[{"external_id":{"isi":["000366295500008"]},"month":"11","oa":1,"has_accepted_license":"1","author":[{"last_name":"Wang","first_name":"Hongzhe","full_name":"Wang, Hongzhe"},{"full_name":"Yang, Kezhen","last_name":"Yang","first_name":"Kezhen"},{"full_name":"Zou, Junjie","first_name":"Junjie","last_name":"Zou"},{"full_name":"Zhu, Lingling","first_name":"Lingling","last_name":"Zhu"},{"full_name":"Xie, Zidian","first_name":"Zidian","last_name":"Xie"},{"last_name":"Morita","first_name":"Miyoterao","full_name":"Morita, Miyoterao"},{"full_name":"Tasaka, Masao","first_name":"Masao","last_name":"Tasaka"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Grotewold, Erich","first_name":"Erich","last_name":"Grotewold"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Sack, Fred","first_name":"Fred","last_name":"Sack"},{"full_name":"Le, Jie","last_name":"Le","first_name":"Jie"}],"status":"public","year":"2015","date_created":"2018-12-11T11:52:34Z","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>.","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.","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.","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>","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).","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>."},"department":[{"_id":"JiFr"}],"title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","publist_id":"5637","_id":"1534","language":[{"iso":"eng"}],"isi":1,"day":"18","intvolume":"         6","file_date_updated":"2020-07-14T12:45:01Z","date_updated":"2025-09-23T14:55:59Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-11-18T00:00:00Z","ddc":["570"],"quality_controlled":"1","article_processing_charge":"No","pubrep_id":"485","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication":"Nature Communications","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"}],"file":[{"relation":"main_file","file_id":"5259","checksum":"3c06735fc7cd7e482ca830cbd26001bf","file_name":"IST-2016-485-v1+1_ncomms9822.pdf","creator":"system","file_size":1852268,"access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:17:07Z","date_updated":"2020-07-14T12:45:01Z"}],"doi":"10.1038/ncomms9822","volume":6,"article_number":"8822","oa_version":"Published Version","publication_status":"published","publisher":"Nature Publishing Group","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","type":"journal_article","fulldoi":"https://doi.org/10.1038/ncomms9822","ec_funded":1},{"day":"01","issue":"2","isi":1,"pmid":1,"language":[{"iso":"eng"}],"_id":"1535","publist_id":"5636","title":"Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-10-01T00:00:00Z","date_updated":"2025-09-23T08:12:18Z","intvolume":"         8","author":[{"orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","first_name":"David H"},{"full_name":"Marcantoni, Andrea","last_name":"Marcantoni","first_name":"Andrea"},{"full_name":"Carbone, Emilio","last_name":"Carbone","first_name":"Emilio"}],"oa":1,"month":"10","external_id":{"pmid":["25966692"],"isi":["000217186100005"]},"department":[{"_id":"PeJo"}],"date_created":"2018-12-11T11:52:35Z","citation":{"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>","short":"D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8 (2015) 149–161.","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>","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>.","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.","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>.","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."},"year":"2015","status":"public","publication_status":"published","oa_version":"Submitted Version","page":"149 - 161","volume":8,"fulldoi":"https://doi.org/10.2174/1874467208666150507105443","type":"journal_article","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/","open_access":"1"}],"scopus_import":"1","publisher":"Bentham Science Publishers","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"}],"article_type":"original","publication":"Current Molecular Pharmacology","article_processing_charge":"No","quality_controlled":"1","acknowledgement":"This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino.","doi":"10.2174/1874467208666150507105443"},{"scopus_import":"1","publisher":"Cell Press","type":"journal_article","fulldoi":"https://doi.org/10.1016/j.cub.2015.01.015","volume":25,"page":"647 - 655","oa_version":"None","publication_status":"published","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.","doi":"10.1016/j.cub.2015.01.015","article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","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."}],"publication":"Current Biology","intvolume":"        25","date_published":"2015-02-12T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T07:57:02Z","publist_id":"5635","title":"Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport","issue":"5","isi":1,"day":"12","_id":"1536","language":[{"iso":"eng"}],"status":"public","department":[{"_id":"JiFr"}],"year":"2015","citation":{"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>.","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>","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.","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>","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.","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.","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>."},"date_created":"2018-12-11T11:52:35Z","month":"02","external_id":{"isi":["000350708800029"]},"author":[{"first_name":"Joëlle","last_name":"Sasse","full_name":"Sasse, Joëlle"},{"full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","last_name":"Gübeli","full_name":"Gübeli, Christian"},{"full_name":"Liu, Guowei","first_name":"Guowei","last_name":"Liu"},{"full_name":"Cheng, Xi","last_name":"Cheng","first_name":"Xi"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"full_name":"Bouwmeester, Harro","first_name":"Harro","last_name":"Bouwmeester"},{"full_name":"Martinoia, Enrico","first_name":"Enrico","last_name":"Martinoia"},{"last_name":"Borghi","first_name":"Lorenzo","full_name":"Borghi, Lorenzo"}]},{"acknowledged_ssus":[{"_id":"SSU"}],"page":"673 - 685","volume":160,"publication_status":"published","oa_version":"Published Version","corr_author":"1","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Cell Press","fulldoi":"https://doi.org/10.1016/j.cell.2015.01.008","type":"journal_article","article_processing_charge":"No","quality_controlled":"1","abstract":[{"text":"3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype.","lang":"eng"}],"project":[{"_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","call_identifier":"FWF"},{"_id":"2527D5CC-B435-11E9-9278-68D0E5697425","grant_number":"I812-B12","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","call_identifier":"FWF"}],"publication":"Cell","pubrep_id":"484","file":[{"relation":"main_file","creator":"system","checksum":"228d3edf40627d897b3875088a0ac51f","file_name":"IST-2016-484-v1+1_1-s2.0-S0092867415000094-main.pdf","file_size":4362653,"file_id":"5003","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-12T10:13:21Z"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"961"}]},"acknowledgement":"We would like to thank R. Hausschild and E. Papusheva for technical assistance and the service facilities at the IST Austria for continuous support. The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel and E. Paluch for exchanging unpublished data. ","doi":"10.1016/j.cell.2015.01.008","publist_id":"5634","title":"Cortical contractility triggers a stochastic switch to fast amoeboid cell motility","day":"12","isi":1,"issue":"4","language":[{"iso":"eng"}],"_id":"1537","file_date_updated":"2020-07-14T12:45:01Z","intvolume":"       160","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"date_published":"2015-02-12T00:00:00Z","date_updated":"2026-04-08T14:22:39Z","month":"02","external_id":{"isi":["000349208800011"]},"author":[{"orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","first_name":"Verena"},{"orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan","first_name":"Stefan","last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrew","last_name":"Callan Jones","full_name":"Callan Jones, Andrew"},{"orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","last_name":"Smutny","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"},{"full_name":"Morita, Hitoshi","first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","last_name":"Morita"},{"orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke","last_name":"Sako","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke"},{"full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","first_name":"Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Monika","last_name":"Ritsch Marte","full_name":"Ritsch Marte, Monika"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"},{"full_name":"Voituriez, Raphaël","first_name":"Raphaël","last_name":"Voituriez"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"has_accepted_license":"1","oa":1,"status":"public","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"citation":{"ista":"Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V, Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685.","chicago":"Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” <i>Cell</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">https://doi.org/10.1016/j.cell.2015.01.008</a>.","ieee":"V. Ruprecht <i>et al.</i>, “Cortical contractility triggers a stochastic switch to fast amoeboid cell motility,” <i>Cell</i>, vol. 160, no. 4. Cell Press, pp. 673–685, 2015.","ama":"Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. <i>Cell</i>. 2015;160(4):673-685. doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">10.1016/j.cell.2015.01.008</a>","short":"V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V. Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160 (2015) 673–685.","apa":"Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K., … Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">https://doi.org/10.1016/j.cell.2015.01.008</a>","mla":"Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” <i>Cell</i>, vol. 160, no. 4, Cell Press, 2015, pp. 673–85, doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">10.1016/j.cell.2015.01.008</a>."},"date_created":"2018-12-11T11:52:35Z","year":"2015"},{"publication_status":"published","oa_version":"Submitted Version","page":"8148 - 8153","volume":112,"fulldoi":"https://doi.org/10.1073/pnas.1423947112","ec_funded":1,"type":"journal_article","publisher":"National Academy of Sciences","scopus_import":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/","open_access":"1"}],"publication":"PNAS","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"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."}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1073/pnas.1423947112","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). ","language":[{"iso":"eng"}],"_id":"1538","day":"30","isi":1,"pmid":1,"issue":"26","title":"Iterative experiment design guides the characterization of a light-inducible gene expression circuit","publist_id":"5633","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-06-30T00:00:00Z","date_updated":"2025-09-23T09:24:24Z","intvolume":"       112","oa":1,"author":[{"first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282"},{"last_name":"Parise","first_name":"Francesca","full_name":"Parise, Francesca"},{"full_name":"Milias Argeitis, Andreas","last_name":"Milias Argeitis","first_name":"Andreas"},{"last_name":"Khammash","first_name":"Mustafa","full_name":"Khammash, Mustafa"},{"full_name":"Lygeros, John","first_name":"John","last_name":"Lygeros"}],"external_id":{"isi":["000357079400070"],"pmid":["26085136"]},"month":"06","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>.","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.","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.","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>","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>","short":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.","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>."},"date_created":"2018-12-11T11:52:36Z","year":"2015","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"status":"public"},{"month":"12","external_id":{"isi":["000370412900068"]},"author":[{"orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","first_name":"Jakob"}],"has_accepted_license":"1","oa":1,"status":"public","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"date_created":"2018-12-11T11:52:36Z","citation":{"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>","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>","short":"J. Ruess, Journal of Chemical Physics 143 (2015).","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>.","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.","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>.","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."},"year":"2015","publist_id":"5632","title":"Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space","day":"22","isi":1,"issue":"24","_id":"1539","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:01Z","intvolume":"       143","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T09:34:48Z","ddc":["000"],"date_published":"2015-12-22T00:00:00Z","article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","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. "}],"project":[{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication":"Journal of Chemical Physics","pubrep_id":"593","file":[{"date_created":"2018-12-12T10:07:43Z","date_updated":"2020-07-14T12:45:01Z","access_level":"open_access","content_type":"application/pdf","file_id":"4641","checksum":"838657118ae286463a2b7737319f35ce","file_size":605355,"creator":"system","file_name":"IST-2016-593-v1+1_Minimal_moment_equations.pdf","relation":"main_file"}],"doi":"10.1063/1.4937937","article_number":"244103","volume":143,"publication_status":"published","oa_version":"Published Version","corr_author":"1","scopus_import":"1","publisher":"American Institute of Physics","ec_funded":1,"fulldoi":"https://doi.org/10.1063/1.4937937","type":"journal_article"},{"status":"public","department":[{"_id":"EvBe"}],"year":"2015","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.","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.","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>.","short":"H. Robert, L. Crhák Khaitová, S. Mroue, E. Benková, Journal of Experimental Botany 66 (2015) 5029–5042.","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>","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>","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>."},"date_created":"2018-12-11T11:52:36Z","month":"05","external_id":{"isi":["000359688300015"]},"author":[{"last_name":"Robert","first_name":"Hélène","full_name":"Robert, Hélène"},{"first_name":"Lucie","last_name":"Crhák Khaitová","full_name":"Crhák Khaitová, Lucie"},{"first_name":"Souad","last_name":"Mroue","full_name":"Mroue, Souad"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        66","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-05-05T00:00:00Z","date_updated":"2025-09-23T13:51:25Z","publist_id":"5631","title":"The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis","issue":"16","isi":1,"day":"05","language":[{"iso":"eng"}],"_id":"1540","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.","doi":"10.1093/jxb/erv256","article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","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."}],"publication":"Journal of Experimental Botany","scopus_import":"1","publisher":"Oxford University Press","type":"journal_article","fulldoi":"https://doi.org/10.1093/jxb/erv256","volume":66,"page":"5029 - 5042","oa_version":"None","publication_status":"published"},{"conference":{"location":"Haifa, Israel","end_date":"2015-11-19","name":"HVC: Haifa Verification Conference","start_date":"2015-11-17"},"author":[{"full_name":"Ray, Rajarshi","first_name":"Rajarshi","last_name":"Ray"},{"first_name":"Amit","last_name":"Gurung","full_name":"Gurung, Amit"},{"full_name":"Das, Binayak","last_name":"Das","first_name":"Binayak"},{"full_name":"Bartocci, Ezio","first_name":"Ezio","last_name":"Bartocci"},{"first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"}],"month":"11","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T11:52:37Z","citation":{"short":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, R. Grosu, 9434 (2015) 3–18.","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>","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>","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>.","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.","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>.","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."},"year":"2015","status":"public","day":"28","_id":"1541","language":[{"iso":"eng"}],"publist_id":"5630","title":"XSpeed: Accelerating reachability analysis on multi-core processors","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-11-28T00:00:00Z","date_updated":"2025-04-15T06:26:02Z","intvolume":"      9434","abstract":[{"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.","lang":"eng"}],"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"}],"quality_controlled":"1","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).","doi":"10.1007/978-3-319-26287-1_1","series_title":"Lecture Notes in Computer Science","publication_status":"published","oa_version":"None","page":"3 - 18","alternative_title":["LNCS"],"volume":9434,"ec_funded":1,"fulldoi":"https://doi.org/10.1007/978-3-319-26287-1_1","type":"conference","scopus_import":1,"publisher":"Springer"},{"abstract":[{"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.","lang":"eng"}],"publication":"Plant Physiology","article_processing_charge":"No","doi":"10.1104/pp.15.00769","oa_version":"None","publication_status":"published","volume":169,"page":"2684 - 2699","type":"journal_article","fulldoi":"https://doi.org/10.1104/pp.15.00769","scopus_import":"1","publisher":"American Society of Plant Biologists","author":[{"full_name":"Olvera Carrillo, Yadira","first_name":"Yadira","last_name":"Olvera Carrillo"},{"full_name":"Van Bel, Michiel","last_name":"Van Bel","first_name":"Michiel"},{"last_name":"Van Hautegem","first_name":"Tom","full_name":"Van Hautegem, Tom"},{"last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699"},{"full_name":"Huysmans, Marlies","first_name":"Marlies","last_name":"Huysmans"},{"last_name":"Šimášková","first_name":"Mária","full_name":"Šimášková, Mária"},{"full_name":"Van Durme, Matthias","last_name":"Van Durme","first_name":"Matthias"},{"first_name":"Pierre","last_name":"Buscaill","full_name":"Buscaill, Pierre"},{"full_name":"Rivas, Susana","first_name":"Susana","last_name":"Rivas"},{"last_name":"Coll","first_name":"Núria","full_name":"Coll, Núria"},{"last_name":"Coppens","first_name":"Frederik","full_name":"Coppens, Frederik"},{"last_name":"Maere","first_name":"Steven","full_name":"Maere, Steven"},{"full_name":"Nowack, Moritz","first_name":"Moritz","last_name":"Nowack"}],"month":"12","external_id":{"isi":["000368472700025"]},"department":[{"_id":"JiFr"}],"year":"2015","citation":{"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>.","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.","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.","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>","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>","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.","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>."},"date_created":"2018-12-11T11:52:38Z","status":"public","issue":"4","isi":1,"day":"01","language":[{"iso":"eng"}],"_id":"1543","publist_id":"5628","title":"A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:28:43Z","date_published":"2015-12-01T00:00:00Z","intvolume":"       169"},{"author":[{"full_name":"Nguyen, Phuong","last_name":"Nguyen","first_name":"Phuong"},{"first_name":"Christine","last_name":"Field","full_name":"Field, Christine"},{"full_name":"Groen, Aaron","last_name":"Groen","first_name":"Aaron"},{"full_name":"Mitchison, Timothy","last_name":"Mitchison","first_name":"Timothy"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"oa":1,"month":"04","external_id":{"isi":["000370490800013"],"pmid":["25997350"]},"department":[{"_id":"MaLo"}],"citation":{"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.","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.","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>.","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>","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>"},"date_created":"2018-12-11T11:52:38Z","year":"2015","status":"public","day":"08","pmid":1,"isi":1,"_id":"1544","language":[{"iso":"eng"}],"publist_id":"5627","title":"Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins","date_updated":"2025-09-29T11:03:06Z","date_published":"2015-04-08T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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"}],"publication":"Building a Cell from its Components Parts","article_processing_charge":"No","quality_controlled":"1","doi":"10.1016/bs.mcb.2015.01.007","publication_status":"published","oa_version":"Submitted Version","corr_author":"1","page":"223 - 241","volume":128,"fulldoi":"https://doi.org/10.1016/bs.mcb.2015.01.007","type":"book_chapter","scopus_import":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/","open_access":"1"}],"publisher":"Academic Press"},{"status":"public","department":[{"_id":"RySh"}],"year":"2015","OA_type":"hybrid","citation":{"ama":"Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. <i>Neuron</i>. 2015;85(1):145-158. doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">10.1016/j.neuron.2014.11.019</a>","short":"Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto, R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158.","apa":"Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto, R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">https://doi.org/10.1016/j.neuron.2014.11.019</a>","mla":"Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” <i>Neuron</i>, vol. 85, no. 1, Elsevier, 2015, pp. 145–58, doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">10.1016/j.neuron.2014.11.019</a>.","chicago":"Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman, Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” <i>Neuron</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">https://doi.org/10.1016/j.neuron.2014.11.019</a>.","ista":"Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 85(1), 145–158.","ieee":"Y. Nakamura <i>et al.</i>, “Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development,” <i>Neuron</i>, vol. 85, no. 1. Elsevier, pp. 145–158, 2015."},"date_created":"2018-12-11T11:52:39Z","month":"01","external_id":{"pmid":["25533484"],"isi":["000348295100015"]},"author":[{"first_name":"Yukihiro","last_name":"Nakamura","full_name":"Nakamura, Yukihiro"},{"orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi","first_name":"Harumi","last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kamasawa, Naomi","last_name":"Kamasawa","first_name":"Naomi"},{"full_name":"Matsui, Ko","first_name":"Ko","last_name":"Matsui"},{"first_name":"Jason","last_name":"Rothman","full_name":"Rothman, Jason"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"full_name":"Silver, R Angus","first_name":"R Angus","last_name":"Silver"},{"first_name":"David","last_name":"Digregorio","full_name":"Digregorio, David"},{"first_name":"Tomoyuki","last_name":"Takahashi","full_name":"Takahashi, Tomoyuki"}],"has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"intvolume":"        85","file_date_updated":"2020-07-14T12:45:01Z","OA_place":"publisher","date_updated":"2025-09-23T09:38:39Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"date_published":"2015-01-07T00:00:00Z","publist_id":"5625","title":"Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development","issue":"1","isi":1,"pmid":1,"day":"07","_id":"1546","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-12T10:15:47Z","relation":"main_file","file_id":"5170","file_name":"IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf","checksum":"725f4d5be2dbb44b283ce722645ef37d","file_size":3080111,"creator":"system"}],"acknowledgement":"This work was supported by the Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.; by the funding provided by Okinawa Institute of Science and Technology (OIST) to T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture, Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la Recherche Scientifique through the Actions Thematiques et Initatives sur Programme, Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01) to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063) to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413) and Principal (095667) Research Fellowship and an ERC advance grant (294667) to RAS.","doi":"10.1016/j.neuron.2014.11.019","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","article_type":"original","abstract":[{"lang":"eng","text":"Synaptic efficacy and precision are influenced by the coupling of voltage-gated Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their proximity to vesicles is unknown, a quantitative understanding of the determinants of vesicular release at nanometer scale is lacking. To investigate this, we combined freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging, and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day 7 and 21, VGCCs formed variable sized clusters and vesicular release became less sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular release are located at the perimeter of VGCC clusters (&lt;30nm) and predict that VGCC number per cluster determines vesicular release probability without altering release time course. This &quot;perimeter release model&quot; provides a unifying framework accounting for developmental changes in both synaptic efficacy and time course."}],"pubrep_id":"482","publication":"Neuron","scopus_import":"1","publisher":"Elsevier","tmp":{"short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"type":"journal_article","fulldoi":"https://doi.org/10.1016/j.neuron.2014.11.019","volume":85,"page":"145 - 158","oa_version":"Published Version","publication_status":"published"},{"external_id":{"isi":["000355776600024"],"arxiv":["0901.3015"]},"month":"05","oa":1,"author":[{"full_name":"Mohammadi, Fatemeh","id":"2C29581E-F248-11E8-B48F-1D18A9856A87","last_name":"Mohammadi","first_name":"Fatemeh"},{"full_name":"Moradi, Somayeh","first_name":"Somayeh","last_name":"Moradi"}],"status":"public","date_created":"2018-12-11T11:52:39Z","citation":{"apa":"Mohammadi, F., &#38; Moradi, S. (2015). Resolution of unmixed bipartite graphs. <i>Bulletin of the Korean Mathematical Society</i>. Korean Mathematical Society. <a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">https://doi.org/10.4134/BKMS.2015.52.3.977</a>","short":"F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015) 977–986.","ama":"Mohammadi F, Moradi S. Resolution of unmixed bipartite graphs. <i>Bulletin of the Korean Mathematical Society</i>. 2015;52(3):977-986. doi:<a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">10.4134/BKMS.2015.52.3.977</a>","mla":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” <i>Bulletin of the Korean Mathematical Society</i>, vol. 52, no. 3, Korean Mathematical Society, 2015, pp. 977–86, doi:<a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">10.4134/BKMS.2015.52.3.977</a>.","ieee":"F. Mohammadi and S. Moradi, “Resolution of unmixed bipartite graphs,” <i>Bulletin of the Korean Mathematical Society</i>, vol. 52, no. 3. Korean Mathematical Society, pp. 977–986, 2015.","chicago":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” <i>Bulletin of the Korean Mathematical Society</i>. Korean Mathematical Society, 2015. <a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">https://doi.org/10.4134/BKMS.2015.52.3.977</a>.","ista":"Mohammadi F, Moradi S. 2015. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 52(3), 977–986."},"year":"2015","department":[{"_id":"CaUh"}],"title":"Resolution of unmixed bipartite graphs","publist_id":"5624","arxiv":1,"_id":"1547","language":[{"iso":"eng"}],"day":"31","isi":1,"issue":"3","publication_identifier":{"eissn":["2234-3016"]},"intvolume":"        52","date_updated":"2025-09-23T10:36:36Z","date_published":"2015-05-31T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","article_processing_charge":"No","publication":"Bulletin of the Korean Mathematical Society","abstract":[{"text":"Let G be a graph on the vertex set V(G) = {x1,…,xn} with the edge set E(G), and let R = K[x1,…, xn] be the polynomial ring over a field K. Two monomial ideals are associated to G, the edge ideal I(G) generated by all monomials xixj with {xi,xj} ∈ E(G), and the vertex cover ideal IG generated by monomials ∏xi∈Cxi for all minimal vertex covers C of G. A minimal vertex cover of G is a subset C ⊂ V(G) such that each edge has at least one vertex in C and no proper subset of C has the same property. Indeed, the vertex cover ideal of G is the Alexander dual of the edge ideal of G. In this paper, for an unmixed bipartite graph G we consider the lattice of vertex covers LG and we explicitly describe the minimal free resolution of the ideal associated to LG which is exactly the vertex cover ideal of G. Then we compute depth, projective dimension, regularity and extremal Betti numbers of R/I(G) in terms of the associated lattice.","lang":"eng"}],"doi":"10.4134/BKMS.2015.52.3.977","page":"977 - 986","volume":52,"publication_status":"published","oa_version":"Preprint","publisher":"Korean Mathematical Society","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0901.3015"}],"scopus_import":"1","fulldoi":"https://doi.org/10.4134/BKMS.2015.52.3.977","type":"journal_article"},{"publication_status":"published","oa_version":"Submitted Version","page":"8135 - 8144","volume":81,"fulldoi":"https://doi.org/10.1128/AEM.02051-15","type":"journal_article","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/","open_access":"1"}],"scopus_import":"1","publisher":"American Society for Microbiology","abstract":[{"lang":"eng","text":"Reproduction within a host and transmission to the next host are crucial for the virulence and fitness of pathogens. Nevertheless, basic knowledge about such parameters is often missing from the literature, even for well-studied bacteria, such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects its hosts via the oral route. To characterize bacterial replication success, we made use of an experimental oral infection system for the red flour beetle Tribolium castaneum and developed a flow cytometric assay for the quantification of both spore ingestion by the individual beetle larvae and the resulting spore load after bacterial replication and resporulation within cadavers. On average, spore numbers increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial stock cultures into nutrient medium, we next investigated outgrowth characteristics of vegetative cells and found that cadaver- derived bacteria showed reduced growth compared to bacteria from the stock cultures. Interestingly, this reduced growth was a consequence of inhibited spore germination, probably originating from the host and resulting in reduced host mortality in subsequent infections by cadaver-derived spores. Nevertheless, we further showed that Bacillus thuringiensis transmission was possible via larval cannibalism when no other food was offered. These results contribute to our understanding of the ecology of Bacillus thuringiensis as an insect pathogen."}],"publication":"Applied and Environmental Microbiology","article_processing_charge":"No","quality_controlled":"1","doi":"10.1128/AEM.02051-15","day":"01","issue":"23","isi":1,"pmid":1,"language":[{"iso":"eng"}],"_id":"1548","publist_id":"5623","title":"Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination","date_published":"2015-12-01T00:00:00Z","date_updated":"2025-09-23T09:22:27Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        81","author":[{"full_name":"Milutinovic, Barbara","orcid":"0000-0002-8214-4758","first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","last_name":"Milutinovic"},{"full_name":"Höfling, Christina","last_name":"Höfling","first_name":"Christina"},{"full_name":"Futo, Momir","last_name":"Futo","first_name":"Momir"},{"full_name":"Scharsack, Jörn","last_name":"Scharsack","first_name":"Jörn"},{"last_name":"Kurtz","first_name":"Joachim","full_name":"Kurtz, Joachim"}],"oa":1,"month":"12","external_id":{"isi":["000364775700018"],"pmid":["26386058"]},"department":[{"_id":"SyCr"}],"citation":{"chicago":"Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” <i>Applied and Environmental Microbiology</i>. American Society for Microbiology, 2015. <a href=\"https://doi.org/10.1128/AEM.02051-15\">https://doi.org/10.1128/AEM.02051-15</a>.","ista":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 81(23), 8135–8144.","ieee":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination,” <i>Applied and Environmental Microbiology</i>, vol. 81, no. 23. American Society for Microbiology, pp. 8135–8144, 2015.","ama":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. <i>Applied and Environmental Microbiology</i>. 2015;81(23):8135-8144. doi:<a href=\"https://doi.org/10.1128/AEM.02051-15\">10.1128/AEM.02051-15</a>","short":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and Environmental Microbiology 81 (2015) 8135–8144.","apa":"Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., &#38; Kurtz, J. (2015). Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. <i>Applied and Environmental Microbiology</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/AEM.02051-15\">https://doi.org/10.1128/AEM.02051-15</a>","mla":"Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” <i>Applied and Environmental Microbiology</i>, vol. 81, no. 23, American Society for Microbiology, 2015, pp. 8135–44, doi:<a href=\"https://doi.org/10.1128/AEM.02051-15\">10.1128/AEM.02051-15</a>."},"date_created":"2018-12-11T11:52:39Z","year":"2015","status":"public"},{"status":"public","citation":{"chicago":"Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak. “Flipping the Photoswitch: Ion Channels under Light Control.” In <i>Novel Chemical Tools to Study Ion Channel Biology</i>, 869:101–17. Advances in Experimental Medicine and Biology. Springer, 2015. <a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">https://doi.org/10.1007/978-1-4939-2845-3_6</a>.","ista":"Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch: Ion channels under light control. In: Novel chemical tools to study ion channel biology. vol. 869, 101–117.","ieee":"C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch: Ion channels under light control,” in <i>Novel chemical tools to study ion channel biology</i>, vol. 869, Springer, 2015, pp. 101–117.","ama":"Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels under light control. In: <i>Novel Chemical Tools to Study Ion Channel Biology</i>. Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117. doi:<a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">10.1007/978-1-4939-2845-3_6</a>","apa":"Mckenzie, C., Sanchez-Romero, I., &#38; Janovjak, H. L. (2015). Flipping the photoswitch: Ion channels under light control. In <i>Novel chemical tools to study ion channel biology</i> (Vol. 869, pp. 101–117). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">https://doi.org/10.1007/978-1-4939-2845-3_6</a>","short":"C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools to Study Ion Channel Biology, Springer, 2015, pp. 101–117.","mla":"Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under Light Control.” <i>Novel Chemical Tools to Study Ion Channel Biology</i>, vol. 869, Springer, 2015, pp. 101–17, doi:<a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">10.1007/978-1-4939-2845-3_6</a>."},"date_created":"2018-12-11T11:52:39Z","year":"2015","department":[{"_id":"HaJa"}],"external_id":{"isi":["000361794300006"]},"month":"09","oa":1,"has_accepted_license":"1","author":[{"first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","last_name":"Mckenzie","full_name":"Mckenzie, Catherine"},{"full_name":"Sanchez Romero, Inmaculada","first_name":"Inmaculada","last_name":"Sanchez Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"}],"file_date_updated":"2020-07-14T12:45:01Z","intvolume":"       869","publication_identifier":{"isbn":["978-1-4939-2844-6"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["571","576"],"date_published":"2015-09-18T00:00:00Z","date_updated":"2025-09-23T08:52:05Z","title":"Flipping the photoswitch: Ion channels under light control","publist_id":"5622","language":[{"iso":"eng"}],"_id":"1549","day":"18","isi":1,"series_title":"Advances in Experimental Medicine and Biology","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-12T10:11:02Z","relation":"main_file","file_size":1919655,"checksum":"bd1bfdf2423a0c3b6e7cabfa8b44bc0f","creator":"system","file_name":"IST-2017-839-v1+1_mckenzie.pdf","file_id":"4854"}],"doi":"10.1007/978-1-4939-2845-3_6","quality_controlled":"1","article_processing_charge":"No","publication":"Novel chemical tools to study ion channel biology","pubrep_id":"839","abstract":[{"text":"Nature has incorporated small photochromic molecules, colloquially termed 'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis and vision. While Nature's ability to employ light-responsive functionalities has long been recognized, it was not until recently that scientists designed, synthesized and applied synthetic photochromes to manipulate many of which open rapidly and locally in their native cell types, biological processes with the temporal and spatial resolution of light. Ion channels in particular have come to the forefront of proteins that can be put under the designer control of synthetic photochromes. Photochromic ion channel controllers are comprised of three classes, photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and photochromic crosslinkers (PXs), and in each class ion channel functionality is controlled through reversible changes in photochrome structure. By acting as light-dependent ion channel agonists, antagonist or modulators, photochromic controllers effectively converted a wide range of ion channels, including voltage-gated ion channels, 'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive ion channels, into man-made photoreceptors. Control by photochromes can be reversible, unlike in the case of 'caged' compounds, and non-invasive with high spatial precision, unlike pharmacology and electrical manipulation. Here, we introduce design principles of emerging photochromic molecules that act on ion channels and discuss the impact that these molecules are beginning to have on ion channel biophysics and neuronal physiology.","lang":"eng"}],"publisher":"Springer","scopus_import":"1","fulldoi":"https://doi.org/10.1007/978-1-4939-2845-3_6","type":"book_chapter","page":"101 - 117","volume":869,"corr_author":"1","publication_status":"published","oa_version":"Submitted Version"},{"publication_status":"published","oa_version":"Submitted Version","page":"989 - 998","volume":87,"fulldoi":"https://doi.org/10.1016/j.neuron.2015.07.011","type":"journal_article","publisher":"Elsevier","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/"}],"publication":"Neuron","abstract":[{"lang":"eng","text":"The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain interneurons. Here, we examine the lineage relationship among MGE-derived interneurons using a replication-defective retroviral library containing a highly diverse set of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor cells enabled us to unambiguously determine their respective lineal relationship. We found that clonal dispersion occurs across large areas of the brain and is not restricted by anatomical divisions. As such, sibling interneurons can populate the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons appeared to be generated from asymmetric divisions of MGE progenitor cells, followed by symmetric divisions within the subventricular zone. Altogether, our findings uncover that lineage relationships do not appear to determine interneuron allocation to particular regions. As such, it is likely that clonally related interneurons have considerable flexibility as to the particular forebrain circuits to which they can contribute."}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1016/j.neuron.2015.07.011","acknowledgement":"Research in the G.F. laboratory is supported by NIH (NS 081297, MH095147, and P01NS074972) and the Simons Foundation. Research in the S.H. laboratory is supported by the European Union (FP7-CIG618444). C.M. is supported by EMBO ALTF (1295-2012). X.H.J. is supported by EMBO (ALTF 303-2010) and HFSP (LT000078/2011-L).\r\n\r\n","language":[{"iso":"eng"}],"_id":"1550","day":"02","issue":"5","pmid":1,"isi":1,"title":"Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries","publist_id":"5621","date_updated":"2025-09-23T08:16:35Z","date_published":"2015-09-02T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        87","oa":1,"author":[{"last_name":"Mayer","first_name":"Christian","full_name":"Mayer, Christian"},{"full_name":"Jaglin, Xavier","last_name":"Jaglin","first_name":"Xavier"},{"first_name":"Lucy","last_name":"Cobbs","full_name":"Cobbs, Lucy"},{"full_name":"Bandler, Rachel","first_name":"Rachel","last_name":"Bandler"},{"last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen"},{"first_name":"Constance","last_name":"Cepko","full_name":"Cepko, Constance"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"last_name":"Fishell","first_name":"Gord","full_name":"Fishell, Gord"}],"external_id":{"isi":["000361146300009"],"pmid":["26299473"]},"month":"09","date_created":"2018-12-11T11:52:40Z","citation":{"mla":"Mayer, Christian, et al. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” <i>Neuron</i>, vol. 87, no. 5, Elsevier, 2015, pp. 989–98, doi:<a href=\"https://doi.org/10.1016/j.neuron.2015.07.011\">10.1016/j.neuron.2015.07.011</a>.","ama":"Mayer C, Jaglin X, Cobbs L, et al. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. <i>Neuron</i>. 2015;87(5):989-998. doi:<a href=\"https://doi.org/10.1016/j.neuron.2015.07.011\">10.1016/j.neuron.2015.07.011</a>","apa":"Mayer, C., Jaglin, X., Cobbs, L., Bandler, R., Streicher, C., Cepko, C., … Fishell, G. (2015). Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2015.07.011\">https://doi.org/10.1016/j.neuron.2015.07.011</a>","short":"C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer, G. Fishell, Neuron 87 (2015) 989–998.","ista":"Mayer C, Jaglin X, Cobbs L, Bandler R, Streicher C, Cepko C, Hippenmeyer S, Fishell G. 2015. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 87(5), 989–998.","chicago":"Mayer, Christian, Xavier Jaglin, Lucy Cobbs, Rachel Bandler, Carmen Streicher, Constance Cepko, Simon Hippenmeyer, and Gord Fishell. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” <i>Neuron</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.neuron.2015.07.011\">https://doi.org/10.1016/j.neuron.2015.07.011</a>.","ieee":"C. Mayer <i>et al.</i>, “Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries,” <i>Neuron</i>, vol. 87, no. 5. Elsevier, pp. 989–998, 2015."},"year":"2015","department":[{"_id":"SiHi"}],"status":"public"},{"_id":"1551","language":[{"iso":"eng"}],"isi":1,"issue":"6","day":"04","title":"Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes","publist_id":"5620","date_published":"2015-06-04T00:00:00Z","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T09:19:00Z","intvolume":"        13","file_date_updated":"2020-07-14T12:45:02Z","oa":1,"has_accepted_license":"1","author":[{"full_name":"El Masri, Leila","id":"349A6E66-F248-11E8-B48F-1D18A9856A87","last_name":"El Masri","first_name":"Leila"},{"full_name":"Branca, Antoine","first_name":"Antoine","last_name":"Branca"},{"full_name":"Sheppard, Anna","first_name":"Anna","last_name":"Sheppard"},{"full_name":"Papkou, Andrei","first_name":"Andrei","last_name":"Papkou"},{"full_name":"Laehnemann, David","first_name":"David","last_name":"Laehnemann"},{"last_name":"Guenther","first_name":"Patrick","full_name":"Guenther, Patrick"},{"full_name":"Prahl, Swantje","first_name":"Swantje","last_name":"Prahl"},{"full_name":"Saebelfeld, Manja","last_name":"Saebelfeld","first_name":"Manja"},{"full_name":"Hollensteiner, Jacqueline","first_name":"Jacqueline","last_name":"Hollensteiner"},{"full_name":"Liesegang, Heiko","last_name":"Liesegang","first_name":"Heiko"},{"full_name":"Brzuszkiewicz, Elzbieta","first_name":"Elzbieta","last_name":"Brzuszkiewicz"},{"full_name":"Daniel, Rolf","last_name":"Daniel","first_name":"Rolf"},{"last_name":"Michiels","first_name":"Nico","full_name":"Michiels, Nico"},{"last_name":"Schulte","first_name":"Rebecca","full_name":"Schulte, Rebecca"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"},{"last_name":"Rosenstiel","first_name":"Philip","full_name":"Rosenstiel, Philip"},{"last_name":"Telschow","first_name":"Arndt","full_name":"Telschow, Arndt"},{"full_name":"Bornberg Bauer, Erich","last_name":"Bornberg Bauer","first_name":"Erich"},{"last_name":"Schulenburg","first_name":"Hinrich","full_name":"Schulenburg, Hinrich"}],"external_id":{"isi":["000357339600009"]},"month":"06","year":"2015","citation":{"ieee":"L. El Masri <i>et al.</i>, “Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes,” <i>PLoS Biology</i>, vol. 13, no. 6. Public Library of Science, pp. 1–30, 2015.","chicago":"El Masri, Leila, Antoine Branca, Anna Sheppard, Andrei Papkou, David Laehnemann, Patrick Guenther, Swantje Prahl, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” <i>PLoS Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002169\">https://doi.org/10.1371/journal.pbio.1002169</a>.","ista":"El Masri L, Branca A, Sheppard A, Papkou A, Laehnemann D, Guenther P, Prahl S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels N, Schulte R, Kurtz J, Rosenstiel P, Telschow A, Bornberg Bauer E, Schulenburg H. 2015. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 13(6), 1–30.","short":"L. El Masri, A. Branca, A. Sheppard, A. Papkou, D. Laehnemann, P. Guenther, S. Prahl, M. Saebelfeld, J. Hollensteiner, H. Liesegang, E. Brzuszkiewicz, R. Daniel, N. Michiels, R. Schulte, J. Kurtz, P. Rosenstiel, A. Telschow, E. Bornberg Bauer, H. Schulenburg, PLoS Biology 13 (2015) 1–30.","apa":"El Masri, L., Branca, A., Sheppard, A., Papkou, A., Laehnemann, D., Guenther, P., … Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002169\">https://doi.org/10.1371/journal.pbio.1002169</a>","ama":"El Masri L, Branca A, Sheppard A, et al. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. <i>PLoS Biology</i>. 2015;13(6):1-30. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002169\">10.1371/journal.pbio.1002169</a>","mla":"El Masri, Leila, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” <i>PLoS Biology</i>, vol. 13, no. 6, Public Library of Science, 2015, pp. 1–30, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002169\">10.1371/journal.pbio.1002169</a>."},"date_created":"2018-12-11T11:52:40Z","department":[{"_id":"SyCr"}],"status":"public","oa_version":"Published Version","publication_status":"published","volume":13,"page":"1 - 30","type":"journal_article","fulldoi":"https://doi.org/10.1371/journal.pbio.1002169","ec_funded":1,"publisher":"Public Library of Science","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","pubrep_id":"481","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"publication":"PLoS Biology","abstract":[{"text":"Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i) high virulence was specifically favoured during pathogen–host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii) the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins.We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen's genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host–pathogen interaction system.","lang":"eng"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1371/journal.pbio.1002169","acknowledgement":"We are very grateful for funding from the German Science Foundation (DFG) to HS (SCHU 1415/8, SCHU 1415/9), PR (RO 2994/3), EBB (BO 2544/7), HL (LI 1690/2), AT (TE 976/2), RDS (SCHU 2522/1), JK (KU 1929/4); from the Kiel Excellence Cluster Inflammation at Interfaces to HS and PR; and from the ISTFELLOW program (Co-fund Marie Curie Actions of the European Commission) to LM.","file":[{"relation":"main_file","file_size":3468956,"checksum":"30dee7a2c11ed09f2f5634655c0146f8","file_name":"IST-2016-481-v1+1_journal.pbio.1002169.pdf","creator":"system","file_id":"5063","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:14:13Z","date_updated":"2020-07-14T12:45:02Z"}]},{"intvolume":"       161","date_published":"2015-04-09T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T07:31:01Z","title":"Actin flows mediate a universal coupling between cell speed and cell persistence","publist_id":"5618","_id":"1553","language":[{"iso":"eng"}],"issue":"2","isi":1,"day":"09","status":"public","year":"2015","citation":{"mla":"Maiuri, Paolo, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” <i>Cell</i>, vol. 161, no. 2, Cell Press, 2015, pp. 374–86, doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.056\">10.1016/j.cell.2015.01.056</a>.","ama":"Maiuri P, Rupprecht J, Wieser S, et al. Actin flows mediate a universal coupling between cell speed and cell persistence. <i>Cell</i>. 2015;161(2):374-386. doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.056\">10.1016/j.cell.2015.01.056</a>","short":"P. Maiuri, J. Rupprecht, S. Wieser, V. Ruprecht, O. Bénichou, N. Carpi, M. Coppey, S. De Beco, N. Gov, C.-P.J. Heisenberg, C. Lage Crespo, F. Lautenschlaeger, M. Le Berre, A. Lennon Duménil, M. Raab, H. Thiam, M. Piel, M.K. Sixt, R. Voituriez, Cell 161 (2015) 374–386.","apa":"Maiuri, P., Rupprecht, J., Wieser, S., Ruprecht, V., Bénichou, O., Carpi, N., … Voituriez, R. (2015). Actin flows mediate a universal coupling between cell speed and cell persistence. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2015.01.056\">https://doi.org/10.1016/j.cell.2015.01.056</a>","chicago":"Maiuri, Paolo, Jean Rupprecht, Stefan Wieser, Verena Ruprecht, Olivier Bénichou, Nicolas Carpi, Mathieu Coppey, et al. “Actin Flows Mediate a Universal Coupling between Cell Speed and Cell Persistence.” <i>Cell</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cell.2015.01.056\">https://doi.org/10.1016/j.cell.2015.01.056</a>.","ista":"Maiuri P, Rupprecht J, Wieser S, Ruprecht V, Bénichou O, Carpi N, Coppey M, De Beco S, Gov N, Heisenberg C-PJ, Lage Crespo C, Lautenschlaeger F, Le Berre M, Lennon Duménil A, Raab M, Thiam H, Piel M, Sixt MK, Voituriez R. 2015. Actin flows mediate a universal coupling between cell speed and cell persistence. Cell. 161(2), 374–386.","ieee":"P. Maiuri <i>et al.</i>, “Actin flows mediate a universal coupling between cell speed and cell persistence,” <i>Cell</i>, vol. 161, no. 2. Cell Press, pp. 374–386, 2015."},"date_created":"2018-12-11T11:52:41Z","department":[{"_id":"MiSi"},{"_id":"CaHe"}],"external_id":{"isi":["000352708300028"]},"month":"04","author":[{"last_name":"Maiuri","first_name":"Paolo","full_name":"Maiuri, Paolo"},{"last_name":"Rupprecht","first_name":"Jean","full_name":"Rupprecht, Jean"},{"orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan","last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633"},{"full_name":"Bénichou, Olivier","first_name":"Olivier","last_name":"Bénichou"},{"full_name":"Carpi, Nicolas","last_name":"Carpi","first_name":"Nicolas"},{"full_name":"Coppey, Mathieu","first_name":"Mathieu","last_name":"Coppey"},{"last_name":"De Beco","first_name":"Simon","full_name":"De Beco, Simon"},{"full_name":"Gov, Nir","first_name":"Nir","last_name":"Gov"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"first_name":"Carolina","last_name":"Lage Crespo","full_name":"Lage Crespo, Carolina"},{"first_name":"Franziska","last_name":"Lautenschlaeger","full_name":"Lautenschlaeger, Franziska"},{"first_name":"Maël","last_name":"Le Berre","full_name":"Le Berre, Maël"},{"last_name":"Lennon Duménil","first_name":"Ana","full_name":"Lennon Duménil, Ana"},{"full_name":"Raab, Matthew","last_name":"Raab","first_name":"Matthew"},{"last_name":"Thiam","first_name":"Hawa","full_name":"Thiam, Hawa"},{"last_name":"Piel","first_name":"Matthieu","full_name":"Piel, Matthieu"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"last_name":"Voituriez","first_name":"Raphaël","full_name":"Voituriez, Raphaël"}],"publisher":"Cell Press","scopus_import":"1","type":"journal_article","ec_funded":1,"fulldoi":"https://doi.org/10.1016/j.cell.2015.01.056","volume":161,"page":"374 - 386","corr_author":"1","oa_version":"None","publication_status":"published","doi":"10.1016/j.cell.2015.01.056","quality_controlled":"1","article_processing_charge":"No","publication":"Cell","project":[{"call_identifier":"FWF","_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation"},{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"_id":"25ABD200-B435-11E9-9278-68D0E5697425","grant_number":"RGP0058/2011","name":"Cell migration in complex environments: from in vivo experiments to theoretical models"}],"abstract":[{"text":"Cell movement has essential functions in development, immunity, and cancer. Various cell migration patterns have been reported, but no general rule has emerged so far. Here, we show on the basis of experimental data in vitro and in vivo that cell persistence, which quantifies the straightness of trajectories, is robustly coupled to cell migration speed. We suggest that this universal coupling constitutes a generic law of cell migration, which originates in the advection of polarity cues by an actin cytoskeleton undergoing flows at the cellular scale. Our analysis relies on a theoretical model that we validate by measuring the persistence of cells upon modulation of actin flow speeds and upon optogenetic manipulation of the binding of an actin regulator to actin filaments. Beyond the quantitative prediction of the coupling, the model yields a generic phase diagram of cellular trajectories, which recapitulates the full range of observed migration patterns.","lang":"eng"}]},{"volume":12,"page":"207 - 210","oa_version":"Submitted Version","publication_status":"published","publisher":"Nature Publishing Group","scopus_import":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/","open_access":"1"}],"type":"journal_article","fulldoi":"https://doi.org/10.1038/nmeth.3279","quality_controlled":"1","article_processing_charge":"No","publication":"Nature Methods","abstract":[{"text":"The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species.","lang":"eng"}],"doi":"10.1038/nmeth.3279","title":"Reporters for sensitive and quantitative measurement of auxin response","publist_id":"5617","language":[{"iso":"eng"}],"_id":"1554","isi":1,"issue":"3","pmid":1,"day":"26","intvolume":"        12","date_published":"2015-02-26T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T10:34:32Z","external_id":{"isi":["000350670300017"],"pmid":["25643149"]},"month":"02","oa":1,"author":[{"full_name":"Liao, Cheyang","last_name":"Liao","first_name":"Cheyang"},{"first_name":"Wouter","last_name":"Smet","full_name":"Smet, Wouter"},{"last_name":"Brunoud","first_name":"Géraldine","full_name":"Brunoud, Géraldine"},{"full_name":"Yoshida, Saiko","first_name":"Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"}],"status":"public","year":"2015","date_created":"2018-12-11T11:52:41Z","citation":{"ieee":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters for sensitive and quantitative measurement of auxin response,” <i>Nature Methods</i>, vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015.","chicago":"Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux, and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” <i>Nature Methods</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nmeth.3279\">https://doi.org/10.1038/nmeth.3279</a>.","ista":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210.","apa":"Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., &#38; Weijers, D. (2015). Reporters for sensitive and quantitative measurement of auxin response. <i>Nature Methods</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nmeth.3279\">https://doi.org/10.1038/nmeth.3279</a>","short":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210.","ama":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive and quantitative measurement of auxin response. <i>Nature Methods</i>. 2015;12(3):207-210. doi:<a href=\"https://doi.org/10.1038/nmeth.3279\">10.1038/nmeth.3279</a>","mla":"Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” <i>Nature Methods</i>, vol. 12, no. 3, Nature Publishing Group, 2015, pp. 207–10, doi:<a href=\"https://doi.org/10.1038/nmeth.3279\">10.1038/nmeth.3279</a>."},"department":[{"_id":"JiFr"}]},{"doi":"10.1093/jxb/erv230","file":[{"date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:14:02Z","content_type":"application/pdf","access_level":"open_access","creator":"system","checksum":"257919be0ce3d306185d3891ad7acf39","file_name":"IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf","file_size":7753043,"file_id":"5051","relation":"main_file"}],"abstract":[{"text":"The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators.","lang":"eng"}],"pubrep_id":"480","publication":"Journal of Experimental Botany","article_processing_charge":"No","quality_controlled":"1","type":"journal_article","fulldoi":"https://doi.org/10.1093/jxb/erv230","scopus_import":"1","publisher":"Oxford University Press","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","publication_status":"published","volume":66,"page":"4631 - 4642","department":[{"_id":"JiFr"}],"year":"2015","date_created":"2018-12-11T11:52:42Z","citation":{"mla":"Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” <i>Journal of Experimental Botany</i>, vol. 66, no. 15, Oxford University Press, 2015, pp. 4631–42, doi:<a href=\"https://doi.org/10.1093/jxb/erv230\">10.1093/jxb/erv230</a>.","ama":"Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. <i>Journal of Experimental Botany</i>. 2015;66(15):4631-4642. doi:<a href=\"https://doi.org/10.1093/jxb/erv230\">10.1093/jxb/erv230</a>","apa":"Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., &#38; Ding, Z. (2015). The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erv230\">https://doi.org/10.1093/jxb/erv230</a>","short":"Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental Botany 66 (2015) 4631–4642.","chicago":"Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml, and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/jxb/erv230\">https://doi.org/10.1093/jxb/erv230</a>.","ista":"Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 66(15), 4631–4642.","ieee":"Y. Jia <i>et al.</i>, “The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development,” <i>Journal of Experimental Botany</i>, vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015."},"status":"public","author":[{"last_name":"Jia","first_name":"Yuebin","full_name":"Jia, Yuebin"},{"full_name":"Tian, Huiyu","last_name":"Tian","first_name":"Huiyu"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Hongjiang","orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang"},{"last_name":"Yu","first_name":"Qianqian","full_name":"Yu, Qianqian"},{"full_name":"Wang, Lei","first_name":"Lei","last_name":"Wang"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"full_name":"Ding, Zhaojun","first_name":"Zhaojun","last_name":"Ding"}],"oa":1,"has_accepted_license":"1","month":"08","external_id":{"isi":["000359687400017"]},"date_published":"2015-08-01T00:00:00Z","date_updated":"2025-09-23T13:42:27Z","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        66","file_date_updated":"2020-07-14T12:45:02Z","issue":"15","isi":1,"day":"01","_id":"1556","language":[{"iso":"eng"}],"publist_id":"5615","title":"The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development"},{"author":[{"first_name":"Fariba","last_name":"Javdani","full_name":"Javdani, Fariba"},{"last_name":"Holló","first_name":"Krisztina","full_name":"Holló, Krisztina"},{"last_name":"Hegedűs","first_name":"Krisztina","full_name":"Hegedűs, Krisztina"},{"full_name":"Kis, Gréta","first_name":"Gréta","last_name":"Kis"},{"last_name":"Hegyi","first_name":"Zoltán","full_name":"Hegyi, Zoltán"},{"first_name":"Klaudia","last_name":"Dócs","full_name":"Dócs, Klaudia"},{"full_name":"Kasugai, Yu","first_name":"Yu","last_name":"Kasugai"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"full_name":"Antal, Miklós","last_name":"Antal","first_name":"Miklós"}],"month":"09","external_id":{"isi":["000358228700006"]},"department":[{"_id":"RySh"}],"date_created":"2018-12-11T11:52:42Z","citation":{"mla":"Javdani, Fariba, et al. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” <i>Journal of Comparative Neurology</i>, vol. 523, no. 13, Wiley-Blackwell, 2015, pp. 1967–83, doi:<a href=\"https://doi.org/10.1002/cne.23774\">10.1002/cne.23774</a>.","ama":"Javdani F, Holló K, Hegedűs K, et al. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. <i>Journal of Comparative Neurology</i>. 2015;523(13):1967-1983. doi:<a href=\"https://doi.org/10.1002/cne.23774\">10.1002/cne.23774</a>","short":"F. Javdani, K. Holló, K. Hegedűs, G. Kis, Z. Hegyi, K. Dócs, Y. Kasugai, Y. Fukazawa, R. Shigemoto, M. Antal, Journal of Comparative Neurology 523 (2015) 1967–1983.","apa":"Javdani, F., Holló, K., Hegedűs, K., Kis, G., Hegyi, Z., Dócs, K., … Antal, M. (2015). Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. <i>Journal of Comparative Neurology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cne.23774\">https://doi.org/10.1002/cne.23774</a>","ista":"Javdani F, Holló K, Hegedűs K, Kis G, Hegyi Z, Dócs K, Kasugai Y, Fukazawa Y, Shigemoto R, Antal M. 2015. Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats. Journal of Comparative Neurology. 523(13), 1967–1983.","chicago":"Javdani, Fariba, Krisztina Holló, Krisztina Hegedűs, Gréta Kis, Zoltán Hegyi, Klaudia Dócs, Yu Kasugai, Yugo Fukazawa, Ryuichi Shigemoto, and Miklós Antal. “Differential Expression Patterns of K+Cl- Cotransporter 2 in Neurons within the Superficial Spinal Dorsal Horn of Rats.” <i>Journal of Comparative Neurology</i>. Wiley-Blackwell, 2015. <a href=\"https://doi.org/10.1002/cne.23774\">https://doi.org/10.1002/cne.23774</a>.","ieee":"F. Javdani <i>et al.</i>, “Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats,” <i>Journal of Comparative Neurology</i>, vol. 523, no. 13. Wiley-Blackwell, pp. 1967–1983, 2015."},"year":"2015","status":"public","day":"01","isi":1,"issue":"13","_id":"1557","language":[{"iso":"eng"}],"publist_id":"5614","title":"Differential expression patterns of K+Cl- cotransporter 2 in neurons within the superficial spinal dorsal horn of rats","date_published":"2015-09-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T08:26:48Z","intvolume":"       523","abstract":[{"text":"γ-Aminobutyric acid (GABA)- and glycine-mediated hyperpolarizing inhibition is associated with a chloride influx that depends on the inwardly directed chloride electrochemical gradient. In neurons, the extrusion of chloride from the cytosol primarily depends on the expression of an isoform of potassium-chloride cotransporters (KCC2s). KCC2 is crucial in the regulation of the inhibitory tone of neural circuits, including pain processing neural assemblies. Thus we investigated the cellular distribution of KCC2 in neurons underlying pain processing in the superficial spinal dorsal horn of rats by using high-resolution immunocytochemical methods. We demonstrated that perikarya and dendrites widely expressed KCC2, but axon terminals proved to be negative for KCC2. In single ultrathin sections, silver deposits labeling KCC2 molecules showed different densities on the surface of dendritic profiles, some of which were negative for KCC2. In freeze fracture replicas and tissue sections double stained for the β3-subunit of GABAA receptors and KCC2, GABAA receptors were revealed on dendritic segments with high and also with low KCC2 densities. By measuring the distances between spots immunoreactive for gephyrin (a scaffolding protein of GABAA and glycine receptors) and KCC2 on the surface of neurokinin 1 (NK1) receptor-immunoreactive dendrites, we found that gephyrin-immunoreactive spots were located at various distances from KCC2 cotransporters; 5.7 % of them were recovered in the middle of 4-10-μm-long dendritic segments that were free of KCC2 immunostaining. The variable local densities of KCC2 may result in variable postsynaptic potentials evoked by the activation of GABAA and glycine receptors along the dendrites of spinal neurons.","lang":"eng"}],"publication":"Journal of Comparative Neurology","article_processing_charge":"No","quality_controlled":"1","acknowledgement":"Funded by:\r\nHungarian Academy of Sciences. Grant Number: MTA-TKI 242\r\nHungarian Brain Research Program. Grant Number: KTIA_NAP_13-1-2013-0001\r\nSolution Oriented Research for Science and Technology from the Japan Science and Technology Agency Japanese Ministry of Education, Culture, Sports, Science and Technology","doi":"10.1002/cne.23774","publication_status":"published","oa_version":"None","page":"1967 - 1983","volume":523,"fulldoi":"https://doi.org/10.1002/cne.23774","type":"journal_article","scopus_import":"1","publisher":"Wiley-Blackwell"}]