Cross-platform comparison of SYBR® Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study

<p>Abstract</p> <p>Background</p> <p>The MicroArray Quality Control (MAQC) project evaluated the inter- and intra-platform reproducibility of seven microarray platforms and three quantitative gene expression assays in profiling the expression of two commercially available Reference RNA samples (<b><it>Nat Biotechnol </it></b>24:1115-22, 2006). The tested microarrays were the platforms from Affymetrix, Agilent Technologies, Applied Biosystems, GE Healthcare, Illumina, Eppendorf and the National Cancer Institute, and quantitative gene expression assays included TaqMan^®Gene Expression PCR Assay, Standardized (Sta) <it>RT</it>-PCR™ and QuantiGene^®. The data showed great consistency in gene expression measurements across different microarray platforms, different technologies and test sites. However, SYBR^®Green real-time PCR, another common technique utilized by half of all real-time PCR users for gene expression measurement, was not addressed in the MAQC study. In the present study, we compared the performance of SYBR Green PCR with TaqMan PCR, microarrays and other quantitative technologies using the same two Reference RNA samples as the MAQC project. We assessed SYBR Green real-time PCR using commercially available RT²Profiler™ PCR Arrays from SuperArray, containing primer pairs that have been experimentally validated to ensure gene-specificity and high amplification efficiency.</p> <p>Results</p> <p>The SYBR Green PCR Arrays exhibit good reproducibility among different users, PCR instruments and test sites. In addition, the SYBR Green PCR Arrays have the highest concordance with TaqMan PCR, and a high level of concordance with other quantitative methods and microarrays that were evaluated in this study in terms of fold-change correlation and overlap of lists of differentially expressed genes.</p> <p>Conclusion</p> <p>These data demonstrate that SYBR Green real-time PCR delivers highly comparable results in gene expression measurement with TaqMan PCR and other high-density microarrays.</p

Rolling element bearing fault diagnosis using laplace-wavelet envelope power spectrum

The bearing characteristic frequencies (BCF) contain very little energy, and are usually overwhelmed by noise and higher levels of macro-structural vibrations. They are difficult to find in their frequency spectra when using the common technique of fast fourier transforms (FFT). Therefore, Envelope Detection (ED) has always been used with FFT to identify faults occurring at the BCF. However, the computation of the ED is suffering to strictly define the resonance frequency band. In this paper, an alternative approach based on the Laplace-wavelet enveloped power spectrum is proposed. The Laplace-Wavelet shape parameters are optimized based on Kurtosis maximization criteria. The results for simulated as well as real bearing vibration signal show the effectiveness of the proposed method to extract the bearing fault characteristic frequencies from the resonant frequency band.Khalid F. Al-Raheem, Asok Roy, K. P. Ramachandran, D. K. Harrison, and Steven Grainge

mRNA Localization of ASXL2

Congenital heart disease (CHD) is the most common birth defect. However, the etiology for the majority of CHD cases have been unknown. Our lab identified a chromatin factor, Additional Sex Combs-Like 2 (ASXL2), as a novel regulator of cardiovascular development. ASXL2 fetuses display congenital heart malformations. To support the notion that ASXL2 plays important roles in cardiovascular development, I conducted whole mount in situ hybridization experiment to examine the distribution of ASXL2 mRNA in mouse embryo at embryonic day 10.5. It resulted in a surprisingly beautiful pattern of high expression level of ASXL2 in the heart and somites. The image in the submission was captured by Andrea using a dissection microscope