Atrial appendage transcriptional profile in patients with atrial fibrillation with structural heart diseases.

During the last few years DNA microarray studies of gene expression changes in human atrial tissues from patients with and without atrial fibrillation (AF) have been performed. For this purpose, tissue samples are usually collected from AF patients undergoing open heart surgery. These investigations have limitations associated with the unavoidable heterogeneity of compared groups which is due to the presence of various structural changes accompanying different sets of underlying heart diseases in both groups. It is thus reasonable to compare the atrial tissue samples from AF patients with those from individuals without signs of cardiovascular disease. To address this, we selected the atrial tissue samples from 12 AF patients (who underwent open heart surgery) and compared them with control atrial tissue samples from 10 individuals with no signs of cardiovascular diseases (those who died due to street accident). cDNA microarray method and reverse transcription-polymerase chain reaction (RT-PCR) analysis were used to identify genes which can discriminate between control and pathologically altered atrial tissues. Thirty-nine genes were found to be differentially expressed in pathologically altered tissues samples independently of the type of the underlying structural heart disease. These genes are involved in signal transduction, gene transcription regulation, cell proliferation, and apoptosis. The greatest alterations were observed for NOR1, DEC1, MSF, and Bcl2A1 genes (5 to 28-fold decrease, P < 0.05). Additional studies are needed to determine the specific role of each selected gene in pathophysiological changes leading to AF.

Simple cDNA normalization using kamchatka crab duplex-specific nuclease.

We developed a novel simple cDNA normalization method [termed duplex-specific nuclease (DSN) normalization] that may be effectively used for samples enriched with full-length cDNA sequences. DSN normalization involves the denaturation-reassociation of cDNA, degradation of the double-stranded (ds) fraction formed by abundant transcripts and PCR amplification of the equalized single-stranded (ss) DNA fraction. The key element of this method is the degradation of the ds fraction formed during reassociation of cDNA using the kamchatka crab DSN, as described recently. This thermostable enzyme displays a strong preference for cleaving ds DNA and DNA in DNA-RNA hybrid duplexes compared with ss DNA and RNA, irrespective of sequence length. We developed normalization protocols for both first-strand cDNA [when poly(A)+ RNA is available] and amplified cDNA (when only total RNA can be obtained). Both protocols were evaluated in model experiments using human skeletal muscle cDNA. We also employed DSN normalization to normalize cDNA from nervous tissues of the marine mollusc Aplysia californica (a popular model organism in neuroscience) to illustrate further the efficiency of the normalization technique.

Total RNA suitable for molecular biology analysis.

Development of methods based on determining expression of individual genes resulted in the need for large amounts of high quality RNA preparations. It is widely accepted that in intact rRNA the 28S and 18S band ratio must be 2:1. It is not quite clear what is the main cause of lower rRNA bands intensity ratio. It is difficult to isolate RNA with 2:1 28S/18S ratio from RNase-rich and some tumor tissues. At the same time this requirement may be excessive and RNA preparations with lower 28S/18S rRNA ratio may be quite adequate for most techniques of determining gene expression. As demonstrated in this study, the level of a particular RNA may be reliably determined by RT-PCR even in a total RNA that is usually considered as degraded (28S to 18S ratio as low as 0.4), provided that random primer is used in RT. In contrast, the use of the oligo(dT) primer in RT-PCR may lead to underestimation of specific mRNA level in the degraded RNA samples, depending on the distance of amplified fragment from the poly(A) end. A criterion based on average degradation level of a number of reference genes is suggested to discriminate specific RNA degradation from random and unspecific ones.