• Male

Dr. D. Speijer PhD

Position: Scientific staff member (UD)
Main activities: Research, Teaching
Specialisation: Molecular evolution, Proteomics, Mass spectrometry, Mitochondrial research
foto
Focus of research: I coordinate research efforts in Proteomics of human lysosomal storage disorders (LSD's), including implementation of ICAT like techniques. I optimized the in gel digestion protocol and colloidal Coomassie staining to get routine identification at very low protein abundancies. I collaborated with many different groups (in and outside of the AMC) in Proteomic studies. In the context of my own research (a.o. Proteomics of HIV-Tcell interaction), I initiated the reproducible large scale DIGE approach in our lab (together with Jeffrey Ringrose and Rienk Jeeninga) and used this to monitor changes in cellular proteins induced by HIV-1 infection. In several collaborations I analysed changes in protein PTM's, identified several biologically important proteins, tested peptidomimetics for biological activities and was involved in immunologcal work. I published several theoretical articles regarding genome architecture and evolution. I started with further Proteomic studies of different classes of parasites (e.g. HIV-1 and -mitochondrial fractions of- trypanosomes). Last but not least, I am also starting research to monitor oxidative damage of proteins, comparing conditions under which most energy is either derived from fatty acid breakdown or glycolysis, to test an hypothesis formulated in BioEssays 33, pp. 88-94.
AMC themes: Infection & Immunity, Metabolic disorders and gastrointestinal diseases
Departments: Medical Biochemistry
Verwer RWH, Sluiter AA, Balesar RA, Baayen JC, Speijer D, Idema S, Swaab DF, Altered Loyalties of Neuronal Markers in Cultured Slices of Resected Human Brain Tissue. BRAIN PATHOL 2016;ahead of print [PubMed]
Kramer G, Woolerton Y, van Straalen JP, Vissers JPC, Dekker N, Langridge JI, Beynon RJ, Speijer D, Sturk A, Aerts JMFG, Accuracy and Reproducibility in Quantification of Plasma Protein Concentrations by Mass Spectrometry without the Use of Isotopic Standards. PLOS ONE 2015;10 (10):e0140097 [PubMed]
Nandal UK, Vlietstra WJ, Byrman C, Jeeninga RE, Ringrose JH, van Kampen AHC, Speijer D, Moerland PD, Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets. BMC BIOINFORMATICS 2015;16 (1):25 [PubMed]
Speijer D, Birth of the eukaryotes by a set of reactive innovations: New insights force us to relinquish gradual models. BIOESSAYS 2015;37 (12):1268-1276 [PubMed]
Speijer D, Lukeš J, Eliáš M, Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life. P NATL ACAD SCI USA 2015;112 (29):8827-8834 [PubMed]
Stax MJ, Mouser EEIM, van Montfort T, Sanders RW, de Vries HJC, Dekker HL, Herrera C, Speijer D, Pollakis G, Paxton WA, Colorectal mucus binds DC-SIGN and inhibits HIV-1 trans-infection of CD4+ T-lymphocytes. PLOS ONE 2015;10 (3):e0122020 [PubMed]
van der Gulik PTS, Speijer D, How amino acids and peptides shaped the RNA world. LIFE (BASEL) 2015;5 (1):230-246 [PubMed]
van der Sluis RM, van Capel TMM, Speijer D, Sanders RW, Berkhout B, de Jong EC, Jeeninga RE, van Montfort T, Dendritic cell type-specific HIV-1 activation in effector T cells: implications for latent HIV-1 reservoir establishment. AIDS 2015;29 (9):1003-1014 [PubMed]
Verwer RWH, Sluiter AA, Balesar RA, Baaijen JC, de Witt Hamer PC, Speijer D, Li Y, Swaab DF, Injury Response of Resected Human Brain Tissue In Vitro. BRAIN PATHOL 2015;25 (4):454-468 [PubMed]
Holt IJ, Speijer D, Kirkwood TBL, The road to rack and ruin: selecting deleterious mitochondrial DNA variants. PHILOS T R SOC B 2014;369 (1646):20130451-(7 p.) [PubMed]
Pannekoek Y, Speijer D, van der Ende A. The Regulatory Small RNAs of Neisseria in: Davies JK, Kahler CM, editors. Pathogenic Neisseria: Genomics, Molecular Biology and Disease Intervention. S.l.: Caister Academic Press; 2014., p. 41-58
Speijer D, How the mitochondrion was shaped by radical differences in substrates: what carnitine shuttles and uncoupling tell us about mitochondrial evolution in response to ROS. BIOESSAYS 2014;36 (7):634-643 [PubMed]
Speijer D, Reconsidering ideas regarding the evolution of peroxisomes: the case for a mitochondrial connection. CELL MOL LIFE SCI 2014;71 (13):2377-2378 [PubMed]
Speijer D, Manjeri GR, Szklarczyk R, How to deal with oxygen radicals stemming from mitochondrial fatty acid oxidation. PHILOS T R SOC B 2014;369 (1646):20130446-(8 p.) [PubMed]
Strang AC, Knetsch MLW, Idu MM, Bisoendial RJ, Kramer G, Speijer D, Koole LH, Stroes ESG, Rotmans JI, Superior in vivo compatibility of hydrophilic polymer coated prosthetic vascular grafts. J VASC ACCESS 2014;15 (2):95-101 [PubMed]
van der Sluis RM, Derking R, Breidel S, Speijer D, Berkhout B, Jeeninga RE, Interplay between viral Tat protein and c-Jun transcription factor in controlling LTR promoter activity in different human immunodeficiency virus type I subtypes. J GEN VIROL 2014;95 (4):968-979 [PubMed]
Buhrman H, van der Gulik PTS, Klau GW, Schaffner C, Speijer D, Stougie L, A Realistic Model Under Which the Genetic Code is Optimal. J MOL EVOL 2013;77 (4):170-184 [PubMed]
van der Sluis RM, van Montfort T, Pollakis G, Sanders RW, Speijer D, Berkhout B, Jeeninga RE, Dendritic cell-induced activation of latent HIV-1 provirus in actively proliferating primary T lymphocytes. PLOS PATHOG 2013;9 (3):e1003259-(15 p.) [PubMed]
Kramer G, Moerland PD, Jeeninga RE, Vlietstra WJ, Ringrose JH, Byrman C, Berkhout B, Speijer D, Proteomic analysis of HIV-T cell interaction: an update. FRONT MICROBIOL 2012;3:240-(6 p.) [PubMed]
Speijer D, Brains have a gut feeling about fat storage. BIOESSAYS 2012;34 (4):275-276 [PubMed]
Speijer D, Penetrating insights?. FRONT MICROBIOL 2012;3:382-(2 p.) [PubMed]
Dekker N, van Dussen L, Hollak CEM, Overkleeft H, Scheij S, Ghauharali K, van Breemen MJ, Ferraz MJ, Groener JEM, Maas M, Wijburg FA, Speijer D, Tylki-Szymanska A, Mistry PK, Boot RG, Aerts JM, Elevated plasma glucosylsphingosine in Gaucher disease: relation to phenotype, storage cell markers, and therapeutic response. BLOOD 2011;118 (16):e118-e127 [PubMed]
Dekker N, Voorn-Brouwer T, Verhoek M, Wennekes T, Narayan RS, Speijer D, Hollak CEM, Overkleeft HS, Boot RG, Aerts JMFG, The cytosolic beta-glucosidase GBA3 does not influence type 1 Gaucher disease manifestation. BLOOD CELL MOL DIS 2011;46 (1):19-26 [PubMed]
Kwakman PHS, Krijgsveld J, de Boer L, Nguyen LT, Boszhard L, Vreede J, Dekker HL, Speijer D, Drijfhout JW, te Velde AA, Crielaard W, Vogel HJ, Vandenbroucke-Grauls CMJE, Zaat SAJ, Native thrombocidin-1 and unfolded thrombocidin-1 exert antimicrobial activity via distinct structural elements. J BIOL CHEM 2011;286 (50):43506-43514 [PubMed]
Speijer D, Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity. BIOESSAYS 2011;33 (5):344-349 [PubMed]
Speijer D, Oxygen radicals shaping evolution: Why fatty acid catabolism leads to peroxisomes while neurons do without it: FADH2/NADH flux ratios determining mitochondrial radical formation were crucial for the eukaryotic invention of peroxisomes and catabolic tissue differentiation. BIOESSAYS 2011;33 (2):88-94 [PubMed]
Hopman CTP, Speijer D, van der Ende A, Pannekoek Y, Identification of a novel anti-sigmaE factor in Neisseria meningitidis. BMC MICROBIOL 2010;10 (1):164 [PubMed]
Kramer G, Sprenger RR, Nessen MA, Roseboom W, Speijer D, de Jong L, Teixeira de Mattos MJ, Back J, de Koster CG, Proteome-wide Alterations in Escherichia coli Translation Rates upon Anaerobiosis. MOL CELL PROTEOMICS 2010;9 (11):2508-2516 [PubMed]
Kwakman PHS, te Velde AA, de Boer L, Speijer D, Vandenbroucke-Grauls CMJE, Zaat SAJ, How honey kills bacteria. FASEB J 2010;24 (7):2576-2582 [PubMed]
Speijer D, Constructive neutral evolution cannot explain current kinetoplastid panediting patterns. P NATL ACAD SCI USA 2010;107 (7):E25-E25 [PubMed]
Boot RG, Speijer D, Bussink AP, Aerts JMFG. The origin and genetics of human chitinases in: Musumeci S, Paoletti MG, editors. Binomium Chitin-Chitinase. Hauppauge, NY 11788-3619, U.S.A.: Nova Science Publishers; 2009., p. 77-99
Boot RG, van Breemen MJ, Wegdam W, Sprenger RR, de Jong S, Speijer D, Hollak CEM, van Dussen L, Hoefsloot HCJ, Smilde AK, de Koster CG, Vissers JPC, Aerts JMFG, Gaucher disease: a model disorder for biomarker discovery. EXPERT REV PROTEOMIC 2009;6 (4):411-419 [PubMed]
Middeldorp J, van den Berge SA, Aronica E, Speijer D, Hol EM, Specific human astrocyte subtype revealed by affinity purified GFAP antibody; unpurified serum cross-reacts with neurofilament-L in Alzheimer. PLOS ONE 2009;4 (11):e7663 [PubMed]
Pannekoek Y, Huis In 't Veld R, Hopman CTP, Langerak AAJ, Speijer D, van der Ende A, Molecular characterization and identification of proteins regulated by Hfq in Neisseria meningitidis. FEMS MICROBIOL LETT 2009;294 (2):216-224 [PubMed]
Speijer D, Defining numbers in terms of their divisors. NATURE 2009;461 (7260):37-37
Stax MJ, van Montfort T, Sprenger RR, Melchers M, Sanders RW, van Leeuwen E, Repping S, Pollakis G, Speijer D, Paxton WA, Mucin 6 in seminal plasma binds DC-SIGN and potently blocks dendritic cell mediated transfer of HIV-1 to CD4(+) T-lymphocytes. VIROLOGY 2009;391 (2):203-211 [PubMed]
van Munster BC, van Breemen MJ, Moerland PD, Speijer D, de Rooij SE, Pfrommer CJ, Levi M, Hollmann MW, Aerts JM, Zwinderman AH, Korevaar JC, Proteomic Profiling of Plasma and Serum in Elderly Patients With Delirium. J NEUROPSYCH CLIN N 2009;21 (3):284-291 [PubMed]
Aerts JM, van Breemen MJ, Bussink AP, Ghauharali K, Sprenger R, Boot RG, Groener JE, Hollak CE, Maas M, Smit S, Hoefsloot HC, Smilde AK, Vissers JP, de Jong S, Speijer D, de Koster CG, Biomarkers for lysosomal storage disorders: identification and application as exemplified by chitotriosidase in Gaucher disease. ACTA PAEDIATR 2008;97 (Suppl. 457):7-14 [PubMed]
Bart A, van der Heijden HM, Greve S, Speijer D, Landman WJ, van Gool T, Intragenomic variation in the internal transcribed spacer 1 region of Dientamoeba fragilis as a molecular epidemiological marker. J CLIN MICROBIOL 2008;46 (10):3270-3275 [PubMed]
Ringrose JH, Jeeninga RE, Berkhout B, Speijer D, Proteomic studies reveal coordinated changes in T-cell expression patterns upon infection with human immunodeficiency virus type 1. J VIROL 2008;82 (9):4320-4330 [PubMed]
Speijer D, Making sense of scrambled genomes. SCIENCE 2008;319 (5865):901-2; author reply 901-2 [PubMed]
van Breemen MJ, Aerts JMFG, Sprenger RR, Speijer D, Potential artefacts in proteome analysis of plasma of Gaucher patients due to protease abnormalities. CLIN CHIM ACTA 2008;396 (1-2):26-32 [PubMed]
van den Bos T, Speijer D, Bank RA, Bromme D, Everts V, Differences in matrix composition between calvaria and long bone in mice suggest differences in biomechanical properties and resorption Special emphasis on collagen. BONE 2008;43 (3):459-468 [PubMed]
Bock VD, Speijer D, Hiemstra H, van Maarseveen JH, 1,2,3-Triazoles as peptide bond isosteres: synthesis and biological evaluation of cyclotetrapeptide mimics. ORG BIOMOL CHEM 2007;5 (6):971-975 [PubMed]
Bussink AP, Speijer D, Aerts JMFG, Boot RG, Evolution of mammalian chitinase(-like) members of family 18 glycosyl hydrolases. GENETICS 2007;177 (2):959-970 [PubMed]
Houterman PM, Speijer D, Dekker HL, de Koster CG, Cornelissen BJC, Rep M, The mixed xylem sap proteome of Fusarium oxysporum-infected tomato plants. MOL PLANT PATHOL 2007;8 (2):215-221 [PubMed]
Rep M, van der Does C, Meijer M, Houterman PM, Dekker HL, Speijer D, de Koster CG, Cornelissen BJC. Secrets of Xylem Colonization - The Xylem Sap Proteome of Tomato Infected with Fusarium oxysorum in: Sanchez S, Lopez-Lara L, Geiger M, editors. Biology of plant-microbe interactions. onbekend: onbekend; 2007. 4, p. 597-601
Speijer D. Evolutionary Aspects of RNA Editing in: Göringer HU, editor. RNA Editing. Berlin: Springer-Verlag; 2008., p. 199-227
van Eijk M, Scheij SS, van Roomen CPAA, Speijer D, Boot RG, Aerts JMFG, TLR- and NOD2-dependent regulation of human phagocyte-specific chitotriosidase. FEBS LETT 2007;581 (28):5389-5395 [PubMed]
Naarding MA, Dirac AM, Ludwig IS, Speijer D, Lindquist S, Vestman EL, Stax MJ, Geijtenbeek TBH, Pollakis G, Hernell O, Paxton WA, Bile salt-stimulated lipase from human milk binds DC-SIGN and inhibits human immunodeficiency virus type 1 transfer to CD4+ T cells. ANTIMICROB AGENTS CH 2006;50 (10):3367-3374 [PubMed]
Ofman R, Speijer D, Leen R, Wanders RJA, Proteomic analysis of mouse kidney peroxisomes: identification of RP2p as a peroxisomal nudix hydrolase with acyl-CoA diphosphatase activity. BIOCHEM J 2006;393 (Part 2):537-543 [PubMed]
Rezaee F, Casetta B, Levels JHM, Speijer D, Meijers JCM, Proteomic analysis of high-density lipoprotein. PROTEOMICS 2006;6 (2):721-730 [PubMed]
Speijer D, Is kinetoplastid pan-editing the result of an evolutionary balancing act?. IUBMB LIFE 2006;58 (2):91-96 [PubMed]
Pannekoek Y, Heurgué-Hamard V, Langerak AAJ, Speijer D, Buckingham RH, van der Ende A, The N-5-glutamine S-adenosyl-L-methionine-dependent methyltransferase PrmC/HemK in Chlamydia trachomatis methylates class 1 release factors. J BACTERIOL 2005;187 (2):507-511 [PubMed]
Peek R, Delbac F, Speijer D, Polonais V, Greve S, Wentink-Bonnema E, Ringrose J, van Gool T, Carbohydrate moieties of microsporidian polar tube proteins are targeted by immunoglobulin G in immunocompetent individuals. INFECT IMMUN 2005;73 (12):7906-7913 [PubMed]
Dekker N, Speijer D, Grün CH, van den Berg M, de Haan A, Hochstenbach F, Role of the alpha-glucanase Agn1p in fission-yeast cell separation. MOL BIOL CELL 2004;15 (8):3903-3914 [PubMed]
Ringrose JH, Meiring HD, Speijer D, Feltkamp TEW, van Els CACM, de Jong APJM, Dankert J, Major histocompatibility complex class I peptide presentation after Salmonella enterica serovar typhimurium infection assessed via stable isotope tagging of the B27-presented peptide repertoire. INFECT IMMUN 2004;72 (9):5097-5105 [PubMed]
Sprenger RR, Speijer D, Back JW, de Koster CG, Pannekoek H, Horrevoets AJG, Comparative proteomics of human endothelial cell caveolae and rafts using two-dimensional gel electrophoresis and mass spectrometry. ELECTROPHORESIS 2004;25 (1):156-172 [PubMed]
Blom D, Speijer D, Linthorst GE, Donker-Koopman WG, Strijland A, Aerts JMFG, Recombinant enzyme therapy for Fabry disease: Absence of editing of human alpha-galactosidase A mRNA. AM J HUM GENET 2003;72 (1):23-31 [PubMed]
Meek B, Diepersloot RJ, van Gool T, Speijer D, Peek R, Igm recognition of recombinant Toxoplasma gondii antigens by sera of acutely or latently infected humans. DIAGN MICR INFEC DIS 2003;45 (1):45-52 [PubMed]
Meek B, Speijer D, de Jong PTVM, de Smet MD, Peek R, The ocular humoral immune response in health and disease. PROG RETIN EYE RES 2003;22 (3):391-415 [PubMed]
Meek B, Back JW, Klaren VNA, Speijer D, Peek R, Conserved regions of protein disulfide isomerase are targeted by natural IgA antibodies in humans. INT IMMUNOL 2002;14 (11):1291-1301 [PubMed]
Meek B, Back JW, Klaren VNA, Speijer D, Peek R, Protein disulfide isomerase of Toxoplasma gondii is targeted by mucosal IgA antibodies in humans. FEBS LETT 2002;522 (1-3):104-108 [PubMed]
Rep M, Dekker HL, Vossen JH, de Boer AD, Houterman PM, Speijer D, Back JW, de Koster CG, Cornelissen BJC, Mass spectrometric identification of isoforms of PR proteins in xylem sap of fungus-infected tomato. PLANT PHYSIOL 2002;130 (2):904-917 [PubMed]
Blom D, van den Burg J, Breek CK, Speijer D, Muijsers AO, Benne R, Cloning and characterization of two guide RNA-binding proteins from mitochondria of Crithidia fasciculata: gBP27, a novel protein, and gBP29, the orthologue of Trypanosoma brucei gBP21. NUCLEIC ACIDS RES 2001;29 (14):2950-2962 [PubMed]
Spelbrink JN, Toivonen JM, Hakkaart GA, Kurkela JM, Cooper HM, Lehtinen SK, Lecrenier N, Back JW, Speijer D, Foury F, Jacobs HT, In vivo functional analysis of the human mitochondrial DNA polymerase POLG expressed in cultured human cells. J BIOL CHEM 2000;275 (32):24818-24828 [PubMed]
Nabholz CE, Speijer D, Schneider A, Chloramphenicol-sensitive mitochondrial translation in Trypanosoma brucei. PARASITOL RES 1999;85 (8-9):779-782 [PubMed]
Nijtmans LG, Taanman JW, Muijsers AO, Speijer D, van den Bogert C, Assembly of cytochrome-c oxidase in cultured human cells. EUR J BIOCHEM 1998;254 (2):389-394 [PubMed]
Vanhamme L, Perez-Morga D, Marchal C, Speijer D, Lambert L, Geuskens M, Alexandre S, Ismaïli N, Göringer U, Benne R, Pays E, Trypanosoma brucei TBRGG1, a mitochondrial oligo(U)-binding protein that co-localizes with an in vitro RNA editing activity. J BIOL CHEM 1998;273 (34):21825-21833 [PubMed]
Breek CK, Speijer D, Dekker H, Muijsers AO, Benne R, Further evidence for the presence of mitochondrially encoded subunits in cytochrome c oxidase of the trypanosomatid Crithidia fasciculata. BIOL CHEM 1997;378 (8):837-841 [PubMed]
Speijer D, Breek CK, Muijsers AO, Hartog AF, Berden JA, Albracht SP, Samyn B, van Beeumen J, Benne R, Characterization of the respiratory chain from cultured Crithidia fasciculata. MOL BIOCHEM PARASIT 1997;85 (2):171-186 [PubMed]
Speijer D, Breek CK, Muijsers AO, Groenevelt PX, Dekker H, de Haan A, Benne R, The sequence of a small subunit of cytochrome c oxidase from Crithidia fasciculata which is homologous to mammalian subunit IV. FEBS LETT 1996;381 (1-2):123-126 [PubMed]
Speijer D, Muijsers AO, Dekker H, de Haan A, Breek CK, Albracht SP, Benne R, Purification and characterization of cytochrome c oxidase from the insect trypanosomatid Crithidia fasciculata. MOL BIOCHEM PARASIT 1996;79 (1):47-59 [PubMed]
Leegwater P, Speijer D, Benne R, Identification by UV cross-linking of oligo(U)-binding proteins in mitochondria of the insect trypanosomatid Crithidia fasciculata. EUR J BIOCHEM 1995;227 (3):780-786 [PubMed]
Arts GJ, van der Spek H, Speijer D, van den Burg J, van Steeg H, Sloof P, Benne R, Implications of novel guide RNA features for the mechanism of RNA editing in Crithidia fasciculata. EMBO J 1993;12 (4):1523-1532 [PubMed]
van der Spek H, Speijer D, Arts GJ, van den Burg J, van Steeg H, Sloof P, Benne R, RNA editing in transcripts of the mitochondrial genes of the insect trypanosome Crithidia fasciculata. EMBO J 1990;9 (1):257-262 [PubMed]
show allhide all
Key publications

Speijer D, Oxygen radicals shaping evolution: Why fatty acid catabolism leads to peroxisomes while neurons do without it: FADH2/NADH flux ratios determining mitochondrial radical formation were crucial for the eukaryotic invention of peroxisomes and catabolic tissue differentiation. BIOESSAYS 2011;33 (2):88-94 [PubMed]
Speijer D, Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity. BIOESSAYS 2011;33 (5):344-349 [PubMed]
Ringrose JH, Jeeninga RE, Berkhout B, Speijer D, Proteomic studies reveal coordinated changes in T-cell expression patterns upon infection with human immunodeficiency virus type 1. J VIROL 2008;82 (9):4320-4330 [PubMed]
Speijer D, How the mitochondrion was shaped by radical differences in substrates: what carnitine shuttles and uncoupling tell us about mitochondrial evolution in response to ROS. BIOESSAYS 2014;36 (7):634-643 [PubMed]
Speijer D, Making sense of scrambled genomes. SCIENCE 2008;319 (5865):901-2; author reply 901-2 [PubMed]


All Publications

Curriculum Vitae

Up till PhD:

Secondary School:

Atheneum: Spinozalyceum, Amsterdam

1968-1974

University Education:


University: University of Amsterdam, Philosophy


Bachelors degree: 1976
Master degree: 1985

 

University: University of Amsterdam, Psychology


First year exam ('propedeuse'): 1976

 

University: University of Amsterdam, Biology


First year exam ('propedeuse'): 1986 (judicium: cum laude)
Master degree: 1989 (judicium: cum laude)


Molecular Biology / Biochemistry
Research project: 'RNA editing in Trypanosomes' Academic Medical Center (Rob Benne), Amsterdam
Extra Research project: 'HLA Genelocus products' NKI (Dutch Cancer Institute; Hidde Ploegh), Amsterdam

PhD: University of Amsterdam, Academic Medical Center, 1997
Thesis Subject: RNA editing in mitochondria of Trypanosomes. Studies on 'edited' and editing proteins

Research programmes

Prof. dr. J.M.F.G. Aerts PhD (Glycosphingolipids in health and disease)

Other research related activities
  • None reported
Current research funding
  • None reported
back to whoiswho