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Huang, Y., Swarge, B. N., Roseboom, W., Bleeker, J. D., Brul, S., Setlow, P., & Kramer, G. (2024). Integrative Metabolomics and Proteomics Allow the Global Intracellular Characterization of Bacillus subtilis Cells and Spores. Journal of Proteome Research, 23(2), 596-608. https://doi.org/10.1021/acs.jproteome.3c00386[details]
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), Article e1011158. https://doi.org/10.1371/journal.ppat.1011158[details]
Liu, S., Huang, Y., Jensen, S., Laman, P., Kramer, G., Zaat, S. A. J., & Brul, S. (2023). Molecular physiological characterization of the dynamics of persister formation in
Staphylococcus aureus. Antimicrobial Agents and Chemotherapy, e0085023. Advance online publication. https://doi.org/10.1128/aac.00850-23
Naalden, D., Dermauw, W., Ilias, A., Baggerman, G., Mastop, M., Silven, J., van Kleeff, P. J. M., Dangol, S., Gaertner, N. F., Roseboom, W., Kwaaitaal, M., Kramer, G., van der Burg, H., Vontas, J., Van Leeuwen, T., Kant, M., & Schuurink, R. (2023). Interaction of whitefly effector G4 with tomato proteins impacts whitefly performance. Molecular Plant-Microbe Interactions. Advance online publication. https://doi.org/10.1094/MPMI-04-23-0045-R
Seekles, S. J., van den Brule, T., Punt, M., Dijksterhuis, J., Arentshorst, M., Ijadpanahsaravi, M., Roseboom, W., Meuken, G., Ongenae, V., Zwerus, J., Ohm, R. A., Kramer, G., Wösten, H. A. B., de Winde, J. H., & Ram, A. F. J. (2023). Compatible solutes determine the heat resistance of conidia. Fungal biology and biotechnology, 10(1), 21. https://doi.org/10.1186/s40694-023-00168-9
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, Article 1161604. https://doi.org/10.3389/fmicb.2023.1161604[details]
van Kleeff, P. J. M., Mastop, M., Sun, P., Dangol, S., van Doore, E., Dekker, H. L., Kramer, G., Lee, S., Ryu, C.-M., de Vos, M., & Schuurink, R. (2023). Discovery of three Bemisia tabaci effectors and their effect on gene expression in planta. Molecular Plant-Microbe Interactions. Advance online publication. https://doi.org/10.1094/MPMI-04-23-0044-R
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), Article 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), Article 1695. https://doi.org/10.3390/microorganisms10091695[details]
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
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), Article 5590. https://doi.org/10.3390/ijms23105590[details]
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), Article 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), Article 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, Article 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), Article 9345. https://doi.org/10.3390/ijms22179345[details]
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. 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]
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
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, Article 103987. Advance online publication. 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), Article 140655. https://doi.org/10.1016/j.bbapap.2021.140655[details]
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), Article 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), Article 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), Article 4315. https://doi.org/10.3390/ijms21124315[details]
Cooke, A., Schwarzl, T., Huppertz, I., Kramer, G., Mantas, P., Alleaume, A-M., Huber, W., Krijgsveld, J., & 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]
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
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), Article 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. Advance online publication. https://doi.org/10.5301/jva.5000166
Wegdam, W., Argmann, C. A., Kramer, G., Vissers, J. P., Buist, M. R., Kenter, G. G., Aerts, J. M. F. G., Meijer, D., & 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), Article 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., Munnik, T., & 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). 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., van den Nieuwendijk, A. M. C. H., Bleijlevens, B., Kramer, G., Florea, B. I., Hooibrink, B., Hollak, C. E. M., Ottenhoff, R., Boot, R. G., van der Marel, G. A., Overkleeft, H. S., & 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 Koning, L. J., Hellingwerf, K. J., de Jong, L., & 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., van Maarseveen, J. H., de Jong, L., Bertozzi, C. R., Hiemstra, H., & 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 Jong, L., van Maarseveen, J. H., & 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
Talk / presentation
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.
2023
Huang, Y. (2023). Multi-omics of Bacillus subtilis spores and cells sheds new light on bacterial survival. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
Chapter 2: Integrative metabolomics and proteomics allow the global intracellular characterization of Bacillus subtilis cells and spores(embargo until 15 November 2025)
Chapter 3: Multi-omics analysis of Bacillus subtilis spores formed at different environmental temperatures reveal differences at the morphological and molecular level(embargo until 15 November 2025)
Chapter 4: Molecular physiological characterization of Bacillus subtilis with Dipicolinic Acid (DPA)-less spores(embargo until 15 November 2025)
Chapter 5: Non-mechanical disruption of Bacillus subtilis spores allows sensitive and deep characterization of the minimal proteome for resuming a cellular life-style(embargo until 15 November 2025)
Chapter 3: Supplementary files(embargo until 30 March 2024)
Chapter 4: Supplementary table(embargo until 30 March 2024)
2021
Tu, Z. (2021). Proteome dynamics during sporulation and heat resistance in Bacillus subtilis spores. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
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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