[{"_id":"6230","scopus_import":"1","file_date_updated":"2020-07-14T12:47:24Z","external_id":{"isi":["000461988300001"]},"type":"journal_article","oa":1,"author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"last_name":"Hermisson","first_name":"Joachim","full_name":"Hermisson, Joachim"},{"last_name":"Nordborg","first_name":"Magnus","full_name":"Nordborg, Magnus"}],"has_accepted_license":"1","citation":{"short":"N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019).","ama":"Barton NH, Hermisson J, Nordborg M. Why structure matters. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.45380\">10.7554/eLife.45380</a>","chicago":"Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure Matters.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.45380\">https://doi.org/10.7554/eLife.45380</a>.","ieee":"N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","ista":"Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380.","apa":"Barton, N. H., Hermisson, J., &#38; Nordborg, M. (2019). Why structure matters. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.45380\">https://doi.org/10.7554/eLife.45380</a>","mla":"Barton, Nicholas H., et al. “Why Structure Matters.” <i>ELife</i>, vol. 8, e45380, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.45380\">10.7554/eLife.45380</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"NiBa"}],"file":[{"creator":"dernst","checksum":"130d7544b57df4a6787e1263c2d7ea43","relation":"main_file","file_id":"6293","date_created":"2019-04-11T11:43:38Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:24Z","file_size":298466,"file_name":"2019_eLife_Barton.pdf"}],"oa_version":"Published Version","date_updated":"2023-08-25T08:59:38Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","date_published":"2019-03-21T00:00:00Z","title":"Why structure matters","date_created":"2019-04-07T21:59:15Z","ddc":["570"],"volume":8,"article_processing_charge":"No","publication":"eLife","year":"2019","publication_identifier":{"eissn":["2050084X"]},"status":"public","abstract":[{"text":"Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies.","lang":"eng"}],"doi":"10.7554/eLife.45380","license":"https://creativecommons.org/licenses/by/4.0/","related_material":{"link":[{"url":"https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/","relation":"press_release","description":"News on IST Homepage"}]},"month":"03","isi":1,"day":"21","publication_status":"published","publisher":"eLife Sciences Publications","intvolume":"         8","article_number":"e45380","language":[{"iso":"eng"}]},{"_id":"6232","external_id":{"isi":["000459681900005"],"arxiv":["1705.05364"]},"scopus_import":"1","type":"journal_article","oa_version":"Preprint","date_updated":"2023-08-25T08:59:11Z","department":[{"_id":"JaMa"}],"citation":{"short":"M. Gerencser, Annals of Probability 47 (2019) 804–834.","ama":"Gerencser M. Boundary regularity of stochastic PDEs. <i>Annals of Probability</i>. 2019;47(2):804-834. doi:<a href=\"https://doi.org/10.1214/18-AOP1272\">10.1214/18-AOP1272</a>","chicago":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2019. <a href=\"https://doi.org/10.1214/18-AOP1272\">https://doi.org/10.1214/18-AOP1272</a>.","ieee":"M. Gerencser, “Boundary regularity of stochastic PDEs,” <i>Annals of Probability</i>, vol. 47, no. 2. Institute of Mathematical Statistics, pp. 804–834, 2019.","ista":"Gerencser M. 2019. Boundary regularity of stochastic PDEs. Annals of Probability. 47(2), 804–834.","mla":"Gerencser, Mate. “Boundary Regularity of Stochastic PDEs.” <i>Annals of Probability</i>, vol. 47, no. 2, Institute of Mathematical Statistics, 2019, pp. 804–34, doi:<a href=\"https://doi.org/10.1214/18-AOP1272\">10.1214/18-AOP1272</a>.","apa":"Gerencser, M. (2019). Boundary regularity of stochastic PDEs. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-AOP1272\">https://doi.org/10.1214/18-AOP1272</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"author":[{"last_name":"Gerencser","full_name":"Gerencser, Mate","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2019-03-01T00:00:00Z","title":"Boundary regularity of stochastic PDEs","quality_controlled":"1","date_created":"2019-04-07T21:59:15Z","year":"2019","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.05364"}],"publication":"Annals of Probability","article_processing_charge":"No","volume":47,"status":"public","publication_identifier":{"issn":["00911798"]},"issue":"2","doi":"10.1214/18-AOP1272","abstract":[{"text":"The boundary behaviour of solutions of stochastic PDEs with Dirichlet boundary conditions can be surprisingly—and in a sense, arbitrarily—bad: as shown by Krylov[ SIAM J. Math. Anal.34(2003) 1167–1182], for any α>0 one can find a simple 1-dimensional constant coefficient linear equation whose solution at the boundary is not α-Hölder continuous.We obtain a positive counterpart of this: under some mild regularity assumptions on the coefficients, solutions of semilinear SPDEs on C1 domains are proved to be α-Hölder continuous up to the boundary with some α>0.","lang":"eng"}],"isi":1,"month":"03","publication_status":"published","day":"01","publisher":"Institute of Mathematical Statistics","intvolume":"        47","page":"804-834","arxiv":1,"language":[{"iso":"eng"}]},{"date_published":"2019-05-01T00:00:00Z","title":"Location of the spectrum of Kronecker random matrices","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"quality_controlled":"1","year":"2019","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.08343"}],"volume":55,"article_processing_charge":"No","publication":"Annales de l'institut Henri Poincare","date_created":"2019-04-08T14:05:04Z","external_id":{"isi":["000467793600003"],"arxiv":["1706.08343"]},"scopus_import":"1","_id":"6240","department":[{"_id":"LaEr"}],"date_updated":"2023-10-17T12:20:20Z","oa_version":"Preprint","oa":1,"author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes","first_name":"Johannes","last_name":"Alt"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"last_name":"Krüger","orcid":"0000-0002-4821-3297","first_name":"Torben H","full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nemish","first_name":"Yuriy","full_name":"Nemish, Yuriy","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7327-856X"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"J. Alt, L. Erdös, T.H. Krüger, Y. Nemish, Annales de l’institut Henri Poincare 55 (2019) 661–696.","ama":"Alt J, Erdös L, Krüger TH, Nemish Y. Location of the spectrum of Kronecker random matrices. <i>Annales de l’institut Henri Poincare</i>. 2019;55(2):661-696. doi:<a href=\"https://doi.org/10.1214/18-AIHP894\">10.1214/18-AIHP894</a>","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Yuriy Nemish. “Location of the Spectrum of Kronecker Random Matrices.” <i>Annales de l’institut Henri Poincare</i>. Institut Henri Poincaré, 2019. <a href=\"https://doi.org/10.1214/18-AIHP894\">https://doi.org/10.1214/18-AIHP894</a>.","ieee":"J. Alt, L. Erdös, T. H. Krüger, and Y. Nemish, “Location of the spectrum of Kronecker random matrices,” <i>Annales de l’institut Henri Poincare</i>, vol. 55, no. 2. Institut Henri Poincaré, pp. 661–696, 2019.","ista":"Alt J, Erdös L, Krüger TH, Nemish Y. 2019. Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. 55(2), 661–696.","apa":"Alt, J., Erdös, L., Krüger, T. H., &#38; Nemish, Y. (2019). Location of the spectrum of Kronecker random matrices. <i>Annales de l’institut Henri Poincare</i>. Institut Henri Poincaré. <a href=\"https://doi.org/10.1214/18-AIHP894\">https://doi.org/10.1214/18-AIHP894</a>","mla":"Alt, Johannes, et al. “Location of the Spectrum of Kronecker Random Matrices.” <i>Annales de l’institut Henri Poincare</i>, vol. 55, no. 2, Institut Henri Poincaré, 2019, pp. 661–96, doi:<a href=\"https://doi.org/10.1214/18-AIHP894\">10.1214/18-AIHP894</a>."},"type":"journal_article","publisher":"Institut Henri Poincaré","language":[{"iso":"eng"}],"arxiv":1,"intvolume":"        55","page":"661-696","issue":"2","abstract":[{"text":"For a general class of large non-Hermitian random block matrices X we prove that there are no eigenvalues away from a deterministic set with very high probability. This set is obtained from the Dyson equation of the Hermitization of X as the self-consistent approximation of the pseudospectrum. We demonstrate that the analysis of the matrix Dyson equation from (Probab. Theory Related Fields (2018)) offers a unified treatment of many structured matrix ensembles.","lang":"eng"}],"doi":"10.1214/18-AIHP894","status":"public","publication_identifier":{"issn":["0246-0203"]},"publication_status":"published","ec_funded":1,"day":"01","month":"05","related_material":{"record":[{"status":"public","id":"149","relation":"dissertation_contains"}]},"isi":1},{"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/newly-discovered-mechanism-of-plant-hormone-auxin-acts-the-opposite-way/"}]},"month":"04","isi":1,"ec_funded":1,"day":"11","publication_status":"published","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"pmid":1,"status":"public","doi":"10.1038/s41586-019-1069-7","abstract":[{"lang":"eng","text":"The plant hormone auxin has crucial roles in almost all aspects of plant growth and development. Concentrations of auxin vary across different tissues, mediating distinct developmental outcomes and contributing to the functional diversity of auxin. However, the mechanisms that underlie these activities are poorly understood. Here we identify an auxin signalling mechanism, which acts in parallel to the canonical auxin pathway based on the transport inhibitor response1 (TIR1) and other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that translates levels of cellular auxin to mediate differential growth during apical-hook development. This signalling mechanism operates at the concave side of the apical hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase 1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically interacts with and phosphorylates two non-canonical transcriptional repressors of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby regulating ARF transcription factors. In contrast to the degradation of Aux/IAA transcriptional repressors in the canonical pathway, the newly identified mechanism stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate gene expression and ultimately inhibit growth. The auxin–TMK1 signalling pathway originates at the cell surface, is triggered by high levels of auxin and shares a partially overlapping set of transcription factors with the TIR1/AFB signalling pathway. This allows distinct interpretations of different concentrations of cellular auxin, and thus enables this versatile signalling molecule to mediate complex developmental outcomes."}],"page":"240-243","article_type":"original","intvolume":"       568","language":[{"iso":"eng"}],"publisher":"Springer Nature","type":"journal_article","author":[{"last_name":"Cao","first_name":"Min","full_name":"Cao, Min"},{"last_name":"Chen","full_name":"Chen, Rong","first_name":"Rong"},{"last_name":"Li","full_name":"Li, Pan","first_name":"Pan"},{"full_name":"Yu, Yongqiang","first_name":"Yongqiang","last_name":"Yu"},{"last_name":"Zheng","first_name":"Rui","full_name":"Zheng, Rui"},{"first_name":"Danfeng","full_name":"Ge, Danfeng","last_name":"Ge"},{"full_name":"Zheng, Wei","first_name":"Wei","last_name":"Zheng"},{"last_name":"Wang","full_name":"Wang, Xuhui","first_name":"Xuhui"},{"last_name":"Gu","first_name":"Yangtao","full_name":"Gu, Yangtao"},{"orcid":"0000-0003-4783-1752","first_name":"Zuzana","full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"},{"full_name":"Zhang, Heng","first_name":"Heng","last_name":"Zhang"},{"last_name":"Liu","full_name":"Liu, Renyi","first_name":"Renyi"},{"first_name":"Jun","full_name":"He, Jun","last_name":"He"},{"last_name":"Xu","full_name":"Xu, Tongda","first_name":"Tongda"}],"oa":1,"citation":{"ista":"Cao M, Chen R, Li P, Yu Y, Zheng R, Ge D, Zheng W, Wang X, Gu Y, Gelová Z, Friml J, Zhang H, Liu R, He J, Xu T. 2019. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 568, 240–243.","mla":"Cao, Min, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” <i>Nature</i>, vol. 568, Springer Nature, 2019, pp. 240–43, doi:<a href=\"https://doi.org/10.1038/s41586-019-1069-7\">10.1038/s41586-019-1069-7</a>.","apa":"Cao, M., Chen, R., Li, P., Yu, Y., Zheng, R., Ge, D., … Xu, T. (2019). TMK1-mediated auxin signalling regulates differential growth of the apical hook. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1069-7\">https://doi.org/10.1038/s41586-019-1069-7</a>","ieee":"M. Cao <i>et al.</i>, “TMK1-mediated auxin signalling regulates differential growth of the apical hook,” <i>Nature</i>, vol. 568. Springer Nature, pp. 240–243, 2019.","ama":"Cao M, Chen R, Li P, et al. TMK1-mediated auxin signalling regulates differential growth of the apical hook. <i>Nature</i>. 2019;568:240-243. doi:<a href=\"https://doi.org/10.1038/s41586-019-1069-7\">10.1038/s41586-019-1069-7</a>","short":"M. Cao, R. Chen, P. Li, Y. Yu, R. Zheng, D. Ge, W. Zheng, X. Wang, Y. Gu, Z. Gelová, J. Friml, H. Zhang, R. Liu, J. He, T. Xu, Nature 568 (2019) 240–243.","chicago":"Cao, Min, Rong Chen, Pan Li, Yongqiang Yu, Rui Zheng, Danfeng Ge, Wei Zheng, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1069-7\">https://doi.org/10.1038/s41586-019-1069-7</a>."},"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"creator":"dernst","relation":"main_file","checksum":"6b84ab602a34382cf0340a37a1378c75","date_created":"2020-11-13T07:37:41Z","success":1,"file_id":"8751","access_level":"open_access","file_size":4321328,"date_updated":"2020-11-13T07:37:41Z","content_type":"application/pdf","file_name":"2019_Nature _Cao_accepted.pdf"}],"department":[{"_id":"JiFr"}],"oa_version":"Submitted Version","date_updated":"2023-09-05T14:58:41Z","_id":"6259","scopus_import":"1","file_date_updated":"2020-11-13T07:37:41Z","external_id":{"isi":["000464412700050"],"pmid":["30944466"]},"date_created":"2019-04-09T08:37:05Z","ddc":["580"],"volume":568,"article_processing_charge":"No","publication":"Nature","year":"2019","quality_controlled":"1","date_published":"2019-04-11T00:00:00Z","title":"TMK1-mediated auxin signalling regulates differential growth of the apical hook","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}]},{"quality_controlled":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"title":"Pinstatic acid promotes auxin transport by inhibiting PIN internalization","date_published":"2019-06-01T00:00:00Z","date_created":"2019-04-09T08:38:20Z","publication":"Plant Physiology","article_processing_charge":"No","volume":180,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.19.00201"}],"year":"2019","_id":"6260","scopus_import":"1","external_id":{"pmid":["30936248"],"isi":["000470086100045"]},"type":"journal_article","citation":{"ista":"Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 180(2), 1152–1165.","apa":"Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., … Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN internalization. <i>Plant Physiology</i>. ASPB. <a href=\"https://doi.org/10.1104/pp.19.00201\">https://doi.org/10.1104/pp.19.00201</a>","mla":"Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” <i>Plant Physiology</i>, vol. 180, no. 2, ASPB, 2019, pp. 1152–65, doi:<a href=\"https://doi.org/10.1104/pp.19.00201\">10.1104/pp.19.00201</a>.","ieee":"A. Oochi <i>et al.</i>, “Pinstatic acid promotes auxin transport by inhibiting PIN internalization,” <i>Plant Physiology</i>, vol. 180, no. 2. ASPB, pp. 1152–1165, 2019.","short":"A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi, T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K. Hayashi, Plant Physiology 180 (2019) 1152–1165.","ama":"Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. <i>Plant Physiology</i>. 2019;180(2):1152-1165. doi:<a href=\"https://doi.org/10.1104/pp.19.00201\">10.1104/pp.19.00201</a>","chicago":"Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy, K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” <i>Plant Physiology</i>. ASPB, 2019. <a href=\"https://doi.org/10.1104/pp.19.00201\">https://doi.org/10.1104/pp.19.00201</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"last_name":"Oochi","first_name":"A","full_name":"Oochi, A"},{"last_name":"Hajny","orcid":"0000-0003-2140-7195","first_name":"Jakub","full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fukui, K","first_name":"K","last_name":"Fukui"},{"last_name":"Nakao","full_name":"Nakao, Y","first_name":"Y"},{"first_name":"Michelle C","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","last_name":"Gallei"},{"last_name":"Quareshy","first_name":"M","full_name":"Quareshy, M"},{"last_name":"Takahashi","first_name":"K","full_name":"Takahashi, K"},{"last_name":"Kinoshita","full_name":"Kinoshita, T","first_name":"T"},{"full_name":"Harborough, SR","first_name":"SR","last_name":"Harborough"},{"last_name":"Kepinski","full_name":"Kepinski, S","first_name":"S"},{"last_name":"Kasahara","first_name":"H","full_name":"Kasahara, H"},{"first_name":"RM","full_name":"Napier, RM","last_name":"Napier"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"},{"first_name":"KI","full_name":"Hayashi, KI","last_name":"Hayashi"}],"oa_version":"Published Version","date_updated":"2024-03-25T23:30:21Z","department":[{"_id":"JiFr"}],"publisher":"ASPB","page":"1152-1165","article_type":"original","intvolume":"       180","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"pmid":1,"status":"public","doi":"10.1104/pp.19.00201","abstract":[{"lang":"eng","text":"Polar auxin transport plays a pivotal role in plant growth and development. PIN auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport."}],"issue":"2","isi":1,"month":"06","related_material":{"record":[{"status":"public","id":"11626","relation":"dissertation_contains"},{"id":"8822","relation":"dissertation_contains","status":"public"}]},"day":"01","ec_funded":1,"publication_status":"published","acknowledgement":"We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis work was supported by the Ministry of Education, Culture, Sports, Science, and Technology (Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.), and the European Union’s Horizon2020 program (European Research Council grant agreement no. 742985 to J.F.)."},{"publisher":"ASPB","intvolume":"       180","page":"22-25","article_type":"letter_note","language":[{"iso":"eng"}],"pmid":1,"status":"public","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"issue":"1","doi":"10.1104/pp.18.01305","abstract":[{"text":"Nitrate regulation of root stem cell activity is auxin-dependent.","lang":"eng"}],"isi":1,"month":"05","publication_status":"published","day":"01","date_published":"2019-05-01T00:00:00Z","title":"Nitrate modulates the differentiation of root distal stem cells","quality_controlled":"1","date_created":"2019-04-09T08:46:17Z","main_file_link":[{"url":"https://doi.org/10.1104/pp.18.01305","open_access":"1"}],"year":"2019","publication":"Plant Physiology","article_processing_charge":"No","volume":180,"_id":"6261","external_id":{"pmid":["30787134"],"isi":["000466860800010"]},"scopus_import":"1","type":"journal_article","oa_version":"Published Version","date_updated":"2023-08-25T10:10:23Z","department":[{"_id":"JiFr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"Y. Wang, Z. Gong, J. Friml, and J. Zhang, “Nitrate modulates the differentiation of root distal stem cells,” <i>Plant Physiology</i>, vol. 180, no. 1. ASPB, pp. 22–25, 2019.","short":"Y. Wang, Z. Gong, J. Friml, J. Zhang, Plant Physiology 180 (2019) 22–25.","ama":"Wang Y, Gong Z, Friml J, Zhang J. Nitrate modulates the differentiation of root distal stem cells. <i>Plant Physiology</i>. 2019;180(1):22-25. doi:<a href=\"https://doi.org/10.1104/pp.18.01305\">10.1104/pp.18.01305</a>","chicago":"Wang, Y, Z Gong, Jiří Friml, and J Zhang. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” <i>Plant Physiology</i>. ASPB, 2019. <a href=\"https://doi.org/10.1104/pp.18.01305\">https://doi.org/10.1104/pp.18.01305</a>.","ista":"Wang Y, Gong Z, Friml J, Zhang J. 2019. Nitrate modulates the differentiation of root distal stem cells. Plant Physiology. 180(1), 22–25.","apa":"Wang, Y., Gong, Z., Friml, J., &#38; Zhang, J. (2019). Nitrate modulates the differentiation of root distal stem cells. <i>Plant Physiology</i>. ASPB. <a href=\"https://doi.org/10.1104/pp.18.01305\">https://doi.org/10.1104/pp.18.01305</a>","mla":"Wang, Y., et al. “Nitrate Modulates the Differentiation of Root Distal Stem Cells.” <i>Plant Physiology</i>, vol. 180, no. 1, ASPB, 2019, pp. 22–25, doi:<a href=\"https://doi.org/10.1104/pp.18.01305\">10.1104/pp.18.01305</a>."},"oa":1,"author":[{"last_name":"Wang","first_name":"Y","full_name":"Wang, Y"},{"last_name":"Gong","full_name":"Gong, Z","first_name":"Z"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří"},{"full_name":"Zhang, J","first_name":"J","last_name":"Zhang"}]},{"scopus_import":"1","file_date_updated":"2020-07-14T12:47:25Z","external_id":{"pmid":["30821050"],"isi":["000473644100008"]},"_id":"6262","author":[{"first_name":"Hana","full_name":"Rakusová, Hana","last_name":"Rakusová"},{"last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","first_name":"Huibin"},{"last_name":"Valošek","id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","full_name":"Valošek, Petr"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"citation":{"mla":"Rakusová, Hana, et al. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” <i>The Plant Journal</i>, vol. 98, no. 6, Wiley, 2019, pp. 1048–59, doi:<a href=\"https://doi.org/10.1111/tpj.14301\">10.1111/tpj.14301</a>.","apa":"Rakusová, H., Han, H., Valošek, P., &#38; Friml, J. (2019). Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. <i>The Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.14301\">https://doi.org/10.1111/tpj.14301</a>","ista":"Rakusová H, Han H, Valošek P, Friml J. 2019. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. The Plant Journal. 98(6), 1048–1059.","chicago":"Rakusová, Hana, Huibin Han, Petr Valošek, and Jiří Friml. “Genetic Screen for Factors Mediating PIN Polarization in Gravistimulated Arabidopsis Thaliana Hypocotyls.” <i>The Plant Journal</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/tpj.14301\">https://doi.org/10.1111/tpj.14301</a>.","short":"H. Rakusová, H. Han, P. Valošek, J. Friml, The Plant Journal 98 (2019) 1048–1059.","ama":"Rakusová H, Han H, Valošek P, Friml J. Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls. <i>The Plant Journal</i>. 2019;98(6):1048-1059. doi:<a href=\"https://doi.org/10.1111/tpj.14301\">10.1111/tpj.14301</a>","ieee":"H. Rakusová, H. Han, P. Valošek, and J. Friml, “Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls,” <i>The Plant Journal</i>, vol. 98, no. 6. Wiley, pp. 1048–1059, 2019."},"has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","checksum":"ad3b5e270b67ba2a45f894ce3be27920","relation":"main_file","date_updated":"2020-07-14T12:47:25Z","content_type":"application/pdf","file_size":1383100,"file_name":"2019_PlantJournal_Rakusov.pdf","file_id":"6304","date_created":"2019-04-15T09:38:43Z","access_level":"open_access"}],"department":[{"_id":"JiFr"}],"oa_version":"Published Version","date_updated":"2025-05-07T11:12:30Z","type":"journal_article","quality_controlled":"1","date_published":"2019-06-01T00:00:00Z","title":"Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":98,"article_processing_charge":"Yes (via OA deal)","publication":"The Plant Journal","year":"2019","date_created":"2019-04-09T08:46:44Z","ddc":["580"],"doi":"10.1111/tpj.14301","abstract":[{"text":"Gravitropism is an adaptive response that orients plant growth parallel to the gravity vector. Asymmetric\r\ndistribution of the phytohormone auxin is a necessary prerequisite to the tropic bending both in roots and\r\nshoots. During hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing\r\ncells to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization to the bottom cell mem-\r\nbranes leads to the auxin accumulation at the lower side of the organ, initiating bending and, later, auxin\r\nfeedback-mediated repolarization restores symmetric auxin distribution to terminate bending. Here, we per-\r\nformed a forward genetic screen to identify regulators of both PIN3 polarization events during gravitropic\r\nresponse. We searched for mutants with defective PIN3 polarizations based on easy-to-score morphological\r\noutputs of decreased or increased gravity-induced hypocotyl bending. We identified the number of\r\nhypocotyl reduced bending (hrb) and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-\r\nlated typically with defective gravity-induced PIN3 relocation whereas all analyzed hhb mutants showed\r\ndefects in the second, auxin-mediated PIN3 relocation. Next-generation sequencing-aided mutation map-\r\nping identified several candidate genes, including SCARECROW and ACTIN2, revealing roles of endodermis\r\nspecification and actin cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.\r\nThe hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms underlying cell\r\npolarity and plant adaptive development.","lang":"eng"}],"issue":"6","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313x"]},"pmid":1,"status":"public","ec_funded":1,"day":"01","publication_status":"published","month":"06","isi":1,"publisher":"Wiley","language":[{"iso":"eng"}],"page":"1048-1059","article_type":"original","intvolume":"        98"},{"year":"2019","article_processing_charge":"No","date_created":"2019-04-09T14:37:06Z","ddc":["575"],"date_published":"2019-02-04T00:00:00Z","title":"Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants 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Version","oa":1,"author":[{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan"}],"citation":{"ista":"Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria.","apa":"Narasimhan, M. (2019). <i>Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:th1075\">https://doi.org/10.15479/at:ista:th1075</a>","mla":"Narasimhan, Madhumitha. <i>Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants </i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/at:ista:th1075\">10.15479/at:ista:th1075</a>.","ieee":"M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ,” Institute of Science and Technology Austria, 2019.","ama":"Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . 2019. doi:<a href=\"https://doi.org/10.15479/at:ista:th1075\">10.15479/at:ista:th1075</a>","short":"M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants , Institute of Science and Technology Austria, 2019.","chicago":"Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants .” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/at:ista:th1075\">https://doi.org/10.15479/at:ista:th1075</a>."},"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","file_date_updated":"2021-02-11T23:30:15Z","_id":"6269","language":[{"iso":"eng"}],"page":"138","supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","day":"04","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","id":"412","relation":"part_of_dissertation"}]},"month":"02","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"doi":"10.15479/at:ista:th1075","abstract":[{"text":"Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking that is constantly regulated for mediating developmental and physiological responses. The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic trafficking in the whole multicellular organ systems of Arabidopsis. The first chapter of my thesis describes the search for new components involved in CME. Tandem affinity purification was conducted using CLC and its interacting partners were identified. Amongst the identified proteins were the Auxilin-likes1 and 2 (Axl1/2), putative uncoating factors, for which we made a full functional analysis. Over-expression of Axl1/2 causes extreme modifications in the dynamics of the machinery proteins and inhibition of endocytosis altogether. However the loss of function of the axl1/2 did not present any cellular or physiological phenotype, meaning Auxilin-likes do not form the major uncoating machinery. The second chapter of my thesis describes the establishment/utilisation of techniques to capture the dynamicity and the complexity of CME and post-endocytic trafficking. We have studied the development of endocytic pits at the PM – specifically, the mode of membrane remodeling during pit development and the role of actin in it, given plant cells possess high turgor pressure. Utilizing the improved z-resolution of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events at the plasma membrane; and using particle detection software, we quantitatively analysed all the endocytic trajectories in an unbiased way to obtain the endocytic rate of the system. This together with the direct analysis of cargo internalisation from the PM provided an estimate on the endocytic potential of the cell. We also developed a methodology for ultrastructural analysis of different populations of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed protoplasts. Structural analysis, together with the intensity profile of CCSs at the PM show that the mode of CCP development at the PM follows ‘Constant curvature model’; meaning that clathrin polymerisation energy is a major contributing factor of membrane remodeling. In addition, other analyses clearly show that actin is not required for membrane remodeling during invagination or any other step of CCP development, despite the prevalent high turgor pressure. However, actin is essential in orchestrating the post-endocytic trafficking of CCVs facilitating the EE formation. We also observed that the uncoating process post-endocytosis is not immediate; an alternative mechanism of uncoating – Sequential multi-step process – functions in the cell. Finally we also looked at one of the important physiological stimuli modulating the process – hormone, auxin. auxin has been known to influence CME before. We have made a detailed study on the concentration-time based effect of auxin on the machinery proteins, CCP development, and the specificity of cargoes endocytosed. To this end, we saw no general effect of auxin on CME at earlier time points. However, very low concentration of IAA, such as 50nM, accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory control with high specificity to PIN2 could be essential in modulating its polarity. ","lang":"eng"}],"status":"public","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]}},{"publisher":"Elsevier","language":[{"iso":"eng"}],"article_type":"original","page":"47-59","abstract":[{"text":"Cell-cell and cell-glycocalyx interactions under flow are important for the behaviour of circulating cells in blood and lymphatic vessels. However, such interactions are not well understood due in part to a lack of tools to study them in defined environments. Here, we develop a versatile in vitro platform for the study of cell-glycocalyx interactions in well-defined physical and chemical settings under flow. Our approach is demonstrated with the interaction between hyaluronan (HA, a key component of the endothelial glycocalyx) and its cell receptor CD44. We generate HA brushes in situ within a microfluidic device, and demonstrate the tuning of their physical (thickness and softness) and chemical (density of CD44 binding sites) properties using characterisation with reflection interference contrast microscopy (RICM) and application of polymer theory. We highlight the interactions of HA brushes with CD44-displaying beads and cells under flow. Observations of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories to be generated, and revealed interactions in the form of stop and go phases with reduced rolling velocity and reduced distance between the bead and the HA brush, compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+ AKR1 T-lymphocytes revealed complementary information about the dynamics of cell rolling and cell morphology, and highlighted the formation of tethers and slings, as they interacted with a HA brush under flow. This platform can readily incorporate more complex models of the glycocalyx, and should permit the study of how mechanical and biochemical factors are orchestrated to enable highly selective blood cell-vessel wall interactions under flow.","lang":"eng"}],"doi":"10.1016/j.matbio.2018.12.002","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_identifier":{"issn":["0945-053X"]},"status":"public","day":"01","publication_status":"published","month":"05","isi":1,"quality_controlled":"1","title":"An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments","date_published":"2019-05-01T00:00:00Z","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"volume":"78-79","article_processing_charge":"No","publication":"Matrix Biology","year":"2019","date_created":"2019-04-11T20:55:01Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:27Z","external_id":{"isi":["000468707600005"]},"_id":"6297","oa":1,"author":[{"last_name":"Davies","first_name":"Heather S.","full_name":"Davies, Heather S."},{"full_name":"Baranova, Natalia S.","first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","last_name":"Baranova"},{"last_name":"El Amri","full_name":"El Amri, Nouha","first_name":"Nouha"},{"full_name":"Coche-Guérente, Liliane","first_name":"Liliane","last_name":"Coche-Guérente"},{"last_name":"Verdier","full_name":"Verdier, Claude","first_name":"Claude"},{"last_name":"Bureau","first_name":"Lionel","full_name":"Bureau, Lionel"},{"last_name":"Richter","full_name":"Richter, Ralf P.","first_name":"Ralf P."},{"first_name":"Delphine","full_name":"Débarre, Delphine","last_name":"Débarre"}],"citation":{"ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 78–79, 47–59.","mla":"Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” <i>Matrix Biology</i>, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:<a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">10.1016/j.matbio.2018.12.002</a>.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. <i>Matrix Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">https://doi.org/10.1016/j.matbio.2018.12.002</a>","ieee":"H. S. Davies <i>et al.</i>, “An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments,” <i>Matrix Biology</i>, vol. 78–79. Elsevier, pp. 47–59, 2019.","ama":"Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. <i>Matrix Biology</i>. 2019;78-79:47-59. doi:<a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">10.1016/j.matbio.2018.12.002</a>","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59.","chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” <i>Matrix Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">https://doi.org/10.1016/j.matbio.2018.12.002</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","file":[{"creator":"dernst","relation":"main_file","checksum":"790878cd78bfc54a147ddcc7c8f286a0","file_size":4444339,"date_updated":"2020-07-14T12:47:27Z","content_type":"application/pdf","file_name":"2018_MatrixBiology_Davies.pdf","date_created":"2020-05-14T09:02:07Z","file_id":"7825","access_level":"open_access"}],"department":[{"_id":"MaLo"}],"date_updated":"2023-08-25T10:11:28Z","oa_version":"Submitted Version","type":"journal_article"},{"publisher":"Elsevier","language":[{"iso":"eng"}],"arxiv":1,"page":"920-940","intvolume":"       349","abstract":[{"text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariskiopen subset of an arbitrary smooth biquadratic hypersurface in sufficiently many variables. The proof uses the Hardy–Littlewood circle method.","lang":"eng"}],"doi":"10.1016/j.aim.2019.04.031","publication_identifier":{"issn":["00018708"],"eissn":["10902082"]},"status":"public","day":"20","publication_status":"published","month":"06","isi":1,"quality_controlled":"1","title":"Counting rational points on biquadratic hypersurfaces","date_published":"2019-06-20T00:00:00Z","volume":349,"article_processing_charge":"No","publication":"Advances in Mathematics","year":"2019","date_created":"2019-04-16T09:13:25Z","ddc":["512"],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:27Z","external_id":{"isi":["000468857300025"],"arxiv":["1810.08426"]},"_id":"6310","oa":1,"author":[{"orcid":"0000-0002-8314-0177","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","last_name":"Browning"},{"last_name":"Hu","full_name":"Hu, L.Q.","first_name":"L.Q."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","citation":{"short":"T.D. Browning, L.Q. Hu, Advances in Mathematics 349 (2019) 920–940.","ama":"Browning TD, Hu LQ. Counting rational points on biquadratic hypersurfaces. <i>Advances in Mathematics</i>. 2019;349:920-940. doi:<a href=\"https://doi.org/10.1016/j.aim.2019.04.031\">10.1016/j.aim.2019.04.031</a>","chicago":"Browning, Timothy D, and L.Q. Hu. “Counting Rational Points on Biquadratic Hypersurfaces.” <i>Advances in Mathematics</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.aim.2019.04.031\">https://doi.org/10.1016/j.aim.2019.04.031</a>.","ieee":"T. D. Browning and L. Q. Hu, “Counting rational points on biquadratic hypersurfaces,” <i>Advances in Mathematics</i>, vol. 349. Elsevier, pp. 920–940, 2019.","ista":"Browning TD, Hu LQ. 2019. Counting rational points on biquadratic hypersurfaces. Advances in Mathematics. 349, 920–940.","mla":"Browning, Timothy D., and L. Q. Hu. “Counting Rational Points on Biquadratic Hypersurfaces.” <i>Advances in Mathematics</i>, vol. 349, Elsevier, 2019, pp. 920–40, doi:<a href=\"https://doi.org/10.1016/j.aim.2019.04.031\">10.1016/j.aim.2019.04.031</a>.","apa":"Browning, T. D., &#38; Hu, L. Q. (2019). Counting rational points on biquadratic hypersurfaces. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2019.04.031\">https://doi.org/10.1016/j.aim.2019.04.031</a>"},"department":[{"_id":"TiBr"}],"file":[{"file_name":"wliqun.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:27Z","file_size":379158,"access_level":"open_access","file_id":"6311","date_created":"2019-04-16T09:12:20Z","checksum":"a63594a3a91b4ba6e2a1b78b0720b3d0","relation":"main_file","creator":"tbrownin"}],"oa_version":"Submitted Version","date_updated":"2023-08-25T10:11:55Z","type":"journal_article"},{"language":[{"iso":"eng"}],"intvolume":"       568","page":"546-550","article_type":"letter_note","publisher":"Springer Nature","publication_status":"published","day":"25","ec_funded":1,"isi":1,"month":"04","related_material":{"record":[{"id":"14697","relation":"dissertation_contains","status":"public"},{"id":"6891","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/"}]},"acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"lang":"eng","text":"During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion."}],"doi":"10.1038/s41586-019-1087-5","pmid":1,"status":"public","year":"2019","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/","open_access":"1"}],"publication":"Nature","volume":568,"article_processing_charge":"No","date_created":"2019-04-17T06:52:28Z","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"name":"Cellular navigation along spatial gradients","grant_number":"724373","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"265FAEBA-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"25A48D24-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1396-2014","name":"Molecular and system level view of immune cell migration"}],"date_published":"2019-04-25T00:00:00Z","title":"Nuclear positioning facilitates amoeboid migration along the path of least resistance","quality_controlled":"1","oa_version":"Submitted Version","date_updated":"2024-03-25T23:30:22Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"citation":{"short":"J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin, R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.","ama":"Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. <i>Nature</i>. 2019;568:546-550. doi:<a href=\"https://doi.org/10.1038/s41586-019-1087-5\">10.1038/s41586-019-1087-5</a>","chicago":"Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K. Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1087-5\">https://doi.org/10.1038/s41586-019-1087-5</a>.","ieee":"J. Renkawitz <i>et al.</i>, “Nuclear positioning facilitates amoeboid migration along the path of least resistance,” <i>Nature</i>, vol. 568. Springer Nature, pp. 546–550, 2019.","ista":"Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 568, 546–550.","mla":"Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” <i>Nature</i>, vol. 568, Springer Nature, 2019, pp. 546–50, doi:<a href=\"https://doi.org/10.1038/s41586-019-1087-5\">10.1038/s41586-019-1087-5</a>.","apa":"Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin, J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along the path of least resistance. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1087-5\">https://doi.org/10.1038/s41586-019-1087-5</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Renkawitz, Jörg","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","last_name":"Renkawitz"},{"full_name":"Kopf, Aglaja","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656","last_name":"Kopf"},{"last_name":"Stopp","full_name":"Stopp, Julian A","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"last_name":"de Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"de Vries, Ingrid","first_name":"Ingrid"},{"last_name":"Driscoll","first_name":"Meghan K.","full_name":"Driscoll, Meghan K."},{"last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"first_name":"Erik S.","full_name":"Welf, Erik S.","last_name":"Welf"},{"full_name":"Danuser, Gaudenz","first_name":"Gaudenz","last_name":"Danuser"},{"last_name":"Fiolka","first_name":"Reto","full_name":"Fiolka, Reto"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"oa":1,"type":"journal_article","external_id":{"isi":["000465594200050"],"pmid":["30944468"]},"scopus_import":"1","_id":"6328"},{"volume":102,"article_processing_charge":"No","publication":"Neuron","year":"2019","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.01.052","open_access":"1"}],"date_created":"2019-04-17T08:28:59Z","quality_controlled":"1","date_published":"2019-04-17T00:00:00Z","title":"Hippocampal reactivation of random trajectories resembling Brownian diffusion","project":[{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"I03713","name":"Interneuro Plasticity During Spatial Learning","_id":"2654F984-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa":1,"author":[{"last_name":"Stella","orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","full_name":"Stella, Federico","first_name":"Federico"},{"id":"361CC00E-F248-11E8-B48F-1D18A9856A87","full_name":"Baracskay, Peter","first_name":"Peter","last_name":"Baracskay"},{"last_name":"O'Neill","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","full_name":"O'Neill, Joseph"},{"last_name":"Csicsvari","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of random trajectories resembling Brownian diffusion. <i>Neuron</i>. 2019;102:450-461. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.01.052\">10.1016/j.neuron.2019.01.052</a>","short":"F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461.","chicago":"Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” <i>Neuron</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neuron.2019.01.052\">https://doi.org/10.1016/j.neuron.2019.01.052</a>.","ieee":"F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation of random trajectories resembling Brownian diffusion,” <i>Neuron</i>, vol. 102. Elsevier, pp. 450–461, 2019.","ista":"Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461.","mla":"Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” <i>Neuron</i>, vol. 102, Elsevier, 2019, pp. 450–61, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.01.052\">10.1016/j.neuron.2019.01.052</a>.","apa":"Stella, F., Baracskay, P., O’Neill, J., &#38; Csicsvari, J. L. (2019). Hippocampal reactivation of random trajectories resembling Brownian diffusion. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.01.052\">https://doi.org/10.1016/j.neuron.2019.01.052</a>"},"department":[{"_id":"JoCs"}],"oa_version":"Published Version","date_updated":"2023-08-25T10:13:07Z","type":"journal_article","scopus_import":"1","external_id":{"pmid":["30819547"],"isi":["000465169700017"]},"_id":"6338","language":[{"iso":"eng"}],"article_type":"original","page":"450-461","intvolume":"       102","publisher":"Elsevier","ec_funded":1,"day":"17","publication_status":"published","month":"04","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/"}]},"isi":1,"abstract":[{"lang":"eng","text":"Hippocampal activity patterns representing movement trajectories are reactivated in immobility and sleep periods, a process associated with memory recall, consolidation, and decision making. It is thought that only fixed, behaviorally relevant patterns can be reactivated, which are stored across hippocampal synaptic connections. To test whether some generalized rules govern reactivation, we examined trajectory reactivation following non-stereotypical exploration of familiar open-field environments. We found that random trajectories of varying lengths and timescales were reactivated, resembling that of Brownian motion of particles. The animals’ behavioral trajectory did not follow Brownian diffusion demonstrating that the exact behavioral experience is not reactivated. Therefore, hippocampal circuits are able to generate random trajectories of any recently active map by following diffusion dynamics. This ability of hippocampal circuits to generate representations of all behavioral outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent cognitive functions such as learning, generalization, and planning."}],"doi":"10.1016/j.neuron.2019.01.052","pmid":1,"status":"public"},{"doi":"10.1038/s41586-019-1110-x","abstract":[{"text":"High-speed optical telecommunication is enabled by wavelength-division multiplexing, whereby hundreds of individually stabilized lasers encode information within a single-mode optical fibre. Higher bandwidths require higher total optical power, but the power sent into the fibre is limited by optical nonlinearities within the fibre, and energy consumption by the light sources starts to become a substantial cost factor1. Optical frequency combs have been suggested to remedy this problem by generating numerous discrete, equidistant laser lines within a monolithic device; however, at present their stability and coherence allow them to operate only within small parameter ranges2,3,4. Here we show that a broadband frequency comb realized through the electro-optic effect within a high-quality whispering-gallery-mode resonator can operate at low microwave and optical powers. Unlike the usual third-order Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear effect, which is much more efficient. Our result uses a fixed microwave signal that is mixed with an optical-pump signal to generate a coherent frequency comb with a precisely determined carrier separation. The resonant enhancement enables us to work with microwave powers that are three orders of magnitude lower than those in commercially available devices. We emphasize the practical relevance of our results to high rates of data communication. To circumvent the limitations imposed by nonlinear effects in optical communication fibres, one has to solve two problems: to provide a compact and fully integrated, yet high-quality and coherent, frequency comb generator; and to calculate nonlinear signal propagation in real time5. We report a solution to the first problem.","lang":"eng"}],"issue":"7752","publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"status":"public","day":"18","publication_status":"published","isi":1,"month":"04","related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-019-1220-5","relation":"erratum"}]},"publisher":"Springer Nature","arxiv":1,"language":[{"iso":"eng"}],"page":"378-381","intvolume":"       568","scopus_import":"1","external_id":{"arxiv":["1808.10608"],"isi":["000464950700053"]},"_id":"6348","citation":{"short":"A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature 568 (2019) 378–381.","ama":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic frequency comb. <i>Nature</i>. 2019;568(7752):378-381. doi:<a href=\"https://doi.org/10.1038/s41586-019-1110-x\">10.1038/s41586-019-1110-x</a>","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1110-x\">https://doi.org/10.1038/s41586-019-1110-x</a>.","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel, “Resonant electro-optic frequency comb,” <i>Nature</i>, vol. 568, no. 7752. Springer Nature, pp. 378–381, 2019.","ista":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant electro-optic frequency comb. Nature. 568(7752), 378–381.","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.” <i>Nature</i>, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:<a href=\"https://doi.org/10.1038/s41586-019-1110-x\">10.1038/s41586-019-1110-x</a>.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., &#38; Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1110-x\">https://doi.org/10.1038/s41586-019-1110-x</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"author":[{"first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez"},{"first_name":"Florian","full_name":"Sedlmeir, Florian","last_name":"Sedlmeir"},{"first_name":"Madhuri","full_name":"Kumari, Madhuri","last_name":"Kumari"},{"first_name":"Gerd","full_name":"Leuchs, Gerd","last_name":"Leuchs"},{"last_name":"Schwefel","full_name":"Schwefel, Harald G.L.","first_name":"Harald G.L."}],"oa_version":"Preprint","date_updated":"2023-08-25T10:15:25Z","department":[{"_id":"JoFi"}],"type":"journal_article","quality_controlled":"1","date_published":"2019-04-18T00:00:00Z","title":"Resonant electro-optic frequency comb","publication":"Nature","article_processing_charge":"No","volume":568,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.10608"}],"year":"2019","date_created":"2019-04-28T21:59:13Z"},{"file":[{"checksum":"4ceba04a96a74f5092ec3ce2c579a0c7","relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"6411","date_created":"2019-05-13T06:12:45Z","file_name":"2019_Cell_Marhava.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:28Z","file_size":10272032}],"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"date_updated":"2024-03-25T23:30:06Z","oa_version":"Published Version","author":[{"last_name":"Marhavá","full_name":"Marhavá, Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra"},{"last_name":"Hörmayer","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926"},{"full_name":"Yoshida, Saiko","first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","last_name":"Yoshida"},{"last_name":"Marhavy","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Marhavy, Peter"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"oa":1,"has_accepted_license":"1","citation":{"mla":"Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>.","apa":"Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., &#38; Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>","ista":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13.","chicago":"Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>.","short":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13.","ama":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. 2019;177(4):957-969.e13. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>","ieee":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” <i>Cell</i>, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","external_id":{"isi":["000466843000015"],"pmid":["31051107"]},"scopus_import":"1","file_date_updated":"2020-07-14T12:47:28Z","_id":"6351","year":"2019","article_processing_charge":"No","volume":177,"publication":"Cell","date_created":"2019-04-28T21:59:14Z","ddc":["570"],"date_published":"2019-05-02T00:00:00Z","title":"Re-activation of stem cell pathways for pattern restoration in plant wound healing","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","ec_funded":1,"day":"02","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/"}],"record":[{"relation":"dissertation_contains","id":"9992","status":"public"}]},"month":"05","isi":1,"acknowledged_ssus":[{"_id":"Bio"}],"issue":"4","abstract":[{"lang":"eng","text":"A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing."}],"doi":"10.1016/j.cell.2019.04.015","pmid":1,"status":"public","publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"language":[{"iso":"eng"}],"intvolume":"       177","page":"957-969.e13","publisher":"Elsevier"},{"quality_controlled":"1","title":"Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure","date_published":"2019-04-12T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (via OA deal)","publication":"Molecular Biology Reports","year":"2019","date_created":"2019-04-28T21:59:14Z","ddc":["570"],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:28Z","external_id":{"isi":["000470332600049"]},"_id":"6352","oa":1,"author":[{"full_name":"Temnov, Andrey Alexandrovich","first_name":"Andrey Alexandrovich","last_name":"Temnov"},{"last_name":"Rogov","full_name":"Rogov, Konstantin Arkadevich","first_name":"Konstantin Arkadevich"},{"last_name":"Sklifas","full_name":"Sklifas, Alla Nikolaevna","first_name":"Alla Nikolaevna"},{"first_name":"Elena Valerievna","full_name":"Klychnikova, Elena Valerievna","last_name":"Klychnikova"},{"first_name":"Markus","full_name":"Hartl, Markus","last_name":"Hartl"},{"first_name":"Kristina","full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo"},{"last_name":"Charnagalov","full_name":"Charnagalov, Alexej","id":"49F06DBA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexej"}],"citation":{"ama":"Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. <i>Molecular Biology Reports</i>. 2019. doi:<a href=\"https://doi.org/10.1007/s11033-019-04765-z\">10.1007/s11033-019-04765-z</a>","short":"A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019).","chicago":"Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo, and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” <i>Molecular Biology Reports</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s11033-019-04765-z\">https://doi.org/10.1007/s11033-019-04765-z</a>.","ieee":"A. A. Temnov <i>et al.</i>, “Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure,” <i>Molecular Biology Reports</i>. Springer, 2019.","ista":"Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports.","mla":"Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” <i>Molecular Biology Reports</i>, Springer, 2019, doi:<a href=\"https://doi.org/10.1007/s11033-019-04765-z\">10.1007/s11033-019-04765-z</a>.","apa":"Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M., Djinovic-Carugo, K., &#38; Charnagalov, A. (2019). Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. <i>Molecular Biology Reports</i>. Springer. <a href=\"https://doi.org/10.1007/s11033-019-04765-z\">https://doi.org/10.1007/s11033-019-04765-z</a>"},"has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_created":"2019-04-30T09:52:36Z","file_id":"6362","access_level":"open_access","file_size":1948014,"date_updated":"2020-07-14T12:47:28Z","content_type":"application/pdf","file_name":"2019_MolecularBioReport_Temnov.pdf","creator":"dernst","relation":"main_file","checksum":"45bf040bbce1cea274f6013fa18ba21b"}],"department":[{"_id":"LeSa"}],"date_updated":"2023-08-25T10:14:26Z","oa_version":"Published Version","type":"journal_article","publisher":"Springer","language":[{"iso":"eng"}],"abstract":[{"text":"Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10%  O2) and normal (21%  O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different  O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure.","lang":"eng"}],"doi":"10.1007/s11033-019-04765-z","publication_identifier":{"eissn":["15734978"],"issn":["03014851"]},"status":"public","day":"12","acknowledgement":"The studies were supported by the Austrian Federal Ministry of Economy, Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding the Center of Optimized Structural Stud-ies, grant No. 253275","publication_status":"published","month":"04","isi":1},{"_id":"6363","file_date_updated":"2021-02-11T11:17:15Z","type":"dissertation","department":[{"_id":"PeJo"}],"file":[{"creator":"cespinoza","checksum":"77c6c05cfe8b58c8abcf1b854375d084","relation":"main_file","embargo":"2020-05-09","date_updated":"2021-02-11T11:17:15Z","content_type":"application/pdf","file_size":13966891,"file_name":"Espinozathesis_all2.pdf","file_id":"6389","date_created":"2019-05-07T16:00:39Z","access_level":"open_access"},{"file_name":"Espinoza_Thesis.docx","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2020-07-14T12:47:28Z","file_size":11159900,"access_level":"closed","file_id":"6390","date_created":"2019-05-07T16:00:48Z","checksum":"f6aa819f127691a2b0fc21c76eb09746","relation":"source_file","creator":"cespinoza"}],"date_updated":"2023-09-15T12:03:48Z","oa_version":"Published Version","author":[{"last_name":"Espinoza Martinez","orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia ","full_name":"Espinoza Martinez, Claudia "}],"oa":1,"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits,” Institute of Science and Technology Austria, 2019.","ama":"Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6363\">10.15479/AT:ISTA:6363</a>","short":"C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria, 2019.","chicago":"Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6363\">https://doi.org/10.15479/AT:ISTA:6363</a>.","ista":"Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria.","apa":"Espinoza Martinez, C. (2019). <i>Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6363\">https://doi.org/10.15479/AT:ISTA:6363</a>","mla":"Espinoza Martinez, Claudia. <i>Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6363\">10.15479/AT:ISTA:6363</a>."},"date_published":"2019-04-30T00:00:00Z","title":"Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits","date_created":"2019-04-30T11:56:10Z","ddc":["570"],"year":"2019","article_processing_charge":"No","status":"public","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-000-8"]},"doi":"10.15479/AT:ISTA:6363","abstract":[{"lang":"eng","text":"Distinguishing  between  similar  experiences  is  achieved  by  the  brain  in  a  process called  pattern  separation.  In  the  hippocampus,  pattern  separation  reduces  the interference of memories and increases the storage capacity by decorrelating similar inputs  patterns  of  neuronal  activity  into  non-overlapping output  firing  patterns. Winners-take-all  (WTA)  mechanism  is  a  theoretical  model  for  pattern  separation  in which  a  \"winner\"  cell  suppresses  the  activity  of  the  neighboring  neurons  through feedback inhibition. However, if the network properties of the dentate gyrus support WTA as a biologically conceivable model remains unknown. Here, we showed that the connectivity rules of PV+interneurons and their synaptic properties are optimizedfor efficient pattern separation. We found using multiple whole-cell in vitrorecordings that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition, a form of  feedback  inhibition  in  which  a  GC  inhibits  other  GCs  but  not  itself  through  the activation of PV+interneurons. Thus, lateral inhibition between GC–PV+interneurons was ~10 times more abundant than recurrent connections. Furthermore, the GC–PV+interneuron  connectivity  was  more  spatially  confined  but  less  abundant  than  PV+interneurons–GC  connectivity,  leading  to  an  asymmetrical  distribution  of  excitatory and inhibitory connectivity. Our network model of the dentate gyrus with incorporated real connectivity rules efficiently decorrelates neuronal activity patterns using WTA as the  primary  mechanism.  This  process  relied  on  lateral  inhibition,  fast-signaling properties  of  PV+interneurons  and  the  asymmetrical  distribution  of  excitatory  and inhibitory connectivity. Finally, we found that silencing the activity of PV+interneurons in  vivoleads  to  acute  deficits  in  discrimination  between  similar  environments, suggesting  that  PV+interneuron  networks  are  necessary  for  behavioral  relevant computations.  Our   results   demonstrate   that   PV+interneurons  possess  unique connectivity  and  fast  signaling  properties  that confer  to  the  dentate  gyrus  network properties that allow the emergence of pattern separation. Thus, our results contribute to the knowledge of how specific forms of network organization underlie sophisticated types of information processing. \r\n"}],"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"21"}]},"month":"04","publication_status":"published","day":"30","publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"page":"140","language":[{"iso":"eng"}]},{"year":"2019","main_file_link":[{"url":"www.doi.org/10.1104/pp.18.01377","open_access":"1"}],"publication":"Plant Physiology","article_processing_charge":"No","volume":180,"date_created":"2019-04-30T15:24:22Z","title":"A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls","date_published":"2019-06-01T00:00:00Z","quality_controlled":"1","date_updated":"2023-09-05T12:25:19Z","oa_version":"Published Version","department":[{"_id":"JiFr"}],"citation":{"ista":"Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M, Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766.","mla":"Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” <i>Plant Physiology</i>, vol. 180, no. 2, ASPB, 2019, pp. 757–66, doi:<a href=\"https://doi.org/10.1104/pp.18.01377\">10.1104/pp.18.01377</a>.","apa":"Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J., … Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. <i>Plant Physiology</i>. ASPB. <a href=\"https://doi.org/10.1104/pp.18.01377\">https://doi.org/10.1104/pp.18.01377</a>","ama":"Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. <i>Plant Physiology</i>. 2019;180(2):757-766. doi:<a href=\"https://doi.org/10.1104/pp.18.01377\">10.1104/pp.18.01377</a>","short":"J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766.","chicago":"Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” <i>Plant Physiology</i>. ASPB, 2019. <a href=\"https://doi.org/10.1104/pp.18.01377\">https://doi.org/10.1104/pp.18.01377</a>.","ieee":"J. Bellstaedt <i>et al.</i>, “A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls,” <i>Plant Physiology</i>, vol. 180, no. 2. ASPB, pp. 757–766, 2019."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"last_name":"Bellstaedt","first_name":"Julia","full_name":"Bellstaedt, Julia"},{"last_name":"Trenner","first_name":"Jana","full_name":"Trenner, Jana"},{"full_name":"Lippmann, Rebecca","first_name":"Rebecca","last_name":"Lippmann"},{"last_name":"Poeschl","full_name":"Poeschl, Yvonne","first_name":"Yvonne"},{"last_name":"Zhang","first_name":"Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"},{"last_name":"Quint","first_name":"Marcel","full_name":"Quint, Marcel"},{"last_name":"Delker","first_name":"Carolin","full_name":"Delker, Carolin"}],"type":"journal_article","external_id":{"pmid":["31000634"],"isi":["000470086100019"]},"scopus_import":"1","_id":"6366","language":[{"iso":"eng"}],"intvolume":"       180","article_type":"original","page":"757-766","publisher":"ASPB","publication_status":"published","day":"01","isi":1,"month":"06","issue":"2","doi":"10.1104/pp.18.01377","abstract":[{"lang":"eng","text":"Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl."}],"pmid":1,"status":"public","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]}},{"title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","date_published":"2019-05-03T00:00:00Z","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"project":[{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","year":"2019","date_created":"2019-05-03T11:55:51Z","ddc":["576","579"],"file_date_updated":"2021-02-11T11:17:13Z","_id":"6371","oa":1,"author":[{"last_name":"Igler","full_name":"Igler, Claudia","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","citation":{"short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6371\">10.15479/AT:ISTA:6371</a>","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6371\">https://doi.org/10.15479/AT:ISTA:6371</a>.","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria.","mla":"Igler, Claudia. <i>On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6371\">10.15479/AT:ISTA:6371</a>.","apa":"Igler, C. (2019). <i>On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6371\">https://doi.org/10.15479/AT:ISTA:6371</a>"},"file":[{"file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","file_size":12597663,"content_type":"application/pdf","date_updated":"2021-02-11T11:17:13Z","access_level":"open_access","date_created":"2019-05-03T11:54:52Z","file_id":"6373","relation":"main_file","checksum":"c0085d47c58c9cbcab1b0a783480f6da","creator":"cigler","embargo":"2020-05-02"},{"relation":"source_file","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","creator":"cigler","access_level":"closed","date_created":"2019-05-03T11:54:54Z","file_id":"6374","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","embargo_to":"open_access","file_size":34644426,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2020-07-14T12:47:28Z"}],"department":[{"_id":"CaGu"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:45:52Z","type":"dissertation","supervisor":[{"full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"page":"152","doi":"10.15479/AT:ISTA:6371","abstract":[{"lang":"eng","text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation.   \r\n"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","status":"public","day":"03","publication_status":"published","month":"05","related_material":{"record":[{"relation":"part_of_dissertation","id":"67","status":"public"},{"status":"public","id":"5585","relation":"popular_science"}]},"alternative_title":["ISTA Thesis"]},{"status":"public","publication_identifier":{"isbn":["9781450359337"]},"abstract":[{"lang":"eng","text":"In today's cryptocurrencies, Hashcash proof of work is the most commonly-adopted approach to mining. In Hashcash, when a miner decides to add a block to the chain, she has to solve the difficult computational puzzle of inverting a hash function. While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it has attracted significant and harsh criticism due to its massive waste of electricity, its carbon footprint and environmental effects, and the inherent lack of usefulness in inverting a hash function. Various other mining protocols have been suggested, including proof of stake, in which a miner's chance of adding the next block is proportional to her current balance. However, such protocols lead to a higher entry cost for new miners who might not still have any stake in the cryptocurrency, and can in the worst case lead to an oligopoly, where the rich have complete control over mining. In this paper, we propose Hybrid Mining: a new mining protocol that combines solving real-world useful problems with Hashcash. Our protocol allows new miners to join the network by taking part in Hashcash mining without having to own an initial stake. It also allows nodes of the network to submit hard computational problems whose solutions are of interest in the real world, e.g.~protein folding problems. Then, miners can choose to compete in solving these problems, in lieu of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners to solve useful problems, such as hard computational problems arising in biology, in a distributed manner. It also gives researchers in other areas an easy-to-use tool to outsource their hard computations to the blockchain network, which has enormous computational power, by paying a reward to the miner who solves the problem for them. Moreover, our protocol provides strong security guarantees and is at least as resilient to double spending as Bitcoin."}],"doi":"10.1145/3297280.3297319","isi":1,"month":"04","related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"publication_status":"published","day":"01","ec_funded":1,"publisher":"ACM","page":"374-381","language":[{"iso":"eng"}],"_id":"6378","external_id":{"isi":["000474685800049"]},"file_date_updated":"2020-07-14T12:47:29Z","scopus_import":"1","pubrep_id":"1069","type":"conference","oa_version":"Submitted Version","date_updated":"2025-06-02T08:53:46Z","department":[{"_id":"KrCh"}],"file":[{"file_name":"2019_ACM_Chatterjee.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:29Z","file_size":1023934,"access_level":"open_access","file_id":"6379","date_created":"2019-05-06T12:09:27Z","checksum":"fbfbcd5a0c7a743862bfc3045539a614","relation":"main_file","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","citation":{"mla":"Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, vol. Part F147772, ACM, 2019, pp. 374–81, doi:<a href=\"https://doi.org/10.1145/3297280.3297319\">10.1145/3297280.3297319</a>.","apa":"Chatterjee, K., Goharshady, A. K., &#38; Pourdamghani, A. (2019). Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i> (Vol. Part F147772, pp. 374–381). Limassol, Cyprus: ACM. <a href=\"https://doi.org/10.1145/3297280.3297319\">https://doi.org/10.1145/3297280.3297319</a>","ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. Proceedings of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing vol. Part F147772, 374–381.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Part F147772:374–81. ACM, 2019. <a href=\"https://doi.org/10.1145/3297280.3297319\">https://doi.org/10.1145/3297280.3297319</a>.","ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In: <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>. Vol Part F147772. ACM; 2019:374-381. doi:<a href=\"https://doi.org/10.1145/3297280.3297319\">10.1145/3297280.3297319</a>","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381.","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving,” in <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Limassol, Cyprus, 2019, vol. Part F147772, pp. 374–381."},"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar"},{"last_name":"Pourdamghani","full_name":"Pourdamghani, Arash","first_name":"Arash"}],"oa":1,"conference":{"name":"ACM Symposium on Applied Computing","end_date":"2019-04-12","start_date":"2019-04-08","location":"Limassol, Cyprus"},"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"title":"Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving","date_published":"2019-04-01T00:00:00Z","quality_controlled":"1","ddc":["004"],"date_created":"2019-05-06T12:11:36Z","year":"2019","publication":"Proceedings of the 34th ACM Symposium on Applied Computing","article_processing_charge":"No","volume":"Part F147772"},{"publisher":"ACM","language":[{"iso":"eng"}],"article_number":"53","intvolume":"         3","issue":"POPL","doi":"10.1145/3290366","abstract":[{"lang":"eng","text":"There is a huge gap between the speeds of modern caches and main memories, and therefore cache misses account for a considerable loss of efficiency in programs. The predominant technique to address this issue has been Data Packing: data elements that are frequently accessed within time proximity are packed into the same cache block, thereby minimizing accesses to the main memory. We consider the algorithmic problem of Data Packing on a two-level memory system. Given a reference sequence R of accesses to data elements, the task is to partition the elements into cache blocks such that the number of cache misses on R is minimized. The problem is notoriously difficult: it is NP-hard even when the cache has size 1, and is hard to approximate for any cache size larger than 4. Therefore, all existing techniques for Data Packing are based on heuristics and lack theoretical guarantees. In this work, we present the first positive theoretical results for Data Packing, along with new and stronger negative results. We consider the problem under the lens of the underlying access hypergraphs, which are hypergraphs of affinities between the data elements, where the order of an access hypergraph corresponds to the size of the affinity group. We study the problem parameterized by the treewidth of access hypergraphs, which is a standard notion in graph theory to measure the closeness of a graph to a tree. Our main results are as follows: We show there is a number q* depending on the cache parameters such that (a) if the access hypergraph of order q* has constant treewidth, then there is a linear-time algorithm for Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy depending on a single parameter, namely, the highest order among access hypegraphs that have constant treewidth; and establish the optimal value q* of this parameter. Finally, we present an experimental evaluation of a prototype implementation of our algorithm. Our results demonstrate that, in practice, access hypergraphs of many commonly-used algorithms have small treewidth. We compare our approach with several state-of-the-art heuristic-based algorithms and show that our algorithm leads to significantly fewer cache-misses. "}],"status":"public","publication_identifier":{"issn":["2475-1421"]},"publication_status":"published","day":"01","ec_funded":1,"related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"month":"01","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"title":"Efficient parameterized algorithms for data packing","date_published":"2019-01-01T00:00:00Z","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2019","publication":"Proceedings of the ACM on Programming Languages","volume":3,"ddc":["004"],"date_created":"2019-05-06T12:18:17Z","file_date_updated":"2020-07-14T12:47:29Z","_id":"6380","date_updated":"2024-03-25T23:30:18Z","oa_version":"Published Version","department":[{"_id":"KrCh"}],"file":[{"file_id":"6381","date_created":"2019-05-06T12:23:11Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:29Z","file_size":1294962,"file_name":"2019_ACM_POPL_Chatterjee.pdf","creator":"dernst","checksum":"c157752f96877b36685ad7063ada4524","relation":"main_file"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data Packing.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 3, no. POPL, 53, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3290366\">10.1145/3290366</a>.","apa":"Chatterjee, K., Goharshady, A. K., Okati, N., &#38; Pavlogiannis, A. (2019). Efficient parameterized algorithms for data packing. <i>Proceedings of the ACM on Programming Languages</i>. ACM. <a href=\"https://doi.org/10.1145/3290366\">https://doi.org/10.1145/3290366</a>","ista":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. 3(POPL), 53.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” <i>Proceedings of the ACM on Programming Languages</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3290366\">https://doi.org/10.1145/3290366</a>.","short":"K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 3 (2019).","ama":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized algorithms for data packing. <i>Proceedings of the ACM on Programming Languages</i>. 2019;3(POPL). doi:<a href=\"https://doi.org/10.1145/3290366\">10.1145/3290366</a>","ieee":"K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient parameterized algorithms for data packing,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 3, no. POPL. ACM, 2019."},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nastaran","full_name":"Okati, Nastaran","last_name":"Okati"},{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"1056","type":"journal_article"}]