BackgroundRT-qPCR is a sensitive and increasingly used method for gene expression quantification. To normalize RT-qPCR measurements between samples, most laboratories use endogenous reference genes as internal controls. There is increasing evidence, however, that the expression of commonly used reference genes can vary significantly in certain contexts.ResultsUsing the Genevestigator database of normalized and well-annotated microarray experiments, we describe the expression stability characteristics of the transciptomes of several organisms. The results show that a) no genes are universally stable, b) most commonly used reference genes yield very high transcript abundances as compared to the entire transcriptome, and c) for each biological context a subset of stable genes exists that has smaller variance than commonly used reference genes or genes that were selected for their stability across all conditions.ConclusionWe therefore propose the normalization of RT-qPCR data using reference genes that are specifically chosen for the conditions under study. RefGenes is a community tool developed for that purpose. Validation RT-qPCR experiments across several organisms showed that the candidates proposed by RefGenes generally outperformed commonly used reference genes. RefGenes is available within Genevestigator at http://www.genevestigator.com.

Smokers have a twofold increased risk to develop Crohn's disease (CD). However, little is known about the mechanisms through which smoking affects CD pathogenesis. Especially Crohn's ileitis is negatively influenced by smoking. Interestingly, the ileum and, more in particular, the Peyer's patches in the terminal ileum are also the sites where the first CD lesions are found. Several chemokines are implicated in the pathogenesis, among which is the CCL20-CCR6 pathway. Here, we studied the gut-associated lymphoid tissue in C57BL/6 wild-type mice and in CCR6-deficient mice after exposure to air or cigarette smoke for 24 weeks. Apoptotic index of the follicle-associated epithelium overlying the Peyer's patches was evaluated. We found that chronic smoke exposure induced apoptosis in the follicle-associated epithelium. Furthermore, immune cell numbers and differentiation along with chemokine expression were determined in Peyer's patches. Important changes in immune cell composition were observed: total dendritic cells, CD4 þ T cells (including regulatory T cells) and CD8 þ T cells increased significantly after smoke exposure. The CD11b þ dendritic cell subset almost doubled. Interestingly, these changes were accompanied by an upregulated mRNA expression of the chemokines CCL9 and CCL20. However, no differences in the increase of dendritic cells were observed between wild-type and CCR6-deficient mice. Our results show that cigarette smoke exposure increases apoptosis in the follicle-associated epithelium and is associated with immune cell accumulation in Peyer's patches.

The specialized epithelium covering the lymphoid follicles of Peyer's patches in the gut mediates transcytosis of antigens to the underlying immune cells, mainly through the membranous, or M, cells. At present, the molecular processes involved in the mucosal immune response, and in antigen transport across the follicle-associated epithelium (FAE) and M cells, are poorly understood. To characterize FAE and M cells, we compared the gene expression profiles of small intestine FAE and villus epithelium (VE) in BALB/c mice by microarray analysis; 91 genes were found to be up-regulated and four down-regulated at least two-fold (p<0.01) in the FAE. The differential expression of a subset of these genes was shown to be confirmed by quantitative RT-PCR. Using immunohistochemistry on BALB/c Peyer's patches, cathepsin H and clusterin expression was increased in the FAE compared to the VE. Moreover, we demonstrated M cell-specific expression of annexin V, which has recently been reported to be important in endocytic transport and membrane scaffolding, suggesting that annexin V has a function in M cell-mediated transcytosis.

In the model organism E. coli, recombination mediated by the related XerC and XerD recombinases complexed with the FtsK translocase at specialized dif sites, resolves dimeric chromosomes into free monomers to allow efficient chromosome segregation at cell division. Computational genome analysis of Helicobacter pylori, a slow growing gastric pathogen, identified just one chromosomal xer gene (xerH) and its cognate dif site (difH). Here we show that recombination between directly repeated difH sites requires XerH, FtsK but not XerT, the TnPZ transposon associated recombinase. xerH inactivation was not lethal, but resulted in increased DNA per cell, suggesting defective chromosome segregation. The xerH mutant also failed to colonize mice, and was more susceptible to UV and ciprofloxacin, which induce DNA breakage, and thereby recombination and chromosome dimer formation. xerH inactivation and overexpression each led to a DNA segregation defect, suggesting a role for Xer recombination in regulation of replication. In addition to chromosome dimer resolution and based on the absence of genes for topoisomerase IV (parC, parE) in H. pylori, we speculate that XerH may contribute to chromosome decatenation, although possible involvement of H. pylori's DNA gyrase and topoisomerase III homologue are also considered. Further analyses of this system should contribute to general understanding of and possibly therapy development for H. pylori, which causes peptic ulcers and gastric cancer; for the closely related, diarrheagenic Campylobacter species; and for unrelated slow growing pathogens that lack topoisomerase IV, such as Mycobacterium tuberculosis.

Hepatitis B virus (HBV) infections cause 500,000 to 700,000 deaths per year as a consequence of chronic hepatitis, cirrhosis, and hepatocellular carcinoma. Efficient and safe antivirals to treat chronically infected patients and consequently to prevent development of hepatocellular carcinoma are still awaited. We isolated five single-domain antibodies (VHHs) that recognize the most abundant envelope protein (S) of HBV. VHHs, when expressed and retained in the endoplasmic reticulum as intrabodies, reduced levels of secreted hepatitis B surface antigen ( H epatitis B virus (HBV) imposes an important burden to human health worldwide. Approximately 350 to 400 million persons are chronically infected. Among these, 15% to 40% will develop cirrhosis, liver failure, and/or hepatocellular carcinoma, resulting in 500,000 to 700,000 deaths each year. 1,2 Potent and safe antivirals to succesfully treat chronically infected HBV patients and to prevent development of hepatocellular carcinoma are still awaited. To date, only interferon-2␤, pegylated interferon-2␣, and four nucleos-(t)ide analogues have been approved for the treatment of chronic HBV infections. However, interferons are only effective in a fraction (20%-40%) of patients and cause numerous side effects. The licensed synthetic nucleos-(t)ide analogues induce fewer side effects, but their therapeutic success is hampered by the appearance of drug-resistant mutants during long-term treatment. Discontinuation of treatment with nucleos(t)ide analogues generally leads to renewed viral replication that can be followed by acute exacerbation of liver disease. [3][4][5][6] Novel strategies to combat viral infections are being explored by several research groups. One approach is the ablation of viral messenger RNA expression by antisense oligonucleotides, peptide aptamers, ribozymes, and RNA interference-mediated gene silencing. 3 Another approach consists of the intrabody-mediated inhibition of viral protein functions or interactions. Intrabodies are antibody fragments that are expressed and function inside the cell. 7,8 Intrabodies can be targeted to a specific cell compartment such as the endoplasmic reticulum (ER), mitochondrium, nucleus, or cytoplasm. The most explored intrabody format is the single-chain variable fragment (scFv), which is derived from the variable antigen-binding domains of a conventional antibody. scFv intrabodies that interfere with viral replication have been developed against human immunodeficiency virus, 9 hepatitis C virus, 10,11 rotavirus, 12 herpesvirus, 13 flavivirus, 14 and HBV. 15,16 Single-domain antibodies (VHHs) are a new generation of recombinant antibody fragments. VHHs consist of the functional variable domain of heavy-chain-only antibodies of the family Camelidae, which are devoid of light chains. [17][18][19] VHHs are the smallest intact antigen-