Absolute quantitation of viremia in human immunodeficiency virus infection by competitive reverse transcription and polymerase chain reaction

HIV Apheresis Tags (HIVAT) Aided Elimination of Viremia

INTRODUCTION

HIV viremia is the essential element for progression of an initial HIV infection into AIDS and death. The currently approved management relies primarily on chemotherapy repressing the HIV replication in the infected CD4+ cells, although with severe systemic adverse effects. The problem is that it does not physically eliminate viruses, which then not only keep infecting healthy cells of these patients, but also promote infections of other people.

SPECIFIC AIM

An overall objective of our work is biomolecular engineering of virus apheresis tags (VAT) that eliminate viremias without adverse effects. The specific aim of this project was biomolecular engineering of Human Immunodeficiency Virus Apheresis Tags (HIVAT): CD4-Au-Fe3O4, CD4-SiO2-Fe3O4, anti-gp120-Au-Fe3O4, and anti-gp120-SiO2-Fe3O4.

HEALTHY DONORS AND PATIENTS

Per the Institutional Review Board's approval and in compliance with Declaration of Helsinki, healthy donors and patients were presented with Patient Bill of Rights and provided Patient Informed Consent, while all the procedures were pursued by the licensed physicians.

MATERIALS AND METHODS

CD4, gp120, gp41, gp160, anti-gp120, p24 were transgenomically expressed. Superparamagnetic core-shell particles (SPM-CSP) were synthesized. SPM-CSP were used as the nucleation centers for assembling the expressed molecules upon them to create virus apheresis tags (VAT). VAT were injected into the blood or lymph acquired from the HIV+ and HBV+ patients followed by apheresis at 0.47 - 9.4 T. VAT efficacy in eliminating viremia was determined through immunoblots, NMR and q-RT-PCR.

RESULTS

Treatment of blood or lymph of the HIV+ patients' with VAT followed by virus apheresis resulted in rapid elimination of the HIV viremia. Efficacy of apheresis was contingent upon the gravity of viremia versus doses and regimens of VAT. Importantly, administration of VAT also effectively improved levels of non-infected CD4+ lymphocytes.

DISCUSSION / CONCLUSIONS

Herein, we present the proof of concept for a new, effective treatment with virus apheresis tags (VAT), specifically Human Immunodeficiency Virus Apheresis Tags (HIVAT), of the HIV+ patients' blood and lymph, which is eliminating the HIV viremia.It can be easily adapted as treatments of viremias perpetrated by other deadly viruses, which we vigorously pursue.

HIV Apheresis Tags (HIVAT) Aided Elimination of Viremia

INTRODUCTION

HIV viremia is the essential element for progression of an initial HIV infection into AIDS and death. The currently approved management relies primarily on chemotherapy repressing the HIV replication in the infected CD4+ cells, although with severe systemic adverse effects. The problem is that it does not physically eliminate viruses, which then not only keep infecting healthy cells of these patients, but also promote infections of other people.

SPECIFIC AIM

An overall objective of our work is biomolecular engineering of virus apheresis tags (VAT) that eliminate viremias without adverse effects. The specific aim of this project was biomolecular engineering of Human Immunodeficiency Virus Apheresis Tags (HIVAT): CD4-Au-Fe3O4, CD4-SiO2-Fe3O4, anti-gp120-Au-Fe3O4, and anti-gp120-SiO2-Fe3O4.

HEALTHY DONORS AND PATIENTS

Per the Institutional Review Board's approval and in compliance with Declaration of Helsinki, healthy donors and patients were presented with Patient Bill of Rights and provided Patient Informed Consent, while all the procedures were pursued by the licensed physicians.

MATERIALS AND METHODS

CD4, gp120, gp41, gp160, anti-gp120, p24 were transgenomically expressed. Superparamagnetic core-shell particles (SPM-CSP) were synthesized. SPM-CSP were used as the nucleation centers for assembling the expressed molecules upon them to create virus apheresis tags (VAT). VAT were injected into the blood or lymph acquired from the HIV+ and HBV+ patients followed by apheresis at 0.47 - 9.4 T. VAT efficacy in eliminating viremia was determined through immunoblots, NMR and q-RT-PCR.

RESULTS

Treatment of blood or lymph of the HIV+ patients' with VAT followed by virus apheresis resulted in rapid elimination of the HIV viremia. Efficacy of apheresis was contingent upon the gravity of viremia versus doses and regimens of VAT. Importantly, administration of VAT also effectively improved levels of non-infected CD4+ lymphocytes.

DISCUSSION / CONCLUSIONS

Herein, we present the proof of concept for a new, effective treatment with virus apheresis tags (VAT), specifically Human Immunodeficiency Virus Apheresis Tags (HIVAT), of the HIV+ patients' blood and lymph, which is eliminating the HIV viremia.It can be easily adapted as treatments of viremias perpetrated by other deadly viruses, which we vigorously pursue.

Detection of slipped-DNAs at the trinucleotide repeats of the myotonic dystrophy type I disease locus in patient tissues

Slipped-strand DNAs, formed by out-of-register mispairing of repeat units on complementary strands, were proposed over 55 years ago as transient intermediates in repeat length mutations, hypothesized to cause at least 40 neurodegenerative diseases. While slipped-DNAs have been characterized in vitro, evidence of slipped-DNAs at an endogenous locus in biologically relevant tissues, where instability varies widely, is lacking. Here, using an anti-DNA junction antibody and immunoprecipitation, we identify slipped-DNAs at the unstable trinucleotide repeats (CTG)n•(CAG)n of the myotonic dystrophy disease locus in patient brain, heart, muscle and other tissues, where the largest expansions arise in non-mitotic tissues such as cortex and heart, and are smallest in the cerebellum. Slipped-DNAs are shown to be present on the expanded allele and in chromatinized DNA. Slipped-DNAs are present as clusters of slip-outs along a DNA, with each slip-out having 1–100 extrahelical repeats. The allelic levels of slipped-DNA containing molecules were significantly greater in the heart over the cerebellum (relative to genomic equivalents of pre-IP input DNA) of a DM1 individual; an enrichment consistent with increased allelic levels of slipped-DNA structures in tissues having greater levels of CTG instability. Surprisingly, this supports the formation of slipped-DNAs as persistent mutation products of repeat instability, and not merely as transient mutagenic intermediates. These findings further our understanding of the processes of mutation and genetic variation.

Over 30 diseases are caused by the expansion of a trinucleotide repeat (TNR) in a specific gene, including the most common adult-onset form of muscular dystrophy, myotonic dystrophy (DM1). The mechanistic contributors to this unstable (TNR) expansion are not fully known, although since the discovery of these types of diseases over twenty years ago, the extrusion of the expanded repeats into mutagenic slipped-DNA conformations has been hypothesized. Here, we show the presence of slipped-DNA at the DM1 disease locus in various patient tissues. The allelic amounts of slipped-DNA in tissues correlate with overall levels of repeat instability. Slipped-DNA was also found to form in clusters along a tract of expanded repeats, which has been previously shown in vitro to impede DNA repair. This is the first evidence for slipped-DNA formation at an endogenous disease-causing gene in patient tissues.

Comparative quantification of human intestinal bacteria based on cPCR and LDR/LCR

AIM: To establish a multiple detection method based on comparative polymerase chain reaction (cPCR) and ligase detection reaction (LDR)/ligase chain reaction (LCR) to quantify the intestinal bacterial components.

METHODS: Comparative quantification of 16S rDNAs from different intestinal bacterial components was used to quantify multiple intestinal bacteria. The 16S rDNAs of different bacteria were amplified simultaneously by cPCR. The LDR/LCR was examined to actualize the genotyping and quantification. Two beneficial (Bifidobacterium, Lactobacillus) and three conditionally pathogenic bacteria (Enterococcus, Enterobacterium and Eubacterium) were used in this detection. With cloned standard bacterial 16S rDNAs, standard curves were prepared to validate the quantitative relations between the ratio of original concentrations of two templates and the ratio of the fluorescence signals of their final ligation products. The internal controls were added to monitor the whole detection flow. The quantity ratio between two bacteria was tested.

RESULTS: cPCR and LDR revealed obvious linear correlations with standard DNAs, but cPCR and LCR did not. In the sample test, the distributions of the quantity ratio between each two bacterial species were obtained. There were significant differences among these distributions in the total samples. But these distributions of quantity ratio of each two bacteria remained stable among groups divided by age or sex.

CONCLUSION: The detection method in this study can be used to conduct multiple intestinal bacteria genotyping and quantification, and to monitor the human intestinal health status as well.

Low-dose combined oral contraceptive and cervicovaginal shedding of human immunodeficiency virus

BACKGROUND

The role of low-dose oral contraceptives on HIV cervicovaginal shedding among HIV-positive women is controversial.

STUDY DESIGN

We evaluated the effect of low-dose oral contraceptives on HIV cervicovaginal shedding in a cohort of 285 HIV-seropositive women followed for a median of 20 months. A sensitive, competitive polymerase chain reaction (cPCR) and a reverse transcription PCR (cRT-PCR) were applied for the quantification of HIV-associated and cell-free RNA and proviral DNA in cervicovaginal cells, as well as HIV-RNA in plasma.

RESULTS

In multivariable logistic generalized estimating equations, plasma viral load >100 copies/mL (OR=1.81, 95% CI=1.3-2.53) and bacterial vaginosis (OR=1.49, 95% CI=1.1-2.02) were associated with an increased risk of HIV-1 DNA shedding, whereas current use of oral contraceptive was associated with a reduced risk (OR=0.55, 95% CI=0.33-0.92). Oral contraceptives were also associated with a reduction of risk (OR=0.38, 95% CI=0.21-0.69) of cell-associated but not cell-free HIV-1 RNA.

CONCLUSIONS

In HIV-positive women with low levels of HIV viremia, low-dose oral contraceptives were associated with a modest but significant reduction of HIV-1 DNA and cell-associated HIV-1 RNA genital shedding.

Performance evaluation of the new Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 2.0 for quantification of human immunodeficiency virus type 1 RNA

Despite FDA approval and CE marking of commercial tests, manufacturer-independent testing of the technical aspects of newly developed tests is important. To evaluate the analytical performance and explore the clinical applicability of the new Roche COBAS AmpliPrep COBAS TaqMan HIV-1 test, version 2.0 (CAP/CTM v2.0), platform comparison was performed with the Roche CAP/CTM test, version 2.0, the COBAS Amplicor HIV-1 Monitor Test, version 1.5 (CAP/CA v1.5), the COBAS AmpliPrep COBAS TaqMan HIV-1 Test (CAP/CTM v1.0), and the Abbott m2000 RealTime HIV-1 assay on panels and diagnostic samples. Specificity was tested for HIV-2 samples. Furthermore, samples from HIV-1-seropositive individuals with CAP/CA v1.5-measured viral loads below 50 HIV-1 RNA copies per ml (cp/ml) and replicates of HIV-1-seronegative plasma were tested in a checkerboard analysis. CAP/CTM v2.0 is HIV-1 specific, with broad genotype inclusivity and no serious underquantification of viral load relative to the other assays used. Low viral loads below the threshold of quantification for CAP/CA v1.5 are observed with CAP/CTM v2.0. A CAP/CTM v2.0-measured viral load of >50 copies/ml in these samples correlated with therapy failure. In conclusion, CAP/CTM v2.0 is an accurate and reliable test for HIV-1 viral load measurement relative to the other assays used with respect to specificity, sensitivity, and genotype inclusivity.

Double-stranded RNA adenosine deaminases enhance expression of human immunodeficiency virus type 1 proteins

ADARs (adenosine deaminases that act on double-stranded RNA) are RNA editing enzymes that catalyze a change from adenosine to inosine, which is then recognized as guanosine by translational machinery. We demonstrate here that overexpression of ADARs but not of an ADAR mutant lacking editing activity could upregulate human immunodeficiency virus type 1 (HIV-1) structural protein expression and viral production. Knockdown of ADAR1 by RNA silencing inhibited HIV-1 production. Viral RNA harvested from transfected ADAR1-knocked-down cells showed a decrease in the level of unspliced RNA transcripts. Overexpression of ADAR1 induced editing at a specific site in the env gene, and a mutant with the edited sequence was expressed more efficiently than the wild-type viral genome. These data suggested the role of ADAR in modulation of HIV-1 replication. Our data demonstrate a novel mechanism in which HIV-1 employs host RNA modification machinery for posttranscriptional regulation of viral protein expression.

Impact of alcaligin siderophore utilization on in vivo growth of Bordetella pertussis

Bordetella pertussis, the causative agent of human whooping cough, or pertussis, is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth. Under iron starvation stress conditions, B. pertussis produces the siderophore alcaligin. The alcaligin siderophore gene cluster, consisting of the alcABCDERS and fauA genes, encodes activities required for alcaligin biosynthesis, the export of the siderophore from the cell, the uptake of the ferric alcaligin complex across the outer membrane, and the transcriptional activation of alcaligin system genes by an autogenous mechanism involving alcaligin sensing. The fauA gene encodes a 79-kDa TonB-dependent outer membrane receptor protein required for the uptake and utilization of ferric alcaligin as an iron source. In this study, using mixed-infection competition experiments in a mouse respiratory model, inactivation of the B. pertussis ferric alcaligin receptor protein was found to have a profound impact on in vivo growth and survival of a fauA mutant compared with a coinfecting wild-type strain. The attenuating effect of fauA inactivation was evident early in the course of the infection, suggesting that the contribution of ferric alcaligin transport to the ecological fitness of B. pertussis may be important for adaptation to iron-restricted host conditions that exist at the initial stages of infection. Alcaligin-mediated iron acquisition by B. pertussis may be critical for successful host colonization and establishment of infection.

Evaluation of the analytical performance of the new Abbott RealTime RT-PCRs for the quantitative detection of HCV and HIV-1 RNA

BACKGROUND

Despite FDA approval and CE marking of commercial tests, manufacturer independent testing of technical aspects is important.

OBJECTIVES

To evaluate the analytical performance of the new Abbott RealTime HCV and HIV-1 viral load tests.

STUDY DESIGN

Sensitivity, specificity and inter-/intra-assay variation were investigated. The HCV and HIV-1 assays were compared with Siemens bDNA 3.0 and Roche Cobas Monitor 2.0, respectively, on diagnostic samples.

RESULTS

Lower isolation volumes on the M1000 gave minor but statistically significant lower quantitative values. Minor differences were observed in the lower limit of detection relative to the specification given by the manufacturer. Inter-/intra-assay coefficients of variations ranged from 0.31 to 4.75 between 5.0 x 10(4) and 5.0 x 10(2) copies/mL. Both the HCV and HIV-1 Abbott RealTime tests did not show a geno-/sub-type dependent under-quantification on WHO reference panels, quality control panels or clinical specimens. The Abbott RealTime HIV-1 viral load assay detected subtype O whereas several other systems failed to detect this subtype.

CONCLUSION

The technical aspects of the HCV and HIV-1 RealTime viral load assays on the M2000 system make it attractive for use in routine diagnostic settings.

Multicenter evaluation of the new Abbott RealTime assays for quantitative detection of human immunodeficiency virus type 1 and hepatitis C virus RNA

The analytical performances of the new Abbott RealTime hepatitis C virus (HCV) and human immunodeficiency virus type 1 viral load assays were compared at nine laboratories with different competitor assays. These included the Abbott LcX, Bayer Versant bDNA, Roche COBAS Amplicor, and Roche COBAS TaqMan assays. Two different protocols used during the testing period with and without a pre-m1000 RNA isolation spin were compared. The difference proved to be nonsignificant. A uracil-N-glycosylase (UNG) contamination control option in the HCV test for previous Roche COBAS Amplicor users was evaluated. It proved to decrease amplicon carryover by 100-fold independent of the amplicon input concentration. The protocol including UNG proved to overcome problems with false-positive negative controls. Comparison with other assays revealed only minor differences. The largest difference was observed between the Abbott HCV RealTime assay and the Roche COBAS Amplicor HCV Monitor version 2.0 assay.

Cervical intraepithelial neoplasia and cervicovaginal shedding of human immunodeficiency virus

OBJECTIVE

Although human immunodeficiency virus (HIV) infection is a well-known risk factor for cervical intraepithelial neoplasia (CIN), the influence of CIN on cervicovaginal shedding of HIV is poorly understood. The purpose of this study was to evaluate the association between CIN and the shedding of HIV in cervicovaginal secretions.

METHODS

Two hundred sixteen HIV-seropositive patients were followed up by Pap test, colposcopy, and targeted cervical biopsies for a median of 16 months (range 0-94). A diagnosis of low-grade CIN was made on the basis of Pap test and either colposcopy or cervical biopsy. High-grade CIN was diagnosed solely on the basis of cervical biopsy. At each follow-up visit, we measured HIV-1 RNA in plasma, proviral HIV-1 DNA, and cell-associated and cell-free HIV-1 RNA in cervicovaginal secretion by competitive polymerase chain reaction (cRT-PCR) and reverse transcriptase PCR. The univariable and multivariable associations between the occurrence of CIN and the presence of HIV-related nucleic acids in cervicovaginal secretions were evaluated with logistic generalized estimating equations.

RESULTS

Overall, at enrollment and during the follow-up period, a diagnosis of either low-grade or high-grade CIN was made in 14.4% (99/689) and 6.7% (46/689) of the visits, respectively. The presence of measurable levels of plasma HIV-1 RNA was a significant risk factor for the detection of cervicovaginal HIV-1 DNA (odds ratio [OR] 1.86, 95% confidence interval [CI] 1.32-2.61, P < .001), cell-associated (OR 1.69, 95% CI 1.18-2.43, P = .004), and cell-free HIV-1 RNA (OR 1.84, 95% CI 1.28-2.63, P = .001). After the adjustment for the effect of plasma HIV-1 RNA, CD4(+) positive cell counts less than 200 mm(3), and bacterial vaginosis, the detection of cell-associated (OR 1.75, 95% CI 1.23-2.49, P = .006) and cell-free HIV-1 RNA (OR 2.0, 95% CI 1.39-2.87, P = .001) in cervicovaginal secretions was significantly associated with the diagnosis of CIN.

CONCLUSION

The presence of CIN lesions is a significant risk factor for genital HIV shedding. Given the high prevalence of cervical disease among HIV-positive women, this finding could have important epidemiological implications in both heterosexual and perinatal transmission of HIV.

LEVEL OF EVIDENCE

II-2.

Increased HIV-DNA load in CCR5-negative lymphocytes without viral phenotypic change

We have previously described a selective increase in HIV-DNA content in CCR5-negative lymphocytes from late stage HIV-infected patients. Here, we show that this increase occurred even in the absence of viral phenotypic switching from CCR5- to CXCR4-tropic. This leads us to hypothesize that early and late CCR5-tropic viruses might be different in the ability to infect CCR5-low or -negative cells. We compared a set of early CCR5-tropic viruses with low viral DNA content in CCR5-negative cells to a set of late CCR5-tropic viruses with high viral DNA content in CCR5-negative cells. We could not find any significant differences between the two sets of viruses in the aspects of relative infectivity in CCR5-low cells and the level of inhibition by beta-chemokine. This suggested that there may be some changes in cellular phenotype or environment that allows an expansion of susceptible cell population in late stages HIV infection. Understanding these changes may provide a novel approach for HIV therapy.

The effect of vaginal candidiasis on the shedding of human immunodeficiency virus in cervicovaginal secretions

OBJECTIVE

The purpose of this study was to evaluate the influence of symptomatic vulvovaginal candidiasis on the shedding of HIV-1 in cervicovaginal secretions of HIV-1-infected women.

STUDY DESIGN

We obtained paired blood and cervicovaginal lavage samples from 66 HIV-infected women with symptomatic vulvovaginal candidiasis, and 249 HIV-infected control patients without genital infection. HIV-1 RNA in plasma, proviral HIV-1 DNA, HIV-1 RNA transcripts, and cell-free HIV-1 RNA in cervicovaginal secretions were quantitatively evaluated by competitive polymerase chain reaction (cPCR) and reverse transcriptase PCR (cRT-PCR). We used logistic regression on ordered data to assess the influence of vulvovaginal candidiasis on the HIV-1 load in cervicovaginal secretions adjusting for potential confounders.

RESULTS

Overall, the amount of HIV-1 RNA in plasma was significantly correlated with HIV-1 DNA (Spearman rank 0.153 +/- 0.059, P = .006), HIV-1 RNA transcripts (Spearman rank 0.169 +/- 0.058, P = .003), and cell free HIV-1 RNA (Spearman rank 0.185 +/- 0.059, P = .001) load in cervicovaginal secretion. Forty-eight out of 182 (26.4%) patients who tested negative for HIV-1 RNA in plasma were positive for HIV-DNA in their cervicovaginal secretions. In logistic regression analysis vulvovaginal candidiasis was significantly associated with increasing loads of HIV-1 RNA transcripts (Odds ratio [OR] 1.97, 95% CI 1.09-3.57, P = .025) and cell free HIV-1 RNA (OR 2.03, 95% CI 1.10-3.73, P = .02) in cervicovaginal secretions.

CONCLUSION

In HIV-infected women, vulvovaginal candidiasis is associated with an increased number of copies of cell-associated and cell-free HIV-1 RNA in cervicovaginal secretions.

Double-step PCR assay to quantify Epstein-Barr viral load in peripheral blood

Posttransplant lymphoproliferative disorders (PTLD) are a severe complication arising in solid organ transplant patients. A strong correlation between Epstein-Barr virus (EBV) infection, the grade and type of immunosuppression, and the development of PTLD has been recognized. This article describes the development of a double-step polymerase chain reaction (PCR) assay for the quantification of EBV-deoxyribonucleic acid (DNA) to monitor EBV infection. Screening of samples containing >/=10(3) viral genomes/10(5) peripheral blood mononuclear cells (PBMC) or 100 micro L serum by a semiquantitative PCR assay is followed by quantification of the samples containing a high number of viral genomes in a quantitative-competitive (QC)-PCR assay. Screening by semiquantitative PCR selects samples with a high number of viral genomes for use in the more labor-intensive and expensive QC-PCR assay and thus provides a handy means for quantitative DNA analysis of large numbers of samples. Our double-step PCR assay can be employed in EBV viral load measurement in PBMC and serum samples to monitor transplanted patients at risk to develop PTLD.

Real-time Fluorescent PCR Techniques to Study Microbial-Host Interactions

This chapter describes how real-time polymerase chain reaction (PCR) performs and how it may be used to detect microbial pathogens and the relationship they form with their host. Research and diagnostic microbiology laboratories contain a mix of traditional and leading-edge, in-house and commercial assays for the detection of microbes and the effects they impart upon target tissues, organs, and systems. The PCR has undergone significant change over the last decade, to the extent that only a small proportion of scientists have been able or willing to keep abreast of the latest offerings. The chapter reviews these changes. It discusses the second-generation of PCR technology-kinetic or real-time PCR, a tool gaining widespread acceptance in many scientific disciplines but especially in the microbiology laboratory.

Cellular HIV-1 DNA load predicts HIV-RNA rebound and the outcome of highly active antiretroviral therapy

OBJECTIVE

To assess whether cellular HIV-1 DNA prior to highly active antiretroviral therapy (HAART) initiation predicts its outcome.

DESIGN AND METHODS

Patients included all 51 hemophiliacs of the Greek component of the Multicenter Hemophilia Cohort Study who had initiated HAART and for whom cryopreserved lymphocyte samples before HAART initiation were available. Cellular HIV-1 DNA quantification was performed by a molecular beacon-based real-time PCR assay in multiple samples per patient with a median (interquartile range) follow-up of 76 (45-102) weeks.

RESULTS

The median (range) baseline HIV-1 DNA load was 297 (< 10 to 3468) copies per 1 x 10(6) peripheral blood mononuclear cells. Baseline HIV-1 DNA load did not predict initial virological response (VR). None of the patients with initial VR and baseline HIV-1 DNA load at or below the median experienced a subsequent virological rebound, while the cumulative probability of virological rebound by week 104 was 55% among those with HIV-1 DNA load greater than the median (P < 0.008). Cellular HIV-1 DNA load was the only parameter associated with sustained virological response as shown by univariate or multivariate analyses [adjusted odds ratio (95% confidence interval) 0.197 (0.048-0.801) per 1 log10 increase in DNA copies, P = 0.023].

CONCLUSION

Low cellular HIV-1 DNA load is a marker of sustained virological response in patients with initial VR and it can reliably predict the long-term success of HAART.

Real-time PCR in the microbiology laboratory

Use of PCR in the field of molecular diagnostics has increased to the point where it is now accepted as the standard method for detecting nucleic acids from a number of sample and microbial types. However, conventional PCR was already an essential tool in the research laboratory. Real-time PCR has catalysed wider acceptance of PCR because it is more rapid, sensitive and reproducible, while the risk of carryover contamination is minimised. There is an increasing number of chemistries which are used to detect PCR products as they accumulate within a closed reaction vessel during real-time PCR. These include the non-specific DNA-binding fluorophores and the specific, fluorophore-labelled oligonucleotide probes, some of which will be discussed in detail. It is not only the technology that has changed with the introduction of real-time PCR. Accompanying changes have occurred in the traditional terminology of PCR, and these changes will be highlighted as they occur. Factors that have restricted the development of multiplex real-time PCR, as well as the role of real-time PCR in the quantitation and genotyping of the microbial causes of infectious disease, will also be discussed. Because the amplification hardware and the fluorogenic detection chemistries have evolved rapidly, this review aims to update the scientist on the current state of the art. Additionally, the advantages, limitations and general background of real-time PCR technology will be reviewed in the context of the microbiology laboratory.

Markers of local immunity in cervico-vaginal secretions of HIV infected women: implications for HIV shedding

OBJECTIVES

To link local proinflammatory cytokines with HIV related nucleic acids in cervico-vaginal secretions and the factors associated with them.

METHODS

An observational study on 60 HIV positive women attending the department of obstetrics and gynaecology, University of Pavia, Italy. HIV-1 RNA in plasma, proviral HIV-1-DNA, cell associated and cell free HIV-1 RNA in cervico-vaginal secretions were evaluated by competitive polymerase chain reaction (c-PCR) and reverse transcriptase PCR (cRT-PCR). IL-1beta, IL-6, and TNF-alpha were measured by ELISA in cervico-vaginal lavages. Multiple regression analysis on ordinal categorical variables was used to test for the simultaneous associations of clinical and microbiological variables on quartiles of cytokine concentrations in lavage samples.

RESULTS

Proviral HIV-1 DNA, cell associated and cell free HIV-1 RNA were detected in 76.7% (46/60), 70% (42/60), and 71.7% (43/60) of the patients, respectively. IL-1beta concentration was directly correlated with proviral HIV-DNA (Spearman rho = 0.35, p = 0.01) and cell associated HIV-RNA levels (Spearman rho = 0.263, p = 0.05). IL-1beta concentration (153.9 pg/ml) was higher (p<0.05) among women with cytological squamous intraepithelial lesion (SIL) than negative controls (73.4 pg/ml). In women with vaginal infection both IL-1beta (41.7 pg/ml) and IL-6 (10.2 pg/ml) were lower (p<0.05) in comparison to negative controls (144.9 pg/ml and 23.7 pg/ml, respectively). Women receiving stable antiretroviral therapy had significantly lower TNF-alpha (34.4 pg/ml versus 44.4 pg/ml, p = 0.04) and higher IL-6 (24.0 pg/ml versus 1.4 pg/ml, p = 0.004) levels in lavage samples compared to untreated women. The associations between the presence of SIL, antiretroviral treatment, vaginal infection and cytokine concentrations in cervico-vaginal secretions were confirmed in multiple regression analysis.

CONCLUSIONS

Local immune activation may modulate HIV-1 shedding in cervico-vaginal secretion with possible influence on vaginal physiology and host defence. Pharmacological agents lowering HIV-1 replication cause a shift to a pattern of cytokine production which seems less favourable to the transmission of the disease.

Development and evaluation of a quantitative competitive reverse transcription polymerase chain reaction (RT-PCR) for hepatitis C virus RNA in serum using transcribed thio-RNA as internal control

A method for quantitation of hepatitis C virus (HCV) RNA was developed based on competitive reverse transcription polymerase chain reaction (RT-PCR) using in vitro transcribed mutated thio-RNA as a competitor template. The thio-RNA is more resistant to RNAse and is stable over a year. This assay was compared with the commercially available Roche Amplicor HCV Monitor assay V 2.0 and real time PCR using SYBR green 1 dye method. A total of 18 pre-therapy serum samples from chronic hepatitis C cases were tested in parallel by the three assays. All samples could be quantitated using the in-house competitive RT-PCR and real time PCR and there was a significant correlation in the virus titer (P<0.05). However, 8 (44%) samples could not be quantified by Amplicor HCV Monitor assay, which has a lower detection range (10(2) to 10(5.5) copies/ml). The in-house method of competitive RT-PCR showed a detection range of 10(3) to 10(10) copies/ml. In the patients the mean viral titer was found to be (9.66+/-9.3)x10(6) copies/ml. Ten (55%) of the samples, assessed by the Amplicor HCV Monitor assay showed a mean viral titre of (1.13+/-0.75)x10(6) copies/ml, which was lower than the other two tests. The competitive PCR method and real time PCR could amplify all prevalent genotypes. This in-house quantitative competitive RT-PCR method is simple, cheap, reproducible and useful for estimation of HCV RNA load.

Polyomavirus BK DNA quantification assay to evaluate viral load in renal transplant recipients

BACKGROUND

Several studies have disclosed a correlation between polyomavirus BK (BKV) and interstitial nephritis in renal transplant recipients and its quantification in urine and serum is therefore required to assess the role of BKV infection in nephropathy.

OBJECTIVE

This paper describes a urine and serum BKV-DNA quantification protocol devised to evaluate the viral load.

STUDY DESIGN

Screening of samples containing > or =10(3)/ml viral genome copies by a semi-quantitative polymerase chain reaction (PCR) assay is followed by precise quantification of the samples containing a high number of viral genomes in a quantitative-competitive (QC)-PCR assay. Generation of the competitor construct relied on the different sizes of wild-type and competitor amplicons.

RESULTS AND CONCLUSIONS

Screening by semi-quantitative PCR selects samples with a high number of viral genomes for use in the more labor-intensive and -expensive QC-PCR assay and thus provides a handy means for quantitative DNA analysis of large numbers of samples. The results obtained in BKV-DNA quantification in urine and serum samples from 51 renal transplant recipients (22 on treatment with tacrolimus (FK506) and 29 on cyclosporine A (Cy A)) are interesting: BKV-DNA findings (43.1%) in urine samples are in agreement with the BKV urinary shedding reported in literature (5-45%). With regard to immunosuppressive treatment, the percentage of activation of the infection (revealed by BKV-DNA detection in urine samples) in the two groups of therapy is similar (40.9% vs 44.8%). The observation that the viral load in urine is dissociated with that of serum suggests that both parameters should be investigated in evaluation of the pathogenetic role of BKV reactivation in renal transplant recipients. Moreover, our BKV-DNA quantification protocol could be used to monitor viral load in urine and serum samples from renal transplant recipients so as to detect those at risk of nephropathy and monitor their response to immunosuppression reduction therapy if it occurs.

Differential expression of rod photoreceptor cGMP-phosphodiesterase alpha and beta subunits: mRNA and protein levels

The catalytic core of photoreceptor-specific cGMP-phosphodiesterase (PDE) consists of two subunits, PDEalpha and PDEbeta, that are homologous and have similar domain organization but are encoded by different genes. We have examined the PDEalpha and PDEbeta mRNA steady-state and protein levels as well as the biosynthesis rate of these proteins in developing and fully differentiated retinas. We have also determined the translational efficiency of PDE subunits and the role of their mRNA structures in regulating protein synthesis. In mature retinas, PDEalpha and PDEbeta are represented by approximately 1.5 x 108 and 7.5 x 108 copies/microg retinal mRNA, respectively. The levels of these transcripts in developing photoreceptors (P10) are approximately 75% of those at P30. Quantification of protein concentration indicated that PDEalpha and PDEbeta are equally expressed in developing and fully differentiated photoreceptors. Furthermore, the PDEalpha/PDEbeta ratios obtained throughout a 2-h pulsechase period revealed a similar turnover rate for both subunits. The observed discordance between the mRNA and protein levels of PDEalpha and PDEbeta suggested post-transcriptional regulation of their expression. We found that PDEalpha mRNA is translated more efficiently than either of the two PDEbeta transcripts expressed in retina. Therefore, the lower level of PDEalpha mRNA is compensated by its more efficient translation to achieve equimolar expression with PDEbeta. We also analyzed the effect of PDEalpha and PDEbeta mRNA 5'- and 3'-untranslated regions as well as that of their coding regions on protein synthesis. We determined that the PDE-coding regions play a critical role in the differential translation of these subunits.

Quantitative expression analysis of a Glyptapanteles indiensis polydnavirus protein tyrosine phosphatase gene in its natural lepidopteran host, Lymantria dispar

In the present study, expression of a newly identified Glyptapanteles indiensis polydnavirus (GiPDV) gene encoding a putative protein tyrosine phosphatase (PDVPTP) was monitored in vivo in the parasitized host, L. dispar, using one step RT-PCR. Expression levels of the PDVPTP transcript were also evaluated in various host tissues at different times post parasitization (pp) using RT quantitative competitive PCR (RT-qcPCR). Expression levels varied, with the most abundant transcript detected in host haemolymph 2 h pp. The high expression level in host haemolymph at an early stage of parasitization suggested a potential role for viral PDVPTP in disruption of the host immune system and protection of the endoparasitoid egg from encapsulation. Additionally, the PDVPTP gene or its homolog(s) mapped to more than one GiPDV genomic DNA segment, which may account for its increased level of expression in the absence of virus replication.

Acute temporal regulation of vascular endothelial growth/permeability factor expression and endothelial morphology in the baboon endometrium by ovarian steroids

We recently showed that endometrial vascular endothelial growth/permeability factor (VEG/PF) mRNA expression was decreased by ovariectomy of baboons and restored by chronic administration of estrogen. However, it remains to be determined whether this effect of estrogen reflects genomic up-regulation of VEG/PF and leads to an increase in microvascular permeability, an early physiological event in angiogenesis. Therefore, we determined the temporal expression of VEG/PF mRNA in glandular epithelial and stromal cells isolated by laser capture microdissection from and width of microvascular paracellular clefts that regulate vessel permeability in the endometrium of ovariectomized baboons after acute estradiol and/or progesterone administration. Endometrial VEG/PF mRNA levels were increased in five of five animals within 2 h of estradiol administration and remained elevated at 4 and 6 h. The net increase in glandular epithelial (7.31 +/- 2.72 attomol/fmol 18S ribosomal rRNA) and stromal (3.13 +/- 0.36) cell VEG/PF mRNA levels after estradiol administration was over 8-fold (P < 0.05) and 2.6-fold (P < 0.01) greater, respectively, than after vehicle (0.90 +/- 0.30, glands and 1.20 +/- 0.33, stroma). In contrast, endometrial VEG/PF mRNA expression was unaltered by progesterone. After estradiol treatment, endometrial paracellular cleft width was increased (P < 0.01) from a mean (+/-SE) of 71.6 +/- 4.6 nm at 0 h to 101.1 +/- 6.4 nm at 6 h, whereas vehicle or progesterone had no effect. We suggest that estrogen has a major role in regulating VEG/PF synthesis and early events in angiogenesis in the primate endometrium.

Antimicrobial activity of a new intact skin antisepsis formulation

Different antiseptic formulations have shown limitations when applied to disinfecting intact skin, notably short-term tolerability and/or efficacy. The purpose of this study was optimizing a new antiseptic formulation specifically targeted at intact skin disinfection and evaluating its in vitro microbicidal activity and in vivo efficacy.

METHODS

The biocidal properties of the antiseptic solution containing 0.5% chloramine-T diluted in 50% isopropyl alcohol (Cloral; Eurospital SpA Trieste, Italy) were measured in vitro versus gram-positive-, gram-negative-, and acid-alcohol-resistant germs and fungi with standard suspension tests in the presence of fetal bovine serum. Virus-inhibiting activity was evaluated in vitro against human cytomegalovirus, herpes simplex virus, poliovirus, hepatitis B virus, and hepatitis C virus. Tests used different methods for the different biologic and in vitro replication capacity of these human viruses. Lastly, Cloral tolerability and skin colonization retardation efficacy after disinfection were studied in vivo.

RESULTS

The antiseptic under review showed fast and sustained antimicrobial activity. The efficacy of Cloral against clinically important bacterial and viral pathogens and fungi was highlighted under the experimental conditions described in this article. Finally, microbial regrowth lag and no side effects were documented in vivo after disinfection of 11 volunteers.

CONCLUSIONS

A stable chloramine-T solution in isopropyl alcohol may be suggested for intact skin antisepsis.

Quantitation of NMDA receptor NR2 mRNA transcripts in human brain by competitive RT-PCR

The NMDA-selective ionotropic receptor constitutes one of the three principal classes of L-glutamate receptors within the mammalian brain. It plays key roles in neuronal differentiation and synapse consolidation, activity-dependent forms of synaptic plasticity, and excitatory amino acid-mediated neuronal toxicity [Lab. Invest., 68 (1993) 372-387]. NMDA receptors exist as multimeric complexes comprising proteins from two families, NR1 and NR2(A-D) [J. Biol. Chem., 271 (1996) 15669-15674]. Studies on recombinant receptors have revealed that while homomeric NR2 receptors are non-functional, co-expression of an NR1 with an NR2 subunit modulates the efficacy of the resulting channel [Nature, 357 (1992) 70-74]. The RT-PCR assay we describe here was developed to allow quantitation of all hNR2 transcripts in a single-tube PCR assay. Each hNR2 isoform is quantified on the basis of standard curves in which a known amount of synthetic ribonucleic acid competitor is co-amplified against total RNA. The protocol has been applied to the quantitation of hNR2 mRNA levels in autopsy brain. Used in conjunction with a method for the quantitation of hNR1 transcripts [Brain Res. Protoc., in press], a complete analysis of NMDA receptor mRNA expression can be obtained.

Tests for mitochondrial function and DNA: potentials and pitfalls

PURPOSE OF REVIEW

In the past few years, mitochondria have been carefully studied to ascertain whether and how in patients affected by HIV antiretroviral therapy is able to alter their functionality and exert a toxic effect on immune cells, as well as on cells present in other districts.

RECENT FINDINGS

A variety of in-vivo and ex-vivo models have been developed to investigate the functionality of mitochondria and DNA during a variety of physiopathological situations, including HIV infection and its treatment. Numerous technologies are available to study at the single-cell or at the single-organelle level a variety of parameters, such as membrane potential, the activity of respiratory chain enzymes, and DNA content or its sequence. As far as in-vitro studies are concerned, a substantial homogeneity of data exists, and several changes in different mitochondrial parameters have been described that depend upon the drug used, the cell model and the parameter investigated. On the other hand, different results have been reported on biological material collected from HIV-positive patients and immediately analysed. Ex-vivo studies showed that changes in mitochondrial DNA content or in the functionality of the organelle exist in some tissues or cells, but not in others.

SUMMARY

One of the possible causes of the discrepancies is the technologies used to investigate mitochondria, and this paper summarizes some of the pros and cons of the main methods used to study mitochondrial function or DNA.

Expression of vascular endothelial growth/permeability factor by endometrial glandular epithelial and stromal cells in baboons during the menstrual cycle and after ovariectomy

Vascular endothelial growth/permeability factor (VEG/PF) has a crucial role in angiogenesis, and neovascularization is essential in preparing the uterine endometrium for implantation. However, the regulation of VEG/PF synthesis by particular cell types of the endometrium during the human menstrual cycle is not well understood. Therefore, in the present study the baboon was used as a nonhuman primate to determine the role of the ovary in vivo in endometrial VEG/PF expression. VEG/PF mRNA levels were quantified by competitive RT-PCR in whole uterine endometrium and in glandular epithelial and stromal cells isolated from the endometrium by laser capture microdissection of baboons during the normal menstrual cycle and after ovariectomy, which decreased serum estradiol and progesterone to undetectable levels. Mean (+/-SE) levels (attomoles per micrograms of total RNA) of the 323-bp VEG/PF mRNA product, which reflected collective expression of all VEG/PF isoforms, in whole endometrium were 785 and 727 +/- 158 during the mid and late follicular phases, respectively, and 1108 +/- 320 during the midcycle surge in serum estradiol. VEG/PF mRNA levels then declined briefly before increasing to 1029 +/- 365 attomoles/ micro g RNA during the late luteal phase of the menstrual cycle. VEG/PF mRNA levels (attomoles per femtomole of 18S rRNA) were similar in glandular epithelial (2.27 +/- 1.11) and stromal (2.54 +/- 0.70) cells at the midcycle estradiol peak and the midluteal phase of the menstrual cycle (2.34 +/- 1.30 and 1.49 +/- 0.53, respectively). Immunocytochemical expression of VEG/PF protein was abundant in glandular and luminal epithelium, stroma, and vascular endothelium. Endometrial vessel density and percent vascularized area, determined by morphometric image analysis, were similar during the various stages of the baboon menstrual cycle. After ovariectomy, VEG/PF mRNA levels (attomoles per femtomole of 18S rRNA) in the endometrial glands (0.52 +/- 0.21) and stroma (0.22 +/- 0.11) were decreased to values that were approximately 20% and 10% (P < 0.05), respectively, of those in intact baboons during the midcycle estrogen surge. Moreover, there was relatively little VEG/PF protein immunostaining in the endometrial glands, stroma, and vascular endothelium after ovariectomy. In summary, VEG/PF mRNA and protein expression in glandular epithelial and stromal cells were markedly suppressed after ovariectomy, indicating that synthesis of this angiogenic factor in these endometrial cells is dependent upon a product(s) secreted by the ovary. Moreover, endometrial VEG/PF expression remained relatively constant and thus was available as a component of the angiogenic system throughout the menstrual cycle, presumably to progressively promote vascular reconstruction of the endometrium.

Quantitation of human immunodeficiency virus type 1 DNA forms with the second template switch in peripheral blood cells predicts disease progression independently of plasma RNA load

There are several forms of human immunodeficiency virus type 1 (HIV-1) DNA in peripheral blood T cells and lymph nodes in untreated HIV-1-infected individuals and in patients whose plasma HIV-1 RNA levels are suppressed by long-term combination antiretroviral therapy. However, it remains to be established whether the concentration of HIV-1 DNA in cells predicts the clinical outcome of HIV-1 infection. In this report, we measured the concentration of HIV-1 DNA forms which has undergone the second template switch (STS DNA) and 2-long-terminal-repeat DNA circles in peripheral blood mononuclear cell (PBMC) samples. To do this, we used molecular-beacon-based real-time PCR assays and studied 130 patients with hemophilia in the Multicenter Hemophilia Cohort Study. We assessed the influence of baseline HIV-1 STS DNA levels on the progression of HIV-1 disease in the absence of combination antiretroviral therapy by Kaplan-Meier and Cox regression analysis. Among the patients who progressed to AIDS, the median levels (interquartile ranges) of STS HIV-1 DNA in PBMC were significantly higher than those of patients who remained AIDS free during the 16 years of follow-up (1,017 [235 to 6,059] and 286 [31 to 732] copies per 10(6) PBMC, respectively; P < 0.0001). Rates of progression to death and development of AIDS varied significantly (log rank P < 0.001) by quartile distribution of HIV-1 STS DNA levels. After adjustment for age at seroconversion, baseline CD4(+) T-cell counts, plasma viral load, and T-cell-receptor excision circles, the relative hazards (RH) of death and AIDS were significantly increased with higher HIV-1 STS DNA levels (adjusted RH, 1.84 [95% confidence interval (CI), 1.30 to 2.59] and 2.62 [95% CI, 1.75 to 3.93] per 10-fold increase per 10(6) PBMC, respectively). HIV-1 STS DNA levels in each individual remained steady in longitudinal PBMC samples during 16 years of follow-up. Our findings show that the concentration of HIV-1 STS DNA in PBMC complements the HIV-1 RNA load in plasma in predicting the clinical outcome of HIV-1 disease. This parameter may have important implications for understanding the virological response to combination antiretroviral therapy.

New methods for the detection of HIV

In the past few years, several strides have been made in the ability to detect the presence of HIV-1 and HIV-2. This article discusses recent advances in serologic testing, including routine ELISA and Western blot tests, rapid HIV tests, home collection kits, and HIV tests using nonserum samples. The clinical application of nucleic acid-based tests also is discussed. Finally, appropriate use of these tests in both acute HIV-1 infection and in infants is reviewed.

Inhibition of HIV-1 Tat activity correlates with down-regulation of bcl-2 and results in reduction of angiogenesis and oncogenicity

The Tat protein of the human immunodeficiency virus type 1 promotes survival and growth and inhibits apoptosis of different cell types. These effects of Tat are attributed to the induction of bcl-2 gene expression. In this study we show that the blocking of both intracellular and extracellular Tat correlates with a decrease of bcl-2 transcripts, leading in vitro to a lower growth rate and attenuation of the transformed phenotype and in vivo to a reduced angiogenic and oncogenic activity of Tat-expressing cells. These results support the notion that bcl-2 is an effector of Tat-induced angiogenesis and oncogenesis and indicate that the blocking of Tat functions by immunoprophylactic, pharmacological, and gene therapy approaches may help to control oncogenesis during AIDS.

Effect of perinatal short-course zidovudine on the clinical and virological manifestations of HIV-1 subtype E infection in infants

BACKGROUND

The perinatal short-course zidovudine (ZDV) chemoprophylaxis that can reduce HIV-1 vertical transmission by 51% has been widely practiced in developing countries such as Thailand because of its simpler and less cost.

OBJECTIVES

To investigate the effects of short-course regimen of oral ZDV for prophylaxis of HIV-1 subtype E vertical transmission among 'break-through' HIV-1 infected infants.

STUDY DESIGN

The study analyzed clinical and virological outcomes of 80 infants, whose mothers received ZDV prophylaxis starting at 36 weeks gestation (group Z) and 37 infants whose mothers never received anti-retroviral drugs (group C), at the ages of 1-2, 4-6, and 12 months.

RESULTS

Of the 12 HIV-1 infected infants, 5/7 (71.4%) from group Z and 1/5 (20%) from group C progressed to a symptomatic clinical stage by the age 4-6 months. The intersample nucleotide distance of HIV-1 pol reverse transcriptase (RT) sequences of isolates collected at age of 1-2 months from group Z was significantly higher than that from group C (3.34 and 2.92%, P=0.02). All twelve virus isolates from infected infants were non syncytium inducing (NSI) and macrophage tropic strains; and 5/6 (83.3%) viruses from symptomatic infants were also T-tropic viruses. The symptomatic infants also had significantly higher HIV-1 nucleic acid quantitation than asymptomatic infants.

CONCLUSION

Our results preliminary suggested that infected infants who were perinatally exposed to ZDV may have a more rapid early disease progression with unfavorable viral manifestations than those without exposure to antiretroviral drug.

Nitroglycerin upregulates matrix metalloproteinase expression by human macrophages

OBJECTIVES

This study aimed to determine whether nitroglycerin (NTG) treatment affects matrix metalloproteinase (MMP) gene expression and activities in human macrophages.

BACKGROUND

Nitroglycerin is one of the most frequently used therapeutic agents for the symptomatic relief of stable or unstable coronary artery disease; however, its effects on vascular biology are poorly characterized. Despite its powerful vasodilator activity, NTG has not been shown to improve outcomes in coronary disease. We now describe evidence that NTG has potentially pro-inflammatory effects in human monocyte-derived macrophages (MDMs).

METHODS

Human monocytes were isolated from whole blood by elutriation and allowed to differentiate into macrophages over eight to 10 days. The MDMs were then treated for 4 or 24 h with control media, pharmacologically relevant doses of NTG or other nitric oxide donors. Matrix metalloproteinase activity was measured by zymography, protein levels measured by enzyme-linked immunosorbent assay and messenger ribonucleic acid (mRNA) levels were quantified by competitive reverse transcription-polymerase chain reaction.

RESULTS

The major MMP expressed by MDMs was MMP-9. Nitroglycerin treatment stimulated a dose-dependent increase in MMP-9 mRNA levels (NTG 200 pmol: 193 +/- 6% and NTG 2,000 pmol: 372 +/- 9% compared to controls, p < 0.005) and MMP-9 activity (NTG 200: 142 +/- 5.5% and NTG 2,000: 167 +/- 11% compared to controls, p < 0.005). Nitroglycerin 2,000 pmol also increased MMP-2 and MMP-7 mRNA levels to 187 +/- 8% and 183 +/- 21% of control values, respectively (p < 0.05). Furthermore, tissue inhibitor of metalloproteinase (TIMP)-1 (the major tissue inhibitor of MMPs) mRNA and protein levels were decreased in NTG 2,000 pmol-treated MDMs compared with control cells (mRNA: 67 +/- 7%, p < 0.005; protein: 45 +/- 5%, p < 0.005).

CONCLUSIONS

Nitroglycerin in pharmacologically relevant concentrations activates MMP but represses TIMP expression in human macrophages. The subsequent imbalance in MMP/TIMP expression associated with NTG treatment could promote matrix degradation, with potentially adverse effects on plaque stability.

Matrilin-3 in human articular cartilage: increased expression in osteoarthritis

OBJECTIVE

Matrilin-3 is a member of the recently described matrilin family of extracellular matrix proteins containing von Willebrand factor A-like domains. The matrilin-3 subunit can form homo-tetramers as well as hetero-oligomers together with subunits of matrilin-1 (cartilage matrix protein). It has a restricted tissue distribution and is strongly expressed in growing skeletal tissues. Detailed information on expression and distribution of extracellular matrix proteins is important to understand cartilage function in health and in disease like osteoarthritis (OA).

METHODS

Normal and osteoarthritic cartilage were systematically analysed for matrilin-3 expression, using immunohistochemistry, Western blot analysis, in situ hybridization, and quantitative PCR.

RESULTS

Our results indicate that matrilin-3 is a mandatory component of mature articular cartilage with its expression being restricted to chondrocytes from the tangential zone and the upper middle cartilage zone. Osteoarthritic cartilage samples with only moderate morphological osteoarthritic degenerations have elevated levels of matrilin-3 mRNA. In parallel, we found an increased deposition of matrilin-3 protein in the cartilage matrix. Matrilin-3 staining was diffusely distributed in the cartilage matrix, with no cellular staining being detectable. In cartilage samples with minor osteoarthritic lesions, matrilin-3 deposition was restricted to the middle zone and to the upper deep zone. A strong correlation was found between enhanced matrilin-3 gene and protein expression and the extent of tissue damage. Sections with severe osteoarthritic degeneration showed the highest amount of matrilin-3 mRNA, strong signals in in situ hybridization, and prominent protein deposition in the middle and deep cartilage zone.

CONCLUSION

We conclude that matrilin-3 is an integral component of human articular cartilage matrix and that the enhanced expression of matrilin-3 in OA may be a cellular response to the modified microenvironment in the disease.

Real-time PCR in virology

The use of the polymerase chain reaction (PCR) in molecular diagnostics has increased to the point where it is now accepted as the gold standard for detecting nucleic acids from a number of origins and it has become an essential tool in the research laboratory. Real-time PCR has engendered wider acceptance of the PCR due to its improved rapidity, sensitivity, reproducibility and the reduced risk of carry-over contamination. There are currently five main chemistries used for the detection of PCR product during real-time PCR. These are the DNA binding fluorophores, the 5' endonuclease, adjacent linear and hairpin oligoprobes and the self-fluorescing amplicons, which are described in detail. We also discuss factors that have restricted the development of multiplex real-time PCR as well as the role of real-time PCR in quantitating nucleic acids. Both amplification hardware and the fluorogenic detection chemistries have evolved rapidly as the understanding of real-time PCR has developed and this review aims to update the scientist on the current state of the art. We describe the background, advantages and limitations of real-time PCR and we review the literature as it applies to virus detection in the routine and research laboratory in order to focus on one of the many areas in which the application of real-time PCR has provided significant methodological benefits and improved patient outcomes. However, the technology discussed has been applied to other areas of microbiology as well as studies of gene expression and genetic disease.

Analytic validation of a competitive polymerase chain reaction assay for measuring Epstein-Barr viral load

Epstein-Barr virus (EBV) is associated with several benign and malignant diseases, and blood tests for EBV viral load show promise as markers of disease burden in affected patients. A commercial quantitative PCR method (BioSource International) was recently introduced to facilitate measuring viral load. It relies on coamplification of EBV DNA and a spiked competitor in plasma or serum, followed by semiautomated product detection on enzyme-linked immunosorbent assay (ELISA) plates. In the current study, analytic performance characteristics were assessed, and the authors describe several methodologic improvements to facilitate laboratory implementation. Rapid DNA extraction was accomplished using commercial silica spin columns, heat-labile uracil-N-glycosylase was used to inhibit amplicon contamination, and inexpensive agarose gels were used to screen for polymerase chain reaction products requiring ELISA plate quantitation. Accuracy and precision were verified using EBV DNA standards derived from two cell lines and plasmid containing viral sequences. The assay was sensitive to as few as five template copies per polymerase chain reaction and was linear across four orders of magnitude (correlation coefficient 0.995). When applied to matched plasma and serum samples from 15 patients with nasopharyngeal carcinoma, both sample types yielded similar viral load results. This commercial EBV viral load assay provides sensitive and quantitative detection of EBV DNA using equipment already available in many molecular diagnostic laboratories.

Developmental regulation of placental insulin-like growth factor (IGF)-II and IGF-binding protein-1 and -2 messenger RNA expression during primate pregnancy

The present study was conducted to determine the developmental expression of placental insulin-like growth factor (IGF)-II, IGF-binding protein (IGFBP)-1 and -2, and IGF-II receptor mRNA expression during baboon pregnancy and whether estrogen, the levels of which increase with advancing pregnancy, regulates placental trophoblast IGF-II mRNA expression. Levels of the IGF-II 6.1-kilobase (kb) and 4.9-kb mRNA transcripts determined by Northern blot analysis progressively increased three- to fourfold in placental syncytiotrophoblast and whole-villous tissue between early (Day 60), mid (Day 100), and late (Day 170) baboon gestation (term = 184 days). In contrast, syncytiotrophoblast IGFBP-1 and -2 mRNA levels decreased, and IGF-II receptor mRNA expression remained relatively constant, with advancing baboon pregnancy. Placental cytotrophoblast IGF-II mRNA levels determined by competitive reverse transcription-polymerase chain reaction on Day 54 of gestation were increased (P < 0.05) almost twofold at 18 h after acute administration of estradiol to baboons, whereas long-term estrogen treatment had no effect. We propose that these changes in trophoblast IGF expression would provide a mechanism for enhancing net bioavailability and bioreactivity of IGF-II locally to promote the growth and development of the placenta and, consequently, of the fetus during primate pregnancy.

Quantification of HIV-1 proviral DNA in patients with undetectable plasma viremia over long-term highly active antiretroviral therapy

OBJECTIVES

To assess the prognostic role of proviral DNA in peripheral blood mononuclear cells (PBMC) of patients with undetectable viremia over long-term highly active antiretroviral therapy (HAART).

METHODS

Eighty-two human immunodeficiency virus (HIV)-1-infected patients, free of acquired immunodeficiency syndrome (AIDS), received zidovudine plus lamivudine plus indinavir. Levels of plasma HIV-RNA, and PBMC proviral DNA and RNA unspliced (US) transcripts were evaluated by using competitive polymerase chain reaction (cPCR) assays, every 3 months over 1 year.

RESULTS

Among patients with undetectable viremia at baseline, 13 of 18 with CD4 cell count 350/mm3 or less and 12 of 16 with CD4 between 351 and 700/mm3, constantly maintained undetectable RNA levels; in these patients, a mean proviral DNA decrease of 0.67 6 0.7 and 1.03 6 0.53 log (P < 0.001), respectively, a significant decrease of RNA-US transcripts (P < 0.001), and significant correlations between decreases of proviral DNA and RNA-US transcripts (P = 0.008 and P < 0.001, respectively) were observed.

CONCLUSIONS

Proviral DNA quantitation permits the continued monitoring of HAART in patients with undetectable viremia.

Target cell populations of human immunodeficiency virus type 1 in peripheral blood lymphocytes with different chemokine receptors at various stages of disease progression

We studied the distribution of human immunodeficiency virus type 1 (HIV-1) DNA in CCR5-positive and -negative peripheral blood lymphocyte populations in HIV-1-infected individuals. While HIV-1 DNA in the CCR5-positive population showed no correlation with CD4 count, the increase of total HIV-1 DNA with lower CD4 count was mainly contributed by the increase of HIV-1 DNA in the CCR5-negative population. This might indicate the change in coreceptor usage from CCR5 to CXCR4 in later stages of disease progression. However, some of the samples with a high viral DNA load in the CCR5-negative population did not have any characteristic of the V3 loop sequence that is compatible with CXCR4 usage or the syncytium-inducing (SI) phenotype. We also did not find any known characteristic change predictive of the SI phenotype in V1 and V2 sequences. Our findings showed that there might be a shift in target cell populations during disease progression, and this shift was not necessarily associated with the genetic changes characteristic of CXCR4 usage.

Aromatase expression in prepuberal Sertoli cells: effect of thyroid hormone

Aromatase activity has recently been assumed as a Sertoli cell functional maturation marker since it is maximally expressed in prepuberal age then it dramatically decreases at puberty and is virtually absent in adult age. Neonatal hypothyroidism is associated with a prolonged proliferation of Sertoli cells. This immature stage persists concomitantly with a dramatic enhancement of aromatase activity reversed by triiodothyronine (T3) either in vivo or in vitro administration. Therefore, in the present study, after immunolocalisation of aromatase in the cytoplasm of cultured Sertoli cells as well as in testis section, we investigate the regulatory effects of T3 in the same cells just at the age when aromatase activity is reported to be maximally expressed. In this aim, the effects of thyroid hormone have been evaluated in 2-weeks-old rats, in basal condition and upon stimulation with dibutyryl cyclic AMP [(Bu)(2)cAMP] by simultaneously analysing three functional levels of aromatase, mRNA expression; protein content; enzymatic activity. Western-blot analysis of Sertoli cell extracts revealed a protein, which co-migrated with a 55 kDa protein detected in human placenta used a positive control. The presence of a functional P450 aromatase protein in purified Sertoli cells was confirmed by the measurement [3H]H(2)O released after incubation with [1beta-(3)H]androst-4-3,17-dione. At the dose used, T3 down-regulates basal aromatase activity, while aromatase mRNA expression was apparently not inhibited. It is noteworthy that aromatase content pattern evaluated by Western blot analysis did not tightly parallel the aromatase activity pattern which clearly displays the inhibitory effects of T3, in basal condition ad upon (Bu)(2)cAMP stimulation, simulating FSH stimulation. The detection of mRNA altered transcript coding for putative protein lacking both aromatic and heme-binding regions upon T3 treatment and unable to convert androgens into estrogens, provides a reasonable explanation for the observed discrepancies between aromatase protein pattern, P450arom mRNA levels and aromatase activity. The authors conclude that although the altered transcript induced by prolonged exposure to T3 is a mechanism by which T3 may down regulate aromatase activity, it cannot be ruled out a direct effect of this hormone at the transcription levels since a recognisable emisite for potential TR(s) binding is located in the promoter region of aromatase gene. Thus a further investigation on T3 modulator role on aromatase gene promoter should be pursued even utilising higher doses of T3.

Factors associated with nucleic acids related to human immunodeficiency virus type 1 in cervico-vaginal secretions

OBJECTIVE

To assess HIV-related nucleic acids in cervico-vaginal secretions and the factors associated with them.

DESIGN

Observational study.

SETTING

Department of Obstetrics and Gynaecology, University of Pavia, Italy.

POPULATION

HIV-positive patients attending a cytology service.

METHODS

Paired blood and cervico-vaginal lavage samples were obtained from 122 known HIV-seropositive patients during periodic visits for cytologic screening for lower genital tract neoplasia. Vaginal specimens for the diagnosis of bacterial vaginosis, trichomonas vaginalis and candida infection were also obtained. HIV-1-RNA in plasma, proviral HIV-1-DNA, cell associated and cell-free HIV-1 RNA in cervico-vaginal secretions were quantitatively evaluated by competitive polymerase chain reaction (c-PCR) and reverse transcriptase PCR (cRT-PCR).

MAIN OUTCOME MEASURE

Prevalences of HIV related nucleic acids in cervico-vaginal secretions and their univariate and multivariate associations with clinical variables.

RESULTS

Proviral HIV-1 DNA, cell-associated and cell-free HIV-1 RNA were detected in 50% (61/122), 37.7% (46/122) and 32.8% (40/122) of the patients, respectively. In logistic regression analysis, the presence of HIV-1 RNA in blood was the factor which correlated best with the detection of HIV-1 DNA (OR = 5.48, 95% CI = 2.28-13.20), cell-associated (OR = 4.85; 95% CI = 1.89-12.45) and cell-free HIV-1 RNA (OR = 4.63, 95% CI = 1.74-12.33) in cervico-vaginal samples. However, between 20% and to 35% of patients who tested negative for blood HIV-1 RNA were positive for either HIV-1 DNA or HIV-1 RNA detection in cervico-vaginal lavages. Bacterial vaginosis was associated with an increased prevalence of cell-associated (OR = 3.58, 95% CI = 1.22-10.54) and cell-free HIV-1 RNA (OR = 2.94, 95% CI = 1.0-8.7) detection in cervico-vaginal secretions. Additional factors associated with increased prevalence of HIV-1 RNA detection were advanced stage of HIV disease and vulvovaginal candidiasis.

CONCLUSIONS

Although the presence of HIV-1 RNA in blood is the factor which correlates best with the detection of HIV-related nucleic acids in cervico-vaginal secretions, the shedding of HIV in the genital tract can occur in 20-30% of non-viremic subjects. Bacterial vaginosis and candida infection could have a facilitating role in local HIV viral replication and shedding.

Developmental regulation of vascular endothelial growth/permeability factor messenger ribonucleic acid levels in and vascularization of the villous placenta during baboon pregnancy

Vascular endothelial growth/permeability factor (VEG/PF) has an important role in angiogenesis; however, very little is known about the developmental regulation of VEG/PF and the vascular system within the placenta during human pregnancy. In the present study, therefore, a developmental approach was used in the baboon to determine the placental source of VEG/PF and its fms-like tyrosine kinase (flt-1) and kinase-insert domain containing (KDR/flk-1) receptors, and whether the rise in estrogen with advancing pregnancy was associated with a corresponding increase in placental VEG/PF expression and vascularization. VEG/PF messenger RNA (mRNA) levels were determined by competitive RT-PCR in villous cell fractions isolated by Percoll gradient centrifugation from placentas obtained on days 45 and 54 (very early), 60 (early), 100 (mid), and 165-170 (late) of baboon pregnancy (term = 184 days). Maternal peripheral serum estradiol increased from very low concentrations early in gestation (0.15-0.20 ng/ml) to an early surge of over 2.5 ng/ml on days 60-85, and peak levels of 4-6 ng/ml late in baboon pregnancy. VEG/PF mRNA was expressed in low level in the syncytiotrophoblast (<2,000 attomol/microgram total RNA), and values in this fraction did not change significantly with advancing gestation. VEG/PF mRNA expression was slightly greater in the inner villous core cell fraction; however, levels decreased (P < 0.05) between early and late gestation. Cytotrophoblasts were a major source of VEG/PF mRNA and levels increased (P < 0.01) from 3,631 +/- 844 attomol/microgram total RNA on day 45 to 25,807 +/- 5,873 attomol/microgram total RNA on day 170. VEG/PF protein expression determined by immunocytochemistry was abundant in cytotrophoblasts and lower in the syncytiotrophoblast and inner villous core cells. The flt-1 and KDR/flk-1 receptors were expressed in the vascular endothelial cells of the baboon villous placenta. The percentage of villous placenta occupied by blood vessels and the number of vessels/mm(2) villous tissue, determined by image analysis, progressively increased (P < 0.001; r = 0.97) from 3.4 +/- 0.2% and 447 +/- 29, respectively, on day 54 to 15.9 +/- 0.9% and 1,375 +/- 71, respectively, on day 170. In summary, the present study shows that villous cytotrophoblasts were a major source of VEG/PF mRNA and protein in the baboon villous placenta, and that cytotrophoblast VEG/PF mRNA levels and vascularization of the villous placenta closely paralleled the increase in estradiol concentrations of advancing pregnancy. These results are consistent with the concept that estrogen has an important role in establishing the new vascular system within the developing placenta during primate pregnancy and that VEG/PF mediates this process.

Matrix metalloproteinases and their inhibitors

Matrix metalloproteinases (MMPs) are a group of 16 enzymes that are capable of degrading extracellular matrix components. Their catalytic function is dependent on a zinc ion in the active center. MMPs are separated in three groups: gelatinases (type IV-collagenases), stromelysins, and interstitial collagenases. Their physiological and pathological significance is to modulate the extracellular matrix-e. g., in embryogenesis, in the ovarian cycles, or in inflammatory diseases such as rheumatoid arthritis or fibrosis of the liver or kidney (1,2).

Use of an internal control in a nested-PCR assay for Mycoplasma hyopneumoniae detection and quantification in tracheobronchiolar washings from pigs

We have previously reported a nested PCR assay for the detection of Mycoplasma hyopneumoniae directly in tracheobronchiolar washings from living pigs in field conditions. Here, we describe the construction and use of an internal control to monitor the presence of PCR inhibitors. A PCR modified target DNA was constructed by insertion of a small DNA fragment into the M. hyopneumoniae specific DNA target. We have demonstrated that the internal control failed to be amplified in only three tracheobronchiolar washings samples out of the 362 tested. This control molecule was inserted in a Spiroplasma citri derived plasmid vector and introduced into S. citri cells by electroporation. After a few passages we ensured that the recombinant plasmid became inserted into the genome of S. citri. PCR amplification of the DNA of this transformed S. citri strain using nested PCR primers led to amplification of a 900-bp fragment which can be discriminated from the M. hyopneumoniae PCR product 700 bp. The S. citri transformants with the integrated internal control were added to the tracheobronchiolar washings prior to PCR and used as an internal control to check the efficiency of sample processing, and to demonstrate the presence of inhibitors. Furthermore, we have been able to estimate the number of mycoplasma cells in the tracheobronchiolar washings. Quantitation was performed by comparing the PCR signal intensity of the specific M. hyopneumoniae template with known concentrations of the S. citri competitor. The titer in tracheobronchiolar washings ranged approximatively from 10(4)to 10(8)M. hyopneumoniae cells per ml of clinical specimen. Quantitative PCR can be a useful tool for monitoring the progression of M. hyopneumoniae in the disease process.

Quantitation of polyomavirus DNA by a competitive nested polymerase chain reaction

A new method to quantitate small amounts of DNA in clinical specimens is described. The method, a nested competitive polymerase chain reaction (ncPCR), is able to quantitate between 10 and 10(6) copies per tube of polyomavirus DNA and shows good reproducibility when clinical samples are analysed. Throughout the whole procedure, an internal standard (IS) competes for the primers with the target DNA. The internal standard, a heterologous sequence containing the four primer recognition sites, was constructed using a modification of the 'MIMIC' approach that is useful for obtaining competitor sequences for any viral, bacterial or eukaryotic target. The ncPCR method for polyomavirus was applied to cerebrospinal fluids (CSF) from AIDS patients with progressive multifocal leukoencephalopathy (PML) and urine specimens from bone marrow transplant patients affected by haemorrhagic cystitis. The results obtained suggest that the ncPCR method is a sensitive and useful method for quantitating genomic load in clinical samples.

Patterns of CYP26 expression in human prenatal cephalic and hepatic tissues indicate an important role during early brain development

CYP26 (P450RAI) catalyzes catabolic retinoic acid (RA) hydroxylation and thereby appears to play a critical role in retinoid signaling pathways during development. In this study, a quantitative competitive reverse transcriptase-polymerase chain reaction (RT-PCR) assay was developed for evaluation of CYP26 message levels in human prenatal tissues. Statistical analyses of transcription levels in 12 prenatal human brains and six prenatal human livers demonstrated good sensitivity and reproducibility. Quantitative profiles of CYP26 gene expression in early (gestational days 57-110) prenatal cephalic and hepatic tissues and comparisons with adult counterparts are reported for the first time. Prenatal cephalic tissues at days 57-67 exhibited values of 1950+/-420 (CYP26 molecules/10(6) GAPDH molecules) whereas prenatal cephalic tissues at days 105-110 exhibited values of 22300+/-4450 (CYP26 molecules/10(6) GAPDH molecules), indicating a sharp developmental increase (approximately 11-fold). Levels in human adult cephalic tissues were slightly less than the prenatal cephalic levels measured during the earliest stages of gestation and were approximately 3-fold lower than those measured in adult human hepatic tissues. Levels in human prenatal hepatic tissues at days 63-110 gestation were less than 800 (CYP26 molecules/10(6) GAPDH molecules) and did not exhibit developmental increases. Considered together, the data have strong implications for the importance of CYP26 in early development of the human brain.