828 research outputs found
Bioavailability of hop-derived bitter acids : key factors for the health-beneficial properties of beer
No full textFrom dysregulated protein expression to histone clipping: the virtue of mass spectrometry: a proteomics tale of serendipity
No full textThroughout the course of this dissertation, the research focus has greatly shifted. The initial objective was reached when the discovered aberrant protein expression patterns in HLAB27 transgenic rat dendritic cells were confirmed with both videomicroscopy and flow cytometry: the dendritic cells from this animal model for Spondyloarthritis exert an endoplasmic reticulum stress due to HLAB27 misfolding, resulting in downregulated cytoskeletal dynamics. This latter deficiency results in lower motility and changed morphology, as well as a less efficient immunological synapse formation with T-cells. The overall downregulation of surface MHCII expression and increased apoptotic sensitivity of the tolerigenic CD4- dendritic cells are most probably also entwined with the deficient cytoskeleton.
An iTRAQ analysis on Chronic Lymphocytic Leukemia B-cells, which was initially set up to optimize the protocol of this new proteomics approach, led to the rediscovery of a histone clipping event that was first described over 35 years ago. In the light of current knowledge, this old proteolytical event could have far-reaching effects on hematopoiesis, through its interaction with the Polycomb Group of epigenetic modifiers. We have now unmasked this so-called “H2A-specific protease” and show that this enzyme actually is Neutrophil Elastase. The obvious parallel between H2A clipping and the recently described histone H3 clipping in embryonic stem cells has inspired us to summarize all previous reports in a review.
More recently, we have set out to validate a new iTRAQ-based approach to identify and quantify phosphorylation events. This MS-based “PiTRAQ”-approach actually focuses on the unphosphotylated counterpart of a peptide after in vitro dephosphorylation to circumvent most MS-related hurdles in phosphoproteomics.
Finally, the LabFBT proteomics platform has been used in collaboration with several different labs to tackle diverse biological and technical challenges
Break it to make it : from fragmented information to computational coherency in mass spectrometry based proteomics
No full textThe wonderful world of histones and stem cells : a fairy tale written by mass spectrometry
No full textMolecular-biological investigation of the anti-inflammatoryproperties of hop (Humulus Lupulus L.)-derived bitteracids.
No full textThe quest for true post-translational protein modifications through label-based quantitative mass spectrometry
No full textMethods matter : towards the implementation of label-free MS in the context of hESC histone epigenetics
No full textTracking changes in the histone modification pattern by untargeted mass spectrometry : how naïve are human embryonic stem cells and data-dependent acquisition?
No full textIn this dissertation, we profile the histone epigenome of hESCs during conversion from the primed to the naive state using an untargeted mass spectrometry (MS)-based approach. In total, 23 histone post-translational modifications (hPTMs) changed significantly over time. H3K27me3 was the most prominently increasing marker hPTM in naive hESCs. This is in line with what was recently described in mouse, prompting us to compare all the shared hPTM fold changes between mouse and human, revealing a set of conserved hPTM markers for the naive state. Principally, we present the first roadmap of the changing human histone epigenome during the conversion of hESCs from the primed to the naive state. This further revealed similarities with mouse, which hint at a conserved mammalian epigenetic signature of the ground state of pluripotency.
Sequential window acquisition of all theoretical fragment ion spectra (SWATH)-MS has great potential for large-scale analysis of hPTMs and their combinatorial patterns, as it allows for untargeted accurate identification and quantification of hPTMs. In this dissertation, we present a complete SWATH workflow specifically adapted for the untargeted study of histones (hSWATH). More specifically, the workflow was optimized to ensure a maximal coverage of the histone code and a high specificity for isobaric and co-eluting peptides. We assessed the validity of the workflow on a technical dataset of a time-lapse deacetylation of a commercial histone extract using HDAC1, which contains a ground truth, i.e. acetylated substrate peptides reduce in intensity. Finally, xe successfully apply this workflow in a biological setting and subsequently investigate the differential response to HDAC inhibition in different breast cancer cell lines
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