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PubMed1976

Studies on the organisation of the chicken genome and its expression during myogenesis in vitro.

DNA from the chicken genome was analysed both by isopycnic centrifugation in cesium salt density gradients and by reassociation analysis using hydroxyapatite (HAP) chromatography. Centrifugation in neutral CsCl revealed a single non-Gaussian band skewed toward the heavy side, but no discrete satellite components. In heavy metal (Ag+ or Hg++)-Cs2SO4 gradients, 4-8 satellite bands were revealed, comprising 5-9% of the total DNA. Purification of the satellites and recentrifugation in neutral CsCl demonstrated that 80-90% of this DNA would band in the shoulder, with the remainder in the main band. These satellites can account at most for 30% of the heavy shoulder DNA, thus most of the heavy shoulder DNA must be of lower repetition frequencies. Reassociation analyses of chicken DNA demonstrated that the complexity of the non-repetitive DNA is 9.49 X 10(8) nucleotide pairs, equivalent to about 90% of the haploid genome. Repetitive DNA comprises only 8-10% of the genome and has the following composition, relative to total DNA: 3.7% intermediate repetitive, 1.9% highly repetitive, and 3.9% "zero-time binding" DNA. This unusually low repetitive DNA content may be related to the small genome size of chickens, relative to other vertebrates, and to the presence of many microchromosomes in the chicken karyotype. Total cell RNA extracted from perfusion myoblasts, post-fusion myotubes, and myoblasts grown in BrdU was incubated in large excess with 3H-TdR labelled non-repetitive DNA and the resulting hybrids assayed by HAP chromatography. The amount of non-repetitive DNA represented in the RNA was found to increase from 7-8% in the myoblast stage to 10-11% in myotubes. An even smaller proportion, about 5%, is represented in the RNA of myoblasts prevented from differentiating by growth in BrdU.

Animals↗
PubMed1978

The ribonucleic acids of Crithidia fasciculata.

Crithidia fasciculata ribosomes were found to be 80S and to dissociate into 58 and 41S subunits; on 5 to 50% sucrose gradients, rRNA was separated into 25, 18, and 5S components. The molecular sizes of the heavier rRNA species, estimated by polyacrylamide gel electrophoresis were 1.24 and 0.84 M (X 10(6) daltons). The 25S RNA has a tendency to interact with the 18S RNA to give a complex that is difficult to separate by sucrose gradient centrifugation. The 25S RNA is also unstable and dissociates into 0.73 and 0.57 M components. The 18S RNA has molecular size (0.84 M) higher than the 0.7 M reported for most eukaryotes, but similar to that of Euglena and Amoeba. Ribosomal RNA hybridized 0.29% of the nuclear DNA. Mitochondrial RNA, extracted by a rapid procedure was resolved into 16 and 5S components in sucrose gradients.

Animals↗
PubMed2006

Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples.

Here we describe the application of metagenomic technologies to construct cDNA libraries from RNA isolated from environmental samples. RNAlater (Ambion) was shown to stabilize RNA in environmental samples for periods of at least 3 months at -20 degrees C. Protocols for library construction were established on total RNA extracted from Acanthamoeba polyphaga trophozoites. The methodology was then used on algal mats from geothermal hot springs in Tengchong county, Yunnan Province, People's Republic of China, and activated sludge from a sewage treatment plant in Leicestershire, United Kingdom. The Tenchong libraries were dominated by RNA from prokaryotes, reflecting the mainly prokaryote microbial composition. The majority of these clones resulted from rRNA; only a few appeared to be derived from mRNA. In contrast, many clones from the activated sludge library had significant similarity to eukaryote mRNA-encoded protein sequences. A library was also made using polyadenylated RNA isolated from total RNA from activated sludge; many more clones in this library were related to eukaryotic mRNA sequences and proteins. Open reading frames (ORFs) up to 378 amino acids in size could be identified. Some resembled known proteins over their full length, e.g., 36% match to cystatin, 49% match to ribosomal protein L32, 63% match to ribosomal protein S16, 70% to CPC2 protein. The methodology described here permits the polyadenylated transcriptome to be isolated from environmental samples with no knowledge of the identity of the microorganisms in the sample or the necessity to culture them. It has many uses, including the identification of novel eukaryotic ORFs encoding proteins and enzymes.

Acanthamoeba↗
PubMed1972

Transcription and transport of virus-specific ribonucleic acids in African green monkey kidney cells abortively infected with type 2 adenovirus.

The techniques of deoxyribonucleic acid-ribonucleic acid (DNA-RNA) hybridization and immunological precipitation were used to compare the synthesis of adenovirus-specific macromolecules in African green monkey kidney (AGMK) cells infected with adenovirus, an abortive infection, and coinfected with both adenovirus and simian virus 40 (SV40), which renders the cells permissive for adenovirus replication. When viral protein synthesis was proceeding at its maximum rate, the incorporation of (14)C-amino acids into adenovirus structural proteins was about 90 times greater in the doubly infected cells than in cells infected only with adenovirus. However, the rates of synthesis of virus-specific ribonucleic acid appeared to be comparable in the two infections at all times measured. A time-dependent increase in the rate of RNA synthesis observed late in the abortive infection was dependent upon the prior replication of viral DNA. Moreover, all virus-specific RNA species that are normally made late in a productive adenovirus infection (i.e., the true late and class II early RNA species) were also detected in the abortive infection. Adenovirus-specific RNA was detected by molecular hybridization in both the cytoplasm and nuclei of abortively infected cells. Comparable amounts of viral RNA were found in the cytoplasmic fractions of AGMK cells infected either with adenovirus or with both adenovirus and SV40. The results of hybridization-inhibition experiments clearly showed that there was a class of virus-specific RNA molecules, representing about 30% of the total, in the nucleus that was not transported to the cytoplasm. This class of RNA was also identified in similar amounts in productively infected human KB cells. The difference in the abilities of cytoplasmic and nuclear RNA to inhibit the hybridization of virus-specific RNA from whole cells was shown not to be due to a difference in the molecular size of the RNA species from the two cell fractions or to the specific loss of a cytoplasmic species during RNA extraction procedures.

Adenoviridae↗
PubMed1996

Serial passage of tobacco rattle virus under different selection conditions results in deletion of structural and nonstructural genes in RNA 2.

The RNA genome of tobacco rattle virus (TRV) is bipartite. RNA 2 of the nematode-transmissible TRV isolate PPK20 encodes the viral coat protein (cp) and proteins with molecular weights of 29,400 and 32,800 (29.4K and 32.8K proteins). When this isolate was serially passaged in tobacco by using phenol-extracted RNA as the inoculum in each transfer, defective interfering (DI) RNAs rapidly accumulated. A number of these DI RNAs were cloned. Six DI RNAs had single internal deletions in RNA 2 that removed most of the cp gene, the 29.4K gene, and the 5' half of the 32.8K gene. The borders of the deletions in these DI RNAs were found to be flanked in the genomic RNA 2 by short nucleotide repeats or sequences resembling the 5' end of TRV genomic and subgenomic RNAs. Two DI RNAs were found to be recombinants containing a 5' sequence derived from RNA 2 and a 3' sequence derived from RNA 1. When serial passage of TRV isolate PPK20 was carried out by using leaf homogenates as inocula in each transfer, accumulation of a DI RNA (designated D7) with a functional cp gene was observed. The deletion in D7 covered the 3' end of the cp gene, the 29.4K gene, and the 5' half of the 32.8K gene. An infectious cDNA clone of D7 RNA was made. In mixed infections, D7 RNA rapidly outcompeted RNA 2 but did not compete with RNA 1. The deletion in D7 RNA abolished the nematode transmissibility of the PPK20 isolate. These results may explain the observation that many laboratory isolates of tobraviruses have lost their nematode transmissibility and contain RNA 2 molecules of widely different lengths.

Culture Media↗
PubMed1987

Different electrophoretypes of human rotaviruses in Hungary.

Polyacrylamide gel electrophoresis of rotaviral double-stranded ribonucleic acid (RNA) extracted directly from faecal specimens collected in three different parts of Hungary was applied to characterize and distinguish 21 randomly selected viral isolates. This technique made it possible to define 7 different electrophoretypes. Of the isolates 11 exhibited an identical "long" electrophoretic migration pattern. "Short" RNA pattern was found in two cases, and one atypical rotavirus was also revealed. This is the first description of rotavirus RNA electrophoretypes in Hungary.

Child, Preschool↗
PubMed1978

Induction of a T-cell specific antigen on bone marrow lymphocytes with thymus RNA.

Expression of a rabbit T-cell specific antigen can be induced on bone marrow lymphocytes following exposure to an RNA extract obtained from the thymuses of young rabbits. The presence of the antigen was demonstrated using goat anti-rabbit T-cell serum in a complement-dependent cytotoxicity assay. The T-cell antigen first appeared 3 h after addition of the thymus RNA to bone marrow cell cultures and the maximum number of cells expressing the T-cell antigen was observed within 24 h. RNA obtained from a source other than the thymus was found to be ineffective in inducing expression of the T-cell antigen. The induction of the antigen appears to be dependent on the presence of intact thymus RNA, as RNase treatment but not trypsin treatment, destroyed the ability of the RNA to induce the T-cell antigen.

Animals↗
PubMedDate not supplied

Early oncogene mRNA expression in HT-29 cells treated with the endogenous colon mitosis inhibitor pyroglutamyl-histidyl-glycine.

BACKGROUND: The tripeptide pyroGlu-His-GlyOH (pEHG), isolated from intestinal extracts (1), suppresses growth of human colonic epithelial cells and human colorectal adenocarcinoma cells (HT-29) both in vitro and in vivo. The present study represents the first attempt to relate alterations in relevant gene expression to the effect on cell growth. MATERIALS AND METHODS: Northern blot with RNA, extracted from HT-29 cells exposed to pEHG, was hybridised with c-fos and c-myc probes. RESULTS: c-fos gene expression was doubled in HT-29 cells after 20 minutes of incubation with pEHG and decreased to half the initial value after 2 hours. The increase at 20 minutes was concentration-dependent at a peptide concentration range from 10(-6)-10(-12) M. The expression of the oncogene c-myc showed only marginal alternations at the concentrations and times tested. CONCLUSION: The colon mitosis-inhibiting peptide pEHG increases gene expression of c-fos, but not that of c-myc.

Antineoplastic Agents↗
PubMed2004

Improvement of extraction and processing of RNA from renal biopsies.

BACKGROUND: Assessment of mRNA levels has the potential to predict renal outcome. The objective of this study was to optimize several steps in the protocol for obtaining cDNA from routine clinical kidney biopsy material. METHODS: RNA integrity was compared between different methods for extraction of RNA, synthesis of cDNA, and storage of renal tissue. Hereby, RNAlater, an RNA-preserving compound, was tested for implementation in a protocol for renal biopsies that combines routine histology and RNA expression studies. Gel electrophoresis and real-time polymerase chain reactions (PCR) were outcome parameters for assessment of RNA integrity. RESULTS: The Trizol method rendered higher RNA yields from fresh renal tissue than the NP40 method and RNeasy spin columns. RNA yields were not affected when renal tissue was stored at -70 degrees C for up to 2 months in phosphate-buffered saline (PBS). cDNA levels obtained using avian myeloblastosis virus (AMV) reverse transcriptase (RT) were at least twice as high as those obtained with Sensiscript and Superscript RT. RNAlater maintained RNA integrity in whole renal cortex stored at 4 degrees C for up to 3 months. Dissection of small biopsies in RNAlater rendered similar RNA yields in comparison with dissection in PBS, but the yield of glomeruli from the cortices was 50% lower (P < 0.005). Integrity of RNAlater-treated tissue, evaluated by light microscopy and immunofluorescence, was diminished. CONCLUSION: This study shows optimization of several steps in the protocol for extraction and handling of RNA in renal cortical tissue. RNA extraction and cDNA synthesis can be optimized by the use of the Trizol method and AMV RT, respectively. RNAlater is beneficial for preserving RNA integrity in whole renal cortex during storage and processing, but is not suitable for implementation in routine diagnostic histologic stainings combined with RNA expression studies in dissected biopsy material.

Aged↗
PubMed2001

Routine HCV PCR screening of blood donations to identify early HCV infection in blood donors lacking antibodies to HCV.

BACKGROUND: Detection of early hepatitis C infection of blood donors is still a major problem for blood transfusion. Common anti-HCV screening assays show differences in sensitivity and specificity. The often mild symptoms of acute hepatitis C also cause difficulties in the identification of early HCV infection. The feasibility and efficacy of routine screening of blood donations for HCV RNA were investigated. STUDY DESIGN AND METHODS: Blood donations (n = 251,737) were screened for HCV RNA over 4 years. RNA extraction, amplification, and detection were done by two commercial HCV PCR kits (HCV Cobas Amplicor and HCV Cobas Amplicor 2.0, Roche Diagnostics). Screening was done by pool testing with a maximum pool size of 40 serum samples. RESULTS: Three donations out of 251,737 were HCV RNA positive and anti-HCV negative. ALT levels of these donations were 271, 32, and 10 U per L. The HCV infection of a fourth HCV RNA-positive donor could not be identified by routine, second-generation HCV EIA (Abbott Diagnostika). In this case, two previous donations were also HCV RNA positive, and three second-generation test systems (Abbott) could not detect anti-HCV, whereas third-generation anti-HCV screening assays detected antibody with different sensitivity. The first HCV RNA-positive donation was identified only by the HCV ELISA 3.0 (Ortho Diagnostic Systems). The results of confirmatory assays like RIBA HCV 3.0 (Ortho) and Matrix (Abbott) indicate a restricted immune response to NS3 only. CONCLUSION: HCV RNA detection by PCR can be carried out routinely in blood donor screening without significant delay of release of the components. The residual risk of transmission can be reduced by identification of early infection, which can lead to an improved safety of blood components. RNA screening can also be advantageous in cases of incomplete or lack of antibody response to HCV.

Alanine Transaminase↗
PubMed1996

Expression of taste reception response of fleshfly in Xenopus oocytes.

Functional expression of the gustatory sensitivity to amino acids and sugars was investigated in Xenopus oocytes injected with poly(A+) RNA extracted from fleshfly labellar taste organs. The current induced by the application of amino acids and sugars that stimulate fleshfly sugar receptor cells was recorded under voltage clamp conditions. L-Phenylalanine and L-valine induced a large transient inward current in poly(A+) RNA-injected oocytes but only small responses in uninjected control oocytes. Glucose and fructose also produced inward currents in the RNA-injected oocytes. N-methylated compounds or D-isomers of these amino acids induced either no response or a much smaller response than L-amino acids as they did in the fleshfly sugar receptor cells. The oocyte expression system is a useful tool for characterizing the taste transduction mechanism.

Animals↗
PubMed1981

Cell-free translation of immunoglobulin G polypeptides by chicken bursal RNA.

The acquisition of messenger RNA controlling the translation of immunoglobulin G was studied in the chicken bursa of Fabricius, using the cell-free translation system of wheat germ lysate. Total cellular RNA extracted by phenol-1% sodium dodecylsulphate (pH 5.0 at 50 degrees) incorporated [3H]-leucine maximally. Sodium dodecylsulphate polyacrylamide gel electrophoresis of the immune precipitates of cell-free products with anti-chick IgG showed that polypeptides of gamma- and light chains were synthesized by bursal RNA from 20-day embryos and one-week-old chicks; in addition, a polypeptide with a molecular size of about 4 x 10(4) was synthesized. No appreciable synthesis of gamma- and light chains by bursal RNA from 12-day embryos was found.

Animals↗
PubMed1984

Introns excised from immunoglobulin pre-mRNAs exist as discrete species.

We have discovered a new class of transcripts of immunoglobulin kappa genes in RNA from B-lineage cells. These transcripts have the properties predicted of free introns excised from kappa mRNA precursors. RNA extracted from populations of normal mouse spleen cells polyclonally activated with B-cell mitogens contains four such transcripts; their electrophoretic mobilities correspond to the distances between the intron-exon boundary of the C kappa region and the four useable J kappa elements, and their relative abundance reflects the relative usage of those J segments. Analysis of RNA from monoclonal kappa-expressing cell lines reveals that one active locus produces one free intron, its size determined by which J element is used in that locus. Apart from their distinctive size, free introns are identified by their lack of polyadenylic acid and their ability to hybridize to cloned probes containing intron sequences, but not to the adjacent V or C exonic sequences. They have a characteristic subcellular distribution, being extractable from nuclei by treatment with nonionic detergent; nuclei thus treated retain most of the primary mRNA precursors, but few of the free introns. A high level of kappa gene expression is not a prerequisite of a cell containing detectable free kappa introns; the lymphoma 38c has only 5% or less of the amount of kappa mRNA that the plasmacytoma MCP-11 contains, yet the ratio of free intron to mRNA precursor is about the same in both cell lines. When analyzed by electrophoretic separation of sufficient resolving power, the free introns due to a single kappa locus resolve into two discrete species. We consider that this most likely reflects the existence of two conformers of the intron, one presumably a covalently intact circle and the other linear molecule.

Animals↗
PubMed1970

In vitro product of a ribonucleic acid polymerase induced by influenza virus.

The ribonucleic acid (RNA)-dependent RNA polymerase induced in the microsomal fraction of cells infected with influenza virus synthesized a mixture of single-and double-stranded RNA in vitro. The single-stranded RNA sedimented mainly in the 8S region on sucrose density gradients, with a smaller proportion of the RNA sedimenting at 18S. This sedimentation pattern corresponds closely to that of incomplete influenza virus RNA. The double-stranded RNA formed in vitro sedimented at 11S, but molecules which may be replicative intermediate, sedimenting at 14 to 20S, were also detected in the in vitro reaction product. Similar species of RNA were detected in vivo by pulse-labeling infected cells at the time of polymerase harvest, but the proportion of each RNA species was different, most of the RNA being single-stranded and sedimenting in the 18S region. An 11S double-stranded RNA was also synthesized in vivo. Pulse chase analysis of the double-stranded RNA synthesized in vitro showed that most is stable, and only a small proportion turns over during the reaction. A proportion of the RNA formed in vitro could be annealed to RNA formed in infected cells and to RNA extracted from purified virus.

Animals↗
PubMed2005

Decreased histone deacetylase activity in chronic obstructive pulmonary disease.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is characterized by chronic airway inflammation that is greater in patients with advanced disease. We asked whether there is a link between the severity of disease and the reduction in histone deacetylase (HDAC) activity in the peripheral lung tissue of patients with COPD of varying severity. HDAC is a key molecule in the repression of production of proinflammatory cytokines in alveolar macrophages. METHODS: HDAC activity and histone acetyltransferase (HAT) activity were determined in nuclear extracts of specimens of surgically resected lung tissue from nonsmokers without COPD, patients with COPD of varying severity, and patients with pneumonia or cystic fibrosis. Alveolar macrophages from nonsmokers, smokers, and patients with COPD and bronchial-biopsy specimens from nonsmokers, healthy smokers, patients with COPD, and those with mild asthma were also examined. Total RNA extracted from lung tissue and macrophages was used for quantitative reverse-transcriptase-polymerase-chain-reaction assay of HDAC1 through HDAC8 and interleukin-8. Expression of HDAC2 protein was quantified with the use of Western blotting. Histone-4 acetylation at the interleukin-8 promoter was evaluated with the use of a chromatin immunoprecipitation assay. RESULTS: Specimens of lung tissue obtained from patients with increasing clinical stages of COPD had graded reductions in HDAC activity and increases in interleukin-8 messenger RNA (mRNA) and histone-4 acetylation at the interleukin-8 promoter. The mRNA expression of HDAC2, HDAC5, and HDAC8 and expression of the HDAC2 protein were also lower in patients with increasing severity of disease. HDAC activity was decreased in patients with COPD, as compared with normal subjects, in both the macrophages and biopsy specimens, with no changes in HAT activity, whereas HAT activity was increased in biopsy specimens obtained from patients with asthma. Neither HAT activity nor HDAC activity was changed in lung tissue from patients with cystic fibrosis or pneumonia. CONCLUSIONS: Patients with COPD have a progressive reduction in total HDAC activity that reflects the severity of the disease.

Acetyltransferases↗
PubMed1993

Differential expression of immediate early genes after transection of the facial nerve.

Facial motoneurons respond to peripheral transection of the facial nerve with a number of molecular changes. In order to obtain insight into the transcriptional mechanisms underlying the changes induced by axotomy, the expression of a number of immediate early genes was investigated after facial nerve lesion in the rat. Some immediate early genes (such as c-fos, c-jun or jun B) are known to encode transcription factors that bind to DNA at sites that regulate gene expression and they could therefore contribute to long-term changes in motoneurons. Northern blot analysis of RNA extracted from the facial nucleus from postoperative intervals covering hours and days revealed that axotomy results in a unique pattern of immediate early gene induction in the facial nucleus. c-Jun, jun B and 12-O-tetradecanoylphorbol-13-acetate-induced sequence (TIS) 11 messenger RNA, also present in low amounts in the unoperated nucleus, were strongly induced in a long-term fashion after nerve injury. Increased levels of these messenger RNAs were first detectable at 5 h, reaching a maximum (300-500% compared to control) within 24 h followed by a gradual decline during the following week. Elevated levels were maintained at least up to eleven days compared to the unoperated side. On the other hand, c-fos messenger RNA was neither expressed in the unoperated nucleus, nor was c-fos messenger RNA induced by axotomy at any of the time-points studied. Another member of the TIS family of immediate early genes TIS 7 (PC4), however, was detectable at low levels in normal facial nucleus, but its expression was unaffected by lesion. The three axotomy-induced messenger RNAs, c-jun, jun B and TIS 11, were all localized in the facial motoneurons by in situ hybridization histochemistry indicating that their induction occurs as part of the retrograde reaction of the motoneurons in response to lesion. These data suggest that c-jun, jun B and TIS 11 may play a role in triggering the regeneration programme of motoneurons.

Animals↗
PubMed2006

Qualitative and quantitative expression profile of muscarinic receptors in human urothelium and detrusor.

PURPOSE: We compared the complete spectrum of receptor subtypes expressed by human detrusor and its primary culture with the expression profile in a human urothelium immortalized cell line, and in fresh urothelium tissue and its primary cell culture. MATERIALS AND METHODS: The levels of mRNA expressed for receptor subtypes M1 through M5 were determined with reverse transcriptase-polymerase chain reaction and quantitative polymerase chain reaction in total RNA extracted individually from different human bladder specimens, including fresh tissue of human urothelium and detrusor, and their respective primary cultures, as well as from the UROtsa cell line. RESULTS: All 5 muscarinic receptors were detected in fresh human bladder tissue by reverse transcriptase-polymerase chain reaction RNA. The same was true in separated urothelium and detrusor tissue except for the lack of the M5 receptor transcript. Receptor subtype mRNA expression in the UROtsa cell line paralleled expression in fresh human bladder. Quantitative polymerase chain reaction data further corroborated these results and showed comparable mRNA expression for M2 and M3 in primary detrusor cultures. Primary cultures also had a decreased copy number of receptor genes than native tissue. The decrease was even more pronounced in primary urothelium culture and the UROtsa cell line in the presence of high calcium. M2 and M3 receptors were also detected in urothelium and detrusor by immunoreactivity. CONCLUSIONS: We identified all 5 existing muscarinic receptor subtypes in detrusor and urothelium, and transcripts levels of M2 and M3 were comparable in detrusor. These results support an alternative site of action in urothelium for anti-muscarinic drugs. Urothelial receptors should be considered in the design of future drugs for overactive bladder.

Adolescent↗