[{"date_published":"2013-01-01T00:00:00Z","author":[{"first_name":"Anika","last_name":"Steffen","full_name":"Steffen, Anika"},{"first_name":"Markus","last_name":"Ladwein","full_name":"Ladwein, Markus"},{"full_name":"Georgi Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A","last_name":"Dimchev"},{"full_name":"Hein, Anke","first_name":"Anke","last_name":"Hein"},{"last_name":"Schwenkmezger","first_name":"Lisa","full_name":"Schwenkmezger, Lisa"},{"full_name":"Arens, Stefan","first_name":"Stefan","last_name":"Arens"},{"first_name":"Kathrin","last_name":"Ladwein","full_name":"Ladwein, Kathrin I"},{"last_name":"Holleboom","first_name":"J.","full_name":"Holleboom, J. Margit"},{"first_name":"Florian","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Florian Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Small, John V","first_name":"John","last_name":"Small"},{"full_name":"Schwarz, Janett","last_name":"Schwarz","first_name":"Janett"},{"full_name":"Gerhard, Ralf","first_name":"Ralf","last_name":"Gerhard"},{"last_name":"Faix","first_name":"Jan","full_name":"Faix, Jan"},{"first_name":"Theresia","last_name":"Stradal","full_name":"Stradal, Theresia E"},{"last_name":"Brakebusch","first_name":"Cord","full_name":"Brakebusch, Cord H"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"}],"doi":"10.1242/jcs.118232","date_updated":"2021-01-12T08:16:57Z","abstract":[{"text":"Cell migration is commonly accompanied by protrusion of membrane ruffles and lamellipodia. In two-dimensional migration, protrusion of these thin sheets of cytoplasm is considered relevant to both exploration of new space and initiation of nascent adhesion to the substratum. Lamellipodium formation can be potently stimulated by Rho GTPases of the Rac subfamily, but alsoby RhoG or Cdc42. Here we describe viable fibroblast cell lines geneticallydeficient for Rac1 that lack detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent lamellipodia, but these structures were restored by expression of either Rac subfamily member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction in wound closure and random cell migration and a notable loss of sensitivity to a chemotactic gradient. Despite these defects, Rac-deficient cells were able to spread, formed filopodia and established focal adhesions. Spreading in these cells was achieved by the extension of filopodia followed by the advancement of cytoplasmic veils between them. The number and size of focal adhesions as well as their intensity were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased the mobility of different components in focal adhesions, potentially explaining how Rac - although not essential - can contribute to focal adhesion assembly. Together, our data demonstrate that Rac signaling is essential for lamellipodium protrusion and for efficient cell migration, but not for spreading or filopodium formation. Our findings also suggest that Rac GTPases are crucial to the establishment or maintenance of polarity in chemotactic migration.","lang":"eng"}],"extern":1,"quality_controlled":0,"publication":"Journal of Cell Science","title":"Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation","publisher":"Company of Biologists","date_created":"2018-12-11T11:48:38Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publist_id":"6840","status":"public","acknowledgement":"This work was supported in part by the Deutsche Forschungsgemeinschaft [grants within programs SFB621 to K.R., and FOR629 and SFB629 to T.E.B.S.]. Deposited in PMC for immediate release.\nWe thank Brigitte Denker and Gerd Landsberg for excellent technical assistance. We are grateful to Robert Geffers (HZI Braunschweig, Germany) for microarray analyses and to Mirko Himmel (UKE Hamburg, Germany) for valuable advice on FRAP analysis.","issue":"20","day":"01","citation":{"mla":"Steffen, Anika, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” <i>Journal of Cell Science</i>, vol. 126, no. 20, Company of Biologists, 2013, pp. 4572–88, doi:<a href=\"https://doi.org/10.1242/jcs.118232\">10.1242/jcs.118232</a>.","short":"A. Steffen, M. Ladwein, G.A. Dimchev, A. Hein, L. Schwenkmezger, S. Arens, K. Ladwein, J. Holleboom, F.K. Schur, J. Small, J. Schwarz, R. Gerhard, J. Faix, T. Stradal, C. Brakebusch, K. Rottner, Journal of Cell Science 126 (2013) 4572–4588.","ista":"Steffen A, Ladwein M, Dimchev GA, Hein A, Schwenkmezger L, Arens S, Ladwein K, Holleboom J, Schur FK, Small J, Schwarz J, Gerhard R, Faix J, Stradal T, Brakebusch C, Rottner K. 2013. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. Journal of Cell Science. 126(20), 4572–4588.","ama":"Steffen A, Ladwein M, Dimchev GA, et al. Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. <i>Journal of Cell Science</i>. 2013;126(20):4572-4588. doi:<a href=\"https://doi.org/10.1242/jcs.118232\">10.1242/jcs.118232</a>","apa":"Steffen, A., Ladwein, M., Dimchev, G. A., Hein, A., Schwenkmezger, L., Arens, S., … Rottner, K. (2013). Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.118232\">https://doi.org/10.1242/jcs.118232</a>","ieee":"A. Steffen <i>et al.</i>, “Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation,” <i>Journal of Cell Science</i>, vol. 126, no. 20. Company of Biologists, pp. 4572–4588, 2013.","chicago":"Steffen, Anika, Markus Ladwein, Georgi A Dimchev, Anke Hein, Lisa Schwenkmezger, Stefan Arens, Kathrin Ladwein, et al. “Rac Function Is Crucial for Cell Migration but Is Not Required for Spreading and Focal Adhesion Formation.” <i>Journal of Cell Science</i>. Company of Biologists, 2013. <a href=\"https://doi.org/10.1242/jcs.118232\">https://doi.org/10.1242/jcs.118232</a>."},"month":"01","volume":126,"page":"4572 - 4588","type":"journal_article","intvolume":"       126","_id":"811","year":"2013","publication_status":"published"},{"volume":24,"page":"2861 - 2875","type":"journal_article","_id":"812","intvolume":"        24","year":"2013","publication_status":"published","acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft Grants RO2414/3-1 (to K.R.) and FA330/6-1 (to J.F.), Austrian \nScience Fund Projects FWF 1516-B09 and FWF P21292-B09 (to  J.V.S.),  the Vienna  Science  and  Technology  Fund  (WWTF,  to \nJ.V.S.  and  C.S.),  and  Australian  National  Health  and  Medical \nResearch Council Grant APP1004175 (to P.W.G.). We thank J. Adams, \nR. Chisholm, A. Hall, L. Machesky, H. G. Mannherz, D. Schafer, and \nR.   Wedlich-Söldner   for   expression   constructs   and   B.   Denker, \nP. Hagendorff, and G. Landsberg for technical assistance.","status":"public","issue":"18","day":"15","citation":{"ama":"Koestler S, Steffen A, Nemethova M, et al. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. <i>Molecular Biology of the Cell</i>. 2013;24(18):2861-2875. doi:<a href=\"https://doi.org/10.1091/mbc.E12-12-0857\">10.1091/mbc.E12-12-0857</a>","short":"S. Koestler, A. Steffen, M. Nemethova, M. Winterhoff, N. Luo, J. Holleboom, J. Krupp, S. Jacob, M. Vinzenz, F.K. Schur, K. Schlüter, P. Gunning, C. Winkler, C. Schmeiser, J. Faix, T. Stradal, J. Small, K. Rottner, Molecular Biology of the Cell 24 (2013) 2861–2875.","ista":"Koestler S, Steffen A, Nemethova M, Winterhoff M, Luo N, Holleboom J, Krupp J, Jacob S, Vinzenz M, Schur FK, Schlüter K, Gunning P, Winkler C, Schmeiser C, Faix J, Stradal T, Small J, Rottner K. 2013. Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. Molecular Biology of the Cell. 24(18), 2861–2875.","mla":"Koestler, Stefan, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” <i>Molecular Biology of the Cell</i>, vol. 24, no. 18, American Society for Biology, 2013, pp. 2861–75, doi:<a href=\"https://doi.org/10.1091/mbc.E12-12-0857\">10.1091/mbc.E12-12-0857</a>.","chicago":"Koestler, Stefan, Anika Steffen, Maria Nemethova, Moritz Winterhoff, Ningning Luo, J. Holleboom, Jessica Krupp, et al. “Arp2/3 Complex Is Essential for Actin Network Treadmilling as Well as for Targeting of Capping Protein and Cofilin.” <i>Molecular Biology of the Cell</i>. American Society for Biology, 2013. <a href=\"https://doi.org/10.1091/mbc.E12-12-0857\">https://doi.org/10.1091/mbc.E12-12-0857</a>.","ieee":"S. Koestler <i>et al.</i>, “Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin,” <i>Molecular Biology of the Cell</i>, vol. 24, no. 18. American Society for Biology, pp. 2861–2875, 2013.","apa":"Koestler, S., Steffen, A., Nemethova, M., Winterhoff, M., Luo, N., Holleboom, J., … Rottner, K. (2013). Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin. <i>Molecular Biology of the Cell</i>. American Society for Biology. <a href=\"https://doi.org/10.1091/mbc.E12-12-0857\">https://doi.org/10.1091/mbc.E12-12-0857</a>"},"month":"09","publication":"Molecular Biology of the Cell","title":"Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin","publisher":"American Society for Biology","date_created":"2018-12-11T11:48:38Z","publist_id":"6841","date_published":"2013-09-15T00:00:00Z","author":[{"first_name":"Stefan","last_name":"Koestler","full_name":"Koestler, Stefan A"},{"first_name":"Anika","last_name":"Steffen","full_name":"Steffen, Anika"},{"last_name":"Nemethova","first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Maria Nemethova"},{"full_name":"Winterhoff, Moritz","last_name":"Winterhoff","first_name":"Moritz"},{"last_name":"Luo","first_name":"Ningning","full_name":"Luo, Ningning"},{"full_name":"Holleboom, J. Margit","first_name":"J.","last_name":"Holleboom"},{"last_name":"Krupp","first_name":"Jessica","full_name":"Krupp, Jessica"},{"last_name":"Jacob","first_name":"Sonja","full_name":"Jacob, Sonja"},{"full_name":"Vinzenz, Marlene","last_name":"Vinzenz","first_name":"Marlene"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Florian Schur"},{"full_name":"Schlüter, Kai","last_name":"Schlüter","first_name":"Kai"},{"full_name":"Gunning, Peter W","last_name":"Gunning","first_name":"Peter"},{"first_name":"Christoph","last_name":"Winkler","full_name":"Winkler, Christoph"},{"first_name":"Christian","last_name":"Schmeiser","full_name":"Schmeiser, Christian"},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"},{"full_name":"Stradal, Theresia E","last_name":"Stradal","first_name":"Theresia"},{"full_name":"Small, John V","last_name":"Small","first_name":"John"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"}],"doi":"10.1091/mbc.E12-12-0857","date_updated":"2021-01-12T08:17:00Z","abstract":[{"lang":"eng","text":"Lamellipodia are sheet-like protrusions formed during migration or phagocytosis and comprise a network of actin filaments. Filament formation in this network is initiated by nucleation/branching through the actin-related protein 2/3 (Arp2/3) complex downstream of its activator, suppressor of cAMP receptor/WASP-family verprolin homologous (Scar/WAVE), but the relative relevance of Arp2/3-mediated branching versus actin filament elongation is unknown. Here we use instantaneous interference with Arp2/3 complex function in live fibroblasts with established lamellipodia. This allows direct examination of both the fate of elongating filaments upon instantaneous suppression of Arp2/3 complex activity and the consequences of this treatment on the dynamics of other lamellipodial regulators. We show that Arp2/3 complex is an essential organizer of treadmilling actin filament arrays but has little effect on the net rate of actin filament turnover at the cell periphery. In addition, Arp2/3 complex serves as key upstream factor for the recruitment of modulators of lamellipodia formation such as capping protein or cofilin. Arp2/3 complex is thus decisive for filament organization and geometry within the network not only by generating branches and novel filament ends, but also by directing capping or severing activities to the lamellipodium. Arp2/3 complex is also crucial to lamellipodia-based migration of keratocytes."}],"extern":1,"quality_controlled":0},{"extern":"1","abstract":[{"lang":"eng","text":"Background: Monoclonal antibodies (mAb), such as trastuzumab are a valuable addition to breast cancer therapy.\r\nData obtained from neoadjuvant settings revealed that antibody-dependent cell-mediated cytotoxicity (ADCC) is a\r\nmajor mechanism of action for the mAb trastuzumab. Conflicting results still call into question whether disease\r\nprogression, prolonged treatment or concomitant chemotherapy influences ADCC and related immunological\r\nphenomena.\r\nMethods: We analyzed the activity of ADCC and antibody-dependent cell-mediated phagocytosis (ADCP) of\r\nperipheral blood mononuclear cells (PBMCs) from human epidermal growth factor receptor 2 (HER2/neu) positive\r\nbreast cancer patients receiving trastuzumab therapy either in an adjuvant (n = 13) or metastatic (n = 15) setting as\r\nwell as from trastuzumab treatment-naive (t-naive) HER2/neu negative patients (n = 15). PBMCs from healthy volunteers\r\n(n = 24) were used as controls. ADCC and ADCP activity was correlated with the expression of antibody binding\r\nFc-gamma receptor (FcγR)I (CD64), FcγRII (CD32) and FcγRIII (CD16) on CD14+ (monocytes) and CD56+ (NK) cells, as well as the expression of CD107a+ (LAMP-1) on CD56+ cells and the total amount of CD4+CD25+FOXP3+ (Treg) cells. In metastatic patients, markers were correlated with progression-free survival (PFS).\r\nResults: ADCC activity was significantly down regulated in metastatic, adjuvant and t-naive patient cohorts as compared to healthy controls. Reduced ADCC activity was inversely correlated with the expression of CD107a on CD56+\r\ncells in adjuvant patients. ADCC and ADCP activity of the patient cohorts were similar, regardless of treatment duration\r\nor additional chemotherapy. PFS in metastatic patients inversely correlated with the number of peripheral Treg cells.\r\nConclusion: The reduction of ADCC in patients as compared to healthy controls calls for adjuvant strategies, such as\r\nimmune-enhancing agents, to improve the activity of trastuzumab. However, efficacy of trastuzumab-specific ADCC\r\nand ADCP appears not to be affected by treatment duration, disease progression or concomitant chemotherapy. This\r\nfinding supports the application of trastuzumab at any stage of the disease."}],"publisher":"Springer Nature","publication":"Journal of Translational Medicine","title":"Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients","date_created":"2020-08-10T11:54:34Z","oa_version":"None","external_id":{"pmid":["24330813"]},"oa":1,"status":"public","publication_identifier":{"issn":["1479-5876"]},"citation":{"mla":"Petricevic, Branka, et al. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” <i>Journal of Translational Medicine</i>, vol. 11, 307, Springer Nature, 2013, doi:<a href=\"https://doi.org/10.1186/1479-5876-11-307\">10.1186/1479-5876-11-307</a>.","short":"B. Petricevic, J. Laengle, J. Singer, M. Sachet, J. Singer, G. Steger, R. Bartsch, E. Jensen-Jarolim, M. Bergmann, Journal of Translational Medicine 11 (2013).","ista":"Petricevic B, Laengle J, Singer J, Sachet M, Singer J, Steger G, Bartsch R, Jensen-Jarolim E, Bergmann M. 2013. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. Journal of Translational Medicine. 11, 307.","ama":"Petricevic B, Laengle J, Singer J, et al. Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. <i>Journal of Translational Medicine</i>. 2013;11. doi:<a href=\"https://doi.org/10.1186/1479-5876-11-307\">10.1186/1479-5876-11-307</a>","apa":"Petricevic, B., Laengle, J., Singer, J., Sachet, M., Singer, J., Steger, G., … Bergmann, M. (2013). Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients. <i>Journal of Translational Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1186/1479-5876-11-307\">https://doi.org/10.1186/1479-5876-11-307</a>","ieee":"B. Petricevic <i>et al.</i>, “Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients,” <i>Journal of Translational Medicine</i>, vol. 11. Springer Nature, 2013.","chicago":"Petricevic, Branka, Johannes Laengle, Josef Singer, Monika Sachet, Judit Singer, Guenther Steger, Rupert Bartsch, Erika Jensen-Jarolim, and Michael Bergmann. “Trastuzumab Mediates Antibody-Dependent Cell-Mediated Cytotoxicity and Phagocytosis to the Same Extent in Both Adjuvant and Metastatic HER2/Neu Breast Cancer Patients.” <i>Journal of Translational Medicine</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1186/1479-5876-11-307\">https://doi.org/10.1186/1479-5876-11-307</a>."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":11,"has_accepted_license":"1","year":"2013","_id":"8245","article_processing_charge":"No","doi":"10.1186/1479-5876-11-307","date_updated":"2022-08-25T14:52:39Z","date_published":"2013-12-12T00:00:00Z","author":[{"first_name":"Branka","last_name":"Petricevic","full_name":"Petricevic, Branka"},{"full_name":"Laengle, Johannes","last_name":"Laengle","first_name":"Johannes"},{"first_name":"Josef","last_name":"Singer","full_name":"Singer, Josef"},{"first_name":"Monika","last_name":"Sachet","full_name":"Sachet, Monika"},{"first_name":"Judit","orcid":"0000-0002-8777-3502","last_name":"Fazekas","full_name":"Fazekas, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Guenther","last_name":"Steger","full_name":"Steger, Guenther"},{"last_name":"Bartsch","first_name":"Rupert","full_name":"Bartsch, Rupert"},{"first_name":"Erika","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika"},{"last_name":"Bergmann","first_name":"Michael","full_name":"Bergmann, Michael"}],"quality_controlled":"1","article_number":"307","file_date_updated":"2020-08-10T13:45:19Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"ddc":["570"],"day":"12","pmid":1,"month":"12","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by/3.0/","file":[{"file_size":777311,"file_name":"2013_JoTM_Petricevic.pdf","file_id":"8247","date_updated":"2020-08-10T13:45:19Z","content_type":"application/pdf","date_created":"2020-08-10T13:45:19Z","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access"}],"publication_status":"published","intvolume":"        11"},{"intvolume":"         4","publication_status":"published","file":[{"file_id":"5903","date_updated":"2020-07-14T12:48:11Z","file_name":"2013_FrontiersPlant_OBrien.pdf","checksum":"fdc25ddd1bf9a99b99f662cdbafeddd4","file_size":953299,"access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2019-01-31T10:40:38Z","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"month":"11","day":"19","ddc":["580"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:48:11Z","article_number":"451","scopus_import":1,"quality_controlled":"1","author":[{"full_name":"O'Brien, José","last_name":"O'Brien","first_name":"José"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"date_published":"2013-11-19T00:00:00Z","doi":"10.3389/fpls.2013.00451","date_updated":"2021-01-12T08:17:50Z","_id":"827","year":"2013","has_accepted_license":"1","volume":4,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>","mla":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>, vol. 4, 451, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>.","short":"J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).","ista":"O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 4, 451.","ieee":"J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","chicago":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>.","apa":"O’Brien, J., &#38; Benková, E. (2013). Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>"},"oa":1,"status":"public","oa_version":"Published Version","date_created":"2018-12-11T11:48:43Z","ec_funded":1,"publist_id":"6821","department":[{"_id":"EvBe"}],"title":"Cytokinin cross talking during biotic and abiotic stress responses","publication":"Frontiers in Plant Science","publisher":"Frontiers Research Foundation","abstract":[{"lang":"eng","text":"As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed."}]},{"month":"12","project":[{"name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"ddc":["580"],"day":"26","file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_created":"2019-01-31T10:36:43Z","date_updated":"2020-07-14T12:48:11Z","file_id":"5902","file_size":710835,"file_name":"2013_FrontiersPlant_Cuesta.pdf","checksum":"0185b3c4d7df9a94bd3ce5a66d213506"}],"publication_status":"published","intvolume":"         4","quality_controlled":"1","scopus_import":1,"doi":"10.3389/fpls.2013.00537","date_updated":"2021-01-12T08:17:52Z","date_published":"2013-12-26T00:00:00Z","author":[{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","last_name":"Cuesta","first_name":"Candela"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","last_name":"Wabnik","first_name":"Krzysztof T"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"537","file_date_updated":"2020-07-14T12:48:11Z","citation":{"chicago":"Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>.","ieee":"C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","apa":"Cuesta, C., Wabnik, K. T., &#38; Benková, E. (2013). Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>","ama":"Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>","ista":"Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 4, 537.","short":"C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013).","mla":"Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>, vol. 4, 537, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>."},"oa":1,"status":"public","has_accepted_license":"1","year":"2013","_id":"828","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":4,"abstract":[{"lang":"eng","text":"The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed."}],"publist_id":"6820","ec_funded":1,"date_created":"2018-12-11T11:48:43Z","oa_version":"Published Version","publisher":"Frontiers Research Foundation","publication":"Frontiers in Plant Science","department":[{"_id":"EvBe"}],"title":"Systems approaches to study root architecture dynamics"},{"volume":76,"page":"446 - 455","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"830","year":"2013","acknowledgement":"The project and F.G. were supported by the CARIPLO Foundation (project 2009-2990) and COST (European Cooperation in Science and Technology) action HAPRECI (Harnessing Plant Reproduction for Crop Improvement). E.B. and C.C. were supported by the European Research Council through a ‘Starting Independent Research’ grant (ERC-2007-Stg-207362-HCPO). We thank A.P. MacCabe (Consejo Superior de Investigaciones Científicas, Valencia, Spain) for critical reading of the manuscript.","status":"public","issue":"3","external_id":{"pmid":["23941199"]},"article_type":"original","citation":{"ama":"Galbiati F, Sinha Roy D, Simonini S, et al. An integrative model of the control of ovule primordia formation. <i>The Plant journal for cell and molecular biology</i>. 2013;76(3):446-455. doi:<a href=\"https://doi.org/10.1111/tpj.12309\">10.1111/tpj.12309</a>","mla":"Galbiati, Francesca, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” <i>The Plant Journal for Cell and Molecular Biology</i>, vol. 76, no. 3, Wiley-Blackwell, 2013, pp. 446–55, doi:<a href=\"https://doi.org/10.1111/tpj.12309\">10.1111/tpj.12309</a>.","short":"F. Galbiati, D. Sinha Roy, S. Simonini, M. Cucinotta, L. Ceccato, C. Cuesta, M. Šimášková, E. Benková, Y. Kamiuchi, M. Aida, D. Weijers, R. Simon, S. Masiero, L. Colombo, The Plant Journal for Cell and Molecular Biology 76 (2013) 446–455.","ista":"Galbiati F, Sinha Roy D, Simonini S, Cucinotta M, Ceccato L, Cuesta C, Šimášková M, Benková E, Kamiuchi Y, Aida M, Weijers D, Simon R, Masiero S, Colombo L. 2013. An integrative model of the control of ovule primordia formation. The Plant journal for cell and molecular biology. 76(3), 446–455.","chicago":"Galbiati, Francesca, Dola Sinha Roy, Sara Simonini, Mara Cucinotta, Luca Ceccato, Candela Cuesta, Mária Šimášková, et al. “An Integrative Model of the Control of Ovule Primordia Formation.” <i>The Plant Journal for Cell and Molecular Biology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/tpj.12309\">https://doi.org/10.1111/tpj.12309</a>.","ieee":"F. Galbiati <i>et al.</i>, “An integrative model of the control of ovule primordia formation,” <i>The Plant journal for cell and molecular biology</i>, vol. 76, no. 3. Wiley-Blackwell, pp. 446–455, 2013.","apa":"Galbiati, F., Sinha Roy, D., Simonini, S., Cucinotta, M., Ceccato, L., Cuesta, C., … Colombo, L. (2013). An integrative model of the control of ovule primordia formation. <i>The Plant Journal for Cell and Molecular Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/tpj.12309\">https://doi.org/10.1111/tpj.12309</a>"},"publication":"The Plant journal for cell and molecular biology","title":"An integrative model of the control of ovule primordia formation","publisher":"Wiley-Blackwell","date_created":"2018-12-11T11:48:44Z","oa_version":"None","publist_id":"6818","abstract":[{"lang":"eng","text":"Upon hormonal signaling, ovules develop as lateral organs from the placenta. Ovule numbers ultimately determine the number of seeds that develop, and thereby contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule primordia formation. We show that expression of the CUC1 and CUC2 genes is required to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required for ovule primordia formation. Furthermore, our results suggest that the auxin response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and promote their transcription. Based on our findings, we propose an integrative model to describe the molecular mechanisms of the early stages of ovule development."}],"extern":"1","intvolume":"        76","publication_status":"published","pmid":1,"day":"19","month":"09","language":[{"iso":"eng"}],"date_published":"2013-09-19T00:00:00Z","author":[{"full_name":"Galbiati, Francesca","last_name":"Galbiati","first_name":"Francesca"},{"last_name":"Sinha Roy","first_name":"Dola","full_name":"Sinha Roy, Dola"},{"full_name":"Simonini, Sara","first_name":"Sara","last_name":"Simonini"},{"first_name":"Mara","last_name":"Cucinotta","full_name":"Cucinotta, Mara"},{"first_name":"Luca","last_name":"Ceccato","full_name":"Ceccato, Luca"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","last_name":"Cuesta","first_name":"Candela"},{"first_name":"Mária","last_name":"Šimášková","full_name":"Šimášková, Mária"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"last_name":"Kamiuchi","first_name":"Yuri","full_name":"Kamiuchi, Yuri"},{"full_name":"Aida, Mitsuhiro","last_name":"Aida","first_name":"Mitsuhiro"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"full_name":"Simon, Rüdiger","first_name":"Rüdiger","last_name":"Simon"},{"last_name":"Masiero","first_name":"Simona","full_name":"Masiero, Simona"},{"full_name":"Colombo, Lucia","last_name":"Colombo","first_name":"Lucia"}],"article_processing_charge":"No","doi":"10.1111/tpj.12309","date_updated":"2022-03-21T07:17:26Z","scopus_import":"1","quality_controlled":"1"},{"publisher":"Nature Publishing Group","publication":"Molecular Systems Biology","title":"Sequential induction of auxin efflux and influx carriers regulates lateral root emergence","publist_id":"6817","date_created":"2018-12-11T11:48:44Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"doi":"10.1038/msb.2013.43","date_updated":"2021-01-12T08:18:03Z","author":[{"last_name":"Péret","first_name":"Benjamin","full_name":"Péret, Benjamin"},{"last_name":"Middleton","first_name":"Alistair","full_name":"Middleton, Alistair M"},{"last_name":"French","first_name":"Andrew","full_name":"French, Andrew P"},{"full_name":"Larrieu, Antoine","first_name":"Antoine","last_name":"Larrieu"},{"full_name":"Bishopp, Anthony","first_name":"Anthony","last_name":"Bishopp"},{"full_name":"Njo, Maria","first_name":"Maria","last_name":"Njo"},{"full_name":"Wells, Darren M","last_name":"Wells","first_name":"Darren"},{"full_name":"Porco, Silvana","last_name":"Porco","first_name":"Silvana"},{"full_name":"Mellor, Nathan","last_name":"Mellor","first_name":"Nathan"},{"first_name":"Leah","last_name":"Band","full_name":"Band, Leah R"},{"full_name":"Casimiro, Ilda","first_name":"Ilda","last_name":"Casimiro"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"first_name":"Ilkka","last_name":"Sairanen","full_name":"Sairanen, Ilkka"},{"full_name":"Mallet, Romain","last_name":"Mallet","first_name":"Romain"},{"full_name":"Sandberg, Göran","last_name":"Sandberg","first_name":"Göran"},{"last_name":"Ljung","first_name":"Karin","full_name":"Ljung, Karin"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková"},{"full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"full_name":"Kramer, Eric","last_name":"Kramer","first_name":"Eric"},{"first_name":"John","last_name":"King","full_name":"King, John R"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"},{"full_name":"Pridmore, Tony","last_name":"Pridmore","first_name":"Tony"},{"full_name":"Owen, Markus","first_name":"Markus","last_name":"Owen"},{"full_name":"Bennett, Malcolm J","first_name":"Malcolm","last_name":"Bennett"}],"date_published":"2013-10-22T00:00:00Z","extern":1,"quality_controlled":0,"abstract":[{"text":"In Arabidopsis, lateral roots originate from pericycle cells deep within the primary root. New lateral root primordia (LRP) have to emerge through several overlaying tissues. Here, we report that auxin produced in new LRP is transported towards the outer tissues where it triggers cell separation by inducing both the auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two cell files overlaying new LRP. To understand how this striking pattern of LAX3 expression is regulated, we developed a mathematical model that captures the network regulating its expression and auxin transport within realistic three-dimensional cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression to be robust to natural variations in root tissue geometry, an efflux carrier is required--later identified to be PIN3. To prevent LAX3 from being transiently expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively, which we later demonstrated to be the case. Our study exemplifies how mathematical models can be used to direct experiments to elucidate complex developmental processes.","lang":"eng"}],"type":"journal_article","volume":9,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","year":"2013","publication_status":"published","_id":"831","intvolume":"         9","day":"22","acknowledgement":"This work was supported by an FEBS Long‐Term Fellowship (BP), an Intra‐European Fellowship for Career Development under the 7th framework of the European Commission (IEF‐2008‐220506 to BP), an EMBO Long‐Term Fellowship (BP), an European Reintegration Grant under the 7th framework of the European Commission (ERG‐2010‐276662 to BP) and the Swedish Research Council (VR 621‐2010‐5720 to IS, GS and KL). AMM, APF, AL, LRB, SP, NM, DMW, MO, JRK and MJB acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC) and Engineering and Physical Sciences Research Council (EPSRC) funding to the Centre for Plant Integrative Biology (CPIB); BBSRC Professorial Research Fellowship funding to DMW and MJB; Belgian Scientific policy (BELSPO contract MARS) to TB and MJB. We thank Bert de Rybel for his help in Multisite Gateway cloning.","status":"public","month":"10","citation":{"ama":"Péret B, Middleton A, French A, et al. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. <i>Molecular Systems Biology</i>. 2013;9. doi:<a href=\"https://doi.org/10.1038/msb.2013.43\">10.1038/msb.2013.43</a>","mla":"Péret, Benjamin, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” <i>Molecular Systems Biology</i>, vol. 9, Nature Publishing Group, 2013, doi:<a href=\"https://doi.org/10.1038/msb.2013.43\">10.1038/msb.2013.43</a>.","ista":"Péret B, Middleton A, French A, Larrieu A, Bishopp A, Njo M, Wells D, Porco S, Mellor N, Band L, Casimiro I, Kleine Vehn J, Vanneste S, Sairanen I, Mallet R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King J, De Smet I, Pridmore T, Owen M, Bennett M. 2013. Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Molecular Systems Biology. 9.","short":"B. Péret, A. Middleton, A. French, A. Larrieu, A. Bishopp, M. Njo, D. Wells, S. Porco, N. Mellor, L. Band, I. Casimiro, J. Kleine Vehn, S. Vanneste, I. Sairanen, R. Mallet, G. Sandberg, K. Ljung, T. Beeckman, E. Benková, J. Friml, E. Kramer, J. King, I. De Smet, T. Pridmore, M. Owen, M. Bennett, Molecular Systems Biology 9 (2013).","chicago":"Péret, Benjamin, Alistair Middleton, Andrew French, Antoine Larrieu, Anthony Bishopp, Maria Njo, Darren Wells, et al. “Sequential Induction of Auxin Efflux and Influx Carriers Regulates Lateral Root Emergence.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/msb.2013.43\">https://doi.org/10.1038/msb.2013.43</a>.","ieee":"B. Péret <i>et al.</i>, “Sequential induction of auxin efflux and influx carriers regulates lateral root emergence,” <i>Molecular Systems Biology</i>, vol. 9. Nature Publishing Group, 2013.","apa":"Péret, B., Middleton, A., French, A., Larrieu, A., Bishopp, A., Njo, M., … Bennett, M. (2013). Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/msb.2013.43\">https://doi.org/10.1038/msb.2013.43</a>"}},{"page":"263-280","volume":57,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        57","_id":"8461","publication_status":"published","year":"2013","status":"public","day":"09","article_type":"original","issue":"3","citation":{"mla":"Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” <i>Journal of Biomolecular NMR</i>, vol. 57, no. 3, Springer Nature, 2013, pp. 263–80, doi:<a href=\"https://doi.org/10.1007/s10858-013-9787-x\">10.1007/s10858-013-9787-x</a>.","ista":"Haller JD, Schanda P. 2013. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. Journal of Biomolecular NMR. 57(3), 263–280.","short":"J.D. Haller, P. Schanda, Journal of Biomolecular NMR 57 (2013) 263–280.","ama":"Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. <i>Journal of Biomolecular NMR</i>. 2013;57(3):263-280. doi:<a href=\"https://doi.org/10.1007/s10858-013-9787-x\">10.1007/s10858-013-9787-x</a>","apa":"Haller, J. D., &#38; Schanda, P. (2013). Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. <i>Journal of Biomolecular NMR</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10858-013-9787-x\">https://doi.org/10.1007/s10858-013-9787-x</a>","chicago":"Haller, Jens D., and Paul Schanda. “Amplitudes and Time Scales of Picosecond-to-Microsecond Motion in Proteins Studied by Solid-State NMR: A Critical Evaluation of Experimental Approaches and Application to Crystalline Ubiquitin.” <i>Journal of Biomolecular NMR</i>. Springer Nature, 2013. <a href=\"https://doi.org/10.1007/s10858-013-9787-x\">https://doi.org/10.1007/s10858-013-9787-x</a>.","ieee":"J. D. Haller and P. Schanda, “Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin,” <i>Journal of Biomolecular NMR</i>, vol. 57, no. 3. Springer Nature, pp. 263–280, 2013."},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0925-2738","1573-5001"]},"month":"10","title":"Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin","publication":"Journal of Biomolecular NMR","publisher":"Springer Nature","oa_version":"None","date_created":"2020-09-18T10:09:05Z","date_published":"2013-10-09T00:00:00Z","author":[{"full_name":"Haller, Jens D.","last_name":"Haller","first_name":"Jens D."},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"}],"date_updated":"2021-01-12T08:19:26Z","doi":"10.1007/s10858-013-9787-x","article_processing_charge":"No","abstract":[{"text":"Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps–μs motions in proteins by solid-state NMR.","lang":"eng"}],"keyword":["Spectroscopy","Biochemistry"],"extern":"1","quality_controlled":"1"},{"status":"public","day":"09","article_type":"original","issue":"15","citation":{"ama":"Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. <i>Journal of Molecular Biology</i>. 2013;425(15):2722-2736. doi:<a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">10.1016/j.jmb.2013.04.028</a>","ista":"Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15), 2722–2736.","short":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736.","mla":"Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” <i>Journal of Molecular Biology</i>, vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:<a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">10.1016/j.jmb.2013.04.028</a>.","ieee":"E. Rennella <i>et al.</i>, “Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure,” <i>Journal of Molecular Biology</i>, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013.","chicago":"Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” <i>Journal of Molecular Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">https://doi.org/10.1016/j.jmb.2013.04.028</a>.","apa":"Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., … Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">https://doi.org/10.1016/j.jmb.2013.04.028</a>"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-2836"]},"month":"08","page":"2722-2736","volume":425,"type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":"       425","_id":"8462","publication_status":"published","year":"2013","author":[{"last_name":"Rennella","first_name":"E.","full_name":"Rennella, E."},{"full_name":"Cutuil, T.","last_name":"Cutuil","first_name":"T."},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606"},{"last_name":"Ayala","first_name":"I.","full_name":"Ayala, I."},{"full_name":"Gabel, F.","first_name":"F.","last_name":"Gabel"},{"full_name":"Forge, V.","last_name":"Forge","first_name":"V."},{"last_name":"Corazza","first_name":"A.","full_name":"Corazza, A."},{"last_name":"Esposito","first_name":"G.","full_name":"Esposito, G."},{"first_name":"B.","last_name":"Brutscher","full_name":"Brutscher, B."}],"date_published":"2013-08-09T00:00:00Z","doi":"10.1016/j.jmb.2013.04.028","date_updated":"2022-08-25T14:56:24Z","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The transition of proteins from their soluble functional state to amyloid fibrils and aggregates is associated with the onset of several human diseases. Protein aggregation often requires some structural reshaping and the subsequent formation of intermolecular contacts. Therefore, the study of the conformation of excited protein states and their ability to form oligomers is of primary importance for understanding the molecular basis of amyloid fibril formation. Here, we investigated the oligomerization processes that occur along the folding of the amyloidogenic human protein β2-microglobulin. The combination of real-time two-dimensional NMR data with real-time small-angle X-ray scattering measurements allowed us to derive thermodynamic and kinetic information on protein oligomerization of different conformational states populated along the folding pathways. In particular, we could demonstrate that a long-lived folding intermediate (I-state) has a higher propensity to oligomerize compared to the native state. Our data agree well with a simple five-state kinetic model that involves only monomeric and dimeric species. The dimers have an elongated shape with the dimerization interface located at the apical side of β2-microglobulin close to Pro32, the residue that has a trans conformation in the I-state and a cis conformation in the native (N) state. Our experimental data suggest that partial unfolding in the apical half of the protein close to Pro32 leads to an excited state conformation with enhanced propensity for oligomerization. This excited state becomes more populated in the transient I-state due to the destabilization of the native conformation by the trans-Pro32 configuration."}],"keyword":["Molecular Biology"],"quality_controlled":"1","extern":"1","title":"Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure","publication":"Journal of Molecular Biology","publisher":"Elsevier","oa_version":"None","date_created":"2020-09-18T10:09:12Z"},{"publist_id":"6752","date_created":"2018-12-11T11:49:04Z","oa_version":"None","publisher":"BioMed Central","publication":"BMC Research Notes","title":"Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R","extern":"1","abstract":[{"text":"Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. Conclusions: Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.","lang":"eng"}],"date_updated":"2021-01-12T08:21:25Z","doi":"10.1186/1756-0500-6-310","date_published":"2013-01-01T00:00:00Z","author":[{"first_name":"Romain","last_name":"Derelle","full_name":"Derelle, Romain"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"full_name":"Arkhipov, Vladimir","first_name":"Vladimir","last_name":"Arkhipov"},{"first_name":"Hélène","last_name":"Corbel","full_name":"Corbel, Hélène"},{"full_name":"Frantz, Adrien","first_name":"Adrien","last_name":"Frantz"},{"full_name":"Gasparini, Julien","last_name":"Gasparini","first_name":"Julien"},{"first_name":"Lisa","last_name":"Jacquin","full_name":"Jacquin, Lisa"},{"first_name":"Gwenaël","last_name":"Jacob","full_name":"Jacob, Gwenaël"},{"full_name":"Thibault, Sophie","first_name":"Sophie","last_name":"Thibault"},{"full_name":"Baudry, Emmanuelle","first_name":"Emmanuelle","last_name":"Baudry"}],"year":"2013","publication_status":"published","_id":"894","intvolume":"         6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":6,"month":"01","language":[{"iso":"eng"}],"citation":{"short":"R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini, L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013).","ista":"Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1).","mla":"Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” <i>BMC Research Notes</i>, vol. 6, no. 1, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1756-0500-6-310\">10.1186/1756-0500-6-310</a>.","ama":"Derelle R, Kondrashov F, Arkhipov V, et al. Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. <i>BMC Research Notes</i>. 2013;6(1). doi:<a href=\"https://doi.org/10.1186/1756-0500-6-310\">10.1186/1756-0500-6-310</a>","apa":"Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini, J., … Baudry, E. (2013). Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R. <i>BMC Research Notes</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1756-0500-6-310\">https://doi.org/10.1186/1756-0500-6-310</a>","chicago":"Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene MC1R.” <i>BMC Research Notes</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1756-0500-6-310\">https://doi.org/10.1186/1756-0500-6-310</a>.","ieee":"R. Derelle <i>et al.</i>, “Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R,” <i>BMC Research Notes</i>, vol. 6, no. 1. BioMed Central, 2013."},"issue":"1","day":"01","acknowledgement":"Romain Derelle was supported by grant from Plan Nacional 004302 BFU2012-31329. Fyodor A Kondrashov was supported by grants HHMI (Howard Hughes Medical Institute) 003803 and EMBO 003691 EUI-EURYIP-2011-4320.","status":"public"},{"title":"Breen et al. reply","publication":"Nature","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:49:05Z","publist_id":"6747","date_published":"2013-05-30T00:00:00Z","author":[{"full_name":"Breen, Michael S","last_name":"Breen","first_name":"Michael"},{"first_name":"Carsten","last_name":"Kemena","full_name":"Kemena, Carsten"},{"full_name":"Vlasov, Peter K","first_name":"Peter","last_name":"Vlasov"},{"last_name":"Notredame","first_name":"Cédric","full_name":"Notredame, Cédric"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov"}],"date_updated":"2021-01-12T08:21:40Z","doi":"10.1038/nature12220","abstract":[{"text":"Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype relationship, is crucial to many areas of biology. Two aspects of fitness landscapes are the focus of contemporary studies of molecular evolution. First, the local shape of the fitness landscape defined by the contribution of individual alleles to fitness that is independent of all genetic interactions. Second, the global, multidimensional fitness landscape shape determined by how interactions between alleles at different loci change each other’s fitness impact, or epistasis. In explaining the high amino-acid usage (u), we focused on the global shape of the fitness landscape, ignoring the perturbations at individual sites.","lang":"eng"}],"quality_controlled":0,"extern":1,"page":"E2 - E3","volume":497,"type":"journal_article","_id":"899","intvolume":"       497","publication_status":"published","year":"2013","status":"public","day":"30","issue":"7451","citation":{"apa":"Breen, M., Kemena, C., Vlasov, P., Notredame, C., &#38; Kondrashov, F. (2013). Breen et al. reply. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12220\">https://doi.org/10.1038/nature12220</a>","chicago":"Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Breen et Al. Reply.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature12220\">https://doi.org/10.1038/nature12220</a>.","ieee":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et al. reply,” <i>Nature</i>, vol. 497, no. 7451. Nature Publishing Group, pp. E2–E3, 2013.","short":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013) E2–E3.","ista":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al. reply. Nature. 497(7451), E2–E3.","mla":"Breen, Michael, et al. “Breen et Al. Reply.” <i>Nature</i>, vol. 497, no. 7451, Nature Publishing Group, 2013, pp. E2–3, doi:<a href=\"https://doi.org/10.1038/nature12220\">10.1038/nature12220</a>.","ama":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Breen et al. reply. <i>Nature</i>. 2013;497(7451):E2-E3. doi:<a href=\"https://doi.org/10.1038/nature12220\">10.1038/nature12220</a>"},"month":"05"},{"date_created":"2018-12-11T11:53:41Z","publist_id":"5402","title":"The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling","publication":"Development","publisher":"Company of Biologists","abstract":[{"text":"The development of a functional tissue requires coordination of the amplification of progenitors and their differentiation into specific cell types. The molecular basis for this coordination during myotome ontogeny is not well understood. Dermomytome progenitors that colonize the myotome first acquire myocyte identity and subsequently proliferate as Pax7-expressing progenitors before undergoing terminal differentiation. We show that the dynamics of sonic hedgehog (Shh) signaling is crucial for this transition in both avian and mouse embryos. Initially, Shh ligand emanating from notochord/floor plate reaches the dermomyotome, where it both maintains the proliferation of dermomyotome cells and promotes myogenic differentiation of progenitors that colonized the myotome. Interfering with Shh signaling at this stage produces small myotomes and accumulation of Pax7-expressing progenitors. An in vivo reporter of Shh activity combined with mouse genetics revealed the existence of both activator and repressor Shh activities operating on distinct subsets of cells during the epaxial myotomal maturation. In contrast to observations in mice, in avians Shh promotes the differentiation of both epaxial and hypaxial myotome domains. Subsequently, myogenic progenitors become refractory to Shh; this is likely to occur at the level of, or upstream of, smoothened signaling. The end of responsiveness to Shh coincides with, and is thus likely to enable, the transition into the growth phase of the myotome.","lang":"eng"}],"quality_controlled":0,"extern":1,"date_published":"2013-04-18T00:00:00Z","author":[{"last_name":"Kahane","first_name":"Nitza","full_name":"Kahane, Nitza"},{"full_name":"Ribes, Vanessa","last_name":"Ribes","first_name":"Vanessa"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Anna Kicheva","orcid":"0000-0003-4509-4998","last_name":"Kicheva","first_name":"Anna"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"full_name":"Kalcheim, Chaya","last_name":"Kalcheim","first_name":"Chaya"}],"doi":"10.1242/dev.092726","date_updated":"2021-01-12T06:52:47Z","intvolume":"       140","_id":"1726","publication_status":"published","year":"2013","page":"1740 - 1750","volume":140,"type":"journal_article","citation":{"chicago":"Kahane, Nitza, Vanessa Ribes, Anna Kicheva, James Briscoe, and Chaya Kalcheim. “The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.” <i>Development</i>. Company of Biologists, 2013. <a href=\"https://doi.org/10.1242/dev.092726\">https://doi.org/10.1242/dev.092726</a>.","ieee":"N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, and C. Kalcheim, “The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling,” <i>Development</i>, vol. 140, no. 8. Company of Biologists, pp. 1740–1750, 2013.","apa":"Kahane, N., Ribes, V., Kicheva, A., Briscoe, J., &#38; Kalcheim, C. (2013). The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.092726\">https://doi.org/10.1242/dev.092726</a>","ama":"Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. <i>Development</i>. 2013;140(8):1740-1750. doi:<a href=\"https://doi.org/10.1242/dev.092726\">10.1242/dev.092726</a>","short":"N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, C. Kalcheim, Development 140 (2013) 1740–1750.","mla":"Kahane, Nitza, et al. “The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.” <i>Development</i>, vol. 140, no. 8, Company of Biologists, 2013, pp. 1740–50, doi:<a href=\"https://doi.org/10.1242/dev.092726\">10.1242/dev.092726</a>.","ista":"Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. 2013. The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. Development. 140(8), 1740–1750."},"month":"04","acknowledgement":"This study was supported by grants from the Israel Science Foundation (ISF) [11/09 to C.K.]; the Association Francaise contre les Myopathies (AFM) [15642 to C.K.]; the German Research Foundation (DFG) [UN 34/27-1 to C.K.]; the UK Medical Research Council (MRC) [U117560541 to J.B. and A.K.]; Fondation Pour la Recherche Médicale (FRM) (post-doctoral fellowship to V.R.). Deposited in PMC for release after 6 months","status":"public","day":"18","issue":"8"},{"status":"public","day":"01","issue":"5","citation":{"chicago":"Kicheva, Anna, Laurent Holtzer, Ortrud Wartlick, Thomas Schmidt, and Marcos González Gaitán. “Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal Discs.” <i>Cold Spring Harbor Protocols</i>. Cold Spring Harbor Laboratory Press, 2013. <a href=\"https://doi.org/10.1101/pdb.top074237\">https://doi.org/10.1101/pdb.top074237</a>.","ieee":"A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, and M. González Gaitán, “Quantitative imaging of morphogen gradients in drosophila imaginal discs,” <i>Cold Spring Harbor Protocols</i>, vol. 8, no. 5. Cold Spring Harbor Laboratory Press, pp. 387–403, 2013.","apa":"Kicheva, A., Holtzer, L., Wartlick, O., Schmidt, T., &#38; González Gaitán, M. (2013). Quantitative imaging of morphogen gradients in drosophila imaginal discs. <i>Cold Spring Harbor Protocols</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/pdb.top074237\">https://doi.org/10.1101/pdb.top074237</a>","ama":"Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. Quantitative imaging of morphogen gradients in drosophila imaginal discs. <i>Cold Spring Harbor Protocols</i>. 2013;8(5):387-403. doi:<a href=\"https://doi.org/10.1101/pdb.top074237\">10.1101/pdb.top074237</a>","ista":"Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. 2013. Quantitative imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor Protocols. 8(5), 387–403.","mla":"Kicheva, Anna, et al. “Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal Discs.” <i>Cold Spring Harbor Protocols</i>, vol. 8, no. 5, Cold Spring Harbor Laboratory Press, 2013, pp. 387–403, doi:<a href=\"https://doi.org/10.1101/pdb.top074237\">10.1101/pdb.top074237</a>.","short":"A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, M. González Gaitán, Cold Spring Harbor Protocols 8 (2013) 387–403."},"month":"05","page":"387 - 403","volume":8,"type":"journal_article","_id":"1727","intvolume":"         8","publication_status":"published","year":"2013","date_published":"2013-05-01T00:00:00Z","author":[{"first_name":"Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","full_name":"Anna Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Holtzer","first_name":"Laurent","full_name":"Holtzer, Laurent"},{"full_name":"Wartlick, Ortrud","last_name":"Wartlick","first_name":"Ortrud"},{"full_name":"Schmidt, Thomas S","last_name":"Schmidt","first_name":"Thomas"},{"full_name":"González-Gaitán, Marcos A","first_name":"Marcos","last_name":"González Gaitán"}],"date_updated":"2021-01-12T06:52:47Z","doi":"10.1101/pdb.top074237","abstract":[{"lang":"eng","text":"Cells at different positions in a developing tissue receive different concentrations of signaling molecules, called morphogens, and this influences their cell fate. Morphogen concentration gradients have been proposed to control patterning as well as growth in many developing tissues. Some outstanding questions about tissue patterning by morphogen gradients are the following: What are the mechanisms that regulate gradient formation and shape? Is the positional information encoded in the gradient sufficiently precise to determine the positions of target gene domain boundaries? What are the temporal dynamics of gradients and how do they relate to patterning and growth? These questions are inherently quantitative in nature and addressing them requires measuring morphogen concentrations in cells, levels of downstream signaling activity, and kinetics of morphogen transport. Here we first present methods for quantifying morphogen gradient shape in which the measurements can be calibrated to reflect actual morphogen concentrations. We then discuss using fluorescence recovery after photobleaching to study the kinetics of morphogen transport at the tissue level. Finally, we present particle tracking as a method to study morphogen intracellular trafficking."}],"quality_controlled":0,"extern":1,"title":"Quantitative imaging of morphogen gradients in drosophila imaginal discs","publication":"Cold Spring Harbor Protocols","publisher":"Cold Spring Harbor Laboratory Press","date_created":"2018-12-11T11:53:41Z","publist_id":"5401"},{"citation":{"short":"N. Ares, V. Golovach, G. Katsaros, M. Stoffel, F. Fournel, L. Glazman, O. Schmidt, S. De Franceschi, Physical Review Letters 110 (2013).","ista":"Ares N, Golovach V, Katsaros G, Stoffel M, Fournel F, Glazman L, Schmidt O, De Franceschi S. 2013. Nature of tunable hole g factors in quantum dots. Physical Review Letters. 110(4).","mla":"Ares, Natalia, et al. “Nature of Tunable Hole g Factors in Quantum Dots.” <i>Physical Review Letters</i>, vol. 110, no. 4, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.046602\">10.1103/PhysRevLett.110.046602</a>.","ama":"Ares N, Golovach V, Katsaros G, et al. Nature of tunable hole g factors in quantum dots. <i>Physical Review Letters</i>. 2013;110(4). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.046602\">10.1103/PhysRevLett.110.046602</a>","apa":"Ares, N., Golovach, V., Katsaros, G., Stoffel, M., Fournel, F., Glazman, L., … De Franceschi, S. (2013). Nature of tunable hole g factors in quantum dots. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.046602\">https://doi.org/10.1103/PhysRevLett.110.046602</a>","chicago":"Ares, Natalia, Vitaly Golovach, Georgios Katsaros, Mathieu Stoffel, Frank Fournel, Leonid Glazman, Oliver Schmidt, and Silvano De Franceschi. “Nature of Tunable Hole g Factors in Quantum Dots.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.046602\">https://doi.org/10.1103/PhysRevLett.110.046602</a>.","ieee":"N. Ares <i>et al.</i>, “Nature of tunable hole g factors in quantum dots,” <i>Physical Review Letters</i>, vol. 110, no. 4. American Physical Society, 2013."},"month":"01","acknowledgement":"We acknowledge financial support from the Nanosciences Foundation (Grenoble, France), DOE under Contract No. DEFG02-08ER46482 (Yale), the Agence Nationale de la Recherche, and the European Starting Grant. G. K. acknowledges support from the European Commission via a Marie Curie Carrer Integration Grant and the FWF for a Lise-Meitner Fellowship","status":"public","oa":1,"day":"23","issue":"4","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1208.0476"}],"_id":"1759","intvolume":"       110","publication_status":"published","year":"2013","volume":110,"type":"journal_article","abstract":[{"text":"We report an electric-field-induced giant modulation of the hole g factor in SiGe nanocrystals. The observed effect is ascribed to a so-far overlooked contribution to the g factor that stems from the mixing between heavy- and light-hole wave functions. We show that the relative displacement between the confined heavy- and light-hole states, occurring upon application of the electric field, alters their mixing strength leading to a strong nonmonotonic modulation of the g factor.","lang":"eng"}],"extern":1,"quality_controlled":0,"date_published":"2013-01-23T00:00:00Z","author":[{"first_name":"Natalia","last_name":"Ares","full_name":"Ares, Natalia"},{"first_name":"Vitaly","last_name":"Golovach","full_name":"Golovach, Vitaly N"},{"last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Georgios Katsaros"},{"full_name":"Stoffel, Mathieu","first_name":"Mathieu","last_name":"Stoffel"},{"last_name":"Fournel","first_name":"Frank","full_name":"Fournel, Frank"},{"full_name":"Glazman, Leonid I","first_name":"Leonid","last_name":"Glazman"},{"first_name":"Oliver","last_name":"Schmidt","full_name":"Schmidt, Oliver G"},{"last_name":"De Franceschi","first_name":"Silvano","full_name":"De Franceschi, Silvano"}],"doi":"10.1103/PhysRevLett.110.046602","date_updated":"2021-01-12T06:53:01Z","date_created":"2018-12-11T11:53:51Z","publist_id":"5365","title":"Nature of tunable hole g factors in quantum dots","publication":"Physical Review Letters","publisher":"American Physical Society"},{"volume":103,"type":"journal_article","intvolume":"       103","_id":"1760","main_file_link":[{"url":"http://arxiv.org/abs/1307.7196","open_access":"1"}],"year":"2013","publication_status":"published","acknowledgement":"We acknowledge the financial support from the Nanosciences Foundation (Grenoble, France), the Commission for a Marie Curie Carrer Integration Grant, the Austrian Science Fund (FWF) for a Lise-Meitner Fellowship (M1435-N30), the DOE under Contract No. DE-FG02-08ER46482 (Yale), the European Starting Grant program, and the Agence Nationale de la Recherche","oa":1,"status":"public","issue":"26","day":"23","citation":{"chicago":"Ares, Natalia, Georgios Katsaros, Vitaly Golovach, Jianjun Zhang, Aaron Prager, Leonid Glazman, Oliver Schmidt, and Silvano De Franceschi. “SiGe Quantum Dots for Fast Hole Spin Rabi Oscillations.” <i>Applied Physics Letters</i>. American Institute of Physics, 2013. <a href=\"https://doi.org/10.1063/1.4858959\">https://doi.org/10.1063/1.4858959</a>.","ieee":"N. Ares <i>et al.</i>, “SiGe quantum dots for fast hole spin Rabi oscillations,” <i>Applied Physics Letters</i>, vol. 103, no. 26. American Institute of Physics, 2013.","apa":"Ares, N., Katsaros, G., Golovach, V., Zhang, J., Prager, A., Glazman, L., … De Franceschi, S. (2013). SiGe quantum dots for fast hole spin Rabi oscillations. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4858959\">https://doi.org/10.1063/1.4858959</a>","ama":"Ares N, Katsaros G, Golovach V, et al. SiGe quantum dots for fast hole spin Rabi oscillations. <i>Applied Physics Letters</i>. 2013;103(26). doi:<a href=\"https://doi.org/10.1063/1.4858959\">10.1063/1.4858959</a>","short":"N. Ares, G. Katsaros, V. Golovach, J. Zhang, A. Prager, L. Glazman, O. Schmidt, S. De Franceschi, Applied Physics Letters 103 (2013).","mla":"Ares, Natalia, et al. “SiGe Quantum Dots for Fast Hole Spin Rabi Oscillations.” <i>Applied Physics Letters</i>, vol. 103, no. 26, American Institute of Physics, 2013, doi:<a href=\"https://doi.org/10.1063/1.4858959\">10.1063/1.4858959</a>.","ista":"Ares N, Katsaros G, Golovach V, Zhang J, Prager A, Glazman L, Schmidt O, De Franceschi S. 2013. SiGe quantum dots for fast hole spin Rabi oscillations. Applied Physics Letters. 103(26)."},"month":"01","publication":"Applied Physics Letters","title":"SiGe quantum dots for fast hole spin Rabi oscillations","publisher":"American Institute of Physics","date_created":"2018-12-11T11:53:52Z","publist_id":"5364","date_published":"2013-01-23T00:00:00Z","author":[{"full_name":"Ares, Natalia","first_name":"Natalia","last_name":"Ares"},{"first_name":"Georgios","last_name":"Katsaros","full_name":"Georgios Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vitaly","last_name":"Golovach","full_name":"Golovach, Vitaly N"},{"first_name":"Jianjun","last_name":"Zhang","full_name":"Zhang, Jianjun"},{"full_name":"Prager, Aaron A","first_name":"Aaron","last_name":"Prager"},{"full_name":"Glazman, Leonid I","last_name":"Glazman","first_name":"Leonid"},{"full_name":"Schmidt, Oliver G","first_name":"Oliver","last_name":"Schmidt"},{"last_name":"De Franceschi","first_name":"Silvano","full_name":"De Franceschi, Silvano"}],"doi":"10.1063/1.4858959","date_updated":"2021-01-12T06:53:02Z","abstract":[{"lang":"eng","text":"We report on hole g-factor measurements in three terminal SiGe self-assembled quantum dot devices with a top gate electrode positioned very close to the nanostructure. Measurements of both the perpendicular as well as the parallel g-factor reveal significant changes for a small modulation of the top gate voltage. From the observed modulations, we estimate that, for realistic experimental conditions, hole spins can be electrically manipulated with Rabi frequencies in the order of 100 MHz. This work emphasises the potential of hole-based nano-devices for efficient spin manipulation by means of the g-tensor modulation technique."}],"quality_controlled":0,"extern":1},{"author":[{"full_name":"Abdumalikov, Abdufarrukh A","last_name":"Abdumalikov","first_name":"Abdufarrukh"},{"orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink"},{"full_name":"Juliusson, K","last_name":"Juliusson","first_name":"K"},{"full_name":"Pechal, M","first_name":"M","last_name":"Pechal"},{"first_name":"Stefan","last_name":"Berger","full_name":"Berger, Stefan T"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"},{"last_name":"Filipp","first_name":"Stefan","full_name":"Filipp, Stefan"}],"date_published":"2013-04-25T00:00:00Z","doi":"10.1038/nature12010","date_updated":"2021-01-12T06:53:11Z","abstract":[{"text":"The geometric aspects of quantum mechanics are emphasized most prominently by the concept of geometric phases, which are acquired whenever a quantum system evolves along a path in Hilbert space, that is, the space of quantum states of the system. The geometric phase is determined only by the shape of this path and is, in its simplest form, a real number. However, if the system has degenerate energy levels, then matrix-valued geometric state transformations, known as non-Abelian holonomies-the effect of which depends on the order of two consecutive paths-can be obtained. They are important, for example, for the creation of synthetic gauge fields in cold atomic gases or the description of non-Abelian anyon statistics. Moreover, there are proposals to exploit non-Abelian holonomic gates for the purposes of noise-resilient quantum computation. In contrast to Abelian geometric operations, non-Abelian ones have been observed only in nuclear quadrupole resonance experiments with a large number of spins, and without full characterization of the geometric process and its non-commutative nature. Here we realize non-Abelian non-adiabatic holonomic quantum operations on a single, superconducting, artificial three-level atom by applying a well-controlled, two-tone microwave drive. Using quantum process tomography, we determine fidelities of the resulting non-commuting gates that exceed 95 per cent. We show that two different quantum gates, originating from two distinct paths in Hilbert space, yield non-equivalent transformations when applied in different orders. This provides evidence for the non-Abelian character of the implemented holonomic quantum operations. In combination with a non-trivial two-quantum-bit gate, our method suggests a way to universal holonomic quantum computing.","lang":"eng"}],"quality_controlled":0,"extern":1,"title":"Experimental realization of non-Abelian non-adiabatic geometric gates","publication":"Nature","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:54:00Z","publist_id":"5329","status":"public","acknowledgement":"This work is supported financially by GEOMDISS, the Swiss National Science Foundation and ETH Zurich","day":"25","issue":"7446","citation":{"mla":"Abdumalikov, Abdufarrukh, et al. “Experimental Realization of Non-Abelian Non-Adiabatic Geometric Gates.” <i>Nature</i>, vol. 496, no. 7446, Nature Publishing Group, 2013, pp. 482–85, doi:<a href=\"https://doi.org/10.1038/nature12010\">10.1038/nature12010</a>.","ista":"Abdumalikov A, Fink JM, Juliusson K, Pechal M, Berger S, Wallraff A, Filipp S. 2013. Experimental realization of non-Abelian non-adiabatic geometric gates. Nature. 496(7446), 482–485.","short":"A. Abdumalikov, J.M. Fink, K. Juliusson, M. Pechal, S. Berger, A. Wallraff, S. Filipp, Nature 496 (2013) 482–485.","ama":"Abdumalikov A, Fink JM, Juliusson K, et al. Experimental realization of non-Abelian non-adiabatic geometric gates. <i>Nature</i>. 2013;496(7446):482-485. doi:<a href=\"https://doi.org/10.1038/nature12010\">10.1038/nature12010</a>","apa":"Abdumalikov, A., Fink, J. M., Juliusson, K., Pechal, M., Berger, S., Wallraff, A., &#38; Filipp, S. (2013). Experimental realization of non-Abelian non-adiabatic geometric gates. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12010\">https://doi.org/10.1038/nature12010</a>","ieee":"A. Abdumalikov <i>et al.</i>, “Experimental realization of non-Abelian non-adiabatic geometric gates,” <i>Nature</i>, vol. 496, no. 7446. Nature Publishing Group, pp. 482–485, 2013.","chicago":"Abdumalikov, Abdufarrukh, Johannes M Fink, K Juliusson, M Pechal, Stefan Berger, Andreas Wallraff, and Stefan Filipp. “Experimental Realization of Non-Abelian Non-Adiabatic Geometric Gates.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature12010\">https://doi.org/10.1038/nature12010</a>."},"month":"04","page":"482 - 485","volume":496,"type":"journal_article","_id":"1785","intvolume":"       496","publication_status":"published","year":"2013"},{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1302.0665"}],"_id":"1786","intvolume":"       110","publication_status":"published","year":"2013","volume":110,"type":"journal_article","citation":{"apa":"Nissen, F., Fink, J. M., Mlynek, J., Wallraff, A., &#38; Keeling, J. (2013). Collective suppression of linewidths in circuit QED. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.203602\">https://doi.org/10.1103/PhysRevLett.110.203602</a>","ieee":"F. Nissen, J. M. Fink, J. Mlynek, A. Wallraff, and J. Keeling, “Collective suppression of linewidths in circuit QED,” <i>Physical Review Letters</i>, vol. 110, no. 20. American Physical Society, 2013.","chicago":"Nissen, Felix, Johannes M Fink, Jonas Mlynek, Andreas Wallraff, and Jonathan Keeling. “Collective Suppression of Linewidths in Circuit QED.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.203602\">https://doi.org/10.1103/PhysRevLett.110.203602</a>.","ista":"Nissen F, Fink JM, Mlynek J, Wallraff A, Keeling J. 2013. Collective suppression of linewidths in circuit QED. Physical Review Letters. 110(20).","short":"F. Nissen, J.M. Fink, J. Mlynek, A. Wallraff, J. Keeling, Physical Review Letters 110 (2013).","mla":"Nissen, Felix, et al. “Collective Suppression of Linewidths in Circuit QED.” <i>Physical Review Letters</i>, vol. 110, no. 20, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.203602\">10.1103/PhysRevLett.110.203602</a>.","ama":"Nissen F, Fink JM, Mlynek J, Wallraff A, Keeling J. Collective suppression of linewidths in circuit QED. <i>Physical Review Letters</i>. 2013;110(20). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.203602\">10.1103/PhysRevLett.110.203602</a>"},"month":"05","oa":1,"acknowledgement":"J. K. acknowledges financial support from EPSRC program “TOPNES” (EP/I031014/1) and EPSRC (EP/G004714/2)","status":"public","day":"15","issue":"20","date_created":"2018-12-11T11:54:00Z","publist_id":"5328","title":"Collective suppression of linewidths in circuit QED","publication":"Physical Review Letters","publisher":"American Physical Society","abstract":[{"lang":"eng","text":"We report the experimental observation and a theoretical explanation of collective suppression of linewidths for multiple superconducting qubits coupled to a good cavity. This demonstrates how strong qubit-cavity coupling can significantly modify the dephasing and dissipation processes that might be expected for individual qubits, and can potentially improve coherence times in many-body circuit QED."}],"extern":1,"quality_controlled":0,"author":[{"full_name":"Nissen, Felix","last_name":"Nissen","first_name":"Felix"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M"},{"full_name":"Mlynek, Jonas A","first_name":"Jonas","last_name":"Mlynek"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"},{"first_name":"Jonathan","last_name":"Keeling","full_name":"Keeling, Jonathan M"}],"date_published":"2013-05-15T00:00:00Z","date_updated":"2021-01-12T06:53:11Z","doi":"10.1103/PhysRevLett.110.203602"},{"publist_id":"5327","date_created":"2018-12-11T11:54:00Z","publisher":"Nature Publishing Group","title":"Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies","publication":"Nature Physics","extern":1,"quality_controlled":0,"abstract":[{"text":"When two indistinguishable single photons impinge at the two inputs of a beam splitter they coalesce into a pair of photons appearing in either one of its two outputs. This effect is due to the bosonic nature of photons and was first experimentally observed by Hong, Ou and Mandel. Here, we present the observation of the Hong-Ou-Mandel effect with two independent single-photon sources in the microwave frequency domain. We probe the indistinguishability of single photons, created with a controllable delay, in time-resolved second-order cross- and auto-correlation function measurements. Using quadrature amplitude detection we are able to resolve different photon numbers and detect coherence in and between the output arms. This scheme allows us to fully characterize the two-mode entanglement of the spatially separated beam-splitter output modes. Our experiments constitute a first step towards using two-photon interference at microwave frequencies for quantum communication and information processing.","lang":"eng"}],"doi":"10.1038/nphys2612","date_updated":"2021-01-12T06:53:11Z","author":[{"last_name":"Lang","first_name":"C","full_name":"Lang, C"},{"full_name":"Eichler, Christopher","last_name":"Eichler","first_name":"Christopher"},{"last_name":"Steffen","first_name":"L.","full_name":"Steffen, L. Kraig"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M"},{"last_name":"Woolley","first_name":"Matthew","full_name":"Woolley, Matthew J"},{"last_name":"Blais","first_name":"Alexandre","full_name":"Blais, Alexandre"},{"full_name":"Wallraff, Andreas","first_name":"Andreas","last_name":"Wallraff"}],"date_published":"2013-06-01T00:00:00Z","publication_status":"published","year":"2013","intvolume":"         9","_id":"1787","type":"journal_article","page":"345 - 348","volume":9,"month":"06","citation":{"chicago":"Lang, C, Christopher Eichler, L. Steffen, Johannes M Fink, Matthew Woolley, Alexandre Blais, and Andreas Wallraff. “Correlations, Indistinguishability and Entanglement in Hong-Ou-Mandel Experiments at Microwave Frequencies.” <i>Nature Physics</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nphys2612\">https://doi.org/10.1038/nphys2612</a>.","ieee":"C. Lang <i>et al.</i>, “Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies,” <i>Nature Physics</i>, vol. 9, no. 6. Nature Publishing Group, pp. 345–348, 2013.","apa":"Lang, C., Eichler, C., Steffen, L., Fink, J. M., Woolley, M., Blais, A., &#38; Wallraff, A. (2013). Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphys2612\">https://doi.org/10.1038/nphys2612</a>","ama":"Lang C, Eichler C, Steffen L, et al. Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies. <i>Nature Physics</i>. 2013;9(6):345-348. doi:<a href=\"https://doi.org/10.1038/nphys2612\">10.1038/nphys2612</a>","ista":"Lang C, Eichler C, Steffen L, Fink JM, Woolley M, Blais A, Wallraff A. 2013. Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies. Nature Physics. 9(6), 345–348.","short":"C. Lang, C. Eichler, L. Steffen, J.M. Fink, M. Woolley, A. Blais, A. Wallraff, Nature Physics 9 (2013) 345–348.","mla":"Lang, C., et al. “Correlations, Indistinguishability and Entanglement in Hong-Ou-Mandel Experiments at Microwave Frequencies.” <i>Nature Physics</i>, vol. 9, no. 6, Nature Publishing Group, 2013, pp. 345–48, doi:<a href=\"https://doi.org/10.1038/nphys2612\">10.1038/nphys2612</a>."},"day":"01","issue":"6","acknowledgement":"This work was supported by the European Research Council (ERC) through a Starting Grant and by ETHZ. L.S. was supported by EU IP SOLID. A.B. and M.J.W. were supported by NSERC, CIFAR and the Alfred P. Sloan Foundation","status":"public"},{"date_updated":"2021-01-12T06:53:13Z","doi":"10.1016/j.neuron.2013.09.019","author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Gaia Novarino","last_name":"Novarino","orcid":"0000-0002-7673-7178","first_name":"Gaia"},{"first_name":"Seungtae","last_name":"Baek","full_name":"Baek, SeungTae"},{"last_name":"Gleeson","first_name":"Joseph","full_name":"Gleeson, Joseph G"}],"date_published":"2013-10-02T00:00:00Z","extern":1,"quality_controlled":0,"abstract":[{"text":"In the September 12, 2013 issue of Nature, the Epi4K Consortium (. Allen etal., 2013) reported sequencing 264patient trios with epileptic encephalopathies. The Consortium focused on genes exceptionally intolerant to sequence variations and found substantial interconnections with autism and intellectual disability gene networks.","lang":"eng"}],"publisher":"Elsevier","publication":"Neuron","title":"The sacred disease: The puzzling genetics of epileptic disorders","publist_id":"5323","date_created":"2018-12-11T11:54:01Z","issue":"1","day":"02","status":"public","month":"10","citation":{"ieee":"G. Novarino, S. Baek, and J. Gleeson, “The sacred disease: The puzzling genetics of epileptic disorders,” <i>Neuron</i>, vol. 80, no. 1. Elsevier, pp. 9–11, 2013.","chicago":"Novarino, Gaia, Seungtae Baek, and Joseph Gleeson. “The Sacred Disease: The Puzzling Genetics of Epileptic Disorders.” <i>Neuron</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.neuron.2013.09.019\">https://doi.org/10.1016/j.neuron.2013.09.019</a>.","apa":"Novarino, G., Baek, S., &#38; Gleeson, J. (2013). The sacred disease: The puzzling genetics of epileptic disorders. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.09.019\">https://doi.org/10.1016/j.neuron.2013.09.019</a>","ama":"Novarino G, Baek S, Gleeson J. The sacred disease: The puzzling genetics of epileptic disorders. <i>Neuron</i>. 2013;80(1):9-11. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.09.019\">10.1016/j.neuron.2013.09.019</a>","short":"G. Novarino, S. Baek, J. Gleeson, Neuron 80 (2013) 9–11.","mla":"Novarino, Gaia, et al. “The Sacred Disease: The Puzzling Genetics of Epileptic Disorders.” <i>Neuron</i>, vol. 80, no. 1, Elsevier, 2013, pp. 9–11, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.09.019\">10.1016/j.neuron.2013.09.019</a>.","ista":"Novarino G, Baek S, Gleeson J. 2013. The sacred disease: The puzzling genetics of epileptic disorders. Neuron. 80(1), 9–11."},"type":"journal_article","volume":80,"page":"9 - 11","year":"2013","publication_status":"published","intvolume":"        80","_id":"1790"},{"day":"01","issue":"5","status":"public","acknowledgement":"This work was funded by the Medical Research Council.","month":"10","citation":{"apa":"Sazanov, L. A., Baradaran, R., Efremov, R., Berrisford, J., &#38; Minhas, G. (2013). A long road towards the structure of respiratory complex I, a giant molecular proton pump. <i>Biochemical Society Transactions</i>. Portland Press. <a href=\"https://doi.org/10.1042/BST20130193\">https://doi.org/10.1042/BST20130193</a>","chicago":"Sazanov, Leonid A, Rozbeh Baradaran, Rouslan Efremov, John Berrisford, and Gurdeep Minhas. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” <i>Biochemical Society Transactions</i>. Portland Press, 2013. <a href=\"https://doi.org/10.1042/BST20130193\">https://doi.org/10.1042/BST20130193</a>.","ieee":"L. A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, and G. Minhas, “A long road towards the structure of respiratory complex I, a giant molecular proton pump,” <i>Biochemical Society Transactions</i>, vol. 41, no. 5. Portland Press, pp. 1265–1271, 2013.","mla":"Sazanov, Leonid A., et al. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” <i>Biochemical Society Transactions</i>, vol. 41, no. 5, Portland Press, 2013, pp. 1265–71, doi:<a href=\"https://doi.org/10.1042/BST20130193\">10.1042/BST20130193</a>.","short":"L.A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, G. Minhas, Biochemical Society Transactions 41 (2013) 1265–1271.","ista":"Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. 2013. A long road towards the structure of respiratory complex I, a giant molecular proton pump. Biochemical Society Transactions. 41(5), 1265–1271.","ama":"Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. A long road towards the structure of respiratory complex I, a giant molecular proton pump. <i>Biochemical Society Transactions</i>. 2013;41(5):1265-1271. doi:<a href=\"https://doi.org/10.1042/BST20130193\">10.1042/BST20130193</a>"},"type":"journal_article","page":"1265 - 1271","volume":41,"publication_status":"published","year":"2013","_id":"1977","intvolume":"        41","doi":"10.1042/BST20130193","date_updated":"2021-01-12T06:54:28Z","date_published":"2013-10-01T00:00:00Z","author":[{"full_name":"Leonid Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989"},{"last_name":"Baradaran","first_name":"Rozbeh","full_name":"Baradaran, Rozbeh "},{"first_name":"Rouslan","last_name":"Efremov","full_name":"Efremov, Rouslan G"},{"last_name":"Berrisford","first_name":"John","full_name":"Berrisford, John M"},{"first_name":"Gurdeep","last_name":"Minhas","full_name":"Minhas, Gurdeep S"}],"quality_controlled":0,"extern":1,"abstract":[{"text":"Complex I (NADH:ubiquinone oxidoreductase) is central to cellular energy production, being the first and largest enzyme of the respiratory chain in mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the inner mitochondrial membrane and is involved in a wide range of human neurodegenerative disorders. Mammalian complex I is composed of 44 different subunits, whereas the 'minimal' bacterial version contains 14 highly conserved 'core' subunits. The L-shaped assembly consists of hydrophilic and membrane domains. We have determined all known atomic structures of complex I, starting from the hydrophilic domain of Thermus thermophilus enzyme (eight subunits, nine Fe-S clusters), followed by the membrane domains of the Escherichia coli (six subunits, 55 transmembrane helices) and T. thermophilus (seven subunits, 64 transmembrane helices) enzymes, and finally culminating in a recent crystal structure of the entire intact complex I from T. thermophilus (536 kDa, 16 subunits, nine Fe-S clusters, 64 transmembrane helices). The structure suggests an unusual and unique coupling mechanism via longrange conformational changes. Determination of the structure of the entire complex was possible only through this step-by-step approach, building on from smaller subcomplexes towards the entire assembly. Large membrane proteins are notoriously difficult to crystallize, and so various non-standard and sometimes counterintuitive approaches were employed in order to achieve crystal diffraction to high resolution and solve the structures. These steps, as well as the implications from the final structure, are discussed in the present review.","lang":"eng"}],"publisher":"Portland Press","title":"A long road towards the structure of respiratory complex I, a giant molecular proton pump","publication":"Biochemical Society Transactions","publist_id":"5106","date_created":"2018-12-11T11:55:00Z"}]