Sensitivity of multiplex real-time PCR reactions, using the LightCycler and the ABI PRISM 7700 Sequence Detection System, is dependent on the concentration of the DNA polymerase

Variability and cost implications of three generations of the Roche LightCycler® 480

Real time PCR has become a dominant method for the highly sensitive detection of pathogens in clinical material. Real time PCR can generate a fluorescence signal by using fluorescence labelled probes, allowing us to detect and semi quantify the amount of amplified DNA. Here we test the variability of the detection system and cost implications of three different versions of the LightCycler® 480 (LC480), focusing on the intensity of fluorescence and Cq in monoplex and multiplex rtPCRs.

For gastro-intestinal pathogens there was no correlation between the intensity of fluorescence and the Cq value in the different LC480 types. For probes with the dyes FAM^TM, HEX^TM, Cy5 and Red610 a higher fluorescence intensity was seen in LC480 type II and III compared to LC480 type I. After lowering the probe concentration for the Cy5 dye three-fold (from 0.3μM to 0.1μM) the Cq value remains the same and the intensity of fluorescence decreases. For the LC480 type II and III the difference in fluorescence intensity was much more extreme. The concentration of the different labelled probes can be lowered at least six-fold in LC480 type II and III cyclers while maintaining a fluorescence intensity as high as achieved in the LC480 type I with undiluted probe. In conclusion, the strength of the fluorescence signal of the LightCycler® 480 type III is superior to that of LightCycler® 480 types I and II, allowing the use of lower probe concentrations for all dyes, particularly for the dyes Red610 and Cy5. This results in a two thirds reduction in PCR probe costs. Switching to these newer machines for real-time PCR can reduce dye labelled probe consumption and thus reduce costs significantly.

Overexpression of p16ink4a regulates the Wnt/β‑catenin signaling pathway in pancreatic cancer cells

The pathogenesis and etiology of pancreatic cancer remain to be fully elucidated; therefore, associated investigations are required to improve the outcome and prognosis of patients. In the present study, the effects of the overexpression of p16ink4a on the Wnt/β‑catenin signaling pathway were investigated in pancreatic cancer cell lines. Two pancreatic cancer cell lines, Bxpc‑3 and Miapaca‑2, characterized by low expression of p16ink4a, were transfected with the pc‑DNA3.0‑p16ink4a plasmid. After 24 h, Reverse transcription‑polymerase chain reaction and western blot analyses were performed to evaluate the expression of p16ink4a, β‑catenin, which is a key molecule in the Wnt/β‑catenin signaling pathway, c‑myc and cyclin D1, which are molecules downstream of β‑catenin. The expression of p16ink4a was significantly upregulated in the transfected cells. Consequently, the expression of β‑catenin was inhibited, whereas the expression levels of c‑myc and cyclin D1 were not altered significantly. The increased expression of p16ink4a may affect the activity of Wnt/β‑catenin signaling through modulation of the expression of β‑catenin. The results of the present study provide information for the future development of targeted treatments for pancreatic cancer.

Advances in multiplex nucleic acid diagnostics for blood-borne pathogens: promises and pitfalls

The large number of blood-borne viruses, bacteria and parasites currently of concern, as well as many newly emerging pathogens, presents a daunting challenge to protection of the safety of blood for transfusion and diagnosing infectious diseases. Focusing on nucleic acid diagnostic tests, multiplex devices are coming into use with many more in various developmental stages that promise to offer solutions to the clinical need. The characteristics, advantages and disadvantages of platforms in clinical use and at the research and development stage are examined here. The presence of multiple assays and associated reagents operating simultaneously on one platform, implementation in traditional clinical laboratories and regulatory review will present special challenges. Fortunately, clinical laboratories have made dramatic technical progress in the last two decades and regulatory agencies have publicly expressed support for development of multiplex devices.

Different real-time PCR systems yield different gene expression values

Most polymerase chain reaction (PCR) systems employ pre-determined settings and proprietary master mixes that differ from one system to another. It is not known whether these differences may affect gene expression values. We compared two major real-time PCR technologies, from Life Technologies (formerly Applied Biosystems; ABI7500) and Roche Applied Science (LC480), using their default settings, proprietary reagents and other potential variables such as ramp rates and magnesium concentrations. We analyzed four genes (IL-8, COX2, ID-1 and CXCR2) in a human breast cancer cell line and found that two of them, though readily detected by ABI, were not detected using the Roche system. By altering some of the parameters and reagents used in the Roche protocol, we were able to detect expression of these two genes, but the level remained far below that detected by ABI, particularly for ID-1. When we tested three additional ID-1 primer pairs, two of these primer pairs yielded higher expression values in the LC system, yet still significantly lower than the values obtained in ABI. These results suggest critical differences in these two PCR systems, which could result in significant discrepancies in results reported by different laboratories.

Comparative evaluation of published cytomegalovirus primers for rapid real-time PCR: which are the most sensitive?

Standardization of human cytomegalovirus (CMV) PCR is highly recommended. As primer design is essential for PCR sensitivity, this study evaluated all published CMV primer pairs to identify the most sensitive for single-round real-time PCR. PubMed (1993-2004) was searched for original papers aimed at CMV PCR. Fifty-seven papers were identified revealing 82 different primer pairs. Of these, 17 primer sets were selected for empirical study, as they were either used in real-time PCR or were evaluated comparatively by conventional PCR. After optimizing the PCR conditions, these primer sets were evaluated by real-time PCR using a SYBR Green format. Analytical sensitivities were assessed by testing the reference standard CMV strain AD169. A blast search was performed to identify mismatches with published sequences. Additionally, 60 clinical samples were tested with the three primer sets showing highest analytical sensitivity and the best match to all CMV strains. Three primer sets located in the glycoprotein B (UL55) gene region were found to be the most sensitive using strain AD169. However, two of these showed a considerable number of mismatches with clinical isolates in a blast search. Instead, two other pairs from the lower matrix phosphoprotein (UL83) gene and DNA polymerase (UL54) gene showed reasonable sensitivity and no mismatches with clinical isolates. These three pairs were further tested with clinical samples, which indicated that the two primer sets from UL55 and UL54 were the most sensitive. Interestingly, the analytical sensitivity of the PCR was inversely correlated with the size of the PCR product. In conclusion, these two primer pairs are recommended for a standardized, highly sensitive, real-time PCR.

Rapid simultaneous detection by real-time PCR of cytomegalovirus UL97 mutations in codons 460 and 520 conferring ganciclovir resistance

Ganciclovir (GCV) resistance is an emerging problem for transplant recipients. A sensitive and rapid real-time PCR approach for simultaneous and semiquantitative detection of human cytomegalovirus (HCMV) UL97 mutations in codons 460/520 was established by LightCycler and confirmed by restriction fragment length polymorphism and sequencing. Results from HCMV laboratory strains were compared with results from 11 GCV-resistant clinical isolates.

Bordetella holmesii DNA is not detected in nasopharyngeal swabs from Finnish and Dutch patients with suspected pertussis

Bordetella holmesii is a Gram-negative bacterium first identified in 1995. It can cause pertussis-like symptoms in humans. B. holmesii contains insertion sequences IS481 and IS1001, two frequently used targets in the PCR diagnosis of Bordetella pertussis and Bordetella parapertussis infections. To investigate the prevalence of B. holmesii in Finnish and Dutch patients with pertussis-like symptoms and whether B. holmesii has caused any false-positive results in diagnostic PCRs, B. holmesii-specific real-time PCRs were developed. The Finnish methods were conventional IS481 PCR and B. holmesii-specific real-time PCR (LightCycler, Roche) targeting the B. holmesii recA gene. The Dutch methods were IS481 and IS1001 PCRs with conventional or real-time formats and B. holmesii-specific real-time PCR targeting the homologue of IS1001. Of 11,319 nasopharyngeal swabs, 2804 were collected from Finnish patients from 2000 to 2003, and 8515 from Dutch patients from 1992 to 2003. B. holmesii DNA was not found in the samples analysed. The results suggest that B. holmesii is not among the causative agents of pertussis-like symptoms in Finnish and Dutch patients and thus does not in practice confound IS481 and IS1001 PCRs.

Real-Time Fluorescent Polymerase Chain Reaction Detection of Phytophthora ramorum and Phytophthora pseudosyringae Using Mitochondrial Gene Regions

ABSTRACT A real-time fluorescent polymerase chain reaction (PCR) detection method for the sudden oak death pathogen Phytophthora ramorum was developed based on mitochondrial DNA sequence with an ABI Prism 7700 (TaqMan) Sequence Detection System. Primers and probes were also developed for detecting P. pseudosyringae, a newly described species that causes symptoms similar to P. ramorum on certain hosts. The species-specific primer-probe systems were combined in a multiplex assay with a plant primer-probe system to allow plant DNA present in extracted samples to serve as a positive control in each reaction. The lower limit of detection of P. ramorum DNA was 1 fg of genomic DNA, lower than for many other described PCR procedures for detecting Phytophthora species. The assay was also used in a three-way multiplex format to simultaneously detect P. ramorum, P. pseudosyringae, and plant DNA in a single tube. P. ramorum was detected down to a 10(-5) dilution of extracted tissue of artificially infected rhododendron 'Cunningham's White', and the amount of pathogen DNA present in the infected tissue was estimated using a standard curve. The multiplex assay was also used to detect P. ramorum in infected California field samples from several hosts determined to contain the pathogen by other methods. The real-time PCR assay we describe is highly sensitive and specific, and has several advantages over conventional PCR assays used for P. ramorum detection to confirm positive P. ramorum finds in nurseries and elsewhere.

Detection of biological threat agents by real-time PCR: comparison of assay performance on the R.A.P.I.D., the LightCycler, and the Smart Cycler platforms

BACKGROUND

Rapid detection of biological threat agents is critical for timely therapeutic administration. Fluorogenic PCR provides a rapid, sensitive, and specific tool for molecular identification of these agents. We compared the performance of assays for 7 biological threat agents on the Idaho Technology, Inc. R.A.P.I.D., the Roche LightCycler, and the Cepheid Smart Cycler.

METHODS

Real-time PCR primers and dual-labeled fluorogenic probes were designed to detect Bacillus anthracis, Brucella species, Clostridium botulinum, Coxiella burnetii, Francisella tularensis, Staphylococcus aureus, and Yersinia pestis. DNA amplification assays were optimized by use of Idaho Technology buffers and deoxynucleotide triphosphates supplemented with Invitrogen Platinum Taq DNA polymerase, and were subsequently tested for sensitivity and specificity on the R.A.P.I.D., the LightCycler, and the Smart Cycler.

RESULTS

Limit of detection experiments indicated that assay performance was comparable among the platforms tested. Exclusivity and inclusivity testing with a general bacterial nucleic acid cross-reactivity panel containing 60 DNAs and agent-specific panels containing nearest neighbors for the organisms of interest indicated that all assays were specific for their intended targets.

CONCLUSION

With minor supplementation, such as the addition of Smart Cycler Additive Reagent to the Idaho Technology buffers, assays for DNA templates from biological threat agents demonstrated similar performance, sensitivity, and specificity on all 3 platforms.

Nucleic acid-based methods for the detection of bacterial pathogens: Present and future considerations for the clinical laboratory

BACKGROUND

Recent advances in nucleic acid-based methods to detect bacteria offer increased sensitivity and specificity over traditional microbiological techniques. The potential benefit of nucleic acid-based testing to the clinical laboratory is reduced time to diagnosis, high throughput, and accurate and reliable results.

METHODS

Several PCR and hybridization tests are commercially available for specific organism detection. Furthermore, hundreds of nucleic acid-based bacterial detection tests have been published in the literature and could be adapted for use in the clinical setting. Contamination potential, lack of standardization or validation for some assays, complex interpretation of results, and increased cost are possible limitations of these tests, however, and must be carefully considered before implementing them in the clinical laboratory.

CONCLUSIONS

A major area of advancement in nucleic acid-based assay development has been for specific and broad-range detection of bacterial pathogens.

Effects of sulfonylureas, α-endosulfine counterparts, on glomerulosclerosis in type 1 and type 2 models of diabetes

BACKGROUND

Previously, we showed the expression of a unique sulfonylurea receptor (SUR) and its putative endogenous ligand, alpha-endosulfine, in mesangial cells and isolated glomeruli. Further, this ligand was up-regulated by high glucose concentration. To investigate the possible role of alpha-endosulfine up-regulation in diabetes, we administered sulfonylureas, the exogenous ligands of SUR, to diabetic animals.

METHODS

In streptozotocin-induced, insulin-deficient, diabetic rats, glomerulosclerosis, albuminuria, glomerular expression of fibronectin mRNA, and glomerular filtration rate (GFR) were studied for various periods up to 36 weeks. Several rat groups received either glibenclamide or tolazamide during the entire study period. Also, glomerulosclerosis and albuminuria were determined in insulin-resistant db/db mice, at 26 weeks of treatment with tolazamide.

RESULTS

Sulfonylureas did not improve hyperglycemia or reduce glycosylated hemoglobin levels. In insulin-deficient diabetic rats, sulfonylureas significantly decreased the degree of glomerulosclerosis and completely reversed the enhanced albumin excretion. Also, glibenclamide reduced diabetes-induced glomerular overexpression of fibronectin mRNA. Because glibenclamide may improve the afferent arteriolar dilatation of diabetes, thereby reducing glomerular hyperfiltration, its effect on GFR was determined. Glibenclamide did not alter glomerular hyperfiltration or renal hypertrophy, regardless of the intensity of hyperglycemia. Finally, in insulin-resistant mice, tolazamide did not alter the extent of diabetic glomerulosclerosis or increased albuminuria.

CONCLUSION

Long-term treatment with sulfonylureas completely prevents glomerular injury in insulin-deficient diabetes in rats. However, this protective effect is not demonstrable in an insulin-resistant model of the disease. We postulate that mesangial alpha-endosulfine up-regulation in the hyperglycemic milieu of insulin-deficient diabetes may retard glomerular extracellular matrix formation and mesangial expansion.

A multiplexed PCR-coupled liquid bead array for the simultaneous detection of four biothreat agents

We have developed a 10-plexed PCR assay coupled to a 12-plexed liquid bead array to rapidly screen environmental samples for B. anthracis, Y. pestis, F. tularensis, and B. melitensis. Highly validated species-specific primer sets were used to simultaneously amplify multiple diagnostic regions unique to each individual pathogen. Resolution of the mix of amplified products was achieved by PCR product hybridization to corresponding probe sequences, attached to unique sets of fluorescent beads. The hybridized beads were processed through a flow cytometer, which detected presence and quantity of each PCR product. The assay was optimized to allow for maximum sensitivity in a multiplexed format. A high-throughput demonstration was performed where 384 simulated environmental samples were spiked with different amounts of B. thuringensis spores and pathogen DNA. The samples were robotically processed to extract DNA and arrayed for multiplexed PCR-liquid bead detection. The assay correctly identified the presence or absence of each pathogen and collected over 3000 individual data points within a single 8-h shift for approximately $4.00 material costs per environmental sample in a 10-plexed assay.

Simultaneous detection of enteric viruses by multiplex real-time RT-PCR

A multiplex real-time RT-PCR protocol for the simultaneous detection of noroviruses ("Norwalk-like viruses") of genogroups I and II, human astroviruses and enteroviruses is described. The protocol was developed and evaluated using the LightCycler and corresponding SYBR Green reagents. New primers were designed within conserved genome regions to optimize the detection range of virus subtypes of each genus. To enable the development of a multiplex PCR assay within one tube (capillary), similar mastermix- and cycling-conditions were respected for each individual primer system. Subsequent melting curve analysis allowed the determination of possible dual-contaminations of entero- and noro- or astroviruses by the formation of dual peaks. Special care was taken to minimize the loss of sensitivity, since the detection of small viral contaminations is a crucial parameter especially for food analysis. The multiplex assay was compared successfully to the single SYBR Green assay, and revealed to be at least 10 times more sensitive than the one obtained with an endpoint PCR thermocycler protocol published previously.