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Variability in Mass Spectrometry-based Quantification of Clinically Relevant Drug Transporters and Drug Metabolizing Enzymes

Wegler, C. (author), Gaugaz, F.Z. (author), Andersson, T.B. (author), Wiśniewski, J.R. (author), Busch, D. (author), Gröer, C. (author), Oswald, S. (author), Norén, A. (author), Weiss, F. (author), Hammer, H.S. (author), Joos, T.O. (author), Poetz, O. (author), Achour, B. (author), Rostami-Hodjegan, A. (author), van de Steeg, E. (author), Wortelboer, H.M. (author), Artursson, P. (author)

Many different methods are used for mass-spectrometry-based protein quantification in pharmacokinetics and systems pharmacology. It has not been established to what extent the results from these various methods are comparable. Here, we compared six different mass spectrometry-based proteomics methods by measuring the expression of clinically...

article 2017

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Recovery of protein from green leaves: verview of crucial steps for utilisation

Tamayo Tenorio, A. (author), Gieteling, J. (author), de Jong, G.A.H. (author), Boom, R.M. (author), van der Goot, A.J. (author)

Plant leaves are a major potential source of novel food proteins. Till now, leaf protein extraction methods mainly focus on the extraction of soluble proteins, like rubisco protein, leaving more than half of all protein unextracted. Here, we report on the total protein extraction from sugar beet leaves (Beta vulgaris L.) by a traditional thermal...

article 2016

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Differential modulation by Akkermansia muciniphila and faecalibacterium prausnitzii of host peripheral lipid metabolism and histone acetylation in mouse gut organoids

Lukovac, S. (author), Belzer, C. (author), Pellis, L. (author), Keijser, B.J. (author), de Vos, W.M. (author), Montijn, R.C. (author), Roeselers, G. (author)

The gut microbiota is essential for numerous aspects of human health. However, the underlying mechanisms of many host-microbiota interactions remain unclear. The aim of this study was to characterize effects of the microbiota on host epithelium using a novel ex vivo model based on mouse ileal organoids. We have explored the transcriptional...

article 2014

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Probing the proteome response to toluene exposure in the solvent tolerant pseudomonas putida S12

Wijte, D. (author), van Baar, B.L.M. (author), Heck, A.J.R. (author), Altelaar, A.F.M. (author)

To enhance target production from biocatalysts, it is necessary to thoroughly understand the molecular mechanisms involved in production, degradation, and, importantly, adaptation to the required environment. One such bacterium with high potential for biocatalysis is the solvent-tolerant bacteria Pseudomonas putida S12, which, among others, is...

article 2011

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Quantitative iTRAQ secretome analysis of aspergillus niger reveals novel hydrolytic enzymes

Adav, S.S. (author), Li, A.A. (author), Manavalan, A. (author), Punt, P. (author), Sze, S.K. (author), TNO Kwaliteit van Leven (author)

The natural lifestyle of Aspergillus niger made them more effective secretors of hydrolytic proteins and becomes critical when this species were exploited as hosts for the commercial secretion of heterologous proteins. The protein secretion profile of A. niger and its mutant at different pH was explored using iTRAQ-based quantitative proteomics...

article 2010

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Identification of resistance and virulence factors in an epidemic Enterobacter hormaechei outbreak strain

Paauw, A. (author), Caspers, M.P.M. (author), Leverstein-van Hall, M.A. (author), Schuren, F.H.J. (author), Montijn, R.C. (author), Verhoef, J. (author), Fluit, A.C. (author), TNO Kwaliteit van Leven (author)

Bacterial strains differ in their ability to cause hospital outbreaks. Using comparative genomic hybridization, Enterobacter cloacae complex isolates were studied to identify genetic markers specific for Enterobacter cloacae complex outbreak strains. No outbreak-specific genes were found that were common in all investigated outbreak strains....

article 2009

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Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles

Yuan, X.-L. (author), van der Kaaij, R.M. (author), van den Hondel, C.A.M.J.J. (author), Punt, P.J. (author), van der Maarel, M.J.E.C. (author), Dijkhuizen, L. (author), Ram, A.F.J. (author), TNO Kwaliteit van Leven (author)

The filamentous ascomycete Aspergillus niger is well known for its ability to produce a large variety of enzymes for the degradation of plant polysaccharide material. A major carbon and energy source for this soil fungus is starch, which can be degraded by the concerted action of α-amylase, glucoamylase and α-glucosidase enzymes, members of the...

article 2008

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Increased infiltration of Chlamydophila pneumoniae in the vessel wall of human veins after perfusion

Kupreishvili, K. (author), ter Weeme, M. (author), Morré, S.A. (author), van den Brule, A.J.C. (author), Huybregts, M.A.J.M. (author), Quax, P.H.A. (author), ten Velden, J. (author), van Hinsbergh, V.W.M. (author), Stooker, W. (author), Eijsman, L. (author), Niessen, H.W.M. (author), TNO Kwaliteit van Leven (author)

Background: Several studies have suggested an association between Chlamydophila pneumoniae (Cp) infection and atherosclerosis. A recent study detected Cp DNA in the saphenous vein of 12% of all patients before bypass grafting and in 38% of failed grafts. We used a system in which human veins were perfused with autologous blood under arterial...

article 2008

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Glycolipid-dependent sorting of melanosomal from lysosomal membrane proteins by lumenal determinants

Groux-Degroote, S. (author), van Dijk, S.M. (author), Wolthoorn, J. (author), Neumann, S. (author), Theos, A.C. (author), de Mazière, A.M. (author), Klumperman, J. (author), van Meer, G. (author), Sprong, H. (author), TNO Kwaliteit van Leven (author)

Melanosomes are lysosome-related organelles that coexist with lysosomes in mammalian pigment cells. Melanosomal and lysosomal membrane proteins share similar sorting signals in their cytoplasmic tail, raising the question how they are segregated. We show that in control melanocytes, the melanosomal enzymes tyrosinase-related protein 1 (Tyrp1)...

article 2008

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Dynamics in prophage content of invasive and noninvasive M1 and M28 Streptococcus pyogenes isolates in the Netherlands from 1959 to 1996

Vlaminckx, B.J.M. (author), Schuren, F.H.J. (author), Montijn, R.C. (author), Caspers, M.P.M. (author), Beitsma, M.M. (author), Wannet, W.J.B. (author), Schouls, L.M. (author), Verhoef, J. (author), Jansen, W.T.M. (author), TNO Kwaliteit van Leven (author)

Invasive group A streptococcal (GAS) disease reemerged in The Netherlands in the late 1980s. To seek an explanation for this resurgence, the genetic compositions of 22 M1 and 19 M28 GAS strains isolated in The Netherlands between 1960s and the mid-1990s were analyzed by using a mixed-genome DNA microarray. During this four-decade period, M1 and...

article 2007

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Identification of outer membrane proteins of Yersinia pestis through biotinylation

Smither, S.J. (author), Hill, J. (author), van Baar, B.L.M. (author), Hulst, A.G. (author), de Jong, A.L. (author), Titball, R.W. (author), TNO Defensie en Veiligheid (author)

The outer membrane of Gram-negative bacteria contains proteins that might be good targets for vaccines, antimicrobials or detection systems. The identification of surface located proteins using traditional methods is often difficult. Yersinia pestis, the causative agent of plague, was labelled with biotin. Tagged proteins were visualised through...

article 2007

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Determination of the relationship between group A streptococcal genome content, M type, and toxic shock syndrome by a mixed genome microarray

Vlaminckx, B.J.M. (author), Schuren, F.H.J. (author), Montijn, R.C. (author), Caspers, M.P.M. (author), Fluit, A.C. (author), Wannet, W.J.B. (author), Schouls, L.M. (author), Verhoef, J. (author), Jansen, W.T.M. (author), TNO Kwaliteit van Leven (author)

Group A streptococci (GAS), or Streptococcus pyogenes, are associated with a remarkable variety of diseases, ranging from superficial infections to life-threatening diseases such as toxic-shock-like syndrome (TSS). GAS strains belonging to M types M1 and M3 are associated with TSS. This study aims to obtain insight into the gene profiles...

article 2007

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Insertion sequence-driven diversification creates a globally dispersed emerging multiresistant subspecies of E. faecium

TNO Kwaliteit van Leven TNO Voeding (author), Leavis, H.L. (author), Willems, R.J.L. (author), van Wamel, W.J.B. (author), Schuren, F.H. (author), Caspers, M.P.M. (author), Bonten, M.J.M. (author)

Enterococcus faecium, an ubiquous colonizer of humans and animals, has evolved in the last 15 years from an avirulent commensal to the third most frequently isolated nosocomial pathogen among intensive care unit patients in the United States. E. faecium combines multidrug resistance with the potential of horizontal resistance gene transfer to...

article 2007

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Response of apolipoprotein E*3-Leiden transgenic mice to dietary fatty acids: Combining liver proteomics with physiological data

de Roos, B. (author), Duivenvoorden, I. (author), Rucklidge, G. (author), Reid, M. (author), Ross, K. (author), Lamers, R.J.A.N. (author), Voshol, P.J. (author), Havekes, L.M. (author), Teusink, B. (author), TNO Kwaliteit van Leven (author)

article 2005

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Advanced glycation end product ligands for the receptor for advanced glycation end products: Biochemical characterization and formation kinetics

Valencia, J.V. (author), Weldon, S.C. (author), Quinn, D. (author), Kiers, G.H. (author), de Groot, J. (author), TeKoppele, J.M. (author), Hughes, T.E. (author), Gaubius instituut TNO (author)

Advanced glycation end products (AGEs) accumulate with age and at an accelerated rate in diabetes. AGEs bind cell-surface receptors including the receptor for advanced glycation end products (RAGE). The dependence of RAGE binding on specific biochemical characteristics of AGEs is currently unknown. Using standardized procedures and a variety of...

article 2004

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Increased fecal bile acid excretion in transgenic mice with elevated expression of human phospholipid transfer protein

Post, S.M. (author), de Crom, R. (author), van Haperen, R. (author), van Tol, A. (author), Princen, H.M.G. (author), Gaubius Instituut TNO (author)

Objective - HDL plays a key role in protection against development of atherosclerosis by promoting reverse cholesterol transport from peripheral tissues to the liver for secretion into bile. Phospholipid transfer protein (PLTP) promotes the transfer of phospholipids between lipoproteins and modulates HDL size and composition, thereby having a...

article 2003

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Structural and functional analysis of the S-layer protein crystallisation domain of Lactobacillus acidophilus ATCC 4356 : evidence for protein : protein interaction of two subdomains

Smit, E. (author), Jager, D. (author), Martinez, B. (author), Tielen, F.J. (author), Pouwels, P.H. (author), Centraal Instituut voor Voedingsonderzoek TNO (author)

The structure of the crystallisation domain, SAN, of the S A-protein of Lactobacillus acidophilus ATCC 4356 was analysed by insertion and deletion mutagenesis, and by proteolytic treatment. Mutant S A-protein synthesised in Escherichia coli with 7-13 amino acid insertions near the N terminus or within regions of sequence variation in SAN (amino...

article 2002

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Stimulation of lipogenesis by pharmacological activation of the liver X receptor leads to production of large, triglyceride-rich very low density lipoprotein particles

Gaubius Instituut TNO (author), Grefhorst, A. (author), Elzinga, B.M. (author), Voshol, P.J. (author), Plösch, T. (author), Kok, T. (author), Bloks, V.W. (author), van der Sluijs, F.H. (author), Havekes, L.M. (author), Romijn, J.A. (author), Verkade, H.J. (author), Kuipers, F. (author)

The oxysterol-activated liver X receptor (LXR) provides a link between sterol and fatty acid metabolism; activation of LXR induces transcription of lipogenic genes. This study shows that induction of the lipogenic genes Srebp-1c, Fas, and Acc1 upon administration of the synthetic LXR agonist T0901317 to C57BL/6J mice (10 mg/kg/day, 4 days) is...

article 2002

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One repeat of the cell wall binding domain is sufficient for anchoring the Lactobacillus acidophilus surface layer protein

Smit, E. (author), Pouwels, P.H. (author)

The N-terminal repeat (SAC1) of the S-protein of Lactobacillus acidophilus bound efficiently and specifically to cell wall fragments (CWFs) when fused to green fluorescent protein, whereas the C-terminal repeat (SAC2) did not. Treatment of CWFs with hydrofluoric acid, but not phenol, prevented binding. Apparently, SAC1 is necessary and...

article 2002

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The S-layer protein of Lactobacillus acidophilus ATCC 4356: Identification and characterisation of domains responsible for S-protein assembly and cell wall binding

Smit, E. (author), Oling, F. (author), Demel, R. (author), Martinez, B. (author), Pouwels, P.H. (author), Centraal Instituut voor Voedingsonderzoek TNO (author)

Lactobacillus acidophilus, like many other bacteria, harbors a surface layer consisting of a protein (SA-protein) of 43 kDa. SA-protein could be readily extracted and crystallized in vitro into large crystalline patches on lipid monolayers with a net negative charge but not on lipids with a net neutral charge. Reconstruction of the S-layer from...

article 2001