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PubMed2005

Quantification of aquabirnaviruses isolated from different host species by real-time RT-PCR.

Real-time reverse transcription (RT)-PCR was developed to detect and quantify successfully aquatic birnaviruses (ABVs) from fish tissue and seawater samples. This method detected marine birnavirus (MABV) RNA in several samples, and the detection was specific for ABVs. Monitoring the MABV strain Y-6 RNA quantification by real-time RT-PCR showed replication kinetics of MABV after experimental infection in vitro. We found the quantity of ABVs isolated from different host species by using combined virus absorption in cell culture and real-time RT-PCR. Although all specimens showed no symptoms of viral infection, ABVs were detected regardless of host species. In conclusion, real-time RT-PCR was shown to be a sensitive and reliable tool to detect and quantify ABVs in cultured fish. This method is useful procedure to show details of horizontal or vertical infections by ABVs in the breeding water of aquatic animals.

Animals↗
PubMed1998

Identification of the respiratory syncytial virus proteins required for formation and passage of helper-dependent infectious particles.

We developed a system to identify the viral proteins required for the packaging and passage of human respiratory syncytial virus (RSV) by reconstructing these events with cDNA-encoded components. Plasmids encoding individual RSV proteins, each under the control of a T7 promoter, were cotransfected in various combinations together with a plasmid containing a minigenome into cells infected with a vaccinia virus recombinant expressing T7 RNA polymerase. Supernatants from these cells were passaged onto fresh cells which were then superinfected with RSV. Functional reconstitution of RSV-specific packaging and passage was detected by expression of the reporter gene carried on the minigenome. As expected, the four nucleocapsid proteins N, P, L, and M2-1 failed to direct packaging and passage of the minigenome. Passage was achieved by further addition of plasmids expressing three membrane-associated proteins, M, G, and F; inclusion of the fourth envelope- associated protein, SH, did not alter passage efficiency. Passage was reduced 10- to 20-fold by omission of G and was abrogated by omission of either M or F. Coexpression of the nonstructural NS1 or NS2 protein had little effect on packaging and passage except through indirect effects on RNA synthesis in the initial transfection. The M2-1 transcription elongation factor was not required for the generation of passage-competent particles. However, addition of increasing quantities of M2-1 to the transfection mediated a dose-dependent inhibition of passage which was alleviated by coexpression of the putative negative regulatory factor M2-2. Omission of the L plasmid reduced passage 10- to 20-fold, most likely due to reduced availability of encapsidated minigenomes for packaging. However, the residual level of passage indicated that neither L protein nor the process of RSV-specific RNA synthesis is required for the production and passage of particles. Omission of N or P from the transfection abrogated passage. Thus, the minimum RSV protein requirements for packaging and passaging a minigenome are N, P, M, and F, although the efficiency is greatly increased by addition of L and G.

Genome, Viral↗
PubMed1982

Regulation of elastin synthesis in developing sheep nuchal ligament by elastin mRNA levels.

Levels of elastin production in explant culture of fetal sheep nuchal ligament and corresponding levels of translatable elastin mRNA were determined in parallel studies during a period of rapid growth of the embryo. The identity of the explant culture and cell-free products was confirmed by peptide mapping, immunoprecipitation, and the characteristic lack of histidine and methionine. Elastin production was quantitated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and radioimmune precipitation. The translation products could be labeled with methionine only when NH2-terminally donated as f-Met-tRNAfMet. Explant cultures showed a large rise in elastin production from 70 days after conception to 150 days after conception. Cell-free translation of RNA demonstrated a parallel in elastin mRNA levels and in elastin mRNA per cell. It appears, therefore, that the marked emphasis the differentiating nuchal ligament places on elastin production is modulated, at least in part, by the quantities of available elastin mRNA.

Aging↗
PubMed2005

Optimization of real time RT-PCR methods for the analysis of gene expression in mouse eggs and preimplantation embryos.

This study was carried out to optimize conditions for using real time RT-PCR as an efficient and precise quantitative method for estimating the transcript levels of genes expressed in samples containing miniscule amounts of RNA, such as single mammalian oocytes and embryos. First, using mouse eggs and blastocysts, we tested three kinds of RNA isolation or collection methods: TRIZOL reagent, oligo-dT conjugated beads, or three freeze/thaw cycles with the reverse transcription buffer. There were no significant differences among three groups in mRNA quantity as assayed by real time RT-PCR analysis. Second, we compared the efficacy of real time analysis between TaqMan fluorescent probes and the SYBR-green dye system. The two systems presented similar real time RT-PCR profiles for the 16s ribosomal protein gene from oocytes to blastocysts. Third, RNA from mouse embryos at defined stages of preimplantation development were isolated and the levels of transcripts encoded by several housekeeping genes (GAPDH, beta-actin, ribosomal protein L7, 16s ribosomal protein, histone H2A.Z) were quantitatively analyzed by real time RT-PCR. The histone H2A.Z and 16s ribosomal protein slightly increased from the egg to blastocyst stages by approximately 10- and 30-fold, respectively. However, other transcripts increased more than 300-fold as a function of developmental stage from eggs to blastocysts. Our results suggest that the simple freezing/thawing method for RNA collection, the economic SYBR-green dye system, and histone H2A.Z gene as an internal control should be useful for the real time RT-PCR analysis of single mouse eggs and preimplantation embryos.

Animals↗
PubMed1989

Relationship between interphasic nucleolar organizer regions and growth rate in two neuroblastoma cell lines.

The relationship between the quantity of silver-stained interphasic nucleolar organizer regions (NORs) and nuclear synthetic activity, caryotype, and growth rate was studied in two established neuroblastoma cell lines (CHP 212 and HTB 10). Statistical analysis of silver-stained NORs revealed four times as many in CHP 212 cells compared with HTB 10 cells. No difference was observed in the ribosomal RNA synthesis between the two cell lines. The caryotype index was 1.2 for CHP 212 and 1.0 for HTB 10 cells. The number of chromosomes carrying NORs and the quantity of ribosomal genes was found to be the same for the two cell lines. Doubling time of CHP 212 cells was 20 hours compared with 54 hours for HTB 10 cells. In CHP 212 cells bindering of cell duplication by serum deprivation induced a progressive lowering (calculated at 48, 72, and 96 hours) of the quantity of silver-stained interphasic NORs. Recovery of duplication by new serum addition induced, after 24 hours, an increase of the quantity of silver-stained interphasic NORs up to control levels. In the light of available data, these results indicate that the quantity of interphasic NORs is strictly correlated only to the growth rate of the cell.

Cell Line↗
PubMed1993

PCR detection of group A bovine rotaviruses in feces.

A polymerase chain reaction (PCR) protocol has been developed for identification of bovine group A rotavirus infection in feces. Primers (20mers) complementary to 3' ends of double-stranded RNA genome segment 6 of bovine rotavirus NCDV strain were synthesized and used in PCR. Bovine rotavirus RNA from infected cell culture was employed to optimize the PCR protocol. Rotavirus-negative fecal samples were spiked with known quantities of bovine rotavirus, and the sensitivity of the PCR assay was determined. Fecal samples were extracted with phenol and treated to eliminate unidentified PCR inhibitor(s) in feces, and PCR was performed. PCR products were either visualized on ethidium bromide-stained agarose gels or detected by chemiluminescent hybridization. The sensitivity of the assay was 6 x 10(4) viral particles/ml of feces with ethidium bromide-stained agarose gel visualization or 6 x 10(2) viral particles/ml of feces with chemiluminescent hybridization. The PCR assay was applied to 18 fecal specimens from clinical cases. All 16 clinical samples that were positive for rotavirus by enzyme-linked immunosorbent assay (ELISA) or by ELISA and electron microscopy (EM) were positive by PCR. The 2 samples that were rotavirus negative by ELISA or by ELISA and EM were also negative on PCR analysis.

Animals↗
PubMed1980

Biochemical and cytochemical studies of the lateral geniculate bodies after optic nerve ligature.

The short term effect of optic nerve ligature was studied by analysing the lateral genuiclate bodies. There was significant difference in total RNA amount per unit tissue between the contralateral and ipsilateral sides 1 week after ligation. There were, however, no observable difference in the acid phosphatase activity and the quantity of contacts between the two sides. The dopamine receptors on the membranes also were much higher in number in the contralateral side.

Acid Phosphatase↗
PubMed1981

Hybrid plasmids carrying part of the Rous sarcoma virus-specific leader sequence.

'Strong-stop' DNA, complementary to the 5'-terminal 101 nucleotides of Rous sarcoma virus genomic RNA and subgenomic mRNAs can be used to isolate RSV-specific mRNA from infected cells. To analyse leader sequences of these mRNAs and to study the mechanism of their translation, relatively large quantities of strong-stop DNA are required. The construction of four plasmids carrying useful strong-stop DNA sequences for mRNA isolation is described. One such hybrid plasmid carries a DNA insertion containing sequences derived from a region starting 42 nucleotides from the 5'-end of RSV RNA, and ending at the tRNATry primer attachment site. Since this plasmid lacks the 20-nucleotide terminal repeat sequence it can be used for the specific isolation of 5'-end fragments of RSV-specific mRNAs and of complementary DNA transcripts of these fragments.

Animals↗
PubMed1995

Simultaneous detection of both hepatitis B virus DNA and hepatitis C virus RNA using a combined one-step polymerase chain reaction technique.

Hepatitis C virus (HCV) RNA polymerase chain reaction (PCR) is widely used for diagnosis of HCV infection and evaluation of therapy. The sensitive hepatitis B virus (HBV) DNA PCR is often reserved for detection of quantities of HBV DNA that are insufficient for hybridization. Application of both PCR techniques is limited by their labor-intensity, potential for contamination, and substantial time required for analysis. To study HCV and HBV infections, occurring alone or in combination, we developed a combined one-step PCR method to detect HCV RNA and HBV DNA in a single serum specimen using oligoprimers from the HCV 5' untranslated region and the HBV preS/S region. Specificity of the HBV and HCV PCR products was confirmed on the basis of their molecular sizes in positive samples, Southern blot hybridization, and negative controls. The sensitivities of the combined PCR were assessed using samples containing a wide range of defined amounts of HBV DNA and HCV RNA and were comparable with those obtained with conventional HBV DNA or HCV RNA PCR methods. The sensitivity of the combined method was further validated by the 100% concordance between results of its HBV and HCV components and those of conventional PCR methods in patients with HBV and/or HCV infections. The combined one-step HBV/HCV PCR is a sensitive, specific, rapid, and cost-effective method, especially suited for epidemiological screening and clinical diagnosis of HBV and HCV infections occurring alone or in combination.

Base Sequence↗
PubMed1968

Effect of lipids, in particular cholesteryl 14-methylhexadecanoate, on the incorporation of labelled amino acids into transfer ribonucleic acid in vitro.

1. Rat liver pH5 enzymes and cell sap extracted with various organic solvents showed a variable decreased incorporation of labelled amino acids into s-RNA (;soluble' or transfer RNA) in vitro. 2. The original enzymic activity could be fully restored, though at different rates, by the addition of lipid extracts in quantities corresponding to those originally present. 3. Of the main lipid groups separated from the extract, only free cholesterol and cholesteryl esters were able to reactivate the extracted pH5 enzymes in the same way as the whole lipid extract. 4. Addition of pure cholesteryl 14-methylhexadecanoate also fully restored the enzymic activity. 5. There was no energy-dependent incorporation of labelled amino acids into ribosomal protein in the presence of extracted cell sap. Addition of cholesteryl 14-methylhexadecanoate fully restored the activity of the cell sap to incorporate labelled leucine and lysine into ribosomal protein and enhanced the incorporation of labelled protein hydrolysate and phenylalanine over the level found with the corresponding non-extracted preparations. 6. It is concluded that lipids play an important role in the synthesis of aminoacyl-s-RNA complexes and that cholesteryl 14-methylhexadecanoate may be the active lipid in this respect.

Amino Acids↗
PubMed1975

Rapid effects of insulin on uridine metabolism in mammary gland explants.

A study was made of the early actions of insulin on uridine metabolism in mammary glang explants. A stimulation of both labeled uridine uptake and its incorporation into RNA was demonstrated as early as 15 min after addition of insulin to medium bathing the tissue; these effects persisted for several hours. The metabolic fate of [3-H] uridine to UMP, UDP, and UTP was observed, whereas insulin had no effect on the quantity of 3-H present as uridine or uracil in these tissues. Further studies were performed in which insulin was also shown to have a rapid stimulatory effect on the incorporation of [32-P] phosphate into RNA; however, the uptake of the labeled phosphate was not affected by insulin. Experiments were also carried out to determine whether the effects of insulin on labeled uridine uptake require ongoing RNA and protein synthesis and whether uridine incorporation depends on concomitant protein synthesis. Incubation of explants with antibiotics which inhibit protein synthesis resulted in the complete suppression of the effects of insulin on labeled uridine uptake and its incorporation into RNA. In contrast, the effect of insulin on labeled uridine uptake does not appear to require ongoing RNA synthesis, since this effect persisted when RNA synthesis was significantly reduced by the presence of actinomycin D.

Animals↗
PubMed2001

Degradation of maternal cdc25c during the maternal to zygotic transition is dependent upon embryonic transcription.

To gain a better understanding of the molecular differences that may contribute to cleavage arrest and the poorer development associated with laboratory produced embryos, a series of experiments were conducted to quantitate the message levels of the cell cycle controller cdc25c, over the maternal to zygotic transition (MZT) in 4-cell in vivo- and in vitro-derived porcine embryos. The experiments were designed to measure both maternal and embryonic derived cdc25c transcripts by quantitative reverse transcription-competitive polymerase chain reaction (RT-cPCR), determine the point of the transition to zygotic genome activation, and study the interaction between initial embryonic transcription and maternal cdc25c degradation. Analysis of in vivo- and in vitro-derived embryos revealed no difference in cdc25c message level for any of the times P4CC (P > 0.05). Comparison of control embryos from 5- to 33-hr P4CC revealed a reduction in transcript quantities in the 10-hr P4CC group that was maintained at later time points (P < 0.05). Embryos cultured in the RNA polymerase inhibitor, alpha-amanitin, from cleavage to 5-, 10-, 18-, 25-, or 33-hr P4CC displayed no difference in cdc25c levels when compared to controls at similar time points (P > 0.05). However, if embryos were first exposed to alpha-amanitin after 18-hr P4CC with this treatment continuing to 33 hr, the levels of cdc25c transcript were reduced (P < 0.04) when compared to those embryos that were first exposed to the inhibitor at either 5- or 10-hr P4CC. This finding and the comparison of these same embryos to the 0-33-hr alpha-amanitin and control groups allowed us to conclude that cdc25c transcription began between 10- and 18-hr P4CC, with the degradation of maternal cdc25c message dependent on transcriptional initiation.

Amanitins↗
PubMed1985

Insulin mediates the asynchronous accumulation of hepatic albumin and malic enzyme messenger RNAs.

We have compared the rate of accumulation of hepatic albumin and malic enzyme mRNAs following insulin treatment of diabetic rats to determine whether insulin coordinately increases mRNA levels or specifically induces the accumulation of individuals mRNAs. Initially, the quantities of both albumin and malic enzyme mRNAs are reduced in diabetic rats compared to normal rats as determined by RNA blot analysis using complementary DNA probes. Following insulin administration for 12 h, albumin and malic enzyme mRNA levels increase at similar rates. However, after 12 h the rate of malic enzyme mRNA accumulation increases dramatically while albumin mRNA continues to increase at its initial rate. This accelerated rate of accumulation of malic enzyme mRNA continued through 60 h of hormone treatment and was associated with the onset of hepatic lipogenesis. Thus, our results suggest that insulin regulates the accumulation of mRNAs encoding these two inducible proteins in an asynchronous manner directly related to the metabolic requirements of the animal.

Animals↗
PubMed1988

Expression of soluble, enzymatically active, human immunodeficiency virus reverse transcriptase in Escherichia coli and analysis of mutants.

We have constructed a plasmid that, when introduced into Escherichia coli, induces the synthesis of large quantities of a protein with an apparent molecular mass of 66 kDa that differs from human immunodeficiency virus (HIV) RNA-dependent DNA polymerase (deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase or reverse transcriptase, EC 2.7.7.49) only in that it has two additional amino-terminal amino acids. This protein is soluble in E. coli extracts, is active in reverse transcriptase assays, and shows inhibition profiles with dideoxy-TTP and dideoxy-GTP that are indistinguishable from the viral enzyme. The deletion of 23 amino-terminal or carboxyl-terminal amino acids or the insertion of 5 amino acids at position 143 substantially decreases the polymerizing activity of the HIV reverse transcriptase made in E. coli. The properties of a 51-kDa reverse transcriptase-related protein made in E. coli suggests that the p51 found in the virion probably does not have substantial polymerizing activity. The full-length HIV reverse transcriptase and the various mutant proteins produced in E. coli should be quite useful for structural and biochemical analyses as well as for the production of antibodies.

Amino Acid Sequence↗
PubMed1991

Purification and characterization of human papillomavirus type 16 E7 protein with preferential binding capacity to the underphosphorylated form of retinoblastoma gene product.

Human papillomavirus type 16 E7 is considered to be a major viral oncoprotein playing an important role(s) in cervical cancers. E7 protein was shown to bind to the protein product of the retinoblastoma gene (RB), while simian virus 40 large T and adenovirus E1A were also shown to possess binding activity to RB protein. The RB protein is a cell cycle regulator that is highly phosphorylated specifically in S, G2, and M, whereas it is underphosphorylated in G0 and G1. Recently, large T was demonstrated to bind preferentially to the underphosphorylated RB protein, which is considered to be an active form restricting cell proliferation. However, it is not known whether E7 can bind to phosphorylated RB protein. We successfully purified large quantities of unfused human papillomavirus type 16 E7 protein expressed in Escherichia coli by using a T7 promoter-T7 RNA polymerase system. The purified E7 protein was demonstrated to bind preferentially to the underphosphorylated RB protein.

Amino Acid Sequence↗
PubMed1994

The two nonallelic insulin-like growth factor-I genes in Xenopus laevis are differentially regulated during development.

To study the potential role of insulin-like growth factor-I (IGF-I) during early embryogenesis, we have used the amphibian Xenopus laevis, a versatile model of vertebrate development. Using polymerase chain reaction (PCR)-based cloning strategies, we have previously identified two different nonallelic Xenopus IGF-I genes (IGF-I' and IGF-I"). Both are expressed in similar quantities in adult liver. We now report the use of a modification of the reverse transcription-PCR method, designated RNA template-specific PCR (RS-PCR), to detect IGF-I messenger RNA (mRNA) from single oocytes and embryos. The same primer pair was used to amplify both IGF-I' and IGF-I" mRNAs. Slot blot analysis of the RS-PCR products with internal oligonucleotide probes that specifically recognize IGF-I' or IGF-I" sequences revealed that only IGF-I' mRNA was present in follicles surrounding mature (stage VI) oocytes; neither IGF-I mRNA was present in follicles surrounding less mature oocytes (stages I and IV) or within oocytes or unfertilized eggs. After fertilization, IGF-I' mRNA was first detected during early organogenesis (stages 21-23), and increased during subsequent stages of development. To localize early IGF-I' expression, a stage 27 embryo was sliced into 24-microns cross-sections; RS-PCR and slot blot analysis were performed on RNA extracts from consecutive sections. IGF-I' mRNA was expressed in all sections, but was most abundant in the body region from which the visceral organs were developing. In contrast, to the early expression of IGF-I', IGF-I" mRNA was not detected until stage 41, a period corresponding to premetamorphic growth. Reverse PCR for Xenopus GH mRNA demonstrated that the onset of GH gene expression was coincident with the onset of IGF-I" gene expression (stage 41). These data suggest that the early expression of IGF-I' may be GH independent, whereas later expression of IGF-I" is GH dependent. We conclude that the two nonallelic IGF-I genes are expressed differentially in a stage-specific manner and suggest that IGF-I' may play an important role during early organogenesis, whereas IGF-I" may be important for premetamorphic growth.

Alleles↗