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[Detection of distemper virus N protein RNA in the brain of dogs with spontaneous distemper encephalitis using a digoxigenin-labeled, double-stranded DNA probe for in situ hybridization].

A digoxigenin-labelled dsDNA-probe of 287 basepairs length complementary to the nucleoprotein-gene of canine distemper virus (CDV) was generated by the polymerase-chain-reaction. The dsDNA-probe hybridized specifically with base sequences of 8 different CDV strains, whereas no hybridization was observed with a porpoise and a canine parainfluenza virus and only a weak signal was obtained with measles virus. In formalin-fixed, paraffin-embedded brain sections of 35 immunohistologically CDV antigen positive dogs with spontaneous distemper encephalitis CDV-RNA could be detected in 25 cases by in situ hybridization. The reason for the lack of RNA detection in some immunohistologically positive dogs may be due to the low stability of DNA-RNA-hybrids. Degradation of RNA by RNAses or diffusion out of autolysed cells can not be excluded.

Animals↗

Prevalence and risk factors for anal squamous intraepithelial lesions in women.

BACKGROUND: Anal cancers are thought to arise from squamous intraepithelial lesions in the anal canal, and women infected with human immunodeficiency virus-1 (HIV) may be at higher risk of anal cancer. Our aim was to determine the prevalence of human papillomavirus (HPV)-related abnormalities of the anal canal in women and to characterize risk factors for these lesions. METHODS: We evaluated HPV-related abnormalities in 251 HIV-positive and in 68 HIV-negative women. We completed physical examinations and obtained questionnaire data on medical history and relevant sexual practices. Univariate and adjusted relative risks (RRs) and 95% confidence intervals (CIs) were computed using the Mantel-Haenszel procedure and regression techniques. All statistical tests were two-sided. RESULTS: Abnormal anal cytology, including atypical squamous cells of undetermined significance, low-grade squamous intraepithelial lesions, or high-grade squamous intraepithelial lesions (HSILs), was diagnosed in 26% of HIV-positive and in 8% of HIV-negative women. HSILs were detected by histology or cytology in 6% of HIV-positive and in 2% of HIV-negative women. HIV-positive women showed increased risk of anal disease as the CD4 count decreased (P<.0001) and as the plasma HIV RNA viral load increased (P =.02). HIV-positive women with abnormal cervical cytology had an increased risk of abnormal anal cytology at the same visit (RR = 2.2; 95% CI = 1.4 to 3.3). Abnormal anal cytology in HIV-positive women was associated with anal HPV RNA detected by the polymerase chain reaction and by a nonamplification-based test (RR = 4.3; 95% CI = 1.6 to 11). In a multivariate analysis, the history of anal intercourse and concurrent abnormal cervical cytology also were statistically significantly (P =.05) associated with abnormal anal cytology. CONCLUSIONS: HIV-positive women had a higher risk of abnormal anal cytology than did HIV-negative women with high-risk lifestyle factors. These data provide strong support for anoscopic and histologic assessment and careful follow-up of women with abnormal anal lesions.

Adult↗

Effects of nucleocapsid mutations on human immunodeficiency virus assembly and RNA encapsidation.

The human immunodeficiency virus (HIV) Pr55Gag precursor proteins direct virus particle assembly. While Gag-Gag protein interactions which affect HIV assembly occur in the capsid (CA) domain of Pr55Gag, the nucleocapsid (NC) domain, which functions in viral RNA encapsidation, also appears to participate in virus assembly. In order to dissect the roles of the NC domain and the p6 domain, the C-terminal Gag protein domain, we examined the effects of NC and p6 mutations on virus assembly and RNA encapsidation. In our experimental system, the p6 domain did not appear to affect virus release efficiency but p6 deletions and truncations reduced the specificity of genomic HIV-1 RNA encapsidation. Mutations in the nucleocapsid region reduced particle release, especially when the p2 interdomain peptide or the amino-terminal portion of the NC region was mutated, and NC mutations also reduced both the specificity and the efficiency of HIV-1 RNA encapsidation. These results implicated a linkage between RNA encapsidation and virus particle assembly or release. However, we found that the mutant ApoMTRB, in which the nucleocapsid and p6 domains of HIV-1 Pr55Gag were replaced with the Bacillus subtilis MtrB protein domain, released particles efficiently but packaged no detectable RNA. These results suggest that, for the purposes of virus-like particle assembly and release, NC can be replaced by a protein that does not appear to encapsidate RNA.

Animals↗

Significance of the 3'-terminal region in minus-strand RNA synthesis of Hibiscus chlorotic ringspot virus.

RNA-dependent RNA polymerase (RdRp) was solubilized from crude extracts of Hibiscus cannabinus infected by Hibiscus chlorotic ringspot virus (HCRSV), a member of the Carmoviridae. After treatment of the extracts with micrococcal nuclease to remove the endogenous templates, the full-length genomic RNA and the two subgenomic RNAs were efficiently synthesized by the partially purified RdRp complex in vitro. When the full-length RNAs of Potato virus X, Tobacco mosaic virus, Odontoglossum ringspot virus and Cucumber mosaic virus were used as templates, no detectable RNA was synthesized. Synthesis of HCRSV minus-strand RNA was shown to initiate opposite the 3'-terminal two C residues at the 3' end in vitro and in vivo. The CCC-3' terminal nucleotide sequence was optimal and nucleotide variations from CCC-3' diminished minus-strand synthesis. In addition, two putative stem-loops (SLs) located within the 3'-terminal 87 nt of HCRSV plus-strand RNA were also essential for minus-strand RNA synthesis. Deletion or disruption of the structure of these two SLs severely reduced or abolished RNA synthesis. HCRSV RNA in which the two SLs were replaced with the SLs of Turnip crinkle virus could replicate in kenaf protoplasts, indicating that functionally conserved structure, rather than nucleotide sequence, plays an important role in the minus-strand synthesis of HCRSV. Taken together, the specific sequence CCC at the 3' terminus and the two SLs structures located in the 3'UTR are essential for efficient minus-strand synthesis of HCRSV.

3' Untranslated Regions↗

Prediction of viremia for cases of hepatitis C virus (HCV) infection using a third-generation anti-HCV enzyme immunoassay test.

BACKGROUND/AIMS: Positive results for anti-hepatitis C virus (HCV) testing reveal subjects are infected by HCV, with presence of HCV RNA indicating persistent infection. In this study, we attempted to evaluate the validity of the HCV viremia using a commercially available, third-generation anti-HCV test. METHODOLOGY: Sample rate/cut-off rate (S/CO) ratios for 1,907 anti-HCV-positive tests (S/CO >1, AxSYM HCV 3.0; Abbott, IL, USA), which had been performed during the last three years, were retrospectively analyzed. Cases with S/CO values between 1 and 100 were divided into 20 groups according to S/CO range (in increments of 10) and ALT (normal or elevated). Ten random cases were obtained for each of the 20 groups. If cases in any group numbered < or =10, all were recruited. Totally, 193 cases were enrolled for HCV RNA detection (COBAS Amplicor; Roche Diagnostics, NJ, USA). RESULTS: The S/CO distribution was biphasic, with two S/CO peaks in the ranges 1-10 (10.7%) and 81-90 (24.2%). Regardless of the ALT level, all samples with S/COs < or =10 were negative for HCV RNA. Of the samples with S/CO values >10, the optimal cut-off was 40 with sensitivity and specificity for both of 81%. In conclusion, subjects with S/CO values < or =10 (10.7%) were more likely to be cases of past infection or of non-specific reaction. Most (90%, 108/120) of the subjects with S/COs >40 represent current or persistent infection. To predict viremia in subjects with S/COs between 10 and 40, 6.7% of all anti-HCV-positive subjects was invalid by a cross-sectional observation. CONCLUSIONS: Follow-up or further study is recommended. The third-generation EIA test plays a semiquantitative role for the prediction of viremia in HCV infection.

Hepacivirus↗

Optimization of nuclear transcript detection by FISH and combination with fluorescence immunocytochemical detection of transcription factors.

Detection of specific nuclear transcripts by fluorescence in situ hybridization (FISH) has constituted a major breakthrough in the study of the organization of transcription in the cell nucleus. Using the model of heat shock genes, we present an optimized procedure for nuclear transcripts that provides high efficiency for RNA detection and good preservation of cell morphology and nuclear texture. Using this procedure, we designed an original high-efficiency methodology combining FISH and fluorescence immunocytochemistry (FICC), which is used here for the simultaneous detection of heat-shock protein (hsp) nuclear transcripts and the specific heat-shock transcription factor 1 (HSF1). We show that the nuclear accumulation sites of HSF1 in heat-shocked cells do not correspond to the sites of transcription of the hsp70 gene.

Cell Nucleus↗

Rapid isolation of plasmid DNA by LiCl-ethidium bromide treatment and gel filtration.

We established a simple and rapid plasmid DNA purification method. Crude plasmid DNA preparations are treated with 4 M LiCl in the presence of 0.6 mg/ml ethidium bromide to precipitate RNA and proteins contained in the DNA preparations. After removal of RNA and protein precipitates, the supernatant is filtered through a Sepharose CL6B column to remove low-molecular-weight contaminants. This procedure takes only 30 min and provides pure plasmid DNA preparations that consist mainly of covalently closed circular plasmid DNA but have no detectable RNA and protein. The purified DNA preparations are susceptible to various six- and four-base-recognition restriction endonucleases, T4 DNA ligase, the Klenow fragment of DNA polymerase I, and T7 and Taq DNA polymerase. Since no special equipment is needed for this purification method, 20 or more samples of microgram to milligram levels can be treated in parallel.

Chemical Precipitation↗

Quantitation of RNA tumor viruses by spectroscopy of density gradient gels.

We have developed a system for virus particle quantitation based on the measurement of the optical absorbance of stained viruses which first have been banded at their buoyant density in an equilibrum 24 to 53% (wt/wt) sucrose density gradient, then fixed in position in the gradient by photopolymerizing an acrylamide-riboflavin mixture in the sucrose, and finally stained and destained. Using plasma from mice infected with leukemia virus (Rauscher) or chickens infected with avian myeloblastosis virus (BAI strain) or suitable controls, we have shown that this technique specifically detects RNA tumor viruses. By using virus stock solutions for which the absolute concentrations were determined by laser beat frequency spectroscopy, we have calibrated the absorbance of the viral bands in terms of virus particle concentration. Using 0.8-ml gradients gels (4 by 45 mm) we can detect as low as 2 x 10(7) viral particles with Coomassie blue staining and 6 x 10(6) viral particles with a more sensitive staining procedure using amido black.

Animals↗

alpha2-Macroglobulin in the marine fish Sparus aurata.

The alpha2-macroglobulin proteinase inhibitors (alpha2Ms) are a family of plasma proteins with the unique ability to inhibit a broad spectrum of proteinases, but are also known as binding proteins for many growth factors and cytokines, including growth hormone and members of the transforming growth factor-beta superfamily. A partial cDNA (475 amino acids) encoding the C-terminus of alpha2M was cloned from the liver of the marine teleostean fish Sparus aurata. The deduced amino acid sequence of the cloned fragment showed 58-60% similarity to carp alpha2Ms. Northern blot analysis of hepatic alpha2M revealed a transcript of about 5 kb. A transcript of a similar size was detected in 1-day larvae. Steady state levels of alpha2M in larvae increased gradually on subsequent days post-hatching. alpha2M expression in embryos was determined by RT-PCR and started in embryos aged 8 h post-fertilization, but not earlier. RT-PCR of muscle RNA detected alpha2M also in fish muscle, albeit with a lower expression than in the liver. Immunoreactive-alpha2M was found in yolk syncytial layer of 3-day larvae and in livers from larvae and adults. Immunoreactive-alpha2M was also identified in soluble total proteins from young larvae with a pattern resembling that of plasma. These data demonstrate that the alpha2M gene is expressed early in fish development. Moreover, in addition to its major expression in liver, alpha2M is expressed also in fish muscle.

Amino Acid Sequence↗

Hepatitis C virus genotypes and reinfection of the graft during long-term follow-up in 35 liver transplant recipients.

To understand the clinical outcome of hepatitis C virus (HCV) recurrence, data from 35 liver transplant recipients who survived more than 6 months were reviewed. The presence of HCV-RNA was evaluated and genotyping was performed. On the basis of alanine aminotransferase (ALT) levels, patients were sorted into four groups. In 20 patients, a chronic elevation in ALT was found; HCV-RNA detection was positive in 17/17 and the following genotypes were found in 15 of them: 1b in ten patients, 2a in four patients, and 3a in one patient. In 11 patients, ALT levels remained normal throughout follow-up; in nine of them HCV-RNA was positive; HCV genotyping was available in eight patients and identified type 1b in two, type 2a in five, and type 3a in another patient. In two patients, ALT fluctuated above and below the upper limits of normality; type 1b HCV-RNA was found in one of them. In two patients, after an initial period of normality, ALT levels showed an abrupt rise; HCV-RNA was positive and type 1b was identified in both patients. Eight patients developed HCV-related deep jaundice and three of them spontaneously recovered. Progressive hepatic injury occurred in eight patients, six with chronic ALT elevation and two showing a late ALT elevation; genotype 1b was present in seven patients while in one, genotype 3a was found; sub-acute graft failure developed in five of them, leading to death in two and retransplantation in the others; the other three patients are alive with recurrent overt cirrhosis. The 1, 3, and 5 year actuarial survivals were 89%, 79%, and 63% respectively. The 1, 3, and 5 year actuarial risks of progressive graft damage were 6%, 7%, and 15%, respectively. In conclusion, HCV reinfection causes a slow decrease in the long-term patients' survival. Persistent elevation of ALT is more frequently observed in patients with genotype 1b infection.

Adolescent↗

Residual risk of transfusion in Ghana.

UNLABELLED: Plasma samples from replacement and volunteer blood donors in Kumasi, Ghana were pooled and tested using a duplex human immunodeficiency virus (HIV) and hepatitis C virus (HCV) RNA detection METHOD: Individual plasmas constitutive of reactive pools were confirmed using reverse transcription-polymerase chain reaction. HIV and HCV infections were significantly higher in 1569 replacement donors than in 1169 volunteers; 2.4 and 1.7 versus 0.3 and 0.7% respectively (P < 0.01). Two duplex RNA-positive plasma pools contained a confirmed/seronegative HIV or HCV RNA individual plasma. The residual post-transfusion risk of HIV and HCV infection of blood collected from replacement blood donors ranged between 1:260 and 1:16 393 after screening for anti-HIV, p24 antigen and anti-HCV. These data indicate that in high-prevalence HIV and HCV blood donor populations, a substantial residual post-transfusion risk of infection remains. This risk might be reduced by collecting blood in younger volunteer donors or by genomic screening.

Adult↗

A protein tyrosine phosphatase-like protein from baculovirus has RNA 5'-triphosphatase and diphosphatase activities.

The superfamily of protein tyrosine phosphatases (PTPs) includes at least one enzyme with an RNA substrate. We recently showed that the RNA triphosphatase domain of the Caenorhabditis elegans mRNA capping enzyme is related to the PTP enzyme family by sequence similarity and mechanism. The PTP most similar in sequence to the capping enzyme triphosphatase is BVP, a dual-specificity PTP encoded by the Autographa californica nuclear polyhedrosis virus. Although BVP previously has been shown to have modest tyrosine and serine/threonine phosphatase activity, we find that it is much more potent as an RNA 5'-phosphatase. BVP sequentially removes gamma and beta phosphates from the 5' end of triphosphate-terminated RNA, leaving a 5'-monophosphate end. The activity was specific for polynucleotides; nucleotide triphosphates were not hydrolyzed. A mutant protein in which the active site cysteine was replaced with serine was inactive. Three other dual-specificity PTPs (VH1, VHR, and Cdc14) did not exhibit detectable RNA phosphatase activity. Therefore, capping enzyme and BVP are members of a distinct PTP-like subfamily that can remove phosphates from RNA.

Acid Anhydride Hydrolases↗

A link between SIVsm in sooty mangabeys (SM) in wild-living monkeys in Sierra Leone and SIVsm in an American-based SM colony.

We have developed a noninvasive method for SIVsm virion RNA detection in feces of captive sooty mangabeys (SMs) (Cercocebus atys). Employing this method to investigate the natural history of SIVsm in endangered SMs is useful for understanding the diversity and evolution of SIVsm and HIV-2. The fecal samples of 61 wild-living SMs and 14 chimpanzees (Pan troglodytes verus) were studied. Samples were collected in rural Sierra Leone in 1993. One SM sample tested positive by reverse transcriptase-PCR. No viral sequence was detected in the feces of 14 chimpanzees. Phylogenetic analysis of the env sequence obtained from SM#13 showed that it clustered within the SIVsm lineage that includes SIVsmH4, B670, and PBj, confirming a direct connection between SIVsm from West Africa and an American-based colony of SM. The virus, designated as SIVsmSL93g, supports a link between the SIVB670/SIVsmH4/SIVPbj lineage and SMs living in Northern Sierra Leone in 1993. The discovery of this strain in a wild-living SM also indicates that noninvasive methods can be used for SIV detection from monkey feces collected in the field.

Animals↗

Staining with pyronin Y detects changes in conformation of RNA during mitosis and hyperthermia of CHO cells.

Cellular RNA in Chinese hamster ovary (CHO) cells synchronized in mitosis (M) or G2 phase, as well as in interphase cells subjected to hyperthermia (42 degrees C, 10 min), was stained with acridine orange (AO), ethidium bromide (EB), or pyronin Y (PY) and the resultant fluorescence was measured by flow cytometry. Total RNA content detected after staining with AO increased in M as compared to G2-phase cells, consistent with continued RNA synthesis during G2 phase. The content of double-stranded RNA, stained with EB (after DNase treatment), was also somewhat higher in M cells. In contrast, the stainability of RNA with PY decreased by 27% in M- compared to G2-phase cells. Furthermore, a decrease in stainability of RNA with PY was observed in G2 cells compared to cells in G1 phase. In separate experiments, RNA stainability with AO or EB was generally unaffected when interphase CHO cells were exposed to 42 degrees C for 10 min, though this same treatment resulted in a 26% decrease in RNA stainability with PY. The decreased PY stainability of cellular RNA in M or heat-treated cells was observed at a relatively narrow range of dye concentration (1.0-2.0 micrograms/ml). The observed hypochromicity of RNA coincides with dissociation of polyribosomes into single ribosomes known to occur during mitosis and following exposure to hyperthermia. It is presumed that the phenomenon involves selective denaturation and condensation of ribosomal (r) RNA by PY in single ribosomes which does not occur in polyribosomes. While the molecular mechanisms responsible for stabilization of rRNA in polyribosomes preventing its denaturation and condensation by PY are unknown, PY appears to be a sensitive probe that can be used to detect and study these changes in rRNA confirmation in situ.

Animals↗

Sedimentation of an RNA polymerase complex from vaccinia virus that specifically initiates and terminates transcription.

A high-molecular-weight protein complex that is capable of accurate transcription initiation and termination of vaccinia virus early genes without additional factors was demonstrated. The complex was solubilized by disruption of purified virions, freed of DNA by passage through a DEAE-cellulose column, and isolated by glycerol gradient sedimentation. All detectable RNA polymerase activity was associated with the transcription complex, whereas the majority of enzymes released from virus cores including mRNA (nucleoside-2'-O)methyltransferase, poly(A) polymerase, topoisomerase, nucleoside triphosphate phosphohydrolase II, protein kinase, and single-strand DNase sedimented more slowly. Activities corresponding to two enzymes, mRNA guanylyltransferase (capping enzyme) and nucleoside triphosphate phosphohydrolase I (DNA-dependent ATPase), partially sedimented with the complex. Silver-stained polyacrylamide gels, immunoblots, and autoradiographs confirmed the presence of subunits of vaccinia virus RNA polymerase, mRNA guanylyltransferase, and nucleoside triphosphate phosphohydrolase I, as well as additional unidentified polypeptides, in fractions with transcriptase activity. A possible role for the DNA-dependent ATPase was suggested by studies with ATP analogs with gamma-S or nonhydrolyzable beta-gamma-phosphodiester bonds. These analogs were used by vaccinia virus RNA polymerase to nonspecifically transcribe single-stranded DNA templates but did not support accurate transcription of early genes by the complex. Transcription also was sensitive to high concentrations of novobiocin; however, this effect could be attributed to inhibition of RNA polymerase or ATPase activities rather than topoisomerase.

Adenosine Triphosphatases↗

Chromogranin-A expression in gastric and colon cancer tissues.

UNLABELLED: We studied the expression of chromogranin A (CgA) in human gastric (n = 17) and colorectal (n = 18) adenocarcinomas by nucleic acid hybridization and immunohistochemical analyses using a specific monoclonal antibody (MAb) to human chromogranin A (CgA). Some corresponding adjacent non-malignant mucosal tissues were also examined. RESULTS: (1) Northern blotting: of 3 normal gastric mucosas examined, 2 (67%) had an easily detected signal for expression of CgA. Only one of 14 gastric carcinomas (7%) and one of 18 colorectal carcinomas (6%) had easily detected RNA signals. (2) Immunohistochemical staining: all non-malignant samples of gastric and colonic mucosa contained CgA-positive neuroendocrine (NE) cells. Two of 17 (12%) gastric adenocarcinomas, and 3 of 18 (17%) of colorectal adenocarcinomas contained CgA-positive tumor cells. Interestingly, the positive cases detected by immunohistochemistry included both cases detected by Northern blotting. Of the 5 cases detected by immunohistochemistry, 2 gastric cancers and 1 rectal carcinoma contained many diffusely scattered positive cells, occurring singly or in small clusters, while 2 colorectal carcinomas contained only occasional single CgA-positive tumor cells. In one of the positive gastric cases, a well-differentiated adenocarcinoma arising in a tubular adenoma, both the adenomatous and the carcinomatous elements contained positively staining cells. Our specific assays for CgA indicate that (1) a NE cell component, either diffusely scattered or occasional, occurs in about 15% of gastric and colorectal tumors; (2) there is no correlation between the presence of NE cells and degree of tumor differentiation; and (3) because only a minority of the tumor cells in positive cases stain for CgA, immunohistochemistry is a more sensitive method than Northern blotting.

APUD Cells↗

A gene that encodes a proline-rich nodulin with limited homology to PsENOD12 is expressed in the invasion zone of Rhizobium meliloti-induced alfalfa root nodules.

To define the early stages of the interaction between Rhizobium and host legumes, we have cloned and characterized three early nodulin-encoding sequences from an alfalfa (Medicago sativa L.) cDNA library by probing with a fragment of a cDNA clone for PsENOD12, an infection-related nodulin from pea (Pisum sativum L.). Although the coding regions of the three clones are 95 to 98% homologous to each other, they are only 43% homologous to the pea clone. However, the putative signal peptide encoded by the alfalfa cDNA clones is 100% homologous to the PsENDO12 signal peptide. The spatial and temporal expression patterns of PsENOD12 and the alfalfa clones were compared. In situ hybridization experiments detected RNA transcripts in the invasion zone of mature nitrogen-fixing nodules, the same site where PsENOD12 mRNAs are found. Transcripts were also found by in situ hybridization in cells of Rhizobium meliloti exoH mutant-induced nodules penetrated by infection threads, but northern analysis did not detect transcripts in inf- (infection thread minus) nodules elicited by R. meliloti exoB nodules or in pseudonodules elicited by treatment with the auxin transport inhibitor N-1-(naphthyl)phthalamic acid. In addition, the alfalfa gene represented by these cDNA clones exhibited a temporal expression pattern that differed from that of PsENOD12, which is transiently expressed. These data, plus information derived from Southern blot analysis, indicate that we have isolated cDNA clones for a novel early nodulin, which we have designated MsENOD10 (Medicago sativa Early Nodulin 10).

Amino Acid Sequence↗

Detection of viral RNA in experimental coxsackievirus B3 myocarditis of mice using the polymerase chain reaction.

The presence of the viral RNA in the myocardium in experimental coxsackievirus B3 myocarditis of mice was investigated using the polymerase chain reaction (PCR). Four-week-old C3H/He mice (n = 35) were inoculated with coxsackievirus B3 (Nancy strain, 10(5) plaque-forming units/mouse). We used a pair of primers, which encompass a part of the 5' end sequence of the coxsackievirus B3 genome and can also detect many enteroviral RNAs. We found that hearts were positive for the viral RNA from 2 to 21 days after virus inoculation by PCR, but negative after day 28 and in non-infected control mice (n = 5). The viral RNA were detected by PCR later than by culture. Thus, the detection of the viral RNA using enzymatic amplification is more rapid and easier and may be more useful for clinical diagnosis of viral myocarditis than conventional culture methods. However, virus persistence in the myocardium long after virus inoculation is unusual in this model.

Animals↗