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PubMedDate not supplied

Rift Valley fever infection of rhesus monkeys: implications for rapid diagnosis of human disease.

Rhesus monkeys inoculated with Rift Valley fever (RVF) virus provide a model in which serial observations of serum viral antigen and antibodies can be made. In 9 non-fatal and 3 fatal infections, either antigen or IgM enzyme-linked immunosorbent assay (ELISA) antibodies were detected in every serum sample during the acute phase. Furthermore, viral nucleic acid could be detected by filter hybridization in most samples taken on days 1 to 3. Circulation of significant quantities of viral RNA provides an additional approach to the diagnosis and study of RVF.

Animals↗
PubMed2003

Evaluation of techniques using amplified nucleic acid probes for gene expression profiling.

Gene expression analyses using spotted cDNA microarrays typically require relatively large quantities of total RNA (up to 100 microg) or polyA+RNA (1-5 microg). However, samples obtained by microdissection, patient biopsies, or embryonic samples often are small and yield an insufficient amount of RNA. Methods such as linear RNA amplification by in vitro transcription (IVT) or cDNA amplification by PCR are currently being used to circumvent these limitations. In the present study, labeled probes from mouse liver and kidney were generated with two amplification methods and were analyzed in terms of reproducibility of intensity values from repeated experiments. In addition, the reliability of differential gene expression detection among the different types of amplified and non-amplified probes was assessed. Data derived from IVT-amplified RNA, as well as from PCR-amplified cDNA probes were reproducible with correlation coefficients of 0.89 and 0.91, respectively. 88-92% of the strongly differentially expressed genes detected with non-amplified probes were also detected as being at least two-folds differentially expressed with the amplified probes. Both the PCR-amplified probe and the IVT-amplified probe were comparable in reproducibility and reliability.

Animals↗
PubMed1975

Purification of SV-40 messenger RNA by hybridization to SV-40 DNA covalently bound to Sepharose.

SV-40 DNA sheared form was coupled in a stable covalent bond to cyanogen bromide activated Sepharose. Under the conditions used at least 80% of the DNA was bound to Sepharose. The T 1/2 of hybridization of 0.5 mug/ml of SV-40 cRNA to SV-40 DNA-Sepharose was 1 hr. This rate of hybridization is sufficiently rapid to purify SV-40 sequences from solutions containing as little as 0.05-0.1 mug/ml. Nonspecific hybridization of RNA is in the range of 0.1-0.2% of the total input RNA. The DNA-Sepharose is fairly stable and can be reused several times to purify RNA. The SV-40 DNA-Sepharose was used to select large quantities of virus specific RNA from SV-40 infected BS-C-1 cells. The virus specific RNA when added to cell-free extracts from wheat germ was shown to direct the synthesis of the major viral structural protein VP-1.

Cells, Cultured↗
PubMed2005

Telomerase catalytic subunit in laryngeal carcinogenesis--an immunohistochemical study.

We recently demonstrated that (1) telomerase catalytic subunit messenger RNA (mRNA) relative quantities increase progressively with the degree of laryngeal epithelial abnormalities and that (2) telomerase catalytic subunit gene re-expression represents an early event in laryngeal carcinogenesis. The aim of the study was to determine whether telomerase catalytic protein immunohistochemisty reflects telomerase catalytic subunit gene expression in different grades of laryngeal epithelial abnormalities and squamous cell carcinomas of the larynx. Telomerase catalytic protein was analysed immunohistochemically in 106 laryngeal epithelial tissue samples: 10 normal epithelia, 15 squamous cell hyperplasias, 14 basal/parabasal cell hyperplasias, 10 atypical hyperplasias, eight intraepithelial carcinomas and 49 squamous cell carcinomas. At least 200 nuclei of each lesion were quantified per slide and the number of positive signals per nucleus was expressed as a telomerase catalytic protein index. The mean telomerase catalytic protein index increased progressively with the degree of laryngeal epithelial abnormalities: from 0.17 in normal epithelia, 0.44 in squamous cell hyperplasia, 0.54 in basal/parabasal cell hyperplasia, 0.91 in atypical hyperplasia, 1.05 in intraepithelial carcinoma to 0.96 in squamous cell carcinomas. Statistical analysis revealed three different groups of laryngeal epithelial changes according to the number of telomerase catalytic protein signals per nucleus: (1) normal epithelium, (2) regenerative epithelium (squamous cell hyperplasia, basal/parabasal cell hyperplasia), and (3) atypical hyperplasia, intraepithelial carcinoma and squamous cell carcinoma (P<0.0033). Telomerase catalytic protein immunohistochemistry parallels well with telomerase catalytic subunit mRNA relative quantities in laryngeal carcinogenesis. In normal and regenerative laryngeal epithelia, telomerase catalytic protein is present in occasional basal/parabasal nuclei, becomes undetectable with maturation or differentiation of epithelial cells, and reflects the regenerative capacity of squamous epithelium. Nevertheless, several telomerase catalytic protein signals in the majority of nuclei in precancerous lesions, intraepithelial carcinomas and squamous cell carcinomas, are consistent with telomerase catalytic subunit gene re-expression, an early event in laryngeal carcinogenesis.

Carcinoma, Squamous Cell↗
PubMed2003

Evaluation of candidate control genes for diagnosis and residual disease detection in leukemic patients using 'real-time' quantitative reverse-transcriptase polymerase chain reaction (RQ-PCR) - a Europe against cancer program.

Real-time quantitative RT-PCR (RQ-PCR) is a sensitive tool to monitor minimal residual disease (MRD) in leukemic patients through the amplification of a fusion gene (FG) transcript. In order to correct variations in RNA quality and quantity and to calculate the sensitivity of each measurement, a control gene (CG) transcript should be amplified in parallel to the FG transcript. To identify suitable CGs, a study group within the Europe Against Cancer (EAC) program initially focused on 14 potential CGs using a standardized RQ-PCR protocol. Based on the absence of pseudogenes and the level and stability of the CG expression, three genes were finally selected: Abelson (ABL), beta-2-microglobulin (B2M), and beta-glucuronidase (GUS). A multicenter prospective study on normal (n=126) and diagnostic leukemic (n=184) samples processed the same day has established reference values for the CG expression. A multicenter retrospective study on over 250 acute and chronic leukemia samples obtained at diagnosis and with an identified FG transcript confirmed that the three CGs had a stable expression in the different types of samples. However, only ABL gene transcript expression did not differ significantly between normal and leukemic samples at diagnosis. We therefore propose to use the ABL gene as CG for RQ-PCR-based diagnosis and MRD detection in leukemic patients. Overall, these data are not only eligible for quantification of fusion gene transcripts, but also for the quantification of aberrantly expressed genes.

Archives↗
PubMed2000

Inhibition of nitric oxide production exacerbates chronic ocular toxoplasmosis.

There is considerable controversy as to the roles of parasite proliferation and the inflammatory response in destruction of the retina during Toxoplasma gondii infection. A murine model was used to investigate the role of nitric oxide in pathogenesis of chronic ocular toxoplasmosis. Increased quantities of messenger RNA (mRNA) transcripts for iNOS were detected in the eyes of chronically infected C57BL/6 mice compared with noninfected control mice. Inhibition of nitric oxide (NO) by the addition of Lomega-nitro-L-arginine methyl ester (L-NAME) to the drinking water of infected mice between weeks 4-6 of infection, exacerbated ocular inflammation. The amount of inflammation was assessed semiquantitatively in histological sections of the eye. Eyes from L-NAME treated mice showed a significant increase in inflammation of the retina (P = 0.02), choroid (P = 0.03), and vitreous (P = 0.02) compared with control mice. These results demonstrate a protective role for NO in the control of chronic, ocular toxoplasmosis.

Animals↗
PubMed2001

Evaluation of the role of heterogeneous nuclear ribonucleoprotein A1 as a host factor in murine coronavirus discontinuous transcription and genome replication.

Viruses with RNA genomes often capture and redirect host cell components to assist in mechanisms particular to RNA-dependent RNA synthesis. The nidoviruses are an order of positive-stranded RNA viruses, comprising coronaviruses and arteriviruses, that employ a unique strategy of discontinuous transcription, producing a series of subgenomic mRNAs linking a 5' leader to distal portions of the genome. For the prototype coronavirus mouse hepatitis virus (MHV), heterogeneous nuclear ribonucleoprotein (hnRNP) A1 has been shown to be able to bind in vitro to the negative strand of the intergenic sequence, a cis-acting element found in the leader RNA and preceding each downstream ORF in the genome. hnRNP A1 thus has been proposed as a host factor in MHV transcription. To test this hypothesis genetically, we initially constructed MHV mutants with a very high-affinity hnRNP A1 binding site inserted in place of, or adjacent to, an intergenic sequence in the MHV genome. This inserted hnRNP A1 binding site was not able to functionally replace, or enhance transcription from, the intergenic sequence. This finding led us to test more directly the role of hnRNP A1 by analysis of MHV replication and RNA synthesis in a murine cell line that does not express this protein. The cellular absence of hnRNP A1 had no detectable effect on the production of infectious virus, the synthesis of genomic RNA, or the quantity or quality of subgenomic mRNAs. These results strongly suggest that hnRNP A1 is not a required host factor for MHV discontinuous transcription or genome replication.

Animals↗
PubMed1997

Improved efficiency for primer extension by using a long, highly-labeled primer generated from immobilized single-stranded DNA templates.

Primer extension is one of the most common methods used to measure the amount and size of RNAs. We demonstrate that the sensitivity and the specificity of this method are improved considerably by using a highly-labeled single-stranded DNA generated from a biotinylated single-stranded DNA template, as a long specific primer in the reverse transcription reaction. This new approach allows the detection of transcripts with a low expression level from microgram quantities of total RNA.

Animals↗
PubMed1992

Expression of the Large ATP Synthase Gene Cluster in Spinach Plastids during Light-Induced Development.

The large ATP synthase gene cluster in spinach (Spinacia oleracea) plastids encodes four of the six chloroplast-encoded ATP synthase subunits. Expression of this cluster was examined to determine its response to light-induced plastid development. Spinach plastid transcripts were isolated from etiolated tissues, etiolated tissues exposed to 24 h of light, young (1-3 cm) leaves, and mature (8-10 cm) leaves. Transcript levels were examined from each developmental stage as a function of either the quantity of total RNA or gene dosage. The relative transcriptional activity of this gene cluster at each of the four developmental stages was also investigated. The stability of these transcripts was deduced by comparing the transcriptional activity with steady-state transcript levels. During the initial 24 h of light-induced development of an etioplast to a chloroplast, transcription decreases in conjunction with increased transcript stability. Transcriptional activity of this cluster per genome then increases between the 24-h and young stages, with a concomitant decrease in the stability of the transcripts. As the young chloroplast matures, the transcripts from this cluster again become markedly more stable, and the transcription of this set of genes declines. Therefore, the regulation of the expression of this cluster is dependent upon a complex interaction between transcriptional and posttranscriptional factors throughout light-induced plastid development.

Journal Article↗
PubMed2001

Detection of differential gene expression in biofilm-forming versus planktonic populations of Staphylococcus aureus using micro-representational-difference analysis.

Microbial proliferation and biofilm formation on biologic or inert substrates are characteristics of invasive Staphylococcus aureus infections and is associated with phenotypic alterations such as reduced antimicrobial susceptibility. To identify genes which are typically expressed in biofilms, a micro-representational-difference analysis (micro-RDA) was adapted for gram-positive bacteria and used with cDNA derived from populations of S. aureus DSM 20231 growing in a biofilm or plankonically. In comparison to previously described cDNA RDA protocols, micro-RDA has the advantages that only minimal quantities of total RNA are needed and, most importantly, that total RNA can be used since the large amount of rRNA in total RNA does not interfere with the micro-RDA procedure. Using a series of spiked controls with various amounts of MS2 RNA in a background of total RNA from S. aureus, the equivalent of five copies of MS2 per cell were detectable after three rounds of subtractive enrichment. Five genes were identified as being differentially expressed in biofilm versus planktonic cultures. These genes revealed homology to a threonyl-tRNA synthetase, a phosphoglycerate mutase, a triosephosphate isomerase, an alcohol dehydrogenase I, and a ClpC ATPase. Differential levels of expression were subsequently confirmed by standard Northern blotting. In conclusion, micro-RDA is a sensitive and specific method to detect transcripts differentially expressed as a function of different S. aureus growth conditions.

Bacterial Proteins↗
PubMed2004

Modified serial analysis of gene expression method for construction of gene expression profiles of microbial eukaryotic species.

Serial analysis of gene expression (SAGE) is a powerful approach for the identification of differentially expressed genes, providing comprehensive and quantitative gene expression profiles in the form of short tag sequences. Each tag represents a unique transcript, and the relative frequencies of tags in the SAGE library are equal to the relative proportions of the transcripts they represent. One of the major obstacles in the preparation of SAGE libraries from microorganisms is the requirement for large amounts of starting material (i.e., mRNA). Here, we present a novel approach for the construction of SAGE libraries from small quantities of total RNA by using Y linkers to selectively amplify 3' cDNA fragments. To validate this method, we constructed comprehensive gene expression profiles of the toxic dinoflagellate Pfiesteria shumwayae. SAGE libraries were constructed from an actively toxic fish-fed culture of P. shumwayae and from a recently toxic alga-fed culture. P. shumwayae-specific gene transcripts were identified by comparison of tag sequences in the two libraries. Representative tags with frequencies ranging from 0.026 to 3.3% of the total number of tags in the libraries were chosen for further analysis. Expression of each transcript was confirmed in separate control cultures of toxic P. shumwayae. The modified SAGE method described here produces gene expression profiles that appear to be both comprehensive and quantitative, and it is directly applicable to the study of gene expression in other environmentally relevant microbial species.

Animals↗
PubMed1976

Rapid micromethod for the purification of Escherichia coli ribonucleic acid polymerase and the preparation of bacterial extracts active in ribonucleic acid synthesis.

A rapid micromethod is described for the preparation of nucleic acid-free extracts from Escherichia coli that involves precipitation with polyethylene glycol. Extracts can be prepared from growing cells in 75 min by three short, low-speed centrifugations. The extract did not inhibit added purified ribonucleic acid (RNA) polymerase, suggesting that major inhibitors of RNA synthesis had been removed. This extract should be ideal for assessing the properties of mutant RNA polymerases. The rapid chromatography of the extracts with step elution from deoxyribonucleic acid- and diethylaminoethyl-cellulose columns resulted in high yields of substantially pure RNA polymerase. We used this technique to purify 35S-labeled RNA polymerase. This system should find application for the purification of small quantities of other bacterial RNA polymerases that share the general chromatographic properties of E. coli RNA polymerase.

Chemical Precipitation↗
PubMed1990

Differential mRNA stability controls relative gene expression within the plasmid-encoded arsenical resistance operon.

The arsenical resistance (ars) operon of the conjugative plasmid R773 encodes an ATP-driven anion extrusion pump, conferring bacterial resistance to arsenicals. The operon contains a regulatory gene, arsR, and three structural genes, arsA, arsB, and arsC. The hydrophilic ArsA and ArsC proteins are produced in large amounts, but the hydrophobic ArsB protein, an integral membrane polypeptide, is synthesized in limited quantities. Northern (RNA-DNA) hybridizations provide evidence that the inducible operon is regulated at the level of transcription. The genes were transcribed in the presence of an inducer (arsenite) as a single polycistronic mRNA with an approximate size of 4.4 kilobases (kb). This transcript was processed to generate relatively stable mRNA species: one of 2.7 kb, encoding the ArsR and ArsA proteins, and a second of 0.5 kb, encoding the ArsC protein. Segmental differences in stability within the polycistronic transcript are proposed to account for the differential expression of the ars genes. In addition, analysis of the mRNA structure at the 5' end of arsB suggests a potential translational block to the synthesis of this membrane protein.

Arsenicals↗
PubMed2006

Induction of a protective immune response against viral nervous necrosis in the European sea bass Dicentrarchus labrax by using betanodavirus virus-like particles.

Betanodaviruses are causative agents of viral nervous necrosis (VNN), a devastating disease of cultured marine fish worldwide. Virus particles contain a single type of coat protein that spontaneously assembles into virus-like particles (VLPs) when expressed in a baculovirus expression system. In the present study, the immunogenicity of betanodavirus VLPs and the protection they confer against VNN in the European sea bass Dicentrarchus labrax were investigated. Enzyme-linked immunosorbent assay and seroneutralization tests performed on plasma from fish vaccinated intramuscularly with doses as low as 0.1 microg of VLPs indicated that the VLPs elicited the synthesis of specific antibetanodavirus antibodies with neutralizing activity. Moreover, fish vaccinated with VLPs were protected from challenge with live virus. Both the immune response and the protective effect against viral challenge were dose dependent. Reverse transcription-PCR data indicated that higher doses of vaccine also reduced the number of fish containing detectable quantities of betanodavirus RNA on day 30 after challenge. Taken together these data strongly support the hypothesis that VLPs obtained in the baculovirus expression system may represent an effective vaccine against VNN.

Animals↗
PubMed1995

Human immunodeficiency virus type 1 Vif- mutant particles from restrictive cells: role of Vif in correct particle assembly and infectivity.

Disruption of the vif gene of human immunodeficiency virus (HIV) type 1 affects virus infectivity to various degrees, depending on the T-cell line used. We have concentrated our studies on true phenotypic Vif- mutant particles produced from CEMx174 or H9 cells. In a single round of infection, Vif- virus is approximately 25 (from CEMx174 cells) to 100 (from H9 cells) times less infectious than wild-type virus produced from these cells or than the Vif- mutant produced from HeLa cells. Vif- virions recovered from restrictive cells, but not from permissive cells, are abnormal both in terms of morphology and viral protein content. Notably, they contain much reduced quantities of envelope proteins and altered quantities of Gag and Pol proteins. Although wild-type and Vif- virions from restrictive cells contain similar quantities of viral RNA, no viral DNA synthesis was detectable after acute infection of target cells with phenotypically Vif- virions. To examine the possible role of Vif in viral entry, attempts were made to rescue the Vif- defect in H9 cells by pseudotyping Vif+ and Vif- HIV particles with amphotropic murine leukemia virus envelope. Vif- particles produced in the presence of HIV envelope could not be propagated when pseudotyped. In contrast, when only the murine leukemia virus envelope was present, significant propagation of Vif- HIV particles could be detected. These results demonstrate that Vif is required for proper assembly of the viral particle and for efficient HIV Env-mediated infection of target cells.

Base Sequence↗
PubMed2001

Rapid CD4(+) T-cell loss induced by human immunodeficiency virus type 1(NC) in uninfected and previously infected chimpanzees.

To investigate the pathogenicity of a virus originating in a chimpanzee with AIDS (C499), two chimpanzees were inoculated with a plasma-derived isolate termed human immunodeficiency virus type 1(NC) (HIV-1(NC)). A previously uninfected chimpanzee, C534, experienced rapid peripheral CD4(+) T-cell loss to fewer than 26 cells/microl by 14 weeks after infection. CD4(+) T-cell depletion was associated with high plasma HIV-1 loads but a low virus burden in the peripheral lymph node. The second chimpanzee, C459, infected 13 years previously with HIV-1(LAV), experienced a more protracted course of peripheral CD4(+) T-cell loss after HIV-1(NC) inoculation, resulting in fewer than 200 cells/microl by 96 weeks postinoculation. The quantities of viral RNA in the plasma and peripheral lymph node from C459 were below the lower limits of detection prior to inoculation with HIV-1(NC) but were significantly and persistently increased after superinfection, with HIV-1(NC) representing the predominant viral genotype. These results show that viruses derived from C499 are more pathogenic for chimpanzees than any other HIV-1 isolates described to date.

Acquired Immunodeficiency Syndrome↗
PubMed1994

Skeletal muscle growth and protein turnover in neonatal boars and barrows.

The objective of this study was to determine the effect of castration, within 24 h after birth, on skeletal muscle growth and protein metabolism in neonatal pigs at 1, 2, and 4 wk of age. Four additional pigs were slaughtered at birth to obtain initial body composition. All other pigs were infused with [14C]tyrosine for 6 h before slaughter to determine in vivo fractional protein synthesis rates (FSR). At slaughter, muscle bundles were removed from the semitendinosus and incubated with [3H]tyrosine to determine in vitro protein synthesis rates. Nucleic acids and protein were determined on the semitendinosus muscle. Testosterone concentrations, determined at weekly intervals, peaked in boars at 3 wk of age. Castration at birth did not affect combined weights of the semitendinosus, longissimus, triceps brachii, and brachialis muscles. Likewise, neither in vitro protein synthesis rates nor in vivo FSR were affected by castration. However, a developmental decline in in vivo FSR and in vitro protein synthesis rates occurred from 1 to 4 wk. Neither concentrations nor total quantity of protein, RNA, or DNA in the semitendinosus muscle differed between neonatal boars and barrows at any age. Concentrations of DNA and RNA at 4 wk were two- and threefold lower, respectively, than at birth. Protein:DNA and protein:RNA ratios increased three- and sixfold, respectively, from birth to 4 wk. Testosterone concentrations had little effect on skeletal muscle growth and protein turnover rates during this neonatal period.

Animals↗
PubMed2002

Extensive oligonucleotide microarray transcriptome analysis of the rat cerebral artery and arachnoid tissue.

Cerebral vessels have certain distinct anatomical and developmental characteristics which are well known, but their characteristic genetic expression profile remains as yet only poorly understood. We investigated gene expression in the rat cerebral artery in comparison with the rat descending aorta, two locations which have obviously different anatomical and developmental characteristics. Since the contamination of cerebral small arteries by arachnoid tissue is to a certain extent inevitable, we also performed a gene expression analysis of arachnoid tissue as a background. In an effort to obtain the necessary quality and quantity of total RNA, a novel freeze-fracture apparatus minimizing the time required for the entire procedure from tissue separation to RNA preparation was used. With the material obtained, a group of genes highly expressed in each tissue was detected by oligonucleotide microarray analysis. In the circle of Willis, peptide-19 (PEP-19), connexin-37 (CXN-37), growth arrest-and DNA damage-inducible gene (GADD45), and the putative G protein coupled receptor RA1c, Notch-1, and jagged-1 were predominantly expressed. In arachnoid tissue, bone morphologic protein (BMP)-7, BMP-6, beta defensin-1, neuroendocrine protein 7B2, thiol-specific antioxidant protein, IL-18, beta-chain clathrin-associated protein complex AP-1, and angiopoietin-2 were highly expressed. In the aorta, most of the abundantly expressed genes related to lipid metabolism. By means of oligonucleotide microarray analysis, the distinct gene expression profiles in the circle of Willis arachnoid tissue, and aorta were made evident. From these findings it is reasonable to conclude that a functional interaction exists between the circle of Willis and arachnoid tissue.

Animals↗