Recent advances in the polymerase chain reaction

Design and evaluation of Bacteroides DNA probes for the specific detection of human fecal pollution

Because Bacteroides spp. are obligate anaerobes that dominate the human fecal flora, and because some species may live only in the human intestine, these bacteria might be useful to distinguish human from nonhuman sources of fecal pollution. To test this hypothesis, PCR primers specific for 16S rRNA gene sequences of Bacteroides distasonis, B. thetaiotaomicron, and B. vulgatus were designed. Hybridization with species-specific internal probes was used to detect the intended PCR products. Extracts from 66 known Bacteroides strains, representing 10 related species, were used to confirm the specificity of these PCR-hybridization assays. To test for specificity in feces, procedures were developed to prepare DNA of sufficient purity for PCR. Extracts of feces from 9 humans and 70 nonhumans (cats, dogs, cattle, hogs, horses, sheep, goats, and chickens) were each analyzed with and without an internal positive control to verify that PCR amplification was not inhibited by substances in the extract. In addition, serial dilutions from each extract that tested positive were assayed to estimate the relative abundance of target Bacteroides spp. in the sample. Depending on the primer-probe set used, either 78 or 67% of the human fecal extracts tested had high levels of target DNA. On the other hand, only 7 to 11% of the nonhuman extracts tested had similarly high levels of target DNA. An additional 12 to 20% of the nonhuman extracts had levels of target DNA that were 100- to 1,000-fold lower than those found in humans.(ABSTRACT TRUNCATED AT 250 WORDS)

Detection of Epstein-Barr virus and human papillomavirus in nasopharyngeal carcinoma by the polymerase chain reaction technique

We used the PCR technique to detect the Epstein-Barr virus (EBV) and human papillomavirus (HPV) DNA in paraffin-embedded tissues from Greek patients with nasopharyngeal carcinoma (NPC). The oligonucleotide primers used for the detection of EBV amplify a 375-bp long sequence from the EcoRI B fragment of the viral genome, whereas for HPV the primers amplify a 151-bp long sequence of the viral genome. The PCR products were analysed by agarose gel electrophoresis and visualised by UV illumination after staining with ethidium bromide. Sixty-three specimens were examined. EBV specific sequence was amplified in 20 (32%) and HPV in 12 (19%) out of the 63 samples. There was no co-infection with EBV and HPV. Although there is a high correlation of EBV infection with poorly differentiated NPC in patients from Southern China and South-East Asia, the restricted distribution suggests genetic or environmental cofactors in the development of the neoplasm. Our results confirm this suggestion since there was only a 32% correlation of EBV with NPC in Greece. HPV may also be involved in the carcinogenesis of EBV-negative squamous cell nasopharyngeal carcinomas.

A rapid, non-radioactive screening test for fragile X mutations at the FRAXA and FRAXE loci

Screening of referrals for the mutations associated with the fragile X syndrome constitutes a significant workload in many genetics laboratories. Since the great majority of these referrals will be negative, there is a need for a rapid and inexpensive screening test. We have developed an assay which allows simultaneous amplification of the triplet repeat sequences at the FRAXA and FRAXE loci by polymerase chain reaction, and detection of the products on non-denaturing gels stained with ethidium bromide. Alleles of normal size are detected, leaving a small minority of samples to be tested by Southern blotting. A PCR based assay for detection of methylation at the CpG island upstream of the FMR-1 gene has also been devised.

DNA enzyme immunoassay of the PCR-amplified HLA-DQ alpha gene for estimating residual leukocytes in filtered blood

Blood is filtered for selective removal of leukocytes (WBC) to reduce the immunological and virological risks of transfusion. Exceedingly low numbers of residual WBC in leukodepleted blood cannot be enumerated by conventional hematologic methods. Therefore, we investigated the application of a DNA enzyme immunoassay (DEIA) for detecting a region of the HLA-DQ alpha gene following amplification by PCR. After hybridization with a specific probe coated onto the wells of a microtiter plate, the PCR-amplified DNA was detected by adding monoclonal antibodies to double-stranded DNA, enzyme tracer, and chromogen substrate for colorimetric measurement. The sensitivities of DEIA and radioisotopic liquid hybridization were similar in five sets of experiments performed with a known number of human WBC. The optical density and the number of spiked human WBC in the range of 1.0 to 0.05 cells per microliter showed good correlation in five calibration experiments performed with human WBC suspended in heterologous blood. Using a calibration curve for DEIA, we estimated the concentration of residual WBC in five individual units of erythrocytes passed through blood filters. The postfiltration WBC count was 1.6 WBC per microliter in one unit, while in four other units it was below the lower detection limit (< 0.05 WBC per microliter) of the DEIA. DEIA obviates the use of radioisotopes in PCR for detection of exceedingly low numbers of residual WBC in filtered blood.

Molecular characterisation of the ADP/ATP-transporter cDNA from the human malaria parasite Plasmodium falciparum

We have isolated a cDNA sequence encoding the ADP/ATP transporter in Plasmodium falciparum. The sequence analysis revealed an open reading frame encoding 301 amino acids and showed significant similarities to known eukaryotic translocases such as that of Chlorella (up to 67.2% identity) and the human transporter (61.2%). RNA blot analysis showed the presence of mRNA encoding for a 33.7-kDa ADP/ATP transporter. During the cell cycle of the parasite the expression levels of the transcripts fluctuate. The mitochondrial ADP/ATP transporter could play a role in energy metabolism of P. falciparum and makes this transporter an excellent target for chemotherapy.

Complete sequence of a mariner transposable element from the predatory mite Metaseiulus occidentalis isolated by an inverse PCR approach

Degenerate primers designed and synthesized based on two conserved regions of the mariner transposase open reading frame were used to amplify a 454 bp DNA fragment from M. occidentalis. Two inverse primers were then synthesized and used to amplify flanking genomic DNA fragments from M. occidentalis by a ligation-mediated inverse PCR. The complete mariner element (Moc1) was 1284 bp long, including the imperfect 28 bp inverted terminal repeat sequences, and shared 59% similarity to an active 1286 bp long D. mauritiana mariner element (Mos1). Insertions, deletions and substitutions were observed in the Moc1 sequence at several positions. No intact open reading frame was detected and the Moc1 element is considered inactive. Stringent Southern blot hybridizations revealed at least twelve copies of mariner sequences similar to Moc1 in the colonies tested.

Novel methods for cloning and engineering genes using the polymerase chain reaction

Use of the polymerase chain reaction (PCR) has become increasingly widespread in virtually all aspects of molecular biology. Recently, novel ligation-independent methods have been developed for the cloning of DNA fragments amplified using PCR. Ligation-independent cloning utilizing the enzyme uracil DNA glycosylase (termed UDG cloning) provides an efficient method for gene cloning and recombinant PCR. This technology is now being applied to site-directed mutagenesis, the generation of nested deletions, and the engineering of novel gene constructs. The ease and flexibility of this methodology, combined with PCR amplification, simplify gene cloning and engineering techniques.

The group A streptococcal virR49 gene controls expression of four structural vir regulon genes

Within a genomic locus termed the vir regulon, virR genes of opacity factor-nonproducing (OF-) group A streptococci (GAS) are known to control the expression of the genes encoding M protein (emm) and C5a peptidase (scpA) and of virR itself. Within the corresponding genomic locus, opacity factor-producing (OF+) GAS harbor additional emm-related genes encoding immunoglobulin G- and immunoglobulin A-binding proteins (fcrA and enn, respectively). The virR gene region of the OF+ GAS M-type 49 strain CS101 was amplified by PCR, and 2,650 bp were directly sequenced. An open reading frame of 1,599 bp exhibited 76% overall homology to published virR sequences. By utilizing mRNA analysis, the 5' ends of two specific transcripts were mapped 370 and 174 bp upstream of the start codon of this open reading frame. The deduced sequences of the corresponding promoters and their locations differed from those of previously reported virR promoters. Transcripts from wild-type fcrA49, emm49, enn49, and scpA49 genes located downstream of virR49 were characterized as being monocistronic. The transcripts were quantified and mapped for their 5' ends. Subsequently, the virR49 gene was inactivated by specific insertion of a nonreplicative pSF152 vector containing recombinant virR49 sequences. The RNA from the resulting vir-mut strain did not contain transcripts of virR49, fcrA49, emm49, or enn49 and contained reduced amounts of the scpA49 transcript when compared with wild-type RNA. The mRNA control from the streptokinase gene was demonstrated not to be affected. When strain vir-mut was rotated in human blood, it was found to be fully sensitive to phagocytosis by human leukocytes. Thus, the present study provides evidence that virR genes in OF+ GAS could be involved in the control of up to five vir regulon genes, and their unaffected regulatory activity is associated with features postulated as crucial for GAS virulence.

Current status of the molecular genetics of hepatitis C virus and its utilization in the diagnosis of infection

BACKGROUND

Since the discovery of hepatitis C virus (HCV) as a major cause of non-A non-B hepatitis, advances have been made in our understanding of the molecular biology of HCV and its relatedness to the flaviviruses and pestiviruses. The use of molecular techniques to construct an antibody assay has enabled the accumulation of information concerning the natural history and pathogenesis of HCV infection.

OBJECTIVES

The objective was to review the literature to March 1994 on the structure, function and genetics of HCV and to correlate these findings with approaches to diagnosis that have contributed to our understanding of HCV infections.

STUDY DESIGN

We reviewed the virological and medical literature from 1988 to March of 1994 with a focus on the stated objectives.

RESULTS

Although the structure of HCV has been well-defined, our knowledge of the function of all the genes of HCV is incomplete. Structural core and envelope proteins as well as enzymes have been described. The 5' end of the polypeptide is most conserved. Genotyping of isolates varies according to the part of the gene examined. Several genotypes exist and tend to predominate in global populations. Antibodies to the various proteins can be measured by EIA assays and positive specimens often require confirmatory testing. Uniquely sensitive nucleic acid detection systems for RNA amplified by PCR have enabled a better understanding of the natural history, epidemiology and responses to treatment.

CONCLUSIONS

Well-designed studies for the detection of nucleic acid, antibodies and antigens using a variety of viral gene products will provide even more information about HCV infections and help lead to treatment and prevention.

Low resolution DNA typing of the HLA-B5 cross-reactive group by nested PCR-SSP

We have established a DNA typing system for the HLA-B5 serologically cross-reactive group (CREG) by means of a two-step PCR amplification with nested sequence-specific primers (nPCR-SSP). The present study provides a low resolution definition of the HLA-B5 CREG, i.e. identifying polymorphism equivalent to serology. Two different primer combinations allow group-specific amplification of all HLA-B5 CREG alleles and other related HLA class I alleles from genomic DNA. The amplified DNA is subjected to a second amplification step using eleven nested primer pairs. This assay permits the detection of the HLA-B5 CREG specificities B35, B51, B52, B53, and B7801 in all homozygous and heterozygous combinations. Sensitivity and specificity as judged by a blind quality control study investigating a reference panel (n = 50) is 100%. Extension of this approach should allow rapid DNA typing of all serologically defined HLA-B specificities by nPCR-SSP.

Molecular biology and its application in paediatric endocrinology

Recent advances in molecular biology and genetics have paved the way to a greater understanding of molecular mechanisms of human disease and, in particular, endocrine disorders. For example, new information concerning the structure and function of different receptors and intracellular signalling has allowed precise definition of the molecular defects involved in various disorders such as McCune-Albright syndrome, growth hormone insensitivity syndromes. Although these conditions might be rare, their susceptibility to analysis was due largely to availability and progress of the molecular biological methods. The aim of this review article is to introduce the language of molecular biology by means of a selected group of endocrine disorders.

Molecular detection of hepatitis C virus: impact of detection methodology on clinical and laboratory correlations

The clinical manifestations of hepatitis C virus (HCV) infection are generally indistinguishable from other causes of viral hepatitis. HCV infections are usually anicteric, asymptomatic, and rarely cause acute fulminant liver failure. Serological testing for HCV in conjunction with epidemiological studies have verified that HCV was the major cause of parenterally transmitted non-A, non-B hepatitis (NANBH). With the widespread introduction of serological screening of blood products for HCV antibody, the risk of transfusion-associated HCV infection has been dramatically reduced (to < 3 cases per 10,000 units transfused). Despite the virtual elimination of transfusion-associated infections, the diagnosis of HCV remains important because > 50% of infections are sporadic in origin, 50 to 70% of infected individuals develop chronic hepatitis, and these individuals are at risk of developing cirrhosis (> 20%) as well as hepatocellular carcinoma. Although currently available anti-HCV immunoassays function well as blood-donor screening assays, they are poor at detecting acute infection because of the prolonged lag time between infection and detection of seroconversion (approximately 10 to 26 weeks for second-generation immunoassays). In contrast, polymerase chain reaction (PCR)-based detection of HCV RNA in serum can detect infection in as little as 1 to 2 weeks after exposure. This review focuses on the impact of modern serologic and nucleic acid-based HCV detection methodology on the clinical understanding of HCV infection, its associated illnesses, and its transmissability. Quantitative and reproducible nucleic acid-based detection assays will be required to provide additional insights into the clinical spectrum of HCV infections as well as to assess the efficacy of antiviral agents.

Applications of DNA amplification techniques in veterinary diagnostics

An overview of the principles of the polymerase chain reaction, ligase chain reaction, self-sustained sequence replication and Q beta replicase is given. The application of these methods for the diagnosis of veterinary infectious and hereditary diseases as well as for other diagnostic purposes is discussed and comprehensive tables of reported assays are provided. Specific areas where these DNA-based amplification methods provide substantial advantages over traditional approaches are also highlighted. With regard to PCR-based assays for the detection of viral pathogens, this article is an update of a previous review by Belák and Ballagi-Pordány (1993).

Immunohistochemical detection of p53 in cervical epithelial lesions with or without infection of human papillomavirus types 16 and 18

Using formalin-fixed and paraffin-embedded cervical tissues, we examined infection with human papillomavirus (HPV) types 16 and 18 by Southern blot analysis following polymerase chain reaction (PCR), and the accumulation of p53 protein by immunohistochemistry in 30 cases of normal or metaplastic cervix, 17 cases of cervical intraepithelial neoplasia grade I (CIN I), 20 cases of CIN II, 37 cases of CIN III and 23 cases of invasive squamous cell carcinoma (ISCC). In addition, we examined the ratio of HPV-infected cells by in situ hybridization (ISH) and the alteration of p53 gene using PCR followed by single-strand conformation polymorphism (PCR-SSCP) in 2 cases of CIN III and 12 cases of ISCC, in which overexpression of p53 was immunohistochemically detected. HPV DNA was detected in 5 cases (16.7%) of normal or metaplastic cervix, 5 cases (29.4%) of CIN I, 9 cases (45.0%) of CIN II, 26 cases (70.3%) of CIN III and 15 cases (65.2%) of ISCC. Positivity for HPV in the groups of CIN III and ISCC was significantly higher than in the normal or metaplastic cervix (P < 0.05). The accumulation of p53 was not detected in the normal or metaplastic cervix, CIN I and CIN II. High-level p53 accumulation was identified in basal and suprabasal atypical cells in 27.0% (10/37) of CIN III and in carcinoma cells in 43.5% (10/23) of ISCC cases, and low-level accumulation was identified in atypical cells of 35.1% (13/37) of CIN III and in carcinoma cells in 30.4% (7/23) of ISCC cases. The accumulation of p53 was found to coexist with infection by HPV in 17 (46.0%) of 37 CIN III cases and 12 (52.2%) of 23 ISCC cases, and high-level p53 accumulation was more frequently detected in HPV-positive ISCC cases. Either HPV infection or accumulation of p53 was found in 16.7% (5/30) of the cases of normal or metaplastic cervix, 29.4% (5/17) of CIN I, 45.0% (9/20) of CIN II, 86.5% (32/37) of CIN III and 87.0% (20/23) of ISCC cases. These results suggest that the inactivation of p53 function by HPV infection or alteration of p53 protein itself precedes the development of tumours with a fully malignant and invasive phenotype and plays an important role in tumorigenesis in the uterine cervix. ISH study provided no correlation between the degree of immunohistochemical positivity for p53 and the ratio of HPV-positive cells in the same lesions.(ABSTRACT TRUNCATED AT 400 WORDS)

Intrahepatic expression of hepatitis C virus antigens in chronic liver disease

Localization of hepatitis C virus (HCV) antigens was studied in fresh frozen and formalin-fixed, paraffin-embedded liver tissue by immunoperoxidase using monoclonal antibodies to nucleocapsid protein and polyclonal human immunoglobulin G purified from plasma containing antibodies to structural and non-structural antigens of hepatitis C virus. The results observed using monoclonal antibody to HCV core were similar to those of polyclonal IgG against HCV antigens in the majority of cases and both correlated well with HCV status as defined by 'nested' polymerase chain reaction. HCV antigens were detected in both hepatocytes and mononuclear cells. Using polyclonal human IgG, a small proportion of biliary epithelial cells were also positive in 6/29 patients. In most of the specimens examined, relatively few cells (1-5 per cent) were found to be positive for HCV antigens. The cryostat sections, using polyclonal IgG against HCV antigens, exhibited greater immunohistochemical staining, suggesting that the fixation and processing of the tissue may be a major factor in the conservation and the outcome of HCV antigen(s) findings. However, the results using monoclonal antibodies may reflect the specificity of antigen expression.

Polymerase chain reaction (PCR) for detection of pathogenic microorganisms in bacteriological monitoring of dairy products

The presence of pathogenic bacteria poses a serious problem in sustaining the safety of dairy products. Microbiological routine controls of these products make use of selective culture techniques. To detect pathogenic species, isolated colonies are characterized by specific metabolic activities and by serotyping. We present an alternative biochemical approach that does not require culture of bacteria. The total bacterial populations of food samples were isolated by centrifugation and analysed by PCRs specific for pathogenic species. A total of 90 raw milk samples and dairy products made from raw milk were screened by this method for the presence of Listeria monocytogenes, Escherichia coli, enterotoxigenic E. coli, Campylobacter jejuni and C. coli. Detection rates were 12/90 (13%) for L. monocytogenes, 41/90 (46%) for E. coli, 18/90 (20%) for enterotoxigenic E. coli producing heat-labile toxin type I or heat-stable toxin type I, and 6/90 (7%) for C. jejuni or C. coli. Except for the use of different amplification primers, this approach is identical for any bacterial species to be detected. Direct PCR analysis of food samples offers rapid screening for the presence of specific bacteria and enables selection of critical samples prior to culture.

Use of the polymerase chain reaction for the detection of Chlamydia trachomatis from endocervical and urine specimens in an asymptomatic low-prevalence population of women

The Amplicor Chlamydia trachomatis test is a polymerase chain reaction (PCR)-based methodology used for the detection of a cryptic plasmid found in C. trachomatis. It was evaluated in comparison with cell culture and the Microtrak II Chlamydia enzyme immunoassay (EIA) for the detection of C. trachomatis in urogenital specimens from women. Endocervical swabs were collected from 993 women attending the women's unit at the Mount Sinai Hospital in Toronto. In addition, concomitant first void urine specimens were collected from 394 of these women for PCR testing only. As compared with culture of the endocervical specimens, PCR and EIA had a sensitivity, specificity, positive predictive value and negative predictive value of 84.6%, 99.2%, 57.9%, and 99.8% and 61.5%, 99.7%, 72.7%, and 99.5%, respectively. As compared with the secondary gold standard of a positive culture and/or a positive PCR using a primer to the major outer membrane protein the sensitivity, specificity, positive, and negative predictive values for culture were 72.2%, 100%, 100%, and 99.5%, respectively. For the Amplicor PCR and EIA the results were 88.9%, 99.7%, 84.2%, and 99.9% and 61.1%, 99.9%, 91.7%, and 99.6%, respectively. When the urine PCR was compared with the same standard, the test had a sensitivity of 91.7% and a specificity of 99.5%. Based on this study the Amplicor C. trachomatis test was found to be sensitive and specific for the detection of C. trachomatis in both endocervical and urine specimens.

Hepatic and extrahepatic hepatitis C virus replication in relation to response to interferon therapy

Response to a 1-yr course of interferon-alpha 2b was assessed in 18 patients with chronic hepatitis C virus infection in relation to clinical, biochemical and histological parameters and to the presence or absence of hepatitis C virus RNA and the presumed replicative form of the virus (negative-strand hepatitis C virus RNA) in serum, liver and peripheral blood mononuclear cells. The findings were compared with those in seven untreated patients studied over the same period. At the start of the study, positive-strand hepatitis C virus RNA was found in sera of all 25 patients, in livers of 24 and in peripheral-blood mononuclear cells of 19 of 22 tested; negative strand was found in livers of 11 and in peripheral-blood mononuclear cells of 15 of 22. Negative-strand hepatitis C virus RNA was not found in the serum of any patient at any stage. All of the five treated patients considered to show complete response during the study period cleared hepatic hepatitis C virus RNA, and four also became seronegative, but three had evidence suggestive of viral replication in their peripheral-blood mononuclear cells; two of these last patients subsequently relapsed. Loss of hepatic hepatitis C virus RNA was the only significant difference between these five and the seven partial and six nonresponders, but it is uncertain whether the observed changes were due specifically to interferon-induced modulation of virus expression because similar (apparently spontaneous) changes were seen in four of the untreated patients.(ABSTRACT TRUNCATED AT 250 WORDS)

Enhancing PCR amplification and sequencing using DNA-binding proteins

The polymerase chain reaction (PCR) is a powerful core molecular biology technique, which when coupled to chain termination sequencing allows gene and DNA sequence information to be derived rapidly. A number of modifications to the basic PCR format have been developed in an attempt to increase amplification efficiency and the specificity of the reaction. We have applied the use of DNA-binding protein, gene 32 protein from bacteriophage T4 (T4gp32) to increase amplification efficiency with a number of diverse templates. In addition, we have found that using single-stranded DNA-binding protein (SSB) or recA protein in DNA sequencing reactions dramatically increases the resolution of sequencing runs. The use of DNA-binding proteins in amplification and sequencing may prove to be generally applicable in improving the yield and quality of a number of templates from various sources.

A touchdown PCR for the differentiation of equine herpesvirus type 1 (EHV-1) field strains from the modified live vaccine strain RacH

More than 50 reference strains and field isolates of equine herpesvirus type 1 (EHV-1) were examined by a touchdown PCR. Primers for specific amplification of EHV-1 DNA were chosen from the terminal and internal repeat regions of the EHV-1 genome where the high-passaged live vaccine strain RacH displays symmetric 850 bp deletions. The positive strand and one negative strand primer were designed to encompass the deletions present in RacH, and the second negative strand primer was designed to hybridize within these deletions. Discrimination between field isolates and the vaccine strain was achieved by the generation of amplification products of different size: In all EHV-1 reference strains and field isolates, a 495 bp DNA fragment was amplified specifically, whereas a 310 bp fragment was amplified when DNA of the vaccine strain RacH was used as a template. PCR amplification was only obtained in the presence of 8-10% dimethylsulfoxide and when the primer annealing temperatures were decreased stepwise from 72 degrees C to 60 degrees C. Under these conditions as little as 100 fg template DNA, corresponding to about 100 genome equivalents, could be detected. The PCR assay allows fast and sensitive discrimination of the modified live vaccine strain RacH from field strains of EHV-1 since it is applicable to viral DNA extracted from organ samples and paraffin-embedded tissues. It may thus be helpful for examining the potential involvement of the RacH live vaccine strain in abortions of vaccinated mares.

Expression and functional role of c-kit ligand (SCF) in human multiple myeloma cells

In this study we investigated the proliferation of three well-documented MM lines and 10 bone marrow samples from myeloma patients in response to rh-SCF alone and combined with Interleukin-6 (IL-6), IL-3 and IL-3/GM-CSF fusion protein PIXY 321. Neoplastic plasma cells were highly purified (> 90%) by immunomagnetic depletion of T, myeloid, monocytoid and NK cells. The number of S-phase cells was evaluated after 3 and 7 d of liquid culture by the bromodeoxyuridine (BRDU) incorporation assay. The proliferation of RPMI 8226 and U266 cell lines was also assessed by a clonogenic assay. All the experiments were performed in serum-free conditions. RPMI 8226 cell line was not stimulated by SCF which also did not augment the proliferative activity of IL-6, IL-3 and PIXY-321. Conversely, SCF addition resulted in 2.4-fold increase of the number of U266 colonies and in a higher number of U266 and MT3 cells in S-phase (24.5 +/- 2% SEM v 14.5 +/- 1% SEM and 32 +/- 3% SEM v 21 +/- 4% SEM, respectively; P < 0.05). The c-kit ligand also enhanced the proliferation of MT3 and U266 cells mediated by the other cytokines. Anti-SCF polyclonal antibodies completely abrogated the proliferative response of MT3 cells to exogenous SCF and markedly reduced the spontaneous growth of the same cell line. Reverse transcriptase-polymerase chain reaction amplification (RT-PCR) did detect SCF mRNA in MT3 and RPMI 8226 cells. Moreover, secreted SCF was found, in a biologically active form, in the supernatant of the two cell lines by the MO7e proliferation assay. When tested on fresh myeloma samples, SCF increased the number of S-phase plasma cells (4.7 +/- 1.6% v 3.4 +/- 1.3% in control cultures: P = 0.02). Significant proliferation was also induced by IL-6 (7 +/- 2.3% of BRDU+ cells; P = 0.006), IL-3 (5.3 +/- 1.3%; P = 0.01) and PIXY-321 (5.4 +/- 1.6%; P = 0.02). The addition of SCF significantly enhanced the proliferation of myeloma cells responsive to IL-6. In summary, our results indicate that SCF is expressed in MM cells and stimulates the proliferation of neoplastic plasma cells.

Molecular characterization of the cfb gene encoding group B streptococcal CAMP-factor

An internal fragment of the cfb gene from group B streptococcal (GBS) strain R268 was amplified by polymerase chain reaction (PCR) using degenerate primers with sequences derived from the CAMP-factor amino acid (aa) sequence of GBS strain NCTC8181 [Rühlmann et al. (1988) FEBS Lett 235:262-266]. After cloning and sequencing this fragment, the remainder of cfb and the adjacent 5' and 3' sequences were amplified by inverted PCR of genomic DNA and directly sequenced from the PCR product. Within the 1560 bp sequenced, a complete cfb gene deviating in two deduced aa residues from the published sequence was identified. In addition, the cfbR268 sequence contained a 29-aa leader peptide. Using primers directed to the 5' and 3' ends of cfb for PCR, a cfb gene of uniform size could be detected in 19 clinical GBS isolates including three phenotypically CAMP-negative strains. Utilizing Northern blot analysis and primer extension assays, the cfbR268 promoter was located and the length of the cfb transcript was assessed at about 1100 bp. In a parallel experiment, no cfb transcript could be detected from the CAMP-negative GBS strain 74-360. The complete cfbR268 gene and different portions of its 5' and 3' ends were cloned into the plasmid pJLA602 and expressed in E. coli DH5 alpha. The recombinant peptides could be detected by Western immunoblots with polyclonal antiserum. Only the full-sized recombinant CAMP-factor was found to exert co-hemolytic activity in a sheep-blood agar assay. This co-hemolytic activity could be inhibited by anti-CAMP antiserum.

Lack of association between obsessive-compulsive disorder and the dopamine D3 receptor gene: some preliminary considerations

Controversial results possibly suggesting an association between Tourette's Syndrome (TS) and excess of homozygosity at a Msc I polymorphism in the Dopamine D3 receptor (DRD3) gene have recently been reported. Since a relationship between Obsessive-Compulsive Disorder (OCD) and Tourette's Syndrome (TS) has been suggested, in this study we assessed the frequency of this 2-allele polymorphism in a sample of 97 OCD patients and in 97 control subjects. No statistically significant differences in allele or genotype frequencies were found. Thus this mutation in the coding sequence of the DRD3 gene is unlikely to confer susceptibility to OCD.

Molecular methods: applications for clinical infectious diseases

The application of molecular biology to microbiology has led to a surge of new information about most infectious microorganisms, the pathogenesis of the infections they cause, and the specific microbial antigens involved in the immune response to these infections. The simultaneous application of the same techniques to diagnosis and epidemiology has also shown great promise, but these developments have not yet had a major effect on the routine practice of medicine. For some purposes, direct probe tests perform as well as other available methods. However, for most infections, these methods have not been proven sufficiently sensitive. The latest generation of highly sensitive diagnostics based on the polymerase chain reaction will overcome this technical obstacle and may revolutionize the management of many infections. Difficulties inherent in performing these tests will require special procedures and training in clinical laboratories to ensure that they are performed reliably. Nucleic acid-based methods for epidemiologic typing of microorganisms and for identification of noncultivatable pathogens are particularly useful for analysis of poorly cultivatable, dangerous, or otherwise untypeable microorganisms.

Binding of Legionella pneumophila to macrophages increases cellular cytokine mRNA

Infection of macrophages with Legionella pneumophila induces formation of interleukin 1 beta (IL-1 beta), but the molecular basis of this is not understood. Binding of bacteria to macrophage surfaces is the first step in an infection process. Therefore, we examined whether this step was sufficient to increase the cellular level of mRNAs for IL-1 beta and other cytokines. To assess the effect of binding of L. pneumophila on the steady-state levels of cytokine mRNAs, cultures of thioglycolate-elicited macrophages from L. pneumophila-susceptible A/J mice were treated with cytochalasin D and infected with L. pneumophila and the total RNA was extracted for analysis by reverse transcription-PCR with primers for IL-1 alpha, IL-1 beta, IL-6, tumor necrosis factor alpha, granulocyte macrophage colony-stimulating factor, and beta interferon (IFN-beta). L. pneumophila treatment increased the cellular steady-state mRNA levels of all cytokines except IFN-beta. To determine the specificity of this effect, macrophage cultures were treated with cytochalasin D and either bacterial lipopolysaccharide, bovine serum albumin-sensitized latex, Salmonella typhimurium, or Escherichia coli. Lipopolysaccharide treatment increased all mRNAs, bovine serum albumin-sensitized latex had no significant effect, and treatment with S. typhimurium or E. coli increased all mRNAs except that of IFN-beta. These results suggested that the binding of gram-negative bacteria to the macrophage surface was sufficient to induce a unique pattern of cytokine mRNAs. Additional studies that examined the characteristics of the bacterial ligands involved indicated involvement of both heat-labile and heat-stable surface ligands.

Sequence variation of the hydroxymethyldihydropterin pyrophosphokinase: dihydropteroate synthase gene in lines of the human malaria parasite, Plasmodium falciparum, with differing resistance to sulfadoxine

Dihydropteroate synthase (H2Pte synthase) is the target of the sulfur-based antimalarial drugs, which are frequently used in synergistic combination with inhibitors of dihydrofolate reductase (H2folate reductase) to combat chloroquine-resistant malaria. We have isolated the H2Pte synthase coding sequence of the most pathogenic human parasite Plasmodium falciparum. It forms part of a longer coding sequence, located on chromosome 8, that also specifies 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (CH2OH-H2pterinPP kinase) at its 5' proximal end. This domain is unusually large, with two long insertions relative to other CH2OH-H2pterinPP kinase molecules. To investigate a possible genetic basis for clinical resistance to sulfa drugs, we sequenced the complete H2Pte synthase domains from eleven isolates of P. falciparum with diverse geographical origins and levels of sulfadoxine resistance. Overall, point mutations in five positions were observed, affecting four codons. Parasite lines exhibiting high-level resistance were found to carry either a double mutation, altering both Ser436 and Ala613, or a single mutation affecting Ala581. The mutations at positions 436 and 581 have the same location relative to each of two degenerate repeated amino acid motifs that are conserved across all other known H2Pte synthase molecules. The amino acid alteration at residue 613 is identically positioned relative to a different conserved motif. The fourth amino acid residue (437) affected by mutation, though adjacent to the apparently crucial residue 436, shows no obvious correlation with resistance. Although these mutations have no exact counterparts in any other organism, that at position 581 falls within a region of three amino acids where H2Pte synthase is modified in various ways in a number of sulfonamide-resistant pathogenic bacteria. Copy-number analysis indicated that there was no amplification of the H2Pte synthase domain in resistant parasite lines of P. falciparum, compared to sensitive lines.

Analysis of the population structure of three phenotypically different PSTVd isolates

Phenotypically dissimilar greenhouse isolates from a Polish collection of potato spindle tuber viroid (PSTVd) were analysed. Partially purified PSTVd genomic RNAs from severe, intermediate and mild isolates was reverse transcribed and the resulting cDNAs enzymatically amplified. Abutting-primer PCR (Ab-P PCR) technology was used to obtain, in a single step, infectious full-length PSTVd cDNA monomers and these were sequenced. The mild isolate was found to be composed of a unique molecular variant (M), closely related to previously described PSTVd mild isolates. In the intermediate isolate, three variants, i2, i3 and i4, were detected. The severe isolate was found to be a mixture containing at least four molecular variants: s23, s27, i4 and i2. Infection of test plants with plasmids carrying monomeric cDNAs corresponding to each of the cloned variants confirmed that they are infectious. In addition, variant M produced mild symptoms, variants i2, i3, i4 intermediate symptoms and variants s23 and s27 severe symptoms. Therefore, the disease symptoms produced by a mixture are determined by the severe variants, masking the presence of milder ones. All the variants detected (except i2 which is identical to previously described PSTVd-DI) represent novel PSTVd sequences with point mutations located in the V and/or P domains. In particular, variants s23 and i4 represent shorter (358 nucleotides) versions of the PSTVd genome.

Detection of Chlamydia pneumoniae in clinical specimens by polymerase chain reaction using nested primers

A nested primers strategy was used to develop a two-step PCR test for the direct species-specific detection of the 16s rRNA gene of Chlamydia pneumoniae. This test was applied to 58 nasopharyngeal or oropharyngeal swab specimens collected from patients in studies of community-acquired pneumonia and in a local outbreak of respiratory disease. Twelve patients (21%) showed evidence of Chlamydia pneumoniae infection in serological tests (7/56; 13%), culture (8/58; 14%) or PCR (10/58; 17%). Nested PCR but not single-step PCR was found to be as sensitive as culture or serology for detection of infection with this organism. In summary, nested PCR can be useful in direct testing of clinical specimens for Chlamydia pneumoniae, making additional DNA purification steps unnecessary.

A method for typing polymorphism at the HLA-A locus using PCR amplification and immobilized oligonucleotide probes

We have developed a simple and rapid method for DNA typing of the HLA-A locus using PCR amplification and hybridization of the PCR product, labeled with biotinylated primers, to an array of immobilized oligonucleotide probes in a single hybridization reaction (reverse dot or line blot). A single primer set (RAP1007 and DB337) is used to specifically amplify a 990-bp fragment containing the HLA-A locus exons 1, 2, and 3 from genomic DNA. This primer set is locus-specific and amplifies all HLA-A alleles. A set of 51 sequence-specific oligonucleotide (SSO) probes, 25 for exon 2 and 26 for exon 3, was immobilized to a nylon membrane by UV-crosslinking oligonucleotide probes containing a poly-thymidine "tail" added with terminal transferase. In the line blot format, all 50 SSO probes plus a control probe are immobilized on a single nylon membrane strip. The probe array was used for typing in a hybridization reaction with DNA amplified from a variety of samples. These probes can identify 37 homozygous HLA-A alleles. In the analysis of heterozygous samples, 604 heterozygous types out of 633 (95.4%) possible heterozygous probe patterns can be detected as a unique probe reactivity pattern. A simple computer program has been developed to assign the alleles and genotypes based on the probe hybridization pattern.

The genome of the THE I human transposable repetitive elements is composed of a basic motif homologous to an ancestral immunoglobulin gene sequence

Amplification of rearranged human immunoglobulin heavy-chain genes using the polymerase chain reaction resulted unexpectedly in the amplification of human transposable repetitive element genomes. These were identified as members of the THE I (transposon-like human element I) transposable element family. Analysis of the THE I sequences revealed the presence of several copies of the ancestral building block described > 10 years ago by Ohno and coworkers as the primordial immunoglobulin sequence. The frequency and degree of homology of the repeats of the basic unit were similar for the two genes, as well as for two murine intracisternal A particles. These findings suggest that both the transposable genetic elements and the immunoglobulin genes originated from a common ancestral building block.

Identification of the alpha 1c-adrenoceptor in rabbit arteries and the human saphenous vein using the polymerase chain reaction

The expression of the alpha 1C-adrenoceptor subtype in human and rabbit blood vessels has been analyzed using the reverse transcriptase/polymerase chain reaction technique (RT/PCR). The 20 bp primers employed were designed from the bovine alpha 1C-adrenoceptor and flank a least conserved region--the putative third cytoplasmic loop. RT/PCR products generated from rabbit and human brain mRNA both had 93% homology to the bovine alpha 1C-adrenoceptor and were used as species and subtype specific probes in Southern blot analysis of vascular RT/PCR products. Poly A+ RNA was purified from the human saphenous vein and rabbit aorta, renal, pulmonary and central ear arteries and amplified by RT/PCR. Size analysis by agarose gel electrophoresis, together with Southern hybridization of the resulting cDNA products confirm the expression of the alpha 1C-adrenoceptor in these vessels.

Search for persistent enterovirus infection of muscle in inflammatory myopathies

To investigate the hypothesis that the inflammatory muscle diseases (IMD) polymyositis (PM) and dermatomyositis (DM) may be due to a chronic, persistent enterovirus (EV) infection we sought to determine the prevalence of these viruses in muscle tissue using both nested polymerase chain reaction (PCR) and dot-blot hybridization assays. Thirty-six frozen muscle biopsies from 32 adult cases of IMD and 42 biopsies from 36 control subjects with other neuromuscular disorders were studied. Primers for PCR were chosen to conserved regions of the 5'-untranslated region of the EV genome. Constitutive Ableson tyrosine kinase (ABL) mRNA was detected by PCR to confirm the integrity of muscle RNA extracts. The sensitivity of the EV PCR was determined to be 40-400 copies (12.5-125 ag) of synthetic EV RNA transcript against a background of 1 microgram of cellular RNA. The specificity was assessed using a range of enteroviral and unrelated viral isolates extracted from cell cultures. Of the 78 samples tested, ABL mRNA was successfully detected in all but four samples. The time the biopsies spent in ultracold storage (1-73 months) did not appear to influence the integrity of extracted RNA. When assayed for EV RNA by nested PCR, none of 29 IMD cases (i.e., 28 PM and 1 DM) nor sequential biopsies from 3 PM patients were found to be positive. All 42 control biopsies were also negative for EV RNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Detection of adenoviruses and enteroviruses in polluted waters by nested PCR amplification

A procedure has been developed for the rapid detection of enteroviruses and adenoviruses in environmental samples. Several systems for virus concentration and extraction of nucleic acid were tested by adding adenovirus type 2 and poliovirus type 1 to different sewage samples. The most promising method for virus recovery involved the concentration of viruses by centrifugation and elution of the virus pellets by treatment with 0.25 N glycine buffer, pH 9.5. Nucleic acid extraction by adsorption of RNA and DNA to silica particles was the most efficient. One aliquot of the extracted nucleic acids was used for a nested two-step PCR, with specific primers for all adenoviruses; and another aliquot was used to synthesize cDNA for a nested two-step PCR with specific primers for further detection of seeded polioviruses or all enteroviruses in the river water and sewage samples. The specificity and sensitivity were evaluated, and 24 different enterovirus strains and the 47 human adenovirus serotypes were recognized by the primers used. The sensitivity was estimated to be between 1 and 10 virus particles for each of the species tested. Twenty-five samples of sewage and polluted river water were analyzed and showed a much higher number of positive isolates by nested PCR than by tissue culture analysis. The PCR-based detection of enteroviruses and adenoviruses shows good results as an indicator of possible viral contamination in environmental wastewater.

Changes in promoter utilization in human and mouse c-myc genes upon transformation induction in temperature-sensitive cell lines

We have previously reported accelerated transcription and rapid accumulation of c-myc mRNAs upon induction of transformation in a temperature-sensitive mouse cell line (Gallant et al., 1989, Oncogene Res., 4:39-46). Here we have used both mouse and human cell lines transformed with a temperature-sensitive mutant of the Simian virus 40 (SV40) virus to investigate whether a shift in promoter utilization within the c-myc gene locus is part of a general mechanism that deregulates c-myc expression during transformation induction. We devised a simple and sensitive method using reverse transcription followed by radioactive polymerase chain reaction (RT-PCR) to measure the relative change in c-myc mRNAs arising from each of the four known promoters. We show that a three to fivefold increase in c-myc transcripts from the P1 and P3 promoters occurs in both human and mouse cell lines within 30 min of the shift to the permissive temperature. The major P2-initiated transcripts are not significantly effected. However, exon 3-containing RNAs increase more gradually up to 24 h postinduction and P1 and P3 transcripts, while remaining elevated, still contribute relatively little to the total c-myc RNA population. These and other results, demonstrating a transient activation of P1 and P3 promoters, suggest an indirect role of the minor transcripts in the deregulated expression of the c-myc gene in transformed cells.

Expression patterns of messenger ribonucleic acids encoding prohormone convertases (PC2 and PC3) in human pituitary adenomas

OBJECTIVE

Prohormone convertases (PC2 and PC3) have been reported to play an important role for prohormone processing in rodent pituitaries. However, expression of mRNAs encoding these enzymes has not been characterized in human pituitaries. In addition, altered or insufficient prohormone processing has been reported in some human pituitary adenomas. Thus, the expression patterns of these mRNAs in non-tumorous and tumorous human pituitaries should be examined.

DESIGN

Total RNAs were extracted from non-tumorous or tumorous human pituitaries to analyse PC2 and PC3 mRNA expression.

SAMPLES

Five ACTH producing adenomas, 11 GH producing adenomas, one PRL producing adenoma and five non-functioning adenomas were obtained at surgery. Two non-tumorous pituitaries were also included in this study.

MEASUREMENTS

The contents were quantitatively measured by Northern blot analysis using rat PC3 cDNA or human PC2 cDNA as a probe. The method was also developed for the detection of PC2 mRNA by Southern blot analysis of reverse transcriptase-polymerase chain reaction (RT-PCR) products.

RESULTS

PC2 and PC3 mRNAs in non-tumorous samples were detected by Northern blot analysis whereas their contents in tumorous samples varied from high levels to undetectable. Marked variation of PC3 mRNA levels was observed among GH producing adenomas. ACTH producing adenomas were observed to express PC3 mRNA. Northern blot analysis also revealed that PC2 mRNA levels in ACTH producing adenomas were low except for one sample. PC2 mRNA expression in GH producing adenomas was confirmed by Southern blot analysis of RT-PCR products. This procedure also confirmed the various levels of PC2 mRNA expression among ACTH producing adenomas.

CONCLUSION

The expression of PC2 and PC3 mRNA in human pituitaries has been confirmed. However, their expression has been observed to vary quantitatively and not to be restricted to certain types of pituitary cells.

The polymerase chain reaction and hepatitis C virus diagnosis

In the absence of tissue culture, electron microscopy or assays for viral antigen, the direct detection of hepatitis C virus (HCV) is by necessity dependent upon nucleic acid hybridisation methods. Of the available methods, amplification of HCV cDNA by polymerase chain reaction (PCR) commends itself by virtue of its extreme sensitivity and its consequent ability to detect the very low levels of HCV-RNA that are present in many clinical samples. In this review the development and evolution of PCR techniques for HCV detection are described and a number of clinical applications are considered in detail. The applications include diagnosis of acute infection during the seronegative window period prior to the appearance of HCV antibodies, and diagnosis of HCV infection in the immunosuppressed. PCR also enables identification of the chronic viraemic carrier state and it permits accurate monitoring of the antiviral effects of drugs such as interferon. Confirmation of the specificity of HCV antibody assays and detection of HCV contamination of blood donations and blood products are other important areas in which PCR techniques have proved invaluable. In addition, PCR-based techniques underlie an increasing number of molecular epidemiological and genotyping studies and they are providing insights into the details of HCV cellular tropism and replication. A number of logistic problems and operational difficulties are also discussed. Despite these limitations it is concluded that PCR will continue to make significant contributions to both clinical practice and to our understanding of the basic biology of HCV infection.

Molecular analysis of rearranged VH genes during B cell chronic lymphocytic leukemia: intraclonal stability is frequent but not constant

Several genetic mechanisms have been shown to diversify the expressed antibody repertoire of committed B lymphocytes. These include V gene replacement, ongoing gene rearrangement and somatic hypermutation. These mechanisms may be operational at discrete points in the B cell differentiation pathway and generate idiotype diversity in various malignant B cell tumors. In particular, V region mutations have been established as a major mechanism of tumor escape from anti-idiotype immunotherapy in some lymphoma. On the other hand, previous studies on a few selected cases have shown that this mutation process does not affect the B cell clone during chronic lymphocytic leukemia. However, to what extent this intraclonal stability is a general phenomenon during B cell CLL is not clear. Therefore, we randomly selected 6 patients suffering from classical B cell CLL (sIgM (+), CD5 (+), CD19 (+)) at different stages of the disease and analysed the intraclonal variability of the expressed variable region of the heavy chain (VH). After PCR amplification of the cDNA corresponding to the rearranged VDJ regions, the products were cloned and sequenced. In five cases, multiple clone analysis did not show any intraclonal variability whatever the stage of the disease. Furthermore, in a single case, this intraclonal stability was confirmed during a three year period of time when the disease progressed. The sixth case behaved differently since we found multiple nucleotide substitutions, apparently accumulating as the malignant clone expanded. Besides the theoretical difficulties that these changes can induce during immunotherapy, two findings merit further discussion: 1) the distribution of the ongoing mutations affecting the VH region was not suggestive of an antigen driven selection, 2) this intraclonal variability was specific for the VH region, since the VL region showed no intraclonal variation.

A group A streptococcal Enn protein potentially resulting from intergenomic recombination exhibits atypical immunoglobulin-binding characteristics

The gene encoding the Enn protein (enn) of the M untypeable group A streptococcal (GAS) strain 64/14 was amplified by polymerase chain reaction, cloned into the expression vector pJLA602 and expressed in Escherichia coli DH5 alpha. Unlike other GAS-Enn proteins, which exhibit IgA-binding activity, the recombinant Enn enn64/14 protein reacted preferentially with human IgG3. The 1050 bp open reading frame comprising the enn64/14 gene was completely sequenced. The region of the gene encoding the signal peptide and the C-terminus exhibited > 95% homology to corresponding sections of other enn genes. The region of enn64/14 encoding the N-terminus of the mature Enn protein was found to be highly homologous to the corresponding section of the gene encoding the M-like protein of GAS serotype M9 (emmL9). The recombinant protein encoded by emmL9 was found to react with all four human IgG subclasses. About 30% of the 1152 bp open reading frame of emmL9 encoding the N-terminus was found to display > 90% homology to the corresponding section of enn64/14 but was < 50% homologous in the remainder of the gene sequence. The functional analysis of the subcloned N-terminal section of emmL9 demonstrated a polypeptide exhibiting selective binding to human IgG3. These findings suggested that enn64/14 was a hybrid gene formed by recombination of an enn gene and an emmL9 gene. The putative recombinational event could have involved a set of flanking 7 bp direct repeats. Since enn64/14 and emmL9 are genes from different phylogenetic lineages of GAS, this report provides evidence that intergenomic recombinations between different types of GAS genes can occur and could lead to hybrid proteins with unique Ig-binding characteristics.

Rapid typing of group A streptococci by the use of DNA amplification and non-radioactive allele-specific oligonucleotide probes

Because of the allelic variations within the M protein gene (emm gene) of group A streptococci, reliable typing of this important human pathogen can be accomplished by the use of emm gene-specific oligonucleotide probes. Two technical modifications (a reverse dot blot and a reverse line blot hybridization assay) of a novel approach for the type-specific identification of emm genes have been developed. Both procedures involved amplification of an emm gene by polymerase chain reaction. The non-radioactively labeled amplicon was subsequently hybridized to a membrane carrying an array of immobilized emm gene-specific oligonucleotide probes, thus allowing the simultaneous analysis of the gene polymorphism in a single hybridization reaction. The feasibility of these rapid and easy to perform methods was shown for the unequivocal identification of reference strains and clinical isolates belonging to 16 different M serotypes.

RecOR suppression of recF mutant phenotypes in Escherichia coli K-12

The recF, recO, and recR genes form the recFOR epistasis group for DNA repair. recF mutants are sensitive to UV irradiation and fail to properly induce the SOS response. Using plasmid derivatives that overexpress combinations of the recO+ and recR+ genes, we tested the hypothesis that high-level expression of recO+ and recR+ (recOR) in vivo will indirectly suppress the recF mutant phenotypes mentioned above. We found that overexpression of just recR+ from the plasmid will partially suppress both phenotypes. Expression of the chromosomal recO+ gene is essential for the recR+ suppression. Hence we call this RecOR suppression of recF mutant phenotypes. RecOR suppression of SOS induction is more efficient with recO+ expression from a plasmid than with recO+ expression from the chromosome. This is not true for RecOR suppression of UV sensitivity (the two are equal). Comparison of RecOR suppression with the suppression caused by recA801 and recA803 shows that RecOR suppression of UV sensitivity is more effective than recA803 suppression and that RecOR suppression of UV sensitivity, like recA801 suppression, requires recJ+. We present a model that explains the data and proposes a function for the recFOR epistasis group in the induction of the SOS response and recombinational DNA repair.