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Items: 1 to 50 of 107

1.

Vegetative Cell and Spore Proteomes of Clostridioides difficile Show Finite Differences and Reveal Potential Protein Markers.

Abhyankar WR, Zheng L, Brul S, de Koster CG, de Koning LJ.

J Proteome Res. 2019 Nov 1;18(11):3967-3976. doi: 10.1021/acs.jproteome.9b00413. Epub 2019 Oct 14.

2.

Proteomics and microscopy tools for the study of antimicrobial resistance and germination mechanisms of bacterial spores.

Abhyankar WR, Wen J, Swarge BN, Tu Z, de Boer R, Smelt JPPM, de Koning LJ, Manders E, de Koster CG, Brul S.

Food Microbiol. 2019 Aug;81:89-96. doi: 10.1016/j.fm.2018.03.006. Epub 2018 Mar 14. Review.

3.

Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and ZapA by BAMG Cross-Linking and Site-Directed Mutagenesis.

Roseboom W, Nazir MG, Meiresonne NY, Mohammadi T, Verheul J, Buncherd H, Bonvin AMJJ, de Koning LJ, de Koster CG, de Jong L, den Blaauwen T.

Int J Mol Sci. 2018 Sep 26;19(10). pii: E2928. doi: 10.3390/ijms19102928.

4.

Correction to "Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach".

Stelder SK, Benito de Moya C, Hoefsloot HCJ, de Koning LJ, Brul S, de Koster CG.

J Proteome Res. 2018 Jul 6;17(7):2562. doi: 10.1021/acs.jproteome.8b00313. Epub 2018 Jun 1. No abstract available.

5.

"One-Pot" Sample Processing Method for Proteome-Wide Analysis of Microbial Cells and Spores.

Swarge BN, Roseboom W, Zheng L, Abhyankar WR, Brul S, de Koster CG, de Koning LJ.

Proteomics Clin Appl. 2018 Sep;12(5):e1700169. doi: 10.1002/prca.201700169. Epub 2018 Apr 16.

6.

Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach.

Stelder SK, Benito de Moya C, Hoefsloot HCJ, de Koning LJ, Brul S, de Koster CG.

J Proteome Res. 2018 Feb 2;17(2):903-917. doi: 10.1021/acs.jproteome.7b00732. Epub 2018 Jan 4. Erratum in: J Proteome Res. 2018 Jul 6;17(7):2562.

7.

Identification and Characterization of (3Z):(2E)-Hexenal Isomerases from Cucumber.

Spyropoulou EA, Dekker HL, Steemers L, van Maarseveen JH, de Koster CG, Haring MA, Schuurink RC, Allmann S.

Front Plant Sci. 2017 Aug 2;8:1342. doi: 10.3389/fpls.2017.01342. eCollection 2017.

8.

In-Culture Cross-Linking of Bacterial Cells Reveals Large-Scale Dynamic Protein-Protein Interactions at the Peptide Level.

de Jong L, de Koning EA, Roseboom W, Buncherd H, Wanner MJ, Dapic I, Jansen PJ, van Maarseveen JH, Corthals GL, Lewis PJ, Hamoen LW, de Koster CG.

J Proteome Res. 2017 Jul 7;16(7):2457-2471. doi: 10.1021/acs.jproteome.7b00068. Epub 2017 May 26.

9.

The Influence of Sporulation Conditions on the Spore Coat Protein Composition of Bacillus subtilis Spores.

Abhyankar WR, Kamphorst K, Swarge BN, van Veen H, van der Wel NN, Brul S, de Koster CG, de Koning LJ.

Front Microbiol. 2016 Oct 13;7:1636. eCollection 2016.

10.

The use of δ(2)H and δ(18)O isotopic analyses combined with chemometrics as a traceability tool for the geographical origin of bell peppers.

de Rijke E, Schoorl JC, Cerli C, Vonhof HB, Verdegaal SJ, Vivó-Truyols G, Lopatka M, Dekter R, Bakker D, Sjerps MJ, Ebskamp M, de Koster CG.

Food Chem. 2016 Aug 1;204:122-8. doi: 10.1016/j.foodchem.2016.01.134. Epub 2016 Feb 4.

PMID:
26988484
11.

Bacillus subtilis Spore Inner Membrane Proteome.

Zheng L, Abhyankar W, Ouwerling N, Dekker HL, van Veen H, van der Wel NN, Roseboom W, de Koning LJ, Brul S, de Koster CG.

J Proteome Res. 2016 Feb 5;15(2):585-94. doi: 10.1021/acs.jproteome.5b00976. Epub 2016 Jan 13.

PMID:
26731423
12.

Proteomic analysis of hyperadhesive Candida glabrata clinical isolates reveals a core wall proteome and differential incorporation of adhesins.

Gómez-Molero E, de Boer AD, Dekker HL, Moreno-Martínez A, Kraneveld EA, Ichsan, Chauhan N, Weig M, de Soet JJ, de Koster CG, Bader O, de Groot PW.

FEMS Yeast Res. 2015 Dec;15(8). pii: fov098. doi: 10.1093/femsyr/fov098. Epub 2015 Nov 5.

PMID:
26546455
13.

Quantitative proteomics analysis of an ethanol- and a lactate-producing mutant strain of Synechocystis sp. PCC6803.

Borirak O, de Koning LJ, van der Woude AD, Hoefsloot HC, Dekker HL, Roseboom W, de Koster CG, Hellingwerf KJ.

Biotechnol Biofuels. 2015 Aug 5;8:111. doi: 10.1186/s13068-015-0294-z. eCollection 2015.

14.

Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression.

Borirak O, Rolfe MD, de Koning LJ, Hoefsloot HC, Bekker M, Dekker HL, Roseboom W, Green J, de Koster CG, Hellingwerf KJ.

Biochim Biophys Acta. 2015 Oct;1854(10 Pt A):1269-79. doi: 10.1016/j.bbapap.2015.05.017. Epub 2015 Jun 4.

15.

Determination of n-alkanes in C. annuum (bell pepper) fruit and seed using GC-MS: comparison of extraction methods and application to samples of different geographical origin.

de Rijke E, Fellner C, Westerveld J, Lopatka M, Cerli C, Kalbitz K, de Koster CG.

Anal Bioanal Chem. 2015 Jul;407(19):5729-38. doi: 10.1007/s00216-015-8755-6. Epub 2015 May 28.

16.

Temperature Dependence of the Proteome Profile of the Psychrotolerant Pathogenic Food Spoiler Bacillus weihenstephanensis Type Strain WSBC 10204.

Stelder SK, Mahmud SA, Dekker HL, de Koning LJ, Brul S, de Koster CG.

J Proteome Res. 2015 May 1;14(5):2169-76. doi: 10.1021/pr501307t. Epub 2015 Apr 22.

PMID:
25853650
17.

Simulation of the rate of transfer of antibiotic resistance between Escherichia coli strains cultured under well controlled environmental conditions.

Smelt JP, Hoefsloot HC, de Koster CG, Schuurmans JM, ter Kuile BH, Brul S.

Food Microbiol. 2015 Feb;45(Pt B):189-94. doi: 10.1016/j.fm.2014.03.019. Epub 2014 Apr 18.

PMID:
25500384
18.

Reinforcement of Bacillus subtilis spores by cross-linking of outer coat proteins during maturation.

Abhyankar W, Pandey R, Ter Beek A, Brul S, de Koning LJ, de Koster CG.

Food Microbiol. 2015 Feb;45(Pt A):54-62. doi: 10.1016/j.fm.2014.03.007. Epub 2014 Mar 18.

PMID:
25481062
19.

Spore proteomics: the past, present and the future.

Abhyankar W, de Koning LJ, Brul S, de Koster CG.

FEMS Microbiol Lett. 2014 Sep;358(2):137-44. doi: 10.1111/1574-6968.12568. Epub 2014 Aug 28. Review.

20.

A gas phase cleavage reaction of cross-linked peptides for protein complex topology studies by peptide fragment fingerprinting from large sequence database.

Buncherd H, Roseboom W, de Koning LJ, de Koster CG, de Jong L.

J Proteomics. 2014 Aug 28;108:65-77. doi: 10.1016/j.jprot.2014.05.003. Epub 2014 May 17.

PMID:
24840472
21.

Isolation of cross-linked peptides by diagonal strong cation exchange chromatography for protein complex topology studies by peptide fragment fingerprinting from large sequence databases.

Buncherd H, Roseboom W, Ghavim B, Du W, de Koning LJ, de Koster CG, de Jong L.

J Chromatogr A. 2014 Jun 27;1348:34-46. doi: 10.1016/j.chroma.2014.04.083. Epub 2014 May 2.

PMID:
24819016
22.

Mutations in SNF1 complex genes affect yeast cell wall strength.

Backhaus K, Rippert D, Heilmann CJ, Sorgo AG, de Koster CG, Klis FM, Rodicio R, Heinisch JJ.

Eur J Cell Biol. 2013 Dec;92(12):383-95. doi: 10.1016/j.ejcb.2014.01.001. Epub 2014 Jan 10.

PMID:
24486034
23.

Cell wall-related bionumbers and bioestimates of Saccharomyces cerevisiae and Candida albicans.

Klis FM, de Koster CG, Brul S.

Eukaryot Cell. 2014 Jan;13(1):2-9. doi: 10.1128/EC.00250-13. Epub 2013 Nov 15. Review.

24.

In pursuit of protein targets: proteomic characterization of bacterial spore outer layers.

Abhyankar W, Hossain AH, Djajasaputra A, Permpoonpattana P, Ter Beek A, Dekker HL, Cutting SM, Brul S, de Koning LJ, de Koster CG.

J Proteome Res. 2013 Oct 4;12(10):4507-21. doi: 10.1021/pr4005629. Epub 2013 Sep 23.

PMID:
23998435
25.

Iron restriction-induced adaptations in the wall proteome of Candida albicans.

Sorgo AG, Brul S, de Koster CG, de Koning LJ, Klis FM.

Microbiology. 2013 Aug;159(Pt 8):1673-82. doi: 10.1099/mic.0.065599-0. Epub 2013 May 31.

PMID:
23728625
26.

Identification of novel candidate phosphatidic acid-binding proteins involved in the salt-stress response of Arabidopsis thaliana roots.

McLoughlin F, Arisz SA, Dekker HL, Kramer G, de Koster CG, Haring MA, Munnik T, Testerink C.

Biochem J. 2013 Mar 15;450(3):573-81. doi: 10.1042/BJ20121639. Erratum in: Biochem J. 2013 Apr 15;451(2):343.

PMID:
23323832
27.

Surface stress induces a conserved cell wall stress response in the pathogenic fungus Candida albicans.

Heilmann CJ, Sorgo AG, Mohammadi S, Sosinska GJ, de Koster CG, Brul S, de Koning LJ, Klis FM.

Eukaryot Cell. 2013 Feb;12(2):254-64. doi: 10.1128/EC.00278-12. Epub 2012 Dec 14.

28.

Beyond the wall: Candida albicans secret(e)s to survive.

Sorgo AG, Heilmann CJ, Brul S, de Koster CG, Klis FM.

FEMS Microbiol Lett. 2013 Jan;338(1):10-7. doi: 10.1111/1574-6968.12049. Epub 2012 Nov 30. Review.

29.

Carbon source-induced reprogramming of the cell wall proteome and secretome modulates the adherence and drug resistance of the fungal pathogen Candida albicans.

Ene IV, Heilmann CJ, Sorgo AG, Walker LA, de Koster CG, Munro CA, Klis FM, Brown AJ.

Proteomics. 2012 Nov;12(21):3164-79. doi: 10.1002/pmic.201200228.

30.

A truncated lamin A in the Lmna -/- mouse line: implications for the understanding of laminopathies.

Jahn D, Schramm S, Schnölzer M, Heilmann CJ, de Koster CG, Schütz W, Benavente R, Alsheimer M.

Nucleus. 2012 Sep-Oct;3(5):463-74. doi: 10.4161/nucl.21676. Epub 2012 Aug 16.

31.

Isoenzyme expression changes in response to high temperature determine the metabolic regulation of increased glycolytic flux in yeast.

Postmus J, Aardema R, de Koning LJ, de Koster CG, Brul S, Smits GJ.

FEMS Yeast Res. 2012 Aug;12(5):571-81. doi: 10.1111/j.1567-1364.2012.00807.x. Epub 2012 Apr 30.

32.

Selective enrichment and identification of cross-linked peptides to study 3-D structures of protein complexes by mass spectrometry.

Buncherd H, Nessen MA, Nouse N, Stelder SK, Roseboom W, Dekker HL, Arents JC, Smeenk LE, Wanner MJ, van Maarseveen JH, Yang X, Lewis PJ, de Koning LJ, de Koster CG, de Jong L.

J Proteomics. 2012 Apr 3;75(7):2205-15. doi: 10.1016/j.jprot.2012.01.025. Epub 2012 Feb 4.

PMID:
22326961
33.

Gel-free proteomic identification of the Bacillus subtilis insoluble spore coat protein fraction.

Abhyankar W, Beek AT, Dekker H, Kort R, Brul S, de Koster CG.

Proteomics. 2011 Dec;11(23):4541-50. doi: 10.1002/pmic.201100003. Epub 2011 Oct 28.

PMID:
21905219
34.

A mass spectrometric view of the fungal wall proteome.

Klis FM, de Koster CG, Brul S.

Future Microbiol. 2011 Aug;6(8):941-51. doi: 10.2217/FMB.11.72. Review.

PMID:
21861624
35.

Identification and differential gene expression of adhesin-like wall proteins in Candida glabrata biofilms.

Kraneveld EA, de Soet JJ, Deng DM, Dekker HL, de Koster CG, Klis FM, Crielaard W, de Groot PW.

Mycopathologia. 2011 Dec;172(6):415-27. doi: 10.1007/s11046-011-9446-2. Epub 2011 Jul 17.

PMID:
21769633
36.

Bis(metallo) capsules based on two ionic diphosphines.

Koblenz TS, Dekker HL, de Koster CG, van Leeuwen PW, Reek JN.

Chem Asian J. 2011 Sep 5;6(9):2431-43. doi: 10.1002/asia.201100073. Epub 2011 Jul 4.

PMID:
21728245
37.

Growth-dependent secretome of Candida utilis.

Buerth C, Heilmann CJ, Klis FM, de Koster CG, Ernst JF, Tielker D.

Microbiology. 2011 Sep;157(Pt 9):2493-503. doi: 10.1099/mic.0.049320-0. Epub 2011 Jun 16.

PMID:
21680638
38.

Diphosphine capsules for transition-metal encapsulation.

Koblenz TS, Dekker HL, de Koster CG, van Leeuwen PW, Reek JN.

Chem Asian J. 2011 Sep 5;6(9):2444-62. doi: 10.1002/asia.201100092. Epub 2011 Jun 9.

PMID:
21661114
39.

Effects of fluconazole on the secretome, the wall proteome, and wall integrity of the clinical fungus Candida albicans.

Sorgo AG, Heilmann CJ, Dekker HL, Bekker M, Brul S, de Koster CG, de Koning LJ, Klis FM.

Eukaryot Cell. 2011 Aug;10(8):1071-81. doi: 10.1128/EC.05011-11. Epub 2011 May 27.

40.

Quantitation of newly synthesized proteins by pulse labeling with azidohomoalanine.

Kramer G, Kasper PT, de Jong L, de Koster CG.

Methods Mol Biol. 2011;753:169-81. doi: 10.1007/978-1-61779-148-2_12.

PMID:
21604123
41.

Hyphal induction in the human fungal pathogen Candida albicans reveals a characteristic wall protein profile.

Heilmann CJ, Sorgo AG, Siliakus AR, Dekker HL, Brul S, de Koster CG, de Koning LJ, Klis FM.

Microbiology. 2011 Aug;157(Pt 8):2297-2307. doi: 10.1099/mic.0.049395-0. Epub 2011 May 20.

PMID:
21602216
42.

Identification of the peroxidase-generated intermolecular dityrosine cross-link in bovine α-lactalbumin.

Heijnis WH, Dekker HL, de Koning LJ, Wierenga PA, Westphal AH, de Koster CG, Gruppen H, van Berkel WJ.

J Agric Food Chem. 2011 Jan 12;59(1):444-9. doi: 10.1021/jf104298y. Epub 2010 Dec 16.

PMID:
21162537
43.

Mass spectrometric quantification of the adaptations in the wall proteome of Candida albicans in response to ambient pH.

Sosinska GJ, de Koning LJ, de Groot PW, Manders EM, Dekker HL, Hellingwerf KJ, de Koster CG, Klis FM.

Microbiology. 2011 Jan;157(Pt 1):136-46. doi: 10.1099/mic.0.044206-0. Epub 2010 Sep 23.

PMID:
20864472
44.

Proteome-wide alterations in Escherichia coli translation rates upon anaerobiosis.

Kramer G, Sprenger RR, Nessen MA, Roseboom W, Speijer D, de Jong L, de Mattos MJ, Back J, de Koster CG.

Mol Cell Proteomics. 2010 Nov;9(11):2508-16. doi: 10.1074/mcp.M110.001826. Epub 2010 Aug 16.

45.

A systematic study of the cell wall composition of Kluyveromyces lactis.

Backhaus K, Heilmann CJ, Sorgo AG, Purschke G, de Koster CG, Klis FM, Heinisch JJ.

Yeast. 2010 Aug;27(8):647-60. doi: 10.1002/yea.1781.

46.

Mass spectrometric analysis of the secretome of Candida albicans.

Sorgo AG, Heilmann CJ, Dekker HL, Brul S, de Koster CG, Klis FM.

Yeast. 2010 Aug;27(8):661-72. doi: 10.1002/yea.1775.

47.

The Candida albicans cell wall protein Rhd3/Pga29 is abundant in the yeast form and contributes to virulence.

de Boer AD, de Groot PW, Weindl G, Schaller M, Riedel D, Diez-Orejas R, Klis FM, de Koster CG, Dekker HL, Gross U, Bader O, Weig M.

Yeast. 2010 Aug;27(8):611-24. doi: 10.1002/yea.1790.

48.

Gaucher disease: a model disorder for biomarker discovery.

Boot RG, van Breemen MJ, Wegdam W, Sprenger RR, de Jong S, Speijer D, Hollak CE, van Dussen L, Hoefsloot HC, Smilde AK, de Koster CG, Vissers JP, Aerts JM.

Expert Rev Proteomics. 2009 Aug;6(4):411-9. doi: 10.1586/epr.09.54. Review.

PMID:
19681676
49.

Flow injection analysis electrospray ionization mass spectrometry for high-throughput screening of a gene library for amidase activity.

Henderickx HJ, Raemakers-Franken PC, van der Wal S, de Koster CG, Duchateau AL, Sonke T.

Anal Biochem. 2009 Nov 15;394(2):159-63. doi: 10.1016/j.ab.2009.07.018. Epub 2009 Jul 16.

PMID:
19615964
50.

Comprehensive genomic analysis of cell wall genes in Aspergillus nidulans.

de Groot PW, Brandt BW, Horiuchi H, Ram AF, de Koster CG, Klis FM.

Fungal Genet Biol. 2009 Mar;46 Suppl 1:S72-81.

PMID:
19585695

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