Posters

We demonstrate that DNA methylation patterns can serve as characteristic markers to distinguish different cell types. We have identified panels of methylation markers that are specific to mesenchymal stem cells or various differentiated cell types in the mesenchymal lineage. This method of cell type identification has a number of advantages over conventional markers in that it is robust, is both qualitative and quantitative.

We have prepared and performed comparison studies using two kinds of resins, Fmoc-Lys(5-FAM)-Rink Amide resin (I) and Fmoc-Lys[5-FAM(trt)]-Rink Amide resin (II), the latter contains a phenolic hydroxyl group protected with a trityl group. Syntheses were carried out under the same standard conditions and the peptides obtained showed no significant difference in purity. The results of these studies showed that resin (I) is adequate for synthesis of C-terminal fluorescent labeled peptide.

The EasyBeacons™ presented here are based on the novel technology Intercalating Nucleic Acid, INA®, linked to a fluorophore and a quencher. INA® is composed of normal DNA nucleotides and Intercalating Pseudo Nucleotides (IPNs). The fact that the EasyBeacons™ are mostly composed of normal DNA nucleotides means that in many respects EasyBeacons™ behave like DNA based probes, allowing use of standard buffers, primers and enzymes and hence reduces the optimisation efforts.

Pacific Northwest National Laboratory (PNNL) has developed a micro/nano particle trap that allows surface-functionalized magnetic or non-magnetic particles to be trapped with subsequent perfusion of sample, reagents and wash solutions, yielding significant (up to 5-fold) improvements in assay speed and sensitivity, while significantly reducing sample matrix effects.

In the present paper we describe results obtained using a miniaturized ProtE instrument and its comparison to the mini- PROTEAN 3-cell (Bio-Rad). Our device is able to perform sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE) in less than 11 min.

In this study we use high-speed photography as a feedback mechanism for adjusting the Nanodrop instrument dispense settings to improve the positional dispense accuracy of low volume (nanoliter) drops. These same parameters can be investigated, with various fluid classes, to reduce deleterious effects on dispensing performance such as deflected streams, satellite formation, secondary pulses and drop deformation.

Afitt is a software package for automated ligand conformation generation and placement within algorithmically identified unfilled electron density. Following real space refinement, the ligand solution is sent for subsequent refinement by Refmac or CNX, via coordinate and dictionary files. We have validated Afitt on forty publicly available data sets, chosen because it contains examples of highly strained ligand conformations.

We use local extrema in microarray time series data as the basis for discretisation. By comparing discretised gene expressions using similarity functions, we discover putative protein-to-protein interactions. We validate the results by use of public true positive and true negative databases for protein-to-protein interactions and demonstrate the high predictiveness of these local extrema as a time series feature.

Identification of low abundant proteins requires relative enrichment. We have tested systems for specific removal of high abundance proteins. Efficiency of albumin and IgG removal was assessed by ELISA and 2-DE. To estimate unspecific binding, six cytokines were spiked into serum. Recovery rates were determined with a cytometric bead assay.