Schlecht U et al. (2003) Reproduction "Mining meiosis and gametogenesis with DNA microarrays."

Schlecht U, Primig M

[Reproduction, 2003]

Gametogenesis is a key developmental process that involves complex transcriptional regulation of numerous genes including many that are conserved between unicellular eukaryotes and mammals. Recent expression-profiling experiments using microarrays have provided insight into the co-ordinated transcription of several hundred genes during mitotic growth and meiotic development in budding and fission yeast. Furthermore, microarray-based studies have identified numerous loci that are regulated during the cell cycle or expressed in a germ-cell specific manner in eukaryotic model systems like Caenorhabditis elegans, Mus musculus as well as Homo sapiens. The unprecedented amount of information produced by post-genome biology has spawned novel approaches to organizing biological knowledge using currently available information technology. This review outlines experiments that contribute to an emerging comprehensive picture of the molecular machinery governing sexual reproduction in eukaryotes.

Douglas S. Portman (2006) WormBook "Profiling C. elegans gene expression with DNA microarrays."

Douglas S. Portman

[WormBook, 2006]

Reinke V (2002) Nat Genet "Functional exploration of the C. elegans genome using DNA microarrays."

Reinke V

[Nat Genet, 2002]

Global changes in gene expression underlie developmental processes such as organogenesis, embryogenesis and aging in Caenorhabditis elegans. Recently developed methods allow gene expression profiles to be determined selectively for individual tissues and cell types. Results from both whole-animal and tissue-specific expression profiling have provided an unprecedented view into genome organization and gene function. Integration of these results with other types of functional genomics data gathered from RNA-mediated interference and yeast two-hybrid analyses will allow rapid identification and exploration of the complex functional gene networks that govern C. elegans development.

Golden TR et al. (2006) Exp Gerontol "Microarray analysis of variation in individual aging C. elegans: approaches and challenges."

Melov S, Golden TR, Hubbard A

[Exp Gerontol, 2006]

Aging is generally defined and studied as a population phenomenon. However, there is great interest, especially when discussing human aging, in the identification of factors that influence the life span of an individual organism. The nematode Caenorhabditis elegans provides an excellent model system for the study of aging at the level of the individual, since young nematodes are essentially clonal yet experience a large range of individual life spans. We are conducting gene expression profiling of individual nematodes, with the aim of discovering genes that vary stochastically in expression between individuals of the same age. Such genes are candidates to modulate the ultimate life span achieved by each individual. We here present statistical analysis of gene expression profiles of individual nematodes from two different microarray platforms, examining the issue of technical vs. biological variance as it pertains to uncovering genes of interest in this paradigm of individual aging.

Steinberg CE et al. (2008) Sci Total Environ "Genes and environment - striking the fine balance between sophisticated biomonitoring and true functional environmental genomics."

Menzel R, Steinberg CE, Sturzenbaum SR

[Sci Total Environ, 2008]

This article provides an overview how the application of the gene profiling (mainly via microarray technology) can be used in different organisms to address issues of environmental importance. Only recently, environmental sciences, including ecotoxicology, and molecular biology have started to mutually fertilize each other. This conceptual blend has enabled the identification of the interaction between molecular events and whole animal and population responses. Likewise, striking the fine balance between biomonitoring and functional environmental genomics will allow legislative and administrative measures to be based on a more robust platform. The application of DNA microarrays to ecotoxicogenomics links ecotoxicological effects of exposure with expression profiles of several thousand genes. The gene expression profiles are altered during toxicity, as either a direct or indirect result of toxicant exposure and the comparison of numerous specific expression profiles facilitates the differentiation between intoxication and true responses to environmental stressors. Furthermore, the application of microarrays provides the means to identify complex pathways and strategies that an exposed organism applies in response to environmental stressors. This review will present evidence that the widespread phenomenon of hormesis has a genetic basis that goes beyond an adaptive response. Some more practical advantages emerge: the toxicological assessment of complex mixtures, such as effluents or sediments, as well as drugs seems feasible, especially when classical ecotoxicological tests have failed. The review of available information demonstrates the advantages of microarray application to environmental issues spanning from bacteria, over algae and spermatophytes, to invertebrates (nematode Caenorhabditis elegans, crustacea Daphnia spp., earthworms), and various fish species. Microarrays have also highlighted why populations of a given species respond differently to similar contaminations. Furthermore, this review points at inherent limits of microarrays which may not yet have been properly addressed, namely epigenetics, which may explain heritable variation observed in natural population that cannot be explained by differences in the DNA sequence. Finally, the review will address promising future molecular biological developments which may supersede the microarray technique.

Valerie Reinke (2006) WormBook "Germline genomics."

Valerie Reinke

[WormBook, 2006]

The completion of the C. elegans genome sequence permits the comprehensive examination of the expression and function of genes. Annotation of virtually every encoded gene in the genome allows systematic analysis of those genes using high-throughput assays, such as microarrays and RNAi. This chapter will center on the use of microarrays to comprehensively identify genes with enriched expression in the germ line during development. This knowledge provides a database for further studies that focus on gene function during germline development or early embryogenesis. Additionally, a comprehensive overview of germline gene expression can uncover striking biases in how genes expressed in the germ line are distributed in the genome, leading to new discoveries of global regulatory mechanisms in the germ line.

Lamitina T (2006) Methods Mol Biol "Functional genomic approaches in C. elegans."

Lamitina T

[Methods Mol Biol, 2006]

The nematode Caenorhabditis elegans is an extraordinarily powerful model organism for the application of functional genomic approaches. Two such approaches, whole genome microarray analysis and genome-wide RNA interference (RNAi)-mediated phenotypic screening, are highly advanced and can be used by virtually any laboratory to study biological processes of interest. Using studies of the osmotic stress response in C. elegans as an example, this chapter describes methods for conducting whole genome microarray experiments and for carrying out genome-wide reverse-genetic screens using a commercially available C. elegans bacterial RNAi feeding library. Both approaches are complimentary and can be used to rapidly gain genome-wide insights into the genes and gene networks controlling specific physiological processes.

Shivers RP et al. (2008) Curr Opin Microbiol "Transcriptional responses to pathogens in Caenorhabditis elegans."

Kim DH, Youngman MJ, Shivers RP

[Curr Opin Microbiol, 2008]

Evolutionarily conserved signaling pathways, such as the p38 and ERK MAPK pathways, the TGF-beta pathway, and the insulin-signaling pathway are required for resistance to pathogens in Caenorhabditis elegans. Recent microarray expression profiling studies have identified both candidate immune effector genes which may recognize and eliminate microbial pathogens as well as uncharacterized gene classes that are broadly induced in response to pathogen. Comparative analysis of these microarray studies is suggestive of basal versus induced components of the ancient innate immune response in C. elegans. In particular, whereas the PMK-1 p38 MAPK pathway regulates genes that are induced by pathogen, the Forkhead family transcription factor DAF-16 confers pathogen resistance through the regulation of genes that are non-overlapping with pathogen-induced genes.

Fleet JC (2007) J Physiol Biochem "Using genomics to understand intestinal biology."

Fleet JC

[J Physiol Biochem, 2007]

The use of microarrays to evaluate the transcriptome has transformed our view of biology. In addition to the focused, hypothesis-testing studies that we have traditionally conducted in cell biology, we are now able to see global changes within the entire system of the cell in response to a treatment. By examining a biological question under multiple complementary perturbations model systems (e.g. yeast, C. Elegans) have revealed new complexity that would have been impossible to see on a gene-by-gene approach. Unfortunately, beyond the use of transcript profiles to define the molecular signature of diseases (e.g. cancer), transcriptomics has not been extensively used to study intestinal biology. This review will provide a roadmap for effective use of gene expression profiling for biological research and will review some of the microarray work that has been done to better understand the nature of intestinal development and enterocyte differentiation.

Millet ACM et al. (2004) Curr Opin Immunol "Immunity in Caenorhabditis elegans."

Millet ACM, Ewbank JJ

[Curr Opin Immunol, 2004]

Until very recently it was not known whether the invertebrate Caenorhabditis elegans was capable of mounting a specific immune response to protect itself from pathogens. It has only just become clear that this simple nematode in fact possesses a complex innate immune system, involving multiple signalling pathways and an armoury of antimicrobial proteins and peptides. Genetic and microarray approaches are now revealing the molecular cross-talk that exists between the different signalling cascades.