Expression profiling using microarrays allows for the detailed characterization of the gene networks that regulate an animal's response to environmental stresses. During nutritional restriction, processes such as protein turnover, connective tissue remodeling, and muscle atrophy take place in the skeletal muscle of the animal. These processes and their regulation are of interest in the context of managing livestock for optimal production efficiency and product quality. Here we expand on recent research applying complementary DNA (cDNA) microarray technology to the study of the effect of nutritional restriction on bovine skeletal muscle. Using a custom cDNA microarray of 9,274 probes from cattle muscle and s.c. fat libraries, we examined the differential gene expression profile of the LM from 10 Brahman steers under three different dietary treatments. The statistical approach was based on mixed-model ANOVA and model-based clustering of the BLUP solutions for the gene x diet interaction effect. From the results, we defined a transcript profile of 156 differentially expressed array elements between the weight loss and weight gain diet substrates. After sequence and annotation analyses, the 57 upregulated elements represented 29 unique genes, and the 99 downregulated elements represented 28 unique genes. Most of these co-regulated genes cluster into groups with distinct biological function related to protein turnover and cytoskeletal metabolism and contribute to our mechanistic understanding of the processes associated with remodeling of muscle tissue in response to nutritional stress.

The ability of cattle to resist tick infestations is partly genetically determined. In order to better define the nature of Bos taurus resistance to the cattle tick Boophilus microplus, skin gene expression was studied using a cattle skin derived cDNA microarray. Expression profiles were determined in skin biopsies sampled from three highly tick resistant animals (HR) and two animals with lower tick resistance (LR) at time 0, immediately before challenge, and again 24 h after challenge. The analysis of the resulting expression data addressed two biological questions: first, for any animal exposed to ticks, which genes are differentially expressed in the 24 h following challenge; and second, which genes are differentially expressed between animals of high and low resistance at 24 h after challenge? In total, 214 genes were found to be differentially expressed in response to larval challenge across all the animals. Seventy-two genes were upregulated and 76 were downregulated at 24 h after challenge. Genes with significantly altered gene expression levels following tick infestation were predominantly keratin genes or mitochondrial genes, as well as odorant binding protein (OBP) and Bos taurus major allergen BDA20. In addition, we identified 66 genes with differential expression between HR and LR animals at 24 h. Of these, genes representing the extracellular matrix and immunoglobulin gene expression pathways were overrepresented. Three differentially expressed genes, OBP, Bos taurus major allergen BDA20 and dendritic cell protein HFL-B5 were further analysed by quantitative reverse transcription PCR (qRT-PCR). The qRT-PCR assay results closely mirrored the expression profiles found in the microarray experiment.

MicroRNAs (miRNAs) are potent regulators of gene transcription and posttranscriptional processes. The majority of miRNAs are localized within intronic regions of protein-coding genes (host genes) and have diverse functions in regulating important cellular processes in animals. To date, few plant intronic miRNAs have been studied functionally. Here we report a comprehensive computational analysis to characterize intronic miRNAs in rice and Arabidopsis. RT-PCR analysis confirmed that the identified intronic miRNAs were derived from the real introns of host genes. Interestingly, 13 intronic miRNAs in rice and two in Arabidopsis were located within seven clusters, of which four polycistronic clusters contain miRNAs derived from different families, suggesting that these clustered intronic miRNAs might be involved in extremely complex regulation in rice. Length analysis of miRNA-carrying introns, promoter prediction and qRT-PCR analysis results indicated that intronic miRNAs are coexpressed with their host genes. Expression pattern analysis demonstrated that host genes had a very broad expression spectrum in different stages of development, suggesting the intronic miRNAs might play an important role in plant development. This comparative genomics analysis of intronic miRNAs in rice and Arabidopsis provides new insight into the functions and regulatory mechanisms of intronic miRNAs in monocots and dicots.

In order to gain new knowledge of the genetic control of biochemical and developmental processes that contribute to beef quality, we constructed a bovine microarray of 9600 elements comprising about 2000 expressed sequence tags (ESTs) and 7300 anonymous cDNA clones from muscle and fat-derived cDNA libraries. The microarray was used in 2 animal experiments aimed at uncovering gene expression differences associated with adipogenesis and protein turnover. The results obtained so far show that expression profiling of bovine muscle using the microarray can reliably identify differentially expressed genes and confirm existing hypotheses. Moreover, the technique can provide new evidence on the detailed involvement of well-characterised genes and can identify genes that have not previously been described as having a role in these processes.