|Identification of novel autoantigensin patients with liver autoimmune diseases by Protein MicroArray|
C. Zingaretti1, M. Arigò1, A. Cardaci1, A. Sinisi1, L. Muratori3, P. Colombatto4, F. Bonino2, P. Invernizzi5, , A.L. Zignego6 MC. Crosti1, M. Moro1, J. Geginat1, Pagani M.1, R. De Francesco1, S. Abrignani1. & M. Bombaci1
The characterization of autoimmune disease-specific biomarkers are of primary importance for the development of diagnostic tools and the comprehension of pathogenetic mechanisms leading to autoimmunity. To this aim a protein microarray was employed to analyze serum samples from patients with autoimmune hepatitis (e.g. AIH & PBC) and of healthy as controls. A panel of autoantigens able to discriminate among the groups of patients was identified for potential use as biomarkers.
Chris de Graaf, Gerdien de Kloe, Henry Vischer, Mark Verheij, Saskia Nijmeijer, Azra Delic, David Maussang, Ken Chow, Anitha Shanmugham, Paul England, Rogier Smits, Rob Leurs and Iwan de Esch
A proprietary and structurally diverse fragment library has been created and screened for a variety of Gprotein coupled receptors (GPCRs) and a number of other drug targets. The data allows for a fragment-based chemogenomics study to interrogate the interactions of GPCRs and their ligands.
|Prognostic Factors for Refeeding Syndrome in Head and Neck Cancer Patients|
James Hare, Rachel Skelly, Samit Ghosh, Terry Jones
Head and neck cancer sufferers are inherently at risk of refeeding syndrome, which had a prevalence of 9.5% in our series. Our results suggest that site of tumour (but not tumour or nodal staging) is a prognostic indicator for developing refeeding syndrome.
|Stephanie Bougel wins Poster Award at the European Biomarkers Summit 2010|
Stephanie Bougel, from the University of Lausanne, France, won the award for best poster at the European Biomarkers Summit and Exhibtion held in Florence, Italy on the 9th - 10th November 2010.
|hTERT methylation: a potential cancer biomarker for metastasis detection in body fluids|
Aim of the study:
1. To develop a specific, sensitive, quantitative, and fast method for detection of hTERT methylation
2. To explore its use as a cancer biomarker in the diagnosis of metastatic tumors in CSF.
|Hepatitis B virus (HBV) and Human immunodeficiency virus (HIV) antibodies detected by peptide microarrays|
ahmed Abd El Wahed1, Ulrike Beutling2, Ronald Frank2, Gerhard Hunsmann1, and Hans-Joachim Fritz3
HBV and HIVenv chips with overlapping oligopeptides encompassing the full amino acid sequences of HBV and HIV polypeptides were produced. In addition, a chip displaying a library of random 4608 different 15-mers peptides (4608-RPL) was prepared. Both chips were used for analyzing monoclonal antibodies and sera from HIV- and HBV-infected individuals. 4608-RPL could be used for identifying target sequences of antibodies without prior knowledge of the corresponding immunizing antigen.
|An improved data processing pipe-line for comprehensive H-NMR and X/MS -omics data|
R. J. O. Torgrip, K. M. Åberg, E. Alm
In the post acqusition analysis of comprehensive -omics data the pre-processing pipe-line is crucial to extract the maximum possible amount of information from the data. Here we show a processing pipe-line for (1D)H-NMR and (2D)X/MS data comprising; feature detection, inter-sample feature alignment and internal-standard free normalization that outperforms today’s state-of-the-art processing schemes.
|Alignment of 1H-NMR data using a Generalized Fuzzy Hough Transform|
Erik Alm, Leonard Csenki, Ralf J.O. Torgrip, K. Magnus Åberg, Lars I. Nord, Ina Schuppe-Koistinen and Johan Lindberg
In metabolic profiling, multivariate data analysis techniques are used to interpret 1D 1H–NMR data. Multivariate data analysis techniques require that peaks are located in the same variables in every spectrum – this requirement is not met in native NMR spectra. Current state-of-the-art alignment algorithms are unable to align peaks when the spatial order of the peaks changes. We present the Fuzzy Generalized Hough Transform alignment which solves the alignment problem.
|Specificity of small molecule inhibitors for deubiquitinating enzymes in living cells assessed by activity-based proteomics|
*Mikael Altun, *Holger B. Kramer, *Lianne Willems, *Mukram Mackeen, *Edward Kogan, *Rebecca Konietzny, *Cynthia Wright, *Roman Fischer, #Benjamin Nicholson, *Benedikt M. Kessler
Small molecular compounds (PR-619 and P22077) was assessed for their abilities to inhibit DUB function in crude extracts and in cells. Activity-based profiling combined with quantitative mass spectrometry revealed the inhibitory capacity of a broad range of DUBs by the PR-619, whereas P22077 showed specificity towards subsets of DUBs including USP7 in cells. Our results demonstrate the usefulness of activity-based quantitative proteomics to monitor inhibition of endogenous DUBs in vivo.