Enumeration of the simian virus 40 early region elements necessary for human cell transformation

While it is clear that cancer arises from the accumulation of genetic mutations that endow the malignant cell with the properties of uncontrolled growth and proliferation, the precise combinations of mutations that program human tumor cell growth remain unknown. The study of the transforming proteins derived from DNA tumor viruses in experimental models of transformation has provided fundamental insights into the process of cell transformation. We recently reported that coexpression of the simian virus 40 (SV40) early region (ER), the gene encoding the telomerase catalytic subunit (hTERT), and an oncogenic allele of the H-ras gene in normal human fibroblast, kidney epithelial, and mammary epithelial cells converted these cells to a tumorigenic state. Here we show that the SV40 ER contributes to tumorigenic transformation in the presence of hTERT and oncogenic H-ras by perturbing three intracellular pathways through the actions of the SV40 large T antigen (LT) and the SV40 small t antigen (ST). LT simultaneously disables the retinoblastoma (pRB) and p53 tumor suppressor pathways; however, complete transformation of human cells requires the additional perturbation of protein phosphatase 2A by ST. Expression of ST in this setting stimulates cell proliferation, permits anchorage-independent growth, and confers increased resistance to nutrient deprivation. Taken together, these observations define the elements of the SV40 ER required for the transformation of human cells and begin to delineate a set of intracellular pathways whose disruption, in aggregate, appears to be necessary to generate tumorigenic human cells.     

Two light-responsive elements of pea chloroplastic fructose-1,6-bisphosphatase gene involved in the red-light-specific gene expression in transgenic tobaccos

The pea chloroplast fructose-1,6-bisphosphatase (FBPase) gene was cloned from a pea genomic library and sequenced. The gene contained three introns and four exons. Both in vitro and in vivo analyses of the promoter region of the gene were carried out simultaneously to elucidate the mechanisms of light-mediated gene expression. Two light-responsive elements were identified in gel mobility shift assays: a GT-1-like sequence for the binding of a GT-1-like factor (termed pea factor 1; PF1) and a binding site for a dark-specific factor (termed pea factor 2; PF2). The binding affinity of PF1 was higher in light-grown peas than in dark-grown peas and was affected by phosphorylation. The binding site was located at nucleotides (nt) -326 to -341. PF2 binding was dark-specific and the binding region was located upstream of the PF1-binding site (nt -492 to -412). In vivo experiments with transgenic tobacco plants suggested that the region between nt -411 and -272 contained a PF1-binding site that promoted light-mediated expression of the pea chloroplast FBPase. In contrast, the 81-bp region between nt -492 and -412, which is located further upstream than the PF1-binding site, negatively regulated light-mediated expression of FBPase. Moreover, activation of gene expression by the region (nt -411 to -272) contained a PF1-binding site that was sensitive to red-light irradiation, suggesting that the expression of the chloroplast FBPase was regulated by the phytochrome system. Interestingly, the binding region for the dark-specific factor (PF2; nt -492 to -412) not only repressed gene expression in the dark, but also acted as a light-dependent activating element of the chloroplast FBPase gene.     

Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions

MOTIVATION: Polymorphisms in human genes are being described in remarkable numbers. Determining which polymorphisms and which environmental factors are associated with common, complex diseases has become a daunting task. This is partly because the effect of any single genetic variation will likely be dependent on other genetic variations (gene-gene interaction or epistasis) and environmental factors (gene-environment interaction). Detecting and characterizing interactions among multiple factors is both a statistical and a computational challenge. To address this problem, we have developed a multifactor dimensionality reduction (MDR) method for collapsing high-dimensional genetic data into a single dimension thus permitting interactions to be detected in relatively small sample sizes. In this paper, we describe the MDR approach and an MDR software package. RESULTS: We developed a program that integrates MDR with a cross-validation strategy for estimating the classification and prediction error of multifactor models. The software can be used to analyze interactions among 2-15 genetic and/or environmental factors. The dataset may contain up to 500 total variables and a maximum of 4000 study subjects. AVAILABILITY: Information on obtaining the executable code, example data, example analysis, and documentation is available upon request. SUPPLEMENTARY INFORMATION: All supplementary information can be found at http://phg.mc.vanderbilt.edu/Software/MDR.     

Application of the C4'-alkylated deoxyribose primer system (CAPS) in allele-specific real-time PCR for increased selectivity in discrimination of single nucleotide sequence variants

This study describes a quantitative real-time PCR-based approach for discrimination of single nucleotide sequence variants, called CAPS (C4' alkylated primer system). To increase the discrimination potential of DNA polymerases against competing sequence variants of single nucleotides, 3'-terminally modified primers were designed carrying a methyl residue bound to the C4' of the thymidylate deoxyribose. In a model sequence system positional dependencies of modified thymidylate (at -1, -2, -3) were tested for their influence on discrimination. Highest discrimination factors were obtained with the modification at the ultimate 3'-position. In a comparison between Taq and Pwo DNA polymerases, substantial better results were obtained by Taq DNA polymerase. In contrast to conventional PCR methods for discrimination of sequence variants, achieving a maximum discrimination potential of about 20, CAPS is capable of obtaining sequence-specific amplifications of a desired target among discriminated templates with a dynamic range of 1:100. Therefore, CAPS is a method able to quantitatively discriminate two sequence variants only differing in a single base (e.g., SNP alleles or point mutations). The range of applications of this easy to perform, fast and reliable technique reaches from medical diagnostics, transplantation medicine, molecular and cell biology to human genetics. Targeting of SNPs assures a universal exertion of this method, since these markers are gender-independent, highly abundant and ubiquitous.     

Aptamers that recognize the lipid moiety of the antibiotic moenomycin A

Moenomycin A is an amphiphilic phosphoglycolipid antibiotic that interferes with the transglycosylation step in peptidoglycan biosynthesis. The antibiotic consists of a branched pentasaccharide moiety, connected to the moenocinol lipid via a glycerophosphate linker. We have previously described the selection of aptamers that require the lipid group and the disaccharide epitopes of the oligosaccharide moiety for moenomycin binding. Here we report that the enriched moenomycin-binding library contains sequences that evolved for specific recognition of the unpolar lipid group of the antibiotic. These results suggest that the evolution of hydrophobic binding pockets in RNA molecules may be much more common than previously assumed.     

Discovery of genes for ginsenoside biosynthesis by analysis of ginseng expressed sequence tags

Expressed sequence tags (ESTs) provide a valuable tool that can be used to identify genes in secondary metabolite biosynthesis. Ginseng (Panax ginseng C.A Meyer) is a medicinal plant that accumulates ginsenosides in roots. We sequenced 11,636 ESTs from five ginseng libraries in order to create a gene resource for biosynthesis of ginsenosides, which are thought to be the major active component in roots. Only 59% of the ginseng ESTs exhibited significant homology to previously known polypeptide sequences. Stress- and pathogen-response proteins were most abundant in 4-year-old ginseng roots. ESTs involved in ginsenoside biosynthesis were identified by a keyword search of BLASTX results and a domain search of ginseng ESTs. We identified 4 oxidosqualene cyclase candidates involved in the cyclization reaction of 2,3-oxidosqualene, 9 nine cytochrome P450 and 12 glycosyltransferse candidates, which may be involved in modification of the triterpene backbone.Abbreviations cDNA Complementary DNA - ESTs Expressed sequence tagsCommunicated by I.S. Chung     

SoFAR: software for fully automatic evaluation of real-time PCR data

Quantitative real-time PCR has proven to be an extremely useful technique in life sciences for many applications. Although a lot of attention has been paid to the optimization of the assay conditions, the analysis of the data acquired is often done with software tools that do not make optimum use of the information provided by the data. Particularly, this is the case for high-throughput analysis, which requires a careful characterization and interpretation of the complete data by suitable software. Here we present a software solution for the robust, reliable, accurate, and fast evaluation of real-time PCR data, called SoFAR. The software automatically evaluates the data acquired with the LightCycler system. It applies new algorithms for an adaptive background correction of signal trends, the calculation of the effective signal noise, the automated identification of the exponential phases, the adaptive smoothing of the raw data, and the correction of melting curve data. Finally, it provides information regarding the validity of the results obtained. The SoFAR software minimizes the time required for evaluation and increases the accuracy and reliability of the results. The software is available upon request.     

Cloning and characterization of genes encoding trehalose-6-phosphate synthase (TPS1) and trehalose-6-phosphate phosphatase (TPS2) from Zygosaccharomyces rouxii

In many organisms, trehalose protects against several environmental stresses, such as heat, desiccation, and salt, probably by stabilizing protein structures and lipid membranes. Trehalose synthesis in yeast is mediated by a complex of trehalose-6-phosphate synthase (TPS1) and trehalose-6-phosphate phosphatase (TPS2). In this study, genes encoding TPS1 and TPS2 were isolated from Zygosaccharomyces rouxii (designated ZrTPS1 and ZrTPS2, respectively). They were functionally identified by their complementation of the tps1 and tps2 yeast deletion mutants, which are unable to grow on glucose medium and with heat, respectively. Full-length ZrTPS1 cDNA is composed of 1476 nucleotides encoding a protein of 492 amino acids with a molecular mass of 56 kDa. ZrTPS2 cDNA consists of 2843 nucleotides with an open reading frame of 2700 bp, which encodes a polypeptide of 900 amino acids with a molecular mass of 104 kDa. The amino acid sequence encoded by ZrTPS1 has relatively high homology with TPS1 of Saccharomyces cerevisiae and Schizosaccharomyces pombe, compared with TPS2. Western blot analysis showed that the antibody against S. cerevisiae TPS1 recognizes ZrTPS1. Under normal growth conditions, ZrTPS1 and ZrTPS2 were highly and constitutively expressed, unlike S. cerevisiae TPS1 and TPS2. Salt stress and heat stress reduced the expression of the ZrTPS1 and ZrTPS2 genes, respectively.     

Micropropagation of calla lily (<Emphasis Type="Italic">Zantedeschia albomaculata</Emphasis>) via <Emphasis Type="Italic">in vitro</Emphasis> shoot tip proliferation

Summary A method for the micropropagation of Zantedeschia albomaculata is presented using shoot tip proliferation onto Murashige and Skoog (MS) medium supplemented with different plant growth regulator concentrations and combinations. Of the four cytokinins tested, 6-benzyladenine (BA) and thidiazuron (TDZ) were found to be more effective. An optimal concentration of BA (8.87 μM) or TDZ (4.54 μM) developed an average of 3.8 and 3.2 shoots per explant, respectively, but increasing concentrations of cytokinins often led to lower proliferation rate and stunted growth. Addition of auxins to the MS medium supplemented with 8.87 μM BA slightly enhanced multiple shoot formation in the explants. Multiplication of six cultivars of Zantedeschia genus comprising different flower types and colors were tested and achieved using only one regeneration medium (MS+8.87 μMBA+2.46 μM IBA). Different MS medium strength, air temperature (15, 20, 25, and 30°C) and light quality [fluorescent, red + blue, red and blue light provided by a LED (light-emitting diode) system] were used (without phytohormone) with the aim of stimulating in vitro shoot and root development. Half-strength MS or MS and cultures maintained at 25°C were found to be equally suitable for shoot tip culture of Z. albomaculata. Shoot elongation as well as fresh and dry weight were significantly increased when cultures were kept under red or blue light.     

Beta 1-adrenergic receptor polymorphisms confer differential function and predisposition to heart failure

Catecholamines stimulate cardiac contractility through beta(1)-adrenergic receptors (beta(1)-ARs), which in humans are polymorphic at amino acid residue 389 (Arg/Gly). We used cardiac-targeted transgenesis in a mouse model to delineate mechanisms accounting for the association of Arg389 with human heart failure phenotypes. Hearts from young Arg389 mice had enhanced receptor function and contractility compared with Gly389 hearts. Older Arg389 mice displayed a phenotypic switch, with decreased beta-agonist signaling to adenylyl cyclase and decreased cardiac contractility compared with Gly 389 hearts. Arg389 hearts had abnormal expression of fetal and hypertrophy genes and calcium-cycling proteins, decreased adenylyl cyclase and G alpha(s) expression, and fibrosis with heart failure This phenotype was recapitulated in homozygous, end-stage, failing human hearts. In addition, hemodynamic responses to beta-receptor blockade were greater in Arg389 mice, and homozygosity for Arg389 was associated with improvement in ventricular function during carvedilol treatment in heart failure patients. Thus the human Arg389 variant predisposes to heart failure by instigating hyperactive signaling programs leading to depressed receptor coupling and ventricular dysfunction, and influences the therapeutic response to beta-receptor blockade.