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PubMed1976

Mediation of cytotoxic immune responses against human tumor-associated antigens by xenogeneic immune RNA.

Xenogeneic immune RNA (I-RNA), extracted from the lymphoid organs of sheep or guinea pigs immunized with human tumor cells, mediated in vitro cytotoxic immune responses that were directed specifically against tumor-associated antigens of human tumor target cells. Normal human peripheral blood lymphocytes from healthy donors became markedly more cytotoxic for human tumor target cells after being incubated with I-RNA extracted from the lymphoid organs of animals that had been immunized with that particular tumor. Gastric carcinoma, malignant melanoma, and carcinoma of the breast were studied. Lymphocytes incubated with RNA from animals immunized with only complete Freund's adjuvant evidenced no increased cytotoxic activity. RNA extracted from the lymphoid organs of animals immunized with normal skin fibroblasts that were autologous to the immunizing tumor, when incubated with normal allogeneic lymphocytes, also mediated cytotoxic immune reactions against tumor target cells. These immune responses probably were directed principally against normal transplantation antigens. However, when lymphocytes that were autologous to the immunizing tumor and/or the tumor target cells were incubated with RNA from animals immunized with autologous normal fibroblasts, cytotoxicity did not increase. Only I-RNA extracted from donor animals specifically immunized with tumor cells mediated cytotoxic antitumor immune responses when incubated with autologous lymphocytes.

Animals↗

PubMed2005

Optimization of liver biopsy RNA sampling and use of reference RNA for cDNA microarray analysis.

In this study, we used the rat liver as a model system to optimize the conditions for extracting RNA from liver biopsies for use in cDNA microarrays. We found that a 5-mm biopsy with a 16-gauge needle and storage in RNA later at 4 degrees C were optimal conditions for RNA extraction. The most important factor for the quantity and quality of RNA extraction was the sample diameter. Using the optimized sampling conditions and a cDNA microarray, we compared the expression of genes in the normal and the fibrotic tissues of the LEC rat liver, a model of liver tumorigenesis, with SD rat liver RNA as a reference. We found 29 genes that were up-regulated and 33 genes that were down-regulated in the fibrotic part of the liver. Furthermore, with the help of the reference RNA, we were able to classify the expression profiles into five groups without complex mathematical analyses; without the reference RNA, the genes could be classified into only two groups. Finally, we found that osteopontin was expressed at a very high level in the fibrotic portion of the LEC rat liver. This cDNA microarray result was validated by immunohistochemistry, which showed an elevated expression of osteopontin in the region of cholangiocarcinoma and a lack of expression in normal tissues. With optimized conditions, we should be able to apply the microarray system for routine practice.

Animals↗

PubMed1996

Detection of gastric cancer micrometastases in lymph nodes by amplification of keratin 19 mRNA with reverse transcriptase-polymerase chain reaction.

A sensitive method for the detection of gastric cancer micrometastases in lymph nodes was developed. The method was based on amplification of keratin 19 mRNA by reverse transcriptase-polymerase chain reaction (RT-PCR). Keratin 19 RT-PCR showed that keratin 19 mRNA was expressed in all 12 gastric cancers, but not in any of 20 normal control lymph nodes, indicating that keratin 19 mRNA is a good target of RT-PCR for the detection of gastric cancer micrometastases in lymph nodes. Serial dilution studies of RNA extracted from gastric cancers against RNA extracted from control lymph nodes demonstrated that the detection sensitivity of the keratin 19 RT-PCR method was one cancer cell in 10(3)-10(5) lymph node cells. Detectability of lymph node metastases was compared between keratin 19 RT-PCR and conventional histological examination, using 100 lymph nodes obtained from 12 gastric cancer patients. Keratin 19 mRNA was detected in all of the seven lymph nodes which were histologically metastasis-positive. Of the 93 lymph nodes which were histologically metastasis-negative, 79 were found not to express keratin 19 mRNA but 14 were found to express keratin 19 mRNA, indicating that these lymph nodes contained micrometastases which could not be detected by histological examination. These results demonstrate that keratin 19 RT-PCR is a more sensitive method than histological examination for the detection of gastric micrometastases in lymph nodes.

Adult↗

PubMed1994

Comparison of methods to detect enteroviral genome in frozen and fixed myocardium by polymerase chain reaction.

BACKGROUND: Understanding the pathogenesis of viral myocarditis is linked to the availability of sensitive assays to detect viral genome in clinical material. Recent advances in molecular techniques permit detection of viral-specific RNA in tissue samples. We describe here a comparison of different methods for RNA extraction, reverse transcription, and gene amplification of Coxsackievirus B3 virus in fixed and frozen mouse myocardium. EXPERIMENTAL DESIGN: Homogenized Coxsackie B3 virus-infected myocardium was assayed for virus titer and formalin fixed, paraffin-embedded sections from the same heart were subjected to RNA extraction by 3 different methods. Optimal conditions were determined for a one-step assay combining reverse transcription and the polymerase chain reaction to detect enteroviral genome in RNA extracted by these different methods. The presence of amplifiable cDNA was confirmed by amplification of porphobilinogen deaminase mRNA as a positive control. RESULTS: Extraction of RNA from paraffin-embedded myocardium after overnight digestion with proteinase K (200 micrograms/ml) and 0.5% sodium dodecyl sulfate was the most efficient of the three methods compared. With our optimized polymerase chain reaction assay, in which the cDNA synthesis and amplification steps are combined, we detected as little as 10 TCID50 of virus from frozen viral stocks and tissue homogenates and 1.0 TCID50 of virus from fixed tissue. CONCLUSIONS: This sensitive polymerase chain reaction assay will facilitate examination of archival clinical samples to establish a retrospective diagnosis of enterovirus infection.

Animals↗

PubMed1991

Antisense probes containing 2-aminoadenosine allow efficient depletion of U5 snRNP from HeLa splicing extracts.

RNA duplexes containing the modified base 2-amino-adenine in place of adenine are stabilized through the formation of three hydrogen bonds in 2-amino A.U base pairs. Antisense 2'-O-alkyloligoribonucleotide probes incorporating 2-aminoadenosine are thus able to efficiently affinity select RNP particles which are otherwise inaccessible. This has allowed the efficient and specific depletion of U5 snRNP from HeLa cell nuclear splicing extracts. U5 snRNP is shown to be essential for spliceosome assembly and for both steps of pre-mRNA splicing. The absence of U5 snRNP prevents the stable association of U4/U6 but not U1 and U2 snRNPs with pre-mRNA.

Adenosine↗

PubMed1981

Rapid, simple method of preparing rotaviral double-stranded ribonucleic acid for analysis by polyacrylamide gel electrophoresis.

A procedure for extracting rotaviral double-stranded ribonucleic acid (RNA) directly from fecal and intestinal specimens collected from calves and pigs is described. This procedure provides a rapid, simple, reproducible method of obtaining rotaviral double-stranded RNA preparations suitable for electrophoretic analysis in polyacrylamide-agarose composite gels. The rotaviral genome electrophoretic migration pattern produced by double-stranded RNA extracted directly from a specimen by this procedure was qualitatively identical to the electrophoretic migration pattern obtained with double-stranded RNA extracted from purified rotavirus derived from the same specimen. Direct extraction of specimens containing porcine rotavirus-like virus by this procedure gave preparations that had electrophoretic migration patterns similar, but not identical, to the characteristic electrophoretic migration pattern of the rotaviral genome. Sufficient rotaviral double-stranded RNA could be extracted from 6 ml of fecal or intestinal specimen by this procedure to permit 15 or more electrophoretic assays.

Animals↗

PubMed2002

Molecular serotyping of dengue viruses in field-caught Aedes mosquitos by in-house RNA extraction/RT-PCR reagent kits.

We developed in-house RNA extraction and RT-PCR reagent kits for the molecular serotyping of dengue viruses in field-caught Aedes mosquitos. Mosquitos that showed positive results by ELISA or IFA were selected for the identification of dengue viruses in order to predict the distribution of the four dengue serotypes. Total RNA was extracted from one whole mosquito as well as from one dissected mosquito by our in-house RNA extraction reagents using the modified method of guanidinium thiocyanate denaturation and isopropanol precipitation. The extracted RNA was amplified by our in-house RT-PCR reagents specific for each dengue serotype under optimized conditions. Dengue viral RNA extracted from a single mosquito as well as from the head and thorax of one dissected mosquito could be detected successfully; it could not be found in the abdomen, however. These results indicated that most of the dengue viruses were located in the head and thorax rather than in the abdomen. The results of dengue serotyping showed a pure specific PCR product for each dengue serotype at 490, 230, 320 and 398 bp for DEN-1, DEN-2, DEN-3, and DEN-4 respectively. In addition, the detection sensitivity was very high: an amount of RNA template equivalent to approximately 1/80 of a single mosquito could be detected by agarose gel electrophoresis and ethidium bromide staining. The coupling of RT-PCR-based surveillance of dengue viral infection with disease mapping data (Geograpical Information System, GIS) could serve as an alternative epidemiological means of providing an early warning of dengue fever/dengue hemorrhagic fever epidemics.

Aedes↗

PubMed2000

Junction phosphate is derived from the precursor in the tRNA spliced by the archaeon Haloferax volcanii cell extract.

RNA splicing in archaea requires at least an endonuclease and a ligase, as is the case for the splicing of eukaryal nuclear tRNAs. Splicing endonucleases from archaea and eukarya are homologous, although they differ in subunit composition and substrate recognition properties. However, they all produce 2',3' cyclic phosphate and 5'-hydroxyl termini. An in vitro-transcribed, partial intron-deleted Haloferax volcanii elongator tRNA(Met) has been used to study splicing by H. volcanii cell extracts. Substrates and products were analyzed by nearest neighbor analyses using nuclease P1 and RNase T2, and fingerprinting analyses using acid-urea gels in the first dimension and gradient thin layer chromatography in the second dimension. The results suggest that 2',3' cyclic phosphate at the 3' end of the 5' exon is converted into the splice junction phosphate forming a 3',5'-phosphodiester linkage. This resembles the animal cell type systems where the junction phosphate preexists in the transcript, and differs from yeast type systems, where GTP is the source of junction phosphate.

Base Sequence↗

PubMed1992

Single- and double-stranded RNAs associated with an isolate of beet soil-borne virus.

Ethidium bromide staining of electrophoretically separated ssRNAs and dsRNAs as well as northern blot analyses with cDNA clones suggested that the genome of the Ahlum serotype of beet soil-borne virus (BSBV) consists of two major ssRNA species of approximately 3.6 and 3.2 kb, respectively, and possibly a minor ssRNA of approximately 6.0 kb. A few of our clones hybridized with both the 3.6-kb and the 3.2-kb RNAs, the majority of the clones, however, hybridized only with the 3.2-kb RNA. The 3.2-kb RNA is, therefore, apparently not a degradation product or a partially deleted form of the 3.6-kb RNA. None of our clones hybridized with the faint band(s) of the 6.0-kb ssRNA(s) which was produced by RNA extracts of some of our virus preparations. A fourth ssRNA of approximately 3.0 kb, which hybridized with the same clones as the 3.2-kb RNA, was found at relatively high concentrations in RNA extracts from purified virus, but not in total RNA extracts from leaves. Its origin is unknown. It is apparently not derived from the 3.2-kb RNA by the loss of a VPg or a poly(A) tail. Hybridization tests with 32P-labelled poly(dT) suggested that none of the RNAs of BSBV is polyadenylated. With respect to size and the lack of a poly(A) tail the RNAs of BSBV are more similar to those of definitive furoviruses than to those of beet necrotic yellow vein virus which is only a possible member of the furovirus group and has RNAs which readily hybridized with poly(dT).

Blotting, Northern↗

PubMed1991

Comparison of IgE expression at the mRNA and protein levels in vitro.

The regulating effects of IL-4 and pokeweed mitogen on IgE synthesis in vitro by human peripheral blood leucocytes has been compared with the corresponding effect of these regulators on the expression of IgE mRNA. The latter was measured by dot blot hybridization with an oligonucleotide coding for a unique six amino acid region of the CH epsilon 2 domain. Specificity of the oligonucleotide probe was established by its inability to hybridize with RNA extracted from HMY-2 (IgG) and XQ-15 (IgM) secreting cell lines whilst producing intense signals with RNA extracted from the IgE secreting cell line U266. Whilst IgE mRNA was detected in RNA extracted from PBL of both atopic and control subjects, spontaneous IgE synthesis was restricted to atopic PBL. IL-4 increased both IgE mRNA and IgE synthesis in all PBL samples but PWM, while significantly increasing IgE mRNA expression either failed to modify IgE synthesis or actively suppressed it. The assay system employed to quantitate IgE synthesis in vitro was shown to be inhibited by both IgE binding factors and IgG anti-IgE autoantibodies which are produced in PBL cultures. IgE mRNA levels might therefore more accurately monitor the regulatory effects of IL-4 and PWM on IgE synthesis than quantitation of the IgE by radioimmunoassay.

Cell Line↗

PubMed1985

Detection of antibodies to small nuclear ribonucleoproteins and small cytoplasmic ribonucleoproteins using unlabeled cell extracts.

RNA molecules immunoprecipitated with sera from patients who have rheumatic diseases can be readily detected in polyacrylamide gels by using ethidium bromide and silver stains. With these stains, we found that RNA patterns characteristic of a broad range of specific small nuclear ribonucleoproteins and small cytoplasmic ribonucleoproteins were recognizable. The stains correctly identified antibodies to ribonucleoproteins in 33 (92%) of 36 patient sera selected for study because of known antibody specificities. The silver stain method detected antibodies to ribonucleoproteins in 25 (76%) of 33 patients with classic systemic lupus erythematosus, a frequency that approximated the frequency observed in the Lerner-Steitz assay, which is based on autoradiography. This approach considerably simplifies the latter radioimmunoassay with minimal loss of precision and sensitivity.

Autoantibodies↗

PubMed1999

[The feature of influenza virus activity and genetic characterization of HA1 gene of influenza A H3N2 viruses isolated from 1994-1997 in Shenzhen].

OBJECTIVE: To understand the feature of influenza virus activity and genetic characterization of HA1 gene of influenza A H3N2 viruses isolated in recently years in Shenzhen. METHODS: The specimens were inoculated into amniotic and allantoic cavities of the embryonated chicken eggs for viral isolation. The isolates were typed with HI test. Virion RNA extracted from allantoic fluid by Rneasy RNA extraction kit was used for RT-PCR amplification. Afterward, the product of PCR was purified with purification kit. RNA sequence analysis was performed by Sanger dideoxy-mediated nucleotide chain termination method. RESULTS: Influenza A H3N2, H1N1 and B viruses were cocirculating in men in Shenzhen in recent years. However, the extent of their activities was not the same in a single year. The influenza B virus was the predominant strain in 1994 and 1997, but the predominant strain was H3N2 virus in 1996. The genetic analysis showed that the substitution of amino acids occured year by year and was mainly located at antigenic determinants or receptor binding site on HA1 domain of H3N2 viruses. CONCLUSION: Influenza A H3N2, H1N1 and B viruses were still co-circulating in men in Shenzhen in recent years, the predominant strain of influenza virus was different in different years. An increase of influenza A H3N2 virus activity in 1996 was due to the substitution of amino acids sequences on viral HA1 domain.

Amino Acid Sequence↗

PubMed1991

Failure to detect paramyxovirus sequences in Paget's disease of bone using the polymerase chain reaction.

It is widely believed that Paget's disease of bone is due to a "slow virus" infection of osteoclasts with one of the paramyxovirus group. Controversy continues to surround the identity of the virus involved, however, since at different times evidence has been presented implicating measles virus (MV), respiratory syncytial virus (RSV), and canine distemper virus (CDV) as putative infective agents. In this study we used the technique of reverse transcription and polymerase chain reaction (PCR) to screen for paramyxovirus sequences in ribonucleic acid (RNA) extracted from pagetic bone. We were able to detect viral amplification products of the appropriate size in RNA extracted from as few as 50 cells experimentally infected with a wide range of paramyxoviruses, including measles, canine distemper, parainfluenza 3, and respiratory syncytial virus, but we found no evidence of viral products in RNA extracts of affected bone from 10 consecutive patients with Paget's disease. This study fails to support the hypothesis that active infection with one of these or a related paramyxovirus is involved in the pathogenesis of Paget's disease.

Aged↗

PubMed2003

Neurokinin 1 receptors and neprilysin modulation of mouse bladder gene regulation.

Neurokinin 1 (NK(1)) receptors play a fundamental role in neurogenic inflammation. We sought to determine the mechanisms downstream from NK(1) receptor (NK(1)R) activation using cDNA arrays and a novel statistical method to analyze gene expression. We used female NK(1)R(-/-) and wild-type (WT) mice that were sensitized actively by intraperitoneal injections of dinitrophenol 4 (DNP(4))-human serum albumin. Cystitis was induced by intravesical instillation of antigen of DNP(4)-ovalbumin, and control mice were challenged with saline. At 1, 4, and 24 h after instillation, bladders were removed for 1) RNA extraction (n = 3), 2) replicate of RNA extraction (n = 3), and 3) morphological analysis (n = 6). For cDNA array experiments, three bladders from each group were homogenized, and total RNA was obtained. DNase-treated RNA was reverse-transcribed to cDNA, labeled with [alpha-(32)P]dATP and hybridized to Atlas Mouse 1.2 Arrays (Clontech). After calculating the mean and SD for background spots, each experimental value was assigned a normalized score S using the formula S' = (S - Av)/SD, where S' is the original pixel value, and Av and SD are the mean and standard deviation of background spots, respectively. Only genes that expressed 3 SD values above background were used. Hypervariable genes were sorted by cluster analysis. Matrices of correlation coefficients were calculated and represented in a connectivity mosaic. As results, we found that in WT mice the most prominent gene cluster had neprilysin in a central position and positively correlated to a group of activator protein-1 (AP-1)-responsive genes, including laminin-alpha3, tissue plasminogen activator 11, fos-B, and TNF-beta. In WT mice, antigen-induced bladder inflammation led to a downregulation in neprilysin expression. In contrast, NK(1)R(-/-) mice failed to mount an inflammatory reaction and presented neprilysin negatively correlated with the same genes described in WT. In conclusion, this work indicates an overriding participation of NK(1)R and neprilysin in bladder inflammation, provides a working model for the involvement of AP-1 transcription factor, and evokes testable hypotheses regarding the role of NK(1)R and neprilysin in inflammation.

Animals↗

PubMed2006

Efficient extraction of high-quality total RNA from various hop tissues (Humulus lupulus L.).

The isolation of high-quality RNA is a prerequisite for gene expression studies. RNA quality is of special relevance if PCR-based strategies such as cDNA-AFLP or RT-PCR are followed. Our molecular investigations of hop (Humulus lupulus L.) focus on genes that determine the biosynthesis of prenylflavonoids with interesting biological activities which accumulate in the lupulin glands. However, optimized protocols for RNA extraction from hop cones are not available. In this study, the RNeasy midi kit protocol was modified to isolate high amounts of total RNA from fresh and freeze-dried hop tissues, specifically leaves, female inflorescences, and lupulin-enriched hop cone fractions. The main difficulties in obtaining high RNA yields were related to specific features of hop, including the abundance of secondary metabolites and their accumulation in the sticky lupulin glands. The introduction of a number of modifications into the RNeasy midi kit protocol resulted in RNA of high quality, as assessed by spectrophotometry and electrophoresis in agarose gels. The protocol developed is currently being used to produce cDNA-AFLP fingerprints of hop cones and leaves for genetic screening. Furthermore, the method could provide RNA for further molecular studies, including Northern blot hybridizations and reverse transcription-polymerase chain reactions.

Blotting, Northern↗

PubMed1978

Evidence that the regulation of diphtheria toxin production is directed at the level of transcription.

It has been known for several decades that iron inhibits the production of diphtheria toxin by Corynebacterium diphtheriae by preventing expression at maximal levels. We examined the inhibition kinetics of toxin production after the addition of either iron or rifampin to iron-limited cultures of C7 (betatox+). Iron-mediated inhibition of toxin production was found to be linear within the range of 16 nM to 16 micron. The inhibition kinetics following the addition of iron or rifampin was almost identical. [3H]RNA extracted from iron-limited toxigenic C. diphtheriae was found to hybridize to a greater extent to corynephage beta DNA than either [3H]RNA extracted from toxigenic C. diphtheriae before the onset of toxin production or [3H]RNA extracted from nonlysogenic, nontoxigenic C. diphtheriae.

Corynebacterium diphtheriae↗

PubMed1981

Skeletal muscle actin mRNA. Characterization of the 3' untranslated region.

Plasmids p749, p106, and p150 contain cDNA inserts complementary to rat skeletal muscle actin mRNA. Nucleotide sequence analysis indicates the following sequence relationships: p749 specifies codons 171 to 360; p150 specifies codons 357 to 374 together with 120 nucleotides of the 3'-non-translated region; p106 specifies the last actin amino acid codon, the termination codon and the entire 3' non-translated region. Plasmid p749 hybridized with RNA extracted from rat skeletal muscle, cardiac muscle, smooth (stomach) muscle, and from brain. It also hybridizes well with RNA extracted from skeletal muscle and brain of dog and chick. Plasmid p106 hybridized specifically with rat striated muscles (skeletal and cardiac muscle) mRNA but not with mRNA from rat stomach and from rat brain. It also hybridized to RNA extracted from skeletal muscle of rabbit and dog but not from chick. Thermal stability of the hybrids and sensitivity to S1 digestion also indicated substantial divergence between the 3' untranslated end of rat and dog skeletal muscle actins. The investigation shows that the coding regions of actin genes are highly conserved, whereas the 3' non-coding regions diverged considerably during evolution. Probes constructed from the 3' non-coding regions of actin mRNAs can be used to identify the various actin mRNA and actin genes.

Actins↗

PubMed1997

Evaluation of commercially available and in-house reverse transcription-PCR assays for detection of hepatitis G virus or GB virus C.

Serum samples from 96 Spanish hemodialysis patients, as well as serial dilutions of RNA extracted from a reference strain of hepatitis G virus (HGV), were tested for HGV or GB virus C (GBV-C) RNA. Two different reverse transcription (RT)-PCR-based methods of detection were compared for the ability to detect RNA extracted from the samples: an RT-nested PCR assay with primers derived from the 5' noncoding region (5'NC) or nonstructural region 3 (NS3) sequences and a commercially available RT-PCR assay with primers derived from the 5'NC or NS5A sequences. When RT-nested PCR was performed on 10-fold serial dilutions of RNA from the HGV reference strain, the last positive dilution was 10(-7) to 10(-8). With the commercial RT-PCR assay, the last positive dilution was 10(-6) to 10(-7). When equal amounts of RNA extracted from serum samples from 96 hemodialysis patients were tested for HGV or GBV-C RNA, 25 patients (26%) were positive by the RT-nested PCR. However, only 21 (84%) of these 25 positive patients were positive for HGV or GBV-C by the commercial RT-PCR assay. Analysis of the 5'NC and NS3 sequences amplified by RT-nested PCR demonstrated that all but two positive patients had unique HGV or GBV-C sequences. In summary, RT-nested PCR and a commercially available RT-PCR assay for HGV or GBV-C gave concordant results for 96% of the patients tested.

Base Sequence↗