Recent advances in the polymerase chain reaction

Competitive amplification and unspecific amplification in polymerase chain reaction with confronting two-pair primers

Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) is an inexpensive, time-saving genotyping method that is applicable for most single nucleotide polymorphisms. To date, we have applied PCR-CTPP successfully for the genotyping of more than 30 polymorphisms. This paper demonstrates the differences in DNA amplification among different annealing temperatures of PCR-CTPP with given melting temperatures for four primers. The NQO1 C609T (Pro187Ser) polymorphism was used as an example. Two sets of four primers were applied for PCR-CTPP; the first set with different melting temperatures (Tms), and the second with similar Tms. The comparisons with one-pair primer PCR (allele-specific PCR) revealed that PCR-CTPP amplified DNA more specifically than allele-specific PCR. The primers with different Tms caused competitive DNA amplification for heterozygous genotype. Four primers with similar Tms amplified both alleles unspecifically at a lower annealing temperature, while the same DNA samples were correctly genotyped under an optimal annealing temperature. These findings are unique for PCR-CTPP, and important characteristics when the primers and annealing temperatures in PCR-CTPP are designed. The knowledge of these characteristics will extend the applicability of PCR-CTPP for polymorphism genotyping.

Downregulation of connexin 43 expression by high glucose reduces gap junction activity in microvascular endothelial cells

Impairment of retinal vascular homeostasis is associated with the development and progression of diabetic retinopathy involving gap junction intercellular communication (GJIC) activity. The principal gap junction protein of intercellular communication, connexin, was investigated to determine the effects of high glucose concentrations on the expression of endothelial-specific connexins (Cx37, Cx40, and Cx43), connexin phosphorylation pattern, and GJIC activity. Rat microvascular endothelial (RME) cells grown in high (30 mmol/l)-glucose medium for 9 days had reduced Cx43 expression: Cx43 mRNA (68 +/- 13% of control; P = 0.019, n = 5) and protein (55.6 +/- 16% of control; P = 0.003, n = 5) levels were reduced; however, Cx37 and Cx40 expression was not affected. Using alkaline phosphatase and Western blot analyses, we identified three forms of Cx43: a nonphosphorylated form (P0) and two phosphorylated forms (P1 and P2). Expression of all three forms was decreased in cells grown in high-glucose medium: PO, 73 +/- 15% of control (P = 0.04); P1, 57 +/- 16% of control (P = 0.01); and P2, 42 +/- 22% of control (P = 0.006). Using immunofluorescence microscopy, we observed Cx43 localization at specific sites of contact (plaques) between adjacent cells. In cells grown in high-glucose medium, we observed reduced plaque counts (63 +/- 6% of control; P = 0.009) and decreased intensity of Cx43 immunofluorescence compared with cells grown in normal medium. Furthermore, using scrape load dye transfer (SLDT) technique, we found that these cells exhibited reduced GJIC activity (60% of control; P = 0.01, n = 5). The reduction in GJIC activity correlated with the decreased Cx43 protein levels (r = 0.9). These results indicate that high glucose concentrations inhibited GJIC activity by reducing Cx43 synthesis in RME cells. Impaired intercellular communication may contribute to breakdown of homeostatic balance in diabetic microangiopathy.

Validity of PCR with emphasis on variable number of tandem repeat analysis

OBJECTIVES

Variable number of tandem repeat polymorphisms (VNTR) are frequently analyzed by PCR in genetic, epidemiologic and forensic studies. We wanted to explore the validity of these PCR analyses.

DESIGN AND METHODS

The amplification of the different alleles of the 17- and the 44-bp VNTR of the serotonin transporter gene and the 39-bp VNTR of the glycoprotein Ibalpha gene was analyzed. We studied the effects of the parameters magnesium, dimethylsulfoxide, 7-deaza-dGTP, formamide, betaine, PCR temperatures and different types of polymerases.

RESULTS

In all three VNTR polymorphisms selective amplification of one of the alleles of heterozygous individuals could be obtained by change of the magnesium concentration. This problem could be minimized by a combination of Taq- and Pwo-polymerases and by use of 7-deaza-dGTP.

CONCLUSION

PCR analysis of all of these VNTRs may give reproducibly wrong results in truly heterozygous subjects due to selective amplification of only one of the alleles.

Antisense oligonucleotides modulate high glucose-induced laminin overexpression and cell proliferation: a potential for therapeutic application in diabetic microangiopathy

Vascular basement membrane (BM) thickening is a prominent and characteristic lesion of diabetic microangiopathy. Studies suggest that increased synthesis of laminin, a BM component, is associated with the development of thickened BM in diabetic vessels. In this study, we evaluated whether an interventive strategy using laminin antisense phosphorothioate oligonucleotides (Lam AS-oligos) could specifically inhibit high-glucose-induced laminin gene overexpression in vascular endothelial cells and normalize cell proliferation. Rat endothelial cells grown in high-glucose (30 mM) medium for 7 days showed increased laminin mRNA and protein level (195% +/- 28% of control, p < 0.05; 143% +/- 26% of control, p < 0.05, respectively) and reduced cell number (79% +/- 6% of control, p < 0.05) compared with cells grown in normal (5 mM) glucose medium. When cells grown in high-glucose medium were transfected with 0.4 microM Lam AS-oligos for 48 hours in the presence of 8 microM lipofectin, the laminin mRNA and protein level decreased (121% +/- 19% and 99% +/- 15% of control, respectively), and the cell number was restored to near normal level (93% +/- 7% of control). The results indicate that the antisense strategy is effective in selectively reducing laminin overexpression and improving endothelial cell proliferation under high-glucose conditions. Thus, the As-oligos may be potentially useful for preventing the development of thickened vascular BM in diabetic microangiopathy.

Comparison of different methods for the isolation of Burkholderia cepacia DNA from pure cultures and waste water

DNA from Burkholderia cepacia was prepared from suspensions of pure cultures and artificially contaminated waste water. The efficacy of four standard methods (lysis buffer containing proteinase K, phenol/chloroform/isoamylalcohol extraction, microwave treatment, heat treatment) and six commercially available kits (Puregene, High Pure PCR Template Preparation Kit, InstaGene, QIAamp Tissue Kit, DNAzol, Elu-Quik) was compared in terms of sensitivity in a subsequent PCR. The results showed that a simple and inexpensive procedure using a lysis buffer containing proteinase K was superior to all other methods tested.

Identification and chromosomal location of tandemly repeated DNA sequences in Allium cepa

A 314-bp tandemly repeated DNA sequence, named pAc074, was characterized in Allium cepa by fluorescence in situ hybridization (FISH) analyses using random amplified fragment as probe. The nucleotide sequences of the clone pAc074 is partially homologous to the satellite DNA sequences, ACSAT1, ACSAT2, and ACSAT3, of A. cepa with 81%, 81% and 78% similarity, respectively. Our sequential C-banding and FISH with pAc074 probe also clearly showed a close relation between Cheterochromatin at telomeric region and pAc074 sequences on all the chromosomes except on chromosome 6. On the long arm of chromosome 7, pAc074 sequences appeared as interstitial band which did not correspond to C-heterochromatin bands. Instead, the C-heterochromatin bands corresponded with the 5S rDNA signals. This is the first evidence of simultaneous banding of the 5S rDNA and C-band in A. cepa.

Sensitive detection and differentiation of Sapporo virus, a member of the family Caliciviridae, by standard and booster nested polymerase chain reaction

Norwalk virus and Sapporo virus (SV) were approved as type species of the genus Norwalk-like viruses and the genus Sapporo-like viruses, respectively, in the family Caliciviridae. Nested polymerase chain reaction (PCR), using newly designed primers in the RNA-dependent RNA polymerase region, was developed to detect and differentiate viruses in the three genetic groups of SV based on the relative size of the PCR products obtained. In addition, a booster nested PCR that performs nested PCR in a single tube was introduced to reduce the chance of contamination during the procedure of standard nested PCR. The specificity of the newly developed PCR was confirmed by testing 77 stool specimens and 16 tissue culture fluids derived from growth of unrelated viruses. The sensitivity of the nested PCR was compared with the conventional PCR using Sapp35/Sapp36 primer pair by testing the three cDNA clones obtained from viruses in the SV/SV82, the SV/London92, and the SV/Parkville virus, respectively. This assay can detect SV in a more sensitive way than the conventional PCR and Southern hybridization. Sensitive and suitable methods to detect and differentiate SV are required to obtain accurate epidemiological data on these viruses and the standard and booster nested PCR should be a very useful tool for this purpose.

Molecular cloning of a Brassica napus thiohydroximate S-glucosyltransferase gene and its expression in Escherichia coli

A genomic clone encoding a thiohydroximate S-glucosyltransferase (S-GT) was isolated from Brassica napus by library screening with probes generated by PCR using degenerated primers. Its corresponding cDNA was amplified by rapid amplification of cDNA ends (RACE) PCR and also cloned by cDNA library screening. The genomic clone was 5 896 bp long and contained a 173-bp intron. At least two copies of the S-GT gene were present in B. napus. The full-length cDNA clone was 1.5 kb long and contained an open reading frame encoding a 51-kDa polypeptide. The deduced amino acid sequence shared a significant degree of homology with other glucosyltransferases characterized in other species, including a highly conserved motif within this family of enzymes corresponding to the glucose-binding domain. The recombinant protein was expressed in Escherichia coli, and the enzyme activity was tested by a biochemical assay based on the measure of glucose incorporation. The high thiohydroximate S-GT activity detected from the recombinant protein confirmed that this clone was indeed a S-glucosyltransferase.

Transplantation of adult human corneal endothelium ex vivo: a morphologic study

PURPOSE

To investigate the feasibility of transplanting untransformed human corneal endothelial cells as a treatment strategy and possible alternative for penetrating keratoplasty by growing donor cells in culture and then transplanting them to denuded Descemet's membrane of recipient corneas.

METHODS

Corneas from adult donors (50-80 years old) were obtained from eye banks. To grow corneal endothelial cells, Descemet's membrane with associated cells was dissected from the stroma. Endothelial cells were released by ethylenediaminetetraacetic acid treatment, grown in medium containing multiple growth factors, and identified as being of endothelial origin by morphology and by reverse-transcription polymerase chain reaction for keratin 12 and collagen type VIII. In transplantation experiments, cultured cells were seeded onto denuded Descemet's membrane of a second donor cornea at 5 x 10(5) cells/mL. The recipient cornea was incubated in organ culture for as long as 2 weeks. The morphology and ultrastructure of the endothelium were evaluated 7 and 14 days after transplantation by transmission electron microscopy, and by immunolocalization of zonula occludins-1 (ZO-1). Endothelial cell density was calculated in transplants by counting ZO-1-stained cells.

RESULTS

Corneal endothelial cells cultured from adult donors consistently grew well in culture medium. Cells were identified as corneal endothelium by characteristic morphology and messenger RNA expression. Morphologic and ultrastructural studies of corneas containing transplanted endothelial cells demonstrated that with time there was an increase in endothelial cell-Descemet's membrane adhesion, in the extent of cell-cell contacts and lateral interdigitation, and in formation of a single cell layer. ZO-1 staining revealed tight junction formation similar to that of corneas in vivo. Mean endothelial cell density in transplanted corneas was 1,895 cells/mm(2) (range, 1,503-2,159 cells/mm(2) ).

CONCLUSION

Untransformed adult human corneal endothelial cells can be efficiently and consistently cultured and transplanted onto denuded Descemet's membrane. Transplanted cells in organ culture exhibit morphologic characteristics and cell densities similar to corneal endothelial cells in vivo. These results provide evidence for the feasibility of developing methods for in vivo transplantation of untransformed corneal endothelial cells cultured from adult donor tissue.

Sequence variation in humans and other primates at six short tandem repeat loci used in forensic identity testing

A large number of alleles from the six different short tandem repeat (STR) loci FGA, D3S1358, vWA, CSF1PO, TPOX and TH01, used in human identity testing were sequenced to provide support for the robustness of fluorescent STR DNA typing by allele size. Sequence information for some of these loci (FGA, vWA, TH01) is an extension of published work, whereas no extensive sequence information is available with respect to the D3S1358, CSF1PO, and TPOX loci. Sequencing of alleles at each locus has provided quantitative data with respect to the true nucleotide length of common alleles, and of alleles that vary in length from the common alleles. All alleles that were identified as "off-ladder" alleles through fluorescent typing at these STR loci have proven to be true length variant alleles. Sequencing at the D3S1358 and CSF1PO loci allowed for the establishment of a common nomenclature for these loci. A correlation between percent stutter and the length of the core tandem repeat is demonstrated at the FGA locus. Alleles in which the core tandem repeat is interrupted by a repeat unit of different sequence have a reduced percent stutter. DNA samples from three non-human primates (chimpanzee, orangutan, and gorilla) were compared to the human sequences, and shown to differ markedly across loci with respect to their homology. The effects of primer binding site mutations on the amplification efficiency at a particular locus, and methods used to interpret amplification imbalance of heterozygous alleles at a locus is also addressed.

Development of a polymerase chain reaction to distinguish monocellate cobra (Naja khouthia) bites from other common Thai snake species, using both venom extracts and bite-site swabs

A PCR technique was used in this study to identify and distinguish monocellate cobra snake bites using snake venoms and swab specimens from snake bite-sites in mice from bites by other common Thai snakes. The sequences of nucleotide primers were selected for the cobrotoxin-encoding gene from the Chinese cobra (Naja atra) since the sequences of monocellate cobra (Naja kaouthia) venom are still unknown. However, the 113-bp fragment of cDNA of the cobrotoxin-encoding gene was detected in the monocellate cobra venom using RT-PCR. This gene was not found in the venoms of Ophiophagus hannah (king cobra), Bungarus fasciatus (banded krait), Daboia russelii siamensis (Siamese Russell's Viper, and Calloselasma rhodostoma (Malayan pit viper). Moreover, direct PCR could detect a 665-bp fragment of the cobrotoxin-encoding gene in the monocellate cobra venom but not the other snake venoms. Likewise, this gene was only observed in swab specimens from cobra snake bite-sites in mice. This is the first report demonstrating the ability of PCR to detect the cobrotoxin-encoding gene from snake venoms and swab specimens. Further studies are required for identification of this and other snakes from the bite-sites on human skin.

Identification of G protein-coupled, inward rectifier potassium channel gene products from the rat anterior pituitary gland

Dopamine (DA) is a physiological regulator of PRL secretion, exerting tonic inhibitory control. DA activates an inward rectifier K(+) (IRK) channel in rat lactotropes, causing membrane hyperpolarization and inhibition of Ca(2+)-dependent action potentials. Both the activation of this effector K(+) channel and the inhibition of PRL release are mediated by D(2)-type receptor activation and pertussis toxin- sensitive G proteins. To study the molecular basis of this physiologically relevant channel, a homology-based PCR approach was employed to identify members of the IRK channel family expressed in the anterior pituitary gland. Nondegenerate primers corresponding to regions specific for IRK channels known to be G protein activated (GIRKs; gene subfamily Kir 3.0) were synthesized and used in the PCR with reverse transcribed female rat anterior pituitary messenger RNA as the template. PCR products of predicted sizes for Kir 3.1, 3.2, and 3.4 were consistently observed by ethidium bromide staining after 16 amplification cycles. The identities of the products were confirmed by subcloning and sequencing. Expression of each of these gene products in anterior pituitary was confirmed by Northern blot analysis. Functional analysis of the GIRK proteins was performed in the heterologous expression system, Xenopus laevis oocytes. Macroscopic K(+) currents were examined in oocytes injected with different combinations of Kir 3.0 complementary RNA (cRNA) and G protein subunit (beta(1)gamma(2)) cRNA. The current-voltage relationships demonstrated strong inward rectification for each individual and pairwise combination of GIRK channel subunits. Oocytes coinjected with any pair of GIRK subunit cRNA exhibited significantly larger inward K(+) currents than oocytes injected with only one GIRK channel subtype. Ligand-dependent activation of only one of the GIRK combinations (GIRK1 and GIRK4) was observed when channel subunits were coexpressed with the D(2) receptor in Xenopus oocytes. Dose-response data fit to a Michaelis-Menten equation gave an apparent K(d) similar to that for DA binding in anterior pituitary tissue. GIRK1 and GIRK4 proteins were coimmunoprecipitated from anterior pituitary lysates, confirming the presence of native GIRK1/GIRK4 oligomers in this tissue. These data indicate that GIRK1 and GIRK4 are excellent candidate subunits for the D(2)-activated, G protein-gated channel in pituitary lactotropes, where they play a critical role in excitation-secretion coupling.

A generic nested-RT-PCR followed by sequencing for detection and identification of members of the alphavirus genus

A specific and sensitive nested RT-PCR method was developed for the detection of members of the alphavirus genus. Based on available sequences, degenerated primers were selected in the nsP4 gene. Reaction components and thermal cycling parameters were investigated and standardised, and optimal ones were selected. As few as 25 pfu/tube could be detected. The identities of the amplified fragments were confirmed by sequencing, and phylogenetic analysis was carried out. The resulting phylogenetic tree could be applied to classify every alphavirus according to its serogroup. This technique is suitable for rapid, sensitive and reliable detection of these viruses and may be very valuable for diagnostic applications and surveillance.

Polymerase chain reaction with confronting two-pair primers for polymorphism genotyping

A novel PCR method using confronting two-pair primers, named PCR-CTPP, is introduced to detect a single nucleotide polymorphism (base X or Y). One primer for the X allele is set to include X' at the 3' end (antisense), where X' is the antisense of X, with the counterpart sense primer upstream. For the Y allele, a sense primer including Y at the 3' end is set, with the antisense primer downstream. One common band and one specific band for each allele are amplified, which allows genotyping directly by electrophoresis. This method is exemplified by application to the polymorphisms of beta-adrenoceptor 2 and interleukin 1B. It is simpler than PCR-RFLP (restriction fragment length polymorphism), which requires incubation with a restriction enzyme, and is suitable for genotyping in studies of genetic epidemiology involving hundreds of samples.

Identification of viable and non-viable Mycobacterium tuberculosis in mouse organs by directed RT-PCR for antigen 85B mRNA

Mycobacterium tuberculosis (MTB) the causative organism of tuberculosis can remain dormant as a non-culturable organism, reactivate and cause disease in man and animals. There is a need for proof of viability of such organisms in order to understand the process of reactivation. PCR for bacterial DNA cannot distinguish between viable and non-viable bacilli. We have tested a previously described two tube directed reverse transcriptase polymerase chain reaction (RT-PCR) for the detection of mRNA of antigen 85B (Ag85B) of MTB that can distinguish between viable and non-viable organisms. Using a set of external and internal primers for Ag85B, a cDNA amplified product (216 bp) was seen among simulated samples containing only viable cfus at a sensitivity of >10 and <100 cfu/ml. Eucaryotic DNA rich normal mouse lung homogenate did not interfere among these samples. The method amplified the 216 bp product also among cfu positive tissues of naturally infected mice. Finally, in a mouse model of dormancy, direct RT-PCR detected a signal among multiple tissues that were negative for cfus and hence non-culturable. Ag85B is abundantly secreted by MTB and hyper-expressed under stress conditions. Thus the method to identify its mRNA message may be useful to detect viable but dormant bacteria.

Genetic diversity of Borrelia burgdorferi sensu lato in ticks from mainland Portugal

To date Borrelia lusitaniae is the only genospecies of Borrelia burgdorferi sensu lato isolated from Ixodes ricinus ticks collected in Portugal and Tunisia. This suggests that the genospecies diversity of B. burgdorferi sensu lato decreases toward the southwestern margin of its Old World subtropical range. In order to further explore the genetic diversity of B. burgdorferi sensu lato from this region, 55 I. ricinus and 27 Hyalomma marginatum questing adults, collected during the spring of 1998 from a sylvatic habitat south of Lisbon, Portugal, were analyzed. Infection prevalences of 75% in I. ricinus ticks and 7% in H. marginatum ticks were detected by a nested PCR that targets the rrf (5S)-rrl (23S) spacer of B. burgdorferi sensu lato. Restriction fragment length polymorphism (RFLP) analysis of the I. ricinus-derived amplicons showed that the sequences in the majority of samples were similar to those of B. lusitaniae type strains (76% for strain PotiB1, 5% for strain PotiB3). Two novel RFLP patterns were obtained from 12% of the samples. The remaining 7% of samples gave mixed RFLP patterns. Phylogenetic analysis of rrf-rrl spacer sequences revealed a diverse population of B. lusitaniae in questing adult I. ricinus ticks (the sequences did not cluster with those of any other genospecies). This population consisted of 10 distinct sequence types, suggesting that multiple strains of B. lusitaniae were present in the local I. ricinus population. We hypothesize that B. lusitaniae has a narrow ecological niche that involves host species restricted to the Mediterranean Basin.

The role of human papillomavirus in gynecological diseases

Papanicolaou (Pap) smears of the cervix and biopsies of the cervix, vagina, vulva, and penis are a substantial portion of the work load of any anatomic pathology laboratory. The importance of samples from these sites is highlighted by the fact that their most common disease is dysplasia, which is sexually transmitted and a recognized risk factor for carcinoma. Human papillomavirus (HPV) is an essential co-factor for the development of lower genital tract dysplasia. Molecular testing for HPV has revealed a great deal about the pathophysiology of dysplasia and its evolution to carcinoma. Importantly, it now allows diagnostic pathologists the opportunity to be more accurate in their assessment of common conditions such as Pap smears of squamous atypia and biopsies equivocal for dysplasia. This review highlights the role of HPV in the evolution of disease in the lower genital tract and stresses the utility of HPV testing to the diagnostic pathologist.

The PCR assay in the preclinical safety evaluation of nucleic acid medicines

The polymerase chain reaction (PCR) is a highly efficient gene amplification procedure which is increasingly being applied to the safety assessment of nucleic acid (NA) medicines such as gene therapies and DNA vaccines. Although clinical experience is limited, a number of potential safety issues exist with these new compounds including toxicity associated with the expression of encoded gene products, autoimmunity due to the induction of anti-DNA antibodies and insertional mutagenesis. PCR enables these questions to be addressed and provides data on mRNA expression, biodistribution and integration. In this review the use of PCR methodologies in the preclinical safety evaluation of NA medicines is discussed. Particular consideration is given to the issues surrounding the use of PCR in regulatory toxicology, including sensitivity requirements, cross-contamination problems, tissue sampling procedures and good laboratory practice (GLP) compliance. In addition, the use of a PCR-based assay to demonstrate the integration of DNA vector into host DNA is described. As the use of PCR in the development of NA medicines will undoubtedly increase over the next few years, it is important that pathologists and toxicologists familiarise themselves with the principles and applications of this technique.

Phylogenetic characterization of several para- and meta-PCB dechlorinating Clostridium species: 16s rDNA sequence analyses

The genus Clostridium has more than 127 species, grouped according to their morphology and functions. Nine Clostridium species were identified based on their ability to dechlorinate meta- and para-PCB (polychlorinated biphenyl) contaminated sediments. The phylogenetic relatedness of these PCB-degrading Clostridium species was studied using ribosomal RNA genes. The diversity of small-subunit rRNA genes associated with the domain bacteria was examined using defined operational taxonomic units (OTUs) in samples from PCB contaminated sediments from Lake Medinah, New York. The RFLP (restriction fragment length polymorphism) of the OTVs was measured. OTUs B (105 clones), A (33 clones) and C (45 clones) accounted for 75% of all the 16S rDNA clones expressing anaerobic para- and meta-PCB dechlorinating activity. In this report we describe complete 16S rDNA sequences of OTU-A and OTU-B, and partial rDNA sequences of OTUs C-J. The OTU-B and OTU-I form a phylogenetically related cluster, closely affiliated with Clostridium hydroxybenzoicum strains. OTUs A, C, D, G, H and J also belong to the genus Clostridium, but they represent separate species. OTU-E, a close affiliate to Bacteroides forsynthus, is a meta-PCB dechlorinator. The Cl. hydroxybenzoicum strains (OTU-B) are primarily para-PCB dechlorinators and are the most common. Some less prevalent OTUs (- E, -G, -H and -I), are also mostly para-PCB dechlorinators. Other Clostridium species such as Cl. beijerinckii (OTU-A), Cl. intestinalis (OTU-D) and Cl. thermolacticum (OTU-J) are primarily meta-PCB dechlorinators. Cl. paraputrificum (OTU-C) and Cl. cellulosi (OTU-F), were less prevalent in the total consortium, but they could dechlorinate both para- and meta-PCB. Although a few less prevalent Clostridium species can degrade both para- and meta-PCBs, this study confirms that para- and meta-PCB dechlorinating species are generally phylogenetically different.

Molecular epidemiology: recent advances and future directions

In 1982 we proposed the concept and a framework for implementing molecular cancer epidemiology. Here, we review progress during the past 17 years in validating and applying this approach to cancer prevention. There have been major advances, notably in the understanding of environment-susceptibility interactions in human cancer. However, a review of major findings to date reveals several urgent research needs to keep pace with the rapid evolution in knowledge of mechanisms in carcinogenesis. Although much valuable progress continues to be made in the study of carcinogens that cause direct DNA damage and are mutagenic, exogenous and endogenous carcinogens can also act by altering gene expression, cell proliferation and differentiation. The mechanisms include aberrant DNA methylation, oxidative damage, effects on metabolism of nitrogen oxide and nitrites, activation of receptors and transcription factors, cyclins and other cell cycle proteins. Sensitive, validated biomarkers are needed to detect these mechanisms in small numbers of cells, tissues or fluids. There is also increasing recognition that individual risk from carcinogen exposure varies as a function of both inherited and acquired factors. Recent advances in genomics, microassay technologies and informatics hold promise for rapid identification of polymorphic variants or changes in expression of genes influencing both response and susceptibility to carcinogens. Another emerging area of molecular epidemiology concerns the role of nutrition and specific dietary factors (including studies on antioxidants, energy metabolism, insulin and various growth factors) and the modulating effect of genetic polymorphisms. Finally, molecular epidemiology has enormous potential in cancer prevention through the early identification of 'at risk' populations and the rapid assessment of intervention efficacy. Its success in fully reaching this potential will depend on the application of validated biomarkers, with adherence to sound epidemiologic and ethical principles.

Hypertrophic scar tissues and fibroblasts produce more transforming growth factor-beta1 mRNA and protein than normal skin and cells

Transforming growth factor-beta1 is a well-known fibrogenic cytokine produced by many types of cells including dermal fibroblasts. To investigate whether this fibrogenic cytokine is involved in development of hypertrophic scar, transforming growth factor-beta1 gene expression was evaluated in small skin samples. Because a sufficient quantity of normal skin from patients with hypertrophic scar is not readily available, a reverse transcription-polymerase chain reaction technique was used. Quantitation of gene expression by reverse transcription-polymerase chain reaction is difficult partly due to the lack of suitable complementary RNA standards. We have established a convenient, reliable procedure to construct an internal standard for transforming growth factor-beta1 starting with a gene specific polymerase chain reaction product. After digestion of the polymerase chain reaction product with endonuclease, a small piece of cDNA from human procollagen alpha1(I) cDNA with compatible ends was inserted into the polymerase chain reaction-DNA fragment. The recombinant cDNA was re-amplified by polymerase chain reaction and subcloned into a plasmid containing bacteriophage T7 and T3 promoters. Complementary RNA was prepared from the recombinant plasmid and amplified by reverse transcription-polymerase chain reaction together with the tissue or cellular RNA. After amplification, the products were electrophoresed in an agarose gel containing ethidium bromide. The bands for internal standard and transforming growth factor-beta1 mRNA were scanned, digitized, and plotted against the amount of internal standard complementary RNA added in the reverse transcription-polymerase chain reaction. The number of mRNA molecules/cell was calculated. We examined the transforming growth factor-beta1 mRNA in hypertrophic scar tissue and in normal skin and found that hypertrophic scar tissues expressed five-fold more transforming growth factor-beta1 mRNA than normal skin per unit of wet weight. We used this procedure to quantitate transforming growth factor-beta1 mRNA expression in 5 pairs of fibroblast cultures derived from hypertrophic scar and normal skin. The results showed that hypertrophic scar fibroblast cultures contain significantly more molecules of mRNA for transforming growth factor-beta1 than normal cells (116 +/- 6 vs. 97 +/- 7, p = 0.017, n = 5). These results were supported by Northern analysis for transforming growth factor-beta1 mRNA in the cells and enzyme-linked immunosorbent assay for TGF-beta1 protein in fibroblast-conditioned medium. In conclusion, hypertrophic scar tissue and fibroblasts produce more mRNA and protein for transforming growth factor-beta1, which may be important in hypertrophic scar formation. The construction of the gene specific internal standard for reverse transcription-polymerase chain reaction is a simple and reliable procedure useful to quantitate gene expression in a small amount of tissue or number of cells.

Single-nucleotide polymorphism analysis by MALDI-TOF mass spectrometry

Single-nucleotide polymorphisms (SNPs) have great potential for use in genetic-mapping studies, which locate and characterize genes that are important in human disease and biological function. For SNPs to realize their full potential in genetic analysis, thousands of different SNP loci must be screened in a rapid, accurate and cost-effective manner. Matrix-assisted laser desorption-ionization-time-of-flight (MALDI-TOF) mass spectrometry is a promising tool for the high-throughput screening of SNPs, with future prospects for use in genetic analysis.

Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection

To understand the high variability of the asymptomatic interval between primary human immunodeficiency virus type 1 (HIV-1) infection and the development of AIDS, we studied the evolution of the C2-V5 region of the HIV-1 env gene and of T-cell subsets in nine men with a moderate or slow rate of disease progression. They were monitored from the time of seroconversion for a period of 6 to 12 years until the development of advanced disease in seven men. Based on the analysis of viral divergence from the founder strain, viral population diversity within sequential time points, and the outgrowth of viruses capable of utilizing the CXCR4 receptor (X4 viruses), the existence of three distinct phases within the asymptomatic interval is suggested: an early phase of variable duration during which linear increases ( approximately 1% per year) in both divergence and diversity were observed; an intermediate phase lasting an average of 1.8 years, characterized by a continued increase in divergence but with stabilization or decline in diversity; and a late phase characterized by a slowdown or stabilization of divergence and continued stability or decline in diversity. X4 variants emerged around the time of the early- to intermediate-phase transition and then achieved peak representation and began a decline around the transition between the intermediate and late phases. The late-phase transition was also associated with failure of T-cell homeostasis (defined by a downward inflection in CD3(+) T cells) and decline of CD4(+) T cells to Collapse

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MESH Headings

• Base Sequence
• DNA, Viral
• Disease Progression
• Evolution, Molecular
• Gene Products, env/genetics
• HIV Infections/immunology
• HIV Infections/physiopathology
• HIV Infections/virology
• HIV-1/classification
• HIV-1/genetics
• Humans
• Male
• Molecular Sequence Data
• Prospective Studies

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Grants

• U01 AI035042 NIAID NIH HHS
• AI34783 NIAID NIH HHS
• U01 AI037984 NIAID NIH HHS
• AI37984 NIAID NIH HHS
• U01 AI035041 NIAID NIH HHS
• P30 AI027757 NIAID NIH HHS
• AI32885 NIAID NIH HHS
• U01 AI035040 NIAID NIH HHS
• U01 AI035039 NIAID NIH HHS

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Affiliation(s)

R Shankarappa Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195-7740, USA
J B Margolick
S J Gange
A G Rodrigo
D Upchurch
H Farzadegan
P Gupta
C R Rinaldo
G H Learn
X He
X L Huang
J I Mullins

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Primary central nervous system lymphomas are derived from germinal-center B cells and show a preferential usage of the V4-34 gene segment

Primary central nervous system lymphomas (PCNSLs) have recently received considerable clinical attention due to their increasing incidence. To clarify the histogenetic origin of these intriguing neoplasms, PCNSLs from 10 HIV-negative patients were analyzed for immunoglobulin (Ig) gene rearrangements. All tumors exhibited clonal IgH gene rearrangements. Of the 10 cases, 5 used the V4-34 gene segment, and all of these lymphomas shared an amino acid exchange from glycine to aspartate due to a mutation in the first codon of the complementarity-determining region 1. No preferential usage of D(H), J(H), V(kappa), J(kappa), V(lambda), or J(lambda) gene segments was observed. All potentially functional rearrangements exhibited somatic mutations. The pattern of somatic mutations indicated selection of the tumor cells (or their precursors) for expression of a functional antibody. Mean mutation frequencies of 13. 2% and 8.3% were detected for the heavy and light chains, respectively, thereby exceeding other lymphoma entities. Cloning experiments of three tumors showed ongoing mutation in at least one case. These data suggest that PCNSLs are derived from highly mutated germinal-center B cells. The frequent usage of the V4-34 gene and the presence of a shared replacement mutation may indicate that the tumor precursors recognized a shared (super) antigen.

Progress toward demonstration of a surface based DNA computation: a one word approach to solve a model satisfiability problem

A multi-base encoding strategy is used in a one word approach to surface-based DNA computation. In this designed DNA model system, a set of 16 oligonucleotides, each a 16mer, is used with the format 5'-FFFFvvvvvvvvFFFF-3' in which 4-8 bits of data are stored in eight central variable ('v') base locations, and the remaining fixed ('F') base locations are used as a word label. The detailed implementations are reported here. In order to achieve perfect discrimination between each oligonucleotide, the efficiency and specificity of hybridization discrimination of the set of 16 oligonucleotides were examined by carrying out the hybridization of each individual fluorescently tagged complement to an array of 16 addressed immobilized oligonucleotides. A series of preliminary hybridization experiments are presented and further studies about hybridization, enzymatic destruction, read out and demonstrations of a SAT problem are forthcoming.

Surface-based DNA computing operations: DESTROY and READOUT

DNA computing on surfaces is where complex combinatorial mixtures of DNA molecules are immobilized on a substrate and subsets are tagged and enzymatically modified (DESTROY) in repeated cycles of the DNA computation. A restriction enzyme has been chosen for the surface DESTROY operation. For the READOUT operation, both cycle sequencing and PCR amplification followed by addressed array hybridization were studied to determine the DNA sequences after the computations.

Development of a single tube nested polymerase chain reaction assay for the detection of Neospora caninum DNA

Sensitive detection techniques are required to study the life cycle of Neospora caninum and to diagnose infections. In this study, we describe the development of a PCR assay for N. caninum based on two successive amplification steps within a single tube. This technique, called single tube nested PCR, was sensitive to a single copy of target sequence, and able to amplify parasite DNA from biological specimens such as formalin-fixed, paraffin-embedded tissues of naturally infected dogs and cattle. An internal standard (or PCR MIMIC) is also described. This assay should prove useful in the study of the biology of N. caninum.

Humoral immune response to equine chorionic gonadotropin in ewes: association with major histocompatibility complex and interference with subsequent fertility

In dairy ewes, the use of eCG as a convenient hormone for the induction of ovulation is necessary for out-of-season breeding and artificial insemination (AI). In this report we show the presence of anti-eCG antibodies in plasma of treated ewes. The major histocompatibility complex (MHC) was involved in the individual variability of the humoral immune responses to eCG. We found significant associations between the anti-eCG response phenotype and some MHC class II alleles. The low immune response phenotype was associated with one MHC class II allele only in Lacaune ewes, and the high immune response phenotype was associated with one MHC class II allele both in Manech and in Lacaune ewes. In herds, the impact of residual anti-eCG antibodies on subsequent fertility after AI seems minimal because of an indirect elimination of high-responder ewes from AI breeding. Therefore, the true magnitude of the association between residual anti-eCG antibody concentration and fertility has been underestimated. An additional experiment without any high-responder female elimination showed a significant correlation between high residual antibody concentrations and lower lambing rate after AI at a fixed time, possibly because of a delayed preovulatory LH surge. The results suggest that anti-eCG antibody concentration is one risk factor for infertility after AI.

POLYMERASE CHAIN REACTION AND ADVANCES IN INFECTIOUS DISEASE DIAGNOSIS

The use of Polymerase Chain Reaction (PCR) in infectious disease diagnosis, has resulted in an ability to diagnose early and treat appropriately diseases due to fastidious pathogens, determine the antimicrobial susceptibility of slow growing organisms, and ascertain the quantum of infection. This article outlines the PCR, some of its modifications and their application in infectious disease diagnosis.

Reverse transcriptase in situ polymerase chain reaction for gene expression in rat mast cells and macrophages

Direct reverse transcriptase in situ polymerase chain reaction (RT-in situ PCR) of selected mRNA expression in rat mast cells (MC) and alveolar macrophages (AM) was optimized. Rat peritoneal mast cells (PMC), rat cultured mast cells (RCMC), rat bronchoalveolar lavage cells (BALC) or rat cultured alveolar macrophages (NR8383) were studied for the detection of mRNA for beta-actin, TNF-alpha and/or CD8alpha. Each type of cell has unique optimal conditions for RT-in situ PCR. The following parameters were carefully evaluated for optimization: protease digestion, DNAse digestion, heparinase digestion, RT, PCR cycle number and signal development with chromagen. Heparinase digestion was required for PMC mRNA detection because they contain large amounts of heparin proteoglycan, which is a potent inhibitor of RT and Taq polymerase enzymes. Only a few PCR cycles were needed to produce a cytoplasmic signal for mRNA transcripts in RCMC, whereas other types of cells (PMC, BALC and NR8383) needed at least 20 cycles for mRNA detection. The mRNA signal in PMC was localized to the perinuclear region, whereas mRNA in other cell types (RCMC, BALC and NR8383) were detected throughout the cytoplasm. Furthermore, modified Southern blot analysis for TNF-alpha in RCMC treated with RT-in situ PCR demonstrated the specificity of amplification product. The modified and optimized protocols for this procedure were successfully applied to detect and localize several mRNA transcripts in rat MC and AM. The approach is valuable and can be used to further study selected gene expression in these and other cell types.

Multiplex detection of four pathogenic retroviruses using molecular beacons

We describe a multiplex nucleic acid assay that identifies and determines the abundance of four different pathogenic retroviruses (HIV-1, HIV-2, and human T-lymphotrophic virus types I and II). Retroviral DNA sequences are amplified in a single, sealed tube by simultaneous PCR assays, and the resulting amplicons are detected in real time by the hybridization of four differently colored, amplicon-specific molecular beacons. The color of the fluorescence generated in the course of amplification identifies which retroviruses are present, and the number of thermal cycles required for the intensity of each color to rise significantly above background provides an accurate measure of the number of copies of each retroviral sequence that were present originally in the sample. Fewer than 10 retroviral genomes can be detected. Moreover, 10 copies of a rare retrovirus can be detected in the presence of 100, 000 copies of an abundant retrovirus. Ninety-six samples can be analyzed in 3 hr on a single plate, and the use of a closed-tube format eliminates crossover contamination. Utilizing previously well characterized clinical samples, we demonstrate that each of the pathogenic retroviruses can be identified correctly and no false positives occur. This assay enables the rapid and reliable screening of donated blood and transplantable tissues.

Transforming growth factor-beta suppresses proliferation of rabbit corneal endothelial cells in vitro

Corneal endothelial cells in vivo appear to be inhibited in G1 phase of the cell cycle. Studies were carried out to determine whether cultured rabbit corneal endothelium expresses transforming growth factor-beta (TGF-beta) receptor types I, II, and III, suggesting they would be sensitive to a TGF-beta-induced signal. In addition, we explored if TGF-beta might mediate this G1 phase inhibition by implementing flow cytometry and 5-bromo-2'-deoxyuridine (BrdU) immunofluorescence. Reverse transcription-polymerase chain reaction (RT-PCR) products of the expected size were obtained for all three TGF-beta receptor types. Flow cytometry revealed a dose-dependent suppression in the percentage of S phase cells in cultures treated with TGF-beta1 or TGF-beta2. The lowest percentage of S phase cells was found for 10 ng/ml TGF-beta1 and 0.1 ng/ml TGF-beta2. BrdU, an S phase marker, was immunolocalized, and semiquantitative analysis of stained cells showed a maximum suppression of S phase entry at 18 h for 10 ng/ml of TGF-beta11 and 24 h for 10 ng/ml of TGF-beta2. In rabbit, the corneal endothelium expresses TGF-beta receptor types I, II, and III, permitting a TGF-beta signal to be transduced. Flow cytometry reveals a dose-dependent response to both TGF-beta1 and TGF-beta2, and the cells are more sensitive to TGF-beta2. At optimal TGF-beta concentrations, the percentage of S phase cells is comparable to that of a non-proliferating culture, suggesting TGF-beta prevents the cells from proceeding through the G1/S phase transition. This suppression was also seen with BrdU labeling. Together, these results indicate that TGF-beta could be one of the pathways that leads to G1 phase arrest in corneal endothelial cells.

The negative effect of repeated equine chorionic gonadotropin treatment on subsequent fertility in Alpine goats is due to a humoral immune response involving the major histocompatibility complex

In dairy goats, the use of eCG as a convenient hormone for the induction of ovulation is necessary for out-of-season breeding and artificial insemination. However, repeated eCG treatments are followed by decreased fertility in goats inseminated at a fixed time after treatment. In this report, we show the presence of anti-eCG antibodies in plasma of treated goats. A 500 IU eCG injection induces a humoral response, with variable concentrations of anti-eCG antibody being produced in individual goats. The analysis of successive anti-eCG immune responses over several years has demonstrated the existence of different populations of goats, defined as low, medium, and high responders. By the use of two caprine microsatellites located inside (OLADRB) and outside (BM1258) the major histocompatibility complex (MHC), a significant association (p < 0.05) between the anti-eCG antibody response and some MHC-DRB alleles was found. Goats with high antibody concentrations at the time of eCG injection (> 2.5 microg/ml) exhibited a much lower kidding rate than did other females (41.3% vs. 66.7%). Lower fertility of these goats, inseminated at a fixed time after eCG treatment, might be due to the observed delay in estrus occurrence and the preovulatory LH surge.

Reverse transcription-polymerase chain reaction in the diagnosis of Helicobacter pylori infection in Finnish children

BACKGROUND

The purpose of this study was to design a simplified polymerase chain reaction (PCR) technique for the detection of Helicobacter pylori and to compare it with conventional diagnostic methods-culture and histology of gastric biopsy specimens. In addition, the capability of this technique to detect H. pylori in the gastric mucosal biopsies of originally H. pylori-negative children with gastritis or recurrent abdominal pain was investigated.

METHODS

Reverse transcriptase polymerase chain reaction (RT-PCR) using polymerase from Thermus thermophilus was applied to detect H. pylori 16S rRNA. Twenty-five children H. pylori-positive by culture and/or histology were used as positive control subjects. Sixteen healthy H. pylori-negative children served as negative control subjects. Biopsy specimens from gastric antrum and corpus from 81 children were examined by RT-PCR. Altogether, 30 had histologic gastritis and 51 had nonspecific abdominal pain only, with no disease in histologic specimens. Histology and culture of H. pylori were negative in both patient groups.

RESULTS

Reverse transcription-polymerase chain reaction detected 24 of 25 tissue-positive and 0 of 16 tissue-negative cases, indicating 96% sensitivity and 100% specificity for the test. None of the culturally and histologically H. pylori-negative samples showed H. pylori colonization when analyzed by RT-PCR.

CONCLUSIONS

RT-PCR using Thermus thermophilus polymerase is a fast and simple means of detecting H. pylori in gastric biopsy specimens. It is at least as specific and sensitive as conventional methods. In pediatric patients it may be necessary to take more than two biopsy specimens to increase sensitivity in cases of local or patchy colonization.

Expression, purification, and characterization of recombinant forms of membrane-bound cytochrome c-550nm from Bacillus subtilis

Bacillus subtilis expresses a cytochrome c-550nm that participates in respiratory electron transfer and is an integral membrane protein. Analysis of the B. subtilis cytochrome c-550nm amino acid sequence predicts a single N-terminal transmembrane helix attached to a water-soluble heme binding domain [C. von Wachenfeldt and L. Hederstedt (1990) J. Biol. Chem. 265, 13939-13948]. We have purified cytochrome c-550nm from wild-type B. subtilis and B. subtilis transformed with the shuttle vector pHP13 containing the gene for B. subtilis cytochrome c-550nm (cccA). In B. subtilis transformed with pHP13/cccA there is better than eightfold more membrane-bound cytochrome c-550nm than in wild-type B. subtilis. The overexpressed cytochrome c-550nm can be purified by chromatography on hydroxylapatite and Q-Sepharose media. A six-histidine tag has been added to the C-terminus of cytochrome c-550nm from B. subtilis as a further aid for purification. This strain produces cytochrome c-550nm to a level fourfold greater than wild type and allows for one-step purification using metal affinity chromatography. UV-Vis spectroscopy detects no change in the heme C spectrum due to the addition of six histidines. Neither form of B. subtilis cytochrome c-550nm is stable in its reduced state in aerated buffer, unless EDTA is added. The two forms, wild-type and his-tagged, of cytochromes c have similar midpoint redox potentials of 195 and 185 mV, respectively, and are equally good substrates for B. subtilis cytochrome c oxidase. We conclude that the addition of the histidine tag eases the purification of cytochrome c-550nm from B. subtilis plasma membranes and that the additional metal binding site does not compromise the stability or functional properties of the protein.

Clear detection and typing of herpes simplex virus types 1 and 2 by an indirect ELISA assay: comparison with three different combined methods--capture ELISA, restriction enzymes, and polymerase chain reaction

The severity and recurrences of Herpes Simplex Virus (HSV) infection depend on the type of the infectious agent (HSV-1 or HSV-2), which induces the necessity of a nonambiguous detecting typing. The commonly used capture ELISA technique has to be often supported by DNA analysis to confirm the detection and the typing of HSV viruses in exposed patients. In this report, we describe a rapid and cheap indirect ELISA method using anti-HSV monospecific polyclonal antibodies prepared in the laboratory. The typing of the studied samples was clear, did not need series of dilution, and allowed the immediate classification of viruses without further control examination. We tested 51 specimens, which were typed 25 HSV-1 and 26 HSV-2 strains. The comparison with capture ELISA, restriction enzyme and polymerase chain reaction analysis definitely allowed our method to be assessed as a useful tool for a routine diagnostic.

Identification of rabbit immunoglobulin latent Ckappa1 allotype genes alters the concept of allelic inheritance

In the rabbit, expression of immunoglobulin Ckappa1 light chain genes is believed to be under allelic control. Conventionally, four nominal allotypic variants, b4, b5, b6 and b9 have been shown to be co-dominantly expressed at the Ckappa1 gene locus. Analogously, the heavy chain allotypes, VHa1, VHa2 and VHa3, found in the V region, are also believed to be inherited co-dominantly. However, after our earlier discovery of non-allelic or latent allotypes in the serum and on cell surfaces. we subsequently reported that cDNA sequences for latent b5 and b6 were identical to nominal b5 and b6, respectively (Ishaq et al., 1990). The latent b5 cDNAs were from two homozygous b4,b4 rabbits; the latent b6 cDNA was found in a heterozygous b4,b9 rabbit. The cDNA sequences had been obtained from lymph nodes and spleens of rabbits which had been infected with Trypanosoma brucei in order to induce latent allotypes more consistently. In this article, employing spleen DNA from three different T. brucei-infected rabbits, (one, heterozygous b4,b9; two others, homozygous, b4,b4), we initially detected two bands by Southern analysis after Hind III digestion using a 624 base pair Ckappa1 b4 probe derived from a b4,b4 rabbit. However, the probe was non-specific allotypically as it hybridized to b5, b6 and b9 Ckappa1 DNA. Therefore, in order to search for the latent genes, we used allotype-specific oligonucleotides for b5, b6 and b9 to probe DNAs from both normal and T. brucei-infected rabbits by Southern blotting. At the outset, employing a b4 oligonucleotide probe, we detected a single 5.8 Kb segment in two b4,b4 rabbit DNAs after Bg1 II digestion. The findings, using the 624 base pair Ckappa1 b4 probe and the b4 oligomer, agreed with earlier data reported by others. Subsequently, we tested kidney, liver and spleen DNAs from one of these and other rabbits for genomic latent b5, b6 and b9 using these specific oligomeric probes. For each latent allotype, Southern analysis revealed latent-allotype specific DNA segments in the genome. After cosmid cloning and sequencing, latent kappa1, b5, b6 and b9 genes were found to be identical in their coding regions with their nominal counterparts. The genes contained at the 5' end the PyPyXPyAG RNA splice acceptor site found in immunoglobulin and many eukaryotic genes. as well as the termination codon TAG, together with AATAAA and the T-rich sites responsible for cleavage-polyadenylation in the untranslated region downstream from the 3' end. Single cosmid clones representing the b5, b6 and b9 genes were mapped for restriction sites which resulted in identifying putative Jk and enhancer regions. The results thus indicate that latent allotype genes are potentially functional. The data provide evidence that allotypes are not strictly controlled by allelic genes but must be regulated by an hierarchical mechanism which provides for synthesis of allelic allotypes mainly (10-20 mg/ml) together with non-allelic allotypes at lower concentrations (2-20 microg/ml) following activation of the latent genes. These results lay to rest the belief that Ckappa1 latent allotypes are the products of scrambled genes or idiotypic mimicry. Importantly, we now have the possibility of investigating the factors leading to latent allotype gene expression, the Vk and Jk regions associated with the genes, and therefore whether antibody diversity is expanded. We do not know, nor do we imply, that latent allotypes are present in all rabbits. However, since the four conventional Ckappa1 allotypes are present in the genome of several of our tested rabbits, and are presumably functional. we are faced with the probability that rabbit allotypes under certain conditions may in fact behave as isotypes and not allotypes.

Bias in template-to-product ratios in multitemplate PCR

Bias introduced by the simultaneous amplification of specific genes from complex mixtures of templates remains poorly understood. To explore potential causes and the extent of bias in PCR amplification of 16S ribosomal DNAs (rDNAs), genomic DNAs of two closely and one distantly related bacterial species were mixed and amplified with universal, degenerate primers. Quantification and comparison of template and product ratios showed that there was considerable and reproducible overamplification of specific templates. Variability between replicates also contributed to the observed bias but in a comparatively minor way. Based on these initial observations, template dosage and differences in binding energies of permutations of the degenerate, universal primers were tested as two likely causes of this template-specific bias by using 16S rDNA templates modified by site-directed mutagenesis. When mixtures of mutagenized templates containing AT- and GC-rich priming sites were used, templates containing the GC-rich permutation amplified with higher efficiency, indicating that different primer binding energies may to a large extent be responsible for overamplification. In contrast, gene copy number was found to be an unlikely cause of the observed bias. Similarly, amplification from DNA extracted from a natural community to which different amounts of genomic DNA of a single bacterial species were added did not affect relative product ratios. Bias was reduced considerably by using high template concentrations, by performing fewer cycles, and by mixing replicate reaction preparations.

Fluorescence cross-correlation: a new concept for polymerase chain reaction

In this article we present a new concept for the detection of any specifically amplified target DNA sequences in multiple polymerase chain reactions (PCR) based on fluorescence correlation spectroscopy (FCS). The accumulation of double-stranded target DNA is monitored by the cross-correlated fluorescence signals provided by two amplification primers which are 5'-tagged with two different kinds of fluorophores (Rhodamine-Green and Cy5). Only the amplified target DNA sequence carrying both primers is observed. Its signal emerges from the background of non-incorporated or non-specifically incorporated primers. Down to 10-25 initial copy numbers of the template in the PCR compartment DNA can presently be detected. No external or internal standards are required for determining the size and the amplified copy number of specific DNA. The PCR amplification process is started with all ingredients in a single compartment (e.g. of a microtiter plate), in which amplification and measurement are performed. This eliminates the need for post-PCR purification steps. The homogeneous one-tube approach does not depend on fluorescence energy transfer between the fluorogenic dyes. Thus, it does not interfere with the enzymatic amplification reaction of PCR and allows the continued use of different conditions for amplifying DNA. The results exemplified by PCR-amplified 217-bp and 389-bp target DNA sequences demonstrate that the analysis based on two-color fluorescence cross-correlation is a powerful method for simplifying the identification of targets in PCR for medical use. For this purpose, an instrument optimized for two-color excitation and detection of two-color emission has been developed, incorporating the principle of confocal arrangement.

Detection of carcinoembryonic antigen mRNA in the mesenteric vein of patients with resectable colorectal cancer

The detection of tumor cells in the drainage venous blood of patients with colorectal cancer was made feasible by demonstrating carcinoembryonic antigen (CEA) mRNA in the mononuclear cell component of the blood, using a nested reverse transcription-polymerase chain reaction. CEA mRNA was detected in the drainage venous blood from 11 (42%) of 26 patients, and the rate of detection increased according to the grade of vessel invasion. CEA mRNA was detected in all patients with synchronous liver metastases, even though there was no significant correlation between the presence of CEA mRNA in the drainage venous blood and the clinicopathological findings. As the presence of CEA mRNA in the drainage venous blood is an indicator of the spread of tumor cells in patients with colorectal cancer, this assay can be used to assess the possible outcome of patients with colorectal cancer, providing one more tool for the physician-oncologist to use in designing appropriate treatments.

Human papillomaviruses in hypopharyngeal squamous cell carcinoma

Human papillomaviruses (HPV) have been detected in squamous cell carcinoma (SCC) of the aerodigestive tract with varying frequency of 10%-100% mainly due to detection methods and primer pairs used. Polymerase chain reaction (PCR) is the most sensitive and Southern blot hybridization (SBH) the most specific detection method of HPV DNA. Both methods achieve the most reliable results. 22 SCC DNA samples of the hypopharynx were analyzed by type specific and consensus primer PCR and Southern blot analysis. HPV was detected in 5/22 (22.6%) hypopharyngeal SCC specimens. HPV 18 and HPV 45 were identified in one case each. An HPV prevalence of 23% is a realistic approximation in hypopharyngeal SCC. The high rate of HPV positive only detected by non type specific detection methods indicates the presence of previously undescribed HPV types.

Inhibition of signal transduction by a splice variant of the growth hormone-releasing hormone receptor expressed in human pituitary adenomas

We have previously shown that some of human growth hormone (GH)-producing pituitary adenomas preferentially express a larger transcript of GH-releasing hormone (GHRH) receptor (GHRH-R). This transcriptional variant is presumed to be produced by alternative messenger RNA splicing and contains premature stop codon in frame, predicted to yield a truncated GHRH-R. Functional expression study indicated that the variant receptor was unable to transduct GHRH signals. To determine the functional relationship between the splice-variant and the wild-type GHRH-R, the expression vector for the variant GHRH-R transcript was transfected into COS-7 cells together with or without that for the wild GHRH-R transcript. In cells transfected with both GHRH-R expression vectors, GHRH-dependent cyclic adenosine monophosphate (cAMP) induction was decreased to 39% of that in the cells transfected with the wild-type GHRH-R expression vector alone. This inhibition was found to be irrespective of the concentration (10(-8) to 10(-5) mol/L) of GHRH. These findings suggest that the splice variant form of GHRH-R functions as a dominant-negative modulator in GHRH-induced cellular signaling.

Genotyping HCV isolates from Italy by type-specific PCR assay in the core region

A revision of the polymerase chain reaction (PCR) core procedure was performed for genotyping hepatitis C virus (HCV) in 139 patients from Italy. This procedure, developed prior to the identification of new genotypes, may be inadequate in several geographical areas. We proposed a new typing mixture in which primers for types 2c and 4, that are reported to be circulating in Italy, were added and a primer for type 2b was substituted. Using the modified procedure, 139 HCV-positive patients were analysed. The HCV genotype was identified in 96.4% of the cases. We observed double infections and unclassified genotypes in 5 (3.6%) and 5 (3.6%) patients, respectively. The classification of isolates into genotypes and subtypes 2b, 2c and 4 was confirmed by sequence analysis. Furthermore, the efficiency and accuracy of the modified core procedure were evaluated by parallel testing of 107 out of 139 samples using the line probe assay, and demonstrated a 98.9% degree of concordance. The results demonstrated the specificity of the selected primers for type 2c, 2b and 4 and confirmed the circulation of types 2c and 4 in Italy. In conclusion, the proposed modified PCR procedure is the only primer-specific PCR genotyping method available for identification of the 2c and 4 genotypes reported to be circulated in Italy and other European countries.

Polymerase chain reaction approaches for the detection of Neospora caninum and Toxoplasma gondii

This review summarizes existing knowledge on the development and use of the polymerase chain reaction for the detection of DNA from Neospora and Toxoplasma. Several strategies which utilise the polymerase chain reaction for the diagnosis of toxoplasmosis in humans and livestock have been described and they principally target the B1 repetitive sequence, the P30 gene or ribosomal DNA. Experience has shown that the polymerase chain reaction has proven insufficiently robust to serve as a diagnostic test alone although when used in conjunction with other diagnostic techniques it does prove to be a useful aid. The marketing of a commercial polymerase chain reaction kit may well solve some of the inadequacies seen using "home made" polymerase chain reaction technology which are commonly used in diagnostic laboratories around the world. Recent progress on the development of polymerase chain reaction diagnostics for Neospora has been rapid and is discussed in detail.