(26):8148-8153. doi:<a href=\"https://doi.org/10.1073/pnas.1423947112\">10.1073/pnas.1423947112</a>","short":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.","apa":"Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., &#38; Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1423947112\">https://doi.org/10.1073/pnas.1423947112</a>","ieee":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” <i>PNAS</i>, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015."},"oa":1,"volume":112,"page":"8148 - 8153","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"publisher":"National Academy of Sciences","quality_controlled":"1","article_processing_charge":"No","month":"06","isi":1,"status":"public","intvolume":"       112","abstract":[{"lang":"eng","text":"Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time."}],"type":"journal_article","publist_id":"5633","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1423947112","oa_version":"Submitted Version","publication_status":"published","day":"30","date_updated":"2025-09-23T09:24:24Z","title":"Iterative experiment design guides the characterization of a light-inducible gene expression circuit","scopus_import":"1","ec_funded":1,"author":[{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","full_name":"Ruess, Jakob","first_name":"Jakob","orcid":"0000-0003-1615-3282"},{"full_name":"Parise, Francesca","first_name":"Francesca","last_name":"Parise"},{"last_name":"Milias Argeitis","full_name":"Milias Argeitis, Andreas","first_name":"Andreas"},{"last_name":"Khammash","first_name":"Mustafa","full_name":"Khammash, Mustafa"},{"first_name":"John","full_name":"Lygeros, John","last_name":"Lygeros"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/","open_access":"1"}],"date_published":"2015-06-30T00:00:00Z"},{"ddc":["000"],"corr_author":"1","publication":"Journal of Chemical Physics","article_number":"244103","_id":"1539","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"},{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"issue":"24","oa":1,"volume":143,"citation":{"ieee":"J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” <i>Journal of Chemical Physics</i>, vol. 143, no. 24. American Institute of Physics, 2015.","apa":"Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. <i>Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4937937\">https://doi.org/10.1063/1.4937937</a>","ama":"Ruess J. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. <i>Journal of Chemical Physics</i>. 2015;143(24). doi:<a href=\"https://doi.org/10.1063/1.4937937\">10.1063/1.4937937</a>","short":"J. Ruess, Journal of Chemical Physics 143 (2015).","ista":"Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103.","mla":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” <i>Journal of Chemical Physics</i>, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1063/1.4937937\">10.1063/1.4937937</a>.","chicago":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” <i>Journal of Chemical Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1063/1.4937937\">https://doi.org/10.1063/1.4937937</a>."},"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"file":[{"creator":"system","content_type":"application/pdf","access_level":"open_access","file_id":"4641","relation":"main_file","file_size":605355,"date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-12T10:07:43Z","checksum":"838657118ae286463a2b7737319f35ce","file_name":"IST-2016-593-v1+1_Minimal_moment_equations.pdf"}],"publisher":"American Institute of Physics","article_processing_charge":"No","quality_controlled":"1","external_id":{"isi":["000370412900068"]},"year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:36Z","publist_id":"5632","language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.1063/1.4937937","publication_status":"published","status":"public","isi":1,"month":"12","intvolume":"       143","abstract":[{"text":"Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. ","lang":"eng"}],"type":"journal_article","scopus_import":"1","pubrep_id":"593","has_accepted_license":"1","ec_funded":1,"author":[{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","first_name":"Jakob","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282"}],"file_date_updated":"2020-07-14T12:45:01Z","date_published":"2015-12-22T00:00:00Z","day":"22","date_updated":"2025-09-23T09:34:48Z","title":"Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space"},{"date_updated":"2025-09-23T13:51:25Z","title":"The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis","day":"05","author":[{"full_name":"Robert, Hélène","first_name":"Hélène","last_name":"Robert"},{"full_name":"Crhák Khaitová, Lucie","first_name":"Lucie","last_name":"Crhák Khaitová"},{"first_name":"Souad","full_name":"Mroue, Souad","last_name":"Mroue"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva","orcid":"0000-0002-8510-9739"}],"date_published":"2015-05-05T00:00:00Z","scopus_import":"1","type":"journal_article","abstract":[{"text":"Plant sexual reproduction involves highly structured and specialized organs: stamens (male) and gynoecia (female, containing ovules). These organs synchronously develop within protective flower buds, until anthesis, via tightly coordinated mechanisms that are essential for effective fertilization and production of viable seeds. The phytohormone auxin is one of the key endogenous signalling molecules controlling initiation and development of these, and other, plant organs. In particular, its uneven distribution, resulting from tightly controlled production, metabolism and directional transport, is an important morphogenic factor. In this review we discuss how developmentally controlled and localized auxin biosynthesis and transport contribute to the coordinated development of plants' reproductive organs, and their fertilized derivatives (embryos) via the regulation of auxin levels and distribution within and around them. Current understanding of the links between de novo local auxin biosynthesis, auxin transport and/or signalling is presented to highlight the importance of the non-cell autonomous action of auxin production on development and morphogenesis of reproductive organs and embryos. An overview of transcription factor families, which spatiotemporally define local auxin production by controlling key auxin biosynthetic enzymes, is also presented.","lang":"eng"}],"status":"public","month":"05","isi":1,"intvolume":"        66","oa_version":"None","doi":"10.1093/jxb/erv256","publication_status":"published","publist_id":"5631","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:36Z","external_id":{"isi":["000359688300015"]},"acknowledgement":"The work was supported by grants from: the Employment of Best Young Scientists for International Cooperation Empowerment/OPVKII programme (CZ.1.07/2.3.00/30.0037) to HSR and LCK; the Czech Science Foundation (GA13-39982S) to EB, LCK and SM; and the SoMoPro II programme (3SGA5602), cofinanced by the South-Moravian Region and the EU (FP7/2007–2013 People Programme), to HSR.","year":"2015","page":"5029 - 5042","department":[{"_id":"EvBe"}],"publisher":"Oxford University Press","article_processing_charge":"No","quality_controlled":"1","issue":"16","volume":66,"citation":{"ieee":"H. Robert, L. Crhák Khaitová, S. Mroue, and E. Benková, “The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis,” <i>Journal of Experimental Botany</i>, vol. 66, no. 16. Oxford University Press, pp. 5029–5042, 2015.","apa":"Robert, H., Crhák Khaitová, L., Mroue, S., &#38; Benková, E. (2015). The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erv256\">https://doi.org/10.1093/jxb/erv256</a>","short":"H. Robert, L. Crhák Khaitová, S. Mroue, E. Benková, Journal of Experimental Botany 66 (2015) 5029–5042.","ama":"Robert H, Crhák Khaitová L, Mroue S, Benková E. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. <i>Journal of Experimental Botany</i>. 2015;66(16):5029-5042. doi:<a href=\"https://doi.org/10.1093/jxb/erv256\">10.1093/jxb/erv256</a>","ista":"Robert H, Crhák Khaitová L, Mroue S, Benková E. 2015. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 66(16), 5029–5042.","mla":"Robert, Hélène, et al. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” <i>Journal of Experimental Botany</i>, vol. 66, no. 16, Oxford University Press, 2015, pp. 5029–42, doi:<a href=\"https://doi.org/10.1093/jxb/erv256\">10.1093/jxb/erv256</a>.","chicago":"Robert, Hélène, Lucie Crhák Khaitová, Souad Mroue, and Eva Benková. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/jxb/erv256\">https://doi.org/10.1093/jxb/erv256</a>."},"_id":"1540","publication":"Journal of Experimental Botany"},{"year":"2015","acknowledgement":"This work was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","alternative_title":["LNCS"],"date_created":"2018-12-11T11:52:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. 2015. XSpeed: Accelerating reachability analysis on multi-core processors. 9434, 3–18.","chicago":"Ray, Rajarshi, Amit Gurung, Binayak Das, Ezio Bartocci, Sergiy Bogomolov, and Radu Grosu. “XSpeed: Accelerating Reachability Analysis on Multi-Core Processors.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-26287-1_1\">https://doi.org/10.1007/978-3-319-26287-1_1</a>.","mla":"Ray, Rajarshi, et al. <i>XSpeed: Accelerating Reachability Analysis on Multi-Core Processors</i>. Vol. 9434, Springer, 2015, pp. 3–18, doi:<a href=\"https://doi.org/10.1007/978-3-319-26287-1_1\">10.1007/978-3-319-26287-1_1</a>.","apa":"Ray, R., Gurung, A., Das, B., Bartocci, E., Bogomolov, S., &#38; Grosu, R. (2015). XSpeed: Accelerating reachability analysis on multi-core processors. Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. <a href=\"https://doi.org/10.1007/978-3-319-26287-1_1\">https://doi.org/10.1007/978-3-319-26287-1_1</a>","ieee":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, and R. Grosu, “XSpeed: Accelerating reachability analysis on multi-core processors,” vol. 9434. Springer, pp. 3–18, 2015.","ama":"Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. XSpeed: Accelerating reachability analysis on multi-core processors. 2015;9434:3-18. doi:<a href=\"https://doi.org/10.1007/978-3-319-26287-1_1\">10.1007/978-3-319-26287-1_1</a>","short":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, R. Grosu, 9434 (2015) 3–18."},"volume":9434,"project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF"}],"quality_controlled":"1","page":"3 - 18","publisher":"Springer","department":[{"_id":"ToHe"}],"_id":"1541","conference":{"location":"Haifa, Israel","end_date":"2015-11-19","name":"HVC: Haifa Verification Conference","start_date":"2015-11-17"},"day":"28","title":"XSpeed: Accelerating reachability analysis on multi-core processors","date_updated":"2025-04-15T06:26:02Z","ec_funded":1,"scopus_import":1,"date_published":"2015-11-28T00:00:00Z","author":[{"last_name":"Ray","full_name":"Ray, Rajarshi","first_name":"Rajarshi"},{"last_name":"Gurung","full_name":"Gurung, Amit","first_name":"Amit"},{"first_name":"Binayak","full_name":"Das, Binayak","last_name":"Das"},{"last_name":"Bartocci","full_name":"Bartocci, Ezio","first_name":"Ezio"},{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365"},{"last_name":"Grosu","full_name":"Grosu, Radu","first_name":"Radu"}],"intvolume":"      9434","month":"11","status":"public","series_title":"Lecture Notes in Computer Science","abstract":[{"lang":"eng","text":"We present XSpeed a parallel state-space exploration algorithm for continuous systems with linear dynamics and nondeterministic inputs. The motivation of having parallel algorithms is to exploit the computational power of multi-core processors to speed-up performance. The parallelization is achieved on two fronts. First, we propose a parallel implementation of the support function algorithm by sampling functions in parallel. Second, we propose a parallel state-space exploration by slicing the time horizon and computing the reachable states in the time slices in parallel. The second method can be however applied only to a class of linear systems with invertible dynamics and fixed input. A GP-GPU implementation is also presented following a lazy evaluation strategy on support functions. The parallel algorithms are implemented in the tool XSpeed. We evaluated the performance on two benchmarks including an 28 dimension Helicopter model. Comparison with the sequential counterpart shows a maximum speed-up of almost 7× on a 6 core, 12 thread Intel Xeon CPU E5-2420 processor. Our GP-GPU implementation shows a maximum speed-up of 12× over the sequential implementation and 53× over SpaceEx (LGG scenario), the state of the art tool for reachability analysis of linear hybrid systems. Experiments illustrate that our parallel algorithm with time slicing not only speeds-up performance but also improves precision."}],"type":"conference","language":[{"iso":"eng"}],"publist_id":"5630","publication_status":"published","doi":"10.1007/978-3-319-26287-1_1","oa_version":"None"},{"type":"journal_article","abstract":[{"text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. ","lang":"eng"}],"intvolume":"       383","isi":1,"month":"10","status":"public","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"doi":"10.1016/j.jtbi.2015.07.011","oa_version":"Published Version","language":[{"iso":"eng"}],"publist_id":"5629","title":"Toward a unifying framework for evolutionary processes","date_updated":"2025-09-23T14:55:02Z","day":"21","date_published":"2015-10-21T00:00:00Z","file_date_updated":"2020-07-14T12:45:01Z","author":[{"first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao"},{"first_name":"Golnaz","full_name":"Badkobeh, Golnaz","last_name":"Badkobeh"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"full_name":"Çörüş, Doğan","first_name":"Doğan","last_name":"Çörüş"},{"first_name":"Duccuong","full_name":"Dang, Duccuong","last_name":"Dang"},{"first_name":"Tobias","full_name":"Friedrich, Tobias","last_name":"Friedrich"},{"last_name":"Lehre","first_name":"Per","full_name":"Lehre, Per"},{"last_name":"Sudholt","full_name":"Sudholt, Dirk","first_name":"Dirk"},{"first_name":"Andrew","full_name":"Sutton, Andrew","last_name":"Sutton"},{"orcid":"0000-0002-6873-2967","first_name":"Barbora","full_name":"Trubenova, Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"has_accepted_license":"1","pubrep_id":"483","scopus_import":"1","_id":"1542","publication":" Journal of Theoretical Biology","corr_author":"1","ddc":["570"],"date_created":"2018-12-11T11:52:37Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","external_id":{"isi":["000362056300005"]},"quality_controlled":"1","article_processing_charge":"No","publisher":"Elsevier","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"file":[{"checksum":"33b60ecfea60764756a9ee9df5eb65ca","date_created":"2018-12-12T10:16:53Z","date_updated":"2020-07-14T12:45:01Z","file_size":595307,"file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","file_id":"5244","access_level":"open_access","content_type":"application/pdf","creator":"system","relation":"main_file"}],"page":"28 - 43","citation":{"ieee":"T. Paixao <i>et al.</i>, “Toward a unifying framework for evolutionary processes,” <i> Journal of Theoretical Biology</i>, vol. 383. Elsevier, pp. 28–43, 2015.","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. <i> Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova,  Journal of Theoretical Biology 383 (2015) 28–43.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. <i> Journal of Theoretical Biology</i>. 2015;383:28-43. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>","ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes.  Journal of Theoretical Biology. 383, 28–43.","chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” <i> Journal of Theoretical Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>.","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” <i> Journal of Theoretical Biology</i>, vol. 383, Elsevier, 2015, pp. 28–43, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>."},"oa":1,"volume":383,"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}]},{"year":"2015","day":"01","external_id":{"isi":["000368472700025"]},"date_created":"2018-12-11T11:52:38Z","title":"A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants","date_updated":"2025-09-22T14:28:43Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 169(4), 2684–2699.","mla":"Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” <i>Plant Physiology</i>, vol. 169, no. 4, American Society of Plant Biologists, 2015, pp. 2684–99, doi:<a href=\"https://doi.org/10.1104/pp.15.00769\">10.1104/pp.15.00769</a>.","chicago":"Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych, Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2015. <a href=\"https://doi.org/10.1104/pp.15.00769\">https://doi.org/10.1104/pp.15.00769</a>.","apa":"Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.15.00769\">https://doi.org/10.1104/pp.15.00769</a>","ieee":"Y. Olvera Carrillo <i>et al.</i>, “A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants,” <i>Plant Physiology</i>, vol. 169, no. 4. American Society of Plant Biologists, pp. 2684–2699, 2015.","short":"Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans, M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere, M. Nowack, Plant Physiology 169 (2015) 2684–2699.","ama":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. <i>Plant Physiology</i>. 2015;169(4):2684-2699. doi:<a href=\"https://doi.org/10.1104/pp.15.00769\">10.1104/pp.15.00769</a>"},"volume":169,"scopus_import":"1","issue":"4","date_published":"2015-12-01T00:00:00Z","article_processing_charge":"No","author":[{"last_name":"Olvera Carrillo","full_name":"Olvera Carrillo, Yadira","first_name":"Yadira"},{"full_name":"Van Bel, Michiel","first_name":"Michiel","last_name":"Van Bel"},{"first_name":"Tom","full_name":"Van Hautegem, Tom","last_name":"Van Hautegem"},{"full_name":"Fendrych, Matyas","first_name":"Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych"},{"full_name":"Huysmans, Marlies","first_name":"Marlies","last_name":"Huysmans"},{"full_name":"Šimášková, Mária","first_name":"Mária","last_name":"Šimášková"},{"last_name":"Van Durme","full_name":"Van Durme, Matthias","first_name":"Matthias"},{"first_name":"Pierre","full_name":"Buscaill, Pierre","last_name":"Buscaill"},{"last_name":"Rivas","full_name":"Rivas, Susana","first_name":"Susana"},{"last_name":"Coll","first_name":"Núria","full_name":"Coll, Núria"},{"first_name":"Frederik","full_name":"Coppens, Frederik","last_name":"Coppens"},{"full_name":"Maere, Steven","first_name":"Steven","last_name":"Maere"},{"last_name":"Nowack","first_name":"Moritz","full_name":"Nowack, Moritz"}],"publisher":"American Society of Plant Biologists","page":"2684 - 2699","department":[{"_id":"JiFr"}],"intvolume":"       169","month":"12","isi":1,"status":"public","_id":"1543","type":"journal_article","abstract":[{"lang":"eng","text":"A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta."}],"language":[{"iso":"eng"}],"publist_id":"5628","publication_status":"published","doi":"10.1104/pp.15.00769","publication":"Plant Physiology","oa_version":"None"},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/"}],"author":[{"last_name":"Nguyen","full_name":"Nguyen, Phuong","first_name":"Phuong"},{"first_name":"Christine","full_name":"Field, Christine","last_name":"Field"},{"full_name":"Groen, Aaron","first_name":"Aaron","last_name":"Groen"},{"full_name":"Mitchison, Timothy","first_name":"Timothy","last_name":"Mitchison"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"}],"date_published":"2015-04-08T00:00:00Z","day":"08","date_updated":"2025-09-29T11:03:06Z","title":"Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins","publist_id":"5627","language":[{"iso":"eng"}],"oa_version":"Submitted Version","doi":"10.1016/bs.mcb.2015.01.007","publication_status":"published","status":"public","isi":1,"month":"04","intvolume":"       128","abstract":[{"text":"Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics of membrane-bound proteins is often difficult to achieve in vivo. Here, we present protocols for the use of supported lipid bilayers to rebuild the cytokinetic machineries of cells with greatly different dimensions: the bacterium Escherichia coli and eggs of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence microscopy, these experimental setups allow for precise quantitative analyses of membrane-bound proteins. The protocols described to obtain glass-supported membranes from bacterial and vertebrate lipids can be used as starting points for other reconstitution experiments. We believe that similar biochemical assays will be instrumental to study the biochemistry and biophysics underlying a variety of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility.","lang":"eng"}],"type":"book_chapter","volume":128,"oa":1,"citation":{"short":"P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell from Its Components Parts, Academic Press, 2015, pp. 223–241.","ama":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: <i>Building a Cell from Its Components Parts</i>. Vol 128. Academic Press; 2015:223-241. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">10.1016/bs.mcb.2015.01.007</a>","apa":"Nguyen, P., Field, C., Groen, A., Mitchison, T., &#38; Loose, M. (2015). Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In <i>Building a Cell from its Components Parts</i> (Vol. 128, pp. 223–241). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">https://doi.org/10.1016/bs.mcb.2015.01.007</a>","ieee":"P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins,” in <i>Building a Cell from its Components Parts</i>, vol. 128, Academic Press, 2015, pp. 223–241.","mla":"Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” <i>Building a Cell from Its Components Parts</i>, vol. 128, Academic Press, 2015, pp. 223–41, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">10.1016/bs.mcb.2015.01.007</a>.","chicago":"Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” In <i>Building a Cell from Its Components Parts</i>, 128:223–41. Academic Press, 2015. <a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">https://doi.org/10.1016/bs.mcb.2015.01.007</a>.","ista":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from its Components Parts. vol. 128, 223–241."},"publisher":"Academic Press","department":[{"_id":"MaLo"}],"page":"223 - 241","article_processing_charge":"No","quality_controlled":"1","external_id":{"isi":["000370490800013"],"pmid":["25997350"]},"pmid":1,"year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:38Z","corr_author":"1","publication":"Building a Cell from its Components Parts","_id":"1544"}]