|Solid Phase Synthesis of a Fluorescent Peptide: Comparison of Fmoc-Lys(5-FAM)-Resin and Fmoc-Lys[5-FAM(Trt)-Resin|
Wenyu Fu, Ling Sheng, Anita Hong and Xiaohe Tong
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.
|EM Algorithm for Gene Copy Number Estimation Using TaqMan® Assays|
Catalin Barbacioru, Kelly Li, Caifu Chen and Raymond Samaha
Recently, TaqMan® assays have been developed for detection of genetic variation at gene level using primers and probes designed for genomic DNA sequences. The R package TaqGCN contains classes and methods that can be used for data reading and plotting, and for predicting gene copy number.
|EasyBeacons™ - new Probes Ideal for Realtime PCR Detection of Methylation Status of Single CpG Duplets and SNPs|
K. Skadhauge, C. Nielsen & U.B. Christensen
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.
|Evaluation of Different RNA Extraction Methods|
Plusquin Michelle, Ellen Geerdens, Karen Smeets, Tony Remans, Ann Cuypers and Tom Artois
The new model-organism, Macrostomum lignano is a marine flatworm that has an average weight of 350 µg and is 1.2 mm long. RNA-isolation from small quantities of tissue needs optimalisation. Our goal was to isolate RNA from small quantities of sample material.
|Real-time PCR Gene Expression Profiling|
Mikael Kubista, José Manuel Andrade, Björn Sjögreen and Amin Forootan
Correct interpretation of real-time PCR data requires appropriate experimental design, accurate data pre-processing and analysis of the data using proper statistical and multivariate methods. For this process we have developed the GenEx software.
|Evaluation of Different Interpretation Strategies to Discover PTM in MS/MS Peptide Fragmentation Data|
Daniel Chamrad, Gerhard Korting, Ken Fantom, Andy West, Klaus Schneider, Ulrike Schweiger-Hufagel, Herbert Thiele and Martin Bluggel
The phenomenon of acquired high quality MS/MS spectra that can not be explained within typical sequence database searches is well known. Although protein identification was successful it is manually very laborious and in most cases even impossible to match these spectra with any suggested protein sequence. The procedure of second pass searches has been developed to overcome this problem. Here we report from our in house developed tool PTM-Explorer.
|Determination of the Autoantibody Repertoire in Autoimmune Diseases with Factor Protein Arrays – A new Approach to Personalized Therapies|
A. Lueking, C. Gutjahr, V. Trappe, M. Ciupke, A. Kowald, K. Schulte, S. Cleves, T. Niehues, S. Schimrigk, M. Schneider, H. E. Meyer, Stefan Müllner and Jens Beator
Recently, we have presented a strategy to identify new marker molecules characteristic for Alopecia areata by combining protein microarray technology with the use of large cDNA expression libraries (Lueking et al., 2005). This strategy is now applied to Juvenile idiopathic Arthritis (JIA), Rheumatoid Arthritis (RA) and Multiple Sclerosis (MS) in a BMBF-funded project.
|Statistical Significance of Proteome Analysis|
Stefan Muellner, Andreas Wattenberg, Katja Aschermann and Petra Lutter
Standard Operation Procedures for each and every step within the work flow of proteome analysis is key for the statistical relevance of the data obtained. We have compared the data sets of four larger proteome studies of different biological samples with regards to the influence of the major steps - sample preparation, protein quantification, study design, analysis, and statistics - on the coefficient of validation of the whole process.
|SAMPL - Sampling And Model-Selection PipeLine : Systematically Combining Stable Gene Selection and Classification|
Chad A Davis, Fabian Gerick, Volker Hintermair, Caroine C Friedel, Katrin Fundel, Robert Kueffner, Ralf Zimmer
Two goals of gene expression analysis are classification and gene selection. Combinations of gene selectors with classifiers were evaluated on random subsets of arrays. Consensus gene signatures are constructed from genes frequently selected. Model reliability is estimated by the variance of the classification performances. The method finds reliable models, even when classification performance is variable. Manual literature screening verified the relevance of the genes identified from an osteoar