Institut für Chemie und Bioanalytik
Dauerhafte URI für die Sammlung
Listen
Neueste Veröffentlichungen
- PublikationMethod to rapidly identify potential solvent systems for crystallization of cocrystals(American Chemical Society, 2023) Codan, Lorenzo; Daza Olivella, Laura; Sirota, Eric [in: Organic Process Research & Development]01A - Beitrag in wissenschaftlicher Zeitschrift
- PublikationDevelopment and validation of a liquid chromatography-triple quadrupole mass spectrometry method for the determination of isopeptide ε-(γ-glutamyl) lysine in human urine as biomarker for transglutaminase 2 cross-linked proteins(Elsevier, 21.06.2023) Dejager, Lien; Jairaj, Mark; Jones, Kieran; Johnson, Timothy; Dudal, Sherri; Dudal, Yves; Shahgaldian, Patrick; Correro, Rita; Qu, Jun; An, Bo; Lucey, Richard; Szarka, Szabolcs; Wheller, Robert; Pruna, Alina; Kettell, Sarah; Pitt, Andrew; Cutler, Paul [in: Journal of Chromatography A]01A - Beitrag in wissenschaftlicher Zeitschrift
- PublikationDesign of a biocatalytic flow reactor based on hierarchically structured monolithic silica for producing galactooligosaccharides (GOSs)(Schweizerische Chemische Gesellschaft, 2023) Dejoma, Riccardo; Buscemi, Andrea; Cutrona, Emilio; Shahgaldian, Patrick [in: CHIMIA]Climate change mitigation requires the development of greener chemical processes. In this context, biocatalysis is a pivotal key enabling technology. The advantages of biocatalysis include lower energy consumption levels, reduced hazardous waste production and safer processes. The possibility to carry out biocatalytic reactions under flow conditions provides the additional advantage to retain the biocatalyst and to reduce costly downstream processes. Herein, we report a method to produce galactooligosaccharides (GOSs) from a largely available feedstock (i.e. lactose from dairy production) using a flow reactor based on hierarchically structured monolithic silica. This reactor allows for fast and efficient biotransformation reaction in flow conditions.01A - Beitrag in wissenschaftlicher Zeitschrift
- PublikationHLA antibody affinity determination. From HLA‐specific monoclonal antibodies to donor HLA specific antibodies (DSA) in patient serum(Wiley, 16.05.2023) Hug, Melanie N.; Keller, Sabrina; Marty, Talea; Gygax, Daniel; Meinel, Dominik; Spies, Peter; Handschin, Joëlle; Kleiser, Marc; Vazquez, Noemi; Linnik, Janina; Buchli, Rico; Claas, Frans; Heidt, Sebastiaan; Kramer, Cynthia S. M.; Bezstarosti, Suzanne; Lee, Jar‐How; Schaub, Stefan; Hönger, Gideon [in: HLA]Organs transplanted across donor‐specific HLA antibodies (DSA) are associated with a variety of clinical outcomes, including a high risk of acute kidney graft rejection. Unfortunately, the currently available assays to determine DSA characteristics are insufficient to clearly discriminate between potentially harmless and harmful DSA. To further explore the hazard potential of DSA, their concentration and binding strength to their natural target, using soluble HLA, may be informative. There are currently a number of biophysical technologies available that allow the assessment of antibody binding strength. However, these methods require prior knowledge of antibody concentrations. Our objective within this study was to develop a novel approach that combines the determination of DSA‐affinity as well as DSA‐concentration for patient sample evaluation within one assay. We initially tested the reproducibility of previously reported affinities of human HLA‐specific monoclonal antibodies and assessed the technology‐specific precision of the obtained results on multiple platforms, including surface plasmon resonance (SPR), bio‐layer interferometry (BLI), Luminex (single antigen beads; SAB), and flow‐induced dispersion analysis (FIDA). While the first three (solid‐phase) technologies revealed comparable high binding‐strengths, suggesting measurement of avidity, the latter (in‐solution) approach revealed slightly lower binding‐strengths, presumably indicating measurement of affinity. We believe that our newly developed in‐solution FIDA‐assay is particularly suitable to provide useful clinical information by not just measuring DSA‐affinities in patient serum samples but simultaneously delivering a particular DSA‐concentration. Here, we investigated DSA from 20 pre‐transplant patients, all of whom showed negative CDC‐crossmatch results with donor cells and SAB signals ranging between 571 and 14899 mean fluorescence intensity (MFI). DSA‐concentrations were found in the range between 11.2 and 1223 nM (median 81.1 nM), and their measured affinities fall between 0.055 and 24.7 nM (median 5.34 nM; 449‐fold difference). In 13 of 20 sera (65%), DSA accounted for more than 0.1% of total serum antibodies, and 4/20 sera (20%) revealed a proportion of DSA even higher than 1%. To conclude, this study strengthens the presumption that pre‐transplant patient DSA consists of various concentrations and different net affinities. Validation of these results in a larger patient cohort with clinical outcomes will be essential in a further step to assess the clinical relevance of DSA‐concentration and DSA‐affinity.01A - Beitrag in wissenschaftlicher Zeitschrift
- PublikationCanIsoNet: a database to study the functional impact of isoform switching events in diseases(Oxford University Press, 17.04.2023) Karakulak, Tülay; Szklarczyk, Damian; Saylan, Cemil Can; Moch, Holger; von Mering, Christian; Kahraman, Abdullah; Ouangraoua, Aida [in: Bioinformatics Advances]Motivation: Alternative splicing, as an essential regulatory mechanism in normal mammalian cells, is frequently disturbed in cancer and other diseases. Switches in the expression of most dominant alternative isoforms can alter protein interaction networks of associated genes giving rise to disease and disease progression. Here, we present CanIsoNet, a database to view, browse and search isoform switching events in diseases. CanIsoNet is the first webserver that incorporates isoform expression data with STRING interaction networks and ClinVar annotations to predict the pathogenic impact of isoform switching events in various diseases. Results: Data in CanIsoNet can be browsed by disease or searched by genes or isoforms in annotation-rich data tables. Various annotations for 11 811 isoforms and 14 357 unique isoform switching events across 31 different disease types are available. The network density score for each disease-specific isoform, PFAM domain IDs of disrupted interactions, domain structure visualization of transcripts and expression data of switched isoforms for each sample is given. Additionally, the genes annotated in ClinVar are highlighted in interactive interaction networks. Availability and implementation: CanIsoNet is freely available at https://www.caniso.net. The source codes can be found under a Creative Common License at https://github.com/kahramanlab/CanIsoNet_Web.01A - Beitrag in wissenschaftlicher Zeitschrift