The polymerase chain reaction

Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen

Rapid turnover of nonsense-containing mRNAs in yeast in dependent on the product of the UPF1 gene (Upf1p). Mutations in UPF1 lead to the selective stabilization of mRNAs containing early nonsense mutations without affecting the decay rates of most other mRNAs. To identify other integral components of this decay pathway, we have employed a two-hybrid screen, seeking those cellular factors that specifically interact with Upf1p. Screening of yeast genomic libraries identified six genes encoding potential Upf1p-interacting proteins. These include four previously uncharacterized genes, NMD1-4 (nonsense-mediated mRNA decay), DBP2, a gene encoding a putative RNA helicase with homology to mammalian p68 RNA helicase, and SNP1, a gene encoding a U1 snRNP 70-kD protein homolog. In this paper we report the identification and characterization of NMD2, a yeast gene that encodes a specific Upf1p-interacting protein. Disruption of NMD2 yields a nonsense-mediated mRNA decay phenotype identical to that obtained in UPF1-deletion strains, indicating that the NMD2 gene product (Nmd2p) is a new factor in the nonsense-mediated mRNA decay pathway. Deletion analysis demonstrated that the acidic carboxyl terminus of Nmd2p constituted the Upf1p-interacting domain. High-level expression of a fragment of Nmd2p containing this domain had a dominant-negative effect on nonsense-mediated mRNA decay when the protein was localized the cytoplasm but not when it was localized to the nucleus, indicating that this decay pathway has a cytoplasmic component. The association of a dominant-negative phenotype with a gene fragment identified in a two-hybrid screen suggests a generalized approach to confirming the function of genes identified in such screens.

The polymerase chain reaction and branching processes

We construct a mathematical model for the polymerase chain reaction and its mutations using the theory of branching processes. Under this model we study the number of mutations in a randomly chosen sequence after n PCR cycles. A method for estimating the mutation is proposed and the variance of this estimator is studied. We also study the distribution of the Hamming distance between two randomly chosen sequences and a method for estimating the mutation rate based on pairwise differences is proposed.

A scheme for sequencing large DNA molecules by identifying local nuclear-induced effects

An experimental scheme for sequencing large DNA molecules is proposed where DNA strands are replicated, with all nucleotides of a given kind marked with radioactive 32P. The marked strands are affixed to an appropriate substrate and are kept until most 32P atoms decay. The local damage caused by the decay is expected to allow the identification of the sites occupied by that particular nucleotide, using atomic scale microscopy (scanning tunneling or atomic force microscopy). Quantitative aspects and methodological considerations associated with the proposed scheme are discussed.

Unusual mitochondrial DNA polymorphism in two local populations of blue tit Parus caeruleus

Mitochondrial DNA (mtDNA) from 25 blue tits Parus caeruleus sampled from two populations of the Grenoble region (France) was assayed for polymorphism with 17 restriction endonucleases. Nine genotypes were found. Several mtDNA genotypes were also analysed by amplification via the polymerase chain reaction (PCR) and direct sequencing of 903 bp of the cytochrome b gene. The mtDNA polymorphism is greater in P. caeruleus than in other comparable bird species and results from the presence of two clearly differentiated mitochondrial lineages. Using the data of restriction polymorphism, the mean sequence divergence between individuals of the two lineages is 1.23%. Therefore, P. caeruleus should fall into the category II of phylogeographic pattern sensu Avise et al. (1987): discontinuous mtDNA genotypes which co-occur in the same region. P. caeruleus, like humans and other mobile species with high gene flow, seems to have lost its geographic structure in terms of mtDNA phylogeny. This unusual mitochondrial polymorphism can be explained by the recent admixture of two long-term isolated populations. This could be accounted for by two different scenarios. One assumes a simultaneous post-glacial colonization of the Grenoble region by two isolated European populations of P. caeruleus. Alternatively, hybridization between P. caeruleus and P. cyanus could have caused the observed pattern of mtDNA variation.

DNA fingerprinting of medically important microorganisms by use of PCR

Selected segments of any DNA molecule can be amplified exponentially by PCR. This technique provides a powerful tool to detect and identify minimal numbers of microorganisms. PCR is applicable both in diagnosis and in epidemiology. By amplification of hypervariable DNA domains, differences can be detected even among closely related strains. PCR fingerprinting is a valuable tool for medical microbiologists, epidemiologists, and microbial taxonomists. The current state of PCR-mediated genotyping is reviewed, and a comparison with conventional molecular typing methods is included. Because of its speed and versatility, PCR fingerprinting will play an important role in microbial genetics, epidemiology, and systematics.

Analysis of type II polyketide beta-ketoacyl synthase specificity in Streptomyces coelicolor A3(2) by trans complementation of actinorhodin synthase mutants

Complementation of defined actinorhodin beta-ketoacyl synthase (KS) mutants by various other KS genes suggested that the ORF1-encoded KS may be relatively generalized in function, whereas the ORF2-encoded KS component may provide specificity in polyketide chain construction. Evidence for differential temporal-spatial expression of the actinorhodin and spore pigment KSs in Streptomyces coelicolor was obtained.

Polymerase chain reaction: basic concepts and clinical applications in dermatology

The polymerase chain reaction (PCR) has been extensively used in basic science research, and the clinical potential of PCR is only now beginning to be realized. The PCR is based on the fundamental DNA replication process that occurs in every living cell. PCR is essentially an in vitro adaptation of the in vivo DNA copying process. Because PCR is so efficient at amplifying even picogram quantities of DNA, contamination with even trace amounts of nucleic acids can lead to the generation of unwanted DNA sequences and false-positive test results. Despite this, there has been rapid growth in the use of PCR in biomedical research and clinical diagnostics. PCR is the most sensitive test for herpes simplex virus, varicella-zoster virus, and human papillomavirus infections. Other diagnostic uses, including tests for genetic diseases, cancers, and other infectious diseases, are evolving.

Regulation of the human cardiac/slow-twitch troponin C gene by multiple, cooperative, cell-type-specific, and MyoD-responsive elements

The cardiac troponin C (cTnC) gene produces identical transcripts in slow-twitch skeletal muscle and in heart muscle (R. Gahlmann, R. Wade, P. Gunning, and L. Kedes, J. Mol. Biol. 201:379-391, 1988). A separate gene encodes the fast-twitch skeletal muscle troponin C and is not expressed in heart muscle. We have used transient transfection to characterize the regulatory elements responsible for skeletal and cardiac cell-type-specific expression of the human cTnC (HcTnC) gene. At least four separate elements cooperate to confer tissue-specific expression of this gene in differentiated myotubes; a basal promoter (between -61 and -13) augments transcription 9-fold, upstream major regulatory sequences (between -68 and -142 and between -1319 and -4500) augment transcription as much as 39-fold, and at least two enhancer-like elements in the first intron (between +58 and +1028 and between +1029 and +1523) independently augment transcription 4- to 5-fold. These enhancers in the first intron increase myotube-specific chloramphenicol acetyltransferase activity when linked to their own promoter elements or to the heterologous simian virus 40 promoter, and the effects are multiplicative rather than additive. Each of the major myotube regulatory regions is capable of responding directly or indirectly to the myogenic determination factor, MyoD.A MyoD expression vector in 10T1/2 cells induced constructs carrying either the upstream HcTnC promoter elements or the first intron of the gene 300- to 500-fold. Expression was inhibited by cotransfection with Id, a negative regulator of basic helix-loop-helix transcription factors. The basal promoter contains five tandem TGGGC repeats that interact with Sp1 or an Sp1-like factor in nuclear extracts. Mutational analysis of this element demonstrated that two of the five repeat sequences were sufficient to support basal level muscle cell-specific transcription. Whereas the basal promoter is also critical for expression in cardiac myocytes, the elements upstream of -67 appear to play little or no role. Major augmentation of expression in cardiomyocytes is also provided by sequences in the first intron, but these are upstream (between +58 and +1028). The downstream segment of the first intron has no enhancer activity in cardiomyocytes. A specific DNA-protein complex is formed by this C2 cell enhancer with extracts from C2 cells but not cardiomyocytes. These observations suggest that tissue-specific expression of the HcTnC gene is cooperatively regulated by the complex interactions of multiple regulatory elements and that different elements are used to regulate expression in myogenic and cardiac cells.

Regulation of the human cardiac/slow-twitch troponin C gene by multiple, cooperative, cell-type-specific, and MyoD-responsive elements

The cardiac troponin C (cTnC) gene produces identical transcripts in slow-twitch skeletal muscle and in heart muscle (R. Gahlmann, R. Wade, P. Gunning, and L. Kedes, J. Mol. Biol. 201:379-391, 1988). A separate gene encodes the fast-twitch skeletal muscle troponin C and is not expressed in heart muscle. We have used transient transfection to characterize the regulatory elements responsible for skeletal and cardiac cell-type-specific expression of the human cTnC (HcTnC) gene. At least four separate elements cooperate to confer tissue-specific expression of this gene in differentiated myotubes; a basal promoter (between -61 and -13) augments transcription 9-fold, upstream major regulatory sequences (between -68 and -142 and between -1319 and -4500) augment transcription as much as 39-fold, and at least two enhancer-like elements in the first intron (between +58 and +1028 and between +1029 and +1523) independently augment transcription 4- to 5-fold. These enhancers in the first intron increase myotube-specific chloramphenicol acetyltransferase activity when linked to their own promoter elements or to the heterologous simian virus 40 promoter, and the effects are multiplicative rather than additive. Each of the major myotube regulatory regions is capable of responding directly or indirectly to the myogenic determination factor, MyoD.A MyoD expression vector in 10T1/2 cells induced constructs carrying either the upstream HcTnC promoter elements or the first intron of the gene 300- to 500-fold. Expression was inhibited by cotransfection with Id, a negative regulator of basic helix-loop-helix transcription factors. The basal promoter contains five tandem TGGGC repeats that interact with Sp1 or an Sp1-like factor in nuclear extracts. Mutational analysis of this element demonstrated that two of the five repeat sequences were sufficient to support basal level muscle cell-specific transcription. Whereas the basal promoter is also critical for expression in cardiac myocytes, the elements upstream of -67 appear to play little or no role. Major augmentation of expression in cardiomyocytes is also provided by sequences in the first intron, but these are upstream (between +58 and +1028). The downstream segment of the first intron has no enhancer activity in cardiomyocytes. A specific DNA-protein complex is formed by this C2 cell enhancer with extracts from C2 cells but not cardiomyocytes. These observations suggest that tissue-specific expression of the HcTnC gene is cooperatively regulated by the complex interactions of multiple regulatory elements and that different elements are used to regulate expression in myogenic and cardiac cells.

Retrospective DNA analysis using fixed tissue specimens

The recent explosion of scientific and technical knowledge in the field of molecular biology has allowed us to make important advances in our understanding of the molecular basis of many human diseases. This technology has now entered the clinical laboratory where identification of specific genetic sequences can aid in the precise diagnosis of hematologic and other malignancies, inherited diseases, specific infectious agents, and inherited predisposition to disease. In addition, it can be applied to prenatal diagnosis, paternity testing, identification of minimal residual disease following treatment, and assessment of drug sensitivity or resistance. In many cases in diagnostic pathology, the need for molecular analysis often is not realized until after a critical tissue specimen has been fixed, embedded, and examined microscopically. Thus, there is a clear need for development of techniques that would allow the retrospective study of archival tissues that have been fixed and embedded in paraffin. This review examines in depth those factors which influence the quality of the DNA available from fixed embedded tissues and discusses the usefulness of polymerase chain reaction amplification in obtaining sufficient diagnostically useful DNA from archival specimens. It is hoped that this review will aid the diagnostic pathologist interested in the application of molecular techniques in the retrospective study of fixed embedded tissues.

The polymerase chain reaction: a tool for molecular medicine

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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.

The expression of B-50/GAP-43 in Schwann cells is upregulated in degenerating peripheral nerve stumps following nerve injury

We have detected mRNA for B-50 (GAP-43, pp46, F1, neuromodulin), which was originally believed to be a neuron-specific protein, in non-neuronal cells in the rat sciatic nerve. In control rats, the level of B-50 mRNA in sciatic nerve tissue was much lower than in dorsal root ganglia. Following nerve crush or transection, the expression of B-50 mRNA in the distal nerve stump increased dramatically between 1 and 2 days post-injury. The B-50 mRNA levels in the distal stump of crushed nerves remained elevated for up to 4 weeks and subsequently returned to control levels after 7 weeks. In contrast, after nerve transection B-50 mRNA levels in the distal nerve portion continued to increase up to 7 weeks post-lesion. No changes in the levels of the B-50 transcript were observed in the proximal portion of either crush-lesioned or transected sciatic nerves. In situ hybridization demonstrated B-50 mRNA associated with Schwann cells in the distal nerve stump. The observation that Schwann cells are capable of producing B-50 mRNA was confirmed by Northern blot analysis of total RNA isolated from primary Schwann cell cultures. Taken together, these data show the expression of B-50 mRNA by Schwann cells and the up-regulation of B-50 mRNA in reactive Schwann cells upon loss of axonal contact.

Deletion screening of Sri Lankan Duchenne muscular dystrophy patients using the polymerase chain reaction

Duchenne muscular dystrophy (DMD) is an X-chromosome-linked myopathy caused by a defect in the DMD gene. Intragenic deletions appear to be the most common gene defect leading to DMD, and the deletion frequency has been estimated to be 66%. Results of this study using a group of 24 DMD patients of Sri Lankan origin employing the technique of multiplex DNA amplification using the polymerase chain reaction indicated a deletion frequency of 62.5%. Eighty per cent of these deletions were localized in a region of the DMD gene regarded as a 'hot spot' for DMD deletions. Our results are in agreement with the results of other studies carried out on Caucasian populations.

Amplification of protein expression in a cell free system

Large quantities of a catalytically active protein have been produced in a cell free system. More than 10(9) copies of protein were produced from each DNA plasmid containing DNAfol, the bacterial gene encoding dihydrofolate reductase (DHFR). The strategy employed, denoted gene amplification with transcription/translation (GATT), involves sequential coupling of (i) DNA amplification by the polymerase chain reaction (PCR) and (ii) in vitro RNA transcription by T7 RNA polymerase, followed by (iii) translation of the run-off transcripts in a rabbit reticulocyte system. The protein product had the expected size (18 kDa) and catalyzed the NADPH-dependent reduction of 7,8-dihydrofolic acid to 5,6,7,8-tetrahydrofolic acid as efficiently as authentic DHFR. Potential applications of the strategy include large scale production of enzymes containing synthetic amino acids and facilitation of the characterization of the function of genes encountered in genomic mapping studies.

Simultaneous amplification and detection of specific DNA sequences

We have enhanced the polymerase chain reaction (PCR) such that specific DNA sequences can be detected without opening the reaction tube. This enhancement requires the addition of ethidium bromide (EtBr) to a PCR. Since the fluorescence of EtBr increases in the presence of double-stranded (ds) DNA an increase in fluorescence in such a PCR indicates a positive amplification, which can be easily monitored externally. In fact, amplification can be continuously monitored in order to follow its progress. The ability to simultaneously amplify specific DNA sequences and detect the product of the amplification both simplifies and improves PCR and may facilitate its automation and more widespread use in the clinic or in other situations requiring high sample throughput.

Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates

An antigen detection system, termed immuno-polymerase chain reaction (immuno-PCR), was developed in which a specific DNA molecule is used as the marker. A streptavidin-protein A chimera that possesses tight and specific binding affinity both for biotin and immunoglobulin G was used to attach a biotinylated DNA specifically to antigen-monoclonal antibody complexes that had been immobilized on microtiter plate wells. Then, a segment of the attached DNA was amplified by PCR. Analysis of the PCR products by agarose gel electrophoresis after staining with ethidium bromide allowed as few as 580 antigen molecules (9.6 x 10(-22) moles) to be readily and reproducibly detected. Direct comparison with enzyme-linked immunosorbent assay with the use of a chimera-alkaline phosphatase conjugate demonstrates that enhancement (approximately x 10(5)) in detection sensitivity was obtained with the use of immuno-PCR. Given the enormous amplification capability and specificity of PCR, this immuno-PCR technology has a sensitivity greater than any existing antigen detection system and, in principle, could be applied to the detection of single antigen molecules.

Epstein-Barr virus DNA recombines via latent origin of replication with the human genome in the lymphoblastoid cell line RGN1

We show here that in a lymphoblastoid cell line Epstein-Barr virus DNA recombines with the human genome. The genetic exchange involves the oriP region of the virus. A junction between viral and human DNA from this line has been cloned and sequenced. The results indicate that the integration of Epstein-Barr virus DNA involves a region of the human genome which contains internal short repetition. An 800-bp probe has been isolated from the human part of the junction. This probe has been used to show that the human region exists as a duplication in normal cells.

The use of radioactively labelled riboprobes for in situ hybridization: background and examples of application

An overview is provided concerning the preparation and use of radiolabelled single-stranded RNA probes (riboprobes) for in situ hybridization. All theoretical aspects are covered as well as some practical examples from the authors' experience. The use of riboprobes for in situ hybridization represents a valid and highly sensitive alternative to oligonucleotide probes. A sample protocol is finally described in detail: this should enable any investigators to design the ISH assay that best fits their particular needs.

Mammalian phylogeny: shaking the tree

Recent palaeontological discoveries and the correspondence between molecular and morphological results provide fresh insight on the deep structure of mammalian phylogeny. This new wave of research, however, has yet to resolve some important issues.

Transcription stimulation of the adenovirus type-12 E1a gene in vitro by a novel factor bound to a region adjacent to a TATA box

The E1a gene of adenovirus (Ad) type-12 possesses two transcription start points (tsp) separated by 139 nucleotides (nt). We previously found that transcription from a tsp distal to the coding region is preferentially stimulated in a cell-free reaction by nuclear factor I (NF-I) bound to a region near the left end of the virus genome. We report here on the identification of a cis-acting DNA region and a trans-acting factor for transcription initiated at the proximal tsp of the Ad12 E1a gene. A deletion in the region between nt -50 and -36 relative to the proximal tsp at +1 caused a significant decrease in the proximal transcription in a cell-free reaction using nuclear extracts of HeLa cells. A cellular factor binding to this region was shown to be responsible for transcription stimulation. This E1A-stimulating factor (ESF-1) appeared to recognize the sequence 5'-TGTCA-3' located immediately upstream from a TATA box. Unlike NF-I, the ESF-1 activity did not seem to be influenced by the E1A protein. Our results indicated that ESF-1 stimulates the proximal transcription of the Ad12 E1a gene by binding to the region adjacent to a TATA box.

The molecular genetic analysis of gene rearrangements in acute lymphoblastic leukaemia

In ALL the majority of cases possess clonal rearrangements of the Ig or TCR gene loci. Detection of these clonal markers by Southern blot analysis over a disease course has provided information on the fate and origin of leukaemic clones during treatment. Detection of these gene rearrangements has been used to detect residual disease during treatment. More recently, methods have been developed for the detection of Ig and TCR gene rearrangements using the polymerase chain reaction (PCR). This amplification technique allows for the rapid detection of gene rearrangements with a greater sensitivity than more conventional methods. The full impact and usefulness of this technique in residual disease detection has yet to be determined. The presence of the Philadelphia chromosome t(9;22) in ALL is associated with poor prognosis. Its detection by Southern blot is technically complicated due to the heterogeneity of chromosome breakpoints involved. The development of PCR-based methods for the detection of the bcr/abl mRNA associated with the Philadelphia chromosome has improved our understanding of the significance and incidence of this disease marker in ALL, emphasizing the importance of establishing Philadelphia status on all patients at diagnosis. Although longitudinal studies in CML have shown the presence of bcr/abl mRNA to be associated with residual disease, and its absence associated with long-term remission, these studies have yet to be reported for ALL. The usefulness of detection of residual disease using bcr/abl has yet to be determined.

Chicken poly(ADP-ribose) synthetase: complete deduced amino acid sequence and comparison with mammalian enzyme sequences

The complete nucleotide (nt) sequence of the cDNA encoding the chicken poly(ADP-ribose) synthetase has been determined. Positive clones overlapping the 5' region or the 3' region of the cDNA have been isolated from a lambda gt 10 hen oviduct cDNA library using two human cDNA probes. The missing middle portion has been obtained by the polymerase chain reaction procedure. A single 3033-nt open reading frame from start codon to stop codon encodes a sequence of 1011 amino acid residues. The alignment of this sequence with those from human and mouse reveals overall identities of 79% and 77%, respectively. However, an identity of about 82% is obtained in the DNA-binding domain within the two zinc fingers, and an even higher similarity (85-87%) is observed in the NAD-binding domain. The isolated clones consistently hybridize on chicken Northern blots to an mRNA species of about 4 kb, whereas they do not cross-hybridize with RNA blots of Drosophila melanogaster. Thus, it appears that, even if the functional properties of the enzyme are maintained, the cDNA identity will be much decreased in nonvertebrate organisms.

The digoxigenin:anti-digoxigenin (DIG) technology--a survey on the concept and realization of a novel bioanalytical indicator system

A review is given on the novel non-radioactive digoxigenin:anti-digoxigenin (DIG) bioanalytical indicator system. After a general introduction on direct and indirect indicator systems based on previous non-radioactive indicator reactions as well as in vitro and in vivo amplification procedures the principle of the new digoxigenin:anti-digoxigenin technology is demonstrated. The novel system is based on the specific high-affinity interaction between the cardenolide digoxigenin from Digitalis plants and a digoxigenin-specific antibody coupled with a reporter group. A variety of methods for digoxigenin modification of nucleic acids, proteins and glycans are presented. In addition, various applications of the novel non-radioactive indicator system in a variety of direct or indirect detection approaches with either insoluble or soluble substrates are described. It is also shown that with these applications alternative reaction formats are used which are partly characterized by additional amplification steps.

The polymerase chain reaction and related techniques

The polymerase chain reaction, and other methods for rapidly amplifying DNA or RNA are versatile tools that can be used in diverse applications that include HLA typing, analyzing the T-cell repertoire, constructing chimaeric antibodies and quantifying cytokine expression. The sensitivity of the polymerase chain reaction has allowed many cellular events to be investigated in vitro and in vivo. Many currently emerging adaptions of the basic technique are of interest to both the research and the clinical immunologist.

Highly polymorphic domains of the human serum amyloid A (SAA) gene GSAA1

The DNA of the human serum amyloid A (SAA) gene GSAA1 contains several repetitive regions within its introns. We have studied length variations at one such region in the 2nd intron by selective amplification using the polymerase chain reaction (PCR) and defined oligonucleotide primers. The lengths of the repetitive regions frequently differ between individual chromosomes and can be transmitted as Mendelian markers, making them useful for genetic linkage analysis.

The polymerase chain reaction

In a short time the PCR techniques has revolutionized research technology in many areas of medicine. Because of the ease and rapidity of the technique it is quickly becoming a standard clinical test for many diseases. Clinical applications continue to emerge from research labs and should rapidly expand to facilitate rapid medical diagnosis.

Toward a unified approach to genetic mapping of eukaryotes based on sequence tagged microsatellite sites

The genomes of all eukaryotes appear to contain a special class of loci, termed microsatellites, which can serve, if sequenced and taken as the substrate for the polymerase chain reaction, as highly informative, locus-specific markers. By analogy to the "sequence tagged sites" recently proposed by Olsen et al. for standardizing the human physical gene map, these microsatellite markers are termed "sequence tagged microsatellite sites" (STMS). Genetic maps based on STMS will share with the Olsen physical maps the advantage that mapping vocabularies will be standardized to the DNA sequence base and that access to any particular locus will not require shipping or storing cloned probes. The species map will consist simply of a listing of nucleotide sequences. Reference populations for developing STMS maps can be chosen on the basis of biological or economic interest. It will not be necessary to maximize for genetic divergence.

Molecular diagnosis of parasites

New developments in molecular biology have generated exciting possibilities for improved diagnosis of parasitic diseases. Through gene cloning and expression and peptide synthesis, defined parasite antigens can be produced in vitro for use in serodiagnosis, while nuclear hybridization techniques offer a vastly improved approach to identification of parasites in the tissue specimens of infected hosts as a means of diagnosis. Furthermore, the advent of the polymerase chain reaction technique has made it possible to increase the sensitivity of nuclear hybridization techniques, through amplification of target DNA sequences of the parasites in test material, by in situ synthesis of these sequences prior to hybridization with the diagnostic probe. Finally, through the use of monoclonal antibody technology, it is possible to design highly specific and sensitive serological assays, as well as assays for parasite antigen detection in tissue fluids and in the excreta of infected hosts, as a means of diagnosis.

Combined use of RFLP and PCR-ASO typing for HLA-DR-Dw and DQw typing

Due to some limitations of restriction fragment length polymorphism (RFLP) analysis in HLA-DR-DQ typing, we present a combined use of RFLP and polymerase chain reaction (PCR)-allele-specific oligonucleotide (ASO) typing. This scheme consists in selectively amplifying the few RFLP ill-defined genes (DR1/DR'Br' and DR4-Dw subsets) using PCR with allele specific primers to avoid cross-hybridization.