archive-be.com » BE » V » VIB-UGENT.BE

Total: 357

Choose link from "Titles, links and description words view":

Or switch to "Titles and links view".
  • Yves Van de Peer Lab
    gene families genomes and genetic networks in plants and other organisms Information about the different research groups can be found here BEG The Bioinformatics and Evolutionary Genomics group is a center of excellence in the fields of gene prediction and genome annotation comparative and evolutionary genomics and systems biology The team is involved in many international genome projects and has a particular interest in genome evolution and gene and genome duplication events CIG The Comparative and Integrative Genomics group has the objective to extract biological knowledge from large scale experimental data sets using data integration comparative sequence and expression analysis and network exploration DBN The Data Integration and Biological Networks group wants to study an organism as an integrated and interacting network of genes proteins and biochemical reactions The team devises new algorithms for data integration and network inference which are applied to all sorts of model systems Projects Yves Van de Peer Group Members Publications Yves Van de Peer 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

    Original URL path: http://www.psb.vib-ugent.be/bioinformatics-yvpee (2016-04-26)
    Open archived version from archive


  • Wout Boerjan Lab
    sugars These sugars can then be further fermented to bio ethanol or other bio based products such as bioplastics We have a main focus on understanding the biosynthesis polymerization and structure of lignin In addition we aim at modifying the cell wall by expressing cell wall degrading enzymes in the plant Our research is heavily supported by metabolomics Successful gene discovery programs in Arabidopsis are followed up by translational research in crops such as poplar and maize Our efforts will underpin the transition from a fossil based to a sustainable bio economy Lignin Lignin is an aromatic heteropolymer that is mainly deposited in the walls of secondary thickened cells Read more Translational Research When reverse genetics in Arabidopsis shows that the biomass is easier to process into glucose the expression of orthologous genes will be modified in poplar or maize Read more Cell Wall Degrading Enzymes Besides altering the lignin content and composition in plants we aim to obtain tailor made cell walls by expressing genes coding for cell wall degrading enzymes Read more Second Generation Biofuel It is now well recognized that burning fossil fuels and deforestation are major contributors to climate change and that plant biomass can serve as an alternative renewable and carbon neutral raw material for the production of bio energy Read more Metabolomics We use secondary metabolite profiling as a tool to help discovering the function of new genes Read more 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

    Original URL path: http://www.psb.vib-ugent.be/bio-energy (2016-04-26)
    Open archived version from archive

  • Applied Bioinformatics & Biostatistics
    Before most analyses in Life Sciences could be conducted on a personal PC But the large amounts of data and the requirements of the HTS analysis algorithms call for dedicated servers 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

    Original URL path: http://www.psb.vib-ugent.be/applied-bioinformatics-biostatistics (2016-04-26)
    Open archived version from archive

  • Compound Screening Facility
    every aspect of plant growth and development We have developed and miniaturized a reporter based assay in Arabidopsis thaliana which marks lateral root development events and allows to screen for novel compounds that promote root branching Screening of a diverse compound collection led to the identification of naxillin the first non auxin like synthetic molecule that selectively induces lateral root development Transcriptome analysis showed that naxillin induces only a subset of the auxin responsive genes In addition the induced auxin response is restricted to the basal meristem the zone where pericycle cells establish their lateral root founder cell identity Genetic and biochemical analysis demonstrated that naxillin enhances the conversion of indole 3 butyric acid IBA into the active auxin indole 3 acetic acid IAA in the root cap The application of naxillin revealed the role of IBA derived IAA as a specific lateral root inducing agent and highlights the contribution of the root cap in root branching as an important source for IBA derived IAA De Rybel B Audenaert D et al 2012 Other chemical biology projects In collaboration with other academic groups we have been involved in assay development and compound screening projects for a diversity of plant biological processes The assays that have been developed include plant cell based assays secondary metabolism flavonoid production and Arabidopsis based assays general growth and development drought tolerance photorespiration lignin biosynthesis auxin signaling gibberellin signaling ethylene signaling which have been successfully implemented for compound screenings VIB Compound Screening Facility VIB CSF Over the last years the Department of Plant Systems Biology VIB UGent has built up significant experience in the field of plant chemical biology In 2007 this has been translated into the VIB Compound Screening Facility VIB CSF a VIB core facility providing fee for service work for both academics and industry to support chemical biology and drug agro discovery research The VIB CSF advises and assists researchers in the process of assay development i e optimization miniaturization and evaluation of screening assays After successful assay development the VIB CSF team provides services for screening of collections in house or custom and data analysis The compound collection of the VIB CSF has been acquired through commercial suppliers and amounts to a total of about 55 000 compounds available as pre plated sets and dissolved in DMSO Diversity of the covered chemical space and increased bioavailability based upon in silico prediction are the most important selection parameters of the compounds The screening platform consists of several liquid handling stations and detection equipment that covers a broad range of detection technologies including image based high content detection The platform set up is compatible with screening in biochemical and cell based systems and screening in the model plant Arabidopsis thaliana For more information on the facility and the screening platform you can contact Dominique Audenaert This email address is being protected from spambots You need JavaScript enabled to view it or visit the VIB CSF website CSF Publications Xuan W Audenaert D Parizot B

    Original URL path: http://www.psb.vib-ugent.be/csf (2016-04-26)
    Open archived version from archive

  • TAP platform
    companies access to our protein complex purification platform Purifications under research service agreement are performed based on well etablished protocols for complex purification from either the Arabidopsis cell suspension cultures PSB D L or Col 0 seedlings We have recently been able to show that our complex purification technology performs equally well in crop species such as corn or rice For purifications from cell cultures we start from delivered ORF clones for purifications from plants we start from delivered plant tissue More details and conditions are given after contacting us at This email address is being protected from spambots You need JavaScript enabled to view it Prev Next Projects Geert De Jaeger Group Members Group in Action Publications Geert De Jaeger Supplementary data TAP fasta Datasets 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

    Original URL path: http://www.psb.vib-ugent.be/tap-platform (2016-04-26)
    Open archived version from archive

  • Bio imaging
    Epub 2012 Jun 5 IF 2 39 BEX5 RabA1b Regulates trans Golgi Network to Plasma Membrane Protein Trafficking in Arabidopsis Feraru E Feraru M I Asaoka R Paciorek T Rycke R D Tanaka H Nakano A et al Plant Cell 24 7 3074 3086 doi 10 1105 tpc 112 098152 2012 IF 2 39 Phloem associated auxin response maxima determine radial positioning of lateral roots in maize Jansen L Roberts I Rycke R D Beeckman T Philosophical Transactions of the Royal Society B Biological Sciences 367 1595 1525 1533 doi 10 1098 rstb 2011 0239 2012 IF 4 6 pFiD188 the linear virulence plasmid of Rhodococcus fascians strain D188 Francis I De Keyser A De Backer P Simón Mateo C Kalkus J Pertry I Ardiles Diaz W et al Molecular Plant Microbe Interactions 25 5 637 647 doi 10 1094 MPMI 08 11 0215 R 2012 IF 5 84 Visualization of the exocyst complex dynamics at the plasma membrane of Arabidopsis thaliana Fendrych M Synek L Pecenková T Drdová EJ Sekeres J de Rycke R Nowack MK Zársky V Mol Biol Cell 2013 Feb 24 4 510 20 doi 10 1091 mbc E12 06 0492 Epub 2013 Jan 2 IF 5 52 AtWRKY15 perturbation abolishes the mitochondrial stress response that steers osmotic stress tolerance in Arabidopsis Vanderauwera S Vandenbroucke K Inzé A van de Cotte B Mühlenbock P De Rycke R Naouar N Van Gaever T Van Montagu MC Van Breusegem F Proc Natl Acad Sci U S A 2012 Dec 4 109 49 20113 8 doi 10 1073 pnas 1217516109 Epub 2012 Nov 19 IF 10 5 Is HUB1 a hub for plant fitness Himanen K Boccardi TM De Rycke R Odeny OP Van Lijsebettens M Plant Signal Behav 2012 Dec 7 12 1537 40 doi 10 4161 psb 22326 Epub 2012 Oct 16 IF 2 78 Characterization of a rabe ras gene from rat brain e GTPase expressed during morphogenesis in the unicellular green alga Micrasterias denticulata Zygnematophyceae Streptophyta Vannerum K De Rycke R Pollier J Goossens A Inzé D Vyverman Wim Journal of Phycology 48 3 682 692 doi 10 1111 j 1529 8817 2012 01170 x 2012 2011 Transcriptional analysis of cell growth and morphogenesis in the unicellular green alga Micrasterias Streptophyta with emphasis on the role of expansin Vannerum K Huysman M J J De Rycke R Vuylsteke M Leliaert F Pollier J Lütz Meindl U et al BMC Plant Biology 11 128 doi 10 1186 1471 2229 11 128 2011 Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family Babiychuk E Vandepoele K Wissing J Garcia Diaz M Rycke R D Akbari H Joubès J et al Proceedings of the National Academy of Sciences of the USA 108 16 6674 6679 doi 10 1073 pnas 1103442108 2011 Previous years Engineering traditional monolignols out of lignin by concomitant up regulation of F5H1 and down regulation of COMT in Arabidopsis Vanholme R Ralph J Akiyama T Lu F

    Original URL path: http://www.psb.vib-ugent.be/bio-imaging (2016-04-26)
    Open archived version from archive

  • Agro-Biotech Valley
    Biotechnology campus employing over 800 persons dedicated to plant biotechnology The bulk of this work force has been established through the department s outstanding scientific achievements and its remarkable ability to identify opportunities for building on scientific results for the exploration of commercial benefits The integration of fundamental research and industrial applications is key to tap into the immense potential plants offer to build a sustainable world The department has

    Original URL path: http://www.psb.vib-ugent.be/agro-biotech (2016-04-26)
    Open archived version from archive

  • Imaging Robots
    details see text A Representative picture of a Petri dish captured with a camera adjusted for IR imaging B Representative picture of a Petri dish captured with a normal single lens reflex camera Red circles indicate non germinated seeds and badly grown plants which should be excluded from the analysis C A mask image containing black disks on the position of selected plants D Automated numbering of the plants based on the position of the disks in the mask image E Selection of the blue channel after an RGB split of the original color figure in B to increase the contrast between the plants and their background F Extraction of the rosettes after the application of a threshold and a reconstructive opening based on the disks in the mask image G I Automatically generated graphs after image and data analysis of the complete time lapse showing data of wild type and AVP1 overexpressing plants grown on different growth media under day night light conditions G Rosette area during development The inset shows the same data with log scale Error bars show SE H Rosette compactness during development The inset shows rosette compactness between day 14 and 15 Error bars show SE I Relative rosette growth rate per hour during development MIRGIS Another phenotyping tool the Multi camera In vivo Rosette Growth Imaging System MIRGIS was developed in the Systems Biology and Yield group It is well known that the physical environment immensely affects plant phenotypes and that growing Arabidopsis plants in soil can lead to increased biological variation within identical genotypes This new platform allows automatic tracking of individual plants after germination The system consists of several single lens reflex cameras and a laptop Three cameras are mounted above six trays of Arabidopsis plants in a custom designed rack together with fluorescent lamps and placed in a controlled growth chamber Figure 5 An in house computer script has been developed so that each camera would take a picture of the two trays underneath on a daily basis The setup can image a total of 144 plants per three cameras The basic concept is that four seeds are sown per pot and followed from early development At a specific point during development a seedling selection is done in order to reduce the variation within the pool of in soil grown plants which mainly arises by differences in germination time This is performed before the plants start to overlap Therefore the projected areas of all seedlings of a specific genotype which are usually spread over the different trays are measured and the median seedling area of that genotype is calculated Then the seedling with an area closest to the median value is selected within each pot of that genotype A selection image is generated in which the selected plant is indicated by a red circle This image is used to manually remove the remaining plants in the pots This methodology ensures that the seedling that is selected per pot is the one

    Original URL path: http://www.psb.vib-ugent.be/infrastructure/330-imaging-robots (2016-04-26)
    Open archived version from archive