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1.
Vanessa Gonzalez‐Covarrubias Marian Beekman Hae‐Won Uh Adrie Dane Jorne Troost Iryna Paliukhovich Frans M. van der Kloet Jeanine Houwing‐Duistermaat Rob J. Vreeken Thomas Hankemeier Eline P. Slagboom 《Aging cell》2013,12(3):426-434
Middle‐aged offspring of nonagenarians, as compared to their spouses (controls), show a favorable lipid metabolism marked by larger LDL particle size in men and lower total triglyceride levels in women. To investigate which specific lipids associate with familial longevity, we explore the plasma lipidome by measuring 128 lipid species using liquid chromatography coupled to mass spectrometry in 1526 offspring of nonagenarians (59 years ± 6.6) and 675 (59 years ± 7.4) controls from the Leiden Longevity Study. In men, no significant differences were observed between offspring and controls. In women, however, 19 lipid species associated with familial longevity. Female offspring showed higher levels of ether phosphocholine (PC) and sphingomyelin (SM) species (3.5–8.7%) and lower levels of phosphoethanolamine PE (38:6) and long‐chain triglycerides (TG) (9.4–12.4%). The association with familial longevity of two ether PC and four SM species was independent of total triglyceride levels. In addition, the longevity‐associated lipid profile was characterized by a higher ratio of monounsaturated (MUFA) over polyunsaturated (PUFA) lipid species, suggesting that female offspring have a plasma lipidome less prone to oxidative stress. Ether PC and SM species were identified as novel longevity markers in females, independent of total triglycerides levels. Several longevity‐associated lipids correlated with a lower risk of hypertension and diabetes in the Leiden Longevity Study cohort. This sex‐specific lipid signature marks familial longevity and may suggest a plasma lipidome with a better antioxidant capacity, lower lipid peroxidation and inflammatory precursors, and an efficient beta‐oxidation function. 相似文献
2.
Marco I. Ries Hazrat Ali Peter P. Lankhorst Thomas Hankemeier Roel A. L. Bovenberg Arnold J. M. Driessen Rob J. Vreeken 《The Journal of biological chemistry》2013,288(52):37289-37295
Metabolic profiling and structural elucidation of novel secondary metabolites obtained from derived deletion strains of the filamentous fungus Penicillium chrysogenum were used to reassign various previously ascribed synthetase genes of the roquefortine/meleagrin pathway to their corresponding products. Next to the structural characterization of roquefortine F and neoxaline, which are for the first time reported for P. chrysogenum, we identified the novel metabolite roquefortine L, including its degradation products, harboring remarkable chemical structures. Their biosynthesis is discussed, questioning the exclusive role of glandicoline A as key intermediate in the pathway. The results reveal that further enzymes of this pathway are rather unspecific and catalyze more than one reaction, leading to excessive branching in the pathway with meleagrin and neoxaline as end products of two branches. 相似文献
3.
Hazrat Ali Marco I. Ries Jeroen G. Nijland Peter P. Lankhorst Thomas Hankemeier Roel A. L. Bovenberg Rob J. Vreeken Arnold J. M. Driessen 《PloS one》2013,8(6)
Profiling and structural elucidation of secondary metabolites produced by the filamentous fungus Penicillium chrysogenum and derived deletion strains were used to identify the various metabolites and enzymatic steps belonging to the roquefortine/meleagrin pathway. Major abundant metabolites of this pathway were identified as histidyltryptophanyldiketopiperazine (HTD), dehydrohistidyltryptophanyldi-ketopiperazine (DHTD), roquefortine D, roquefortine C, glandicoline A, glandicoline B and meleagrin. Specific genes could be assigned to each enzymatic reaction step. The nonribosomal peptide synthetase RoqA accepts L-histidine and L-tryptophan as substrates leading to the production of the diketopiperazine HTD. DHTD, previously suggested to be a degradation product of roquefortine C, was found to be derived from HTD involving the cytochrome P450 oxidoreductase RoqR. The dimethylallyltryptophan synthetase RoqD prenylates both HTD and DHTD yielding directly the products roquefortine D and roquefortine C without the synthesis of a previously suggested intermediate and the involvement of RoqM. This leads to a branch in the otherwise linear pathway. Roquefortine C is subsequently converted into glandicoline B with glandicoline A as intermediates, involving two monooxygenases (RoqM and RoqO) which were mixed up in an earlier attempt to elucidate the biosynthetic pathway. Eventually, meleagrin is produced from glandicoline B involving a methyltransferase (RoqN). It is concluded that roquefortine C and meleagrin are derived from a branched biosynthetic pathway. 相似文献
4.
Proposed minimum reporting standards for chemical analysis 总被引:4,自引:0,他引:4
Lloyd W. Sumner Alexander Amberg Dave Barrett Michael H. Beale Richard Beger Clare A. Daykin Teresa W.-M. Fan Oliver Fiehn Royston Goodacre Julian L. Griffin Thomas Hankemeier Nigel Hardy James Harnly Richard Higashi Joachim Kopka Andrew N. Lane John C. Lindon Philip Marriott Andrew W. Nicholls Michael D. Reily John J. Thaden Mark R. Viant 《Metabolomics : Official journal of the Metabolomic Society》2007,3(3):211-221
There is a general consensus that supports the need for standardized reporting of metadata or information describing large-scale
metabolomics and other functional genomics data sets. Reporting of standard metadata provides a biological and empirical context
for the data, facilitates experimental replication, and enables the re-interrogation and comparison of data by others. Accordingly,
the Metabolomics Standards Initiative is building a general consensus concerning the minimum reporting standards for metabolomics
experiments of which the Chemical Analysis Working Group (CAWG) is a member of this community effort. This article proposes
the minimum reporting standards related to the chemical analysis aspects of metabolomics experiments including: sample preparation,
experimental analysis, quality control, metabolite identification, and data pre-processing. These minimum standards currently
focus mostly upon mass spectrometry and nuclear magnetic resonance spectroscopy due to the popularity of these techniques
in metabolomics. However, additional input concerning other techniques is welcomed and can be provided via the CAWG on-line
discussion forum at or . Further, community input related to this document can also be provided via this electronic forum.
The contents of this paper do not necessarily reflect any position of the Government or the opinion of the Food and Drug Administration
Sponsor: Metabolomics Society http://www.metabolomicssociety.org/
Reference: http://msi-workgroups.sourceforge.net/bio-metadata/reporting/pbc/
http://msi-workgroups.sourceforge.net/chemical-analysis/
Version: Revision: 5.1
Date: 09 January, 2007 相似文献
5.
van der Werf MJ Overkamp KM Muilwijk B Coulier L Hankemeier T 《Analytical biochemistry》2007,370(1):17-25
Achieving metabolome data with satisfactory coverage is a formidable challenge in metabolomics because metabolites are a chemically highly diverse group of compounds. Here we present a strategy for the development of an advanced analytical platform that allows the comprehensive analysis of microbial metabolomes. Our approach started with in silico metabolome information from three microorganisms-Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae-and resulted in a list of 905 different metabolites. Subsequently, these metabolites were classified based on their physicochemical properties, followed by the development of complementary gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry methods, each of which analyzes different metabolite classes. This metabolomics platform, consisting of six different analytical methods, was applied for the analysis of the metabolites for which commercial standards could be purchased (399 compounds). Of these 399 metabolites, 380 could be analyzed with the platform. To demonstrate the potential of this metabolomics platform, we report on its application to the analysis of the metabolome composition of mid-logarithmic E. coli cells grown on a mineral salts medium using glucose as the carbon source. Of the 431 peaks detected, 235 (=176 unique metabolites) could be identified. These include 61 metabolites that were not previously identified or annotated in existing E. coli databases. 相似文献
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7.
Michelle Janssens Jeroen van Smeden Gert S. Gooris Wim Bras Guiseppe Portale Peter J. Caspers Rob J. Vreeken Thomas Hankemeier Sanja Kezic Ron Wolterbeek Adriana P. Lavrijsen Joke A. Bouwstra 《Journal of lipid research》2012,53(12):2755-2766
A hallmark of atopic eczema (AE) is skin barrier dysfunction. Lipids in the stratum corneum (SC), primarily ceramides, fatty acids, and cholesterol, are crucial for the barrier function, but their role in relation to AE is indistinct. Filaggrin is an epithelial barrier protein with a central role in the pathogenesis of AE. Nevertheless, the precise causes of AE-associated barrier dysfunction are largely unknown. In this study, a comprehensive analysis of ceramide composition and lipid organization in nonlesional SC of AE patients and control subjects was performed by means of mass spectrometry, infrared spectroscopy, and X-ray diffraction. In addition, the skin barrier and clinical state of the disease were examined. The level of ceramides with an extreme short chain length is drastically increased in SC of AE patients, which leads to an aberrant lipid organization and a decreased skin barrier function. Changes in SC lipid properties correlate with disease severity but are independent of filaggrin mutations. We demonstrate for the first time that changes in ceramide chain length and lipid organization are directly correlated with the skin barrier defects in nonlesional skin of AE patients. We envisage that these insights will provide a new therapeutic entry in therapy and prevention of AE. 相似文献
8.
van der Kloet FM Tempels FW Ismail N van der Heijden R Kasper PT Rojas-Cherto M van Doorn R Spijksma G Koek M van der Greef J Mäkinen VP Forsblom C Holthöfer H Groop PH Reijmers TH Hankemeier T 《Metabolomics : Official journal of the Metabolomic Society》2012,8(1):109-119
Diabetic kidney disease (DKD) is a devastating complication that affects an estimated third of patients with type 1 diabetes mellitus (DM). There is no cure once the disease is diagnosed, but early treatment at a sub-clinical stage can prevent or at least halt the progression. DKD is clinically diagnosed as abnormally high urinary albumin excretion rate (AER). We hypothesize that subtle changes in the urine metabolome precede the clinically significant rise in AER. To test this, 52 type 1 diabetic patients were recruited by the FinnDiane study that had normal AER (normoalbuminuric). After an average of 5.5?years of follow-up half of the subjects (26) progressed from normal AER to microalbuminuria or DKD (macroalbuminuria), the other half remained normoalbuminuric. The objective of this study is to discover urinary biomarkers that differentiate the progressive form of albuminuria from non-progressive form of albuminuria in humans. Metabolite profiles of baseline 24?h urine samples were obtained by gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) to detect potential early indicators of pathological changes. Multivariate logistic regression modeling of the metabolomics data resulted in a profile of metabolites that separated those patients that progressed from normoalbuminuric AER to microalbuminuric AER from those patients that maintained normoalbuminuric AER with an accuracy of 75% and a precision of 73%. As this data and samples are from an actual patient population and as such, gathered within a less controlled environment it is striking to see that within this profile a number of metabolites (identified as early indicators) have been associated with DKD already in literature, but also that new candidate biomarkers were found. The discriminating metabolites included acyl-carnitines, acyl-glycines and metabolites related to tryptophan metabolism. We found candidate biomarkers that were univariately significant different. This study demonstrates the potential of multivariate data analysis and metabolomics in the field of diabetic complications, and suggests several metabolic pathways relevant for further biological studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-011-0291-6) contains supplementary material, which is available to authorized users. 相似文献
9.
Jagodzinski M Breitbart A Wehmeier M Hesse E Haasper C Krettek C Zeichen J Hankemeier S 《Journal of biomechanics》2008,41(9):1885-1891
Until now, there has been no in vitro model that duplicates the environment of bone marrow. The purpose of this study was to analyze proliferation and differentiation of human bone marrow stromal cells (hBMSC) under the influence of continuous perfusion and cyclic mechanical loading. hBMSC of seven individuals were harvested, grown in vitro, and combined. 10(6) hBMSC were seeded on a bovine spongiosa disc and incubated in a bioreactor system. Cell culture was continued using three different conditions: Continuous perfusion (group A), 10% cyclic compression at 0.5Hz (group B) and static controls (group C). After 24h, 1, 2, and 3 weeks, we determined cell proliferation (MTS-assay) and osteogenic differentiation (osteocalcin ELISA, Runx2 mRNA). Tenascin-C mRNA was quantified to exclude fibroblastic differentiation. In groups A and B, proliferation was enhanced after 2 weeks (48.6+/-19.6x10(3) (A) and 44.6+/-14.3 x 10(3) cells (B)) and after 3 weeks (46.6+/-15.1 x 10(3) (A) and 44.8+/-10.2 x 10(3) cells (B)) compared with controls (26.3+/-10.8 x 10(3) (2 weeks) and 17.1+/-6.5 x 10(3) cells (3 weeks), p<0.03). Runx2 mRNA was upregulated in both stimulated groups after 1, 2, and 3 weeks compared to control (group A, 1 week: 5.2+/-0.7-fold; p<0.01, 2 weeks: 4.4+/-1.9-fold; p<0.01, 3 weeks: 3.8+/-1.7-fold; p=0.013; group B, 1 week: 3.6+/-1.1-fold, p<0.01, 2 weeks: 4.2+/-2.2-fold, p<0.01; 3 weeks: 5.3+/-2.7-fold, p<0.01). hBMSC stimulated by cyclic compression expressed the highest amount of osteocalcin at all time points (1 week: 294.5+/-88.4 mg/g protein, 2 weeks: 294.4+/-73.3mg/g protein, 3 weeks: 293.1+/-83.6 mg/g protein, p0.03). The main stimulus for cell proliferation in a 3-dimensional culture of hBMSC is continuous perfusion whereas mechanical stimulation fosters osteogenic commitment of hBMSC. This study thereby contributes to the understanding of physical stimuli that influence hBMSC in a 3-dimensional cell culture system. 相似文献
10.
Strategies to assess and optimize stability of endogenous amines during cerebrospinal fluid sampling
Marek J. Noga Ronald Zielman Robin M. van Dongen Sabine Bos Amy Harms Gisela M. Terwindt Arn M. J. M. van den Maagdenberg Thomas Hankemeier Michel D. Ferrari 《Metabolomics : Official journal of the Metabolomic Society》2018,14(4):44