High-throughput analysis of mRNA expression: microarrays are not the whole story

Large-scale tag/PCR-based gene expression profiling

An intriguing enigma in molecular biology is how genes within a single genome are differentially expressed in different cell types of a multicellular organism, or in response to different developmental or environmental queues in a single cell type. Quantification of transcript levels on a genome-wide scale, often termed transcript profiling, provides a powerful approach to identifying protein-coding and non-coding RNAs functionally relevant to a given biological process. Indeed, transcriptome analysis has been a key area of biological inquiry for decades and successfully produced discoveries in a multitude of processes and disease states, and in an increasingly large number of organisms. The evolution of technologies with increasing levels of informational content, ranging from hybridization-based technologies such as Northern blot analysis and microarrays to tag/polymerase chain reaction (PCR)- and sequence-based technologies including differential display and SAGE, along with the next-generation sequencing, has provided hope for revealing the molecular details of biological systems as they respond to change. This review is an overview of selected high throughput tag/PCR-based methods for genome-wide expression profiling amenable to high-throughput automated operation in any standard laboratory.

Application of HiCEP to screening of radiation stress-responsive genes in the soil microarthropod Folsomia candida (Collembola)

The field of ecotoxicogenomics has received increasing attention for its potential to provide insight into pressing ecological issues. However, its applications are limited due to a lack of genetic sequence information for organisms used in ecotoxicological studies. We used high-coverage expression profiling (HiCEP), a method that requires no prior sequence knowledge, to examine stress-responsive genes and their dose dependence in the springtail Folsomia candida using gamma radiation as the stressor. Radiation-responsive genes and their dose dependency were detected at effective doses for reproduction, and 16 up-regulated transcript-derived fragments (TDFs) were sequenced. Quantitative PCR analysis also found that most of the TDFs were up-regulated. The sequences of the TDFs showed resemblance to known genes, such as glutathione S-transferase and poly(ADP-ribose) polymerase, but most showed no similarity to any genes in the gene databases. These results suggest that HiCEP is effective for discovering differently expressed genes and their dose dependence, even in organisms for which few sequence data are available. The limited length of the TDFs, however, may impede functional annotation of the genes. In conclusion, HiCEP is useful for ecotoxicogenomic studies in which various organisms with few available genomic resources are involved.

Use of molecular techniques to elucidate the mechanisms of action of fungal biocontrol agents: a review

Biological control of fungal plant pathogens appears as an attractive and realistic approach, and numerous microorganisms have been identified as biocontrol agents. There have been many efforts to understand the mechanisms of action of fungal biocontrol agents. Microbiological, microscopic, and biochemical techniques applied over many years have shed light on these mechanisms without fully demonstrating them. More recently, the development of molecular techniques has yielded innovative alternative tools for understanding and demonstrating the mechanisms underlying biocontrol properties. To date, more than 70 publications describe the use of molecular techniques for this purpose. They describe work exploiting targeted or non-targeted gene isolation, gene expression profiling, gene inactivation and/or overexpression, the study of regulatory factors. This work has shed considerable light on mechanisms underlying biocontrol properties. It has also fully demonstrated a number of targeted action mechanisms of some biocontrol agents. This review describes the techniques used in such studies, with their potential and limitations. It should provide a guide for researchers wanting to study the molecular basis of the biocontrol in diverse biocontrol agents.