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Publications - Stress and Develop Biology

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Strehmel, C.; Zhang, Z.; Strehmel, N.; Lensen, M. Cell phenotypic changes of mouse connective tissue fibroblasts (L-929) to poly(ethylene glycol)-based gels Biomaterials Sci 1, 850–859, (2013) DOI: 10.1039/C3BM60055F

Cellular responses to various gels fabricated by photoinitiated crosslinking using acrylated linear and multi-arm poly(ethylene glycol) (PEG)-based and poly(propylene glycol)-b-poly(ethylene glycol) precursors were investigated. While no protein adsorption and cell adhesion were observed on the hydrophilic PEG-based gels, protein adsorption and cell adhesion did occur on the more hydrophobic gel generated from the block copolymer precursor. Murine fibroblast viability on the poly(ethylene glycol)-based gels was studied in the course of 72 h and the results indicated no cytotoxicity. In a systematic study, extra- and intracellular metabolites of the murine fibroblasts cultured on these PEG-based gels were examined by GC-MS. Distinct intra- and extracellular changes in primary metabolism, namely amino acid metabolism, glycolysis and fatty acid metabolism, were observed. Cells cultured on the polymeric gels induced more intense intracellular changes in the metabolite profile by means of higher metabolite intensities with time in comparison to cells cultured on the reference substrate (tissue culture polystyrene). In contrast, extracellular changes of metabolite intensities were comparable.

Rasche, F.; Svatoš, A.; Maddula, R. K.; Böttcher, C.; Böcker, S. Computing Fragmentation Trees from Tandem Mass Spectrometry Data Anal Chem 83, 1243-1251, (2011) DOI: 10.1021/ac101825k

The structural elucidation of organic compounds in complex biofluids and tissues remains a significant analytical challenge. For mass spectrometry, the manual interpretation of collision-induced dissociation (CID) mass spectra is cumbersome and requires expert knowledge, as the fragmentation mechanisms of ions formed from small molecules are not completely understood. The automated identification of compounds is generally limited to searching in spectral libraries. Here, we present a method for interpreting the CID spectra of the organic compound’s protonated ions by computing fragmentation trees that establish not only the molecular formula of the compound and all fragment ions but also the dependencies between fragment ions. This is an important step toward the automated identification of unknowns from the CID spectra of compounds that are not in any database.
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