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PubMed1995

Simultaneous quantitation of multiple cytokine mRNAs by RT-PCR utilizing plate based EIA methodology.

Cytokines are small protein hormones produced during an immune response that are responsible for mediation and regulation of many aspects of immunity. Measurement of cytokines by several different methods has led to a broader understanding of the immune response. This paper describes a sensitive, reproducible, and quantitative RT-PCR assay for the simultaneous measurement of multiple cytokines. The main features of the methodology are: RNA competitors which control for all aspects of the process from RNA extraction, through reverse transcription (RT) and PCR amplification; a general cloning vector, pQPCR1, for building RNA competitors that does not require prior analyte cDNA cloning; and analysis by plate based EIA. This RT-PCR-EIA system is shown to be more sensitive than agarose gel electrophoresis followed by EtBr staining, measuring PCR product in the sub-nanogram range. It also extends the linear dynamic range of detection to a four log fold range of analyte concentration. The assay is reproducible, with coefficients of variation (CVs) in the 10-20% range. Moreover, the cloning vector is designed to accommodate multiple primer templates, thus allowing simultaneous quantitation of many different analytes from a single RT reaction. The described system is versatile and adapts to numerous analytes.

Animals↗
PubMed1998

Genetic analysis of the G and P genes in ungulate respiratory syncytial viruses by RNase A mismatch cleavage method.

The G and P genes of bovine, ovine and caprine respiratory syncytial (RS) viruses were analyzed by RNase A one-dimensional fingerprinting, using A 51908 as the reference strain. Antisense G or P RNA probes of bovine RS virus strain A 51908 were hybridized to total RNA extracted from bovine turbinate cells infected with bovine, ovine or caprine RS virus strains. The RNA:RNA heteroduplexes were digested with RNase A and the resistant products were analyzed by gel electrophoresis. Comparative analysis of the cleavage patterns revealed heterogeneity among bovine, ovine and caprine RS virus isolates. Ovine RS virus strains generated RNA cleavage patterns more distantly related to the bovine or caprine RS virus strains, particularly in the G gene. Statistical analysis of the results obtained indicated that genetic differences between bovine and ovine viruses were larger, compared with the ones among bovine strains themselves. The same analysis also revealed a close genetic relation among bovine and caprine strains. These results are discussed in terms of ungulate RS virus genetic variation and vaccine development.

Animals↗
PubMed1973

Inhibition of transcription of the histidine operon in vitro by the first enzyme of the histidine pathway.

An in vitro system was developed for transcription of the histidine operon of Esherichia coli carried in the genome of a defective varphi80 transducing phage. The messenger RNA (mRNA) of the histidine operon synthesized in the in vitro system was detected by hybridization to single strands of both varphi80 and varphi80dhis DNA, and by competition of this hybridization with unlabeled histidine mRNA that had been synthesized in vivo (RNA extracted from cells in which the histidine operon had been derepressed). Under the conditions used, RNA complementary to the histidine operon was about 15% of the total RNA that was synthesized in vitro from the varphi80dhis DNA template. The RNA complementary to the histidine operon was synthesized on the "sense" strand (the R strand) of varphi80dhis in the form of a polycistronic message with a sedimentation coefficient (about 38 S) very close to that observed for the histidine mRNA synthesized in vivo. Synthesis of the histidine operon RNA appears to be subject to control in vitro. Addition of the first enzyme of the pathway for histidine biosynthesis blocked transcription of the histidine operon specifically, strongly suggesting that this enzyme acts as a regulatory protein for the histidine operon.

Cell-Free System↗
PubMed2006

Laser capture microdissection of epithelial cancers guided by antibodies against fibroblast activation protein and endosialin.

Transcriptional profiling of cancer biopsies is used extensively to identify expression signatures for specific cancer types, diagnostic and prognostic subgroups, and novel molecular targets for therapy. To broaden these applications, several challenges remain. For example, the integrity of RNA extracted even from small tissue samples has to be insured and monitored. Moreover, total tumor RNA may hide the marked histologic heterogeneity of human cancers. A principle approach to this heterogeneity has been provided by laser capture microdissection performed on antibody-stained tissue sections (immuno-LCM; iLCM). In this study, we have established a procedure to assess the quality of RNA obtained from tissue sections, coupled with immunostaining using antibodies to different tumor stromal markers, and subsequent iLCM to selectively capture the cancer stroma compartments. The procedure was applied to 53 frozen specimens of human epithelial cancers. Sections were stained for histopathological evaluation, and RNA was isolated from adjacent serial sections. RNA quality was assessed by the Agilent-Bioanalyzer (Agilent, Palo Alto, CA) and by multiplex RT-PCR. Two thirds of the specimens were found to yield good to excellent RNA quality. For microdissection of the tumor stroma with reactive fibroblasts and tumor blood vessels, a rapid incubation protocol with antibodies against fibroblast activation protein (FAP) and against endosialin was developed to ensure RNA integrity for subsequent iLCM. Using these procedures, RNA from distinct tumor compartments can be isolated, analyzed, amplified, and used for transcription profiling.

Antibodies, Neoplasm↗
PubMed1992

Defective RNAs in mosquito cells persistently infected with Bunyamwera virus.

Viral protein and RNA synthesis were compared in BHK and Aedes albopictus C6/36 (mosquito) cells infected with Bunyamwera virus. In BHK cells host protein synthesis was inhibited and viral proteins were detected until the cells died; in C6/36 cells there was little inhibition of host proteins and viral proteins could not be detected after 36 h post-infection. Relatively more S segment RNA than L or M segment RNA was produced in infected C6/36 cells compared to BHK cells. A persistent infection of C6/36 cells was established and the cells were passaged at weekly intervals for over a year. The titre of virus released from the cells and the level of viral RNA in the cells at different passages fluctuated markedly, but there was no simple relationship between virus titre and the amount of viral RNA. Northern blot analysis of viral RNA extracted from persistently infected cells revealed the presence of subgenomic RNAs derived from the L RNA segment. These defective RNAs were not packaged into nucleocapsids. The presence of the defective RNAs did not correlate with resistance of cells cloned from the persistently infected population to superinfection with homologous virus. Hence the role of these defective RNAs in the maintenance of the persistent state remains to be elucidated.

Animals↗
PubMed1987

En-1 and En-2, two mouse genes with sequence homology to the Drosophila engrailed gene: expression during embryogenesis.

Two mouse genes, En-1 and En-2, have sequence homology to the engrailed (en) and invected (inv) genes of Drosophila (Joyner et al. 1985). Partial nucleotide sequence analyses of genomic and cDNA clones show that the homologous sequences can encode a stretch of 107 amino acids, including a centrally located, 60-amino-acid homeo box. Within the homologous regions of the mouse and Drosophila genes, 78 (73%) of the amino acids are identical. Such extensive conservation of sequence outside the homeo box between vertebrate and Drosophila homeo box-containing genes is thus far unique. En-1 and En-2 are expressed during mouse embryogenesis. Transcripts from both genes were detected in RNA samples from teratocarcinoma cells, which serve as in vitro models for the early embryo, and from embryos at 9.5 through 17.5 days of development. For each gene we observed a unique pattern of changes in the number and relative intensities of transcripts detectable during embryonic development. Transcripts from both genes are represented abundantly in RNA extracted from the posterior portion of the fetal brain, and are much less abundant in RNA from other fetal tissues, including the anterior portion of the brain and the spinal cord. The chromosome map positions of En-1 and En-2 were determined by recombinant inbred strain analyses. Unlike their Drosophila counterparts, they are unlinked: En-1 is in the central portion of the mouse chromosome 1 and En-2 is in the proximal portion of mouse chromosome 5. Both genes map in the vicinity of mutations that are known to cause abnormalities during development.

Amino Acid Sequence↗
PubMed1981

Effects of insulin on ribonucleic acid synthesis in toad urinary bladder.

We previously found that the sustained rise in active sodium transport by the toad urinary bladder after exposure to insulin is associated with the synthesis of a membrane protein with a molecular weight of 25,000. Studying the effects of insulin on the incorporation of uridine into RNA of epithelial cells of the bladder, we now report that insulin causes a 39% increase in the incorporation of [3H]uridine into poly(A)-containing RNA extracted from granular cells, the predominant epithelial cell type. The increased accumulation of label in RNA, most notably species ranging from 5-10S, could be demonstrated whether cells were pulsed with [3H]uridine or continuously exposed to the label. Using a reticulocyte lysate system, we compared the translation products of RNA from untreated and insulin-treated granular mucosal cells. Exposure to insulin was associated with the expression of a mRNA coding for a protein with molecular weight of approximately 25,000, similar in size to the insulin-induced membrane protein we previously identified in the intact tissue.

Animals↗
PubMed1991

Coexpression of functionally active receptors for thyrotropin and platelet-derived growth factor in human thyroid carcinoma cells.

In the present study we show the simultaneous expression of functionally active receptors for TSH and platelet-derived growth factor (PDGF) in a newly established human anaplastic thyroid carcinoma cell line, HTh 74. In Northern blot analysis of RNA extracted from HTh 74 cells a low expression of both TSH and PDGF receptor messenger RNA was found. These observations in conjunction with the fact that the cells contain cytokeratin clearly demonstrate that the cells are bona fide epithelial thyroid cells. Stimulation of HTh 74 cells with TSH led to a concentration-dependent increase in cAMP formation, showing a functional activity of the TSH receptors. Northern blot analysis, immunoprecipitation, immunofluorescence staining, and binding experiments showed the presence of both alpha- and beta-type PDGF receptors in the HTh 74 cells. The functional activity of the PDGF receptors was demonstrated by ligand-induced internalization of the receptors and PDGF-induced growth of the HTh 74 cells. The significance of the expression of PDGF receptors on thyroid epithelial cells is not clear. However, it might reflect the gain of a new growth stimulatory pathway participating in the transformation of the epithelial thyroid cells. Alternatively, the PDGF receptors may be remnants from an immature progenitor cell from which the undifferentiated carcinoma has evolved.

Carcinoma↗
PubMed1998

Quantitative analysis of the expression of apoptosis-related genes.

BACKGROUND: The development and subsequent introduction of current molecular biology techniques allows the elucidation of some of the mechanisms of the programmed cell death (apoptosis). The overexpression of the genes directly (B-cell leukemia/lymphoma-2, BCL-2) or indirectly (multidrug resistance gene-1, MDR1) involved in the suppression of apoptosis, as well as the low-level expression of their antagonists (BCL-2 associated X-protein, BAX) result in longer survival and the development of drug resistance in malignant cells. AIM: The objective of this study was to design our own appropriate primers and to synthesize internal RNA standards and this way to evaluate the rate of expression of the MDR1, BCL-2 and BAX genes using a competitive reverse transcription and polymerase chain reaction (cRT-PCR). MATERIAL AND METHODS: Peripheral blood or bone marrow aspirates from 5 patients and 3 healthy controls were used for RNA extraction. Competitive RT-PCR was employed utilizing the constructed specific primers and synthesized internal RNA standards. Following electrophoresis, the PCR products stained with ethidium bromide were evaluated on the "Gel Doc 1000TM" video image system. RESULTS: The constructed primers specific for each of the three genes and synthesized internal RNA standards with a suitable deletion allow receiving the yield of well-separated competitive amplicons. The measured band's intensity of light and the calculated standard/patient ratio were employed in the analysis of the MDR1, BCL-2 and BAX gene expression. CONCLUSIONS: Competitive RT-PCR is a non-radioactive and comparatively rapid molecular biology method suitable for everyday laboratory practice. The possibility for simultaneous evaluation of the expression of several genes could help in the elucidation of some of the mechanisms underlying the prolonged survival of malignant cells.

Apoptosis↗
PubMed1992

Pig testicular 20 beta-hydroxysteroid dehydrogenase exhibits carbonyl reductase-like structure and activity. cDNA cloning of pig testicular 20 beta-hydroxysteroid dehydrogenase.

cDNA inserts encoding 20 beta-hydroxysteroid dehydrogenase (EC 1.1.1.53) were, for the first time, isolated and cloned from a pig testis cDNA library using synthetic oligonucleotides deduced from the partially determined amino acid sequences. The cDNA contains an open reading frame predicted to encode 289 amino acid residues. Surprisingly, it has 85% amino acid homology to human carbonyl reductase. The purified enzyme exhibited carbonyl reductase activity. Adenine-rich sequence was located in the 3'-untranslated nine-rich sequence was located in the 3'-untranslated region, which may mean that the gene originates by retroposition. RNA transcripts of 1.3, 3, and 6 kilobases were detected in poly(A)+ RNA extracted from pig testis by Northern blot hybridization. The steady-state level of the RNA species increased to a maximum in testes from 10-day-old pigs, but rapidly declined thereafter to the same levels found in testes of mature animals.

Alcohol Oxidoreductases↗
PubMed1991

Expression of Madin-Darby canine kidney cell Na(+)-and Cl(-)-dependent taurine transporter in Xenopus laevis oocytes.

Expression of a Madin-Darby canine kidney (MDCK) cell taurine transporter was examined in Xenopus oocytes that had been injected with poly(A)+ RNA extracted from MDCK cells. Compared with water-injected oocytes, injection of total poly(A)+ RNA resulted in an increase in Na(+)-dependent taurine uptake which was directly related to the amount of RNA injected. The magnitude of expression in poly(A)+ RNA-injected oocytes was 5-10-fold higher than that of water-injected oocytes. Since the Vmax of taurine uptake in MDCK cells is increased by culture in hypertonic medium, we compared oocyte taurine uptake after injection with poly(A)+ RNA from MDCK cells cultured in hypertonic medium with uptake in oocytes injected with poly(A)+ RNA from hypertonic cells elicited twice the taurine uptake elicited by poly(A)+ RNA from isotonic cells. The transporter expressed in oocytes was like that in MDCK cells: it was completely dependent on external sodium and was also anion dependent (Cl- greater than or equal to Br- greater than SCN- much greater than gluconate-). Other beta-amino acids, beta-alanine and hypotaurine, inhibited taurine uptake, but L-alanine and 2-(methylamino) isobutyric acid did not. The apparent Km of the transporter was 7.0 microM. After size fractionation on a sucrose density gradient, poly(A)+ RNA encoding for the MDCK taurine transporter was found in the fraction whose average size was 4.4 kilobases.

Animals↗
PubMed1979

Translation in vivo and in vitro of proteins resembling apoproteins of rat plasma very low density lipoprotein.

Antibodies raised against rat plasma apoVLDL and a purified fraction of arginine-rich peptides (ARP) were labeled with Na125I and were shown to bind to polyribosomes isolated from rat liver. Antibody fractions enriched by selective affinity chromatography exhibited increased levels of binding to polysomes. Anti-apoVLDL immunoreactivity was further resolved into anti-ARP and anti apoB components, each reactive with a distinct polysome population. Binding was specific for rat polysomes, and was directed toward nascent polypeptide chains. About 2% of normal rat liver polysomes were recovered by indirect immunoprecipitation with anti-apoVLDL. Ribonucleic acid (RNA) extracted from this immunoprecipitate contained species with polyadenylate (poly[A] sequences characteristic of eukaryotic messenger RNA (mRNA). These species, purified by affinity chromatography on poly(U)-Sepharose, stimulated the in vitro synthesis of immunoprecipitable apoVLDL-like proteins by about 17-fold when compared to unfractionated rat liver mRNA. Most of the in vitro translation products precipitated by purified anti-ARP migrated identically on polyacrylamide gel electrophoresis with unlabeled purified ARP. Some implications of these findings with respect to plasma VLDL biosynthesis are discussed.

Animals↗
PubMed1982

The extraction, characterization and in vitro translation of RNA from adult Schistosoma mansoni.

We have extracted RNA from Schistosoma mansoni using the lithium chloride-urea method which gives good yields of undegraded RNA. The results of agarose gel electrophoresis of RNA extracted by this procedure suggest that S. mansoni has an in vivo nick in the large rRNA sub-unit. Translation of the RNA in a rabbit reticulocyte lysate gave significant incorporation of [35S]methionine into synthesized proteins. Immunoprecipitation of these translation products using a hyperimmune monkey serum sedimented between 5 and 8% of the radioactivity, which appeared to be present in approximately 13 proteins of molecular weights 18, 20, 21, 22, 23, 35, 40, 54, 60, 70, 74, 78 and 105 K Daltons.

Animals↗
PubMed1992

Determination of coexisting nuclear transcription rates and cytoplasmic mRNA levels for gonadotropin subunit genes in rat anterior pituitary.

Nuclear run-on transcription assays allow the study of those factors that regulate the expression of a given gene. Because previously published protocols may have been presented in abbreviated form or not developed for nuclei derived from specific tissues, we have established a comprehensive protocol for those who wish to measure transcription of the gonadotropin subunit genes (alpha, LH-beta, FSH-beta) in the anterior pituitary of the rat. The protocol also allows the determination of simultaneously existing cytoplasmic subunit mRNA levels within the same cells. An especially critical step in nuclear run-on transcription assays is the isolation of newly formed labeled mRNA transcripts from the DNA template. In previously published protocols such isolation has been accomplished through rather tedious, multistep methods. To simplify this isolation process, we have evaluated the use of the commercially available product RNAzol. Nascent mRNA transcripts are attached to chromatin and the DNA template; proteinase K and DNase I are typically utilized to disrupt this attachment, thereby facilitating subsequent extraction. We have found that strict adherence to proteinase K and DNase I digestion prior to RNA extraction with RNAzol, followed by two ethanol/NH4OAc precipitations, will enable one to successfully isolate nascent mRNA transcripts free of unincorporated nucleotides. In summary, we present a comprehensive protocol for determining transcription rates and cytoplasmic mRNA levels for the gonadotropin subunit genes in the anterior pituitary of the rat. RNAzol was found to simplify the extraction of newly formed transcripts and should prove applicable with transcription assays utilizing nuclei from a variety of tissue.

Animals↗
PubMed2004

A comparison of RT-PCR-based assays for the detection of HAV from shellfish.

The hepatitis A virus (HAV) is the most common cause of viral infection linked to shellfish consumption. The lack of correlation between the fecal coliform indicators and the presence of enteric viruses in shellfish and their harvesting waters points to the need for molecular methods to detect viruses. We compared two RT-PCR based techniques currently available for the detection of the hepatitis A virus (HAV) in shellfish. Both approaches involve extraction of viral particles by glycine buffer and concentration of virus particles by one or two PEG precipitation steps. One procedure involves as RNA extraction method the use of oligo (dT) cellulose to select poly (A) RNA, and the other uses a system in which total RNA is bound on silica membrane. Comparison of the two RT-PCR based methods highlighted the efficiency of the first approach which is less time-consuming and technically demanding than the second.

Animals↗
PubMed1986

Evidence for the existence in the nuclei of Friend cells of a new type of ribonucleoprotein network.

We have isolated fragments of a novel nuclear structure exhibiting the morphological and biochemical characteristics of a ribonucleoprotein network. Under transmission electron microscopy it is visualized as irregularly interconnected branches assembled by tightly packed particles with sizes between 100A and 300A. RNA extracted from this structure shows a complex pattern: as well as ribosomal 28 S and 18 S RNA, small amounts of heterogeneous nuclear RNA and small nuclear RNA are also present. The protein composition of the network indicates a strong domination of ribosomal polypeptides. This fact, considered together with the sedimentation characteristics of the prevailing type of particles isolated directly from the network, supports the conclusion that ribosomal particles are the representative particulate elements. Further electrophoretic analysis of the protein has pointed out that it also contains a significant number of acidic polypeptides. Control experiments have suggested that the site of origin of the network fragments studied is not nucleolar: the fragments are released during extraction, most probably from the nuclear periphery. It is not yet clear whether this structure is localized only at the nuclear periphery or represents an extensive structure, occupying the entire volume of the nucleus. It is speculated that the network is involved in the extranucleolar transport and maturation of ribosomes.

Autoradiography↗
PubMed1977

Nucleic acid synthesis in preimplantation rabbit embryos. III. A "dark period" immediately following fertilization, and the early predominance low molecular weight RNA synthesis.

This report stems from efforts to characterize the products of transcription during the initial stages of cleavage in the rabbit embryo, since previous studies have suggested that RNA synthesis is required during this period for the continuation of normal development. Early cleaving embryos were exposed to radiolabeled precursors of nucleic acids in vitro and RNA extracted and analyzed by polyacrylamide gel electrophoresis and BD-cellulose chromatography. No unequivocal evidence of RNA synthesis could be obtained during the first three cleavage divisions; all apparent "embryonic" RNA synthesis could be ascribed to contaminating follicle cells. After the fourth cleavage, however, there is readily detectable incorporation of radioisotope into RNA by embryos which have been denuded of follicle cells. Two-thirds of the cytoplasmic RNA labeled during a 4-hour period is 25-30 X 10(3) daltons in size, and some of this low molecular weight RNA can be aminoacylated and shown to be transfer RNA. A low level of ribosomal RNA synthesis is detectable at this stage. The contribution, if any, of the rabbit embryonic genome to development prior to the 16-cell stage remains to be defined.

Amino Acyl-tRNA Synthetases↗
PubMed1991

Evolution of the G and P genes of human respiratory syncytial virus (subgroup A) studied by the RNase A mismatch cleavage method.

The G and P genes of human respiratory syncytial viruses (subgroup A), isolated between 1961 and 1989, were analyzed by RNase A one-dimensional fingerprinting, using the Long strain as the reference. Total RNA extracted from cells infected with the different isolates was hybridized to radiolabeled antisense G or P RNA probes of the Long virus. The RNA:RNA heteroduplexes were digested with RNase A and the resistant products analyzed by gel electrophoresis. Comparative analysis of the cleavage patterns revealed extensive genetic heterogeneity in both genes among viruses isolated in different epidemics. In contrast, 13 viruses isolated in Montevideo during a 3-month period showed much more restricted heterogeneity; thus, 11 viruses represented the predominant type of this outbreak and only 2 other viruses generated different RNA cleavage patterns distantly related to the major type. Statistical analysis of the results obtained indicated progressive accumulation of genetic changes with time along cocirculating evolutionary lineages within the same antigenic subgroup of RS virus. The results are discussed in terms of a model for RS virus evolution.

Antigens, Viral↗