title: Development and evaluation of different normalization strategies for gene expression studies in Candida albicans biofilms by real-time PCR.
abstract: BACKGROUND
  Candida albicans biofilms are commonly found on indwelling medical devices. However, the molecular basis of biofilm formation and development is not completely understood. Expression analysis of genes potentially involved in these processes, such as the ALS (Agglutinine Like Sequence) gene family can be performed using quantitative PCR (qPCR). In the present study, we investigated the expression stability of eight housekeeping genes potentially useful as reference genes to study gene expression in Candida albicans (C. albicans) biofilms, using the geNorm Visual Basic Application (VBA) for Microsoft Excel. To validate our normalization strategies we determined differences in ALS1 and ALS3 expression levels between C. albicans biofilm cells and their planktonic counterparts.
  
  
  RESULTS
  The eight genes tested in this study are ranked according to their expression stability (from most stable to least stable) as follows: ACT1 (beta-actin)/PMA1 (adenosine triphosphatase), RIP (ubiquinol cytochrome-c reductase complex component), RPP2B (cytosolic ribosomal acidic protein P2B), LSC2 (succinyl-CoA synthetase beta-subunit fragment), IMH3 (inosine-5'-monophosphate dehydrogenase fragment), CPA1 (carbamoyl-phosphate synthethase small subunit) and GAPDH (glyceraldehyde-3-phosphate dehydrogenase). Our data indicate that five genes are necessary for accurate and reliable normalization of gene expression data in C. albicans biofilms. Using different normalization strategies, we found a significant upregulation of the ALS1 gene and downregulation of the ALS3 gene in C. albicans biofilms grown on silicone disks in a continous flow system, the CDC reactor (Centre for Disease Control), for 24 hours.
  
  
  CONCLUSIONS
  In conclusion, we recommend the use of the geometric mean of the relative expression values from the five housekeeping genes (ACT1, PMA1, RIP, RPP2B and LSC2) for normalization, when analysing differences in gene expression levels between C. albicans biofilm cells and planktonic cells. Validation of the normalization strategies described above showed that the ALS1 gene is overexpressed and the ALS3 gene is underexpressed in C. albicans biofilms grown on silicone in the CDC reactor for 24 hours.
authors.affiliation: Laboratory for Pharmaceutical Microbiology, Ghent University, Harelbekestraat 72, B-9000, Ghent, Belgium. Heleen.Nailis@UGent.be
authors.forename: Heleen
authors.initials: H
authors.lastname: Nailis
authors.forename: Tom
authors.initials: T
authors.lastname: Coenye
authors.forename: Filip
authors.initials: F
authors.lastname: Van Nieuwerburgh
authors.forename: Dieter
authors.initials: D
authors.lastname: Deforce
authors.forename: Hans J
authors.initials: HJ
authors.lastname: Nelis
mesh_terms: D018441:Biofilms; D002176:Candida albicans / Q000235:genetics / Q000378:metabolism*; D018076:DNA, Complementary / Q000032:analysis; D004526:Efficiency; D005656:Fungal Proteins / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012313:RNA / Q000032:analysis; D020871:RNA Stability
chemical_list: C093538:ALS1 protein, Candida albicans; C113620:ALS3 protein, Candida albicans; D018076:DNA, Complementary; D005656:Fungal Proteins; D012313:RNA