Microarray analysis of gene expression in olive flounder liver infected with viral haemorrhagic septicaemia virus (VHSV).

The most fatal viral pathogen in olive flounder Paralichthys olivaceus, is viral hemorrhagic septicemia virus, which afflicts over 48 species of freshwater and marine fish. Here, we performed gene expression profiling on transcripts isolated from VHSV-infected olive flounder livers using a 13 K cDNA microarray chip. A total of 1832 and 1647 genes were upregulated and down-regulated over two-fold, respectively, after infection. A variety of immune-related genes showing significant changes in gene expression were identified in upregulated genes through gene ontology annotation. These genes were grouped into categories such as antibacterial peptide, antigen-recognition and adhesion molecules, apoptosis, cytokine-related pathway, immune system, stress response, and transcription factor and regulatory factors. To verify the cDNA microarray data, we performed quantitative real-time PCR, and the results were similar to the microarray data. In conclusion, these results may be useful for the identification of specific genes or for the diagnosis of VHSV infection in flounder.

HBx induces the proliferation of hepatocellular carcinoma cells via AP1 over-expressed as a result of ER stress.

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and chronic hepatitis B virus (HBV) infection is the most common risk factor for HCC. The HBV proteins can induce oncogenic or synergy effects with a hyperproliferative response on transformation into HCC. CREBH (cAMP-responsive, element-binding protein H), activated by stress in the endoplasmic reticulum (ER), is an ER-resident transmembrane bZIP (basic leucine zipper) transcription factor that is specifically expressed in the liver. In the present study, we address the role played by CREBH activated by ER stress in HBV-induced hepatic cell proliferation. We confirmed CREBH activation by ER stress and showed that it occurred as a result of/via hepatitis B virus X (HBx)-induced ER stress. CREBH activated by HBx increased the expression of AP-1 target genes through c-Jun induction. Under pathological conditions such as liver damage or liver regeneration, activated CREBH may have an important role to play in hepatic inflammation and cell proliferation, as an insulin receptor with dual functions under these conditions. We showed that CREBH activated by HBx interacted with HBx protein, leading to a synergistic effect on the expression of AP-1 target genes and the proliferation of HCC cells and mouse primary hepatocytes. In conclusion, in HBV-infected hepatic cells or patients with chronic HBV, CREBH may induce proliferation of hepatic cells in co-operation with HBx, resulting in HCC.

Molecular characterization and expression analysis of a peroxiredoxin 1 cDNA from Korean rose bitterling (Rhodeus uyekii).

Peroxiredoxins (Prxs), also known as natural killer cell enhancing factors in fish, role as antioxidant proteins and participate in a variety of biological processes, including H2O2-mediated cell signaling, molecular chaperoning, and mitochondrial function. In this study, we isolated and characterized a Prx 1 cDNA from the Korean rose bitterling Rhodeus uyekii, and designated it RuPrx 1. The RuPrx 1 cDNA encodes a 197-amino-acid polypeptide that belongs to the class of typical 2-Cys Prxs that contain peroxidatic and resolving cysteines. The deduced RuPrx 1 protein shows strong homology (77.38-92.89 %) with Prx 1 proteins from other species, including fish, amphibians, and mammals, and it is most closely related to rainbow smelt Prx 1. RuPrx 1 mRNA was ubiquitously detected in all tested tissues and its expression was comparatively high in the brain, intestine, kidney, liver, ovary, stomach, and testis. Expression of RuPrx 1 mRNA in liver peaked 3 h post-infection with Aeromonas hydrophila and decreased 24 h post-infection while the expression in intestine decreased 24 h post-infection. These results suggest that RuPrx 1 is conserved through evolution and may play roles similar to its mammalian counterparts.

Characterization, expression profile, and promoter analysis of the Rhodeus uyekii vitellogenin Ao1 gene.

The fish Vitellogenin (Vg) gene has been applied as a biomarker for exposure to estrogenic compounds in the aquatic environment. In this study, we cloned and characterized Vg cDNA from the Korean rose bitterling Rhodeus uyekii (Ru-Vg). The Ru-Vg cDNA encodes a 1424-amino-acid polypeptide that belongs to the VgAo1 family and contains a putative signal peptide, lipovitellin I, phosvitin, and lipovitellin II, but does not contain the vWFD domain or the C-terminal peptide. The deduced Ru-Vg protein has high amino acid identity (73.97%-32.17%) with fish Vg proteins. Pairwise alignment and phylogenetic analysis revealed that Ru-Vg is most closely related to Acheilognathus yamatsutae Vg. Ru-Vg transcripts were detected using quantitative polymerase chain reaction in all tissues tested, with the highest level of expression observed in the ovary. Ru-Vg mRNA was upregulated in R. uyekii hepatopancreas cells in response to treatment with 17ß-estradiol (E2) or 17α-ethinylestradiol (EE2). Luciferase reporter expression, driven by the 5'-regulatory region of the Ru-Vg gene spanning from -1020 bp to the start codon was induced by the estrogen receptor and was synergistically activated by treatment with E2 or EE2. These results suggest that R. uyekii and the Ru-Vg gene may be useful as biomarkers for exposure to E2 or EE2.

Molecular and functional analyses of the fast skeletal myosin light chain2 gene of the Korean oily bitterling, Acheilognathus koreensis.

We identified and characterized the primary structure of the Korean oily bitterling Acheilognathus koreensis fast skeletal myosin light chain 2 (Akmlc2f), gene. Encoded by seven exons spanning 3955 bp, the deduced 168-amino acid AkMLC2f polypeptide contained an EF-hand calcium-binding motif and showed strong homology (80%-98%) with the MLC2 proteins of Ictalurus punctatus and other species, including mammals. Akmlc2f mRNA was highly enriched in skeletal muscles, and was detectable in other tissues. The upstream regions of Akmlc2f included a TATA box, one copy of a putative MEF-2 binding site and several putative C/EBPß binding sites. The functional activity of the promoter region of Akmlc2f was examined using luciferase and red fluorescent protein reporters. The Akmlc2f promoter-driven reporter expressions were detected and increased by the C/EBPß transcription factor in HEK293T cells. The activity of the promoter of Akmlc2f was also confirmed in the developing zebrafish embryo. Although the detailed mechanism underlying the expression of Akmlc2f remains unknown, these results suggest the muscle-specific expression of Akmlc2f transcript and the functional activation of Akmlc2f promoter by C/EBPß.

Characterization of Paralichthys olivaceus peroxisome proliferator-activated receptor-α gene as a master regulator of flounder lipid metabolism.

Peroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that play key roles in lipid and energy homeostasis. Paralichthys olivaceus PPARα (PoPPARα) cDNA was isolated by initial reverse transcription-polymerase chain reaction (RT-PCR) using conserved region among fish species and rapid amplification of cDNA ends (RACE). The full-length of PoPPARα cDNA is 2040-bp long encoding a polypeptide with 505 amino acids and containing a DNA binding domain (C4-type zinc finger) and a ligand-binding domain. PoPPARα was detected from 1 day post-hatch and was highly expressed in the stomach, liver, and intestine of continuously fed flounder, approximately 16 cm in size. PoPPARα mRNA expression was down-regulated in the kidney, stomach, and liver of the 4.5-month-old flounder after a 30 day food-deprivation period. PoPPARα activates the PPAR response element (PPRE)-driven reporter, and treatment with Wy14643, a PPARα agonist, augmented PoPPARα-stimulated peroxisome proliferator response element activity in HINAE and HepG2 cells. PoPPARα activated the expression of fatty acid ß-oxidation related genes such as carnitine palmitoyltransferase 1A, medium chain acyl-CoA dehydrogenase, and acyl-CoA oxidase 1 and inhibited the expression of sterol regulatory element binding protein and fatty acid synthase by competitively inhibiting LXR/RXR heterodimer formation. These results suggest that PoPPARα plays an important role in lipid metabolism of olive flounder and that it is functionally and evolutionarily conserved in olive flounder and mammals.

Endoplasmic reticulum stress induced by hepatitis B virus X protein enhances cyclo-oxygenase 2 expression via activating transcription factor 4.

Chronic hepatitis B is a disease of the liver that can progress to cirrhosis and liver cancer. The HBx (hepatitis B virus X) protein of hepatitis B virus is a multifunctional regulator that induces ER (endoplasmic reticulum) stress by previously unknown mechanisms. ER stress plays a critical role in inflammatory induction and COX2 (cyclo-oxygenase 2) is an important mediator of this inflammation. In the present study, we demonstrate the molecular mechanisms of HBx on induction of ER stress and COX2 expression. In addition, HBx reduced expression of enzymes which are involved in mitochondrial ß-oxidation of fatty acids and the mitochondrial inner membrane potential. The reduction in intracellular ATP levels by HBx induced the unfolded protein response and COX2 expression through the eIF2α (eukaryotic initiation factor 2α)/ATF4 (activating transcription factor 4) pathway. We confirmed that ATF4 binding to the COX2 promoter plays a critical role in HBx-mediated COX2 induction. The results of the present study suggest that HBV infection contributes to induction of hepatic inflammation through dysfunction of cellular organelles including the ER and mitochondria.

SHP (small heterodimer partner) suppresses the transcriptional activity and nuclear localization of Hedgehog signalling protein Gli1.

Gli (glioma-associated oncogene homologue) proteins act as terminal effectors of the Hedgehog signalling pathway, which is implicated in the development of many human malignancies. Gli activation is important for cell proliferation and anti-apoptosis in various cancers. Several studies have suggested that nuclear receptors have anti-cancer effects by inhibiting the activation of various oncoproteins. However, the involvement of nuclear receptors on the Hedgehog/Gli signalling pathway is poorly defined. In the present study we identified SHP (small heterodimer partner) as a nuclear receptor that decreased the expression of Gli target genes by repressing the transcriptional activity of Gli1. The inhibitory effect of SHP was associated with the inhibition of Gli1 nuclear localization via protein-protein interaction. Finally, SHP overexpression decreased the expression of Gli target genes and SHP knockdown increased the expression of these genes. Taken together, these results suggest that SHP can play a negative role in Hedgehog/Gli1 signalling.

Forest cover classification by optimal segmentation of high resolution satellite imagery.

This study investigated whether high-resolution satellite imagery is suitable for preparing a detailed digital forest cover map that discriminates forest cover at the tree species level. First, we tried to find an optimal process for segmenting the high-resolution images using a region-growing method with the scale, color and shape factors in Definiens(®) Professional 5.0. The image was classified by a traditional, pixel-based, maximum likelihood classification approach using the spectral information of the pixels. The pixels in each segment were reclassified using a segment-based classification (SBC) with a majority rule. Segmentation with strongly weighted color was less sensitive to the scale parameter and led to optimal forest cover segmentation and classification. The pixel-based classification (PBC) suffered from the "salt-and-pepper effect" and performed poorly in the classification of forest cover types, whereas the SBC helped to attenuate the effect and notably improved the classification accuracy. As a whole, SBC proved to be more suitable for classifying and delineating forest cover using high-resolution satellite images.

The SDF-1alpha/CXCR4 axis induces the expression of fatty acid synthase via sterol regulatory element-binding protein-1 activation in cancer cells.

Fatty acid synthase (FASN), a key enzyme that synthesizes long-chain fatty acids, is involved in both normal lipid synthesis and cancer development. Overexpression and increased activity of FASN represents one of the most frequent phenotypic alterations in cancer cells. Multiple growth factors and growth factor receptors have emerged as major contributors to FASN overexpression. However, the ultimate mechanisms responsible for tumor-associated FASN overexpression are not completely understood. Here, we show that the stromal cell-derived factor-1 alpha (SDF-1alpha)/CXCR4 axis can induce the FASN expression via the nuclear translocation of sterol regulatory element-binding protein-1, a major modulator of FASN transcription. We also identified that recombinant SDF-1alpha-induced phosphatidylinositol-3'-kinase/protein kinase B (Akt) phosphorylation was involved in the expression or activities of FASN. Finally, we demonstrated that FASN inhibition significantly reduced the SDF-1alpha-mediated G(1) cyclin expression and cell viability. Taken together, our findings manifest that the SDF-1alpha/CXCR4 axis is a novel upstream pathway of FASN expression and is associated with mediating its prosurvival effect.

Characterization of the flounder IL-6 promoter and its regulation by the p65 NF-kappaB subunit.

Interleukin (IL)-6 plays important roles in the regulation of the immune response and inflammation in many cell types and its induction by bacterial endotoxins or cytokines is regulated at the transcriptional level. The present study demonstrates the isolation and characterization of the flounder IL-6 promoter sequence and its transcriptional regulation in olive flounder (hirame) natural embryo (HINAE) cells. The promoter region (-400 to +79 bp from the transcription initiation site) of the flounder IL-6 gene contains putative cis-regulatory elements for CCAAT-enhancer-binding proteins (C/EBP; -346 to -355 bp and -166 to -160 bp), cAMP response element binding (CREB; -81 to -85 bp), the activator protein 1 (AP-1; -56 to -62 bp), and NF-kappaB (-39 to -48 bp). Transfection of p65 stimulated the PoIL-6-luc-WT reporter, but not the PoIL-6-luc-kappaB mt reporter, and treatment with LPS augmented p65-stimulated reporter activity in HINAE cells. In contrast, transfection of C/EBPbeta or c-Jun failed to induce synergistic effects in the LPS-driven PoIL-6-luc-WT reporter activity. These results give us new insight into the regulation of flounder IL-6 transcription by the p65 NF-kappaB subunit.

Activating transcription factor 2 increases transactivation and protein stability of hypoxia-inducible factor 1alpha in hepatocytes.

HIF-1 (hypoxia inducible factor 1) performs a crucial role in mediating the response to hypoxia. However, other transcription factors are also capable of regulating hypoxia-induced target-gene transcription. In a previous report, we demonstrated that the transcription factor ATF-2 (activating transcription factor 2) regulates hypoxia-induced gene transcription, along with HIF-1alpha. In the present study, we show that the protein stability of ATF-2 is induced by hypoxia and the hypoxia-mimic CoCl2 (cobalt chloride), and that ATF-2 induction enhances HIF-1alpha protein stability via direct protein interaction. The knockdown of ATF-2 using small interfering RNA and translation-inhibition experiments demonstrated that ATF-2 plays a key role in the maintenance of the expression level and transcriptional activity of HIF-1alpha. Furthermore, we determined that ATF-2 interacts directly with HIF-1alpha both in vivo and in vitro and competes with the tumour suppressor protein p53 for HIF-1alpha binding. Collectively, these results show that protein stabilization of ATF-2 under hypoxic conditions is required for the induction of the protein stability and transactivation activity of HIF-1alpha for efficient hypoxia-associated gene expression.

Estimating stem volume and biomass of Pinus koraiensis using LiDAR data.

The objective of this study was to estimate the stem volume and biomass of individual trees using the crown geometric volume (CGV), which was extracted from small-footprint light detection and ranging (LiDAR) data. Attempts were made to analyze the stem volume and biomass of Korean Pine stands (Pinus koraiensis Sieb. et Zucc.) for three classes of tree density: low (240 N/ha), medium (370 N/ha), and high (1,340 N/ha). To delineate individual trees, extended maxima transformation and watershed segmentation of image processing methods were applied, as in one of our previous studies. As the next step, the crown base height (CBH) of individual trees has to be determined; information for this was found in the LiDAR point cloud data using k-means clustering. The LiDAR-derived CGV and stem volume can be estimated on the basis of the proportional relationship between the CGV and stem volume. As a result, low tree-density plots had the best performance for LiDAR-derived CBH, CGV, and stem volume (R (2) = 0.67, 0.57, and 0.68, respectively) and accuracy was lowest for high tree-density plots (R (2) = 0.48, 0.36, and 0.44, respectively). In the case of medium tree-density plots accuracy was R (2) = 0.51, 0.52, and 0.62, respectively. The LiDAR-derived stem biomass can be predicted from the stem volume using the wood basic density of coniferous trees (0.48 g/cm(3)), and the LiDAR-derived above-ground biomass can then be estimated from the stem volume using the biomass conversion and expansion factors (BCEF, 1.29) proposed by the Korea Forest Research Institute (KFRI).

An immune responsive complement factor D/adipsin and kallikrein-like serine protease (PoDAK) from the olive flounder Paralichthys olivaceus.

The cDNA encoding of a complement factor D/adipsin and kallikrein-like serine protease, designated PoDAK, was isolated from the olive flounder Paralichthys olivaceus. PoDAK cDNA encodes a polypeptide with 277 amino acids containing conserved catalytic triad residues of serine proteases. The amino acid sequence of PoDAK showed high similarity to the kallikrein-like protein of medaka, mammalian adipsin/complement factor D and tissue kallikrein homolog, KT-14 of trout, complement factor D of zebrafish, and shared 31.6-36.8% homology with complement factor D/adipsin known from other species, including mammals. Phylogenetic analysis revealed that PoDAK clustered with the kallikrein-like protein of medaka and mammalian adipsin/complement factor D and tissue kallikrein homolog KT-14 of trout. The expression of PoDAK mRNA was high in the gills and heart, moderate in muscle, liver, intestine, stomach, kidney, and spleen of healthy flounder, and increased in the kidney, liver, and spleen of flounder challenged by the viral hemorrhagic septicemia virus (VHSV) or Streptococcus iniae. In situ hybridization confirmed that PoDAK mRNA is localized in the kidney and heart of individuals infected with VHSV. Further investigations are needed to clarify the function of PoDAK in vivo and in vitro.

Molecular cloning of Kazal-type proteinase inhibitor of the shrimp Fenneropenaeus chinensis.

Proteinase inhibitors play important roles in host defence systems involving blood coagulation and pathogen digestion. We isolated and characterized a cDNA clone for a Kazal-type proteinase inhibitor (KPI) from a hemocyte cDNA library of the oriental white shrimp Fenneropenaeus chinensis. The KPI gene consists of three exons and two introns. KPI cDNA contains an open reading frame of 396 bp, a polyadenylation signal sequence AATAAA, and a poly (A) tail. KPI cDNA encodes a polypeptide of 131 amino acids with a putative signal peptide of 21 amino acids. The deduced amino acid sequence of KPI contains two homologous Kazal domains, each with six conserved cysteine residues. The mRNA of KPI is expressed in the hemocytes of healthy shrimp, and the higher expression of KPI transcript is observed in shrimp infected with the white spot syndrome virus (WSSV), suggesting a potential role for KPI in host defence mechanisms.

Molecular cloning and characterization of olive flounder (Paralichthys olivaceus) peroxisome proliferator-activated receptor gamma.

Peroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that play key roles in lipid and energy homeostasis. Olive flounder (Paralichthys olivaceus) PPARgamma cDNA (olPPARgamma) was isolated by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The full-length cDNA is 1667-bp long and encodes a polypeptide with 532 amino acids containing a C4-type zinc finger and a ligand-binding domain. Quantitative RT-PCR revealed that olPPARgamma transcription was detected from 7days post-hatching, and its expression was increased under a starved condition. Overexpression of olPPARgamma stimulated PPAR response element (PPRE) activity, and treatment with rosiglitazone, a PPARgamma agonist, augmented olPPARgamma-stimulated PPRE activity in HINAE olive flounder cells. Cotransfection of olPPARgamma and olRXRbeta, in the absence or presence of rosiglitazone and ciglitazone, produced a synergistic effect on PPRE transactivation in 3T3L1 adipocytes. Moreover, olPPARgamma, in the presence or absence of rosiglitazone, regulated the expression of lipid synthesis- and adipogenesis-related proteins in NIH3T3 and 3T3L1 cells. Taken together, these results suggest that olPPARgamma is functionally and evolutionarily conserved in olive flounder and mammals.

Identification of softness syndrome-associated candidate genes and DNA sequence variation in the sea squirt, Halocynthia roretzi.

The mortality of sea squirts, Halocynthia roretzi, with softness syndrome threatens the sea squirt aquaculture industry in Asian countries. The molecular approach to understanding the pathogenesis of softness syndrome began with differential gene expression analysis of tissues from normal and dying organisms. In the present study, we show that the expression of Halocynthia roretzi metalloproteinase (HrMMP) was significantly upregulated in the tissues of dying organisms through screening of differentially expressed genes, reverse transcription-polymerase chain reaction (RT-PCR), and real-time PCR. HrMMP is composed of 482 amino acids, contains a conserved domain found in the astacin family, and has typical metalloproteinase activity. To discriminate between the differential expression of the HrMMP gene in normal and dying organisms, we cloned the HrMMP gene promoter and identified a polymorphism in the HrMMP promoter region that resulted in distinct polymorphisms (G/T) at position - 308 bp. These results suggest that organisms with the GT genotype may have more resistance to softness syndrome than those with the TT genotype. These findings suggest that the HrMMP promoter polymorphism may be associated with an increased risk of softness syndrome in cultivated sea squirts and should be evaluated as a candidate molecular marker for the selective breeding of softness syndrome-resistant sea squirts.

Generation of expressed sequence tags for immune gene discovery and marker development in the sea squirt, Halocynthia roretzi.

Expresssed sequence tag (EST) analysis was developed from three cDNA libraries constructed from cells of the digestive tract, gonad, and liver of sea squirt. Randomly selected cDNA clones were partially sequenced to generate a total of 922 ESTs, in which 687 unique ESTs were identified respectively. Results of BLASTX search showed that 612 ESTs (89%) have homology to genes of known function whereas 75 ESTs (11%) were unidentified or novel. Based on the major function of their encoded proteins, the identified clones were classified into ten broad categories. We also identified several kinds of immune-related genes as identifying novel genes. Sequence analysis of ESTs revealed the presence of microsatellite-containing genes that may be valuable for further gene mapping studies. The accumulation of a large number of identified cDNA clones is invaluable for the study of sea squirt genetics and developmental biology. Further studies using cDNA microarrays are needed to identify the differentially expressed transcripts after disease infection.

Phosphorylation of the large subunit of replication factor C is associated with adipocyte differentiation.

Adipocyte differentiation is an ordered multistep process requiring the sequential activation of several groups of adipogenic transcription factors, including CCAAT/enhancer-binding protein-alpha and peroxisome proliferator-activated receptor-gamma, and coactivators. Here we show that replication factor C 140, which was known to act as a coactivator for CCAAT/enhancer-binding protein-alpha in our previous study, was phosphorylated on the proliferating cell nuclear antigen-bindng domain during the adipocyte differentiation process. Calmodulin-dependent protein kinase II was responsible for phosphorylating replication factor C 140 in the process of adipocyte differentiation. Ser518 of replication factor C 140 was identified as a major target of calmodulin-dependent protein kinase II phosphorylation in vitro. Calmodulin-dependent protein kinase II inhibitor attenuated phosphorylation of replication factor C 140 by differentiation inducers and blocked replication factor C 140-derived transcriptional activation. Taken together, these findings demonstrate that calmodulin-dependent protein kinase II signaling leads the cooperative transactivation of CCAAT/enhancer-binding protein-alpha and replication factor C 140 through an increase in replication factor C 140 phosphorylation, and subsequently enhances the transcriptional activation of target genes involved in adipocyte differentiation.

Hepatitis B virus X increases immune cell recruitment by induction of chemokine SDF-1.

Hepatitis B virus X protein is a major factor in the HBV-induced disease developments. Stromal cell-derived factor-1 is a small cytokine that is strongly chemotactic for lymphocytes. We explored the role of HBx on recruitment of HBV-induced virus-nonspecific immune cells into liver. Immune cell recruitment and SDF-1 expression level significantly increased in livers of HBx-transgenic mice and X-box binding protein-1 significantly increased SDF-1 gene expression. Finally, we confirmed that immune cell recruitment into liver tissues of HBx-TG mice was diminished by a chemokine receptor antagonist. Therefore, HBx increases ER stress-dependent SDF-1 expression and induces HBV-induced immune cell recruitment into liver.