Yin et al. BMC Genomics 2010, 11:612 http://www.biomedcentral.com/1471-2164/11/612 Page 11 of 18 Figure 4 Proteomics analyses of E. purpurea phytocompound effects on mouse bone-marrow derived immature dendritic cells (iBMDCs). Effect of Echinacea purpurea extract on differential protein expression in iBMDCs was evaluated by 2D gel electrophoretic analysis. 500 μg of total cell proteins from various treatments of iBMDCs were applied to pH 5-8 IPG strips. After isofocusing and 2D gel separation, SYPRO Ruby was used to stain proteins. Images on gel were analyzed using PD-Quest software. Forty-two differentially-expressed proteins were trypsin- digested in situ, and 23 protein spots were identified by MALDI-TOF MS, with their locations in gel assigned a number. These protein ID numbers are listed in Table 4. A, Up-regulated and B, down-regulated protein spots are reported on a representative two-dimensional gel corresponding to protein expression profile of iBMDCs. The expression ratios are shown in bold print. Gels shown here are representative of thee independent experiments. appears to be readily distinguishable from the LPS- induced DC mobility. Discussion By using a combination of genomic and proteomic experimental approaches, we investigated the ex vivo effects of a candidate medicinal plant extract, [BF/S+L/ Ep], on the differentiation and modulation activities of mouse BMDCs. This study extends our previous report [9,10], where human DCs were used in a similar func- tional genomics study. In addition to the ex vivo test system, this study also examined the in vivo effect of [BF/S+L/Ep] in experimental mice. Together, our cur- rent and previous findings on both human and mouse DCs, under in vitro as well as in vivo conditions, have provided us with a comprehensive information base for future translational research into potential clinical appli- cation of [BF/S+L/Ep] as botanical drugs or nutritional supplements. As demonstrated in Fig 2, our DNA microarray test systems and the experimental cell cul- ture replicate samples were highly reproducible and consistent. We identified that close to 0.36% of the genes from the BMDC genome are significantly affected by treatment with [BF/S+L/Ep]. These differentially expressed and responsive genes were mostly related to cell adhesion and motility, immune response, signaling molecules and specialty enzymes. Some of these genes have been previously reported to be related to functions of DCs, but a large portion are reported here for the first time. In this study, flow cytometry analysis on a number of CD markers showed that expression of several mouse DC surface markers was not significantly affected by treatment with [BF/S+L/Ep], this finding was not consis- tent with our previous data for human DCs [10]. This result may suggest that specific biochemical and cellular effects of herbal extract on DC maturation may vary considerably between different mammalian species,