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  • Second Generation Biofuel
    and biodiesel it is expected that lignocellulosic biomass crops with improved yield and optimized cell wall composition will become the second generation biofuel crops Fast growing perennial grasses such as switchgrass and Miscanthus and trees such as poplar and willow have large potential to become the major energy crops for the future Second generation bio ethanol is made by fermentation of sugars that are released from lignocellulosic biomass by cocktails of cell wall degrading enzymes In this process lignin is the main limiting factor because it restricts the accessibility of the cellulose microfibrils to enzymatic depolymerization Therefore lignocellulosic plant biomass needs to be pretreated by chemicals or steam explosion to break down lignin making saccharification a costly process However there is enormous potential to engineer plant cell walls by exploiting the available genetic resources and by genetic modification This potential has remained largely unexplored First bottle of ethanol from greenhouse grown transgenic trees Prev Next Projects Wout Boerjan Group Members Lab Members and Alumni Group in Action Publications Wout Boerjan 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

    Original URL path: http://www.psb.vib-ugent.be/bio-energy/317-second-generation-biofuel (2016-04-26)
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  • Lignin
    in reducing the lignin amount in plants cell walls or in altering its composition such that the lignin polymer becomes easier to process during biomass pretreatments Composition of the plant cell wall Both approaches require a deep understanding of the biosynthesis pathway of the monolignols and how this pathway is integrated in and interacts with plant metabolism To this end we have identified all Arabidopsis genes that share homology with known genes in monolignol biosynthesis Raes et al 2003 and characterized the corresponding mutants by combined microarray analyses metabolomics LC MS GC MS and FTMS and computational analyses Vanholme et al 2012 Subsequently we have identified genes that are closely co expressed with known genes of the monolignol biosynthesis pathway The function of a selection of these genes is now studied by reverse genetics in Arabidopsis For example we recently identified a new gene encoding caffeoyl shikimate esterase CSE an enzyme central to the lignin biosynthetic pathway Vanholme et al 2013 The knock out mutant deposits 36 less lignin and 44 of the remaining lignin is composed of p coumaryl alcohol H units that are normally below 1 in wild type plants resulting in a four fold higher conversion of cellulose into glucose For genes with potential agricultural value translational research to poplar and maize is envisaged as proof of concept Enhanced color confocal microscopy image of a cross section of an Arabidopsis stem The cell walls in blue contain lignin which provides strength to the walls The magenta color in the cortex cells reflects the presence of chlorophyll Cover Science Vol 341 Issue 6150 Prev Next Projects Wout Boerjan Group Members Lab Members and Alumni Group in Action Publications Wout Boerjan Research Groups Alain Goossens Lab Ann Depicker Lab Bruno Cammue Lab Daniel Van Damme Lab Dirk Inzé Lab

    Original URL path: http://www.psb.vib-ugent.be/bio-energy/313-lignin (2016-04-26)
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  • Cell Wall Degrading Enzymes
    and composition in plants we aim to obtain tailor made cell walls by expressing genes coding for cell wall degrading enzymes This allows the modification of the cell wall composition during plant growth and development and could improve the downstream processing of the biomass In order to screen for promising enzymes we optimized a transformation pipeline to test the enzymes in Arabidopsis and analyze the cell wall composition and saccharification yield of the engineered lines For genes with potential agricultural value translational research to poplar and maize is envisaged as proof of concept Current view on fungal enzymatic degradation of cellulose based on Horn et al 2012 Prev Next Projects Wout Boerjan Group Members Lab Members and Alumni Group in Action Publications Wout Boerjan 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 Boerjan Lab About PSB PSB Missions The Department Infrastructure Core Facilities International Projects Publications News Seminars Research

    Original URL path: http://www.psb.vib-ugent.be/bio-energy/315-cell-wall-degrading-enzymes (2016-04-26)
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  • Metabolomics
    invested in the profiling and structural characterization of metabolites based on their MS MS or MS n spectra with a special focus on aromatics lignomics and other secondary metabolites Morreel et al 2010a 2010b Vanholme et al 2012 Dima et al 2015 This knowledge has been exploited to generate a new algorithm called CSPP to systematically characterize the structures of unknown metabolites This method serves the main bottleneck in metabolomics i e the fact that the structures of most metabolites in any tissue are still unknown Morreel et al 2014 Our cutting edge metabolomics platform include a GC MS and several UHPLC MS instruments ion trap MS FT MS and Q Tof MS supplemented with laboratory scale preparative chromatography systems flash chromatography and 2D UHPLC Currently these technologies are used for assembling secondary metabolite databases of model plants such as Arabidopsis and various bio energy crops such as maize and sugarcane Metabolite profile of wild type poplar xylem Sequencing small lignin polymers Lignin is made from the combinatorial radical radical coupling of monolignols and many other less abundant monomers This polymerization process leads to a plethora of units and linkage types that affect the physicochemical characteristics of the cell wall Current methods to analyze the lignin structure focus only on the frequency of the major monomeric units and interunit linkage types We have developed a mass spectrometry based tool to determine the sequence of units in small lignin polymers as well as the bonds connecting these units Morreel et al 2010a This technique is used to identify lignin polymers composed of still unknown units and bond types This knowledge will be instrumental in engineering plants with new lignin structures that are more easily degraded during the pretreatment of plant biomass Sequencing of small lignin molecules The figure shows an example

    Original URL path: http://www.psb.vib-ugent.be/bio-energy/316-metabolomics (2016-04-26)
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  • Translational Research
    exposed to the different seasons deep soil wind rain pathogens and pests In addition outdoor the trees can be grown under agricultural practices typical for biomass plantations The biomass produced in this way can then be processed in the Bio Base Europe pilot biorefinery at the port of Ghent A field trial with transgenic poplars downregulated for the lignin biosynthesis gene cinnamoyl CoA reductase CCR has been started in May 2009 after obtaining regulatory permission from the authorities Wood from these trees has been shown to be easier converted to fermentable sugars Van Acker et al 2014 The full story on the field trial can be downloaded here Another field trial with poplars downregulated in cinnamyl alcohol dehydrogenase CAD that were generated at the INRA in France has been established in May 2014 Field trial of transgenic poplars Breeding with rare defective alleles BRDA Genetic engineering is but one strategy to genetically improve plant biomass Alternatively the natural variation present in the wild germplasm can be exploited by next generation breeding for example when a genetically engineered knock out of a gene improves biomass processing naturally defective genetic variants can be identified from the wild germplasm by Next Generation Sequencing NGS and introduced into the breeding population As proof of concept we have identified a natural mutant in poplar that is defective in HCT a gene of the lignin biosynthesis pathway Vanholme et al 2013 Accordingly the natural mutant had a modified lignin composition BRDA is therefore a straightforward approach to accelerate breeding Natural populations are used for to search for and breed with rare defective genes Prev Next Projects Wout Boerjan Group Members Lab Members and Alumni Group in Action Publications Wout Boerjan Research Groups Alain Goossens Lab Ann Depicker Lab Bruno Cammue Lab Daniel Van Damme Lab Dirk

    Original URL path: http://www.psb.vib-ugent.be/bio-energy/314-translational-research (2016-04-26)
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  • Projects
    and an optimized storage solution The Applied Bioinformatics Biostatistics group has been founded with three goals in mind enable wetlab scientists to perform everyday bioinformatic analyses through a user friendly interface provide expertise to tackle custom data and statistical analysis offer consultancy and training This core facility within PSB is also available for industrial collaborations If you have further questions This email address is being protected from spambots You need JavaScript enabled to view it get in touch with us Bioinformatics Currently our main focus is in High Throughput Sequencing HTS analysis ranging from RNA seq over ChIP seq to variant and methylation calling Next to the data analysis we also provide expertise in setting up your experiment see also biostatistics and identifying the appropriate technology for you research question Read more Biostatistics The main task of the statistical consultant is to advise the scientific staff about the design of an experiment and data analysis using modern techniques The goal is to enable scientists to perform the statistical analyses of their data Read more Projects Group Members Lab Members and Alumni Tools Research Groups Alain Goossens Lab Ann Depicker Lab Bruno Cammue Lab Daniel Van Damme Lab Dirk Inzé Lab

    Original URL path: http://www.psb.vib-ugent.be/projects-frcop (2016-04-26)
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  • Group Members
    Alumni Tools 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 Boerjan Lab About PSB PSB Missions The Department Infrastructure

    Original URL path: http://www.psb.vib-ugent.be/group-members-frcop (2016-04-26)
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  • Lab Members and Alumni
    related Postdoctoral Researchers Bram Slabbinck Postdoctoral fellow Bram Slabbinck graduated as bioscience engineer in 2004 He also achieved a one year master in applied informatics in 2005 From 2006 to 2009 he worked towards a PhD in the field of machine learning and microbiology at Ghent University In 2010 he joined the Yves Van de Peer lab of VIB where he worked as a post doc on internal and industrial bioinformatics projects In 2013 he moved to the Applied Bioinformatics and Statistics group His main interests are solving biological problems through bioinformatics data mining and modeling approaches and software development Michiel Van Bel Postdoctoral fellow As a postdoctoral researcher in the ABB group I m involved in the bioinformatics sections of PSB projects both internal experiments and industrial collaborations With a master degree in computer science a PhD in comparative genomics and experience with expression data I m well equipped to easily answer most questions by either chaining existing tools together or by developing new software Q A for wet lab scientists and continuous support for in house developed software platforms make up the rest of my responsibilities Biostatistician Véronique Storme Biostatistician Véronique Storme has a master degree in biochemistry 1989 and statistical data analysis 2008 awarded with a Quetelet prize She started at VIB in 1995 in the bio energy group of Wout Boerjan where she was involved in genetic mapping and QTL analysis of poplar trees Her interest in statistics grew more and more while analyzing microarray data Her area of expertise is statistical genetics mixed model analysis multivariate statistics and data mining Her favorite statistical language is SAS followed by R Software Developer Nicolas Cybulski Software Developer Nicolas Cybulski text Former Members Matthias De Smet Prev Projects Group Members Lab Members and Alumni Tools Research Groups Alain

    Original URL path: http://www.psb.vib-ugent.be/lab-members-and-alumni-frcop (2016-04-26)
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