|Biomarkers and Metabolomics: Practical Implication|
Vladimir V. Tolstikov
Current presentation is dedicated to case studies and illustrates diversity of the projects. Cases representing different projects combine the same analytical platform we utilize for metabolomics study of blood plasma and urine. While pattern recognition presents certain challenges but rather ones that can be resolved, identification of low abundant unknown biomarkers is critical for the field and offers significant technical challenge in spite of considerable progress in modern analytical techn
|Application of genetic programming in analysis of quantitative gene expression profiles for identification of nodal status in bladder cancer|
Anirban P. Mitra, Arpit A. Almal, Ben George, David W. Fry, Peter F. Lenehan, Vincenzo Pagliarulo, Richard J. Cote, Ram H. Datar, William P. Worzel
Nodal involvement in bladder cancer is an independent indicator of prognosis. This study employed an iterative machine learning process called genetic programming on quantitative expression values of 70 genes to classify primary urothelial carcinoma samples into those associated with or without nodal metastasis. The generated rules showed a strong predilection for ICAM1, MAP2K6 and KDR resulting in gene expression motifs that cumulatively suggested a pattern ICAM1>MAP2K6>KDR for node positive ca
|How to Perform High Throughput siRNA Transfection|
Mark Hewitson, Hanno Hermann and Neil Benn
We demonstrate the optimization of siRNA transfection process for time and costs in a high throughput application with two independent measurements of the RNAi effect: The visual monitoring of Eg5 expression and the quantitative PCR measurement of GAPDH mRNA after transfection of Hela cells. The results show, that 1 wash cycle is sufficient for the removal of any remnants of the transfection complex from disposable tips, making the tips re-usable.
|Introducing the new FLUOstar Omega: Performing the Bradford Assay|
Franka Ganske, and E.J. Dell
The Bradford Assay is a fast and homogeneous assay to determine the protein concentration of samples. The shift of the dye can be followed with the new spectrometer tool. The FLUOstar Omega offers entirely new possibilities with its spectrometer. A whole absorbance spectrum can be read in about 1 sec per well. The speed of the spectrometer and the easy work-up in the software provide users with unmatched flexibility.
|Transcreener™ KINASE Fluorescence Polarization Assay Performed on the PHERAstar|
Franka Ganske, E.J. Dell
Transcreener™ KINASE ASSAY kits are far-red competitive fluorescence polarization immunoassays based on the detection of ADP. Any enzymatic reaction that uses ATP in a range from 1-250 µM can be monitored. With its dual emission detection and five photomultiplier tubes, BMG LABTECH´s PHERAstar provides the speed and sensitivity needed to take full advantage of BellBrook Labs Transcreener™ technology. Furthermore, a specific optical module was developed, thereby making assay setup simple.
|Calcium Detection Using the NOVOstar and Screen QuestT Fluo-8 NW Calcium Kit|
Jennifer Liao and E.J. Dell
The Screen Quest™ Fluo-8 NW Calcium Assay Kits provide an optimized assay method for monitoring G-protein-coupled receptors (GPCRs) and calcium channels. The assay was successfully performed on the NOVOstar. The NOVOstar from BMG LABTECH is the ideal platform to perform cell-based, fast kinetic assays such as intracellular calcium measurements, because it has a unique pipetting system that can add small amounts of agonist or antagonist (< 1.0 µl) to cells.
|Microwave-Assisted Rapid Access to Bio-active Heterocycles |
Vivek Polshettiwar and Rajender S. Varma
Environmentally benign protocols have been developed for the synthesis of various pharmaceutically active heterocycles namely 1,3,4-oxadiazoles, 1,3,4-thiadiazoles, 1,3-dioxanes, pyrazoles, hydrazones and 3,4-dihydropyrimidin-2(1H)-ones, which proceed under the influence of microwave irradiation and using eco-friendly conditions. These greener protocols were catalyzed efficiently by solid supported Nafion®NR50, phosphorus pentasulfide on alumina under solvent-free conditions.
|New Protein Biomarkers for Histopathological Classification of Breast Cancer |
Brozkova Kristyna, Knoflickova Dana, Bouchal Pavel, Nenutil Rudolf and Vojtesek Borivoj
We used Ciphergen technology based on SELDI TOF-MS (Surface Enhanced Laser Desorption/Ionisation Time-of-Flight Mass Spectrometry) for analysis of protein expression profiles of 105 breast cancer tissue samples. The aim of this study was the identification of single proteins or protein patterns specific for different tumour subgroups, which should take advantage of the biomarker as an alternative to commonly used diagnostic and prognostic characteristics.
|Development of an Automated siRNA Screening of Host Macrophages Genes Involved in Mycobacterium Tuberculosis Infection|
Jean-Philippe Carralot, Chang-Bok Lee, Annette Boese, Boris Lenseigne, Auguste Genovesio, Peter Sommer, Thierry Christophe and Priscille Brodin
In order to identify host genes required for M. tuberculosis infection and persistence, we developed a phenotypic cell-based assay in both murine and human cells and adapted it for high throughput and high content screening purposes. Knock-down efficiencies above 80% were achieved in “hard-to-Transfect” macrophage cells. Validation of the assay performed with control siRNAs will be discussed.