Real-time PCR based on SYBR-Green I fluorescence: an alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions

Macrophage migration inhibitory factor contributes to host defense against acute Trypanosoma cruzi infection

Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine that is involved in the host defense against several pathogens. Here we used MIF-/- mice to determine the role of endogenous MIF in the regulation of the host immune response against Trypanosoma cruzi infection. MIF-/- mice displayed high levels of blood and tissue parasitemia, developed severe heart and skeletal muscle immunopathology, and succumbed to T. cruzi infection faster than MIF+/+ mice. The enhanced susceptibility of MIF-/- mice to T. cruzi was associated with reduced levels of proinflammatory cytokines, such as tumor necrosis factor alpha, interleukin-12 (IL-12), IL-18, gamma interferon (IFN-gamma), and IL-1beta, in their sera and reduced production of IL-12, IFN-gamma, and IL-4 by spleen cells during the early phase of infection. At all time points, antigen-stimulated splenocytes from MIF+/+ and MIF-/- mice produced comparable levels of IL-10. MIF-/- mice also produced significantly less Th1-associated antigen-specific immunoglobulin G2a (IgG2a) throughout the infection, but both groups produced comparable levels of Th2-associated IgG1. Lastly, inflamed hearts from T. cruzi-infected MIF-/- mice expressed increased transcripts for IFN-gamma, but fewer for IL-12 p35, IL-12 p40, IL-23, and inducible nitric oxide synthase, compared to MIF+/+ mice. Taken together, our findings show that MIF plays a role in controlling acute T. cruzi infection.

Structural variation in the human genome

The first wave of information from the analysis of the human genome revealed SNPs to be the main source of genetic and phenotypic human variation. However, the advent of genome-scanning technologies has now uncovered an unexpectedly large extent of what we term 'structural variation' in the human genome. This comprises microscopic and, more commonly, submicroscopic variants, which include deletions, duplications and large-scale copy-number variants - collectively termed copy-number variants or copy-number polymorphisms - as well as insertions, inversions and translocations. Rapidly accumulating evidence indicates that structural variants can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility.

Carbohydrate components of Taenia crassiceps metacestodes display Th2-adjuvant and anti-inflammatory properties when co-injected with bystander antigen

Common helminth infections promote Th2-skewed immune responses in their hosts. We have studied the role of intact carbohydrate structures on Taenia crassiceps compounds in the induction of biased type 2 and anti-inflammatory immune responses on peptide-stimulated T cells by using DO11.10 transgenic (OVA Tg) mice. While OVA Tg mice co-injected with OVA peptide (323-339) (OVA(323-339)) plus intact Taenia soluble antigens (iTSA) displayed significantly higher titers of OVA-specific IgG1 and total IgE, low amounts of these antibodies were detectable in sera from OVA Tg mice co-injected with OVA(323-339) plus periodate-carbohydrate altered TSA (paTSA). Spleen cells from OVA Tg mice failed to efficiently produce OVA-specific IFN-gamma but displayed higher IL-4, IL-5 and IL-10 production when they received OVA(323-339) plus iTSA, compared with OVA Tg mice similarly co-injected with OVA(323-339) plus paTSA. Moreover, after in vivo stimulation with OVA(323-339) plus iTSA, spleen cells did show elevated mRNA transcripts for Arginase 1, Ym1, IL-4, IL-10, TGF-beta, and Mannose Receptor (MR) genes, all them associated with Th2-type and anti-inflammatory responses. Similar results were obtained using TLR4 mutant mice. Together these findings suggest that carbohydrate components in TSA are involved in modulating immune responses to bystander antigens and that do not signal via TLR4.

Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples

Due to the advanced development of fluorogenic chemistry, quantitative real-time polymerase chain reaction (qRT-PCR) has become an emerging technique for the detection and quantification of microorganisms in the environment. Compared with the conventional hybridization- and PCR-based techniques, qRT-PCR not only has better sensitivity and reproducibility, but it is also quicker to perform and has a minimum risk of amplicon carryover contamination. This article reviews the principle of this emerging technique, its detection reagents, target DNAs, quantification procedures, and affecting factors. The applications of qRT-PCR for the quantification of microorganisms in the environment are also summarized.

Development of a human mitochondria-focused cDNA microarray (hMitChip) and validation in skeletal muscle cells: implications for pharmaco- and mitogenomics

Mitochondrial research has influenced our understanding of human evolution, physiology and pathophysiology. Mitochondria, intracellular organelles widely known as 'energy factories' of the cell, also play fundamental roles in intermediary metabolism, steroid hormone and heme biosyntheses, calcium signaling, generation of radical oxygen species, and apoptosis. Mitochondria possess a distinct DNA (mitochondrial DNA); yet, the vast majority of mitochondrial proteins are encoded by the nuclear DNA. Mitochondria-related genetic defects have been described in a variety of mostly rare, often fatal, primary mitochondrial disorders; furthermore, they are increasingly reported in association with many common morbid conditions, such as cancer, obesity, diabetes and neurodegenerative disorders, although their role remains unclear. This study describes the creation of a human mitochondria-focused cDNA microarray (hMitChip) and its validation in human skeletal muscle cells treated with glucocorticoids. We suggest that hMitChip is a reliable and novel tool that will prove useful for systematically studying the contribution of mitochondrial genomics to human health and disease.

The optimization of quantitative reverse transcription PCR for verification of cDNA microarray data

cDNA microarray analysis is highly useful for monitoring genome-wide changes in gene expression that occur in biological processes. Current standards require that microarray observations be verified by quantitative (Q)-PCR or other techniques. Few studies have optimized Q-PCR for verification of microarray findings. The current study assessed several variables affecting Q-PCR fidelity, including RNA extraction methods, mRNA enrichment, primers for reverse transcription, and cDNA amplification detection methods. Also assessed was the choice of reference gene on which other gene expression changes are based. The RNA for ribosomal protein S28 was found to be ideal for this purpose, with minimal variance in expression among isogenic drug-resistant cell lines. We also found that oligo (dT) primers were superior to random hexamers and that RNA extracted by the RNeasy method gave consistent S28 gene amplification without the need for mRNA enrichment, particularly when TaqMan probes were used. Nevertheless, sensitivity was sufficiently high with SYBR Green I that it was the preferred, least costly method for amplification product detection, even for low-abundance transcripts. Using the optimal method, 91-95% of the differences in gene expression identified between the cell lines by cDNA microarray analysis could be confirmed by Q-PCR, significantly superior to previously described methods.

Loss of E-cadherin mRNA and gain of osteopontin mRNA are useful markers for detecting early recurrence of HCV-related hepatocellular carcinoma

BACKGROUND AND OBJECTIVES

We investigated whether expression of E-cadherin (E-cad) and osteopontin (OPN) mRNAs could predict the early recurrence of HCV-associated hepatocellular carcinoma (HCV-HCC) after curative surgery.

METHODS

Forty-four HCV-HCC patients who underwent curative hepatectomy were divided into three categories: category 1--recurrence (3 mR+: n = 6) or non-recurrence (3 mR-: n = 38) within 3 months; category 2--recurrence (6 mR+: n = 4) or non-recurrence (6 mR-: n = 34) between 3-6 months; category 3--recurrence (1 yR+: n = 4) or non-recurrence (1 yR-: n = 30) between 6-12 months. Levels of expression of E-cad and OPN mRNAs were analyzed quantitatively by real-time PCR and calculated using the formula: t = (copy of E-cad or OPN/copy of GAPDH) x 1,000.

RESULTS

The t-value for E-cad was significantly lower in 3 mR+ than in 3 mR- (0.4 and 28.1, P < 0.05), in 6 mR+ than in 6 mR- (4.0 and 30.6, P < 0.05), and in 1 yR+ than in 1 yR- (9.2 and 32.9, respectively, P < 0.05). The t-value for OPN was higher in 3 mR+ than in 3 mR- (92.6 and 65.7, P = 0.57), in 6 mR+ than in 6 mR- (457.1 and 58.15, respectively, P = 0.24), and in 1 yR+ than in 1 yR- (221.8 and 53.5, respectively, P = 0.06).

CONCLUSIONS

Low expression of E-cad mRNA and high expression of OPN mRNA are associated with a higher likelihood of early recurrence of HCV-HCC.

Dysregulation of the Hedgehog pathway in human hepatocarcinogenesis

Hedgehog (Hh) pathway activation promotes tumors in several endodermally derived tissues, but its role in the pathogenesis of hepatocellular carcinoma (HCC) is unknown. Although normal hepatocytes lack Hh signaling, activation of the Hh pathway in endodermal progenitors is required for liver development. Thus, we hypothesized that hepatocarcinogenesis may involve regulation of Hh signaling. This pathway is activated when Hh ligand binds to its receptor, Patched (PTC). In an unoccupied state, PTC normally functions as a tumor suppressor that inhibits Smoothened (SMO), a proto-oncoprotein, from activating downstream components and transcription of target genes. Here we show that in HCCs, overexpression of the Smo proto-oncogene, as well as an increase in the stoichiometric ratio of Smo to Ptc mRNA levels, correlated with tumor size, a prognostic indicator in HCC biology. In one tumor we identified a novel Smo mutation in an evolutionarily conserved residue. We also demonstrated that HCC cell lines (HepG2 and Hep3B) expressed Hh pathway components and activated Hh transcriptional targets. In Hep3B cells, cyclopamine, an inhibitor of wild-type SMO, had no effect, but KAAD-cyclopamine, a blocker of oncogenic SMO, inhibited Hh signaling activity by 50%, decreased expression of the hepatocarcinogenic oncogene, c-myc, by 8-fold, and inhibited the growth rate of Hep3B cells by 94%. These data support our hypothesis that Hh signaling is dysregulated in human hepatocarcinogenesis. We demonstrate that overexpression and/or tumorigenic activation of the Smo proto-oncogene mediates c-myc overexpression which plays a critical role in hepatocarcinogenesis and suggests that Smo is a prognostic factor in HCC tumorigenesis.

CD38 expression is insensitive to steroid action in cells treated with tumor necrosis factor-alpha and interferon-gamma by a mechanism involving the up-regulation of the glucocorticoid receptor beta isoform

Evidence shows that the CD38 molecule, recently involved in the two main features of asthma, bronchial hyper-responsiveness and airway inflammation, could represent a new potential therapeutic target for asthma. In this study, we investigated whether glucocorticoid (GC), the most effective treatment for lung diseases, can affect CD38 expression in human airway smooth muscle (ASM) cells treated with different pro-inflammatory cytokines, such as tumor necrosis factor-alpha (TNFalpha) and interferons (IFNs). We found that CD38 expression induced by TNFalpha alone was completely abrogated by fluticasone (100 nM), dexamethasone (1 microM), or budesonide (100 nM). In contrast, the synergistic induction of CD38 by the combination of TNFalpha with IFNgamma or IFNbeta, but not with IL-1beta or IL-13, was completely insensitive to the GC inhibitory effects. We also found that TNFalpha and IFNgamma impaired GC responsiveness by inhibiting steroid induced both 1) GRalpha-DNA binding activity and 2) GC-responsive element-(GRE)-dependent gene transcription. Although levels of the GC receptor (GR) alpha isoform remained unchanged, expression of GRbeta, the dominant-negative GR isoform, was synergistically increased by TNFalpha and IFNgamma with a GRalpha/GRbeta ratio of 1 to 3. More importantly, fluticasone failed to induce GRE-dependent gene transcription and to suppress TNFalpha-induced CD38 expression in ASM cells transfected with constitutively active GRbeta. We conclude that, upon pro-inflammatory cytokine stimulation, CD38 expression becomes insensitive to GC action by a mechanism involving the up-regulation of GRbeta isoform, thus providing a novel in vitro cellular model to dissect GC resistance in primary cells.

Over-production of IFN-gamma and IL-12 in AhR-null mice

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that mediates toxicity of environmental pollutants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin. The exposure to AhR agonists results in profound suppression of cellular and humoral immune responses and compromises host to infectious disease. Therefore, to define the role of AhR in the immune response, spleen cells from ovalbumin (OVA)-immunized and naïve mice were removed and stimulated in vitro with either OVA or mitogen concanavalin-A (Con A), respectively. Proliferation, CD19+, F4/80+, CD4+ and CD8+ T cells expansion and cytokines production were measured in C57BL/6-AhR-/- mice (AhR-/-) and compared with immune response in similarly immunized age-matched wild type (AhR+/+) mice. In response to OVA immunization, AhR-/- mice had similar levels of serum OVA-specific IgG2a, IgG1, and IgG2b compared with AhR+/+ animals. However, AhR-/- mice showed splenomegalia and an increase in B cells. No changes were observed on proliferation and IL-4 secretion, although AhR-/- cells produced more IFN-gamma and IL-12 than AhR+/+ cells. Similar results were observed with Con A stimulation, a decrease on IL-5 and no change on IL-2 secretion were observed on AhR-/- cells compared with AhR+/+ cells in response to Con A stimulation. High levels of IFN-gamma mRNA were detected in AhR-/- lymphocytes, but IL-4 mRNA levels in AhR-/- cells were similar to those in AhR+/+ mice. These data suggest that AhR may play an important role in the normal development and function of immune system by down-regulating IFN-gamma and IL-12 expression.

Insulin-producing cells derived from human pancreatic non-endocrine cell cultures reverse streptozotocin-induced hyperglycaemia in mice

AIMS/HYPOTHESIS

The aim of the study was to investigate the potential of human pancreatic non-endocrine cells to transdifferentiate into endocrine cells that would be capable of secreting insulin in response to glucose and ameliorating insulin-deficient diabetes after transplantation.

MATERIALS AND METHODS

Cell fractions enriched with exocrine cells after human islet isolation were treated with streptozotocin to remove residual beta cells, grown in monolayer culture to allow de-differentiation, transferred to cluster culture for redifferentiation in the presence of activin A, betacellulin, nicotinamide and glucose, supplemented with 10% FCS, and administered to streptozotocin-induced diabetic SCID mice. A subset of cells was transfected with the IPF1 gene (also known as PDX1) before transdifferentiation.

RESULTS

No insulin was detectable in cell preparations after 5 days of treatment with streptozotocin. In monolayer culture, 90% of the streptozotocin-treated pancreatic cells co-expressed cytokeratin-19 and vimentin at 2 weeks and 60% expressed nestin at 4 weeks. Cell cultures with a high proportion of nestin-expressing cells had greater plasticity for transdifferentiation into cells with phenotypic and functional markers of beta cells, this property being significantly enhanced by transfection with IPF1 gene and leading to 15+/-6.7% insulin-positive cells after transplantation vs. 0.01% of cells transplanted after streptozotocin treatment alone. These cells improved glucose control in all of 42 diabetic mice after transplantation, restoring normoglycaemia in 40%.

CONCLUSIONS/INTERPRETATION

Human pancreatic cells are a potential source of new glucose-responsive insulin-producing cells that may be developed further for clinical use.

Rapid quantitative analysis of human cytomegalovirus DNA by the real-time polymerase chain reaction method

CONTEXT

Human cytomegalovirus (CMV) infection is a progressive and life-threatening complication in immunocompromised patients even now. Therefore, early and accurate treatment based on rapid and certain detection is needed to prevent fatal CMV infection diseases.

OBJECTIVE

To study a quicker, simpler, and less expensive method of quantitative analysis using real-time polymerase chain reaction based on the SYBR Green I method of CMV detection for appropriate treatment of CMV infection in immunocompromised patients.

DESIGN

We quantified 50 samples tested by direct immunoperoxidase staining of leukocytes with peroxidase-labeled monoclonal antibody (C7-HRP test), 30 samples from healthy persons, and 47 samples from 7 patients suspected of having CMV infection diseases. We used the primer set in the pp65 gene of CMV and whole blood without a preparatory process. The setting for the study was the First Department of Pathology, Kurume University School of Medicine, St Mary's Hospital, and the Gene Section of the Clinical Laboratory at St Mary's Hospital, Fukuoka, Japan.

RESULTS

The results obtained with this method corresponded well with conventional C7-HRP tests and demonstrated excellent reproduction. Additionally, the results were better correlated with the clinical course than were C7-HRP tests.

CONCLUSIONS

This method was more useful than the C7-HRP test as a rapid diagnostic test for early treatment of CMV infection. This test also demonstrated its usefulness for monitoring CMV infection during treatment using ganciclovir. Moreover, it was quicker, simpler, and cheaper than other real-time polymerase chain reaction methods.

Monoamine oxidase-A is a major target gene for glucocorticoids in human skeletal muscle cells

Skeletal myopathy is a common complication of endogenous and exogenous glucocorticoid excess, yet its pathogenetic mechanisms remain unclear. There is accumulating evidence that mitochondrial dysfunction and oxidative stress are involved in this process. To explore the glucocorticoid-induced transcriptional adaptations that may affect mitochondrial function in skeletal muscle, we studied gene expression profiles in dexamethasone-treated primary human skeletal myocytes using a cDNA microarray, which contains 501 mitochondria-related genes. We found that monoamine oxidase A (MAO-A) was the most significantly up-regulated gene. MAO-A is the primary enzyme metabolizing catecholamines and dietary amines, and its role in skeletal muscle remains largely unexplored. Dexamethasone induced dose- and time-dependent increases of MAO-A gene and protein expression, while its effects on MAO-B were minimal. Both the glucocorticoid receptor (GR) and the Sp1 transcription factor were required for dexamethasone-induced MAO-A mRNA expression, as blockade of the GR with RU 486 or ablation of Sp1 binding with mithramycin abrogated MAO-A mRNA induction. The observed dexamethasone effect was biologically functional, as this steroid significantly increased MAO-mediated hydrogen peroxide production. We suggest that MAO-A-mediated oxidative stress can lead to cell damage, representing a novel pathogenetic mechanism for glucocorticoid-induced myopathy and a potential target for therapeutic intervention.

Novel Regulators of Kidney Development from the Tips of the Ureteric Bud

Mammalian nephrogenesis depends on the interaction between the ureteric bud and the metanephric mesenchyme. As the ureteric bud undergoes branching and segmentation, the stalks differentiate into the collecting system of the mature kidney, while the tip cells interact with the adjacent cells of the metanephric mesenchyme, inducing their conversion into nephrons. This induction is mediated by secreted factors. For identifying novel mediators, the tips of the ureteric tree were isolated and microarray analyses were performed using manually refined, multistep gene ontology annotations. For identifying conserved factors, two databases were developed, one from mouse E12.5 and one from rat E13.5 ureteric buds. The overlap of mouse and rat data sets yielded 20 different transcripts that were enriched in the ureteric bud compared with metanephric mesenchyme and predicted to code for secreted proteins. Real-time reverse transcriptase-PCR and in situ hybridization confirmed these identifications. One of the genes that was highly specific to the ureteric bud tip was cytokine-like factor 1 (CLF-1). Recombinant CLF-1 in complex with its physiologic ligand, cardiotrophin-like cytokine (CLC), triggered phosphorylation of signal transducer and activator of transcription 3 in mesenchyme, a pathway characteristic of mesenchymal-to-epithelial conversion. Indeed, when applied to isolated rat metanephric mesenchyme, CLF-1/CLC (3 nM) induced mature nephron structures expressing glomerular and tubular markers. These results underline the power of this first comprehensive gene expression analysis of the ureteric bud tip to identify bioactive molecules.

Real-time PCR method for the quantitative analysis of human T-cell receptor gamma and beta gene rearrangements

Analyzing the status of T-cell receptor (TCR) gene rearrangements has been an essential part of deciphering the stages of thymocyte development, understanding the alphabeta vs. gammadelta lineage decision, and characterizing T-cell leukemias. Methods such as PCR and quantitative Southern blotting provide useful information, but also have significant shortcomings such as lack of quantitation in the case of PCR and technical challenges in the case of Southern blotting. Here we describe a real-time PCR method that overcomes many of these shortcomings. This new method shows comparable results for the fraction of unrearranged TCRgamma and TCRbeta genes in human thymocytes and peripheral blood T cells as Southern blotting, and has the advantages of being simple to perform, highly quantitative, and requiring nanogram quantities of DNA. We also describe a real-time PCR method to quantitate T-cell receptor excision circles formed during TCRbeta rearrangements.

Mechanistic data and cancer risk assessment: the need for quantitative molecular endpoints

The cancer risk assessment process as currently proposed by the U.S. Environmental Protection Agency allows for the use of mechanistic data to inform the low-dose tumor response in humans and in laboratory animals. The aim is to reduce the reliance on defaults that introduce a relatively high level of uncertainty to the risk estimates. The types of data required for this purpose are those that help identify key events in tumor formation following exposure to environmental chemicals. Informative biomarkers of tumor responses could then be developed for describing the shape of a dose-response curve at low doses (i.e., a qualitative assessment) and for predicting tumor frequency at these low doses (i.e., a quantitative assessment). A number of recently developed molecular approaches could aid in the development of qualitatively and quantitatively informative biomarkers. An overview of these with examples of their use is presented. These methods include quantitative gene expression array techniques, quantitative proteomic assays, and the assessment of DNA alterations at the single gene level and at the genome level of detection. It is most likely that a combination of approaches at different levels of cellular organization (i.e., DNA, RNA, and protein) will be the most productive for biomarker development. The rapid progress that is being made will make this tool kit even more applicable for the cancer risk assessment process.

A kinetic model of quantitative real-time polymerase chain reaction

Real-time polymerase chain reaction (PCR) is one of the most sensitive and accurate methods for quantifying transcript levels especially for those expressed at low abundance. The selective amplification of target DNA over multiple cycles allows its initial concentration to be determined. The amplification rate is a complex interplay of the operating conditions, initial reactant concentrations, and reaction rate constants. Experimentally, the compounded effect of all factors is quantified in terms of an effective efficiency, which is estimated by curve fitting to the amplification data. We present a comprehensive model of PCR to study the effect of various reactant concentrations on the amplification efficiency. The model is used to calculate the kinetic progression of the target DNA concentration with cycle number under conditions when different species are stoichiometrically or kinetically limiting. The reaction efficiency remains constant for the initial cycles. As the primer concentration becomes limiting, the efficiency is marked by a gradual decrease. This is in contrast to a steep decline under nucleotide limiting conditions. Under some conditions, commonly used experimentally, increasing primer concentration has the adverse effect of reducing the final amplified template concentration. This phenomenon seen at times experimentally is explained by the simulation results under rate limiting enzyme concentrations. Primer dimer formation is shown to significantly affect the reaction rates, effective efficiency, and the estimated initial concentrations. This model, by describing the interplay of the many operating variables, will be a useful tool in designing PCR conditions and evaluating its results.

Optimised real-time quantitative PCR assays for RANKL regulated genes

Osteoclasts are multinucleated giant cells that differentiate from precursors of the monocyte-macrophage lineage. We used receptor activator of NF-kappa B ligand (RANKL) and macrophage colony stimulating factor (M-CSF) to differentiate authentic human osteoclasts from peripheral blood mononuclear cells (PBMCs). We previously described a series of genes that are strongly regulated by RANKL. Here, we provide a set of reliable quantitative real-time PCR based assays of RANKL regulated genes as reference genes that may prove useful in the study of human osteoclasts. The SYBR-green I assays are free of primer dimer and other artefacts, and are designed to amplify in parallel, thus permitting simultaneous analysis of 12 genes. Optimised primers for 18S rRNA provide a valid housekeeping reference gene. Standard curves have been constructed for all assays, thus allowing for absolute quantification of mRNA transcript copy number. As an example, the regulation of expression of the chemokine RANTES in osteoclasts is demonstrated. These gene assays have potential utility in a variety of cell types, tissues and organs, in addition to macrophages and osteoclasts.

Quantitative real-time PCR detection of oral Enterococcus faecalis in humans

OBJECTIVE

Enterococcus faecalis is consistently associated with recurrent root canal infections. Only low concentrations of E. faecalis in the human mouth have been demonstrated by culture techniques. Quantitative detection strategies more sensitive than culturing, such as quantitative PCR (qPCR), could provide more illuminating data.

DESIGN

Thirty outpatients attending the University of Michigan Graduate Endodontic Clinic for endodontic treatment provided oral rinse samples that were analysed for E. faecalis using qPCR and microbiological culturing. A SYBR Green I qPCR protocol was developed for the quantifiable detection of E. faecalis and total bacteria in oral rinse samples using primers designed to target the 16S rRNA gene. Annealing temperature and primer, magnesium ion, and dimethyl sulfoxide concentrations were investigated for optimisation of the protocol; a minimum sensitivity limit of 23 rRNA copies (an estimated six E. faecalis cells) was established for E. faecalis in pure culture, and 104 rRNA copies (an estimated 26 E. faecalis cells) in mixed culture.

RESULTS

In qPCR assays, based on extrapolation from estimated rRNA gene copy numbers, E. faecalis comprised 0.0006-0.0047% of a total bacteria load that ranged from 5.92 x 10(5) to 5.69 x 10(7) cells/ml of oral rinse. E. faecalis was detected in five (17%) samples in concentrations from 114 to 490 cells/ml. In parallel culture assays E. faecalis were detected in only two samples (7%) of the five identified by qPCR and in concentrations 30 and 240 CFU/ml.

CONCLUSIONS

qPCR reported a higher incidence of E. faecalis in oral rinse samples than culture techniques and afforded greater sensitivity.

Use of real-time PCR for determining copy number and zygosity in transgenic plants

This review examines how real-time PCR can be used to determine copy number and zygosity in transgenic plants. Distinguishing between plants that harbor one and two copies of a transgene or are hemizygous and homozygous requires the ability to routinely distinguish twofold differences, a detection difference which approaches the resolution of PCR-based quantification methods. After explaining the basic principles, especially the threshold cycle (Ct value) as the basic measuring unit in real-time PCR, we introduce three quantitation methods currently in use. While the absolute and relative standard curve approaches are qualitative methods that distinguish high-copy from low-copy transformants, the comparative (2(-DeltaDeltaCt)) method with double-dye oligonucleotides (TaqMan probes) is able to detect twofold differences. In order to obtain reliable results, Ct values for an amplicon should be below 25 and the standard deviation below 0.3. Although real-time PCR can deliver exact copy number determinations, the procedure is not fail-safe. Therefore, real-time PCR should to be viewed as complementary to--rather than as a replacement of--other methods such as Southern analysis, but it is particularly useful as a preliminary screening tool for estimating copy numbers of a large number of transformants.

Effects of herbal compound 861 on human hepatic stellate cell proliferation and activation

AIM: To investigate the effects of herbal compound 861 (Cpd 861) on cell proliferation in human hepatic stellate cells (LX-2) and human hepatocellular liver carcinoma cells (HepG2), and expression of α-smooth muscle actin (α-SMA) in LX-2 cells.

METHODS: LX-2 and HepG2 cells were incubated with various concentrations of Cpd 861 (0.1-0.003 mg/mL) for 1, 2, 3, 5 and 7 d. Cell proliferation was analyzed by 3-(4, 5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay. Effects of Cpd861 on the expression of α-SMA mRNA in LX-2 cells were measured by real-time quantitative PCR method using SYBR Green I technology.

RESULTS: Cpd 861, at 0.1 mg/mL, significantly inhibited LX-2 cell proliferation (15% decrease relative to control, P < 0.05) after 3 d of incubation. The inhibitory effects seemed to increase with the treatment time (25% decrease after 5 d of incubation and 35% decrease after 7 d of incubation, P < 0.01). However, Cpd 861 did not affect HepG2 cell proliferation at the same concentration used for LX-2 cells. The expression levels of α-SMA mRNA decreased significantly when LX-2 cells were exposed to Cpd 861 for 48 h (59% decrease relative to control, P < 0.05) or 72 h (60% decrease relative to control, P < 0.01).

CONCLUSION: Cpd 861 can significantly inhibit LX-2 cell proliferation in a dose-dependant manner, and reduce the expression levels of α-SMA mRNA in LX-2 cells. Since hepatic cell proliferation and high level of α-SMA are associated with liver fibrosis, the results suggest that Cpd 861 may be useful in the treatment of this disease.

Rapid identification of female carriers of DMD/BMD by quantitative real-time PCR

Recently developed PCR systems offer online-monitoring of amplification and allow simple and reliable DNA quantification. We have used the LightCycler system to develop a simple and rapid method for direct identification of female carriers of deletions and duplications in the dystrophin gene. The challenge resides in the ability to identify the presence of a deleted or duplicated allele over the background contributed by the normal allele. Quantification is based on the determination of the ratio between potentially deleted/duplicated dystrophin exons and non-deleted/-duplicated reference exons using the unspecific dsDNA-dye SYBRgreen I. In a retrospective study, we evaluated our method in female relatives of DMD/BMD patients with known carrier status by comparative analysis of deleted or duplicated versus non-deleted/-duplicated exons. Carrier status was accurately attributed in 100% of cases, the mean ratios being 0.52+/-0.12 for deletion carriers (expected value: 0.5) and 1.56+/-0.18 for duplication carriers (expected value: 1.5) vs. 1.022+/-0.17 for non-carriers (expected value: 1.0). The method proved to be simple, rapid, reliable, and cost-effective. It may be used for direct determination of deletions/duplications in potential DMD/BMD carriers and may easily be adapted for other genetic conditions involving deletions and duplications.

Rapid detection of subtelomeric deletion/duplication by novel real-time quantitative PCR using SYBR-green dye

Telomeric chromosome rearrangements may cause mental retardation, congenital anomalies, miscarriages, and hematological malignancies. Automated detection of subtle deletions and duplications involving telomeres is essential for high-throughput screening procedures, but impractical when conventional cytogenetic methods are used. Novel real-time PCR quantitative genotyping of subtelomeric amplicons using SYBR-green dye allows high-resolution screening of single copy number gains and losses by their relative quantification against a diploid genome. To assess the applicability of the technique in the screening and diagnosis of subtelomeric imbalances, we describe here a blinded study in which DNA from 20 negative controls and 20 patients with known unbalanced cytogenetic abnormalities involving at least one or more telomeres were analyzed using a novel human subtelomere-specific primer set, producing altogether 86 amplicons, in the SYBR-green I-based real-time quantitative PCR screening approach. Screening of the DNA samples from 20 unrelated controls for copy number polymorphism do not detect any polymorphism in the set of amplicons, but single-copy-number gains and losses were accurately detected by quantitative PCR in all patients, except the copy number alterations of the subtelomeric p-arms of the acrocentric chromosomes in two cases. Furthermore, a detailed mapping of the deletion/translocation breakpoint was demonstrated in two cases by novel real-time PCR "primer-jumping." Because of the simplicity and flexibility of the SYBR-green I-based real-time detection, the primer-set can easily be extended, either to perform further detailed molecular characterization of breakpoints or to include amplicons for the detection and/or analysis of syndromes that are associated with genomic copy number alterations, e.g., deletion/duplication-syndromes and malignant cancers.