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Mechanisms responsible for dominant expression of human growth hormone gene mutations.

Point mutations of the donor splice site of intron 3 of the human GH-1 gene cause autosomal dominant inherited isolated growth hormone deficiency (IGHD II). The mechanism by which a defect in one GH-1 allele results in GH deficiency is obscure. Previously reported reverse transcription-nested PCR data suggested an overexpression of the mutant GH-1 allele. We employed alternative methods to determine the relative expression of mutant (C for G at +1 of intron 3) and normal GH-1 allele. The use of a second round PCR primer bridging exons 2 and 3 and specific for normal GH-1 messenger ribonucleic acid (mRNA) indicated equal quantities in mutant and control cells. Large scale messenger RNA extraction from Epstein-Barr virus-transformed lymphoblasts permitted assay by ribonuclease protection. In normal pituitary, there were three GH-1 mRNA species. The variant lacking exon 3 comprised 5% of the total GH-1 mRNA. The proband's lymphoblasts contained equal amounts of mRNA with and without exon 3. Only normal GH-1 mRNA was detected in controls. Secreted GH, measured by enzyme-linked immunosorbent assay was present in equal concentrations in media from normal and mutant cells. Thus, GH-1 mRNA lacking exon 3 was expressed in proportion to the dosage of the mutant gene, and dominant effects on GH secretion were not observed in lymphoblasts. These findings are compatible with a dominant negative mechanism involving interaction between normal and mutant proteins in secretory vesicles of somatotropes.

Adolescent↗

Effects of centrifugation speed and freezing on composition of ruminal bacterial samples collected from defaunated sheep.

Triplicate ruminal samples from four rumen-cannulated defaunated sheep (50 kg BW) were used in a completely randomized design experiment with a 2 x 3 factorial arrangement of treatments to test effects of two pretreatments (fresh vs. freezing) and three centrifugation speeds (4640 x g for 30 min; 9820 x g for 20 min; 25,900 x g for 20 min) or quantity of ruminal bacteria harvested and composition of ruminal bacterial samples. There were no differences among centrifugation speeds on quantity of ruminal bacterial harvested, organic matter, total N, RNA, and diaminopimelic acid concentrations (% of DM), or RNA:N, RNA:organic matter, N:organic matter, and diaminopimelic acid:organic matter ratios. However, there were differences between fresh and frozen samples for all measurements except diaminopimelic acid concentration, and the diaminopimelic acid:organic matter ratio, suggesting that freezing ruminal fluid is not appropriate for obtaining truly representative bacterial samples.

Animals↗

Biochemical, pharmacological, and phase I clinical evaluation of pseudoisocytidine.

Pseudoisocytidine (psi ICyd) is a C-nucleoside with enhanced stability and resistance to enzymatic deamination when compared to 5-azacytidine and 1-beta-D-arabinofuranosylcytosine. Elimination kinetics in plasma using [14C]psi ICyd showed a beta-phase for t1/2 for 14C of 2 hr and a beta-phase t1/2 of unchanged psi ICyd of 1.5 hr. Net recovery of radioactivity in urine over 24 hr varied between 40 and 80% of the administered dose; 50 to 90% was unchanged drug and the rest was pseudouridine. Human leukemic cells in vitro deaminated psi ICyd very slowly, formed appreciable quantities of pseudoisocytidine triphosphate, and incorporated small amounts into RNA and DNA. Clinical trials were done using a daily i.v. injection for 5 consecutive days. Hematological or intestine toxicities were not seen, nor was depression of white blood cell count observed in leukemic patients. Hepatic toxicity proved to be dose limiting; this was characterized by an early phase with elevation of prothrombin time and aspartate aminotransferase. A later phase with cirrhosis was observed in two patients. Autopsy showed massive hepatic necrosis in patients dying of acute toxicity and micronodular cirrhosis in one patient dying with the chronic form.

Antineoplastic Agents↗

Persistence of hepatitis C virus in patients successfully treated for chronic hepatitis C.

It is unclear whether the current antiviral treatment for chronic hepatitis C virus (HCV) infection results in complete elimination of the virus, or whether small quantities of virus persist. Our study group comprised 17 patients with chronic HCV who had sustained virological response (SVR) after interferon/ribavirin treatment. Serum and peripheral blood mononudear cells were collected 2 to 3 times at 3- to 6-month intervals starting 40 to 109 months (mean, 64.2 +/- 18.5 months) after the end of therapy. In addition, lymphocyte and macrophage cultures were established at each point. In 11 patients, frozen liver tissue samples were available from follow-up biopsies performed 41 to 98 months (mean, 63.6 +/- 16.7 months) after therapy. Presence of HCV RNA was determined by sensitive reverse-transcriptase polymerase chain reaction, and concentration of positive and negative strands was determined by a novel quantitative real-time reverse transcriptase polymerase chain reaction. Only 2 of 17 patients remained consistently HCV RNA negative in all analyzed compartments. HCV RNA was detected in macrophages from 11 patients (65%) and in lymphocytes from 7 patients (41%). Viral sequences were also detected in 3 of 11 livers and in sera from 4 patients. Viral replicative forms were found in lymphocytes from 2 and in macrophages from 4 patients. In conclusion, our results suggest that in patients with SVR after therapy, small quantities of HCV RNA may persist in liver or macrophages and lymphocytes for up to 9 years. This continuous viral presence could result in persistence of humoral and cellular immunity for many years after therapy and could present a potential risk for infection reactivation.

Adult↗

Low plasma human immunodeficiency virus type 2 viral load is independent of proviral load: low virus production in vivo.

Levels of virus in the plasma are closely related to the pathogenicity of human immunodeficiency virus type 1 (HIV-1). HIV-2 is much less pathogenic than HIV-1, and infection with HIV-2 leads to significantly lower plasma viral load. To identify the source of this difference, we measured both viral RNA and proviral DNA in matched samples from 34 HIV-2-infected individuals. Nearly half had undetectable viral RNA loads (<100 copies/ml), but levels of proviral DNA were relatively high and confirmed that quantities of provirus in HIV-1 and HIV-2 infection were similar. Overall, HIV-2 proviral DNA load did not correlate with viral RNA load, and higher viral RNA load was associated with increased production of plasma virus from the proviral template. These results suggest that low viral load in HIV-2 infection is due to decreased rates of viral production, rather than differences in target cell infectivity.

CD4 Lymphocyte Count↗

Enhanced sensitivity RNA gel loading buffer that enables efficient RNA separation on native gels.

RNA gel analysis is essential for quality assessment of RNA preparations for subsequent analysis such as microarrays and real-time PCRs. The routinely used standard electrophoresis of RNA through formaldehyde-containing agarose gels is not only labor-intensive and time-consuming, but also involves sizeable quantities of hazardous materials. Above all, it is not sensitive, requiring more than 1 microgram of RNA for the assay. Current gene expression profiling with microarrays and real-time PCR often involves limiting amounts of RNA. It is therefore important to have a more sensitive way to analyze RNA. Here we report an improved ethidium bromide-based RNA gel analysis system with our Superload buffer that increases sensitivity to 12.5 ng of total RNA and allows RNA analysis on a regular native Tris-acetate EDTA (TAE) agarose gel.

Animals↗

Selective precipitation of ribonucleic acid from a mixture of total cellular nucleic acids extracted from cultured mammalian cells.

A simple and reproducible method is described for precipitating RNA selectively from total mammalian-cell nucleic acids extracted by the phenol-sodium dodecyl sulphate procedure at pH8.0. Under specified conditions bulk RNA is precipitated almost quantitatively whereas bulk DNA remains in solution. Minor components of RNA (detected by pulse-labelling and chromatography on methylated albumin-kieselguhr) and rapidly labelled components of DNA containing single-stranded regions are also precipitated. The usefulness of the method is discussed in the context of isolating separately both RNA and DNA from cultured cells that are difficult to obtain in quantity.

Animals↗

Injection of bovine parathyroid poly(A)+ RNA into Xenopus oocytes confers sensitivity to high extracellular calcium.

Parathyroid cells detect increments in the extracellular [Ca2+], which lead to substantial increases in intracellular free Ca2+ ([Ca2+]i) and, ultimately, to suppression of parathyroid hormone (PTH) secretion. To determine whether mRNA from parathyroid tissue could confer sensitivity to high extracellular Ca2+, we isolated and injected total bovine parathyroid poly(A)+ RNA into Xenopus laevis oocytes. To assess translational activity of the RNA, PTH released into the media was measured. Intact PTH was detected in the medium for < or = 48 h, and injection of increasing amounts of RNA (approximately 0.5-50 ng/oocyte) led to the release of greater quantities of PTH. We screened for the expression of a putative Ca2+ sensor molecule by measuring 45Ca efflux from preloaded oocytes, in response to raising extracellular [Ca2+] from 0.7 to 5.7 mM. This increment in [Ca2+] stimulated 45Ca efflux by 249 +/- 52 cpm over 20 min from eggs injected with parathyroid poly(A)+ RNA (n = 22). This response was significantly greater than 45Ca efflux from any group of controls exposed to the same change in extracellular Ca2+ (p < 0.02), including oocytes injected with either water, cRNA for the platelet-derived growth factor (PDGF) BB receptor, or T cell poly(A)+ RNA. Size-fractionation of poly(A)+ RNA over sucrose gradients demonstrated that mRNA, which induced responsiveness to high extracellular Ca2+, was present in fractions with transcripts of approximately 5-9 kB. Injection of these fractions also conferred sensitivity to the presence of Ba2+ or Sr2+ (both at 5 mM) in the media.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Efficient replication of human immunodeficiency virus type 1 requires a threshold level of Rev: potential implications for latency.

The Rev protein of human immunodeficiency virus type 1 (HIV-1) is essential for the expression of the structural genes of HIV-1. To determine whether a functional threshold level of Rev is required to allow efficient HIV-1 replication, CD4-positive HeLa cells, constitutively expressing a Rev-deficient provirus, were transfected with various quantities of a Rev-expressing plasmid. Compared with the quantity of the Rev-producing plasmid transfected, HIV-1 replication was distinctly nonlinear as measured by HIV-1 p24 antigen and HIV-1-specific RNA production. A quantitative RNA polymerase chain reaction (PCR) demonstrated that Rev mRNA expression was linearly correlated with the quantity of Rev-expressing plasmid which was transfected into these cells. These data suggest that a critical threshold of Rev is required for a highly productive HIV-1 infection. This threshold level of Rev may be involved in the generation and maintenance of HIV-1 proviral latency.

Amino Acid Sequence↗

Enhanced macromolecular binding of N-[4-(5-nitro-2-furyl)-2-thiazolyl]- formamide in germfree versus conventional rats.

To investigate the binding of a nitrofuran to tissue macromolecules in vivo, the urinary bladder carcinogen N-[4-(5-nitro-2-furyl)- 2-[35S]thiazolyl]formamide [[35S]FANFT; 94 mCi/mmol] was given p.o. to conventional [n = 4; 115 +/- 8 g (S.D.)] and germfree [n = 4; 105 + 5 g] female CD rats [1.23 mCi/rat]. After 18 hr, organs were removed, and macromolecules were then isolated from individual livers and kidneys and from pooled urinary bladders. A hydroxylapatite isolation procedure was followed (Beland et al., J. Chromatogr., 174: 177-186, 1979), and the nucleic acids obtained were further purified by digestion with appropriate nucleases and/or centrifugation (105,000 X g). The results are as follows and are given in pairs (conventional/germ-free) expressed as pmol FANFT bound per mg macromolecule. Protein binding levels were: liver, 165 +/- 40/307 +/- 31; kidney, 72 +/- 19/88 +/- 24; bladder, 272/322. RNA levels were: liver, 217 +/- 184/413 +/- 196; kidney, 219 +/- 60/617 +/- 196; bladder, 448/1373. DNA levels were: liver, 9.8 +/- 7.5/17.0 +/- 7.5; kidney, 0.69 +/- 0.38/4.5 +/- 1.0. The quantity of bladder DNA was insufficient for accurate measurement. Diethylaminoethyl cellulose chromatography of liver RNA from a germfree rat, either before or after RNase digestion, showed that the majority of the radioactivity was associated with a polynucleotide fraction that appeared to be RNase resistant and accounted for only a small portion of the total RNA but that also permitted the intercalation of ethidium bromide. The deformylated FANFT metabolite, 2-amino-4-(5-nitro-2-fury)thiazole, reacted with transfer RNA upon reduction with sodium dithionite in vitro to give adduct(s) that also appeared to be RNase resistant. Thus, these results show that the urinary bladder carcinogen FANFT or its metabolites react in vivo with protein and nucleic acid of both target and nontarget organs and that binding levels are elevated in germfree rats.

Animals↗

Gene expression in a pure population of odontoblasts isolated by laser-capture microdissection.

Studies of odontoblast differentiation and function have been limited due to difficulties in obtaining sufficient numbers of intact cells. We describe a novel approach of laser-capture microdissection to obtain homogenous populations of pre-odontoblasts and odontoblasts from tissue sections of mouse molar cusp tips. Fixation, processing, and staining conditions were assessed for the optimal retrieval of total RNA from microdissected odontoblasts. Fluorometric assays and RT-PCR analysis of alpha1(I) collagen, dentin sialophosphoprotein (Dspp), and osteocalcin (OC) confirmed that the total RNA from three-day-old captured odontoblasts was sufficient in quantity and quality. Odontoblast-specific gene expression was studied by RT-PCR analysis performed in a single streptavidin-coated tube. At E15.5, Days 0 and 3, gene expression in laser-captured odontoblasts resembled that seen in vivo by in situ hybridization. The use of LCM is thus a valuable means of retrieving quality RNA from discrete populations of odontoblasts at different stages of dentinogenesis.

Animals↗

Isolation and point of action of a factor from Escherichia coli required to reconstruct translation.

To study the mechanism of translation we have attempted to reconstruct the process from purified components. Protein synthesis was programmed by the RNAs of wild-type or amber mutants of bacteriophages f2 or MS2. Translation programmed by MS2 or f2am3 RNA does not occur using ribosomes, precharged aminoacyl-tRNAs, and the sum of the purified proteins involved in initiation (initiation factors; IF-1, IF-2, and IF-3), propagation (elongation factors; EF-Tu, EF-Ts, and EF-G) and termination (release factors; RF-1 or RF-2) of protein synthesis. The requirement for a protein called W was demonstrated. Protein W was purified free of all translation factors, activating enzymes, and other proteins such as the RR, "rescue," and EF-P implicated in translation. The stimulation of propagation by W depended on the position of the amino acid residue to be added in the synthesis of the NH2-terminal hexapeptide of the coat protein. In the reconstructed system, with the sum of all translation factors but in the absence of W, only dipeptides and smaller quantities of tripeptides were synthesized under the direction of f2am3 RNA. W stimulated the synthesis of the hexapeptide, fMet-Ala-Ser-AspNH2-Phe-Thr directed by this RNA. In addition, W stimulated ejection of non-cognate tRNAs that bind to ribosomal particles.

Bacterial Proteins↗

Thermodynamic cycle between DNA and RNA constituents for conformation of the sugar ring from nuclear magnetic resonance study.

The effect of a structural change of ribose to deoxyribose, by replacement of 2'-OH by 2'-H, on the conformational equilibrium of the sugar ring is described in terms of one thermodynamic cycle. The method is based on the observation that conformational correlations of the sugar ring--side chain ensemble in DNA and RNA components show one general pattern, reflecting an intrinsic physical property of this ensemble. The pattern determines a choice of model systems to study. The systems consist of pairs of DNA and RNA components, nucleosides and nucleotides in aqueous solution, where all conformational factors are fully controlled. This approach allowed us to describe the thermodynamic cycle and measure its fundamental parameters, equilibrium constants and free energy differences, delta delta G, from a nuclear magnetic resonance study. The delta delta G values as determined for pairs of ribo- and deoxyribo-nucleosides in classes of syn-constrained and anti-preferred models, are comparable and lie in a narrow range, delta delta G = 1.7 +/- 0.1 [kJ/mol]. For pairs of ribo- and deoxyribo-nucleotides, the delta delta G values also lie in narrow ranges, delta delta G = 1.7 +/- 0.1 [kJ/mol] for 5'-phosphate nucleotides and delta delta G = 1.9 +/- 0.1 [kJ/mol] for 3'-phosphate nucleotides, i.e. similar to those observed for nucleosides. The measured quantity, delta delta G, is generally observed in a relatively narrow range, delta delta G = 1.75 +/- 0.15 [kJ/mol], irrespective of the class of the model system. This quantity represents a "pure" constant contribution, pe one sugar moiety, as a "driving force" for the N-->S shift in the sugar ring conformational equilibrium, when one compares RNA and DNA. This important thermodynamic quantity, delta delta G, has not hitherto been determined for nucleic acids. Ultimately the delta delta G quantity is revealed in the tendency to adopt S(C2'endo) sugar puckering domain by the majority of DNA structures, whereas RNA generally adopt an N(C3'endo) puckering domain. A possible biological significance of the delta delta G quantity may include evolutionary aspects of nucleic acids.

DNA↗

Quantitative RT-PCR for measuring gene expression.

Classical Northern blot analysis for measuring mRNA requires too many cells to be practical for cell sorting. Yet, measurement of gene expression in small subsets within a heterogeneous population of cells is often desired. The PCR in combination with prior reverse transcription (RT-PCR) of the mRNA of interest provides a means for measuring gene expression using as few as one cell. When RT-PCR is performed, the reliability of the data can be highly subjective due to the efficiency of both RT and PCR steps. This subjectivity can be eliminated by a technique for quantitating specific RNA molecules using an internal RNA competitive reference standard (RNA-CRS), which is identical to the sequence of interest except for a deletion of 80 bases. Here we illustrate a strategy for quantitative PCR using a RNA-CRS, synthesized solely using nonplasmid-based PCR techniques. The competitive reaction consists of a constant quantity of wild-type mRNA (from 100-1000 cells) added individually to tubes containing a serially decreasing amount of RNA-CRS. The RT-PCR is performed on these samples, then the resulting product is analyzed by gel electrophoresis and densitometry. The procedure for preparing the RNA-CRS and subsequent RT-PCR steps are described in detail.

Animals↗

Functional and structural heterogeneity of nucleoli: the dependence of the activity of transport of newly synthesized rRNA on nucleolar size and phase of the cell cycle.

On the basis of radioactivity of interphase cells in the antheridial filaments of Chara vulgaris after a 20 min. incubation with 3H-uridine and after a 40 min. postincubation the activity of synthesis and transport of newly synthesized RNA has been studied in different-sized nucleoli. Investigations of their ultrastructure have been also performed. It was found that the smallest nucleoli from 0.2-0.5 micron in diameter indicate the structure typical of nucleoli inactive in RNA synthesis. Nucleoli ranging from 0.5-2.0 microns in diameter which constitute the most numerous population were evidenced to be active both in synthesis and transport of newly synthesized RNA. Their structure is characterized by nucleoloneme-like appearance with small quantity of granular components. The largest nucleoli which are present in small numbers at the onset of interphase gradually increase in number till G2 phase. They indicate similar transcriptional activity as the latter category of nucleoli but a lower activity of transport of newly synthesized RNA; moreover, they abound in granular components surrounding the nucleoloneme. Nucleoli from all size-classes increase their transcriptional activity in middle S and middle G2 phases. Transport of newly synthesized RNA, however, is differentiated and it depends on both the phase of the cell cycle and nucleolar size.

Cell Cycle↗

Selective gene expression in failing human heart. Quantification of steady-state levels of messenger RNA in endomyocardial biopsies using the polymerase chain reaction.

BACKGROUND: Evaluation of gene expression in failing human heart has been limited by the availability of cardiac tissue. METHODS AND RESULTS: We used the polymerase chain reaction (PCR) to assess gene expression in small quantities of failing and nonfailing human heart. PCR is a powerful new molecular biological tool that allows a small quantity of DNA to be amplified as much as 1 million-fold. Total RNA was extracted from 3-5 mg samples of human heart and reverse-transcribed to complementary DNA (cDNA). With selected oligonucleotide primers, we used PCR to amplify cDNAs encoding atrial natriuretic peptide, beta-myosin heavy chain, phospholamban, and cytoskeletal beta-actin. To quantify the relative levels of messenger RNA (mRNA) in human heart, a known amount of a control RNA was present in the reverse transcription and PCR reactions. The amount of mRNA in the sample could therefore be assessed in relation to the amount of control product. The control RNA was transcribed from a synthetic DNA template containing primers complementary to those used to amplify the cDNAs of interest. Atrial natriuretic factor mRNA could not be detected in nonfailing human heart but was abundant in ventricular myocardium from failing human heart. In contrast, steady-state levels of phospholamban mRNA decreased, whereas levels of beta-myosin heavy-chain mRNA were unchanged with heart failure. CONCLUSIONS: Alterations in gene expression in the failing human heart appear to be selective. In addition, the present study suggests that PCR provides a rapid and economical way to quantify the expression of multiple genes of interest in endomyocardial biopsy specimens and may therefore be used to advance our understanding of heart muscle disease.

Biopsy↗

Genetically engineered transgenic plants with the domain 1 sequence of tobacco mosaic virus 126 kDa protein gene are completely resistant to viral infection.

In many plant RNA viruses, Domains 1, 2 and 3 are conserved in replicase proteins. In order to examine the interference of viral replication by the Domain 1 sequence, we generated transgenic plants transformed with DNA corresponding to the Domain 1 sequence of the TMV 126 kDa protein. This DNA sequence includes the TMV RNA from nucleotides 1 to 2,149, which comprises both the 5'-untranslated and methyl transferase region. The transgenic plants obtained showed complete resistance to TMV infection. The presence of the Domain 1 sequence in the plants completely prevented local necrosis in Nicotiana tabacum cv. Xanthi nc, and any systemic development of symptoms in Nicotiana tabacum Xanthi upon TMV inoculation. Most transgenic plants sustained the conferred resistance even under TMV inoculum concentrations up to as high as 1,000 microg/ml. To detect any accumulation of TMV coat protein or viral RNA in infected transgenic plants, immunochemical tests and Northern blot analyses were carried out. Neither viral RNA or coat protein was detectable in the systemic leaves of the completely resistant transgenic plants, whereas they were accumulated in large quantities in all of the control plants. Because of the conservation of Domain 1 in many plant RNA viruses, the acquisition of resistance to virus infection using the Domain 1 sequence appears to be a very effective strategy for breeding of viral resistant plants.

Genes, Viral↗

Biogenesis of poxviruses: role for the DNA-dependent RNA polymerase II of the host during expression of late functions.

The participation of host RNA polymerase II in the vaccinia life cycle was examined by comparing efficiency of multiplication after treating the Ama+ sensitive and Ama 102 drug resistant lines with alpha-amanitin. In the latter, resistance is due to a mutation in RNA polymerase II. The toxin profoundly reduces synthesis of virus-specified polypeptides and morphopoeisis in Ama+ but not in Ama 102 rat myoblasts without appreciably altering vaccinia DNA replication in either cell type. This implicates RNA polymerase II in the expression of late virus functions. Circumstantial evidence from a model system indicates that gamma irradiation of the host prior to infection might disrupt transcription into functional mRNA from the nucleus. Irradiation does not, however, alter the capability of the host to support vaccinia multiplication fully. Therefore, ongoing host nuclear transcription may not be required by this virus. The above results are consistent with the ability of cytoplasts to produce small quantities of mature progeny. Our studies lead us to hypothesize that RNA polymerase II or a subunit of the host enzyme may participate directly in late transcription of the vaccinia genome.

Amanitins↗