Genes In Various Tissues Research Articles

Estimation of an optimum intake level of epigallocatechin gallate for suppression of inflammation in type 2 diabetic GK rats

Previous studies have suggested that epigallocatechin gallate (EGCG) exerts anti‐oxidative and anti‐inflammatory actions in various tissues, which might be beneficial for reducing risks of development of diabetes. However, it is unknown whether there is an optimum intake level of EGCG. In this study, we have examined the effect of a diet containing various concentrations of EGCG on the expression of inflammation‐related genes in various tissues including visceral adipose tissue and the liver of non‐obese type‐2 diabetes animal model, Goto‐Kakizaki (GK) rats. GK rats at 5 weeks of age were fed a control high‐fat diet (45 energy% as fat) or the high‐fat diet containing 0.1%, 0.2% or 0.5% EGCG for 34 weeks. The mRNA levels of IL‐1β, IL‐18, TNF‐α and resistin were significantly reduced in the adipose tissue of rats fed a diet containing 0.1% EGCG, but not in those fed diets containing 0.2% or more EGCG, as compared with control. The mRNA levels of IL‐1β and IL‐18 in the liver of rats fed a diet containing 0.1% EGCG were also significantly lower than those in the control. These results suggest that there is an optimum range of intake of EGCG, which may suppress the expression of genes involved in inflammation in the adipose tissue and the liver.

Expression and characterization of a new valosin‐containing protein from silkworm

Abstract Valosin‐containing protein (VCP) is a type‐II adenosine triphosphatase (ATPase) wih extensive biological function in organisms. Silkworm is the second insect model for genetic studies and a bioreactor for proteinaceous drugs and biomaterials. In this paper, a new VCP‐like gene was amplified from the fat body of silkworm following genome prediction and spliced expressed sequence tag sequences, using both reverse transcription polymerase chain reaction (RT‐PCR) and 3′‐RACE (rapid amplification of complementary DNA ends) methods. Bioinformatical analysis showed that the translated amino acid sequence contained a highly conserved domain of VCPs similar to that of many insects. This domain consists of the conserved structure motifs of the ATP binding site and the catalytical center, which is closely related to the insect VCPs in a phylogenetic tree. The silkworm VCP‐like gene was successfully inserted into the plasmid and transformed into Escherichia coli cells to express VCP‐like protein with ATPase activity. The expression of silkworm VCP‐like protein was also confirmed by Western blotting and mass spectrometric analyses. Distribution of the VCP‐like gene in various tissues of the silkworm was also studied by real‐time PCR. Results showed that the messenger RNA (mRNA) of VCP‐like protein is widely expressed in fat body, reproductive organs (testis or ovary), silk gland, head, Malpighian tubule, epidermis and midgut. Among them, fat body has the highest mRNA expression level of the VCP‐like gene, while the midgut has the lowest expression level. This study provides groundwork for further study on the structure and function of the new VCP‐like protein.

Control of iron metabolism – Lessons from neonatal hemochromatosis

When hepatologists begin their investigations at the scene of liver damage, iron is certainly on the list of ‘‘usual suspects’’ to be rounded up. Hemochromatosis, a well-known cause of chronic liver disease, is the most prevalent genetic disorder in adults [1]. Serum iron parameters are therefore included in most guidelines on how to investigate patients with elevated transaminases or chronic liver disease [2]. The hemochromatosis (HFE) genotype is an important piece of evidence in patients with liver disease and elevated transferrin saturation with hyperferritinemia, because homozygosity for the C282Y allele of HFE is considered sufficient to diagnose hemochromatosis under these circumstances [1]. Compound heterozygosity for C282Y and H63D has been almost removed from the watch-list and is currently considered a mere risk factor for liver diseases – sufficient to cause hemochromatosis or even cirrhosis only in combination with other health burdens. Hence, a partner in crime for HFE mutation must be found in patients with liver disease and C282Y/H63D compound heterozygosity [3]. If there is evidence for iron overload in the absence of hemochromatosis-associated HFE genotypes and the hepatopathologist finds iron confined to hepatocytes, sharp investigators are well advised to search for the culprit in the genes encoding transferrin receptor 2 (TFR2) and ferroportin (SLC40A1) or even to hunt for combined mutations in these genes if a patient presents with severe iron overload or early-onset disease [4]. If the patient is adolescent or before the 3rd decade of life and presents with heart failure or hypogonadism in addition to – often overlooked – liver disease, other genes will be committed in custody. Mutations in HJV and HAMP, which respectively encode hemojuvelin and hepcidin, will be sufficient to identify juvenile hemochromatosis [5]. Through the power of genetics, iron-related diseases are now subject to close scrutiny. In addition, genetic studies have greatly advanced our understanding of hemochromatosis. This progress is reflected in the proposed re-classification of human iron

Abstract P346: Regulation of GRK5 in Myocytes Is Mediated by Nuclear Transcription Factor [ê]B: A New Clue in Heart Disease

G protein coupled receptor kinase-5 (GRK5) plays a key role in the heart and it’s expression is increased in heart failure. Moreover, a human mutation within its amino-terminus appears to play a role in therapeutic responses to β-blockers in heart failure patients. Nuclear transcription factor kappa B (NF-κB), a ubiquitous transcription factor, is involved in the regulation of numerous genes in various tissues and activation of NF-κB has also been shown to be associated with heart disease. Here, we investigated the role of NF-κB signaling in the regulation of the GRK5 gene and GRK5 expression in neonatal rat ventricular myocytes (NRVMs). In analyzing the 5’-flanking DNA of GRK5 , the presence of a potential NF-κB binding site was observed in the promoter. Phorbol myristate acetate (PMA), a known stimulator of NF-κB, increased the levels of GRK5 in NRVMs. Conversely, treatment of NRVMs with N-acetyl cysteine (NAC), a known inhibitor of NF-κB, decreased the levels of GRK5 compared to control cells. Utilizing electrophoretic mobility shift assay (EMSA) with nuclear extracts from NRVMs treated with or without PMA, it was found that proteins bound to the GRK5 promoter containing the putative NF-κB binding site. When an antibody specific for NF-κB was utilized, a super-shift of the proteins binding to the putative NF-κB binding site was observed. Furthermore, interaction of NF-κB with GRK5 was confirmed by shift Western blot. Chromatin immunoprecipitation (ChIP) showed dynamic recruitment of both p50 and p65 to the NF-κB site of GRK5 promoter after treatment of NRVMs with PMA. Treatment of myocytes with siRNA and subsequent knock-down of NF-κB p65 decreased the levels of GRK5 as judged by real time quantitative PCR. Finally, adenovirus mediated overexpression of a dominant negative IκB-α in NRVMs inhibited the levels of GRK5. Taken together, our present studies suggest that NF-κB plays a potential role in the regulation of GRK5 transcription in myocytes and this may translate to key expressional changes seen in heart disease.

Stimulating the immune response of Litopenaeus vannamei using the phagocytosis activating protein ( PAP) gene

High mortality in the shrimp farming industry is caused by several pathogens such as white spot syndrome virus (WSSV), yellow head virus (YHV) and Vibrio harveyi ( V. harveyi). A PAP (Phagocytosis activating protein) gene able to activate phagocytosis of shrimp hemocytes was cloned into the eukaryotic expression vector phMGFP. In vitro expression was confirmed by transfection of PAP-phMGFP into CHO (Chinese Hamster Ovary) cells and the expression of the Green Fluorescent Protein (GFP) was observed. In order to activate the phagocytic activity of shrimp, 20, 40 and 80 μg/shrimp of this PAP-phMGFP vector were injected into Litopenaeus vannamei muscle. After challenged with WSSV, 40 μg/shrimp produced the highest relative percent survival (77.78 RPS). Analysis for the expression of the GFP gene in various tissues showed the expression mostly in the hemolymph of the immunized shrimp. The expression level of PAP and proPO ( Prophenoloxidase) gene were highest at 7 days after immunization. This agreed with the efficiency of protection against WSSV that also occurred 7 days after immunization with the highest RPS of 86.61%. However there was no protection 30 days after immunization. Hemocytes of shrimp injected with PAP-phMGFP had 1.9 folds and 3 folds higher percentage phagocytosis and phagocytic index than the shrimp injected with PBS. Accordingly, copies of WSSV reduced in the PAP-phMGFP injected shrimp. In addition, PAP-phMGFP also protected shrimp against several pathogens: WSSV, YHV and V. harveyi, with RPS values of 86.61%, 63.34% and 50% respectively. This finding shows that the immune cellular defense mechanisms in shrimp against pathogens can be activated by injection of PAP-phMGFP and could indicate possible useful ways to begin to control this process.

DNA methylation analyses of the connexin gene family reveal silencing of GJC1 (Connexin45) by promoter hypermethylation in colorectal cancer

Gap junctions are specialized plasma membrane domains consisting of channels formed by members of the connexin protein family. Gap junctional intercellular communication is often lost in cancers due to aberrant localization or downregulation of connexins, and connexins are therefore suggested to act as tumor suppressor genes in various tissues. The aim of this study was to investigate the expression pattern and DNA promoter methylation status of connexins in colorectal cancer. Expression of six (GJA1, GJA9, GJB1, GJB2, GJC1 and GJD3) connexin genes was detected in normal colonic tissue samples. GJC1 expression was reduced in colorectal carcinomas compared to normal tissue samples. All analyzed connexins were hypermethylated in colon cancer cell lines, although at various frequencies. GJA4, GJB6 and GJD2 were hypermethylated in 60% (29/48), 25% (12/48) and 96% (46/48) of primary colorectal carcinomas, respectively. However, the methylation status was not associated with gene expression. GJC1 has two alternative promoters, which were methylated in 42% (32/76) and 38% (25/65) of colorectal tumors, and in none of the normal mucosa samples. Expression of GJC1 was significantly lower in methylated compared with unmethylated samples (p < 0.01) and was restored in cell lines treated with the demethylating drug 5-aza-2'deoxycytidine. Taken together, DNA hypermethylation of the promoter region of GJC1, encoding connexin45, is an important mechanism in silencing gene expression in colorectal cancer.

Vertebrate Paralogous MEF2 Genes: Origin, Conservation, and Evolution

BackgroundThe myocyte enhancer factor 2 (MEF2) gene family is broadly expressed during the development and maintenance of muscle cells. Although a great deal has been elucidated concerning MEF2 transcription factors' regulation of specific gene expression in diverse programs and adaptive responses, little is known about the origin and evolution of the four members of the MEF2 gene family in vertebrates.Methodology/Principal FindingsBy phylogenetic analyses, we investigated the origin, conservation, and evolution of the four MEF2 genes. First, among the four MEF2 paralogous branches, MEF2B is clearly distant from the other three branches in vertebrates, mainly because it lacks the HJURP_C (Holliday junction recognition protein C-terminal) region. Second, three duplication events might have occurred to produce the four MEF2 paralogous genes and the latest duplication event occurred near the origin of vertebrates producing MEF2A and MEF2C. Third, the ratio (Ka/Ks) of non-synonymous to synonymous nucleotide substitution rates showed that MEF2B evolves faster than the other three MEF2 proteins despite purifying selection on all of the four MEF2 branches. Moreover, a pair model of M0 versus M3 showed that variable selection exists among MEF2 proteins, and branch-site analysis presented that sites 53 and 64 along the MEF2B branch are under positive selection. Finally, and interestingly, substitution rates showed that type II MADS genes (i.e., MEF2-like genes) evolve as slowly as type I MADS genes (i.e., SRF-like genes) in animals, which is inconsistent with the fact that type II MADS genes evolve much slower than type I MADS genes in plants.ConclusionOur findings shed light on the relationship of MEF2A, B, C, and D with functional conservation and evolution in vertebrates. This study provides a rationale for future experimental design to investigate distinct but overlapping regulatory roles of the four MEF2 genes in various tissues.

Cloning and expression analysis of a ubiquitin gene (Ub L40 ) in the haemocytes of Crassostrea hongkongensis under bacterial challenge

Ubiquitin, a highly conserved stress-related protein, is assigned multiple functions, such as DNA processing, protein degradation, and ribosome synthesis. The Crassostrea hongkongensis ubiquitin gene (designated ChUbL40) was cloned by a combination of suppressive subtractive hybridization (SSH) and rapid amplification of cDNA ends (RACE). The full-length cDNA of ChUbL40 is 496 bp in length, consisting of a 5' untranslated region (UTR) of 34 bp, a 3'-UTR of 75 bp and an open reading frame of 387 bp encoding a ubiquitin fusion protein of 128 amino acids. Analysis of the amino acid sequence of ChUbL40 reveals that UbL40 is highly conservative during evolution. The expression patterns of ChUbL40 gene in various tissues were examined by real-time PCR. The expression level of ChUbL40 in haemocytes is down-regulated at 4 h and gradually returned to its original level from 6 h to 24 h after Vibrio alginolyticus challenge. Our results suggest that ChUbL40 is ubiquitously expressed and plays an important role in immune defense against bacterial challenge.

Molecular characterization and tissue-specific expression of invariant chain in the muscovy duck (Cairina moschata)

The invariant chain (Ii) plays an important role as a chaperone for MHC II maturation and facilitates antigen presentation in vertebrates. We cloned, characterized and made a homology analysis of healthy adult muscovy duck Ii (MDIi), from a poultry farm in the suburban district of Hefei city in China, by rapid amplification of cDNA ends (RACE)-PCR and by measuring expression of the MDIi gene in various tissues by real-time quantitative PCR. A full-length cDNA sequence of MDIi was obtained, 1188-bp long, encoding a 222-amino acid protein. A comparison of the amino acid sequence of Ii between muscovy duck and other birds showed high similarity (66.3-95.3%). Characteristic functional domains found in Ii of other species, such as cytoplasmic domain, transmembrane domain, class II-associated Ii-derived peptide (CLIP) and trimerization domain, were identified in MDIi. Although all functional domains of Ii were found to be highly conserved, small differences in the CLIP sequence occur among the various species. Expression of MDIi was detected in all tissues at different levels. A higher expression level was found in the spleen, intestinal mucosa and the bursa stipe (bursa of Fabricius stipe) than other tissues. This tissue-specific expression suggests that MDIi plays an essential role in all tissues and differential expression may be a function of the innate structures and essential functions of these tissues.

Effects of dietary cadmium exposure on tissue-specific cadmium accumulation, iron status and expression of iron-handling and stress-inducible genes in rainbow trout: Influence of elevated dietary iron

Recent evidences suggest that dietary cadmium (Cd) uptake likely occurs via the dietary iron (Fe) uptake pathway in freshwater fish, at least in part. The present study investigated the interactive effects of dietary Cd and Fe in juvenile rainbow trout ( Oncorhynchus mykiss). Fish were treated for four weeks with four different diets: normal Fe, high Fe, normal Fe plus Cd, and high Fe plus Cd. Physiological parameters, tissue-specific Fe and Cd level, plasma Fe status, and tissue-specific mRNA expression of transferrin, metallothioneins (MT-A and MT-B) and heat shock proteins 70 (HSP70a and HSP70b) were analyzed. Exposure to dietary Cd increased Cd burden in the following order: intestine > kidney > stomach > liver > gill > carcass. Interestingly, high dietary Fe reduced Cd accumulation in the stomach and intestine as well as in the wholebody of fish. Dietary Cd increased hepatic transferrin mRNA expression and total Fe binding capacity in the plasma, indicating the effect of Cd on Fe handling in fish. The mRNA expression of MTs and HSP70s was also increased in various tissues following dietary Cd exposure, however the response profile of different MT and HSP70 genes was not consistent among different tissues. In general, MT-A was more responsive to Cd exposure in the intestine and liver, whereas MT-B was more responsive in the kidney. Similarly, HSP70a expression was more sensitive to Cd exposure than HSP70b, particularly in the intestine. Interestingly, high Fe diet suppressed Cd-induced induction of transferrin, MT and HSP70 genes in various tissues. Overall, our study suggests that elevated dietary Fe can reduce Cd accumulation and ameliorate Cd-induced stress responses in freshwater fish.

Quantitative profiling of mRNA expression of glutathione S‐transferase superfamily genes in various tissues of bighead carp (Aristichthys nobilis)

The expression of glutathione S-transferase (GST) is a crucial factor in determining the sensitivity of cells and organs in response to a variety of toxicants. In this study, we cloned the core nucleotide of alpha, kappa, mu, mGST, pi, rho, and theta-like GST genes from bighead carp (Aristichthys nobilis). Their derived amino acid sequences were clustered with other vertebrate GSTs in a phylogenetic tree, and the bighead carp GST sequences have the highest similarity with those from common carp and zebrafish. We quantified the constitutive mRNA transcription of GST isoforms in eight different tissues (liver, kidney, spleen, intestine, muscle, heart, brain, and gill). The information obtained from the present study could be distilled into a few generalized principles: multiple GST isoenzymes were ubiquitously expressed in all tissues; majority of GSTs had high constitutive expression in intestine, liver, and kidney. These findings are in agreement with the roles of these tissues in xenobiotic metabolism. At the same time, some unique findings were detected in the current experiment: (1) higher expression of most GSTs was observed in spleen; (2) the expression of GST pi was highest in almost all the studied tissues except muscle; the other two isoforms, GST alpha and rho, were also highly expressed in liver, kidney, intestine, spleen, heart, and brain of bighead carp. All these results strongly imply an important role of these GST isoforms in detoxification of ingested xenobiotics.

Silencing MR-1 attenuates inflammatory damage in mice heart induced by AngII

Myofibrillogenesis regulator-1(MR-1) can aggravate cardiac hypertrophy induced by angiotensin(Ang) II in mice through activation of NF-κB signaling pathway, and nuclear transcription factor (NF)-κB and activator protein-1(AP-1) regulate inflammatory and immune responses by increasing the expression of specific inflammatory genes in various tissues including heart. Whether inhibition of MR-1 expression will attenuate AngII-induced inflammatory injury in mice heart has not been explored. Herein, we monitored the activation of NF-κB and AP-1, together with expression of pro-inflammatory of interleukin(IL)-6, tumor necrosis factor(TNF)-α, vascular-cell adhesion molecule (VCAM)-1, platelet endothelial cell adhesion molecule (PECAM), and inflammatory cell infiltration in heart of mice which are induced firstly by AngII (PBS),then received MR-1-siRNA or control-siRNA injecting. We found that the activation of NF-κB and AP-1 was inhibited significantly, together with the decreased expression of IL-6, TNF-α, VCAM-1, and PECAM in AngII-induced mice myocardium in MR-1-siRNA injection groups compared with control-siRNA injecting groups. However, the expression level of MR-1 was not an apparent change in PBS-infused groups than in unoperation groups, and MR-1-siRNA do not affect the expression of MR-1 in PBS-infused mice. Our findings suggest that silencing MR-1 protected mice myocardium against inflammatory injury induced by AngII by suppression of pro-inflammatory transcription factors NF-κB and AP-1 signaling pathway.

Time course of expression of the retinoid X receptor gene and induction of imposex in the rock shell, Thais clavigera, exposed to triphenyltin chloride

To examine the role of the retinoid X receptor (RXR) in the development of imposex in gastropods, we investigated the time course of expression of the RXR gene in various tissues (ctenidium, ovary or testis, digestive gland, penis-forming area or penis, and head ganglia) of female and male rock shells (Thais clavigera) exposed to triphenyltin (TPT) in a flow-through exposure system for 3 months. Accumulations of TPT in tissues were clearly observed in exposed individuals, whereas no accumulation of TPT was observed in the control groups. In females, 3-month exposure to TPT resulted in the development of imposex, and penis lengths in imposex-exhibiting females were significantly longer in small females (shell height <20 mm) than in large females (shell height > or = 20 mm). RXR gene expression in the ovary, penis-forming area or penis, and head ganglia of females exposed for 3 months was significantly higher than expression in control females, and the highest RXR gene expression was found in the penis-forming area or penis. Moreover, RXR gene expression in the penis-forming area or penis of each female exposed to TPT seemed to be associated with an increase in penis length. In males, the ratio of penis length to shell height was significantly larger in the exposed groups than in the controls. Although RXR gene expression in males exposed for 3 months was not significantly higher than expression in control males in any tissues, the highest gene expression was observed in the penis of exposed males. These results suggest that RXR plays an important role in the development of male genitalia (i.e., penis and vas deferens) in gastropods, although RXR might also have other physiological functions.

Expression of Critical Lignin Metabolism Genes in Flax (&lt;I&gt;Linum usitatissimum&lt;/I&gt;)

Flax (Linum usitatissimum) is an important bast fiber crop. High lignin content in the flax fiber greatly affects the per- formance and quality in the flax textile industry. CCoAOMT1, 4CL1, 4CL2, COMT, F5H1, F5H2, and F5H3 are putative genes coding the key enzymes involved in lignin accumulation. The expression patterns of these genes were analyzed by semi-quantitative RT-PCR in different flax tissues and in xylem and phloem (bark) at different development stages of the variety Baihua. The results revealed that all genes were detected to express in seedlings, roots, florescent xylem, florescent phloem, leaves, flowers, and young fruits excluding F5H1 in roots. Expression of CCoAOMT1 was consistently high in all the tissues detected. There existed complementary expression between two 4CL genes and among the three F5H genes in various tissues. In the phloem, all genes lowly expressed except for 4CL2 at florescence and highly expressed after flowering. The expression of 4CL1 was high, and that of F5H3 was low in the phloem at all stages compared with that of other genes. In the xylem, expression of 4CL1 gene was low at all the developing stages, that of F5H1 reached a peak before flowering and that of the other genes in the xylem reached the highest at 30 d after emergence of seedlings and gradually declined at late growing stages, with a sharp de- crease to very lower level after flowering. The expression of 4CL1compared with other genes was significantly higher in phloem

Visfatin gene expression in chickens is sex and tissue dependent

The present study investigated the expression of visfatin mRNA in various tissues of male and female broiler chickens. We also studied the effect of leptin, cerulenin, and food deprivation, known effectors of energy balance and insulin action, on visfatin gene expression in chickens. Using reverse transcription polymerase chain reaction (RT-PCR) and Northern blot analysis, we detected chicken visfatin mRNA transcript in the kidney, hypothalamus, gizzard, liver, pancreas, proventriculus, breast and leg muscle, ovary, testis, lung, intestine, adipose tissue, and heart. Expression of the visfatin gene in various tissues of male and female chickens was determined by real-time quantitative PCR and found to be tissue and sex dependent. In both sexes, compared to other tissues, the visfatin gene is highly expressed in the muscle. Females exhibited greater ( P < 0.001) abundance of visfatin mRNA in adipose tissue compared to males, whereas compared to females, males showed greater ( P < 0.05) visfatin mRNA abundance in the kidney. Also, the regulation of visfatin gene expression by leptin, cerulenin, and food deprivation is tissue specific. Leptin decreased ( P < 0.05) visfatin mRNA abundance in the liver and hypothalamus, but not in muscle. In contrast, cerulenin increased ( P < 0.01) visfatin gene expression in the liver and in muscle, but not in the hypothalamus. Interestingly, visfatin mRNA levels increased ( P < 0.05) in the liver after 24-h food deprivation, but not in muscle or in the hypothalamus of genetically selected fat and lean line chickens. Our results showed that the visfatin gene is ubiquitously expressed in chickens with greater abundance in muscle, and that it is regulated in a tissue-specific manner by energy balance–related factors.

Differential CpG island methylation of murine adenine nucleotide translocase genes

Adenine nucleotide translocase (Ant) mediates the exchange of ADP and ATP across the inner mitochondrial membrane in eukaryotes. Mice possess three distinct but highly homologous Ant isoforms, encoded by independent genes, whose transcription depends upon tissue type . Ant1 is expressed selectively in heart and skeletal muscles, Ant2 is ubiquitously expressed in most tissues but lower in skeletal muscle and testis, while Ant4 is exclusively expressed in the testis. Of interest, each of these Ant genes contains CpG islands in their proximal promoter regions. We investigated the methylation status of the three Ant genes in various tissues with active and inactive transcription. In contrast to the Ant4 gene in which CpG island methylation is essential for gene repression, the CpG islands of Ant1 and Ant2 are hypomethylated regardless of the gene expression status throughout the tissues of male mice. Despite the tissue specific expression profile of Ant1, CpG methylation is unlikely involved in the regulation of the gene. Consistent with these findings, addition of a CpG-demethylating agent, 5-aza-2′-deoxycitidine, to fibroblasts increased the expression of Ant4 but not Ant1 or Ant2 genes. This study provides insight regarding the differential regulation of Ant isoforms in mammals, whereby both the Ant1 and Ant2 genes are capable of expression, but the Ant4 gene is completely repressed throughout somatic tissues. To the best of our knowledge, this is a first example to clearly demonstrate a differential usage of CpG island methylation within a family of genes.

Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification

BackgroundLarge-scale compilation of gene expression microarray datasets across diverse biological phenotypes provided a means of gathering a priori knowledge in the form of identification and annotation of bimodal genes in the human and mouse genomes. These switch-like genes consist of 15% of known human genes, and are enriched with genes coding for extracellular and membrane proteins. It is of interest to determine the prediction potential of bimodal genes for class discovery in large-scale datasets.ResultsUse of a model-based clustering algorithm accurately classified more than 400 microarray samples into 19 different tissue types on the basis of bimodal gene expression. Bimodal expression patterns were also highly effective in differentiating between infectious diseases in model-based clustering of microarray data. Supervised classification with feature selection restricted to switch-like genes also recognized tissue specific and infectious disease specific signatures in independent test datasets reserved for validation. Determination of "on" and "off" states of switch-like genes in various tissues and diseases allowed for the identification of activated/deactivated pathways. Activated switch-like genes in neural, skeletal muscle and cardiac muscle tissue tend to have tissue-specific roles. A majority of activated genes in infectious disease are involved in processes related to the immune response.ConclusionSwitch-like bimodal gene sets capture genome-wide signatures from microarray data in health and infectious disease. A subset of bimodal genes coding for extracellular and membrane proteins are associated with tissue specificity, indicating a potential role for them as biomarkers provided that expression is altered in the onset of disease. Furthermore, we provide evidence that bimodal genes are involved in temporally and spatially active mechanisms including tissue-specific functions and response of the immune system to invading pathogens.

Role of HNF-1α and HNF-1β on insulin, IGF-1 and other potential target genes

Hepatocyte nuclear factor (HNF)-1α and HNF-1β are transcription factors that regulate many target genes in various tissues including liver, pancreas and kidney. Heterozygous mutations in the HNF-1α and HNF-1β genes result in maturity-onset diabetes of the young (MODY)3 and MODY5, respectively. The discovery of these ‘hepatocyte nuclear factors’ as MODY-responsible genes provided a breakthrough in the field of diabetes. Patients with HNF-1α and HNF-1β mutations, as well as their model mice, show impaired pancreatic β-cell function. The mechanism of impaired β-cell function and the target genes has been intensively investigated by considerable in vitro and in vivo studies. The insulin gene is one of the target genes of HNF-1α and HNF-1β in the β-cells, and may contribute to the diabetes. The IGF-1 gene is also regulated by HNF-1α and HNF-1β, and its decreased expression may contribute to growth failure and impaired β-cell proliferation. Mutations in HNF-1β result in symptoms in multiple organs, including kidney and liver, and several target genes have been reported to be involved in the pathogenesis. HNF-1α and HNF-1β may be one of the master regulators of hepatocyte and islet transcription, and further investigations by microarray and genome-scale analyses are providing information for the better understanding of the complex transcriptional network involving HNF-1α and -1β.

Analysis of Rice OsPLD3 and OsPLD4 Genes and Promoters

Phospholipase Ds (PLDs) are present in many plants. PLDs catalyze the hydrolysis of phospholipids (e.g. phosphatidylcholine) in cell membrane into phosphatidic acid (PA) and polar free heads (e.g. choline). Two PLD members from rice, OsPLD3 and OsPLD4, were studied by reverse genetics approach. The results showed that the promoters of OsPLD3 and OsPLD4 could drive the expression of the reporter gene in various tissues of the rice flower organs at different levels. The expression of both genes was induced by wounding and by applying methyl jasmonate (MeJA) but with different intensity at different time intervals. No prominent phenotypes were observed by RNA interference with gene-specific artificial miRNAs strategy or overexpression of the target genes in rice plants implying the functional redundancy among different members of the rice PLD family.

Gonadotropin-releasing hormone receptor ( GnRHR) gene expression is differently modulated in gender types of the hermaphroditic fish Kryptolebias marmoratus by endocrine disrupting chemicals

Gonadotropin-releasing hormone (GnRH) plays a pivotal role in the regulation of reproduction in vertebrates through interaction with a specific receptor. The GnRH-stimulated gonadotropin synthesis and release are regulated by the GnRH receptors (GnRHRs). In this study, we have identified a GnRH receptor ( GnRHR) gene from the hermaphroditic fish Kryptolebias marmoratus. K. marmoratus GnRHR showed typical vertebrate GnRHR domains and motifs, and its cDNA contained 1634 bp including an open reading frame (ORF) of 1263 bp encoding a putative protein of 420 amino acids. To analyze expression patterns of GnRHR gene in various tissues and developmental stages of K. marmoratus, we carried out quantitative real-time reverse transcriptase polymerase chain reaction (RT-PCR). The K. marmoratus GnRHR gene expression was detected in all the tissues of adult fish with highest level in brain and gonad. The expression of K. marmoratus GnRHR mRNA increased from stage 1 (2 day post fertilization, dpf) to stage 4 (12 dpf) but steeply decreased at hatching stage (stage 5). Expression of K. marmoratus GnRHR after exposure to endocrine-disrupting chemicals such bisphenol A (BPA, 600 μg/L for 96 h) and 4- tert-octylphenol (OP, 300 μg/L for 96 h) in hermaphrodites as well as secondary males was highly up-regulated in almost all the tissues. Another EDC, 4-nonylphenol (NP, 300 μg/L for 96 h) showed no consistent response. 17β-estrodiol (E2, 100 ng/L for 96 h), a known natural estrogen, suppressed expression of GnRHR in most of the tissues from hermaphrodites as well as secondary males. Tamoxifen (TMX, 10 μg/L), an estrogen antagonist, on the other hand, caused upregulation of GnRHR expression in the liver of hermaphrodites and the gonad and liver of secondary males. This is the first report of a GnRHR gene from K. marmoratus and modulation of its expression by EDCs. This study provides an insight into the molecular mechanism of endocrinological functions of this unique fish.