DNA-Microarray Technology: Comparison of Methodological Factors of Recent Technique Towards Gene Expression Profiling

Gene Expression Measurement Module (GEMM) for space application: Design and validation

In order to facilitate studies on the impact of the space environment on biological systems, we have developed a prototype of GEMM (Gene Expression Measurement Module) - an automated, miniaturized, integrated fluidic system for in-situ measurements of gene expression in microbial samples. The GEMM instrument is capable of (1) lysing bacterial cell walls, (2) extracting and purifying RNA released from cells, (3) hybridizing the RNA to probes attached to a microarray and (4) providing electrochemical readout, all in a microfluidics cartridge. To function on small, uncrewed spacecraft, the conventional, laboratory protocols for both sample preparation and hybridization required significant modifications. Biological validation of the instrument was carried out on Synechococcus elongatus, a photosynthetic cyanobacterium known for its metabolic diversity and resilience to adverse conditions. It was demonstrated that GEMM yielded reliable, reproducible gene expression profiles. GEMM is the only high throughput instrument that can be deployed in near future on space platforms other than the ISS to advance biological research in space. It can also prove useful for numerous terrestrial applications in the field.

Establishment of a protocol for large-scale gene expression analyses of laser capture microdissected bladder tissue

PURPOSE

Lower urinary tract symptoms (LUTS) can be caused by structural and functional changes in different compartments of the bladder. To enable extensive investigations of individual regions even in small bladder biopsies, we established a combination protocol consisting of three molecular techniques: laser capture microdissection microscopy (LCM), RNA preamplification and quantitative polymerase chain reaction (qPCR).

METHODS

Urinary bladders of ten mice were resected and frozen immediately or after a delay of 15 min. Cryosections were obtained and smooth muscle was isolated using the LCM technique. Then, RNA was extracted, including protocols with and without DNase digestion as well as with and without the addition of carrier RNA. Extracted RNA was either used for reverse transcriptase (RT)-PCR plus qPCR or for a combination of RNA preamplification and qPCR.

RESULTS

Our data showed that with RNA preamplification, 10 μg cDNA can be regularly generated from 2.5 ng RNA. Depending on expression levels, this is sufficient for hundreds of pPCR reactions. The efficiency of preamplification, however, was gene-dependent. DNase digestion before preamplification lead to lower threshold cycles in qPCR. The use of partly degraded RNA for RNA preamplification did not change the results of the following qPCR.

CONCLUSIONS

RNA preamplification strongly enlarges the spectrum of genes to be analyzed in distinct bladder compartments by qPCR. It is an easy and reliable method that can be realized with standard laboratory equipment. Our protocol may lead in near future to a better understanding of the pathomechanisms in LUTS.

Glycosylation and post-translational modification gene expression analysis by DNA microarrays for cultured mammalian cells

DNA microarray analysis of gene expression has become a valuable tool for bioprocessing research aimed at improving therapeutic protein yields. The highly parallel nature of DNA microarray technology allows researchers to assess hundreds of gene simultaneously, essentially enabling genome-wide snapshots. The quality and amount of therapeutic proteins produced by cultured mammalian cells rely heavily on the culture environment. In order to implement beneficial changes to the culture environment, a better understanding of the relationship between the product quality and culture environment must be developed. By analyzing gene expression levels under various environmental conditions, light can be shed on the underlying mechanisms. This paper describes a method for evaluating gene expression changes for cultured NS0 cells, a mouse-derived myeloma cell line, under culture environment conditions, such as ammonia buildup, known to affect product quality. These procedures can be easily adapted to other environmental conditions and any mammalian cell lines cultured in suspension, so long as a sufficient number of gene sequences are publicly available.

An optimized RNA amplification method for prokaryotic expression profiling analysis

DNA microarray technology has been extensively used for gene expression analysis of both eukaryotic and prokaryotic organisms. For eukaryotic gene expression profiling, the poly(A)-based reverse transcription of messenger RNA (mRNA) followed by T7 RNA polymerase-based in vitro transcription is generally required to produce enough RNA targets for hybridization with the microarray chips. However, the same method cannot be directly applied to prokaryotic mRNAs due to the lack of poly(A) sequences at the 3' ends. Conventional methods usually require large amounts of starting RNAs and lead to high background noise. Recently developed amplification methods enable smaller amounts of prokaryotic RNA to be used from samples with species-specific primers, oligo(dT) primers, or random primers. In this study, three target preparation methods, including the direct labeling, polyadenylation-involved oligo-dT priming, and random priming amplification (respectively referred to as DL, PAOD, and RPA hereafter) were evaluated through expression profiling of a heat shock model of Escherichia coli. The PAOD method was found to be more sensitive and more specific in differential gene expression measurements than either DL and RPA, even when the E. coli RNA was only a small proportion of the simulated eukaryotic host RNA. The results suggest that PAOD is the preferred target preparation method for prokaryotic transcriptome.