TEM

TEM_Morph_AraRoot_web The Transmission Electron Microscopy (TEM) facility located on the campus ‘Ledeganck’ of the UGent is providing expertise in the use and application of transmission electron microscopy to serve biological or biomedical sciences.

The facility was established in 2003 and uses the equipment of the UGent Department of Biology. Its aim is to support research projects of all scientific groups of VIB1, Center of Inflammation Research (DMBR), including projects in cell biology, inflammation, glycobiology, virology, cancer biology, cell death, developmental biology, immunology… and VIB2, Center of Plant Systems Biology (PSB), including projects dealing with cell cycle, cell death, gene regulation, plant microbes, root development, secondary metabolites…

Equipment

TEM_Equipment_web

Possible applications

IEM (Immuno-gold Electron Microscopy)

Embedding medium : LR-White
Chemical fix. (aldehydes)

Immunolocalization using PA:g or conjugates as gold-markers
Advantages: less limited in size
Disadvantages: morphol. artefacts and less sensitive

HPF = high-pressure freezing (EM-Pact)

Immunolocalization using PA:g or conjugates as gold-markers.
Advantages: better structural preservation and retains antigenicity
Disadvantages: limited in size

Examples

TEM IEM-Full-Picture web v2

Morphological analysis

Embedding medium : Spurr's resin
Chemical fix. (aldehydes + OsO4)

Advantages: less limited in size
Disadvantages: morphol. artefacts and less sensitive

HPF = high-pressure freezing (EM-Pact)

Advantages: better structural preservation and an "in vivo" impression
Disadvantages: limited in size

Examples

TEM_Morph-Full-Picture_web

For all information

contact Tom Beeckman (This email address is being protected from spambots. You need JavaScript enabled to view it.)
or Riet Derycke (This email address is being protected from spambots. You need JavaScript enabled to view it.)

Most recent publications with TEM contribution

(publications involving PSB with TEM contribution, for more details, and the complete list of publications since 2003 with TEM contribution, visit http://users.ugent.be/~rderycke/)

2014

Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis
Satoshi Naramoto, Marisa S. Otegui, Natsumaro Kutsuna, Riet de Rycke, Tomoko Dainobu, Michael Karampelias, Masaru Fujimoto, Elena Feraru, Daisuke Miki, Hiroo Fukuda, Akihiko Nakano and Ji?í Friml
The Plant Cell, 2014

Nanoporous Hydrogen Bonded Polymeric Microparticles : Facile and Economic Production of Cross Presentation Promoting Vaccine Carriers
Marijke Dierendonck, Kaat Fierens, Riet De Rycke, Lien Lybaert, Samarendran Maji, Zhiyue Zhang, Qilu Zhang, Richard Hoogenboom, Bart N. Lambrecht, Johan Grooten, Jean Paul Remon, Stefaan De Koker, and Bruno G. De Geest
Journal of Advanced Functional Materials, 2014

Accumulation of GlcNAc oligomers in the plant cell wall affects plant architecture in a dose-dependent and conditional manner
Bartel Vanholme, Ruben Vanholme, Halbay Turumtay, Geert Goeminne, Igor Cesarino, Florence Goubet, Kris Morreel, Jorge Rencoret, Vincent Bulone, Cortwa Hooijmaijers, Riet De Rycke, Godelieve Gheysen, John Ralph, Marc De Block, Frank Meulewaeter, Wout Boerjan
Plant Physiology, 2014

Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling
Tongda Xu, Ning Dai, Jisheng Chen, Shingo Nagawa, Min Cao, Hongjiang Li, Zimin Zhou, Xu Chen, Riet De Rycke, Wuyi Wang, , Alan M. Jones, Jiri Friml, Sara E. Patterson , Anthony B. Bleecker , and Zhenbiao Yang
Science, 2014

The unfolded-protein-response sensor IRE-1? regulates the function of CD8alpha+ dendritic cells
Fabiola Osorio, Simon J Tavernier, Eik Hoffmann, Yvan Saeys, Liesbet Martens, Jessica Vetters, Iris Delrue, Riet De Rycke, Eef Parthoens, Philippe Pouliot, Takao Iwawaki, Sophie Janssens & Bart N Lambrecht
Nature Immunology, 2014

SAC domain phosphoinositide phosphatases at tonoplast mediate vacuolar function in Arabidopsis
Petra Nováková, SibylleHirsch, Elena Feraru, Ricardo Tejos, Tom Viaene, Riet De Rycke, Ringo van Wijk, Mugurel Feraru, Peter Grones, Ingo Heilmann, Teun Munnik, Marc C.E. Van Montagu, Ji?í Friml
PNAS, 2014

2013

Just spray it – Next generation of electrostatic assembly
Marijke Dierendonck, Stefaan De Koker, Riet De Rycke, Bruno De Geest
Soft Matter, 2013

Salt Plays a Pivotal Role in the Temperature-Responsive Aggregation and Layer-by-Layer Assembly of Polymer-Decorated Gold Nanoparticles
Zhang Zhiyue, Maji Samarendra, Antunes André, De Rycke Riet, Zhang Qilu, Hoogenboom Richard, De Geest Bruno
Chemistry of Materials, 2013

Enhanced membrane protein expression by engineering increased Intracellular Membrane production
Mouna Guerfal, Katrien Claes, Oskar Knittelfelder, Riet De Rycke, Sepp D Kohlwein and Nico Callewaert
Microbial Cell Factories, 2013

Hard X-ray nanoprobe investigations of the subtissue metal distributions within Daphnia magna
B. De Samber, K. A. C. De Schamphelaere, C. R. Janssen, B. Vekemans, R. De Rycke, G. Martinez-Criado, R. Tucoulou, P. Cloetens, L. Vincze
Anal Bioanal Chem, 2013

Radiation-induced myosin IIA-dependent collagen type I matrix reorganization affects breast cancer cell death
Stéphanie Blockhuys, Bart Van Rompaye, Riet De Rycke, Kathleen Lambein, Marc Bracke, Carlos De Wagter, Olivier De Wever.
Radiotherapy and Oncology, 2013

Matrix metalloproteinase 13 modulates intestinal epithelial barrier integrity in inflammatory diseases by activating TNF.
Roosmarijn E. Vandenbroucke, Eline Dejonckheere, Filip Van Hauwermeiren, Sofie Lodens, Riet De Rycke, Elien Van Wonterghem, An Staes, Kris Gevaert, Carlos Lopez-Otin, and Claude Libert.
EMBO Molecular Medicine, 2013

Nodule development on the tropical legume Sesbania virgata under flooded and non-flooded conditions.
Bomfeti, C. A., Ferreira, P. A. A., Carvalho, T. S., De Rycke, R., Moreira, F. M. S., Goormachtig, S., & Holsters, M.
Plant Biology, 15(1), 93-98. doi:10.1111/j.1438-8677.2012.00592.x (2013).

Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis.
Nodzynski T, Feraru MI, Hirsch S, De Rycke R, Niculaes C, Boerjan W, Van Leene J, De Jaeger G, Vanneste S, Friml J.
Mol Plant. 2013 Nov;6(6):1849-62. doi: 10.1093/mp/sst044. Epub 2013 Jun 14. IF 5.54

Cell polarity and patterning by PIN trafficking through early endosomal compartments in Arabidopsis thaliana.
Tanaka H, Kitakura S, Rakusová H, Uemura T, Feraru MI, De Rycke R, Robert S, Kakimoto T, Friml J.
PLoS Genet. 2013 May;9(5):e1003540. doi: 10.1371/journal.pgen.1003540. Epub 2013 May 30. IF 6.69

Generation of VHH antibodies against the Arabidopsis thaliana seed storage proteins.
De Meyer T, Eeckhout D, De Rycke R, De Buck S, Muyldermans S, Depicker A.
Plant Mol Biol. 2014 Jan;84(1-2):83-93. doi: 10.1007/s11103-013-0118-0. Epub 2013 Aug 21. IF 2.5

2012

Nodule development on the tropical legume Sesbania virgata under flooded and non-flooded conditions.
Bomfeti CA, Ferreira PAA, Carvalho TS, De Rycke R, Moreira FMS, Goormachtig S, Holsters M
Plant Biol (Stuttg). 2013 Jan;15(1):93-8. doi: 10.1111/j.1438-8677.2012.00592.x. 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., Pazo, J. R., Kim, H., Christensen, J. H., et al.
Plant Journal, 64(6), 885–897. doi:10.1111/j.1365-313X.2010.04353.x (2010).

The AP-3 ? adaptin mediates the biogenesis and function of lytic vacuoles in Arabidopsis.
Feraru, E., Paciorek, T., Feraru, M. I., Zwiewka, M., De Groodt, R., De Rycke, R., Kleine-Vehn, J., et al.
Plant Cell, 22(8), 2812–2824. doi:10.1105/tpc.110.075424 (2010).

Comparison of developmental and stress-induced nodule senescence in Medicago truncatula.
Pérez Guerra, J. C., Coussens, G., De Keyser, A., De Rycke, R., De Bodt, S., Van De Velde, W., Goormachtig, S., et al.
Plant Physiology, 152(3), 1574–1584. doi:10.1104/pp.109.151399 (2010).

Developmental stage specificity and the role of mitochondrial metabolism in the response of Arabidopsis leaves to prolonged mild osmotic stress.
Skirycz, A., De Bodt, S., Obata, T., De Clercq, I., Claeys, H., De Rycke, R., Andriankaja, M., et al.
Plant Physiology, 152(1), 226–244. doi:10.1104/pp.109.148965 (2010).

Calcium spiking patterns and the role of the calcium/calmodulin-dependent kinase CCaMK in lateral root base nodulation of Sesbania rostrata.
Capoen, W., Den Herder, J., Sun, J., Verplancke, C., De Keyser, A., De Rycke, R., Goormachtig, S., et al.
Plant Cell, 21(5), 1526–1540. doi:10.1105/tpc.109.066233 (2009).

Fluorescence imaging-based screen identifies ARF GEF component of early endosomal trafficking.
Tanaka, H., Kitakura, S., De Rycke, R., De Groodt, R., & Friml, J.
Current Biology, 19(5), 391–397. doi:10.1016/j.cub.2009.01.057 (2009).

Seven in absentia proteins affect plant growth and nodulation in Medicago truncatula.
Den Herder, G., De Keyser, A., De Rycke, R., Rombauts, S., Van de Velde, W., Clemente, M. R., Verplancke, C., et al.
Plant Physiology, 148(1), 369–382. doi:10.108.119453 (2008).

Downregulation of cinnamoyl-coenzyme A reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure.
Leplé, J.-C., Dauwe, R., Morreel, K., Storme, V., Lapierre, C., Pollet, B., Naumann, A., et al.
Plant Cell, 19(11), 3669–3691. doi:10.1105/tpc.107.054148 (2007).

Nod factor perception during infection thread growth fine-tunes nodulation.
Den Herder J, Vanhee C, De Rycke R, Corich V, Holsters M, Goormachtig S
Molecular Plant-Microbe Interactions, 20(2), 129-137. doi:10.1094/MPMI-20-2-0129 (2007).

AtGRP2, a cold-induced nucleo-cytoplasmic RNA-binding protein, has a role in flower and seed development.
Fusaro AF, Bocca SN, Ramos RL, Barroco RM, Magioli C, Jorge VC, Coutinho TC, Rangel-Lima CM, De Rycke R, Inzé D, Engler G, Sachetto-Martins G
Planta, 225(6), 1339-1351. doi:10.1007/s00425-006-0444-4 (2007). 

Somatic Cytokinesis and Pollen Maturation in Arabidopsis Depend on TPLATE, Which Has Domains Similar to Coat Proteins.
Van Damme D, Coutuer S, De Rycke R, Bouget FY, Inzé D, Geelen D
Plant Cell, 18(12), 3502-3518. doi: 10.1105/tpc.106.040923 (2006).

Serpin1 of Arabidopsis thaliana is a Suicide Inhibitor for Metacaspase 9.
Vercammen D, Belenghi B, van de Cotte B, Beunens T, Gavigan JA, De Rycke R, Brackenier A, Inze D, Harris JL, Van Breusegem F
Journal of Molecular Biology, 364(4), 625-636. doi:10.1016/j.jmb.2006.09.010 (2006).

Aging in legume symbiosis. A molecular view on nodule senescence in Medicago truncatula.
Van de Velde W, Pérez Guerra JC, De Keyser A, De Rycke R, Rombauts S, Maunoury N, Mergaert P, Kondorosi E, Holsters M, Goormachtig S
Plant Physiology, 141(2), 711-720. doi: 10.1104/pp.106.078691 (2006).

Cell cycle-dependent targeting of a kinesin at the plasma membrane demarcates the division site in plant cells.
Vanstraelen M, Van Damme D, De Rycke R, Mylle E, Inzé D, Geelen D
Current Biology, 16(3), 308-314. doi:10.1016/j.cub.2005.12.035 (2006).

Lipopolysaccharides as a communication signal for progression of legume endosymbiosis.
Mathis R, Van Gijsegem F, De Rycke R, D'Haeze W, Van Maelsaeke E, Anthonio E, Van Montagu M, Holsters M, Vereecke D
Proceedings of the National Academy of Sciences of the USA, 102(7), 2655-2660. doi:10.1073/pnas.0409816102 (2005).

SrSymRK, a plant receptor essential for symbiosome formation.
Capoen W, Goormachtig S, De Rycke R, Schroeyers K, Holsters M
Proceedings of the National Academy of Sciences of the USA, 102(29), 10369-10374. doi:10.1073/pnas.0504250102 (2005).

An easy and versatile embedding method for transverse sections.
De Smet I, Chaerle P, Vanneste S, De Rycke R, Inzé D, Beeckman T
Journal of Microscopy 213(1), 76-80. doi:10.1111/j.1365-2818.2004.01269.x (2004).

Structural characterization of extracellular polysaccharides of Azorhizobium caulinodans and importance for nodule initiation on Sesbania rostrata.
D'Haeze W, Glushka J, De Rycke R, Holsters M, Carlson RW
Molecular Microbiology 52(2), 485-500. doi:10.1111/j.1365-2958.2004.03989.x (2004).

Molecular phenotyping of the pal1 and pal2 mutants of Arabidopsis thaliana reveals far-reaching consequences on phenylpropanoid, amino acid, and carbohydrate metabolism.
Rohde A, Morreel K, Ralph J, Goeminne G, Hostyn V, De Rycke R, Kushnir S, Van Doorsselaere J, Joseleau J-P, Vuylsteke M, Van Driessche G, Van Beeumen J, Messens E, Boerjan W
Plant Cell 16(10), 2749-2771. doi:10.1105/tpc.104.023705 (2004).

Reactive oxygen species and ethylene play a positive role in lateral root base nodulation of a semiaquatic legume.
D'Haeze W, De Rycke R, Mathis R, Goormachtig S, Pagnotta S, Verplancke C, Capoen W, Holsters M
Proceedings of the National Academy of Sciences of the USA, 100(20), 11789-11794. doi:10.1073/pnas.1333899100 (2003).