Recent advances in the polymerase chain reaction

A RT-PCR assay for the differential diagnosis of vesicular viral diseases of swine

A RT-PCR assay based on specific amplification of RNA sequences from each of the etiological agents of three important vesicular diseases that affect swine, foot-and-mouth disease virus (FMDV), swine vesicular disease virus (SVDV), and vesicular stomatitis virus (VSV), was developed. Genotype-specific primers that amplified DNA fragments of differential size from SVDV 3D gene or VSV L gene were selected with the aid of a computer program. Experimental testing of the primers predicted as SVDV-specific identified a primer pair, SA2/SS4, that rendered a specific product from SVDV RNAs, but did not amplify RNA from either FMDV or coxsackie B5 virus (CV-B5), a highly related picornavirus. Primers SA2/SS4 were used in combination with primers 3D2/3D1, which amplify a product of different size on FMDV 3D gene (Rodriguez et al., 1992). This combined RT-PCR reaction allowed a sensitive and specific differential detection of FMDV and SVDV RNAs in a single tube, by means of the analysis of the amplified products in agarose gels. The results obtained were similar when RNA extracted from viral stocks or plastic wells coated with either viral supernatants or extracts from lesions of infected animals, were used as starting material in the reactions. Using a similar approach, VSV serotype-specific primers IA/IS and NA/NS were selected for the specific amplification of VSV-Indiana and VSV-New Jersey RNAs, respectively. The combined use of SVDV, FMDV and VSV specific primers in a single reaction resulted in a genotype-specific amplification of each of the viral RNAs. Thus, differential diagnosis of FMDV from SVDV and/or VSV can be carried out in a single RT-PCR reaction, using a rapid and simplified methodology.

Linear amplification mapping of polycyclic aromatic hydrocarbon-reactive sequences in H-ras gene

Linear amplification, or primer directed single-strand DNA synthesis, is commonly used in applications such as cycle sequencing and mapping replication block sites in DNA. Although linear amplification reactions would be expected to synthesize full-length single-stranded DNA, the synthesis is often prematurely terminated. We describe the optimization of a linear amplification protocol for synthesizing a full-length (985-nt) single-stranded pBR322 segment. The enzyme activities of five DNA polymerases commonly used in PCR amplification, namely, AmpliTaq, Stoffel fragment, Tth, Pfu, and Vent, were tested either singly or in combination. The results indicate that the additive action of small amounts of proofreading DNA polymerases to a nick-translating polymerase is optimum for linear amplification. From these results, a linear amplification protocol was developed to map DNA synthesis-blocking sites generated by the reaction of (+/-) anti-benzo[a]pyrene-7,8-diol-9,10-epoxide, or anti- or syn-dibenzo[a,l]pyrene-9,10-diol-11,12-epoxide with H-ras DNA surrounding the oncogenic codon 61 region. The results indicate that the central A of H-ras codon 61 (CAA) reacts with these polycyclic aromatic hydrocarbons.

Molecular detection and quantitation of the chemokine RANTES mRNA in neurological brain

Accumulation of T-cells in the brains of patients with neurological disorders prompted a molecular analysis of brain tissue for expression of the chemokine RANTES, which is known to be a T-cell activator and chemoattractant. A fast, sensitive and reproducible technique was developed, based on the polymerase chain reaction and nonradioactive detection. The method could detect and quantitate RANTES in small amounts of brain tissue from all patients with multiple sclerosis, and in some patients with other neural or inflammatory diseases. The data indicate constitutive expression of RANTES in brain from some neurological disorders where its downregulation can have therapeutic benefits.

Removal of inhibitors of CSF-PCR to improve diagnosis of herpesviral encephalitis

CSF-PCR is currently the most sensitive test to diagnose encephalitis due to cytomegalovirus or herpes simplex virus. However, false negative results sometimes arise due to inhibitors in CSF. We have shown that the inhibitory effects may be due to increased levels of proteins and increased cell numbers, but are not due to cellular DNA. Simple techniques were used to remove the inhibitors and successfully apply these methods to CSF specimens that gave equivocal results when tested untreated.

Comparison of polymerase chain reaction assay with culture for detection of genital mycoplasmas in perinatal infections

The polymerase chain reaction (PCR) technique was compared with culture for the detection of Ureaplasma urealyticum, Mycoplasma hominis, and Mycoplasma genitalium in clinical samples (vaginal secretions, throat and endotracheal secretions, and skin swabs) obtained from 47 high-risk pregnant women peripartum and eight newborn infants. Detection using PCR with homologous primers was highly specific, as a product with the expected length was consistently amplified with homologous but not with heterologous species. The limit of detection of the PCR assay was 10 color-changing units (CCU) of Mycoplasma strains. The PCR technique facilitated detection of Ureaplasma urealyticum DNA in 31 of 55 patients studied, of Mycoplasma hominis in seven samples, and of Mycoplasma genitalium in two samples. Four PCR-positive patients yielded culture-negative results. In one case a culture-positive sample was negative by PCR. The results show that PCR is a valuable tool for rapid detection of genital mycoplasmas in clinical samples. It is fast, sensitive, specific, and easy to perform, requiring minimal preparation of the clinical sample.

Mycobacterial DNA not detected in liver sections from patients with primary biliary cirrhosis

BACKGROUND/AIMS

Recent studies in primary biliary cirrhosis have reported the detection of serum antibodies against Mycobacterium gordonae and of mycobacterial DNA in liver sections. The aim of this study was to investigate whether mycobacterial DNA is present in liver biopsy material in primary biliary cirrhosis.

METHODS

Archival liver biopsy specimens from 11 patients with primary biliary cirrhosis (10 female, mean age 52 years) and 11 patients with autoimmune hepatitis (10 female, mean age 53 years) were identified. Positive control tissue comprised five archival lymph node specimens from patients with tuberculous lymphadenopathy, three of which had stained positive on ZN staining, and also a liver biopsy specimen from a patient with tuberculous hepatitis (ZN positive). Fixed sections were deparaffinised and DNA was extracted by mechanical disruption with glass beads. DNA was purified by use of diatoms and lysis in guanidinium thiocyanate in a technique previously validated for archival DNA. Primers were directed to amplify a partial 16S ribosomal RNA gene yielding the species-specific character for mycobacteria, and also to amplify the constitutively-expressed human gene GAPDH.

RESULTS

The polymerase chain reaction was shown to be capable of detecting 1 fg of M. gordonae DNA in 'spiked' samples, equivalent to 1-5 bacterial cells. No mycobacterial DNA was detected in liver biopsy samples from either the primary biliary cirrhosis or autoimmune hepatitis groups. Of the tuberculous control sections, mycobacterial DNA was detected in four of five lymph nodes and the liver biopsy specimen. GAPDH amplification was detected in all tested samples from liver disease and tuberculous control samples.

CONCLUSION

These data do not support a role for mycobacteria in the aetiology of primary biliary cirrhosis.

In situ PCR for in vivo detection of foreign genes transferred into rat brain

Here we describe the use of in situ PCR to detect a viral transgene in rat brain. Previously, we have reported in vivo gene transfer by using a defective herpes simplex viral vector in mammalian brain (Kaplitt, M.G., Pfaus, J.G., Kleopoulos, S.P., Hanlon, B.A., Rabkin, S.D., Pfaff, D.W., Mol. Cell. Neurosci. 2 (1991) 320-330). For detection of the LacZ transgene, we have used histochemical staining for the protein product, beta-galactosidase, and in situ hybridization for its mRNA, but the DNA itself cannot be reliably detected with conventional methods. Therefore we have adapted the technique of in situ PCR, so that we may detect minute quantities of transgenic vector DNA following in vivo gene. The brain sections, prefixed, were treated with PBS-detergent before PCR amplification to increase permeability for peptides and oligonucleotides across cellular barriers in brain tissue. Pretreatment with detergent retained better brain morphology than the more widely used proteinase treatment. The PCR mixture containing dNTPs, primers, digoxigenin-dUTP (Dig-dUTP) and buffer was loaded onto each brain section. Slides containing brain sections were placed in an aluminum boat and then on the block of the thermal cycler. Temperature was brought to 82 degrees C before adding Taq polymerase ('hot start' method). Dig-labeled PCR amplified fragments were then detected by alkaline-phosphatase-linked anti-digoxigenin-antibody. Positive signals were seen within the nucleus of transduced neurons, indicating presence of viral DNA. Enhanced specificity was observed with the use of Dig-labeled primers which eliminates the possibility of non-specific viral DNA detection through primer-independent reactions. Overall, this technique can serve not only as an internal control for transgene presence during comparisons of experimental groups of animals, but may also have clinical applications including the detection of viral infection in human brain such as HIV in pathology specimens.

Clinical usefulness of RT-PCR detection of hematogenous prostate cancer spread

Understaging is commonly associated with therapeutic failure of surgical intervention in apparently localized prostate cancers. Methods that specifically detect prostate cancer cells in the circulation may be able to identify metastatic cancers and thus aid in the selection of the most adequate therapy. The high sensitivity and specificity of the reverse transcriptase-polymerase chain reaction (RT-PCR) encouraged various groups to investigate the mRNA expression of prostate-specific markers in the peripheral blood of patients with prostate cancer. However, probably due to methodological differences, many contradictory results have been obtained with the markers studied so far: prostate-specific antigen (PSA) and prostate-specific membrane antigen (PSM). For this reason, clinical decisions should not be based yet on RT-PCR results. Future research and long-term follow-up on the patients may point out whether RT-PCR assays, following appropriate standardization, will have an additive value in prostate cancer staging and in prediction of tumor progression.

Ty3/gypsy-like retrotransposon sequences in tomato

Polymerase chain reactions (PCRs) were carried out with DNAs of eight tomato species using primers directed at the reverse transcriptase domain of Ty3/gypsy-like LTR retrotransposons. All DNAs gave PCR products of the expected size which, after cloning and sequencing, were confirmed as representing Ty3/gypsy-like elements. The sequences were heterogeneous, only 3 of the 16 being identical and the most diverse showing 124/426 pairwise nucleotide differences. Multiple alignment and construction of neighbor joining trees divided the sequences into six groups, three comprising five, three, and five sequences respectively, and the other three containing a single sequence each.

Detection of adenovirus outbreak at a municipal swimming pool by nested PCR amplification

In July 1995 an outbreak of pharyngoconjuctivitis caused by adenoviruses occurred among athletes participating in a swimming contest in a town in southern Greece (Peloponnese). At least 80 persons displayed symptoms of the illness, with the predominant ones being high fever, sore throat, conjuctivitis, headache, and abdominal pain. Poor chlorination was probably the cause of the outbreak (residual chlorine <0.2 mg/l), as after hyperchlorination the spread of adenoviruses stopped. Rapid detection of adenoviruses in the municipal swimming pool water by nested polymerase chain reaction (PCR) amplification allowed quick control of the outbreak.

cDNA selection with YACs

Identification of expressed sequence tags (ESTs) in large genomic segments is an important step in positional cloning and genomic mapping studies. A simple and efficient polymerase chain reaction (PCR)-based approach is described here to identify coding sequences in large genomic fragments of DNA cloned in vectors such as yeast artificial chromosome (YAC) vectors. The method is based on blocking of sequences such as repetitive and GC rich sequences in the genomic DNA immobilized on nylon paper discs prior to hybridization of the discs to cDNA library, and recovery of the selected cDNAs by the PCR. Single or multiple cDNA libraries can be used in the selection procedure. The procedure has been used successfully also with total yeast DNA containing a YAC.

Simultaneous detection and typing of plum pox potyvirus (PPV) isolates by heminested-PCR and PCR-ELISA

Two techniques for simultaneous detection and typing of plum pox potyvirus (PPV) isolates belonging to the D or M serotypes, heminested PCR (H-PCR) and PCR-ELISA, have been developed. Ten PPV isolates typed using PPV-D and PPV-M specific monoclonal antibodies by ELISA-DASI were used to validate these two methods. The results obtained show a complete coincidence of the nucleic acid-based techniques with the serological data. When serial dilutions of infected plant extracts were assayed, H-PCR and PCR-ELISA were found to be 100 times more sensitive than the more conventional immunocapture-PCR (IC-PCR) assay. Testing of 228 PPV-infected fruit tree samples coming from different hosts and locations indicated that so far only PPV type D appears to be present in Spain and in Chile. Coupled with print-capture sample preparation (Olmos et al., Nucl. Acids Res. 24, 2192-2193, 1996) the increased sensitivity provided by heminested-PCR allowed the detection of PPV targets of D and M types, in wingless individuals of the aphid vector Aphis gossypii.

Molecular diagnostics of infectious diseases

Over the past several years, the development and application of molecular diagnostic techniques has initiated a revolution in the diagnosis and monitoring of infectious diseases. Microbial phenotypic characteristics, such as protein, bacteriophage, and chromatographic profiles, as well as biotyping and susceptibility testing, are used in most routine laboratories for identification and differentiation. Nucleic acid techniques, such as plasmid profiling, various methods for generating restriction fragment length polymorphisms, and the polymerase chain reaction (PCR), are making increasing inroads into clinical laboratories. PCR-based systems to detect the etiologic agents of disease directly from clinical samples, without the need for culture, have been useful in rapid detection of unculturable or fastidious microorganisms. Additionally, sequence analysis of amplified microbial DNA allows for identification and better characterization of the pathogen. Subspecies variation, identified by various techniques, has been shown to be important in the prognosis of certain diseases. Other important advances include the determination of viral load and the direct detection of genes or gene mutations responsible for drug resistance. Increased use of automation and user-friendly software makes these technologies more widely available. In all, the detection of infectious agents at the nucleic acid level represents a true synthesis of clinical chemistry and clinical microbiology techniques.

Cloning and expression of the panallergen profilin and the major allergen (Ole e 1) from olive tree pollen

BACKGROUND

Olive tree (Olea europaea) pollen allergy is one of the main causes of allergy in Mediterranean countries and some areas of North America.

OBJECTIVE

To clone olive allergens and to characterize immunologically the purified recombinant allergens.

METHODS

Full-length complementary deoxyribonucleic acid (cDNA) strands encoding olive allergens (Ole e 1) were cloned by polymerase chain reaction amplification and sequenced. Recombinant proteins were produced in Escherichia coli by the use of two different expression systems. Immunoreactivity of the recombinant proteins was tested by ELISA and Western blot with serum from patients with allergy to olive.

RESULTS

Significant sequence polymorphism was found in both allergens. The panallergen profilin was expressed as a nonfusion protein and was purified to homogeneity after a single step of affinity chromatography with a poly-L-proline Sepharose column. One cDNA encoding an Ole e 1 isoform was expressed as a fusion protein consisting of the glutathione S-transferase of Schistosoma japonicum and Ole e 1. The fusion protein was purified to homogeneity by gel filtration chromatography and affinity chromatography with a glutathione-Sepharose column, and digested with thrombin. Both recombinant allergens shared B cell epitopes with the corresponding natural allergens.

CONCLUSION

IgE-reactive Ole e 1 and olive profilin expressed in bacteria were purified after simple chromatographic procedures and may be useful for diagnostic purposes.

Water deprivation upregulates ANG II AT1 binding and mRNA in rat subfornical organ and anterior pituitary

We studied angiotensin II (ANG II) receptor subtype expression in selected brain nuclei and pituitary gland after water deprivation by in vitro receptor autoradiography using 125I-labeled [Sar1]ANG II and by in situ hybridization using 35S-labeled AT1A, AT1B, and AT2 receptor-specific riboprobes. In control rats we found binding to AT1 receptors in the subfornical organ, paraventricular nucleus, median eminence, and anterior pituitary; AT1A mRNA expression in the subfornical organ and paraventricular nucleus; and AT1B mRNA expression in the anterior pituitary. No receptor mRNA was found in the median eminence. AT1 receptors and AT1A receptor mRNA levels were increased in the subfornical organ, and, in the anterior pituitary, AT1 receptors and AT1B receptor mRNA were increased, only after 5 days of water deprivation. No significant changes occurred after 1 or 3 days of water deprivation, and no regulation of ANG II receptor expression was detected in other brain areas. Our results show that prolonged water deprivation selectively regulates AT1 receptor expression and AT1A and AT1B receptor mRNA levels in the subfornical organ and anterior pituitary, respectively, supporting a role for these receptors during sustained dehydration.

Clonal X-inactivation analysis of human tumours using the human androgen receptor gene (HUMARA) polymorphism: a non-radioactive and semiquantitative strategy applicable to fresh and archival tissue

Assessment of clonality of cellular proliferations is important in experimental and clinical cancer research. X-chromosome inactivation studies are widely used to assess clonality, but most assays require relatively large amounts of high molecular weight DNA. Two PCR-based strategies, the phosphoglycerate kinase (PGK) and the human androgen receptor (HUMARA) clonality assays allow studies of small tissue samples. The HUMARA assay was adapted to non-radioactive analysis taking advantage of an automated sequencer providing high resolution of alleles and immediate quantitation. This assay was validated by comparison with X-inactivation patterns obtained by Southern analysis with the probes M27 beta and PGK. Fifteen gastrointestinal carcinomas, 25 benign goiter nodules and normal peripheral leukocytes of 27 individuals (12 who were under 15 years and 15 over 80 years) were analysed. Furthermore, DNA extracted from formalin-fixed paraffin-embedded tissue (FPT) was analysed with the two PCR-based methods and compared with X-inactivation patterns determined by Southern analysis of high molecular weight (HMW) DNA. This modified HUMARA assay is reliable in most patients; as with other clonality assays, constitutive skewing in normal tissue precludes clonal analysis in some individuals. Extremely skewed X-inactivation patterns were found in normal peripheral leukocytes of 7 out of 15 old females (over 80 years) and in 1 of 12 of the young females tested (under 15 years). Comparison of results obtained with HMW and FPT DNA yielded consistent results for the HUMARA assay whereas the PGK PCR assay was much less reliable. The HUMARA assay thus permits studies of selected areas of tissue sections without significant stromal components, allowing correlation of histological and genotype findings in fresh and archival specimens.

Infrared fluorescent detection of D1S80 alleles

A genetic locus D1S80 containing a variable number of tandem repeats (VNTR) has been used extensively in forensic analysis and paternity testing. In the current research, the D1S80 locus was amplified using polymerase chain reaction (PCR) technology and the alleles detected using a high sensitivity infrared (IR) fluorescence automated DNA sequencer. IR-labeled amplification products were generated using oligonucleotide primers which were covalently linked to an infrared fluorescent dye (IRD41) at the 5'-end. Human genomic DNA (1.0 ng or less) isolated from blood and various simulated forensic samples was successfully amplified using this technology. Allelic bands were detected by incorporation of the IR fluorescent dye into PCR products. Both Long Ranger and polyacrylamide denaturing gels permitted clear resolution of individual alleles that differ by only one repeat unit. In the smaller gels a separation distance of only 15 cm allowed separation of the alleles in less than 2 h from sample loading to visualization. This system combines IR fluorescence chemistry and laser technology thus eliminating the need for post-electrophoretic gel handling for the detection of D1S80 alleles. Real-time detection is valuable for immediate visualization of the data and the alleles are displayed as familiar autoradiogram-like images which can also be analyzed by computer. By loading a 64-lane gel twice it is possible to type at least 120 samples in 1 day using a single gel.

Absence of cell-surface annexin V is accompanied by defective collagen matrix binding in the Swarm rat chondrosarcoma

Annexin V has been characterized as a major collagen type II binding cell-surface component of normal chondrocytes and is also called anchorin CII in chondrogenic populations. Herein we present evidence that in vitro cultured Swarm rat chondrosarcoma cells are not capable of binding collagen type II in significant quantities to their surfaces, as compared to normal rat chondrocytes. This finding coincides with a deficiency of annexin V on the surface of these cells. A small quantity of an intracellular polypeptide could be detected which is immunologically cross-reactive with annexin V but displayed a mobility in SDS-PAGE of less than 34 kD compared to the M(r) 36 kD of intact rat annexin V. By immunohistochemistry the protein could be localized in the cytoplasm of in vitro and in vivo grown tumor cells. By reverse transcription-polymerase chain reaction and Northern blot analysis, a regular-sized mRNA for annexin V could be detected in the chondrosarcoma cells that is expressed in only slightly lower quantities than in normal chondrocytes. Taken together, the data suggest a modified processing or turnover for annexin V in the chondrosarcoma excluding it from being a functionally active collagen type II binding protein. The findings support the hypothesis of cell-surface annexin V as a key component for the formation of the pericellular matrix of chondrocytes.

A PCR assay for identification of Enterococcus faecium

Enterococcus faecium has recently emerged as a serious nosocomial pathogen. The prevalence and severity of enterococcal infections, the mortality rate from such infections, and the antibiotic resistance of enterococci are often species dependent. Since conventional biochemical methods fail to differentiate E. faecium from certain newly described enterococcal species, a PCR-based assay was developed for the rapid identification of E. faecium.

Gene amplification in the diagnosis of mycobacterial infections

The number of importance of infections caused by Mycobacterium tuberculosis and other mycobacterial species is increasing. Since the detection and identification of mycobacteria by conventional laboratory methods (cultivation, staining, and biochemical tests) is a slow and complex procedure, rapid diagnostic methods are urgently needed. Several amplification methods based on different techniques have been applied in the detection of mycobacteria directly from clinical specimens. Most experience has been obtained from different polymerase chain reaction (PCR) assays and their general performance is good. However, their sensitivity in the analysis of samples containing small amounts of mycobacteria or samples containing inhibitory substances has been low. Furthermore, the risk of false positives caused by contamination is high, and the clinical relevance of the results may be unclear. Thus, these gene amplification techniques are a valuable adjunct to the diagnosis of mycobacteria, but so far they cannot replace conventional microbiological methods.

A sensitive reverse transcriptase polymerase chain reaction assay for measuring the effects of dehydration and gestation on rat amounts of vasopressin and ocytocin mRNAs

This study describes a competitive reverse transcriptase polymerase chain reaction (RT-PCR) method for assaying the amounts of vasopressin (AVP) and ocytocin (OT) mRNAs in the rat hypothalamus and uterus. Despite the low concentrations of these mRNAs, the RT-PCR method readily measured both AVP and OT mRNAs in the same sample. A common internal standard for both reactions was designed to quantify the reaction. Both AVP and OT mRNAs were readily quantified in a 75 ng sample of total RNA from the hypothalamus. Water deprivation stimulated AVP mRNA production 3-fold and OT mRNA production 1.7-fold in the hypothalamus. Gestation only influenced the amount of OT mRNA in the hypothalamus (3-fold increase) and uterus (38-fold increase). The amount of AVP mRNA in the hypothalamus remained unchanged and no AVP mRNA was detected in the uteri of either non-pregnant or pregnant rats. This competitive RT-PCR is a powerful tool that provides rapid and precise assays of AVP and OT mRNAs.

Purification and properties of a new virus from black currant, its affinities with nepoviruses, and its close association with black currant reversion disease

ABSTRACT Black currant reversion is a virus-like disease whose causal agent has not been identified. In rooted cuttings of a black currant plant affected with the severe form of the disease, pronounced chlorotic line patterns and ringspots developed in newly emerging leaves. From such symptom-bearing leaves, a virus was mechanically transmitted with difficulty to Chenopodium quinoa and, from this host, to other herbaceous test plants. The virus was purified and partially characterized, and the purified viri-ons were used for antiserum production. Virus particles were isometric, approximately 27 nm in diameter, and sedimented as two nucleoprotein components. They contained a protein species with a molecular mass of 55 kDa, which was readily degraded into a 54-kDa protein and two major RNA components of about 6,700 and 7,700 nucleotides (nt), each with a poly(A) tail. Most of these properties are shared by nepoviruses, but the virus was serologically unrelated to 14 nepoviruses or putative nepovi-ruses tested. However, the deduced sequence of 1,260 nt at the 3' end of one of the viral RNA species was distinct from any known viral sequence, except that it contained short regions of homology to the 3' terminal sequences of RNAs of seven other nepoviruses and two comovi-ruses. To detect this virus in Ribes plants, primers were designed from the known sequence to amplify a 210-nt region of the cDNA of the virus RNA using an immunocapture reverse transcriptase polymerase chain reaction (IC-RT-PCR) protocol. Using this assay for the virus, we associated its presence with two recognized forms of black currant reversion disease occurring in Finland, Scotland, or New Zealand. We also detected the virus in vector gall mites from reverted plants and in black currant plants on which such vector mites had fed. However, the virus was not detected by IC-RT-PCR in known healthy Ribes plants; in Ribes plants free from reversion, but affected by three other distinct virus-like diseases of Ribes; or in plants infected with arabis mosaic, strawberry latent ringspot, or raspberry ringspot nepoviruses. These data suggest that this virus may be the causal agent of reversion disease, and it is tentatively called black currant reversion associated virus.

Detection of Chlamydia pneumoniae in human nonrheumatic stenotic aortic valves

OBJECTIVES

We sought to study the possible presence of Chlamydia pneumoniae in aortic valve stenosis (AVS).

BACKGROUND

Inflammation and immune mechanisms are considered important for the pathogenesis of nonrheumatic AVS. All chlamydial species are able to cause heart infections, and seroepidemiologic studies have indicated an association between chronic C. pneumoniae infection and coronary artery disease. Furthermore, the organism has been demonstrated in atherosclerotic lesions.

METHODS

Aortic valve specimens with varying degrees of macroscopic disease were obtained from 35 subjects--17 consecutive patients undergoing aortic valve replacement for treatment of nonrheumatic AVS and 18 age-matched subjects at autopsy. The possible presence of C. pneumoniae in aortic valves was studied by immunohistochemical analysis, polymerase chain reaction or transmission electron microscopy, or a combination of these.

RESULTS

Positive immunohistochemical staining with C. pneumoniae specific antibody was found in 9 (53%) of 17 patients with advanced aortic valve disease requiring surgical treatment (group A), 8 (80%) of 10 cadavers with clearly macroscopic aortic valve pathology (group B) and 1 (12%) of 8 grossly normal cadaver control subjects (group C). Statistical significance with regard to the presence of C. pneumoniae was found when combined diseased subjects (groups A and B: total 17 of 27 subjects) were compared with group C (p = 0.018). However, when group A was compared with group C, there was only marginal statistical significance (p = 0.088). Finally, there was a strong statistical significance (p = 0.015) when groups B and C were compared. Chlamydia pneumoniae DNA was also found in three stenotic valves, and in two of the three tested valve specimens chlamydia-like particles were seen by electron microscopy.

CONCLUSIONS

Chlamydia pneumoniae is frequently present in nonrheumatic AVS. Similarly, the high number of C. pneumoniae infections detected in the early lesions of "degenerative" AVS suggest that this pathogen may play an etiologic role in the development of this disease. The validity of this relation requires additional study.

Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry

We report a simple method, the PinPoint assay, for detecting and identifying single-base variations (polymorphisms) at specific locations within DNA sequences. An oligonucleotide primer is annealed to the target DNA immediately upstream of the polymorphic site and is extended by a single base in the presence of all four dideoxynucleotide triphosphates and a thermostable DNA polymerase. The extension products are desalted, concentrated, and subjected to delayed-extraction MALDI-TOF mass spectrometry. The base at the polymorphic site is identified by the mass added onto the primer. Heterozygous targets produce two mass-resolved species that represent the addition of both bases complementary to those at the polymorphic site. The assay is suitable for double-stranded PCR products without purification or strand separation. More than one primer can be simultaneously extended and then mass-analyzed. The mass spectrometric method thus shows promise for high-volume diagnostic or genotyping applications.

The complete sequence, expression in Escherichia coli, purification and some properties of carbonic anhydrase from Neisseria gonorrhoeae

The complete nucleotide sequence of the carbonic anhydrase gene from Neisseria gonorrhoeae has been determined. The gene encodes a 252-residue polypeptide with a molecular mass of 28085 Da. The gene has been cloned and overexpressed in Escherichia coli, and the enzyme has been purified. A 26-residue signal peptide is cleaved off by the E. coli processing machinery. Thus, the isolated enzyme contains 226 amino acid residues with a molecular mass of 25314 Da. Most of the enzyme seems to be produced as a soluble protein located in the periplasm of E. coli. The enzyme is homologous to carbonic anhydrases from the animal kingdom; it is an alpha-carbonic anhydrase. A comparison with the amino acid sequences of human carbonic anhydrases I and II suggests that the secondary structures are essentially intact in the bacterial enzyme but that several loops are much shorter than in the human forms. Most of the active-site residues are identical to those found in the high-activity human isozyme II. The bacterial enzyme has a high CO2 hydration activity with a k(cat) of 1.1 x 10(6) s(-1) and Km of 20 mM at pH 9 and 25 degrees C. The enzyme also catalyzes the hydrolysis of 4-nitrophenyl acetate. The pH/rate profile can be described as a titration curve with pKa of 6.7 and a maximal value of the catalytic second-order rate constant, k(enz), of 130 M(-1) x s(-1).

Development of a nested PCR assay for detection of feline infectious peritonitis virus in clinical specimens

A diagnostic test for feline infectious peritonitis virus (FIPV) infection based on a nested PCR (nPCR) assay was developed and tested with FIPV, feline enteric coronavirus (FECV), canine coronavirus (CCV), and transmissible gastroenteritis virus (TGEV) and clinical fluid samples from cats with effusive feline infectious peritonitis (FIP). The target sequence for the assay is in the S1 region of the peplomer protein E2 gene. A vaccine strain of FIPV and two wild-type FIPV strains tested positive, but FECV, TGEV, and CCV tested negative. Preliminary tests with 12 cats with clinical evidence of effusive FIP and 11 cats with an illness associated with effusions, but attributed to other causes, were performed. Eleven of the 12 cats with effusive FIP tested positive, while 1 was negative. Ten of the 11 cats ill from other causes tested negative, while 1 was positive. On the basis of clinical laboratory and histopathologic criteria, the preliminary sensitivity and specificity of the assay were 91.6 and 94%, respectively.

Demonstration of Chlamydia pneumoniae in the walls of abdominal aortic aneurysms

BACKGROUND

Seroepidemiologic studies have indicated an association between chronic Chlamydia pneumoniae infection and coronary heart disease. The organism, which is a common respiratory pathogen, has been demonstrated in atherosclerotic lesions of the aorta and coronary arteries. Abdominal aortic aneurysms are frequently associated with atherosclerosis, and inflammation may actually be an important factor in aneurysmal dilatation. Hence it could be assumed that C. pneumoniae may play a role in maintaining an inflammation and triggering the development of aortic aneurysms.

METHODS AND RESULTS

Specimens from abdominal aortic aneurysm were examined for the presence of C. pneumoniae by immunohistochemical analysis, the polymerase chain reaction amplifying omp 1 gene, transmission electron microscopy, and culture methods with histologically atherosclerosis-negative human aortic tissues used as a control group. Chlamydial lipopolysaccharide and C. pneumoniae specific antigens were found by immunohistochemistry in 12 and 8 of 12 aneurysm specimens, respectively, and C. pneumoniae DNA could be demonstrated in 6 of 6 aneurysm specimens studied. Furthermore electron microscopy revealed the presence of Chlamydia-like elementary bodies in three of four aneurysm specimens tested. None of the control samples gave positive reaction in the polymerase chain reaction, and C. pneumoniae antigens were not detected in any of them.

CONCLUSIONS

C. pneumoniae is frequently found in the vessel wall of abdominal aortic aneurysm. The potential etiopathogenetic role of C. pneumoniae in the development of these aneurysms remains to be studied.

Product differentiation by analysis of DNA melting curves during the polymerase chain reaction

A microvolume fluorometer integrated with a thermal cycler was used to acquire DNA melting curves during polymerase chain reaction by fluorescence monitoring of the double-stranded DNA specific dye SYBR Green I. Plotting fluorescence as a function of temperature as the thermal cycler heats through the dissociation temperature of the product gives a DNA melting curve. The shape and position of this DNA melting curve are functions of the GC/AT ratio, length, and sequence and can be used to differentiate amplification products separated by less than 2 degrees C in melting temperature. Desired products can be distinguished from undesirable products, in many cases eliminating the need for gel electrophoresis. Analysis of melting curves can extend the dynamic range of initial template quantification when amplification is monitored with double-stranded DNA specific dyes. Complete amplification and analysis of products can be performed in less than 15 min.

Growth factor control of growth and epithelial differentiation in embryonic lungs

embryonic lung cultures were exposed to either EGF (10 ng/ml) or TGF beta 1 (2 ng/ml) for 72 h, and branching morphogenesis, cell proliferation, and epithelial differentiation (the expression of DSPC synthesis and of surfactant protein C (SP-C) mRNA) were studied. EGF treatment stimulated branching morphogenesis (measured as the number of terminal left lung buds), epithelial differentiation, and cell proliferation. Branching morphogenesis was increased compared to controls after 48 h of culture by 47% and after 72 h by 34% (P < 0.0005). Choline incorporation into DSPC was stimulated by 343% (P = 0.05). SP-C expression was increased sixfold. Thymidine incorporation was stimulated by 49% (P < 0.05). The effects of EGF on thymidine labeling were distributed among epithelial cells of the airway walls and of the branching tips, and also the mesenchyme (P < 0.01 for each area compared to controls). In contrast, TGF beta 1 did not alter the number of terminal left lung buds, inhibited choline incorporation into DSPC by 35% (P < 0.05), and had no effect on thymidine incorporation (87% of control). There was increased thymidine labeling at the branching tips (P < 0.01), while other areas were not different from controls. We conclude that both EGF and TGF beta 1 affect the development of branching morphogenesis and of epithelial differentiation in the embryonic lung.

Achalasia is not associated with measles or known herpes and human papilloma viruses

Achalasia is an esophageal motility disorder of unknown etiology. Several studies suggest possible herpes or measles virus etiology, but results are inconclusive. The aim of this study was to test whether herpesvirus (HV), measles (MV), or human papilloma virus (HPV) sequences could be detected in myotomy specimens from a wide spectrum of achalasia patients, using the polymerase chain reaction (PCR) technique. Myotomy specimens from 13 achalasia patients, esophagectomy specimens from nine esophageal cancer patients, and autopsy specimens from six fetuses were studied with the PCR technique. Paired oligonucleotide primers of HV (HSV-1 and 2, CMV, EBV, VZV, and HHV-6), MV and HPV sequences and exon 3 of the HPRT gene were used for the PCR DNA amplification. Amplified products were resolved on agarose gels and stained with ethidium bromide. All specimens yielded the appropriate-sized products for exon 3 of the HPRT and viral controls. No amplified products were seen in the achalasia specimens or controls corresponding to any of the virus sequences tested. The absence of HV, MV, and HPV sequences suggests that these viruses are not associated with achalasia but does not exclude the possibility of a previously unidentified virus as a causal agent. Further studies aimed at identifying an unknown viral agent as a cause for achalasia are warranted.

PCR in laboratory diagnosis of human Borrelia burgdorferi infections

The laboratory diagnosis of Lyme borreliosis, the most prevalent vector-borne disease in the United States and endemic in parts of Europe and Asia, is currently based on serology with known limitations. Direct demonstration of Borrelia burgdorferi by culture may require weeks, while enzyme-linked immunosorbent assays for antigen detection often lack sensitivity. The development of the PCR has offered a new dimension in the diagnosis. Capable of amplifying minute amounts of DNA into billions of copies in just a few hours, PCR facilitates the sensitive and specific detection of DNA or RNA of pathogenic organisms. This review is restricted to applications of PCR methods in the diagnosis of human B. burgdorferi infections. In the first section, methodological aspects, e.g., sample preparation, target selection, primers and PCR methods, and detection and control of inhibition and contamination, are highlighted. In the second part, emphasis is placed on diagnostic aspects, where PCR results in patients with dermatological, neurological, joint, and ocular manifestations of the disease are discussed. Here, special attention is given to monitoring treatment efficacy by PCR tests. Last, specific guidelines on how to interpret PCR results, together with the advantages and limitations of these new techniques, are presented.

Detection of Epstein-Barr virus DNA in gastric carcinoma with lymphoid stroma

Gastric carcinoma with lymphoid stroma (GCLS) was considered to be one of the virus-associated neoplasms. However, the precise mechanism of Epstein-Barr virus (EBV) oncogenesis for GCLS remains unclear. We used polymerase chain reaction (PCR) and DNA in situ hybridization (ISH) methods to detect the presence of EBV DNA in 14 cases of gastric carcinoma, including 8 cases of GCLS. Epstein-Barr virus DNA was detected by both PCR and ISH in 3 of the 8 GCLS cases (37.5%) and was negative in the other 6 cases of non-GCLS. In situ DNA hybridization showed that the EBV DNA was in the carcinoma cells in all cases that were positive by PCR. Among the positive cases, one early gastric carcinoma showed that EBV DNA was not only in the carcinoma cells, but also in the normal epithelium. This study provides the interpretation of the finding of EBV DNA in nonneoplastic gastric epithelium. Some genetic changes may be initiated in the EBV-infected nonneoplastic cells, which would lead to oncogenesis.

RAPD typing in microbiology--a technical review

Many biochemical and molecular techniques can be used for distinguishing isolates of a given bacterial species. Traditional typing techniques based on phenotypic characteristics such as serotyping are being increasingly challenged by the use of DNA-based methods. The introduction of the polymerase chain reaction (PCR) has led to typing techniques based on DNA amplification. Randomly amplified polymorphic DNA (RAPD) typing (also known as arbitrarily primed-polymerase chain reaction, APPCR) is one such technique which is being used increasingly to type micro-organisms, especially during clinical outbreaks. The application and potential problems and solutions of RAPD typing are discussed and the role of such techniques among established typing methods is addressed.

Long range-inverse PCR (LR-IPCR): extending the useful range of inverse PCR

The inverse PCR technique (IPCR) has proven to be very useful for the amplification of uncharacterized stretches of DNA upstream or downstream of regions that have already been cloned and sequenced. In practice, however, chromosome walking using standard IPCR is often a slow, repetitive process because only small DNA fragments are effectively amplified. The development of long and accurate PCR methodology has greatly expanded the range of DNA fragment sizes that is amenable to amplification by conventional PCR. We reasoned that combining long range PCR with IPCR would also extend the useful range of the IPCR technique. In this paper we demonstrate the utility of the hybrid, long range-inverse PCR (LR-IPCR) technique by generating clones containing long stretches of DNA flanking endogenous chicken proviral elements.

Peptide rescue of an N-terminal truncation of the Stoffel fragment of taq DNA polymerase

Deletion of the first 289 amino acids of the DNA polymerase from Thermus aquaticus (Taq polymerase) removes the 5' to 3' exonuclease domain to yield the thermostable Stoffel polymerase fragment (Lawyer et al., 1989). Preliminary N-terminal truncation studies of the Stoffel fragment suggested that removal of an additional 12 amino acids (the Stof delta 12 mutant) had no significant effect on activity or stability, but that the further truncation of the protein (the Stof delta 47, in which 47 amino acids were deleted), resulted in a significant loss of both activity and thermostability. A 33-amino acid synthetic peptide, based on this critical region (i.e., residues 303-335 inclusive), was able to restore 85% of the Stof delta 12 activity when added back to the truncated Stof delta 47 protein as well as return the temperature optimum to that of the Stof delta 12 and Stoffel proteins. Examination of the crystal structure of Taq polymerase (Kim et al., 1995) shows that residues 302-336 of the enzyme form a three-stranded beta-sheet structure that interacts with the remainder of the protein. CD analysis of the 33-amino acid peptide indicates that the free peptide also adopts an ordered structure in solution with more than 50% beta-sheet content. These data suggest that this 33-amino acid peptide constitutes a stable beta-sheet structure capable of rescuing the truncated polymerase in a fashion analogous to the well-documented complementation of Ribonuclease S protein by the 15-residue, alpha-helical, S peptide.

The Nramp1 antimicrobial resistance gene segregates independently of resistance to virulent Mycobacterium tuberculosis

Nramp1 is a recently cloned gene that is involved in resistance of mice to infection with certain microbial pathogens, including the attenuated bacillus Calmette-Guérin (BCG) strain of Mycobacterium bovis, as well as certain other mycobacteria. With a view to determining whether Nramp1 influences resistance of mice to infection with virulent M. tuberculosis, BALB/c mice homozygous for the susceptibility allele of Nramp1, and DBA/2 mice homozygous for the resistance allele, as well as their F1 and F2 progeny, were typed according to their possession of these alleles using a 'hot start' polymerase chain reaction (PCR) procedure. As assessed by the ability of the mice to survive infection, the results show that Nramp1 plays no discernible role in resistance to tuberculosis.

Quantitation and purification of polymerase chain reaction products by high-performance liquid chromatography

This work describes the application of the fully automated high-performance liquid chromatographic system to the analysis of PCR-amplified products. Efficient separations of both DNA restriction fragments and PCR products were performed using an anion-exchange DEAE-NPR column, packed with 2.5-microns nonporous particles. The automated HPLC method was employed for the separation, quantitation, and purification of PCR products in less than 10 min in a single step.

Individualisation of HIV therapy based on HIV RNA load: the virologist's perspective

There is increasing evidence that direct quantification of viral load by quantitative HIV RNA polymerase chain reaction (PCR) may be one of the more useful markers of disease status and antiviral treatment efficacy. Given the central role of viral replication in the pathogenesis of HIV infection, it is logical to assume that monitoring levels of cell-free virus in the plasma will be predictive of disease status. Furthermore, since the primary aim of treatment with current antiretroviral therapies is reduction of viral load, changes in plasma viraemia may be expected to be predictive of treatment effects. Preliminary data indeed suggest that viral load, is a useful marker of baseline prognosis, disease status and the effectiveness of antiretroviral therapy in individual patients. These data support the concept that measurement of viral RNA may eventually be of clinical utility in managing therapy of individual patients. However, prospective viral load studies are required to validate such a strategy.

Role of Borrelia burgdorferi in the pathogenesis of morphea/scleroderma and lichen sclerosus et atrophicus: a PCR study of thirty-five cases

Morphea (localized scleroderma), and lichen sclerosus et atrophicus (LSA) share common features with acrodermatitis chronica atrophicans (ACA), a known chronic form of borreliosis. These include similar histologic findings such as diffuse dermal fibrosis. These observations have led several investigators to consider the possibility of Borrelia burgdorferi (Bb) as a common etiologic factor among all of these diseases. The aim of this study is to investigate the role of Bb in the pathogenesis of morphea and LSA, by assaying for its presence in lesional skin biopsies from patients with these diseases. We utilized the nested polymerase chain reaction (PCR) technique to selectively amplify a longer segment of a Bb-specific somatic gene, on DNA from paraffin-embedded, formalin-fixed tissues. The results revealed no Bb-specific DNA sequence in 28 specimens of morphea/scleroderma and 7 of LSA with varying stages of disease. Furthermore, confirmatory Southern blot of the PCR product, resulted in similar findings. These data seriously question the role played by this spirochete in the pathogenesis of morphea and LSA, at least in the southeastern part of the USA.

Recombinant technique and gonadotropins production: new era in reproductive medicine

OBJECTIVE

To review current knowledge regarding recombinant DNA technology and its safety and efficacy in relation to recombinant gonadotropin production.

DATA IDENTIFICATION AND SELECTION

Studies that relate specifically to recombinant DNA technology, method of laboratory production, and the clinical aspects of using recombinant gonadotropins were identified through literature and Medline searches.

RESULTS

Recent developments in recombinant DNA technology have resulted in a rapidly expanding range of new diagnostic and therapeutic opportunities. This technology paves the way to the identification, isolation, cloning, and production of specific proteins. Recently, recombinant human gonadotropins became available for clinical use. The pharmacokinetics, receptor availability, pharmacodynamics, and safety were studied extensively and the drugs were found to be identical if not superior to urinary gonadotropins that have been used in reproductive medicine for the last 30 years. It is clear today that the use of recombinant human gonadotropins is expected to provide better batch-to-batch consistency, steady supply, and most importantly, a purified compound with high specific activity, which accounts for >99% of the preparation's protein content, allowing SC administration.

CONCLUSION

There is no doubt that recombinant gonadotropins produced by genetic engineering technology are here to stay and will represent an important treatment modality in various fertility disturbances.

Theoretical uncertainty of measurements using quantitative polymerase chain reaction

Current quantitative polymerase chain reaction (PCR) protocols are only indicative of the quantity of a target sequence relative to a standard, because no means of estimating the amplification rate is yet available. The variability of PCR performed on isolated cells has already been reported by several authors, but it could not be extensively studied, because of lack of a system for doing kinetic data acquisition and of statistical methods suitable for analyzing this type of data. We used the branching process theory to simulate and analyze quantitative kinetic PCR data. We computed the probability distribution of the offspring of a single molecule. We demonstrated that the rate of amplication has a severe influence on the shape of this distribution. For high values of the amplification rate, the distribution has several maxima of probability. A single amplification trajectory is used to estimate the initial copy number of the target sequence as well as its confidence interval, provided that the amplification is done over more than 20 cycles. The consequence of possible molecular fluctuations in the early stage of amplification is that small copy numbers result in relatively larger intervals than large initial copy numbers. The confidence interval amplitude is the theoretical uncertainty of measurements using quantitative PCR. We expect these results to be applicable to the data produced by the next generation of thermocyclers for quantitative applications.

Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments

The phylogenetic compositions of bacterioplankton assemblages from San Francisco Bay and Tomales Bay, Calif., differed substantially when analyzed by PCR-denaturing gradient gel electrophoresis; these differences are consistent with the results of previous studies demonstrating differences in their metabolic capabilities. PCR-denaturing gradient gel electrophoresis analysis of complex microbial assemblages was sensitive and reliable, and the results were reproducible as shown by experiments with constructed and naturally occurring assemblages.