Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue

BACKGROUND: Low density arrays (LDAs) have recently been introduced as a novel approach to gene expression profiling. Based on real time quantitative RT-PCR (QRT-PCR), these arrays enable a more focused and sensitive approach to the study of gene expression than gene chips, while offering higher throughput than more established approaches to QRT-PCR. We have now evaluated LDAs as a means of determining the expression of multiple genes simultaneously in human tissues and cells. RESULTS: Comparisons between LDAs reveal low variability, with correlation coefficients close to 1. By performing 2-fold and 10-fold serial dilutions of cDNA samples in the LDAs we determined a clear linear relationship between the gene expression data points over 5 orders of magnitude. We also showed that it is possible to use LDAs to accurately and quantitatively detect 2-fold changes in target copy number as well as measuring genes that are expressed with low and high copy numbers in the range of 1 × 10(2 )– 1 × 10(6 )copies. Furthermore, the data generated by the LDA from a cell based pharmacological study were comparable to data generated by conventional QRT-PCR. CONCLUSION: LDAs represent a valuable new approach for sensitive and quantitative gene expression profiling

ACE2 gene expression is up-regulated in the human failing heart

BACKGROUND: ACE2 is a novel homologue of angiotensin converting enzyme (ACE). ACE2 is highly expressed in human heart and animal data suggest that ACE2 is an essential regulator of cardiac function in vivo. Since overactivity of the renin-angiotensin system contributes to the progression of heart failure, this investigation assessed changes in gene expression of ACE2, ACE, AT(1 )receptor and renin in the human failing heart. METHODS: The sensitive technique of quantitative reverse transcriptase polymerase chain reaction was used to determine the level of mRNA expression of ACE and ACE2 in human ventricular myocardium from donors with non-diseased hearts (n = 9), idiopathic dilated cardiomyopathy (IDC, n = 11) and ischemic cardiomyopathy (ICM, n = 12). Following logarithmic transformation of the data, a one-way analysis of variance was performed for each target gene followed by a Dunnett's test to compare the two disease groups IDC and ICM versus control. RESULTS: As anticipated, ACE mRNA was found to be significantly increased in the failing heart with a 3.1 and 2.4-fold up-regulation found in IDC and ICM relative to non-diseased myocardium. Expression of ACE2 mRNA was also significantly up-regulated in IDC (2.4-fold increase) and ICM (1.8-fold increase) versus non-diseased myocardium. No change in angiotensin AT(1 )receptor mRNA expression was found in failing myocardium and renin mRNA was not detected. CONCLUSIONS: These data suggest that ACE2 is up-regulated in human IDC and ICM and are consistent with the hypothesis that differential regulation of this enzyme may have important functional consequences in heart failure. This strengthens the hypothesis that ACE2 may be a relevant target for the treatment of heart failure and will hopefully spur further studies to clarify the functional effects in human myocardium of ACE2 derived peptides

Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue-0

<p><b>Copyright information:</b></p><p>Taken from "Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue"</p><p>BMC Genomics 2006;7():34-34.</p><p>Published online 24 Feb 2006</p><p>PMCID:PMC1403755.</p><p>Copyright © 2006 Goulter et al; licensee BioMed Central Ltd.</p> best fit has been plotted

Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue-3

<p><b>Copyright information:</b></p><p>Taken from "Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue"</p><p>BMC Genomics 2006;7():34-34.</p><p>Published online 24 Feb 2006</p><p>PMCID:PMC1403755.</p><p>Copyright © 2006 Goulter et al; licensee BioMed Central Ltd.</p>represents the geometric mean copy number (n = 3) +95 % CI

Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue-2

<p><b>Copyright information:</b></p><p>Taken from "Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue"</p><p>BMC Genomics 2006;7():34-34.</p><p>Published online 24 Feb 2006</p><p>PMCID:PMC1403755.</p><p>Copyright © 2006 Goulter et al; licensee BioMed Central Ltd.</p> dilution. A line of best fit and Rvalue were derived using PRISM software

Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue-4

<p><b>Copyright information:</b></p><p>Taken from "Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue"</p><p>BMC Genomics 2006;7():34-34.</p><p>Published online 24 Feb 2006</p><p>PMCID:PMC1403755.</p><p>Copyright © 2006 Goulter et al; licensee BioMed Central Ltd.</p>(B) post-thrombin. Targets that were altered by less than 50 % from the control were excluded from this figure

Characterisation of above-ground endophytic and soil fungal communities associated with dieback-affected and healthy plants in five exotic invasive species

In Australia, several well-established invasive plant species have experienced unexplained dieback. To investigate this issue, we used internal transcribed spacer (ITS) amplicon pyrosequencing to characterise fungal communities within stems (endophytes) and soils associated with dieback-affected and healthy plants from populations of five exotic invasive species (Jatropha gossypiifolia, Mimosa pigra, Parkinsonia aculeata, Tamarix aphylla and Vachellia nilotica) across northern Australia. M. pigra and P.\ua0aculeata were sampled from multiple geographic regions. A total of 353 and 4926 fungal operational taxonomic units (OTUs) were identified in stem and soil samples, respectively. Members of Ascomycota were common, representing 75% of stem and 49% of soil OTUs. Four common endophytes, including Cladosporium perangustum, were at least 50% more prevalent in healthy than dieback-affected samples for the five invasive species combined. Fungal community structure within stem and soil samples varied among invasive species. For the two species sampled across multiple regions, M. pigra had similar fungal communities within stems among regions, but a significant difference in associated soil fungi, suggesting that host plant rather than environment determined endophytic communities in this species. Irrespective of the invasive species and sample type (stem vs. soil), no significant differences were observed in fungal richness, diversity or community structure between dieback-affected and healthy plants, either locally or regionally. Our work failed to identify fungi that were either unique or relatively more abundant in dieback than healthy plants in these invasive species. Future investigations of biotic factors other than fungi, such as bacteria, archaea and oomycetes, may provide more insights into the mechanism of the dieback phenomenon affecting these species