Internal Oligonucleotide Research Articles

Cloning of the classical guinea pig pancreatic lipase and comparison with the lipase related protein 2.

Starting from total pancreatic mRNAs, the classical guinea pig pancreatic lipase was cloned using rapid amplification of 3' and 5' cDNA ends. Internal oligonucleotide primers were designed from a partial cDNA clone including the region coding for the lid domain. Using this strategy, we did not amplify the cDNA corresponding to the pancreatic lipase related protein 2 in which the lid domain is deleted. Amino acid sequences of the classical guinea pig pancreatic lipase and the related protein 2 were compared based on the primary and tertiary structures of the classical human pancreatic lipase. Their distinct physiological roles are discussed in the light of functional amino acid differences.

Solid-phase polymerase chain reaction.

The polymerase chain reaction (PCR) has facilitated the diagnosis of infectious diseases and genetic disorders, because of its ability to amplify minute amounts of nucleic acids. To distinguish genes of interest from nonspecifically amplified DNA, PCR products commonly are fractionated by electrophoresis, transferred to membranes, and then probed with a labeled internal sequence-specific oligonucleotide. Alternatively, the PCR products have been labeled directly, and hybridized to immobilized oligonucleotide probes. These methods require the tedious physical transfer of the PCR products. In order to amplify and immobilize genes simultaneously, we have developed a simple solid-phase PCR method. The technique enabled us to detect the HIV envelope gene readily without any transfer of amplified DNA.

Exclusion in liver by polymerase chain reaction of hepatitis B and C viruses in acute liver failure attributed to sporadic non-A, non-B hepatitis

Hepatitis B and C viruses have been implicated in a few cases of acute liver failure attributed to sporadic (community acquired) non-A, non-B hepatitis, but reports are conflicting. We determined whether hepatitis B virus and hepatitis C virus were detectable in prospectively stored hepatectomies from seven British patients grafted for acute liver failure attributed to sporadic non-A, non-B hepatitis. For hepatitis B virus, we used nested polymerase chain reaction with primers to the core and surface regions. For hepatitis C virus, we used one round of reverse transcription polymerase chain reaction with primers to the 5' untranslated region and Southern hybridization using an internal oligonucleotide probe as well as nested PCR for the E1 region. Positive controls were native livers from two patients with unequivocal fulminant hepatitis B and from four patients with cirrhosis attributed to hepatitis C virus. Our negative findings suggest that, in the UK, acute liver failure attributed to sporadic non-A, non-B hepatitis most likely is caused by agent/s other than hepatitis B and C viruses.

Molecular identification of cardioviruses by enzymatic amplification

Cardiovirus specific sequences located in the 5′ NTR are used to amplify viral RNA by PCR. General primers were selected for the amplification of cardioviruses, including encephalomyocarditis virus (EMCV), mengovirus and Theiler's murine encephalomyelitis virus (TMEV. Additionally, ECHO virus type 22, an atypical enterovirus, could also be detected with the general cardiovirus primers. An internal encephalomyocarditis virus specific probe and a general cardiovirus probe are used to discriminate EMCV from other cardioviruses. The sensitivity of the PCR was determined at 10 pfu after hybridization with an internal oligonucleotide probe. Specificity was tested with a broad range of picornaviruses and other nonrelated RNA and DNA viruses. The applicability of the assay was demonstrated by the detection of TMEV RNA in tissue samples from experimentally-infected mice.

Colorimetric diagnosis of prolonged bluetongue viremia in sheep, using an enzyme-linked oligonucleotide sorbent assay of amplified viral nucleic acids

Summary Each of 5 US-origin serotypes of bluetongue virus (btv) was inoculated into a separate pair of sheep. The duration of each animal's ensuing viremia was monitored, using a btv serogroup-specific nested polymerase chain reaction (pcr) method and an embryonating chicken egg (ece) inoculation procedure. Mean duration of viremia was 100 and 38 days for the pcr and ece methods, respectively. This difference was significant (P < 0.001) and documents a more prolonged viremia in virus-exposed sheep than has been reported. A dual internal oligonucleotide solution hybridization procedure was developed for the rapid (2 hours) colorimetric detection and identification of btv-specific pcr products. This enzyme-linked oligonucleotide sorbent assay (elosa) relied on annealing of separate biotinylated and fluores-ceinated probes to the amplified btv nucleic acid; these complexes were captured on streptavidin-coated microtitration wells and were detected, using a horseradish peroxidase-labeled antifluorescein antibody conjugate. End-point dilution analyses of pcr products indicated that the elosa was more sensitive than gel electrophoretic or comparable colorimetric slot-blot hybridization techniques. The btv pcr-elosa system represents a more sensitive and expeditious means of diagnosing btv-induced viremia than does the ece procedure currently used. The combination of elosa with pcr should facilitate practical application of nucleic acid technology to diagnostic veterinary medicine.

Regulation of Expression of B7 by Murine Langerhans Cells: A Direct Relationship Between B7 mRNA Levels and the Level of Surface Expression of B7 by Langerhans Cells

Cultured BALB/c epidermal Langerhans cells express high levels of the costimulatory molecule B7 on their surfaces relative to levels expressed on fresh Langerhans cells. Quantitation of relative amounts of B7 mRNA in fresh epidermal cells and cultured epidermal cells following amplification of mRNA signals via reverse transcriptase-polymerase chain reaction, hybridization of PCR products with radiolabeled internal oligonucleotide probes, resolution of hybrids in non-denaturing polyacrylamide gels, and detection by autoradiography revealed dramatically (approximately one thousandfold) higher levels of B7 mRNA in cultured epidermal cells (10-40% I-A+) as compared with fresh epidermal cells (1-4% I-A+). Levels of B7 mRNA in cultured epidermal cells were also substantially greater than those detected in a reference B lymphoma cell line (CH-1). Analysis of B7 mRNA expression in subpopulations of cultured epidermal cells demonstrated that essentially all of the B7 mRNA was present in Langerhans cells; cells bearing I-A and CD45 antigens. Cultured keratinocytes did not contain appreciable amounts of B7 mRNA. These results are consistent with previous data regarding surface expression of B7 by cLC and also demonstrate that fLC are essentially devoid of B7 mRNA and surface protein.

Spatiotemporal expression of pregnancy-specific glycoprotein gene rnCGM1 in rat placenta.

As a basis towards a better understanding of the role of the pregnancy-specific glycoprotein (PSG) family in the maintenance of pregnancy, detailed investigations are described on the expression of a recently identified rat PSG gene (rnCGM1) at the mRNA and protein levels. Using specific oligonucleotide primers, rnCGM1 transcripts were identified after reverse transcription, polymerase chain reaction, and hybridization with a radiolabelled, internal oligonucleotide. Transcripts were only found in significant amounts in placenta. In situ hybridization visualized rnCGM1 transcripts at day 14 post coitum (p.c.), in secondary trophoblast giant cells and in the spongiotrophoblast. Only those secondary giant cells lining the maternal decidua were positive. In contrast, primary giant cells did not contain rnCGM1 mRNA. At day 18 p.c., rnCGM1 transcripts were almost exclusively detectable in the spongiotrophoblast. No rnCGM1 transcripts were found in rat embryos of these two developmental stages. Rabbit antisera were generated against the amino-terminal immunoglobulin variable-like domain and against a synthetic peptide containing the last 13 carboxy-terminal amino acids of rnCGM1. Both antisera recognized a 124 kDa protein in day 18 rat placental extracts as identified by Western blot analysis. The anti-peptide antiserum recognized a 116 kDa protein in the serum of a 14 day p.c. pregnant rat that is absent from the sera of non-pregnant females. Taken together, these results confirm exclusive expression of rnCGM1 in the rat trophoblast, but unlike human PSG, negligible or no expression is found in other organs, such as fetal liver or salivary glands, indicating a more specialized function of rnCGM1. Its spatiotemporal expression pattern is conducive with a potential role of PSG in protecting the fetus against the maternal immune system and/or in regulating the invasive growth of trophoblast cells.

Investigation of bcr-abl transcription by Ph-positive chronic myeloid leukemia progenitors.

It is now feasible to investigate bcr-abl transcription by the progeny of Ph-positive (Ph+) early and committed hemopoietic progenitor cells from patients with chronic myeloid leukemia (CML). Cells from individual colonies can be bisected and each half analyzed by cytogenetics or the reverse transcriptase-polymerase chain reaction (RT-PCR) method to detect the bcr-abl transcript using internal nested oligonucleotide primers that flank the chimeric gene junction. We previously showed that some Ph+ colonies have undetectable PCR products for bcr-abl. When colonies are generated in the presence of alpha interferon (IFN-alpha) bcr-abl transcripts are undetectable in the majority of Ph+ colonies. These data suggest a potential mechanism for the action of IFN-alpha in Ph+ CML and indicate the need for a combined approach with cytogenetics and RT-PCR in analyzing the bcr-abl gene.

Different genomic structure of mouse and human Lmp7 genes: characterization of MHC-encoded proteasome genes.

The 20S proteasome or multicatalytic proteinase is a high relative molecular mass proteinase consisting of at least 12 different subunits of a relative mass of 2 0 30 kDa (reviewed in Rivett 1989; Monaco 1992). Recently, in mouse and humans the genes for two subunits (Lmp2 and Lmp7) were found to be encoded in the class II region of the Major histocompatibility complex (MHC; Brown et al. 1991; Glynne et al. 1991; Kelly et al. 1991; Ortiz-Navarrete et al. 1991). This has nurtured the speculation that the highly conserved proteasome is involved in the cytosolic degradation of antigens, which is a prerequisite for MHC class I mediated peptide presentation. So far no direct evidence has been obtained to support this intriguing hypothesis (Momburg et al. 1992; Arnold et al. 1992), but more studies are required. The genomic structure of the human LMP2 and LMP7 genes has been described by Frfih and co-workers (1992). Both genes reveal only a limited polymorphism (van Endert et al. 1992). In this study we present the complete genomic sequences of mouse and human Lmp7 genes and show that the mouse Lmp-7 gene lacks the first exon found in the human LMP7 gene. Subclones of the genes were derived from cosmid II 5.9 derived from a BALB/c(H-2 ~ ) mouse (Steinmetz et al. 1986) or cosmid U15 for humans (Blanck and Strominger 1988) and sequenced using the pBluescript system (Sambrook et al. 1989) with internal oligonucleotide primers derived from mouse and human cDNA clones (Glynne et al. 1991; Frentzel et al. 1992).

Detection of C-type natriuretic peptide (CNP) transcript in the rat heart and immune organs

Previous studies suggested the expression of mRNA, coding for CNP, exclusively in the central nervous system. In the present study, using the polymerase chain reaction (PCR) technique instead of the less sensitive Northern blot hybridization, CNP-specific sequences have also been detected in rat atria and ventricles of the heart as well as in organs of the immune system (thymus, spleen and lymph nodes). Parallel PCR-assays documented ANP-mRNA in these tissues. To verify specificity of the PCR-products, Southern blots have been hybridized with a third internal oligonucleotide and amplification products have been sequenced. The relative level of CNP-mRNA in these tissues was estimated to be in the range of 1-9% of total brain CNP transcripts. The results suggest that the peptide may have a peripheral as well as a central site of action. In light of its pronounced effect on cell proliferation, particular interest should focus on a possible role of CNP in the immune system.

Detection of C-type natriuretic peptide (CNP) transcript in the rat heart and immune organs.

Previous studies suggested the expression of mRNA, coding for CNP, exclusively in the central nervous system. In the present study, using the polymerase chain reaction (PCR) technique instead of the less sensitive Northern blot hybridization, CNP-specific sequences have also been detected in rat atria and ventricles of the heart as well as in organs of the immune system (thymus, spleen and lymph nodes). Parallel PCR-assays documented ANP-mRNA in these tissues. To verify specificity of the PCR-products, Southern blots have been hybridized with a third internal oligonucleotide and amplification products have been sequenced. The relative level of CNP-mRNA in these tissues was estimated to be in the range of 1-9% of total brain CNP transcripts. The results suggest that the peptide may have a peripheral as well as a central site of action. In light of its pronounced effect on cell proliferation, particular interest should focus on a possible role of CNP in the immune system.

Specific amplification of Aspergillus fumigatus DNA by polymerase chain reaction

We have developed a specific and sensitive method to detect the human pathogen Aspergillus fumigatus by polymerase chain reaction (PCR) with an objective of detecting the organism in peripheral blood and urine which can be obtained by non-invasive procedures. A pair of oligonucleotide primers for PCR were designed based on the published partial protein sequences of an 18 K D IgE-binding protein of A. fumigatus Asp f1 and the ribotoxins mitogillin and restrictocin of A. restrictus, and alpha-sarcin of A. giganteus. The primers were specific in amplifying an expected 315 bp region of the homologous genes in A. fumigatus and A. restrictus but not in A. giganteus. Also, there was no amplification of human DNA or DNA of A. flavus, A. niger, A. fischeri, Penicillium sp., Candida albicans and Pneumocystis carinii. The sensitivity of the PCR detection of A. fumigatus DNA is about 20 pg on an ethidium bromide gel and 0·6 pg by Southern analysis using a 32 P-labelled internal oligonucleotide. In preliminary analysis of 13 urine specimens of patients suspected of invasive aspergillosis (IA), two were PCR positive, one of whom died of IA with brain lesion. Further analyses of both urine and blood specimens of IA are in progress to determine the comparative utility of PCR over the conventional antigen tests.

Molecular dynamics simulations of B-DNA: an analysis of the role of initial molecular configuration, randomly assigned velocity distribution, long integration times, and nonconstrained termini.

Molecular dynamics simulations of three DNA sequences using the AMBER 3.0 force field were performed with implicit inclusion of water through a distance-dependent dielectric constant and solvated counterions. Simulations of the self-complementary DNA dodecamer d(CGCGAATTCGCG) were started from a regular B-DNA structure and the x-ray single crystal B-DNA structure. Although mean convergence during the 89-ps calculation was confirmed, localized differences in backbone torsionals and base-pair helicoidals were observed. A nanosecond simulation of the nonself-complementary 14 base-pair DNA d(GGCGGAATTGGCGG) indicates that most structural parameters stabilize within the first 100-200 ps, while isolated features show low-frequency oscillations throughout the calculation. The lack of harmonic constraints on the ends of the molecules was shown not to perturb the structural dynamics of the internal oligonucleotide beyond the external 2 base pairs. Comparison of three simulations of the nonself-complementary 14 base-pair DNA d(GGCGAAATTCGCGG), identical in all respects other than the assignment of initial Maxwellian atomic velocity distributions, revealed the inherent systematic variability. The three calculations result in nearly superimposable global structures, with localized variations in torsionals and helicoidals. Our results provide a basis for performing a comparative analysis of the effect of DNA sequence on localized structure.

Use of the polymerase chain reaction and 16S rRNA sequences for the rapid detection of Brochothrix spp. in foods.

Oligonucleotide primers were designed against rRNA sequences to give a DNA-based PCR assay for the rapid identification/detection of Brochothrix spp. The PCR products could be confirmed by hybridization to an internal oligonucleotide probe. The method successfully and sensitively detected/identified these organisms in pure cultures but was of limited value as a detection method because the detection sensitivity, in relation to conventional plate counts, varied and the assay sensitivity was reduced in the presence of staphylococci. Furthermore, sensitivity was also lost when the assay was applied directly to meat samples. However, a separation step using a lectin (from Agaricus bisporus) immobilized on magnetic beads prior to the PCR assay, allowed the direct detection of low numbers (> 10(2) cfu g-1) of Brochothrix in meat samples within a working day.

Detection of Echinococcus multilocularis DNA in fox faeces using DNA amplification.

In order to identify Echinococcus multilocularis DNA in fox faeces for epidemiological purposes, we have developed a new method to prepare DNA suitable for PCR amplification. DNA isolation from fox excrement was performed according to a novel procedure involving lysis in KOH, phenol-chloroform extraction and a purification step on a matrix (Prep-A-Gene). The target sequence for amplification was the E. multilocularis U1 snRNA gene. PCR products were indistinguishable for 32 different E. multilocularis isolates and no signal was observed after ethidium bromide staining with DNAs from other tapeworm species, including E. granulosus. The sensitivity of amplification was monitored by the addition of E. multilocularis DNA or eggs to faeces free of E. multilocularis and was estimated to be 1 egg per 4 g of faeces. PCR products were blotted onto nylon membranes and hybridized with an internal oligonucleotide probe in order to confirm the results. Twenty nine faecal samples from foxes shot in Franche-Comté (East France) were tested. Out of 10 samples from foxes in which no E. multilocularis adult worms could be observed after necropsy, 7 were PCR positive, showing that the PCR test is more sensitive than microscopical examination. Out of 19 samples from foxes harbouring E. multilocularis adult worms, 18 were PCR positive. The remaining PCR-negative sample could be due either to the misidentification of the species of adult worm (E. granulosus and E. multilocularis), or to DNA variation between different isolates of E. multilocularis. Further work in the field should be initiated in order to confirm these results.

A PCR-based method for high stringency screening of DNA libraries.

A rapid method for cloning genomic DNA utilizing a PCR-based screening protocol is described. A murine genomic library in lambda phage was subdivided into 64 wells, each containing 1000 clones, and propagated in bacteria. Amplified phage from each of 8 wells across columns, and each of 8 wells down rows, were pooled. The pooled phage were screened for the presence of murine M-CSF DNA by PCR using specific oligonucleotide primers. A single well that contained an M-CSF genomic clone was identified by the synthesis of a PCR product of the correct size that hybridized to an internal M-CSF oligonucleotide probe. This well was subdivided into 64 wells, each containing approximately 30 individual phage, reamplified, and rescreened utilizing the same protocol. A positive well was then subdivided and amplified a third time starting with an average of 2 phage per well, and rescreened for M-CSF DNA by PCR. Phage from a PCR-positive well, now highly enriched for M-CSF DNA, were grown as individual plaques. PCR-screening of randomly picked plaques demonstrated that the majority contained an M-CSF genomic insert. This method obviates the more labor and time intensive method of plaque hybridization screening of DNA libraries, and is more stringent since three oligonucleotides (the two PCR primers, and the hybridization probe) are required to give a true positive signal. Similar methodology has also been used to clone a cDNA gene contained within a plasmid library.

The Expression of .ALPHA.2B-Adrenoceptor mRNA in Sprague-Dawley Rat Kindey.

Based on radio-ligand binding assays, most of the α2B-adrenoceptors in rat kidney are found in the proximal tubules and are of the α2B-adrenoceptors subtype. To determine more accurately the distribution of the α2B-adrenoceptors in the rat kidney, we studied the expression of α2B-adrenoceptors mRNA in rat kidney slices and microdissected nephron fragments using reverse transcription-polymerase chain reaction (RT-PCR) technique. Sprague-Dawley rat kidney was dissected into cortex, outer medulla and inner medulla. Total RNA was prepared from the kidney slices. Microdissected single nephron segments about 1mm in length were transferred to tubes containing lysis buffer. RT-PCR was performed using a GeneAmp RNA PCR kit from Perkin-Elmer Corporation. The PCR primers were designed based on the sequences of the third cytoplasmic loop of the rat α2B-gene. After the PCR, the products were analyzed by agarose gel electrophoresis. The specificity of PCR amplified products was examined by restriction endonuclease digestion and internal oligonucleotide hybridization. Our results indicate that α2B-adrenoceptors mRNA is expressed in rat kidney cortex, outer medulla and inner medulla. Microdissection and RT-PCR showed that α2B-adrenoceptor mRNA was expressed in the proximal straight tubules (S3), cortical and medullary thick ascending limbs of Henle (CTALH, MTALH) and cortical and outer medullary collecting tubules (CCT, OMCT). (Hypertens Res 1993; 16: 259-263)

Persistence of viral genome into late stages of murine myocarditis detected by polymerase chain reaction.

Enteroviruses have been considered as the most common etiologic agents in clinical myocarditis and dilated cardiomyopathy; however, their pathogenetic role remains unknown. Hence, the relation of viral replication and development of cardiomyopathy has been determined in a murine model of myocarditis by evaluating the persistence of viral genome during acute and chronic stages of myocarditis by means of Northern blot hybridization and polymerase chain reaction (PCR). DBA/2 mice (n = 146) were injected peritoneally with 10 plaque-forming units of encephalomyocarditis (EMC) virus, and the control mice (n = 33) were injected with normal saline. Animals were randomly killed at 4, 7, 10, 14, 21, 28, 35, and 42 days after infection. Histology revealed acute myocardial necrosis with massive inflammatory cell infiltrate peaking on day 14 followed by increasing fibrosis and declining chronic inflammation features compatible with dilated cardiomyopathy between days 21 and 42. Northern blot analysis of control and infected hearts showed detectable viral RNA in the infected hearts initially at day 4, peaking by day 7, diminishing between day 7 and day 14, and absent at day 21 and day 28. However, potential viral remnants present in low quantities and undetectable by Northern blot were further detected by PCR followed by confirmation with an internal oligonucleotide probe after day 14 up to day 42. Viral RNA signals on Northern blot showed a strong correlation with massive myocyte necrosis on day 14, but the viral RNA fragment was consistently detectable into late stages of cardiomyopathy on days 21, 28, 35, and 42 by PCR. This indicated that the mature virions are fully developed early in infection and are capable of persisting in the myocardium after virus-mediated myocytolysis stage. Therefore, PCR is an extremely sensitive method for detecting residual viral genome and viral persistence in the myocardium and may offer insights into the pathogenesis of chronic myocarditis leading to dilated cardiomyopathy.

Langerhans Cells Are the Major Source of mRNA for IL-1β and MIP-1α Among Unstimulated Mouse Epidermal Cells

Immunocompetent cells of the epidermis can interact by the elaboration and recognition of cytokines. Although much new information has been reported concerning the cytokines secreted by keratinocytes, little is known about cytokines derived from Langerhans cells (LC). To address this deficiency, we examined cytokine mRNA profiles in different epidermal preparations from BALB/c mice, taking advantage of the sensitive technique of polymerase chain reaction (PCR), after reverse transcription of mRNA. In assays of epidermal sheets separated from dermis by ammonium thiocyanate, mRNA for IL-1 alpha, IL-1 beta, IL-6, IL-7, tumor necrosis factor alpha (TNF alpha), TNF beta, granulocyte macrophage/colony-stimulating factor (GM-CSF), and macrophage inflammatory protein-1 alpha (MIP-1 alpha) were unequivocally present. By contrast, faint bands were detected for IL-4, IL-5, and interferon gamma (IFN gamma), and no PCR signal was detected for IL-2. Importantly, assays of epidermal cells (EC) dissociated with trypsin revealed similar mRNA profiles. To determine the effects of cell isolation, fluorescence-activated cell sorter (FACS)-purified Ia- EC were first analyzed; all of the previously cited cytokine mRNA were present except for IL-1 beta and MIP-1 alpha. EC depleted of LC by a second technique, lysis using anti-Ia monoclonal antibody and complement, revealed similar profiles, with substantially reduced PCR signals for IL-1 beta and MIP-1 alpha. Finally, FACS-purified LC (Ia+ EC) clearly expressed IL-1 beta and MIP-1 alpha mRNA, a finding that was verified by Southern blotting using internal oligo probes. We conclude that these cell-isolation procedures did not produce substantial alterations in basal mRNA profiles and that LC are the principal source of mRNA for IL-1 beta and MIP-1 alpha among unstimulated EC in mice.

Rapid detection of tuberculous and non-tuberculous mycobacteria by polymerase chain reaction amplification of a 162 bp DNA fragment from antigen 85.

A polymerase chain reaction (PCR) assay was developed for detection of mycobacteria using amplification of a 162 bp region of the genes coding for the mycobacterial antigen 85 complex. Strains belonging to the Mycobacterium tuberculosis complex were further differentiated from non-tuberculous mycobacteria by hybridization of the PCR derived Southern blot with an internal oligonucleotide probe and washing under stringent conditions. The method allowed rapid and sensitive detection of mycobacterial DNA in uncultured clinical samples. PCR results obtained for Mycobacterium tuberculosis in 206 specimens from 180 untreated patients gave a sensitivity of 93.9% and a specificity of 94.3% compared with the culture. PCR detected DNA from Mycobacterium tuberculosis in seven samples from patients with clinically evident tuberculosis in whom culture was negative. The results suggest that this PCR assay could be used for early and specific diagnosis of tuberculosis.