Recent advances in the polymerase chain reaction

Improved detection of human papillomavirus infection in genital intraepithelial neoplasia in human immunodeficiency virus positive (HIV +) women by polymerase chain reaction-in situ hybridization

The prevalence of genital human papillomavirus (HPV) infection was evaluated in 30 consecutive human immunodeficiency virus (HIV) + women by polymerase chain reaction (PCR)-in situ hybridization (ISH) on paraffin-embedded tissue sections and compared with that found with standard ISH. Biopsies were removed from normal or neoplastic areas in the cervix, vagina, and vulva, and ISH was performed with biotinylated or fluorescein isothiocyanate genomic DNA probes. One probe was used for HPV screening and others for HPV typing (types 6, 11, 16, 18, 31, and 33). Sequences were amplified by the "hot-start" PCR method and followed by standard ISH. Among the 30 HIV + women, 90% scored HPV + in one or several locations by PCR-ISH, whereas only 67% were positive by ISH. Oncogenic HPV types were found in 63% by PCR-ISH and in only 43% by ISH. The same HPV types detected by standard ISH were also recognized by PCR-ISH, but with the latter the signal was amplified. Moreover, some HPV types were found with PCR-ISH but not by ISH. We conclude that PCR-ISH is a valuable and sensitive method for specific detection of HPV.

Preferential virological response to interferon-alpha 2a in patients with chronic hepatitis C infected by virus genotype 3a and exhibiting a low gamma-GT/ALT ratio

Hepatitis C virus infection causes acute and often chronic hepatitis. Therapy with interferon-alpha has been shown to induce remission of the inflammatory process within the liver and also elimination of the virus. However, only about 50% of treated patients respond in terms of at least a transient disappearance of viral RNA from the circulation below the limit of detection. In order to find prognostic factors for responsiveness, patients with chronic hepatitis C virus infection were analyzed for virus genotype and pretreatment biochemical liver parameters including serum AST, ALT, and gamma-GT activities. Whereas the initial biochemical response to interferon-alpha 2a was found not to be related to virus genotype, the initial virological response was found to be closely related to infection by genotype 3a and to a low pretreatment ratio of serum gamma-GT/ALT activity. These data confirm and extend the importance of virus genotype for responsiveness to interferon-alpha therapy and introduce an additional, host-specific parameter with a potential predictive value, namely the pretreatment ratio of serum gamma-GT/ALT activity.

Detection of human papillomavirus in cervical intra-epithelial neoplasia, using in situ hybridization and various polymerase chain reaction techniques

One hundred and forty-eight randomly chosen neutral-buffered formaldehyde-fixed cervical biopsies in which cervical intra-epithelial neoplasia (CIN) I-III had been diagnosed were tested for HPV (human papilloma virus) DNA by in situ hybridization (ISH) and polymerase chain reaction (PCR). For ISH, we utilized a biotinylated panprobe and type-specific, genomic probe sets. For PCR, we used the general primers GP5/GP6 and their recently described, elongated version GP5+/GP6+, and included the modification of hot-start PCR. Amplified DNA was detected by gel electrophoresis and slot blot hybridization. The positivity rate of ISH was 59% for all biopsies and 69%, 62% and 46% for CIN I, II and III, respectively. The sensitivity of GP5/GP6 was 74% with cold-start PCR and 78% with hot-start PCR. When GP5+/GP6+ was used, the sensitivity increased to 89% with cold-start PCR and to 95% with hot-start PCR. Based on the most sensitive PCR technique, HPV detection was 93%, 95% and 96% in CIN I, II and III, respectively. The number of HPV types decreased with the severity of the lesion, and HPV 16 was the predominant type. Multiple HPVs were rare and almost all HPV-positive cases could be typed. ISH and slot blot hybridization correlated well regarding HPV typing specificity. Our results confirm that distinct HPV types are present in a high proportion of cases of CIN. The sensitivity of ISH is lower than that of PCR. Furthermore, the modified general primers GP5+/GP6+ give a higher yield than GP5/GP6, while hot-start PCR increases sensitivity even further.

Remarkable preservation of biomolecules in ancient radish seeds

Desiccated seeds from a 6th century AD storage vessel recovered from Qasr Ibrîm, Egypt, were examined for the presence of lipids and nucleic acids. A remarkable degree of lipid preservation was discovered, the fatty acid and sterol profiles being very similar to those of modern radish seeds. The only significant differences were hydrolysis of triacylglycerols and depletion of the polyunsaturated fatty acids (C18:2 and C18:3). The delta 13 C values of the principal fatty acids were in the range -25.4 to -29.2/1000, which is congruent with modern radish (C3 seeds) taking account of isotopic shifts caused by recent changes in atmospheric CO2. Deoxyribonucleosides and nucleic acid bases were detected by direct chemical analysis, and polymerase chain reactions gave products with sequences comparable to those from modern radish. The degree of lipid preservation, which was much greater than that reported for other archaeological remains, suggests that the microenvironment within desiccated seeds retards biomolecular decay. The results illustrate the utility of combined lipid-nucleic acid analysis in chemotaxonomic and genotypic studies of archaeobotanical remains.

Isolation and sequence analysis of a cDNA encoding the c subunit of a vacuolar-type H(+)-ATPase from the CAM plant Kalanchoë daigremontiana

We report the sequence of a cDNA clone encoding the c ("16 kDa') subunit of a vacuolar-type H(+)-ATPase (V-ATPase) from Kalanchoë daigremontiana, a plant in which the cell vacuole plays a pivotal role in crassulacean acid metabolism. The clone, pKVA211, was isolated from a K. daigremontiana leaf cDNA library constructed in lambda ZAP II using a homologous PCR-generated cDNA probe for the V-ATPase c subunit. The KVA211 cDNA was 839 nucleotides long and included a 20 bp poly(A)+ tail together with a complete 495 bp coding region for a polypeptide with a predicted molecular mass of 16659 Da. The deduced amino acid sequence was highly conserved across the wide range of eukaryotes (vertebrates, invertebrates, fungi, plants and protozoa) in which this gene has now been identified. Sequence comparison of several PCR products and genomic Southern analysis indicated that the V-ATPase c subunit in K. daigremontiana is encoded by a small multi-gene family. Steady-state levels of the KVA211 mRNA were much higher in leaves than in roots or flowers, and expression of this transcript in leaves was shown to be strongly light-dependent.

Oligonucleotides containing 2-aminoadenine and 5-methylcytosine are more effective as primers for PCR amplification than their nonmodified counterparts

Oligonucleotides containing the modified bases 5-methylcytosine and 2-aminoadenine in place of cytosine and adenine, respectively, have higher than normal affinity for complementary sequences The strong binding oligonucleotides (SBO) are much better than their normal counterparts in PCR amplification: they yield significantly more product per cycle, allow amplification at annealing temperatures as high as 72 degrees C and, unlike their normal counterparts, allow efficient priming from within a palindromic sequence. We propose that such strong binding oligonucleotides will be valuable in numerous PCR applications, including: (i) minimization of the frequency of mutants among PCR products; (ii) when only short specific primers can be designed based on available sequence information; (iii) when the material available for the analysis is limited in quantity; and (iv) when primer binding is blocked by DNA secondary structure involving a primer binding site, or chain extension is impeded by secondary structure in downstream sequences.

Amplification of genes, single transcripts and cDNA libraries from one cell and direct sequence analysis of amplified products derived from one molecule

We report a procedure to generate and amplify cDNA libraries and to amplify and sequence genes and single RNA transcript molecules from the same cell without cloning. An absence of cloning steps minimizes potential sources of contamination, which can be especially problematic when working at the single cell level. Potential contamination is further reduced by an absence of any purification step prior to PCR amplification. Amplifications are designed to minimize the production of aberrant molecules in favor of full-length products, which is especially advantageous when generating cDNA libraries. Genes are amplified from isolated single nuclei, which are segregated from cytoplasmic lysates by microcentrifugation. Specific cDNA, total cDNA or both are synthesized from aliquots of the cytoplasmic lysate, and single cDNA molecules are isolated from others of the same species by limiting dilution prior to PCR amplification. In this way, the frequency of amplified products provides for a direct calculation of cDNA copy number by a Poisson analysis. Incorporation errors by Taq DNA polymerase occur at a low frequency and can be eliminated by sequencing independently amplified cDNA molecules from the same cell. Single molecule amplifications provide sufficient material for numerous (approximately 150) direct DNA sequencing reactions. The limiting dilution approach also permits sequence information to be obtained from a single cDNA, when highly related transcripts derived from distinct genes are present in the same cell and simultaneously amplified with the same primers. In sum, this method provides for a maximum amount of nucleic acid information to be extracted from one cell. It has a wide range of applications to studies of the immune system where, to a first approximation, each lymphocyte has a unique receptor identity, where specific states of differentiation may be difficult to assess in a mixed cell population, and where cell immortalization procedures are not always possible nor practical.

Development of a simplified polymerase chain reaction-enzyme immunoassay for the detection of Chlamydia pneumoniae

The 16S rRNA genes of two Chlamydia pneumoniae and two C. psittaci strains of different serovars were sequenced then compared to previously reported Chlamydia 16S rRNA gene sequences. Chlamydia pneumoniae-specific regions were identified and specific primers for nested PCR were synthesized. Nested PCR reactions were performed, in a single tube, by varying the annealing temperature of the amplification cycles. The initial thermal cycles were selected to allow annealing and extension of only the outer primer pair, whilst in later cycles a temperature that allowed inner primer annealing was employed. The inner primers were labelled, one with biotin and the other with fluorescein and consequently the dual labelled amplicon could be immobilized onto antibiotin-coated microtitre plates and detected colorimetrically via an antifluorescein-enzyme conjugate. The assay was found to be sensitive and specific. No cross reactions were observed with C. trachomatis, C. psittaci or other common respiratory pathogens.

Sequence analysis of the DNA binding domain of the estrogen receptor gene in ER (+)/PR (-) breast cancer

Estrogen stimulates the proliferation of breast cancer cells and regulates the expression of other proteins, including the progesterone receptor (PR), via interaction with a unique estrogen receptor (ER), a ligand-inducible transcription factor that binds to regulatory DNA sequences associated with target genes. The best indirect evidence of an intact ER gene signaling system in a tumor is the demonstration of both ER and PR cytosol protein. The molecular basis of the ER (+)/PR (-) phenotype is unknown and may reflect either defective PR gene expression or alterations in the ER-specifically, inability of the ligand-receptor complex to effectively bind to regulatory sequences in DNA. To test the latter possibility, we evaluated 10 ER (+)/PR (-) resected human breast cancers for small deletions and point mutations in the DNA binding domain of the ER gene. Exons 2 and 3 and their flanking intron sequences were selectively amplified using the polymerase chain reaction and then directly sequenced using the Sanger dideoxynucleotide method. A normal gene sequence was found in all cases studied. We conclude that sequence aberrations in the DNA binding domain of the ER are not a common cause of absent PR expression in ER (+)/PR (-) breast carcinomas.

Rapid diagnosis of Mycobacterium tuberculosis bacteremia by PCR

A method based on DNA amplification and hybridization has been used for the rapid detection of Mycobacterium tuberculosis in blood samples from 38 hospitalized patients (15 human immunodeficiency virus [HIV] positive and 23 HIV negative) in whom localized or disseminated forms of tuberculosis were suspected. In 32 of these patients, the diagnosis of tuberculosis was eventually confirmed by conventional bacteriological or histological procedures. M. tuberculosis DNA was detected with the PCR technique in the peripheral blood mononuclear cells from 9 of 11 (82%) HIV-infected patients and in 7 of 21 (33%) HIV-negative patients (P < 0.01), while M. tuberculosis blood cultures were positive in 1 of 8 (12.5%) and 1 of 18 (5.5%) patients, respectively. PCR was positive in all cases with disseminated disease in both HIV-negative and HIV-positive patients and also in the HIV-positive patients with extrapulmonary tuberculosis. Seven samples from patients with documented illness other than tuberculosis and 12 specimens from healthy volunteers, including seven volunteers with a recent positive purified protein derivative test, were used as controls and had a negative PCR. These results suggest that detection of M. tuberculosis DNA in peripheral blood mononuclear cells may be a useful tool for rapid diagnosis of disseminated and extrapulmonary forms of tuberculosis, especially in an HIV-positive population.

The design of strain-specific polymerase chain reactions for discrimination of the racoon rabies virus strain from indigenous rabies viruses of Ontario

Since its recognition as a discrete epizootic in Florida in the early 1950s, the raccoon strain of rabies virus (RV) has spread over almost the entire eastern seaboard of the US and now threatens to enter the southernmost regions of Canada. To characterise this RV strain in more detail, nucleotide sequencing of the N and G genes, encoding the nucleoprotein and glycoprotein, respectively, of representative isolates has been undertaken. This sequence information generated a conserved restriction map of the N gene, thereby permitting unequivocal identification of this strain by molecular techniques. Comparisons of the predicted nucleoprotein and glycoprotein products with those of other RV strains identified a number of amino acid sequence variations conserved only in the raccoon strain. This information was used to design strain-specific primers targeted to the N gene sequences encoding these residues. The incorporation of these primers into a multiplex polymerase chain reaction (PCR) protocol permitted easy and rapid discrimination between the raccoon RV strain and indigenous Ontario RVs.

C-kit ligand (SCF) in human multiple myeloma cells

Here we review our recent experience addressing the role of SCF in multiple myeloma (MM). We first investigated the proliferation of MM cell lines and 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 days 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. 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. These results suggest that an autocrine proliferative loop may be operative in MT3 cell line. When tested on fresh myeloma samples, SCF increased the number of S-phase plasma cells (4.7 +/- 1.6% vs 3.4 +/- 1.3% in control cultures; p = 0.02). Significant proliferation was also induced by IL6, IL-3 and PIXY-321. The addition of SCF significantly enhanced the proliferation of myeloma cells responsive to IL-6. Preliminary experiments performed on circulating plasma cells and myeloma precursors further supported the role of SCF on the proliferation of the neoplastic clone in MM.

Detection of microinjected genes in bovine preimplantation embryos with combined DNA digestion and polymerase chain reaction

We have developed a simple digestion-polymerase chain reaction (PCR) assay for a simultaneous transgene detection and sexing of pronucleus-injected bovine preimplantation embryos. Bovine embryos were microinjected with dam-methylated gene construct and cultured in vitro for 6-7 days after the injections. The developed blastocysts and compact morulae were bisected and the embryonic biopsies representing mainly trophoblasts were subjected to the digestion-PCR, while the biopsied embryos remained in culture. Embryonic DNA was released with proteinase K and the samples were digested with a Dpnl-Bal31 mixture before the PCR amplification of the transgene, bovine alpha S1-casein, and bovine Y-chromosome fragments in the same reaction. The whole assay from biopsy to electrophoresis took less than 6 hr. The digestion removed up to 50 fg of dam-methylated transgene copies (unintegrated or contaminants) and also a few hundred copies of contaminating PCR products from the embryonic samples. The digestion-PCR assay eliminated all transgene contaminations from noninjected blastocysts, which were exposed to the microinjection DNA during the stay in injection chambers, and reduced the amount of transgene-positive embryos among pronucleus-injected blastocysts as compared with unmodified PCR. Analysis of 486 microinjected bovine embryo biopsies in 13 separate experiments revealed that we were able to sex 398 (82%) of the biopsies and 77 (19%) of the biopsies were scored as transgene positive and 57 (14%) as transgene questionable. Upon reanalysis of 41 of the biopsied embryos, 38 (93%) of the embryos were observed to be transgene negative and 2 questionable in both assays and uneven distribution of transgene copies was observed in one embryo. The results from sexing were in accordance with biopsies and remaining embryos in 38 (93%) of the embryos.

Combined PCR-heteroduplex and PCR-SSCP analysis for matching of HLA-A, -B and -C allotypes in marrow transplantation

We describe a method for rapid matching of HLA-A, -B and -C allotypes using simultaneous polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and heteroduplex analysis. Electrophoresis is performed at ambient temperature without requirements for buffer cooling. SSCP and heteroduplexes are revealed as discrete spatially separated band clusters. Using HLA-A, -B and -C locus-specific PCR primers, matching for alleles at these loci can be performed in 5 h. We tested 17 serologically matched patient-unrelated donor pairs and found considerable microheterogeneity at the DNA level. We propose that this technology has several advantages over conventional low-resolution typing methods and represents a potentially valuable screening method in unrelated donor selection.

The polymerase chain reaction: applications for the detection of foodborne pathogens

Faster methods for the detection of foodborne microbial pathogens are needed. The polymerase chain reaction (PCR) can amplify specific segments of DNA and is used to detect and identify bacterial genes responsible for causing diseases in humans. The major features and requirements for the PCR are described along with a number of important variations. A considerable number of PCR-based assays have been developed, but they have been applied most often to clinical and environmental samples and more rarely for the detection of foodborne microorganisms. Much of the difficulty in implementing PCR for the analysis of food samples lies in the problems encountered during the preparation of template DNAs from food matrices; a variety of approaches and considerations are examined. PCR methods developed for the detection and identification of particular bacteria, viruses, and parasites found in foods are described and discussed, and the major features of these reactions are summarized.

Technical report: Part 2. Basic requirements for designing optimal PCR primers

Designing optimal polymerase chain reaction (PCR) primer sequences is one of the critical factors for successful PCR with sensitive, specific, and assay-to-assay reproducible results. In this review, all the requirements of PCR primer sequences are summarized, such as location, size of amplicon, length of primers, nucleotide composition, Tm, 3' terminal hybridization strength and frequency, hairpin formation energy, primer-to-primer interaction, specificity, and location of mismatches to sequences of cross-hybridization. The report also discusses how to explore these various types of information for more advanced PCR applications, which include nested PCR, multiplex PCR, competitive PCR, long PCR, point mutation detection, degenerate primers, and PCR cloning.

Direct hybridization and amplification applications for the diagnosis of infectious diseases

We are entering an exciting new era of molecular diagnostics in the clinical microbiology laboratory. A number of perspectives are presented in this review. First presented was a discussion of molecular diagnostics for detection of the bacterium, Chlamydia trachomatis. This is especially relevant since the tests available for this organism represent the forefront of commercial systems. Also, these tests exemplify the difficulties and advantages inherent to future molecular diagnostics for all types of disease processes. Next, a discussion of the techniques thus far employed in the field of clinical microbiology is presented. Obvious overlap exists with other areas of molecular pathology. However, the emphasis is on which techniques have proven most useful in identifying infectious agents. Finally, the features of a successful clinical microbiology diagnostics laboratory are presented, including test component requirements, laboratory personnel, quality assurance techniques, and physical laboratory setting. It is hoped that helpful advice and references are provided that will assist individual clinical laboratories as they enter the field of molecular diagnostics of infectious diseases.

The effects of nested primer binding sites on the reproducibility of PCR: mathematical modeling and computer simulation studies

The polymerase chain reaction (PCR) has become an indispensable tool in modern biological research. Although the application of PCR is a standard routine, we widely lack a theoretical understanding of the dynamic processes involved, especially with respect to the amplification of nonreproducible and/or unexpected amplification products. For one potential source of uncertainty, the presence of nested primer binding sites within an amplifyable DNA locus, we consider a simple stochastic model for the dynamics of PCR amplification of competing products. For commonly used thermostable DNA polymerases lacking a 5'-3'-exonuclease activity, we predict the relative amplification frequencies of competing PCR products dependent on the primer binding probability, the number of PCR cycles, and the number of initial DNA template molecules. At low primer binding probabilities and low numbers of initial DNA template molecules and PCR cycles, we expect the amplification of two products. At high primer binding probabilities and/or high copy numbers of initial template molecules only one main amplification product is predicted at increasing cycle numbers. Furthermore, by means of computer simulation studies we quantify the stochastic variation for the amplification frequencies of competing products.

Molecular diversity of GABA-gated chloride channels in the rat anterior pituitary

mRNA expression of GABA-gated Cl(-)-channels in rat antepituitary was evaluated by using an reverse-transcribed (RT)-polymerase chain reaction (RT-PCR) method with degenerate and specific oligonucleotides. The main result of our findings is that the antepituitary expresses mRNAs encoding alpha 4 and rho 1 GABA receptor subunits. These two subunits are believed to be, respectively, constituents of benzodiazepine-insensitive GABAA and GABAC receptors in the CNS. This molecular analysis is consistent with the pharmacological diversity of GABA receptors in pituitary cells.

A method for determining the position and size of optimal sequence regions for phylogenetic analysis

The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optimize this kind of study, we suggest a heuristic procedure for detection of the shortest region whose informational content can be considered sufficient for significant phylogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of reference to those obtained for different windows of variable size and position by means of a simple index. We also present an approach for testing whether the informative content in the stretches selected in this way is significantly different from the corresponding content shown by the larger genomic regions used as reference. Application of this test to the analysis of the VP1 protein gene of foot-and-mouth-disease type C virus allowed us to define optimal stretches whose informative content is not significantly different from that displayed by the complete VP1 sequence. We showed that the predictions made for type C sequences are valid for type O sequences, indicating that the results of the procedure are consistent.

PCR and single-strand conformational polymorphism for recognition of medically important opportunistic fungi

The application of PCR technology to molecular diagnostics holds great promise for the early identification of medically important pathogens. PCR has been shown to be useful for the detection of the presence of fungal DNA in both laboratory and clinical samples. Considerable interest has been focused on the utility of selecting universal primers, those that recognize constant regions among most, if not all, medically important fungi. Once an amplicon, or piece of amplified DNA determined by the unique pair of oligonucleotide primers, has been generated, several different methods may be used to distinguish between genera and between species. The two major approaches have utilized differences in restriction enzyme digestion patterns or hybridization with specific probe. We report the application of single-strand conformational polymorphism (SSCP) as a technique to delineate the differences between fungal species and/or genera. Minor sequence variations in small single-stranded DNA cause subtle changes in conformation, allowing these strands to be separated on polyacrylamide gels by SSCP. We used a 197-bp fragment amplified from the 18S rRNA gene, common to all medically important fungi. After amplification, the fragments were denatured and run on an acrylamide-glycerol gel at room temperature or 4 degrees C for 4.5 or 4 h, respectively. Under room temperature conditions, the SSCP patterns for Candida albicans, Candida tropicalis, and Candida parapsilosis were identical and all strains within each species demonstrated the same pattern. These patterns differed markedly from those of the genus Aspergillus. The SSCP patterns of major and minor bands at room temperature permitted distinction between strains of Aspergillus fumigatus and Aspergillus flavus. There also was consistency of the SSCP banding pattern among different strains of the same Aspergillus species. The SSCP patterns for other medically important opportunistic fungi, such as Cryptococcus neoformans, Pseudallescheria boydii, and Rhizopus arrhizus, were sufficiently unique to permit distinction from those of C. albicans and A. fumigatus. We conclude that the technique of PCR-SSCP provides a novel method by which to recognize and distinguish medically important opportunistic fungi and which has potential applications to molecular diagnosis, taxonomic classification, molecular epidemiology, and elucidation of mechanisms of antifungal drug resistance.

HLA-DQB1 and DQA1 matching by ambient temperature PCR-SSCP

We have developed a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) protocol for rapid matching of DQA1 and DQB1 alleles. Electrophoresis can be performed at ambient temperature within the range 18-28 degrees C without continuous gel cooling. The method has been tested on 27 patient-potential bone marrow donor pairs for DQB1 and 31 pairs for DQA1. Bone marrow pairs were chosen to represent a broad range of common alleles based upon previous restriction fragment length polymorphism (RFLP) analysis type assignments. Samples were re-typed by PCR with sequence-specific primers (PCR-SSP) and the results compared to matching by PCR-SSCP analysis. There was a 100% correlation between PCR-SSP and PCR-SSCP analysis for DQB1, and a 97% correlation for DQA1 matching.

Viral serology and detection

Viral detection is an important part of clinical hepatology. For many years practical clinical tests have been serological but recently newer molecular techniques have become available for virus detection, although these have yet to become routine and some, such as PCR of viral nucleic acid in blood or tissue are not yet consistently reliable. Serology remains the mainstay at present for routine diagnosis. Hepatitis A testing in clinical practice is entirely serological, the IgM response representing acute infection and the IgG response immunity, although more sophisticated molecular techniques have been applied experimentally. A second agent of epidemic enteral hepatitis, the hepatitis E virus, has recently been cloned and sequenced and serological tests for this virus are available, although experience in their use is necessarily limited and a commercial IgM assay has yet to be produced. Serological tests for the hepatitis B virus are well developed. The IgM anticore response differentiates acute infection from chronic, the latter being characterized by the persistence of hepatitis B surface antigen for over six months. Chronic carriers are at risk of liver damage and this risk is best assessed by the amount of viral DNA circulating, which can be determined using a hybridization assay. More sensitive techniques such as the branched chain DNA assay or PCR can detect lower levels of viral DNA but their clinical relevance remains to be established. The hepatitis D virus is defective and relies on hepatitis B to replicate. Serology for antibody and antigen is well established although PCR for circulating viral genome may come to supplant hepatic viral antigen as a test for hepatitis D replication. For hepatitis C serology is feasible only for antibodies, not antigens; although early tests were prone both to false positives and false negatives, current versions are more reliable. PCR has been much used for detection of hepatitis C RNA in blood and tissues and a bDNA assay is now commercially available. Cytomegalovirus detection is confounded by the problem of distinguishing asymptomatic viral replication from disease. Serology is helpful, especially in primary infections, but viral culture is a widely used method. PCR (especially quantitative modifications) or the pp65 antigenaemia assay are experimental approaches which may prove specific enough for general use.

Prevention of product carry-over by single tube two-round (ST-2R) PCR: application to BCR-ABL analysis in chronic myelogenous leukemia

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Mycobacterium paratuberculosis DNA not detected in Crohn's disease tissue by fluorescent polymerase chain reaction

The role of mycobacteria in the aetiology of Crohn's disease has been a contentious subject for many years. Mycobacterium paratuberculosis is known to cause a chronic granulomatous enteritis in animals (Johne's disease) and has been implicated as a possible infectious cause of Crohn's disease. However this fastidious organism is only rarely detected by conventional microbiological techniques. This study used oligonucleotide primers to the species-specific M paratuberculosis IS900 DNA insertion element and the polymerase chain reaction to amplify any M paratuberculosis DNA from intestinal tissue DNA extracts. One oligonucleotide primer was fluorochrome-labelled and the presence of fluorescent amplified product was determined using an automated DNA sequencer with a computerised gel-scanning laser. This method was shown capable of detecting 1-2 mycobacterial genomes. Intestinal tissue samples were obtained from 68 patients with histologically confirmed Crohn's disease, 49 patients with histologically confirmed ulcerative colitis, and 26 non-inflammatory bowel disease controls. In no case was M paratuberculosis detected in any of the inflammatory bowel disease tissue samples and only one non-inflammatory bowel disease case was positive. These results do not support the hypothesis that M paratuberculosis has an aetiological role in Crohn's disease.

An infrared fluorescent dATP for labeling DNA

Near-infrared fluorescence provides a nonradioactive method of detection with high sensitivity and low background. An infrared fluorophore has been attached covalently to the nucleotide deoxyadenosine triphosphate (dATP) to provide a reagent for enzymatic labeling of various types of DNA molecules and for facilitating their detection with an automated DNA sequencing and analysis system. DNA sequencing reaction products can be labeled internally by performing limited polymerization utilizing infrared-labeled dATP (IR-dATP) as the sole source of adenine deoxynucleotide prior to a dideoxy-specific termination reaction. PCR products can be labeled fluorescently by the addition of limited quantities of IR-dATP to the amplification reaction. This latter strategy has been utilized for detection of short tandem repeat polymorphisms (STRPs) which are useful for gene mapping, genetic diagnostics, forensic analysis, and paternity testing. Restriction fragments can be labeled also by fill-in reactions of appropriate 5' overhangs. Diminutive amounts of such fluorescently labeled DNA molecules can be visualized rapidly and conveniently using infrared detection technology.

Interleukin-11 (IL-11) acts as a synergistic factor for the proliferation of human myeloid leukaemic cells

Interleukin-11 is a stromal cells derived cytokine which stimulates the proliferation of primitive haemopoietic progenitor cells. For this paper we have studied the constitutive expression of IL-11 mRNA in a panel of wellknown leukaemic cell lines and samples from AML patients at diagnosis. Moreover, the same cellular populations were evaluated for their proliferative response to recombinant-human-(r-hu). IL-11 alone and combined with r-hu-IL-3, granulocyte-macrophage colony stimulating factor (GM-CSF) and stem cell factor (SCF, c-kit ligand). The colony-forming ability of HL60, K562, KG1 cells and eight fresh AML cell populations was assessed by a clonogenic assay in methylcellulose. In eight additional AML cases the number of S-phase leukaemic cells induced by IL-11 was determined by the bromodeoxyuridine (BRDU) incorporation assay after 3d of liquid culture. IL-11, as single cytokine, did not stimulate the colony formation of the three myeloid cell lines under serum-containing and serum-free conditions. In contrast, the proliferation of the leukaemic cells in response to IL-3, GM-CSF and SCF was enhanced by co-incubation with IL-11, and this effect was reversed in blocking experiments by the anti-IL-11 Moab. When tested on primary AML samples, IL-11 alone showed little, if any, proliferative activity. However, it increased the IL-3-dependent blast colony formation in eight out of eight cases and GM-CSF in seven cases. IL-11 also augmented synergistically the number of CFU-L stimulated by SCF in seven cases. A combination of three factors (IL-11, SCF and IL-3) yielded optimal colony formation. The BRDU studies showed the significant increase of AML cells in S-phase when IL-11 was combined with SCF, whereas the two CSF had no activity on their own. Positive interaction was also observed when IL-11 was added to IL-3 supplemented cultures in five out of eight cases tested. Reverse transcriptase-polymerase chain reaction amplification (RT-PCR) demonstrated the constitutive expression of IL-11 mRNA in all the cell lines and 11/12 AML samples studied at diagnosis. These results indicate that IL-11 is expressed in leukaemic myeloid cells and that their proliferation is regulated by the cytokine which acts as a synergistic factor.

Differential gene expression during early murine yolk sac development

The visceral yolk sac (VYS), composed of extraembryonic mesoderm and visceral endoderm, is the initial site of blood cell development and serves important nutritive and absorptive functions. In the mouse, the visceral endoderm becomes a morphologically distinct tissue at the time of implantation (E4.5), while the extraembryonic mesoderm arises during gastrulation (E6.5-8.5). To isolate genes differentially expressed in the developing yolk sac, polymerase chain reaction (PCR) methods were used to construct cDNA from late primitive streak to neural plate stage (E7.5) murine VYS mesoderm and VYS endoderm tissues. Differential screening led to the identification of six VYS mesoderm-enriched clones: ribosomal protein L13a, the heat shock proteins hsc 70 and hsp 86, guanine-nucleotide binding protein-related gene, cellular nucleic acid binding protein, and alpha-enolase. One VYS endoderm-specific cDNA was identified as apolipoprotein C2. In situ hybridization studies confirmed the differential expression of these genes in E7.5 yolk sac tissues. These results indicate that representative cDNA populations can be obtained from small numbers of cells and that PCR methodologies permit the study of gene expression during early mammalian postimplantation development. While all of the mesoderm-enriched genes were ubiquitously expressed in the embryo proper, apolipoprotein C2 expression was confined to the visceral endoderm. These results are consistent with the hypothesis that at E7.5, the yolk sac endoderm provides differentiated liver-like functions, while the newly developing extraembryonic mesoderm is still a largely undifferentiated tissue.

Generation of entire human papillomavirus genomes by long PCR: frequency of errors produced during amplification

Recently, several improvements of traditional PCR techniques have facilitated the amplification of significantly longer DNA target sequences. Here we report an improved method for amplification of entire human papillomavirus (HPV) genomes. Using rTth DNA polymerase, XL (Perkin-Elmer, Foster City CA), and the accompanying XL PCR buffer system, we have successfully amplified 8-kb genomes from approximately 10 copies of input reference strain HPV16 DNA. This long PCR (LPCR) method was subsequently used to amplify the entire HPV16 genome from clinical specimens. The fidelity with which the rTth DNA polymerase XL amplified target sequences under our chosen amplification conditions was estimated by partial sequencing of cloned LPCR products generated from cloned reference strain HPV16 genomes. A region spanning the HPV16 E6, E7, and part of the E1 open reading frames (ORFs) was sequenced in 29 clones. A total of 33 nucleotide substitutions were observed in the 23.5 kb sequenced. This corresponds to an error frequency of approximately one error per 700 bases. Finally, LPCR methods were used to amplify entire, novel HPV genomes from clinical specimens. LPCR primer pairs were designed for amplification of seven potentially novel HPV types. Amplicons of approximately 8 kb were generated from five of the seven HPV types targeted. One of the LPCR-generated novel genomes, CP141, was subsequently cloned and a partial sequence was determined.

Detection of cytomegalovirus using 'boosted' nested PCR

As a part of a study of an outbreak of CMV infections in a neonatal care intensive care unit, a modified nested PCR was developed for detection of CMV DNA in clinical specimens. Standard nested PCR involves a critical step; passage of PCR products from the first reaction round to the second round. We have adapted a 'boosted' nested PCR which implies amplification in one single step, thus reducing the contamination problems. Nasopharyngeal aspirates and urine samples from patients with perinatal CMV infections, breast milk from some of their mothers, amniotic fluids, urine samples and lymphocytes from seropositive healthy adults were examined by PCR and culture. In the total of 614 of clinical specimens, the PCR test yielded positive results in 51 samples from 14 patients, whereas CMV was isolated in 25 samples from 11 cases only. All samples from healthy individuals were negative. CMV DNA was detected in all culture-positive samples, but all samples from healthy adults were negative. 29/68 culture negative specimens were positive by PCR. No cross-reactivity to other herpes viruses or to human DNA was observed. Our findings show a high sensitivity and a high specificity of the 'boosted' nested PCR. We conclude that the described PCR method can be used for the rapid detection of CMV in clinical specimens with a greatly reduced risk of contamination, and it has proved to be a very useful tool in diagnostic work.

Novel actin crosslinker superfamily member identified by a two step degenerate PCR procedure

Actin-crosslinking proteins link F-actin into the bundles and networks that constitute the cytoskeleton. Dystrophin, beta-spectrin, alpha-actinin, ABP-120, ABP-280, and fimbrin share homologous actin-binding domains and comprise an actin crosslinker superfamily. We have identified a novel member of this superfamily (ACF7) using a degenerate primer-mediated PCR strategy that was optimized to resolve less-abundant superfamily sequences. The ACF7 gene is on human chromosome 1 and hybridizes to high molecular weight bands on northern blots. Sequence comparisons argue that ACF7 does not fit into one of the existing families, but represents a new class within the superfamily.

Anti-DNA and anti-platelet specificities of SLE-derived autoantibodies: evidence for CDR2H mutations and CDR3H motifs

Although polyreactivity appears to be a characteristic feature of natural autoantibodies, polyreactive anti-DNA autoantibodies can be derived both from patients with autoimmune disease and from normal individuals. It is unclear whether these autoantibodies differ depending on their origin, but previous studies from our laboratory have suggested that polyreactive systemic lupus erythematosus (SLE)-derived platelet-binding anti-DNA autoantibodies have more restricted antigen reactivity and greater functional activity than normal-derived polyreactive autoantibodies. The objective of the present study was to characterize the VH and VL region sequences of 10 human hybridoma anti-DNA autoantibodies derived from peripheral blood lymphocytes of different origins [SLE, rheumatoid arthritis (RA), or normal] to determine whether there are structural differences between these autoantibodies. We show that although some unmutated germline structures (VH and VL) are represented, these are not restricted to anti-DNA autoantibodies from normal individuals and that two normal-derived anti-DNA antibodies showed quite extensively mutated VH genes. However, these mutations, unlike those found in the CDR2H of several of the SLE-derived antibodies, did not appear to be antigen-selected. Three different amino acid motifs, putatively involved in antigen binding specificity, were observed in the CDR3H segments of some of the autoantibodies. One was the previously described YYGSG motif, which was found in a normal-derived anti-DNA autoantibody, while two new potential motifs were observed only in SLE-derived platelet-binding anti-DNA autoantibodies. These data suggest that antigenic and functional differences between SLE-derived and normal-derived platelet-binding anti-DNA autoantibodies may be due to antigen-selected mutations in the CDR2H and specific amino acid motifs in the CDR3H.

Detection of Pseudomonas (Burkholderia) cepacia using PCR

Pseudomonas cepacia colonization of the lung is associated with increased morbidity and mortality for cystic fibrosis (CF) patients. The lack of a sensitive detection method for Pseudomonas cepacia in CF sputum has resulted in controversy regarding its epidemiology. We designed a PCR method to detect P. cepacia using P. cepacia 16 S rRNA sequences as the amplification target region. The PCR amplification with purified DNA as template yielded the expected 209-bp products from P. cepacia, but not from related Pseudomonas species of medical importance or other bacteria which have been reported to colonize CF patients. In serial dilution experiments as few as 10(2) P. cepacia CFU were detectable. When sputum samples from three CF patients chronically colonized with P. cepacia and P. aeruginosa were analyzed, P. cepacia was detected in all three specimens by PCR, but only in two when selective culture was performed. Our data support the potential role of PCR technology in the rapid, sensitive, and definitive detection of P. cepacia in CF sputum samples, even in the context of concomitant P. aeruginosa colonization.

The diagnosis of congenital infections: contemporary strategies

Congenital infections remain an important source of neurologic, ophthalmologic, and audiologic disability for thousands of children throughout the world. This review summarizes the clinical features and describes contemporary approaches to the microbiologic diagnosis of congenital infections. In particular, this review emphasizes the important roles that molecular methods, especially the polymerase chain reaction, have in detecting the many infectious agents capable of damaging the developing nervous system.

Fractal dimension of error sequence dynamics in quantitative modeling of syntheses of short oligonucleotide and single-stranded DNA sequences

Oligonucleotides are becoming more and more important in molecular biomedicine; for example, they are used as defined primers in polymerase chain reaction and as antisense oligonucleotides in gene therapy. In this paper, we model the dynamics of polymer-supported oligonucleotide synthesis to an inverse power law of driven multi-cycle synthesis on fixed starting sites. The mathematical model is employed by presenting the accompanying view of error sequences dynamics. This model is a practical one, and is applicable beyond oligonucleotide synthesis to dynamics of biological diversity. Computer simulations show that the polymer support synthesis of oligonucleotides and single-stranded DNA sequences in iterated cyclic format can be assumed as scale-invariant. This synthesis is quantitatively described by nonlinear equations. From these the fractal dimension Da (N,d) is derived as the growth term (N = number of target nucleotides, d = coupling probability function). Da(N,d) is directly measurable from oligonucleotide yields via high-performance liquid chromatography or capillary electrophoresis, and quantitative gel electrophoresis. Different oligonucleotide syntheses, including those with large-scale products can be directly compared with regard to error sequences dynamics. In addition, for short sequences the fractal dimension Da (N,d) is characteristic for the efficiency with which a polymer support of a given load allows oligonucleotide chain growth. We analyze the results of separations of crude oligonucleotide product from the synthesis of a 30 mer. Preliminary analysis of a 238 mer single-stranded DNA sequence is consistent with a simulated estimate of crude synthesis product, although the target sequence itself is not detectable. We characterize the oligonucleotide support syntheses by simulated and experimentally determined values of the fractal dimension Da (N,d0) within limitations (d0 = constant (average) coupling probability).

Topographical characterization of the DNA polymerase from Thermus aquaticus. Defining groups of inhibitor mAbs by epitope mapping and functional analysis using surface plasmon resonance

Among 24 unique monoclonal antibodies (mAb) generated against Taq polymerase (TaqPol) 13 are potent inhibitors of polymerase activity. These antibodies have been sorted into groups defined by their topographical or functional properties using surface plasmon resonance-based methods to examine three different types of interactions. An epitope map of all the pairwise interactions among all 24 antiTaqPol antibodies revealed the surface of TaqPol as a complex space populated by isolated antigenic domains with no evident relationship to each other. 11 discrete epitopes or epitope clusters were defined and potent inhibitors bound to sites within seven of them. The second method examined the ability of antiTaqPol mAbs to bind to recombinant forms of the constituent functional domains of TaqPol, the N-terminal 5'-nuclease domain and the C-terminal polymerase domain. Most of the antibodies demonstrated a clear specificity for one domain or the other. The third method measured the ability of each mAb to block the interaction of TaqPol with a preformed, immobilized primer:template complex (PTC). Some antibodies had no effect on this interaction while others effectively blocked it. Together these latter two methods resolved many of the antibodies into five distinct groups. In addition, antibodies that bound to overlapping epitopes in the pairwise interaction analysis were members of the same group by their interaction with the polymerase fragment and PTC. Three groups of polymerase inhibitors were clearly resolved by these analyses: (1) those that recognize an epitope on the 5'-nuclease domain and have no effect on the interaction of TaqPol with PTC; (2) those that recognize an epitope on the polymerase domain and block the interaction of TaqPol and PTC; and (3) those that recognize an epitope on the polymerase domain, but have no effect on the interaction of TaqPol with PTC. The surface of TaqPol bears at least three antigenic regions that are topographically and functionally distinct and may correspond to sites for inhibition of different steps in the enzymatic activity of TaqPol.

Sequence identity of the n-1 product of a synthetic oligonucleotide

After synthesis and purification of an oligonucleotide, the final product usually contains a low level of n-1 congeneric species. We have sequenced the n-1 population of a 25mer phosphodiester oligonucleotide. The n-1 band was cut from the gel and eluted. Oligonucleotides were tailed with dA and annealed to a dT-tailed plasmid. The recombinant plasmid was ligated and used to transform competent bacteria. Our results show that the n-1 population was heterogeneous. The frequency of truncated nucleotides at the 3'-end was much higher than at the 5'-end of the oligomer. No truncated nucleotides were found in the last four nucleotides at the 5'-end. Our results also show that the chain of oligonucleotides can grow on unreacted sites of a controlled-pore glass support.

Application of dual internal standards for precise sizing of polymerase chain reaction products using capillary electrophoresis

Capillary electrophoresis (CE) is an analytical technique which provides rapid, high resolution analysis of amplified DNA fragments produced by the polymerase chain reaction (PCR). In this study, two internal standards are used as size markers to bracket und precisely size PCR products. The technique is applied to typing PCR products from the short tandem repeat locus HUMTH01. HUMTH01 consists of five to seven major alleles in the size range of 179-203 bp, with each allele four bp apart. Using this genetic marker, a population containing 97 individuals was examined with both polyacrylamide gel electrophoresis and CE. Identical genotypes were obtained with both techniques demonstrating the reliability of CE in DNA typing applications. The DNA analysis took place in sets of 10 with a calibration of the CE being performed between each set of samples. For the 97 samples examined, the pooled standard deviation was 0.3 bp. The observed genotype frequencies determined from the sample set did not deviate significantly from Hardy-Weinberg expectations. From these CE results, we conclude that HUMTH01 PCR products can be accurately and precisely sized by capillary electrophoresis using the method described.

CMV-DNA detection in parenchymatous organs in cases of SIDS

A nested PCR approach has been developed especially for the detection of small amounts of cytomegalovirus (CMV) DNA in autopsy samples. Lung tissue and submandibular glands in 118 cases of infant death (92 SIDS cases, 13 natural deaths due to other defined causes and 13 unnatural deaths) were investigated by this technique and compared to the results obtained by other CMV detection methods (histology, immunohistochemistry, in situ hybridization and PCR). CMV-DNA could be detected in the lung tissue in 7 cases of SIDS using nested PCR. Compared to conventional PCR (3 positive cases in lung tissue) the nested approach always gave glear results and showed less additional bands. In all cases where CMV could be detected in the lungs, positive results were also obtained in the submandibular glands. The nested PCR method proved to be a more sensitive technique than the other detection methods including PCR and hot start, and even minimal amounts of target DNA could be detected in the presence of human and bacterial background DNA.

Characterization of a gene coding for a type IIo bacterial IgG-binding protein

Two antigenic classes of non-immune IgG-binding proteins can be expressed by group A streptococci. One antigenic group of proteins is recognized by an antibody prepared against the product of a cloned fcrA gene (anti-FcRA). In this study, the immunogen used to prepare the antibody that defines the second antigenic class was shown to be the product of the emm-like (emmL) gene of M serotype 55 group A isolate, A928. The emmL55 gene expressed in E. coli produced an M(r) approximately 58,000 molecule which bound human IgG1, IgG2, IgG3 and IgG4, as well as horse, rabbit and pig IgG in a non-immune fashion. These properties are characteristic of the previously described type IIo IgG-binding protein isolated from this strain. In addition, the recombinant protein was reactive with human serum albumin and fibrinogen. The emmL 55 gene sequence was analysed and found to have the organization and sequence characteristics of a typical class I emm-like gene.

A single tube nested PCR for the detection of hepatitis C virus RNA

An assay was developed for the detection of hepatitis C virus RNA in serum which combined cDNA synthesis and a hot start nested polymerase chain reaction (PCR) in a single tube. This was made possible by separation of the reagents necessary for cDNA synthesis and PCR during cDNA synthesis with a high melting temperature wax interface and by the use of 'drop in-drop out' nested primers which enabled each primer set to be selectively extended within the same reaction tube. The increase in sensitivity following amplification with the internal primer pair was comparable to that achieved when nested reactions are carried out separately.

A quantitative assay for IGF-I and IGF binding protein mRNAs: expression in malignant melanoma cells

The quantification of messenger RNA is central in studies of gene expression. We describe a quantitative assay for specific mRNAs (QASM) that measures mRNAs for insulin-like growth factor-I, IGF binding proteins (IGFBPs) -2, -3, -4, and -5, and beta-actin. The assay utilizes reverse transcription and polymerase chain reaction, followed by an ELISA based DNA assay technique. The use of internal (competitive) quantification standards gave poorly linear results, while external standards gave linear and reproducible results. QASM results correlated with IGFBP protein concentrations in conditioned medium and with mRNA levels determined by Northern blotting. QASM was used to study IGFBP expression in human malignant melanoma cells. Messenger RNA for IGFBP-2, -3, and -5 were present, while IGF-I and IGFBP-4 mRNAs were not detected. IGFBP-2 and -3 expression was increased in a dose dependent manner by treatment with IGF-I. Protein concentrations in conditioned media paralleled mRNA levels. QASM is a sensitive, specific, and reproducible approach to determining mRNA levels.

Early diagnosis and monitoring of human cytomegalovirus pneumonia in patients with adult T-cell leukemia by DNA amplification in serum

A nested polymerase chain reaction (PCR) was used to detect human cytomegalovirus (HCMV) DNA in serum of patients with adult T-cell leukemia (ATL). Serum samples were collected consecutively from 11 patients with HCMV pneumonia diagnosed histopathologically and 7 HCMV-seropositive patients without HCMV disease. Serum samples obtained from 24 HCMV-seropositive healthy volunteers were used as controls. The HCMV DNA was detected in serum a mean of 14 days before the onset of HCMV pneumonia, which suggests that DNAemia exists prior to the development of HCMV pneumonia. The amount of viral DNA in serum increased with disease progression and decreased with disease improvement. Thus, the detection of HCMV DNA in serum by nested PCR is useful for monitoring and the early diagnosis of HCMV pneumonia in patients with ATL. In addition, quantitation of HCMV DNA may be useful for monitoring HCMV infection, because it appears to correlate with the activity of the disease.