Dr. G. (Gertjan) Kramer
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Swammerdam Institute for Life Sciences
Bezoekadres
- Science Park 904
- Kamernummer: C2.263
Postadres
- Postbus 94215
1090 GE Amsterdam
Contactgegevens
Social media
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Publicaties
2023
Alvarado, M., Gómez-Navajas, J. A., Blázquez-Muñoz, M. T., Gómez-Molero, E., Berbegal, C., Eraso, E., Kramer, G., & De Groot, P. W. J. (2023). Integrated post-genomic cell wall analysis reveals floating biofilm formation associated with high expression of flocculins in the pathogen Pichia kudriavzevii. PLoS Pathogens, 19(5), [e1011158]. https://doi.org/10.1371/journal.ppat.1011158 [details]- Yu, B., Kanaan, J., Shames, H., Wicander, J., Aryal, M., Li, Y., Korza, G., Brul, S., Kramer, G., Li, Y., Nichols, F. C., Hao, B., & Setlow, P. (2023). Identification and characterization of new proteins crucial for bacterial spore resistance and germination. Frontiers in Microbiology, 14, [1161604]. https://doi.org/10.3389/fmicb.2023.1161604 [details]
2022
- Gao, X., Swarge, B. N., Roseboom, W., Setlow, P., Brul, S., & Kramer, G. (2022). Time-Resolved Proteomics of Germinating Spores of Bacillus cereus. International Journal of Molecular Sciences, 23(21), [13614]. https://doi.org/10.3390/ijms232113614 [details]
- Gao, X., Swarge, B. N., Roseboom, W., Wang, Y., Dekker, H. L., Setlow, P., Brul, S., & Kramer, G. (2022). Changes in the Spore Proteome of Bacillus cereus in Response to Introduction of Plasmids. Microorganisms, 10(9), [1695]. https://doi.org/10.3390/microorganisms10091695 [details]
- Hertzberger, R., May, A., Kramer, G., van Vondelen, I., Molenaar, D., & Kort, R. (2022). Genetic Elements Orchestrating Lactobacillus crispatus Glycogen Metabolism in the Vagina. International Journal of Molecular Sciences, 23(10), [5590]. https://doi.org/10.3390/ijms23105590 [details]
2021
- Gao, X., Swarge, B. N., Dekker, H. L., Roseboom, W., Brul, S., & Kramer, G. (2021). The membrane proteome of spores and vegetative cells of the food-borne pathogen Bacillus cereus. International Journal of Molecular Sciences, 22(22), [12475]. https://doi.org/10.3390/ijms222212475 [details]
- Guerrieri, A., Floková, K., Vlaar, L. E., Schilder, M. L., Kramer, G., Chojnacka, A., van Dijk, Y. R., Bouwmeester, H. J., & Dong, L. (2021). UPLC-MS/MS analysis and biological activity of the potato cyst nematode hatching stimulant, solanoeclepin A, in the root exudate of Solanum spp. Planta, 254(6), [112]. https://doi.org/10.1007/s00425-021-03766-2 [details]
- Roeters, S. J., Golbek, T. W., Bregnhøj, M., Drace, T., Alamdari, S., Roseboom, W., Kramer, G., Šantl-Temkiv, T., Finster, K., Pfaendtner, J., Woutersen, S., Boesen, T., & Weidner, T. (2021). Ice-nucleating proteins are activated by low temperatures to control the structure of interfacial water. Nature Communications, 12, [1183]. https://doi.org/10.1038/s41467-021-21349-3 [details]
- Tu, Z., Dekker, H. L., Roseboom, W., Swarge, B. N., Setlow, P., Brul, S., & Kramer, G. (2021). High resolution analysis of proteome dynamics during bacillus subtilis sporulation. International Journal of Molecular Sciences, 22(17), [9345]. https://doi.org/10.3390/ijms22179345 [details]
- Tu, Z., Setlow, P., Brul, S., & Kramer, G. (2021). Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate. Microorganisms, 9(3), [667]. https://doi.org/10.3390/microorganisms9030667 [details]
- Ursem, R., Swarge, B., Abhyankar, W. R., Buncherd, H., de Koning, L. J., Setlow, P., Brul, S., & Kramer, G. (2021). Identification of Native Cross-Links in Bacillus subtilis Spore Coat Proteins. Journal of Proteome Research, 20(3), 1809–1816. https://doi.org/10.1021/acs.jproteome.1c00025 [details]
- de Jong, L., Roseboom, W., & Kramer, G. (2021). A composite filter for low FDR of protein-protein interactions detected by in vivo cross-linking. Journal of Proteomics, 230, [103987]. https://doi.org/10.1016/j.jprot.2020.103987 [details]
- de Jong, L., Roseboom, W., & Kramer, G. (2021). Towards low false discovery rate estimation for protein-protein interactions detected by chemical cross-linking. Biochimica et Biophysica Acta. Proteins and Proteomics, 1869(7), [140655]. https://doi.org/10.1016/j.bbapap.2021.140655 [details]
2020
- Swarge, B., Abhyankar, W., Jonker, M., Hoefsloot, H., Kramer, G., Setlow, P., Brul, S., & de Koning, L. J. (2020). Integrative Analysis of Proteome and Transcriptome Dynamics during Bacillus subtilis Spore Revival. mSphere, 5(4), [e00463-20]. https://doi.org/10.1128/mSphere.00463-20 [details]
- Swarge, B., Nafid, C., Vischer, N., Kramer, G., Setlow, P., & Brul, S. (2020). Investigating Synthesis of the MalS Malic Enzyme during Bacillus subtilis Spore Germination and Outgrowth and the Influence of Spore Maturation and Sporulation Conditions. mSphere, 5(4), [e00464-20]. https://doi.org/10.1128/mSphere.00464-20 [details]
- Tu, Z., Abhyankar, W. R., Swarge, B. N., van der Wel, N., Kramer, G., Brul, S., & de Koning, L. J. (2020). Artificial Sporulation Induction (ASI) by kinA Overexpression Affects the Proteomes and Properties of Bacillus subtilis Spores. International Journal of Molecular Sciences, 21(12), [4315]. https://doi.org/10.3390/ijms21124315 [details]
2019
- Cooke, A., Schwarzl, T., Huppertz, I., Kramer, G., Mantas, P., Alleaume, A-M., ... Hentze, M. W. (2019). The RNA-Binding Protein YBX3 Controls Amino Acid Levels by Regulating SLC mRNA Abundance. Cell Reports, 27(11), 3097-3106, e1-e5. https://doi.org/10.1016/j.celrep.2019.05.039 [details]
2017
- Huis In 't Veld, R. A. G., Kramer, G., van der Ende, A., Speijer, D., & Pannekoek, Y. (2017). The Hfq regulon of Neisseria meningitidis. FEBS OPEN BIO, 7(6), 777-788. https://doi.org/10.1002/2211-5463.12218
- Pannekoek, Y., Huis In 't Veld, R. A. G., Schipper, K., Bovenkerk, S., Kramer, G., Brouwer, M. C., van de Beek, D., Speijer, D., & van der Ende, A. (2017). Neisseria meningitidis Uses Sibling Small Regulatory RNAs To Switch from Cataplerotic to Anaplerotic Metabolism. MBio, 8(2). https://doi.org/10.1128/mBio.02293-16
- Pannekoek, Y., Huis In 't Veld, R., Schipper, K., Bovenkerk, S., Kramer, G., Speijer, D., & van der Ende, A. (2017). Regulation of Neisseria meningitidis cytochrome bc1 components by NrrF, a Fur-controlled small noncoding RNA. FEBS OPEN BIO, 7(9), 1302-1315. https://doi.org/10.1002/2211-5463.12266
2016
- Kramer, G., & Krijgsveld, J. (2016). Turning Over Paradigms in Protein Decay. Developmental Cell, 39(3), 284-285. https://doi.org/10.1016/j.devcel.2016.10.018
- Kramer, G., Wegdam, W., Donker-Koopman, W., Ottenhoff, R., Gaspar, P., Verhoek, M., Nelson, J., Gabriel, T., Kallemeijn, W., Boot, R. G., Laman, J. D., Vissers, J. P. C., Cox, T., Pavlova, E., Moran, M. T., Aerts, J. M., & van Eijk, M. (2016). Elevation of glycoprotein nonmetastatic melanoma protein B in type 1 Gaucher disease patients and mouse models. FEBS OPEN BIO, 6(9), 902-913. https://doi.org/10.1002/2211-5463.12078
2015
- Brackeva, B., De Punt, V., Kramer, G., Costa, O., Verhaeghen, K., Stangé, G., Sadones, J., Xavier, C., Aerts, J. M. F. G., Gorus, F. K., & Martens, G. A. (2015). Potential of UCHL1 as biomarker for destruction of pancreatic beta cells. Journal of Proteomics, 117, 156-167. https://doi.org/10.1016/j.jprot.2015.01.009
- Brackeva, B., Kramer, G., Vissers, J. P. C., & Martens, G. A. (2015). Quantitative proteomics of rat and human pancreatic beta cells. Data in Brief, 3, 234-9. https://doi.org/10.1016/j.dib.2015.02.019
- Kramer, G., Woolerton, Y., van Straalen, J. P., Vissers, J. P. C., Dekker, N., Langridge, J. I., Beynon, R. J., Speijer, D., Sturk, A., & Aerts, J. M. F. G. (2015). Accuracy and Reproducibility in Quantification of Plasma Protein Concentrations by Mass Spectrometry without the Use of Isotopic Standards. PLoS ONE, 10(10), [e0140097]. https://doi.org/10.1371/journal.pone.0140097
- Mirzaian, M., Kramer, G., & Poorthuis, B. J. H. M. (2015). Quantification of sulfatides and lysosulfatides in tissues and body fluids by liquid chromatography-tandem mass spectrometry. Journal of Lipid Research, 56(4), 936-43. https://doi.org/10.1194/jlr.M057232
- Mirzaian, M., Wisse, P., Ferraz, M. J., Gold, H., Donker-Koopman, W. E., Verhoek, M., Overkleeft, H. S., Boot, R. G., Kramer, G., Dekker, N., & Aerts, J. M. F. G. (2015). Mass spectrometric quantification of glucosylsphingosine in plasma and urine of type 1 Gaucher patients using an isotope standard. Blood cells, molecules, & diseases, 54(4), 307-14. https://doi.org/10.1016/j.bcmd.2015.01.006
2014
- Martens, G. A., Motté, E., Kramer, G., Stangé, G., Gaarn, L. W., Hellemans, K., Nielsen, J. H., Aerts, J. M., Ling, Z., & Pipeleers, D. (2014). Functional characteristics of neonatal rat β cells with distinct markers. Journal of molecular endocrinology, 52(1), 11-28. https://doi.org/10.1530/JME-13-0106
- Plug, T., Kramer, G., & Meijers, J. C. M. (2014). A role for arginine-12 in thrombin-thrombomodulin-mediated activation of thrombin-activatable fibrinolysis inhibitor. Journal of Thrombosis and Haemostasis, 12(10), 1717-1725. https://doi.org/10.1111/jth.12674
- Strang, A. C., Knetsch, M. L. W., Idu, M. M., Bisoendial, R. J., Kramer, G., Speijer, D., Koole, L. H., Stroes, E. S. G., & Rotmans, J. I. (2014). Superior in vivo compatibility of hydrophilic polymer coated prosthetic vascular grafts. Journal of Vascular Access, 15(2), 95-101. https://doi.org/10.5301/jva.5000166
- Wegdam, W., Argmann, C. A., Kramer, G., Vissers, J. P., Buist, M. R., Kenter, G. G., ... Moerland, P. D. (2014). Label-free LC-MSe in tissue and serum reveals protein networks underlying differences between benign and malignant serous ovarian tumors. PLoS ONE, 9(9), [e108046]. https://doi.org/10.1371/journal.pone.0108046
2013
- Jiang, L., Brackeva, B., Ling, Z., Kramer, G., Aerts, J. M., Schuit, F., Keymeulen, B., Pipeleers, D., Gorus, F., & Martens, G. A. (2013). Potential of protein phosphatase inhibitor 1 as biomarker of pancreatic β-cell injury in vitro and in vivo. Diabetes, 62(8), 2683-2688. https://doi.org/10.2337/db12-1507
- McLoughlin, F., Arisz, S. A., Dekker, H. L., Kramer, G., de Koster, C. G., Haring, M. A., ... Testerink, C. (2013). Identification of novel candidate phosphatidic acid-binding proteins involved in the salt-stress response of Arabidopsis thaliana roots. Biochemical Journal, 450(3), 573-581. https://doi.org/10.1042/BJ20121639 [details]
2012
- Kramer, G., Moerland, P. D., Jeeninga, R. E., Vlietstra, W. J., Ringrose, J. H., Byrman, C., Berkhout, B., & Speijer, D. (2012). Proteomic analysis of HIV-T cell interaction: an update. Frontiers in Microbiology, 3, 240. https://doi.org/10.3389/fmicb.2012.00240
2011
- Aerts, J. M. F. G., Kallemeijn, W. W., Wegdam, W., Joao Ferraz, M., van Breemen, M. J., Dekker, N., Kramer, G., Poorthuis, B. J., Groener, J. E. M., Cox-Brinkman, J., Rombach, S. M., Hollak, C. E. M., Linthorst, G. E., Witte, M. D., Gold, H., van der Marel, G. A., Overkleeft, H. S., & Boot, R. G. (2011). Biomarkers in the diagnosis of lysosomal storage disorders: proteins, lipids, and inhibodies. Journal of inherited metabolic disease, 34(3), 605-619. https://doi.org/10.1007/s10545-011-9308-6 [details]
- Kramer, G., Kasper, P. T., de Jong, L., & de Koster, C. G. (2011). Quantitation of newly synthesized proteins by pulse labeling with azidohomoalanine. In K. Gevaert, & J. Vandekerckhove (Eds.), Gel-free proteomics: methods and protocols (pp. 169-181). (Methods in molecular biology; No. 753). [S.l.]: Humana Press. https://doi.org/10.1007/978-1-61779-148-2_12 [details]
2010
- Kramer, G., Sprenger, R. R., Nessen, M. A., Roseboom, W., Speijer, D., de Jong, L., Teixeira de Mattos, M. J., Back, J. W., & de Koster, C. G. (2010). Proteome-wide alterations in Escherichia coli translation rates upon anaerobiosis. Molecular & Cellular Proteomics, 9(11), 2508-2516. https://doi.org/10.1074/mcp.M110.001826
- Witte, M. D., Kallemeijn, W. W., Aten, J., Li, K-Y., Strijland, A., Donker-Koopman, W. E., ... Aerts, J. M. F. G. (2010). Ultrasensitive in situ visualization of active glucocerebrosidase molecules. Nature chemical biology, 6(12), 907-913. https://doi.org/10.1038/nchembio.466
2009
- Kramer, G., Sprenger, R. R., Back, J. W., Dekker, H. L., Nessen, M. A., van Maarseveen, J. H., ... de Koster, C. G. (2009). Identification and quantitation of newly synthesized proteins in Escherichia coli by enrichment of azidohomoalanine-labeled peptides with diagonal chromatography. Molecular & Cellular Proteomics, 8(7), 1599-1611. https://doi.org/10.1074/mcp.M800392-MCP200 [details]
- Nessen, M. A., Kramer, G., Back, J. W., Baskin, J. M., Smeenk, L. E. J., de Koning, L. J., ... de Koster, C. G. (2009). Selective enrichment of azide-containing peptides from complex mixtures. Journal of Proteome Research, 8(7), 3702-3711. https://doi.org/10.1021/pr900257z [details]
2007
- Bekker, M., Kramer, G., Hartog, A. F., de Koster, C. G., Hellingwerf, K. J., & Teixeira De Mattos, M. J. (2007). Changes in the redox state and composition of the quinone pool of Escherichia coli during aerobic batch-culture growth. Microbiology, 153, 1974-1980. https://doi.org/10.1099/mic.0.2007/006098-0 [details]
2005
- Back, J. W., David, O. R. P., Kramer, G., Masson, G. S., Kasper, P. T., de Koning, L. J., ... de Koster, C. G. (2005). Mild and chemoselective peptide-bond cleavage of peptides and proteins at azido homoalanine. Angewandte Chemie, International Edition, 44, 7946-7950. https://doi.org/10.1002/anie.200502431 [details]
- Back, J. W., David, O. R. P., Kramer, G., Masson, G. S., de Jong, L., de Koning, L. J., ... de Koster, C. G. (2005). Selective and mild chemical protein cleavage. The FEBS Journal, 272, S1-151. [details]
- Cremazy, F. G. E., Manders, E. M. M., Bastiaens, P. I. H., Kramer, G., Hager, G. L., van Munster, E. B., Verschure, P. J., Gadella, T. W. J., & van Driel, R. (2005). Imaging in situ protein-DNA interactions in the cell nucleus using FRET-FLIM. Experimental Cell Research, 309, 390-396. https://doi.org/10.1016/j.yexcr.2005.06.007 [details]
2004
- de Ruijter, A. J. M., Kemp, S., Kramer, G., Meinsma, R. J., Kaufmann, J. O., Caron, H. N., & van Kuilenburg, A. B. P. (2004). The novel histone deacetylase inhibitor BL1521 inhibits proliferation and induces apoptosis in neuroblastoma cells. Biochemical pharmacology, 68(7), 1279-88. https://doi.org/10.1016/j.bcp.2004.05.010
Spreker
- Nessen, M. (speaker), Kramer, G. (speaker), Back, J. W. (speaker), van Maarseveen, J. H. (speaker), de Koning, L. J. (speaker), de Jong, L. (speaker), Hiemstra, H. (speaker) & de Koster, C. G. (speaker) (2-11-2009). Selective enrichment of azide-labelled peptides for mass spectrometric analysis of cellular proteome dynamics., Annual Meeting NWO/CW and NVMS, Lunteren, the Netherlands.
- Nessen, M. (speaker), Kramer, G. (speaker), Back, J. W. (speaker), van Maarseveen, J. H. (speaker), de Koning, L. J. (speaker), de Jong, L. (speaker), Hiemstra, H. (speaker) & de Koster, C. (speaker) (26-3-2009). Selective purification of azide-containing peptides from complex mixtures., Ned. Ver. voor Massaspectrometrie, Kerkrade, the Netherlands.
- Kramer, G. (speaker) (8-12-2008). Identification of newly synthesized protein in E.coli., NWO/CW Studiegroep, Veldhoven, The Netherlands.
- Kramer, G. (speaker) (3-11-2008). Enrichment of azido homoalanine labeled peptides with diagonal chromatography., NWO/CW Analytische Scheikunde, Lunteren, the Netherlands.
2022
- Kramer, G. (2022). MassIVE MSV000090154 - Time-resolved proteomics of germinating spores of Bacillus cereus. MassIVE. https://doi.org/10.25345/c5jq0t02m
- Gao, X., Swarge, B., Roseboom, W., Wang, Y., Dekker, H. L., Setlow, P., Brul, S. & Kramer, G. (2022). MassIVE MSV000090153 - Changes in the spore proteome of Bacillus cereus in response to introduction of plasmids.. MassIVE. https://doi.org/10.25345/c5pg1hs5v
2021
- Kramer, G., Tu, Z., Setlow, P., Brul, S. & Kramer, G. (2021). MassIVE MSV000087080 - Molecular physiological characterization of a high heat resistant spore forming Bacillus subtilis food isolate. UC San Diego. https://doi.org/10.25345/c5zn5n
- Ursem, R., Swarge, B., Abhyankar, W., Buncherd, H., de Koning, L., Setlow, P., Kramer, G. & Brul, S. (2021). MassIVE MSV000086681 - Identification of Native Cross-links in Bacillus subtilis Spore Coat Proteins. MassIVE. https://doi.org/10.25345/c5fn50
- Kramer, G., Wang, Y., Breedijk, R., Hink, M., Bults, L., Vischer, N., Setlow, P. & Brul, S. (2021). MassIVE MSV000088726 - Dynamics of Germinosome Formation Interactions between GerD and Germinant Receptor Subunits in Bacillus cereus Spores. UC San Diego. https://doi.org/10.25345/c5j87w
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Nevenwerkzaamheden
Geen nevenwerkzaamheden
Alvarado, M., Gómez-Navajas, J. A., Blázquez-Muñoz, M. T., Gómez-Molero, E., Berbegal, C., Eraso, E., Kramer, G., & De Groot, P. W. J. (2023). Integrated post-genomic cell wall analysis reveals floating biofilm formation associated with high expression of flocculins in the pathogen Pichia kudriavzevii. PLoS Pathogens, 19(5), [e1011158].