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  • Publications Dirk Inzé
    Inzé Lab Members and Alumni Group Members Publications Dirk Inzé News Research Groups Alain Goossens Lab Ann Depicker Lab Bruno Cammue Lab Daniel Van Damme Lab Dirk Inzé Lab Frank Van Breusegem Lab Geert De Jaeger Lab Ive De Smet Lab Jenny Russinova Lab Lieven De Veylder Lab Mieke Van Lijsebettens Lab Moritz Nowack Lab Sofie Goormachtig Lab Steven Maere Lab Tom Beeckman Lab Yves Van de Peer Lab Wout

    Original URL path: http://www.psb.vib-ugent.be/publications-dirk-inze (2016-04-26)
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  • News
    can be used to obtain higher yields during plant breeding movie in Dutch Prev Next Projects Yield Booster Website Collaborations Dirk Inzé Lab Members and Alumni Group Members Publications Dirk Inzé News Research Groups Alain Goossens Lab Ann Depicker Lab Bruno Cammue Lab Daniel Van Damme Lab Dirk Inzé Lab Frank Van Breusegem Lab Geert De Jaeger Lab Ive De Smet Lab Jenny Russinova Lab Lieven De Veylder Lab Mieke

    Original URL path: http://www.psb.vib-ugent.be/news-diinz (2016-04-26)
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  • Introduction
    supplying a sustainable CO 2 neutral source for the ever increasing energy needs There is an obvious and urgent need to further increase crop productivity As yield is the most important trait for breeding a considerable amount of eco physiological research has been conducted on yield performance of crops In contrast surprisingly little is known about the molecular networks underpinning crop yield and plant organ size partly because of its multifactorial nature in which many physiological processes such as photosynthesis water mineral uptake and stress tolerance determine the resources available to produce new cells tissues and organs Albeit plant growth and stress tolerance are obviously high complex processes novel approaches collectively called systems biology allow us to better understand this complexity It is our ambition to decipher the molecular networks underpinning yield and organ growth both under standard as well as mild drought stress conditions in Arabidopsis and the C4 crop maize Systems biology will ultimately provide a holistic view enabling the optimalization of plant productivity either by advanced plant breeding or genetic engineering Next Projects Yield Booster Website Collaborations Dirk Inzé Lab Members and Alumni Group Members Publications Dirk Inzé News Research Groups Alain Goossens Lab Ann Depicker Lab

    Original URL path: http://www.psb.vib-ugent.be/systems-biology-of-yield/238-introduction (2016-04-26)
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  • Organ Size Regulation
    interactions analyses to study the mode of action of growth promoting genes and identify new potential growth regulators We have in the past identified and studied several growth promoting genes and we are now further investigating their function as well as their targets and or interacting proteins to expand the growth regulatory network To discover new growth regulators and growth regulatory pathways in a non a priori manner we also make use of a chemical genomics approach We will use our expertise in imaging to s creen chemical libraries of small molecules to find compounds positively influencing leaf growth Whereas much research is done on single genes affecting leaf size the interactions between these growth regulators remain unexplored Therefore to build a more integrated growth regulatory network we study the connections existing between the different molecular players of the various processes driving leaf growth Our final aim is to be able model regulatory networks to understand leaf growth People involved Nathalie Gonzalez Project leader Stijn Dhondt Hannes Vanhaeren Jonas Blomme Youn Joeng Nam Judith Van Dingenen Jasmien Vercruysse Liesbeth De Milde Twiggy Van Daele Mattias Vermeersch Selected publications Gonzalez N Pauwels L Baekelandt A De Milde L Van Leene J Besbrugge N Heyndrickx KS Pérez AC Durand AN De Clercq R Van De Slijke E Vanden Bossche R Eeckhout D Gevaert K Vandepoele K De Jaeger G Goossens A Inzé D 2015 A Repressor Protein Complex Regulates Leaf Growth in Arabidopsis Plant Cell PMID 26232487 Vanhaeren H Gonzalez N Inzé D 2015 A Journey Through a Leaf Phenomics Analysis of Leaf Growth in Arabidopsis thaliana Arabidopsis Book PMID 26217168 Vercruyssen L Tognetti VB Gonzalez N Van Dingenen J De Milde L Bielach A De Rycke R Van Breusegem F Inzé D 2015 GROWTH REGULATING FACTOR5 stimulates Arabidopsis chloroplast division photosynthesis and leaf longevity Plant Physiol Mar 167 3 817 32 PMID 25604530 Vanhaeren H Gonzalez N Coppens F De Milde L Van Daele T Vermeersch M Eloy NB Storme V Inzé D 2014 Combining growth promoting genes leads to positive epistasis in Arabidopsis thaliana Elife PMID 24843021 Vercruyssen L Verkest A Gonzalez N Heyndrickx KS Eeckhout D Han SK Jégu T Archacki R Van Leene J Andriankaja M De Bodt S Abeel T Coppens F Dhondt S De Milde L Vermeersch M Maleux K Gevaert K Jerzmanowski A Benhamed M Wagner D Vandepoele K De Jaeger G Inzé D 2014 ANGUSTIFOLIA3 binds to SWI SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development Plant Cell PMID 24443518 Gonzalez N Vanhaeren H Inzé D 2012 Leaf size control complex coordination of cell division and expansion Trends Plant Sci 17 6 332 40 Eloy NB Gonzalez N Van Leene J Maleux K Vanhaeren H De Milde L Dhondt S Vercruysse L Witters E Mercier R Cromer L Beemster GT Remaut H Van Montagu MC De Jaeger G Ferreira PC Inzé D 2012 SAMBA a plant specific anaphase promoting complex cyclosome regulator is involved in early development and A type cyclin

    Original URL path: http://www.psb.vib-ugent.be/systems-biology-of-yield/239-regulating-organ-size (2016-04-26)
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  • Unravel Leaf Growth
    publicly available data sources to unravel the molecular mechanisms of leaf growth In addition we try to identify new leaf growth regulators through gene prioritization in these molecular networks Bioinformatics tool development CORNET a user friendly tool for data mining and integration We have developed the tool CORNET which allows the interrogation of currently available microarray protein protein interaction regulatory interaction gene gene association and functional annotation data De Bodt et al 2010 2012 Different search options are implemented to enable the construction of integrated networks centered around multiple input genes or proteins Networks and associated evidence of the majority of currently available data types are visualized in Cytoscape see Fig 2 CORNET is currently available for Arabidopsis and maize Figure 1 Transcript profiling using RNA seq xpres Figure 2 CORNET co expression and protein protein interaction network People involved Frederik Coppens Dorota Herman Steven Maere Bram Slabbinck Michiel Van Bel Relevant publications De Bodt S Carvajal D Hollunder J Van den Cruyce J Movahedi S Inzé D 2010 CORNET a user friendly tool for data mining and integration Plant Physiology 152 1167 1179 De Bodt S Hollunder J Nelissen H Meulemeester N Inzé D 2012 CORNET 2 0 integrating plant coexpression protein protein interactions regulatory interactions gene associations and functional annotations New Phytologist 195 707 720 Andriankaja M Dhondt S De Bodt S Vanhaeren H Coppens F De Milde L Mühlenbock P Skirycz A Gonzalez N Beemster G T Inzé D 2012 Exit from proliferation during leaf development in Arabidopsis thaliana a not so gradual process Development Cell 22 64 78 Skirycz A Claeys H De Bodt S Oikawa A Shinoda S Andriankaja M Maleux K Eloy N B Coppens F Yoo S D Saito K Inzé D 2011 Pause and stop the effects of osmotic stress on cell

    Original URL path: http://www.psb.vib-ugent.be/systems-biology-of-yield/240-unravel-leaf-growth (2016-04-26)
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  • Drought Tolerance
    showed that ERF6 regulates the inactivation of the growth stimulating GA pathway but also induces multiple other transcription factors involved in stress response Dubois et al 2013 In total we identified 20 transcription factors around ERF6 and observed that these transcription factors are regulating each other s expression thereby forming a dense and complex transcriptional network It is now our aim to use mathematical modeling to unravel the dynamics of this network under stress and to link the status of the network to leaf growth Lisa Van den Broeck As a first piece of this puzzle the regulatory relationship between two transcription factors of this network ERF6 and ERF11 was recently characterized Dubois et al 2015 To extend the network even further without a bias towards transcription factors we are performing a large scale forwards genetics screen for new genes potentially involved in leaf growth regulation under stress Ting Li Besides the in vitro work we also aim to unravel the growth regulatory pathways active under in soil mild drought stress We use the Weighing Imaging and Watering Machine WIWAM to establish an appropriate setup enabling the capture of early drought responses in actively growing Arabidopsis leaves by tracking leaf growth over time and measuring expression changes with a high time resolution Growth and transcriptional responses to in soil drought are extremely complex with the time of day as a crucial factor influencing the extent the specificity and sometimes also the direction of the expression changes While the response to in soil drought does not seem to involve the same molecular players as under in vitro stress the general mechanisms including ethylene and gibberellin mediated growth inhibition are most likely conserved We also make use of the genetic variation in Arabidopsis to identify new genes potentially involved in the response to mild drought by means of transcriptomic and genome wide association studies Clauw et al 2015 People involved Nathalie Gonzalez project leader Pieter Clauw Marieke Dubois Lisa Van den Broeck and Li Ting Selected publications Dubois M Van den Broeck L Claeys H Van Vlierberghe K Matsui M Inzé D 2015 The ETHYLENE RESPONSE FACTORS ERF6 and ERF11 antagonistically regulate mannitol induced growth inhibition in Arabidopsis Plant Physiol PMID 25995327 Clauw P Coppens F De Beuf K Dhondt S Van Daele T Maleux K Storme V Clement L Gonzalez N Inzé D 2015 Leaf responses to mild drought stress in natural variants of Arabidopsis Plant Physiol PMID 25604532 Claeys H Van Landeghem S Dubois M Maleux K Inzé D 2014 What Is Stress Dose Response Effects in Commonly Used in Vitro Stress Assays Plant Physiol PMID 24710067 Dubois M Skirycz A Claeys H Maleux K Dhondt S De Bodt S Vanden Bossche R De Milde L Yoshizumi T Matsui M Inzé D 2013 Ethylene Response Factor6 acts as a central regulator of leaf growth under water limiting conditions in Arabidopsis Plant Physiol 162 1 319 32 Claeys H Skirycz A Maleux K Inzé D 2012 DELLA Signaling Mediates Stress Induced

    Original URL path: http://www.psb.vib-ugent.be/systems-biology-of-yield/241-drought-tolerance (2016-04-26)
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  • Maize Leaf Development
    division and cell expansion and thus determine organ growth The combinatory approach of cellular and molecular analysis allowed to identify distinct ways to regulate the dynamics in growth Hormone and transcript measurements along the growth zone combined with the cellular analysis of mutants and overexpression lines of enzymes in the GA biosynthetic pathway showed that the transition from cell division to cell expansion TZ1 was characterized by a local accumulation of GA Nelissen et al 2012 Tandem affinity purification on samples enriched for dividing and expanding tissues revealed that growth zone dependent protein protein interactions were crucial to determine TZ1 Nelissen et al 2015 Besides the information from our molecular studies in maize we also take advantage of the plethora of knowledge affecting growth obtained in Arabidopsis thaliana intrinsic yield genes stress tolerance genes and the molecular yield networks and assess its translatability to maize Nelissen et al 2014 Therefore we combine the phenotyping of lines perturbing the function of selected growth regulators with the genetic and molecular interactions around these nodes to build growth regulatory networks We also aim to understand the relevance of our greenhouse based research for agriculture by performing field trials with growth phenotypes Nelissen et al 2014 Besides biotech research we also study the variation in leaf growth parameters by using different inbreds recombinant inbred lines and hybrids Dell Acqua et al 2015 The maize leaf of the future Up to now we gathered a substantial toolbox to perform maize biotech research varying from efficient transformation optimized growth conditions kinematic analysis bio informatics and computational tools genome wide technologies to field trials and automated systems to phenotype the plants Our aim is to continue to optimize and develop technologies to gain a better understanding of the processes driving growth and to expand our knowledge on growth regulatory networks Furthermore we are evaluating how the growth regulatory mechanisms operating in the leaf function in controlling the maize ear growth People involved Hilde Nelissen project leader Joke Baute Michiel Bontinck Jolien De Block Kirin Demuynck Kim Feys Katrien Maleux Stien Mertens Xiaohuan Sun Tom Van Hautegem Lennart Verbraeken Liesbeth Vercruyssen Charlot Versteele Astrid Welvaert Nathalie Wuyts Visiting scientist Hironori Takasaki Relevant publications Nelissen H Rymen B Jikumaru Y Demuynck K Van Lijsebettens M Kamiya Y Inzé D and Beemster Gerrit T S 2012 A local maximum in gibberellin levels regulates maize leaf growth by spatial control of cell division Current Biology 22 1183 1187 Nelissen H Rymen B Coppens F Dhondt S Fiorani F and Beemster G S 2013 Kinematic analysis of cell division in leaves of mono and dicotyledonous species A basis for understanding growth and developing refined molecular sampling strategies In Plant Organogenesis Methods in Molecular Biology Vol 959 I De Smet ed New York Humana Press pp 247 264 Nelissen H Moloney M and Inzé D 2014 Translational research from pot to plot Plant Biotechnol J 12 3 277 85 Candaele J Demuynck K Mosoti D Beemster G T Inzé D and Nelissen H

    Original URL path: http://www.psb.vib-ugent.be/systems-biology-of-yield/242-maize-leaf-development (2016-04-26)
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  • Frank Van Breusegem
    B 9052 Gent BELGIUM Fax 32 0 9 33 13 809 Prev Projects Frank Van Breusegem Group Members Lab Members and Alumni Publications Frank Van Breusegem Research Groups Alain Goossens Lab Ann Depicker Lab Bruno Cammue Lab Daniel Van Damme Lab Dirk Inzé Lab Frank Van Breusegem Lab Geert De Jaeger Lab Ive De Smet Lab Jenny Russinova Lab Lieven De Veylder Lab Mieke Van Lijsebettens Lab Moritz Nowack Lab

    Original URL path: http://www.psb.vib-ugent.be/frank-van-breusegem (2016-04-26)
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