Recent advances in the polymerase chain reaction

Detection of hepatitis C virus RNA in serum, by combining reverse transcription and polymerase chain reaction in one tube

Reverse transcription of viral RNA into cDNA and its subsequent amplification by polymerase chain reaction (PCR) are generally carried out as two separate reactions. Here we describe a novel method for the detection of HCV RNA in serum combining both steps in one reaction tube using a wax interface to separate the two sets of reactants during initial cDNA synthesis. This enabled optimisation of both reactions, simplified the test and thereby reduced the risk of cross-contamination.

Detection of bovine herpesvirus-1 in bovine semen by a nested PCR assay

A nested PCR assay targeting a portion of the glycoprotein IV gene has been developed for the detection of Bovine Herpesvirus-1 (BHV-1). Rapid and sensitive detection of the PCR products was achieved using a nonisotopic reverse dot-blot format with a visible color readout. Cross-reactivity of this PCR assay was not observed with the closely related BHV-3. The sensitivity of this assay when tested on a supernatant from a BHV-1 cell culture was approximately 4.5 TCID50 (50% tissue culture infectious dose). A procedure using the chelating resin Chelex 100 was used to prepare viral DNA from artificially inoculated samples of extended and raw semen for use in the PCR assay. In combination with nested PCR and reverse dot blot, this method allowed the detection of 5 x 10(3) TCID per 0.5 ml of semen, which is comparable to the detection in the Cornell Semen Test. The whole procedure can be completed in approximately 8 h. This assay has therefore the potential of replacing the currently available yet time consuming and costly detection methods for BHV-1 in bovine semen.

Retinoblastoma. Interphotoreceptor retinoid binding protein mRNA analysis by polymerase chain reaction

The authors used the polymerase chain reaction (PCR) to detect the mRNA for interphotoreceptor retinoid-binding protein (IRBP/RBP3), a photoreceptor specific protein, in small samples. They carried out these experiments to assess the feasibility of applying this technique to small tumor samples. Surgically excised tumor samples from four enucleations were analyzed. Messenger RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction was followed by phenol-chloroform purification, reverse-transcription and amplification. The primers used were 5' TGATGACTCTGTCAGTG 3' in exon 3 (sense) and 5' TTGTGCTGGAGCATCTC 3' in exon 4 (antisense). Controls included an IRBP cDNA pIRBP 20-700 and RNA from normal human retina. All samples amplified the same size band if detected. Three tumor samples contained IRBP mRNA as indicated by amplified 234 bp band. These three samples showed a high IRBP protein level by slot blot and RNA for IRBP detected by northern blot. Hematoxylin-eosin staining of one of these samples revealed a well differentiated tumor with numerous Flexner-Wintersteiner rosettes. In the fourth tumor, a poorly differentiated neoplasm, no IRBP mRNA was detected. The authors' results showed a qualitative variation of IRBP mRNA levels, usually related to the histologic differentiation, with IRBP expressed in well differentiated tumors as well as in the normal human retina in contrast to a poorly differentiated tumor with no detectable IRBP. The feasibility of the reverse transcriptase-PCR (RT-PCR) technique to detect IRBP mRNA in small retinoblastoma tumors, was demonstrated.

Typing of Legionella pneumophila strains by polymerase chain reaction-mediated DNA fingerprinting

Well-defined Legionella pneumophila strains were analyzed by amplification of variable genomic regions with arbitrary and repeat sequence primers. Clinical and environmental outbreak-related isolates showed closely related amplicon patterns. Eleven strains of unrelated origins displayed 10 distinct patterns. Fingerprinting of L. pneumophila by polymerase chain reaction appeared to have the potential of being as epidemiologically useful as other genotypic methods.

Concordant clonal delineation of methicillin-resistant Staphylococcus aureus by macrorestriction analysis and polymerase chain reaction genome fingerprinting

Pulsed-field gel electrophoresis of DNA macrorestriction fragments (macrorestriction analysis) allows epidemiologic typing and delineation of genetic relatedness of methicillin-resistant Staphylococcus aureus (MRSA) by indexing variations in the global chromosome architecture. Polymerase chain reaction (PCR)-mediated genome fingerprinting can also discriminate MRSA strains by detecting locally variable DNA motifs. To assess the correlation between these methods, 48 epidemic MRSA strains collected from 20 hospitals over a 10-year period were tested in a blind comparison by (i) macrorestriction analysis with SstII or SmaI endonuclease and (ii) PCR fingerprinting with four primer sets aimed at the mecA gene, enterobacterial repetitive intergenic consensus sequences, and arbitrary sequences. Isolates were discriminated into 22 macrorestriction patterns and 15 PCR fingerprints. MRSA strains belonging to 12 distinct clones by macrorestriction analysis showed 11 distinct PCR genotypes distinguished by multiple band differences. In contrast, 34 of 37 MRSA strains found to be clonally related by macrorestriction analysis clustered in two highly related PCR genotypes that differed by a single DNA fragment (P < 0.0001). These data demonstrate concordant clonal delineation of epidemic MRSA by macrorestriction analysis and PCR fingerprinting and thereby indicate that the rapid PCR assay may be an efficient epidemiologic typing system.

DNA amplification fingerprinting using arbitrary oligonucleotide primers

DNA amplification fingerprinting (DAF) is a strategy for genetic typing and mapping that uses one or more very short (> or = 5 nt) arbitrary oligonucleotides to direct the enzymatic amplification of discrete portions of a DNA template resulting in a spectrum of products characteristic of the DNA starting material. Polymorphisms from simple banding patterns are useful as genetic markers while more complex and informative patterns are suitable for DNA fingerprinting. The use of polyacrylamide gel electrophoresis and silver staining can adequately resolve the spectrum of DAF products into detailed and reproducible patterns.

Detection of bovine viral diarrhea virus RNA in formalin-fixed, paraffin-embedded brain tissue by nested polymerase chain reaction

Isolation and amplification of RNA from formalin-fixed, paraffin-embedded tissues is delicate due to its fragility and ubiquitous ribonucleases. For retrospective studies, however, a convenient procedure for the detection of RNA in archived material is of great value. Bovine viral diarrhea (BVD) virus is a member of the pestivirus genus in the family Flaviviridae. Different protocols for the isolation of BVD virus RNA from fresh and autolytic as well as from routinely formalin-fixed and paraffin-embedded brain tissue of BVDV-infected calves were compared. The polymerase chain reaction (PCR) after reverse transcription (RT-PCR) was carried out subsequently for the detection of viral RNA. Using proteinase K digestion of deparaffinized tissue sections without additional ribonuclease inhibitors and subsequent nested PCR, a 803 bp fragment of the gene coding for the nonstructural protein p125 of BVD virus could be consistently detected. In addition, BVD virus RNA was detected by RT-PCR from non-fixed brain tissue after 10 days of autolysis.

Absence of human papillomavirus type 16 E6 transcripts in HPV 16-infected, cytologically normal cervical scrapings

By a combination of reversed transcription and subsequent polymerase chain reaction (RNA-PCR), 23 cytologically normal cervical scrapings, positive for the presence of human papillomavirus type 16 (HPV 16) DNA, were analyzed for the presence of transcripts originating from the E6 region of the viral genome. This region is thought to be involved in transformational, tumorigenic events. No mRNAs of the E6 region were detectable using the most sensitive PCR-mediated procedure currently available. Since it was previously shown that in cytological abnormal cervical scrapings about one-half of the samples positive for HPV 16 DNA express mRNAs of the E6 region, a difference between normal and abnormal cervical scrapings, when the HPV 16 is present, exists. The observed difference between cytologically normal and abnormal, HPV-DNA-positive cervical scrapes may eventually be used as a prognostic marker for screening of women at risk for the development of cervical carcinoma. However, firm establishment of the putative correlation between tumor progression and the presence of E6 transcripts requires extensive follow-up analysis of HPV-positive patients.

Comparison of plasmid- and chromosome-based polymerase chain reaction assays for detecting Chlamydia trachomatis nucleic acids

Several laboratories have demonstrated that the polymerase chain reaction (PCR) is more sensitive than culture or enzyme immunoassay (EIA) for detecting Chlamydia trachomatis in genitourinary tract specimens when various DNA targets are used for amplification, including the cryptic plasmid, major outer membrane protein (MOMP), or rRNA genes. We compared the performances of five different PCR assays, including assays with two plasmid, two MOMP, and one rRNA targets, by amplifying serial dilutions of C. trachomatis DNA and testing genitourinary tract specimens. By using published procedures, two different plasmid primers had sensitivities of 0.1 fg for C. trachomatis plasmid DNA and 10 fg for total cellular DNA. The sensitivities of the assays with the two MOMP primers were 0.1 and 10 pg, and the sensitivity for the assay with the rRNA primers was 1 pg for cellular DNA. Both plasmid-based assays detected 38 of 38 confirmed Chlamydiazyme-positive specimens, whereas the assays with the MOMP and rRNA primers detected 36 of 38 and 29 of 38 confirmed Chlamydiazyme-positive specimens, respectively. Six of 18 Chlamydiazyme-negative specimens collected from individuals whose specimens were positive by culture or immunofluorescence were positive by both plasmid-based PCRs; 4 of these were positive by PCR with the MOMP primers and 3 were positive by PCR with the rRNA primers. The results obtained with both purified DNA and genitourinary tract specimens indicated that the plasmid-based PCRs are more sensitive than bacterial chromosome-based PCRs for detecting C. trachomatis.

The origin of HIV-1 isolate HTLV-IIIB

The striking similarity between the first two human immunodeficiency virus type 1 (HIV-1) isolates Lai/LAV (formerly LAV, isolated at the Pasteur Institute) and Lai/IIIB (formerly HTLV-IIIB, reported to be isolated from a pooled culture at the Laboratory of Tumor Cell Biology (LTCB) of the National Cancer Institute) provoked considerable controversy in light of the high level of variability found among subsequent HIV-1 isolates. In November 1990, the Office of Scientific Integrity at the National Institutes of Health commissioned our group to analyse archival samples established at the Pasteur Institute and LTCB between 1983 and 1985. Retrospective analyses have shown that contamination of a culture derived from patient BRU by one from patient LAI was responsible for the provenance of HIV-1 Lai/LAV; the contaminated culture (M2T-/B) was sent to LTCB in September 1983. Our goals were to determine which HIV-1 variants were present in the samples and the sequence diversity among HIV-1 isolates from the earliest stages of the AIDS epidemic. We examined archival specimens and report here the detection of six novel HIV-1 sequences in the cultures used to establish the pool: none is closely related to HIV-1 Lai/IIIB. A sample derived from patient LAI contained variants of both HIV-1 Lai/IIIB and HIV-1 Lai/LAV, and a sequence identical to a variant of HIV-1 Lai/IIIB was detected in the contaminated M2T-/B culture. We conclude that the pool, and probably another LTCB culture, MoV, were contaminated between October 1983 and early 1984 by variants of HIV-1 Lai from the M2T-/B culture. Therefore, the origin of the HIV-1 Lai/IIIB isolate also was patient LAI.

Development of species-specific DNA probes for Campylobacter jejuni, Campylobacter coli, and Campylobacter lari by polymerase chain reaction fingerprinting

The application of polymerase chain reaction (PCR) fingerprinting assays enables discrimination between species and strains of microorganisms. PCR primers aiming at arbitrary sequences in combination with primers directed against the repetitive extragenic palindrome (REP) or enterobacterial repetitive intergenic consensus (ERIC) motifs generate isolate-specific DNA banding patterns. Analysis of these PCR fingerprints obtained for 33 isolates of Campylobacter jejuni, 30 isolates of Campylobacter coli, and 8 isolates of Campylobacter lari revealed that besides generation of isolate-specific fragments, species-specific DNA fragments of identical size were synthesized. It appeared that these DNA fragments could be used as species-specific probes, since they are unique for the pattern which they are deriving from. The probes do not cross-react with amplified DNA originating from a large panel of nonrelated microorganisms. Moreover, these probes displayed species specificity, as they reacted with a single restriction fragment on Southern blots containing DNA from C. jejuni, C. coli, and C. lari and other Campylobacter species. This combination of PCR fingerprinting and probe hybridization results in a highly specific identification assay and provides an example of specific test development without the prior need for DNA sequence information. The principle of the procedure holds great promise for the rapid isolation of DNA probes which, in combination with a general PCR assay, may lead to efficient typing and detection procedures for a multitude of medically important nonviral microorganisms.

Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases

Previously known 5' exonucleases of several eubacterial DNA polymerases have now been shown to be structure-specific endonucleases that cleave single-stranded DNA or RNA at the bifurcated end of a base-paired duplex. Cleavage was not coupled to synthesis, although primers accelerated the rate of cleavage considerably. The enzyme appeared to gain access to the cleavage site by moving from the free end of a 5' extension to the bifurcation of the duplex, where cleavage took place. Single-stranded 5' arms up to 200 nucleotides long were cleaved from such a duplex. Essentially any linear single-stranded nucleic acid can be targeted for specific cleavage by the 5' nuclease of DNA polymerase through hybridization with an oligonucleotide that converts the desired cleavage site into a substrate.

Sexing and detection of gene construct in microinjected bovine blastocysts using the polymerase chain reaction

We present a polymerase chain reaction (PCR)-based procedure for rapid bovine embryo sexing and classifying embryos for the presence of exogenous DNA. Fourteen bovine blastocysts microinjected with gene construct DNA at the pronuclear stage were divided into quarters and subjected to amplification with construct-specific and sex gene-specific (ZFY/ZFX) primers in the same initial PCR reaction. Blastocysts carrying microinjected construct DNA could be identified by the presence of construct-specific PCR product in approximately 4 h. Approximately half of the microinjected and two of 16 non-microinjected blastocysts typed PCR-positive for the construct DNA. Owing to erroneous amplifications in the two non-microinjected control blastocysts, and the inability of the system to distinguish integrated from non-integrated copies of the microinjected construct, the number of construct-positive blastocysts determined in our assay most likely overestimates the number of true transgenic embryos. Nevertheless, using this assay, we were able to determine that approximately half of the microinjected embryos were negative for the transgene construct and thus could be eliminated from transfer to a recipient cow. Embryo sexing was achieved in less than 6 h by restriction fragment length polymorphism analysis of nested ZFY/ZFX PCR products reamplified from initial PCR reactions. In 11/14 microinjected blastocysts all sections assayed unambiguously as the same sex. In one embryo, only one section was analysed, while two other blastocysts showed some discrepancies of sexing results between the sections analysed.(ABSTRACT TRUNCATED AT 250 WORDS)

Detection of bovine immunodeficiency-like virus by the polymerase chain reaction

This report describes a test for the bovine lentivirus, bovine immunodeficiency-like virus, in which polymerase chain reaction (PCR) technology is employed. Two pairs of oligonucleotide primers directed to sequences within the coding regions of the gag and pol genes generated the expected PCR products from molecular BIV clones and from DNA of BIV-infected cell cultures but not from DNA of uninfected cultures. Data indicating the specificity and sensitivity of these PCRs for BIV detection and the potential utility of this technology for diagnostic applications are presented.

Differentiation of major genotypes of Giardia intestinalis by polymerase chain reaction analysis of a gene encoding a trophozoite surface antigen

The polymerase chain reaction (PCR) has been used to amplify in vitro a semi-conserved region of a gene encoding an M(r) 68-72,000 surface antigen of Giardia intestinalis trophozoites. Using primers specific for conserved nucleotide sequences identified within the promoter-distal portion of two homologous genes (tsp11 and tsa417) cloned previously from the G. intestinalis isolates Ad-1 (from Australia) and WB (from Afghanistan), a single PCR-amplified DNA fragment of the expected size (0.52 kilobases) was obtained in high yield from either purified DNA or whole trophozoites of the Ad-1 isolate and from every 1 to 9 other axenic G. intestinalis isolates belonging to genetic groups I and II (defined previously on the basis of allozyme electrophoresis data--Andrews et al. 1989). Discernible product was recovered from as few as 2-4 trophozoites. In contrast, 6 G. intestinalis isolates that were assigned by allozymic analysis to genetic groups III/IV yielded small amounts of a 0.37-kilobase (kb) amplification product (with evidence in some samples of an additional 0.4 or 0.18 kb fragment) but no 0.52 kb product. Two animal-derived isolates of G. duodenalis (one from an Australian native rodent, Notomys alexis, the other from a domestic cat) also yielded a single 0.37 kb PCR-amplified fragment, whereas an isolate from another cat produced a 0.34 kb fragment. No product was recovered from G. muris, a morphologically distinct species of Giardia. The results demonstrate that different genotypes of G. duodenalis can be distinguished using this assay and that it is diagnostic for isolates belonging to two major clusters (groups I/II and III/IV) of G. intestinalis. The amplified DNA segment appears to be relatively conserved among group I and group II isolates of G. intestinalis. A related but clearly distinct sequence seems to be conserved among group III/IV isolates of G. intestinalis and some isolates of G. duodenalis.

Detection of genomic and intermediate replicative strands of hepatitis C virus in liver tissue by in situ hybridization

Nonisotopic in situ hybridization using a digoxigenin-labeled cDNA probe to the 3' nonstructural region (NS5) of hepatitis C virus (HCV) was performed on liver tissue from 33 patients. The results were compared with PCR detection of HCV RNA performed on 24 of the biopsies. Nonisotopic in situ hybridization correlated well with PCR findings. Hybridization signals were detected, within the cytoplasm and nuclei/nucleoli of hepatocytes, mononuclear, and biliary epithelial cells. In patients with clinically and histologically defined chronic active hepatitis related to active HCV infection, HCV genome was frequently detected in biliary epithelium and correlated well with biliary damage, an otherwise uncommon finding in chronic active hepatitis due to other hepatotropic viruses. Further studies using sense and antisense probes synthesized from the 5' non-coding region of the HCV genome confirmed the localization of positive strand of HCV in the above cell populations. The replicative intermediate strand was also present in all cells, although less frequently observed, apart from biliary epithelium, where negative strand of HCV was undetectable. The findings of HCV genome in liver biopsies of two patients with no significant histological abnormalities may suggest that the damage seen in chronic HCV infection is immune mediated, although the cytopathic effect of the virus may also be important.

Isolation of a goat acetyl-CoA carboxylase complementary DNA and effect of milking frequency on the expression of the acetyl-CoA carboxylase and fatty acid synthase genes in goat mammary gland

1. Using the polymerase chain reaction we have isolated a partial complementary DNA for goat acetyl-CoA carboxylase which is 90 and 82% homologous to the published rat and chicken complementary DNA sequences, respectively. 2. Frequent milking causes an upregulation of the acetyl-CoA carboxylase and fatty acid synthase genes in goat mammary gland that parallels the increase in the respective enzyme activities. 3. The sequence for goat acetyl-CoA carboxylase is in the EMBL data base, Accession Number Z17803.

Simultaneous amplification of multiple HIV-1 DNA sequences from clinical specimens by using nested-primer polymerase chain reaction

A sensitive and specific polymerase chain reaction (PCR) protocol with nested primers was developed for simultaneous amplification of three independent human immunodeficiency virus type 1 (HIV-1) DNA sequences from clinical specimens. DNA samples were first amplified with gag, pol, and env outer primer pairs and then with the corresponding three inner primer pairs in the same two-step reaction. Detection of the different amplification products was readily accomplished by simple agarose gel electrophoresis of the reaction product, even when starting with a single copy of HIV-1 DNA. Equivalent amounts of the three PCR products were generated, provided that the relative concentrations of the inner primer pairs were optimized. In addition, a beta-globin control primer pair could be conveniently included in the internal amplification step to verify that the DNA sample was suitable for PCR analysis. One nested multiplex PCR test was sufficient to detect HIV-1 DNA in all of 80 HIV-1-seropositive individuals and none of 50 HIV-1-seronegative healthy blood donors. The nested multiplex PCR procedure provides an attractive means for simple, rapid, and cost-effective direct detection of HIV-1 DNA in patient samples.

Identification of Bacteroides forsythus in subgingival plaque from patients with advanced periodontitis

Bacteroides forsythus has been associated with destructive adult periodontitis. Up to now, detailed analysis by classical means was hampered by the fastidious nature of the organism. There is hope that the application of molecular detection methods such as indirect immunofluorescence or in situ hybridization (ISH) will allow for more rapid and accurate identification. Here we describe a B. forsythus-specific probe (BFV530), complementary to 16S rRNA, which correctly identified all B. forsythus isolates as confirmed by biochemical, protein, or fatty acid analysis. To assess whether this probe might be suitable for direct identification of B. forsythus in clinical specimens, a total of 92 subgingival plaque samples were analyzed. Fifty-five specimens were tested in parallel by culture, light microscopy, and filter hybridization. Unfortunately, the overall agreement between results of filter hybridization and conventional methods was 70.9% only. We therefore examined 37 new specimens by ISH and indirect immunofluorescence by using fluorescently labeled probe BFV530 or B. forsythus-specific monoclonal antibody 116BF1.2 (kindly provided by R. Gmür, Zurich, Switzerland), respectively. Agreement between these methods was 100%, indicating that ISH with probe BFV530 might be used to accurately identify B. forsythus directly in subgingival plaque samples.

Analysis of prevalence of human papillomavirus in laryngeal carcinomas. Study of 40 cases using polymerase chain reaction and consensus primers

In this study we determined the frequency of association of human papillomavirus (HPV) and laryngeal carcinomas and investigated the possibility that HPV may be associated with larger or more aggressive tumors. Laryngeal squamous cell carcinomas from 40 patients who did not have preexisting papillomas by clinical history were retrieved from formalin-fixed, paraffin-embedded blocks and analyzed for HPV. Twenty-two cases were tumors of the true vocal folds, and 18 were supraglottic. Clinical follow-up was available for 25 patients. We used the polymerase chain reaction (PCR) with the "hot start" modification and consensus primers that can detect over 30 distinct HPV types. Three of the 40 patients (8%) had detectable HPV DNA. These 3 patients did not have unusual age demographics and were smokers. All but 1 of the 22 HPV-negative patients who were questioned were also smokers. We compared the outcomes for large (4 cm or greater) HPV-positive and -negative tumors. Six of the 40 tumors were 4 cm or greater and involved contiguous structures. Two of these 6 were HPV-positive, and these patients died of disease after 3 and 16 months, respectively. Of the 4 HPV-negative patients with tumors greater than 4 cm, 3 are disease-free at 41, 42, and 3 months, respectively, and 1 was lost to follow-up. The third HPV-positive patient had a tumor less than 1 cm, and is disease-free after 38 months. While the number of HPV-positive cases is too small for definitive conclusions, it is possible that for large tumors the presence of HPV DNA may portend a worse prognosis.(ABSTRACT TRUNCATED AT 250 WORDS)

Typing of the 3' hypervariable region of the apolipoprotein B gene: approaches, pitfalls, and applications

Apolipoprotein B-100 is the principal protein component of lipoproteins with very low, intermediate, and low density. The interaction of apoB-100 with low density lipoprotein (LDL) receptors is responsible for the uptake of LDL into cells. An AT-rich hypervariable region is located adjacent to the 3' end of the apoB gene. It consists of a variable number of tandemly repeated sequences (VNTR). Two approaches were used to analyze this polymorphism. In both, the region harboring the VNTR was amplified with the polymerase chain reaction (PCR). In the first method, fluorescently labeled primers were used in the PCR reactions and products were separated in agarose gels by means of an automated fluorescent fragment analyzer. In the second method, PCR products were analyzed in denaturing polyacrylamide gels and detected with silver staining. Even in the highly sophisticated automated system, agarose gel electrophoresis did not always enable unequivocal assignment of VNTR alleles. In contrast, denaturing polyacrylamide gel electrophoresis made it possible to distinguish the 15 bp differences between the VNTR alleles in a precise and simple manner. The VNTR polymorphism was typed in 234 individuals. Among these were 136 patients with coronary artery disease and 74 healthy controls. Thirteen alleles could be distinguished. The allele containing 49 repeats (VNTR-49) was found in 9.2% of the coronary artery disease patients and in 4.7% of the controls. Thus, the VNTR-49 allele increases relative coronary risk by about twofold. It is concluded that the apoB VNTR polymorphism is a potentially useful genetic marker. Since agarose gel electrophoresis may lead to ambiguous results, we prefer typing by denaturing polyacrylamide gel electrophoresis.(ABSTRACT TRUNCATED AT 250 WORDS)

PCR-dependent amplification and sequence characterization of partial cDNAs encoding myosin-like proteins in Anemia phyllitidis (L.) Sw. and Arabidopsis thaliana (L.) Heynh

Partial cDNAs encoding for myosin-like proteins from Anemia phyllitidis and Arabidopsis thaliana have been isolated using PCR technology. The deduced amino acid sequences show an average similarity up to 62% with known myosin heavy chain genes. From northern blot analysis we were able to estimate that transcripts of ca. 6.1 kb size are expressed in A. phyllitidis.

Use of NS3 consensus primers for the polymerase chain reaction amplification and sequencing of dengue viruses and other flaviviruses

Consensus primers for the polymerase chain reaction were designed based on conserved motifs within the serine protease and RNA helicase domains encoded by the NS 3 genes of dengue and other flaviviruses. Target fragments of 470 bp were amplified on cDNA templates synthesized from RNAs of dengue types 1, 2, 3, and 4, Japanese encephalitis, Kunjin, and yellow fever viruses using random or specific downstream primers. PCR of oligo(dT)-primed cDNAs from Japanese encephalitis and Kunjin viral RNAs did not yield target bands. As few as 10(3) copies of dengue viral RNA could be detected. Direct DNA sequencing of PCR products of reference strains of dengue 2 (NGC), Kunjin (MRM 61C) and yellow fever (17 D) viruses demonstrated complete concurrence with published data. However, 2 nucleotide differences were observed between our data for dengue 3 H87 strain and the published sequence, resulting in a single amino acid disparity. Differences at 21, 16, and 11 nucleotide positions were noted between dengue 1 Hawaii and S 275/90; dengue 4 H 241 and 814669; Japanese encephalitis Nakayama and JaOArS 982 viral strains, culminating in only 4, 1 and 1 amino acid residue differences, respectively. These amino acid disparities occurred outside putative active sites of the enzymatic domains, emphasizing the important role of the NS3 protein in flaviviral replication. This RNA-PCR consensus primer strategy coupled with DNA sequencing represents a valuable tool for the molecular diagnosis and epidemiology of dengue and other flaviviral infections.

Detection of Epstein-Barr virus in a case of undifferentiated nasopharyngeal carcinoma by in situ hybridization with digoxigenin-labelled PCR-generated probes

A case of nasopharyngeal carcinoma is presented. Epstein-Barr viral genome was identified in the neoplastic cells by in situ hybridization with digoxigenin-labelled polymerase chain reaction-generated probes. We report the development of this technique in paraffin-embedded sections and propose that such identification may prove valuable for the diagnosis of this tumour in routine material.

Four recombinant isoforms of Cor a I, the major allergen of hazel pollen, show different IgE-binding properties

Previous studies showed that pollens from trees of the order Fagales (e.g. birch, alder, hazel and hornbeam) all contain one major allergen. These proteins are cross-reactive between these tree species, and approximately 95% of tree-pollen-allergic patients display IgE binding to these allergens. Using the reported N-terminal amino acid sequence of the hazel pollen allergen Cor a I, it was possible to amplify Cor-a-I cDNA by use of the polymerase chain reaction. Four clones with cDNA inserts were isolated. All four clones contained an open reading frame of 477 nucleotides (159 amino acids) but differed in length of their 3'-non-coding regions. Within the overlapping regions, the nucleotide sequence of the 3'-non-coding regions of the four clones were nearly identical. The open reading frames coded for different isoforms of the major hazel pollen allergen, Cor a I. The clones were designated Cor a I/5, 6, 11 and 16, respectively. Comparison of the deduced amino acid sequences of these Cor a I isoforms revealed identities of 96-99%. The sequence identities between the Cor a I isoforms and Bet v I, the major birch pollen allergen, were 71-73% (80.5-83% similarity). Comparing amino acid sequences of Cor a I isoforms with the published sequences of Aln g I, the major allergen from alder, and Car b I and isoforms, the major allergen from hornbeam, 75.5-76.7% identity (83.6-85% similarity) and 83.6-89.9% sequence identity (89.3-95% similarity), respectively, was found. The four Cor a I cDNAs were subcloned into plasmid pKK223-3 and expressed in Escherichia coli as non-fusion proteins; their capacity to bind serum IgE from tree-pollen-allergic patients was investigated. The four cloned isoforms showed an apparent molecular mass of 17 kDa in SDS/PAGE, identical to the natural, pollen-derived Cor a I. IgE antibodies from tree-pollen-allergic patients reacted with all four recombinant isoforms. However, we noted marked differences in the IgE-binding patterns of the distinct isoforms. Furthermore, Cor a I/11 was the only isoform recognized by the anti-(Bet v I) mAb, BIP 1. Our results demonstrate that Cor a I isoforms display different antigenic and allergenic properties, very likely due to few but significant changes in their amino acid sequences. These findings have implications for the development of reagents for diagnosis and immunotherapy of type I allergies.

Polymerase chain reaction (PCR): a possible alternative to immunochemical methods assuring safety and quality of food. Detection of wheat contamination in non-wheat food products

A rapid, sensitive and specific analysis of food samples determining wheat contamination was established using polymerase chain reaction (PCR) technology. First, primers specific for highly conserved eukaryote DNA sequences were used to prove isolated nucleic acid substrate accessibility to PCR amplification. Subsequently, a highly repetitive and specific genomic wheat DNA segment was amplified by PCR for wheat detection. This assay was tested with 35 different food samples ranging from bakery additives to heated and processed food samples. In addition, the PCR method was compared to an immunochemical assay that detected the wheat protein component gliadin. Combination of both assays allowed a detailed characterization of wheat contamination. Hence, wheat flour contamination could be distinguished from gliadin used as a carrier for spices as well as from wheat starch addition.

Expression of interleukins 1, 3, 6, stem cell factor and their receptors in acute leukemia blast cells and in normal peripheral lymphocytes and monocytes

Reverse transcriptase-polymerase chain reaction amplification (RT-PCR) and Southern blot analysis were used to evaluate ligand and receptor expression of interleukin 1 alpha (IL-1 alpha), interleukin 3 (IL-3), interleukin 6 (IL-6) and stem cell factor (SCF) in peripheral blood lymphocytes and monocytes and in several acute leukemia blast cell populations. Resting peripheral lymphocytes and monocytes expressed both ligand and receptor of the four cytokines at considerable levels. The leukemic blast cells of the M1-M4 phenotypes are characterized by almost complete lack of expression of IL-1 alpha, IL-3 and IL-6 and the constant and usually high expression of SCF. On the other hand, these myeloid blast cells express generally high levels of the four cytokine receptors. The data suggest that the regulation of the expression of IL-1 alpha, IL-3 and IL-6, at least in our limited number of leukemic cell populations studied, is independent of that of SCF. The results indicate that, at least in most of the leukemic myeloid blasts cells, the expression of SCF and its receptor, the c-kit oncogene, may permit an autocrine regulation of cell cycling.

Colorimetric detection for PCR amplified HIV-1 DNA using magnetic beads

A rapid and nonradioactive detection method for polymerase chain reaction (PCR) amplified HIV-1 DNA was developed using a colorimetric detection system. Hybridization between biotin-labeled amplified targets and digoxigenin-capture probes occurs in solution followed by efficient and rapid capture onto streptavidin-magnetic beads. The presence of the digoxigenin-capture probe hybridized with biotin-labeled targets is then detected by antidigoxigenin-alkaline phosphatase conjugates using a colorimetric substrate. This approach is highly sensitive and can detect less than 10 HIV targets prior to PCR in approximately 50 min.

High output genetic mapping of polyploids using PCR-generated markers

The polymerase chain reaction (PCR) with arbitrarily selected primers has been established as an efficient method to generate fingerprints that are useful in genetic mapping and genomic fingerprinting. To further increase the productivity of mapping and fingerprinting efforts, we have altered existing protocols to include the use of the Stoffel fragment, which is derived from genetically engineered Taq polymerase. We also optimized the thermal profile of the reaction to increase the number of useful primers. In mapping of the genome of Saccharum spontaneum 'SES 208', a polyploid wild relative of sugarcane, these modifications allowed for an increase of 30% in the number of loci screened per primer, and an 80% increase in the number of polymorphisms per primer. Furthermore, the enzyme cost per reaction was decreased approximately 1.6-fold. Finally, there was an increase from about 70% to about 97% in the number of primers that were useful (i.e., gave a reproducible fingerprint) using our protocol. We have placed some of these markers into linkage groups.

Quantitative titration of nucleic acids by enzymatic amplification reactions run to saturation

In vitro enzymatic amplification of nucleic acids by PCR or other techniques is a very sensitive method to detect rare DNA segments. We present here a protocol that allows the rapid, sensitive and precise quantification of DNA molecules using PCR amplification run to saturation. The DNA (or cDNA) to be assayed is co-amplified with known amounts of an internal standard DNA. We show that the latter must be almost identical to the assayed DNA, otherwise quantification at the plateau is unreliable. The read-out of the amplification involves one or two additional oligonucleotides. Using fluorescent oligonucleotides as primers in run-off reactions together with an automated DNA sequencer, we could measure the level of expression of several genes, like the murine MHC class I H-2Kd or a specific T cell receptor beta chain transcript in the course of an immunization. mRNA levels were normalized by measuring in a similar manner the number of transcripts encoding the housekeeping gene HPRT. Finally, our procedure might allow the rapid analysis of a large number of samples at the same time, as illustrated by the simultaneous analysis of the mRNAs encoding the CD4 and CD8 murine T cell markers.

Diagnostic molecular microbiology. Current challenges and future directions

The advent of nucleic acid amplification techniques for the clinical laboratory provides not only new diagnostic opportunities but new responsibilities as well. Problems associated with the introduction of this technology include contamination with the products of amplification reactions, and difficulty in interpreting test results. Eventually, however, many of these problems will be overcome, and new applications of diagnostic molecular microbiology such as sequence-based microbial identification will become established. Clinical microbiologists will successfully negotiate the transition to tests based on nucleic acid chemistry if they are willing to educate and become educated in the new technology.

Three different types of organization of the vir regulon in group A streptococci

The DNA of group A streptococci (GAS) encodes several important virulence factors such as the antiphagocytic M protein, the Ig-Fc-binding M-related proteins (FcrA-like and EnnX-like) and the complement factor-inactivating C5a peptidase. The corresponding genes emm, fcrA, ennX, and scpA, respectively, were assumed to be located close together in the GAS genome. Additionally, emm and scpA have been found to be under the positive, coordinate control of the virR locus, which led to the designation "vir regulon" for the corresponding genomic segment. In order to map the vir regulons of many GAS serotypes and to analyse any correlation between the organization of vir regulons and circumscribed heterogeneities within the emm, virR, and scpA genes, an approach using several distinct sets of polymerase chain reaction (PCR) experiments was chosen. By examination of the genomic DNA of 42 GAS isolates from 36 different M serotypes three patterns of vir regulon topography were found. The first, designated "large vir regulon" (LVR), consists of virR--fcrA(-like)--emm--ennX(-like)--scpA. The second, designated "small vir regulon" (SVR), contains virR--emm--scpA, and the last, designated "unusual vir regulon" (UVR), resembles SVR but contains additional heterogeneous sequences between emm and scpA. The patterns correlate with heterogeneities at the 3' ends of the virR and scpA genes, with the M classification system and the occurrence of specific non-coding intervening sequences within the vir regulons. The potential impact of these patterns on models to account for generation of vir regulons is discussed.

A computer program for the design of PCR primers for diagnosis of highly variable genomes

PCRDiag (Diagnosis by PCR) is a computer program which allows the localization of pairs of oligonucleotides with optimal thermodynamic requirements for use in a PCR assay. The program is designed for the selection of pairs of primers complementary to sequences present in a group, whose identification is intended, but are absent in other non-specific sequences. The program constitutes a powerful tool, specially in systems which display a high degree of sequence heterogeneity, as is the case of RNA viruses. The program runs on IBM-PC and compatible computers and has no special software requirements. It does not need the previous alignment of the sequences analyzed.

Comparison of indirect and direct in-situ polymerase chain reaction in cell preparations and tissue sections. Detection of viral DNA, gene rearrangements and chromosomal translocations

Different approaches to the in-situ polymerase chain reaction (in-situ PCR) were compared in the detection and in-situ localization of chromosomal translocations (t14; 18) immunoglobulin gene rearrangements and viral DNA (cytomegalovirus, hepatitis B-virus) in cell suspensions, cytospins and tissue sections. Single and multiple primer pairs were compared in the amplification step of indirect in-situ PCR and long genomic probes or internal oligonucleotide probes in the subsequent in-situ hybridization (ISH). For direct in-situ PCR, in which amplification products were directly labeled with digoxigenin-11-dUTP during PCR and detected immunohistochemically, only single primer pairs were used for amplification. In-situ PCR yielded best results in the cell suspensions and worked less efficiently in cytospins or tissue sections. Quantification of the results obtained in artificial cell mixtures yielded only an approximate correlation between the number of expected and observed positive cells. The specificity of the results was greater with indirect in-situ PCR than direct in-situ PCR, where false positive results were frequent. Successful indirect in-situ PCR in tissue sections required the use of multiple primer pairs for amplification and genomic probes for detection by ISH. False positive results in direct in-situ PCR were caused by primer-independent, but DNA polymerase- and cycling-dependent incorporation of digoxigenin-labeled nucleotides into cellular DNA, possibly related to DNA repair and/or internal priming. Non-specific results were most marked in tissue sections and were much less frequent in cell suspensions. In-situ PCR includes a number of different techniques, which are not equally applicable to different starting materials. Accurate interpretation of the results requires vigorous controls.

An improved method for the detection of hepatitis C virus RNA in plasma utilizing heminested primers and internal control RNA

The majority of transfusion-associated, non-A, non-B hepatitis cases are caused by hepatitis C virus (HCV), a positive-stranded RNA virus. Although high titers of HCV in clinical specimens have been reported, in some cases extremely low titers of virus are not uncommon. Therefore, an extremely sensitive and reliable assay is required to determine viremia and replication of HCV accurately. We report here the systematic investigation of factors influencing the detection of HCV RNA by a reverse transcription-polymerase chain reaction (RT-PCR) assay utilizing "drop in-drop out" heminested primers derived from the conserved 5' non-coding region of the viral genome. A genetically engineered 5' noncoding region has been constructed and used as an internal control. Addition of the control RNA to each test not only allowed semiquantitation of positive reactions but also validated the performance of reverse transcription and PCR for every specimen. The optimized heminested PCR (HN-PCR) protocol is capable of amplifying one molecule of cloned HCV DNA or 10 molecules of in vitro-transcribed HCV RNA to levels detectable in ethidium bromide-stained agarose gels. We evaluated the improved method for the detection of HCV RNA on a human plasma sample containing the pedigreed strain H of HCV with a chimpanzee infectious dose of 10(6)/ml. Utilizing the internal control RNA, we calculated 2 x 10(7) virions in 1 ml of the original human plasma. The HN-PCR achieves the sensitivity and specificity of the double-nested PCR (DN-PCR) in a simplified format that avoids the false-positive results associated with DN-PCR.

CD4 molecules with a diversity of mutations encompassing the CDR3 region efficiently support human immunodeficiency virus type 1 envelope glycoprotein-mediated cell fusion

The third complementarity-determining region (CDR3) within domain 1 of the human CD4 molecule has been suggested to play a critical role in membrane fusion mediated by the interaction of CD4 with the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein. To analyze in detail the role of CDR3 and adjacent regions in the fusion process, we used cassette mutagenesis to construct a panel of 30 site-directed mutations between residues 79 and 96 of the full-length CD4 molecule. The mutant proteins were transiently expressed by using recombinant vaccinia virus vectors and were analyzed for cell surface expression, recombinant gp120-binding activity, and overall structural integrity as assessed by reactivity with a battery of anti-CD4 monoclonal antibodies. Cells expressing the CD4 mutants were assayed for their ability to form syncytia when mixed with cells expressing the HIV-1 envelope glycoprotein. Surprisingly in view of published data from others, most of the mutations had little effect on syncytium-forming activity. Normal fusion was observed in 21 mutants, including substitution of human residues 85 to 95 with the corresponding sequences from either chimpanzee, rhesus, or mouse CD4; a panel of Ser-Arg double insertions after each residue from 86 to 91; and a number of other charge, hydrophobic, and proline substitutions and insertions within this region. The nine mutants that showed impaired fusion all displayed defective gp120 binding and disruption of overall structural integrity. In further contrast with results of other workers, we observed that transformant human cell lines expressing native chimpanzee or rhesus CD4 efficiently formed syncytia when mixed with cells expressing the HIV-1 envelope glycoprotein. These data refute the conclusion that certain mutations in the CDR3 region of CD4 abolish cell fusion activity, and they suggest that a wide variety of sequences can be functionally tolerated in this region, including those from highly divergent mammalian species. Syncytium formation mediated by several of the CDR3 mutants was partially or completely resistant to inhibition by the CDR3-directed monoclonal antibody L71, suggesting that the corresponding epitope is not directly involved in the fusion process.(ABSTRACT TRUNCATED AT 400 WORDS)

Polymerase chain reaction and transfusion microbiology

Polymerase chain reaction (PCR) involves alternate denaturing and re-annealing of DNA in test samples in the presence of appropriate oligonucleotide primers complementary to opposite strands of the target DNA together with a heat-stable DNA polymerase, Mg2+ and the four nucleotide triphosphates. DNA target segments can be 'amplified' ten-millionfold by 25-35 such cycles. Even greater amplification (approximately 10(12)-fold) with enhanced specificity can be obtained by a second set of amplification cycles using a further pair of 'nested' primers sited within the DNA sequence defined by the original primers. PCR can be applied to the study of the whole range of transfusion-transmitted infections, both plasma and cell associated; RNA viruses can be analyzed if a DNA copy is made from the viral RNA by treatment with reverse transcriptase. In a transfusion context, the retroviruses (HIV-1, HIV-2, HTLV-I, HTLV-II), HCV and HBV have been the viruses most intensively subjected to PCR analysis. The advantages of PCR in this context include its ability to detect virus during the 'window period' or seronegative stages of infections and its value as a marker for viraemia and for the detection of viruses in products made from large pools of plasma. True immunity may also be differentiated from persistent infection in the presence of antibody. Similarly, PCR can overcome problems of diagnosis of acute infection caused by the presence of passively transferred antibody. Detailed strain differentiation is also possible by PCR, in conjunction with sequencing or with the aid of restriction endonucleases.(ABSTRACT TRUNCATED AT 250 WORDS)

Application of the polymerase chain reaction (PCR) in veterinary diagnostic virology

The polymerase chain reaction has become an important diagnostic tool for the veterinary virologist. Conventional methods for detecting viral diseases can be laborious or ineffective. In many cases PCR can provide a rapid and accurate test. In this article we explain the basic principles of PCR and supply a reference list of its uses in diagnostic veterinary virology.

Competitor mRNA fragments for quantitation of cytokine specific transcripts in cell lysates

Synthetic RNAs (sRNAs) specific for four human cytokines were constructed and used as an exogenous internal standard in a quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). The sequences of the sRNA and the target mRNA were identical except for a duplication or deletion of approximately 100 nucleotides. The size difference between these two templates permitted easy electrophoretic separation of their PCR products. The sRNA has polyadenylated sequences at the 3' end and can be added directly either to a cell lysate before RNA purification or to a reverse transcription reaction. One pair of primers is used to amplify the internal standard and the target simultaneously, and the ratio of the two PCR products remains constant throughout the amplification. This technique can be applied to quantitate specific mRNA in as few as 10 cells when the exogenous control is added directly to cell lysates. This method is sensitive, accurate and adaptable for quantitation of other transcripts.