SK-Hep1 cells were stably transfected with pDsRed2-mito vectors (Clontech) containing the mt signal sequence of COXVIII in front of red fluorescent protein (Red2). The cDNAs of several candidate proteins were synthesized from the total RNA of r + cells by RT-PCR, sub-cloned into the T-easy vector (Promega), and then cloned into the N-terminus of the pEGFP-N3 vector (BD Bioscience). The resulting GFP-hybrid plasmids of pZCD1-EGFP, pGPT2-EGFP, pPYCR2-EGFP, pCTSD-EGFP, and pHSPBP1-EGFP were transfected using Superfect (QIAGEN, Valencia, CA) into DsRed2-mito-SK-Hep1 cells. At 48 h post-transfection, the transfected cells were fixed with 4% paraformaldehyde, mounted, and imaged using a confocal microscope (Carl Zeiss LSM 5). The mt localizations of candidate proteins were determined by the overlap of EGFP and DsRed signals. Figure S1 Workflow of comparative cICAT analysis of mitochondria proteomes. See Materials and Methods for details. (TIF) Figure S2 The reproducibility of the changes in protein abundances detected by cICAT quantification. Thirtythree mt proteins were observed from both cICAT and 2DE proteome datasets. Similar expression patterns between our mt proteomics data (black) and 2DE analysis (light gray) are shown. (TIF) Figure S3 The level of protein expression in cytoplasm and mitochondria. Western blot analysis of five proteins in cytosolic and mitochondrial fractions isolated from r + and r 0 cells. b-actin was used as a loading control. (TIF) Figure S4 Confirmations of mtDNA depletion in r 0 cells. (A) PCR amplification of mtDNA. Genomic DNAs isolated from r + or r 0 cells were utilized as templates to amplify mtDNA and nuclear DNA-encoded b-actin control. (B) Cellular nucleotide staining. Cells were treated with PicoGreen for 1 h, washed with DPBS, and then stained with Mitotracker orange (Mito-T, 100 nM) for 10 min. The cells were fixed with paraformaldehyde for 20 min and visualized by conformal microscopy (61000). mtDNA was observed only in r + cells. (TIF) Figure S5 Identification of purified mitochondria. Mitochondria were isolated using gradient-based ultracentrifugation as described. Proteins from a total lysate (30 mg), and mitochondria (10 mg) were resolved using 12% SDS-PAGE and analyzed by western blot. Antibodies against the following marker proteins were used: COXI, COXIV, and HSPD1 (HSP60) for mitochondria, HDAC1 for nucleus, NF-kB and SOD1 for cytoplasm, GRP78 for ER, and LAMP1 for lysosome. b-actin served as a loading control. (TIF)  Claudins in lung diseases Tight junctions are the most apically localized part of the epithelial junctional complex. They regulate the permeability and polarity of cell layers and create compartments in cell membranes. Claudins are structural molecules of tight junctions. There are 27 claudins known, and expression of different claudins is responsible for changes in the electrolyte and solute permeability in cells layers. Studies have shown that claudins and tight junctions also protect multicellular organisms from infections and that some infectious agents may use claudins as targets to invade and weaken the host's defense. In neoplastic diseases, claudin expression may be up- or downregulated. Since their expression is associated with specific tumor types or with specific locations of tumors to a certain degree, they can, in a restricted sense, also be used as tumor markers. However, the regulation of claudin expression is complex involving growth factors and integrins, protein kinases, proto-oncogens and transcription factors. In this review, the significance of claudins is discussed in lung disease and development. Tight junctions are membranous structures present in epithelial, endothelial and mesothelial cells [1, 2] They form barriers between cells in cell layers regulating diffusion of molecules and ions through the intercellular space [3] . They also form a fence separating the apical part of the cell from other parts thus preventing membrane proteins from mixing up with each other [3] . They play a part in the formation of cellular polarity and attachment [2, 3] (Figure 1 ). The barrier formed by the tight junctions prevents pathogens from penetrating through the epithelial layers thus serving as components of innate immunity [4] . They also participate in the immune defense by forming secluded areas such as the brain, eye or testis, where they contribute to sealing these tissues from the immune system [5, 6] . Tight junctional proteins also participate in regulation of cell differentiation and proliferation [7] .