Quantitative proteomic studies, based on two-dimensional gel electrophoresis, are commonly used to find proteins that are differentially expressed between samples or groups of samples. These proteins are of interest as potential diagnostic or prognostic biomarkers, or as proteins associated with a trait. The complexity of proteomic data poses many challenges, so while experiments may reveal proteins that are differentially expressed, these are often not significant when subjected to rigorous statistical analysis. However, this can be addressed through appropriate experimental design. A good experimental design considers the impact of different sources of variation, both analytical and biological, on the statistical importance of the results. The design should address the number of samples that must be analyzed and the number of replicate gels per sample, in the context of a particular minimum difference that one is seeking to achieve. In this study, we explore the ways to improve the quality of protein expression data from 2-DE gels, and describe an approach for defining the number of samples required and the number of gels per sample. It has been developed for the simplest of situations, two groups of samples with variation at two levels: between samples and between gels. This approach will also be useful as a guide for more complex designs involving more than two groups of samples. We describe some Internet-accessible tools that can assist in the design of proteomic studies.

The mammalian testis-determining gene Sry and the related Sox genes define a family of transcriptional regulators widely expressed during embryogenesis. Tightly controlled temporal profiles of expression are a feature of the Sox gene family and may be required for initiation of a cascade of gene expression, yet the molecular mechanisms that control Sox gene expression are unknown. We now show that human SOX4 is expressed in the normal breast and in breast cancer cells. In these cells SOX4 is a progesterone-regulated gene, the expression of which is increased by progestins, leading to a marked increase in SOX-mediated transcriptional activity. Treatment of T-47D breast cancer cells with the synthetic progestin ORG 2058 directly increased SOX4 transcription, resulting in a 4-fold increase in SOX4 mRNA levels within 4 h of treatment. No effect of ORG 2058 was noted on other SOX genes measured, nor were other hormone-regulated HMG box proteins detected in this system, suggesting that the observed ability of progestin to increase SOX mRNA expression was confined to SOX4. The increase in SOX4 transcription was reflected in increased SOX4 protein expression, as progestin treatment of T-47D cells transfected with a SOX-responsive reporter resulted in a marked increase in reporter gene expression. Progesterone is essential for normal development and differentiation of the female reproductive system, plays an essential role in regulating growth and differentiation of the mammary gland and is required for opposing the proliferative effects of estrogen in specific cell types. The detection of SOX4 expression in the normal and malignant breast and the demonstration that SOX4 expression is under progesterone control suggests that changes in SOX4 gene expression may play a role in commitment to the differentiated phenotype in the normal and malignant mammary gland.

Trichoderma atroviride has a natural ability to parasitise phytopathogenic fungi such as Rhizoctonia solani and Botrytis cinerea, therefore providing an environmentally sound alternative to chemical fungicides in the management of these pathogens. Two-dimensional electrophoresis was used to display cellular protein patterns of T. atroviride (T. harzianum P1) grown on media containing either glucose or R. solani cell walls. Protein profiles were compared to identify T. atroviride proteins up-regulated in the presence of the R. solani cell walls. Twenty-four protein spots were identified using matrix-assisted laser desorption ionisation mass spectrometry, liquid chromatography mass spectrometry and N-terminal sequencing. Identified up-regulated proteins include known fungal cell wall-degrading enzymes such as N-acetyl-beta-D: -glucosaminidase and 42-kDa endochitinase. Three novel proteases of T. atroviride were identified, containing sequence similarity to vacuolar serine protease, vacuolar protease A and a trypsin-like protease from known fungal proteins. Eukaryotic initiation factor 4a, superoxide dismutase and a hypothetical protein from Neurospora crassa were also up-regulated as a response to R. solani cell walls. Several cell wall-degrading enzymes were identified from the T. atroviride culture supernatant, providing further evidence that a cellular response indicative of biological control had occurred.

The SOX genes define a family of transcriptional regulators whose diverse patterns and tightly controlled temporal profiles of expression suggest that they play key roles in determination of cell fate during development. One of the family members, Sox4, is expressed in the gonads of adult mice, but expression in the reproductive tissues has not been studied. As previous studies in this laboratory had shown that the SOX4 gene was regulated by ovarian hormones in breast cancer cells, murine Sox4 expression was analyzed in the reproductive tissues of mice by Northern blot analysis and ribonuclease protection assays. Sox4 mRNA expression was detected in the uterus and, at a lower level, in the mammary glands of pubertal and adult mice. Expression was modulated in the uterus of intact mice at various stages of the estrous cycle and was reduced by estradiol treatment of ovariectomized mice. Progesterone treatment partially reversed the estradiol effect. Although no modulation of Sox4 expression in the mammary glands was detected by Northern blot analysis, further evaluation of Sox4 protein expression at a cellular level is required. No modulation of Sox4 levels was observed in the thymus. The results presented here suggest that expression of the Sox4 gene is under ovarian hormone control in the uterus and implicate Sox4 in the complex effects controlled by ovarian hormones in the female reproductive system.