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At least 73 records · Page 4Linked to original sources
PubMed2002

A single nucleotide polymorphism of the low molecular mass polypeptide 7 gene influences the interferon response in patients with chronic hepatitis C.

Transporter associated with antigen processing (TAP) and low molecular mass polypeptides (LMP) play crucial roles in the human leukocyte antigen (HLA) class I-restricted antigen presenting systems. This study was performed to elucidate whether these antigen-presenting gene polymorphisms could influence the response to interferon (IFN) treatment in patients with chronic hepatitis C. Polymorphisms of TAP and LMP genes in 175 hepatitis C virus (HCV) patients were determined by polymerase chain reaction-restriction fragment length polymorphism. The frequencies of these genes were compared between sustained-responders (n=49) and nonresponders (n=126), classified by biochemical and virological responses to IFN. The distributions of TAP1*, TAP2*, and LMP2 genes between sustained-responders and nonresponders did not differ. However, LMP7-K gene frequency in sustained-responders was higher than that in nonresponders [odds ratio 2.3 (95% confidence interval 1.1-4.6); 16%vs 7.9%]. Multivariate analysis revealed that LMP7-K and HCV-RNA quantity were independent factors influencing the outcome of IFN therapy [4.5 (1.4-14); P=0.011, 0.40 (0.24-0.65); P=0.0003, respectively]. Furthermore, among patients with a low viral load (< or = 2.0 Meq/mL), the LMP7-K positive patients had an even higher ratio of sustained response compared to those without LMP7-K [5.9 (1.6-22); 82%vs 44%; P=0.0062]. These findings suggest that a single nucleotide polymorphism of LMP7 gene is one of the important host factors which independently influence the response to IFN in patients with chronic hepatitis C.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2001

[Involvement of TAP2 and LMP7 gene polymorphisms in HCV infection].

We aimed to study whether TAP and LMP polymorphisms could influence the severity of liver disease or the response to IFN treatment in patients with chronic HCV infection. TAPZ*0103 gene frequencies in carriers with normal ALT was significantly higher than that in CLD patients. As for the results of IFN responses, LMP7-K gene frequency in sustained-responders was higher than that in non-responders. Multivariate analysis revealed that LMP7-K and HCV RNA quantity were independent factors influencing the outcome of IFN therapy. Furthermore, among patients with a low viral load, the LMP7-K positive patients had a significantly higher ratio of sustained response compared to those without LMP7-K. The TAP2 polymorphism may be closely associated with low hepatitis activity, whereas the LMP7 polymorphism influences the efficacy of IFN treatment and can be a useful predictive parameter in HCV patients with a low viral load.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMedDate not supplied

Study of housekeeping gene expression in human keratinocytes using OLISA, a long-oligonucleotide microarray and q RT-PCR.

In recent years, applications of microarray platforms have been extended to different areas of research including cosmetic and pharmaceutical. Although microarray technology is still improving its sensitivity and flexibility, researchers often turn toward quantitative RT-PCR for data validation. Assessment of messenger RNA quantity by these methods is based on comparison with internal standard genes, mainly housekeeping genes, so called because their synthesis occurs normally at a constant level. However, numerous studies showed that expression of these genes could vary in given situations. Here, we report results on four housekeeping genes (GAPDH, beta-2 microglobulin, S40 and S26 ribosomal sub-units) with constant expression levels established on OLISA microarray using different keratinocyte cultures. Moreover, qRT-PCR validation demonstrates that S26 ribosomal is a good housekeeping gene on keratinocytes and skin studies. Our data indicate that S26 gene can be routinely used to standardize results to investigate differentially expressed genes in a healthy human skin.

Cells, Cultured↗
PubMed2025

Systematic comparison of quantity and quality of RNA recovered with commercial FFPE tissue extraction kits.

BACKGROUND: FFPE tissue samples are commonly used in biomedical research and are a valuable source for next-generation sequencing in oncology, however, extracting RNA from these samples can be difficult the quantity and quality achieved can impact the downstream analysis. This study compared the effectiveness of seven different commercially available RNA extraction kits specifically designed for use with FFPE samples in terms of the quantity and quality of RNA recovered. METHODS: This study used 9 samples of FFPE tissue from three different types of tissue (Tonsil, Appendix and lymph node of B-cell lymphoma) to evaluate RNA extraction methods. Three sections of 20&#xa0;&#xb5;m of each sample were combined per sample. The slices were distributed in a systematic manner to prevent any biases. Each of the 7 commercially available RNA extraction kits were used according to manufacturer's instructions, with each sample being tested in triplicate resulting in a total of 189 extractions. The concentration, RNA quality score (RQS) and DV200 of each extraction was analysed using a nucleic acid analyser to determine the quantity and quality of the recovered RNA. RESULTS: This study found that despite processing the FFPE samples in the same standardized way, there were disparities in the quantity and quality of RNA recovered across the different tissue types. Additionally, the study found notable differences in the quantity of RNA recovered when using different extraction kits. In terms of quality, three of the kits performed better than the other four in terms of RQS and DV200 values. CONCLUSION: Though many laboratories have developed their own protocols for specific tissue types, using commercially available kits is still a popular option. Although these kits use similar processes and extraction procedures, the amount and quality of RNA obtained can vary greatly between kits. In this study, among the kits tested, while the Roche kit, provided a nearly systematic better-quality recovery than other kits, the ReliaPrep FFPE Total RNA miniprep from Promega yielded the best ratio of both quantity and quality on the tested tissue samples.

Paraffin Embedding↗
PubMed1997

[AIDS; new developments. III. Predictive value of the quantity of HIV-RNA for the course of the HIV infection and the effect of the treatment].

Standardized tests to measure the quantity of HIV-RNA in blood have been available since early 1995. Individual differences in quantity of HIV-RNA in blood are determined mainly by differences in virus production. Most of the HIV production takes place in infected and activated CD4+ T lymphocytes. The concentration of HIV-RNA in plasma or serum is an important predictor of AIDS and death, in the early stage of the infection even the only one. High concentrations (> or = 10(4) HIV-RNA copies/ml) in the early stage of the infection increase the probability of AIDS from 2.5 to 5 times that with concentrations < 10(4) HIV-RNA copies/ml. The degree of reduction of the HIV-RNA concentration during anti-HIV therapy is of great predictive value for the clinical course. The percentage of persons in whom the amount of HIV-RNA decreases to below the limit of detectability is a good second indicator of a favourable prognosis. Consequently, anti-HIV treatment should be started as early as possible in the infection, and not postponed until the first symptoms of immunodeficiency occur; only then can the virus production be kept at a minimal level as early and as long as possible. The current guideline reads: determination of HIV-RNA concentrations in serum or plasma should be part of the standard clinical practice in monitoring HIV-infected persons. Treatment is started as soon as occasioned by the quantity of HIV-RNA (limit: 10,000 copies/ml), the CD4+ cell count (limit: 500 x 10(6)/l) or the onset of HIV-related symptoms. The quantity of HIV-RNA should diminish substantially during the first three months of treatment. If this is the case, one checkup every three months will suffice. If the HIV-RNA concentration does not decrease sufficiently, resistance or poor compliance may be involved.

Acquired Immunodeficiency Syndrome↗
PubMed2004

Gene expression profiling of human adrenocortical tumors using complementary deoxyribonucleic Acid microarrays identifies several candidate genes as markers of malignancy.

The aim of this study was to identify predictor sets of genes whose over- or underexpression in human sporadic adrenocortical tumors would help to identify malignant vs. benign tumors and to predict postsurgical metastatic recurrence. For this, we analyzed the expression of 230 candidate genes using cDNA microarrays in a series of 57 well-characterized human sporadic adrenocortical tumors (33 adenomas and 24 carcinomas). We identified two clusters of genes (the IGF-II cluster containing eight genes, including IGF-II, and the steroidogenesis cluster containing six genes encoding steroidogenic enzymes plus eight other genes) whose combined levels of expression appeared to be good predictors of malignancy. This predictive value was as strong as that of the pathological score of Weiss. The analysis of the population of carcinomas (13 tumors) for genes whose expression would be strongly different between recurring and nonrecurring tumors allowed identification of 14 genes meeting these criteria. Among these genes, there are probably new markers of tumor evolution that will deserve additional validation on a larger scale. Taken together, these results show that the parallel analysis of the expression levels of a selected group of genes on microgram quantities of tumor RNA (a quantity that can be obtained from fine needle aspirations) appears as a complementary method to histopathology for the diagnosis and prognosis of evolution of adrenocortical carcinomas.

Adolescent↗
PubMedDate not supplied

Large quantity of ribosomal RNA exists extracellularly in mouse spleen.

When BALB/c mouse spleens were gently homogenized in saline, the resultant supernatant (without cells and tissue debris) contained significant amount of 28S and 18S ribosomal RNA, reaching up to 70% of the total spleen RNA. Haemoglobin assays indicated that less than 15% of the spleen cells were lysed during the homogenization process, indicating that the majority of the spleen 'supernatant RNA' was from the extracellular space of the organ rather than released by the splenocytes as a consequence of grinding. Quantitative RNA analysis showed that the ratio of spleen supernatant RNA/total RNA of BALB/c mice was inversely correlated with age (from approximately 70% at 3 weeks to 45% at 6 months), but that of BXSB mice (an animal model for systemic lupus erythematosus) remained at about 70% irrespective of age. Methyl Green-Pyronin Y staining of paraffin sections of mouse spleen revealed that extracellular RNA was distributed mainly in the sinuses of the organ. Culture supernatants of apoptotic splenocytes contained significant amounts of RNA, suggesting that the extracellular RNA in the spleen might have come from apoptotic lymphocytes. This is supported by the fact that 'thymus supernatant' also contained significant amount of RNA. A possible correlation between spleen extracellular RNA and autoimmune diseases is discussed.

Age Factors↗
PubMed2004

Evaluation of vector-primed cDNA library production from microgram quantities of total RNA.

cDNA sequences are important for defining the coding region of genes, and full-length cDNA clones have proven to be useful for investigation of the function of gene products. We produced cDNA libraries containing 3.5-5 x 10(5) primary transformants, starting with 5 mug of total RNA prepared from mouse pituitary, adrenal, thymus, and pineal tissue, using a vector-primed cDNA synthesis method. Of approximately 1000 clones sequenced, approximately 20% contained the full open reading frames (ORFs) of known transcripts, based on the presence of the initiating methionine residue codon. The libraries were complex, with 94, 91, 83 and 55% of the clones from the thymus, adrenal, pineal and pituitary libraries, respectively, represented only once. Twenty-five full-length clones, not yet represented in the Mammalian Gene Collection, were identified. Thus, we have produced useful cDNA libraries for the isolation of full-length cDNA clones that are not yet available in the public domain, and demonstrated the utility of a simple method for making high-quality libraries from small amounts of starting material.

Animals↗
PubMed1990

Amplified RNA synthesized from limited quantities of heterogeneous cDNA.

The heterogeneity of neural gene expression and the spatially limited expression of many low-abundance messenger RNAs in the brain has made cloning and analysis of such messages difficult. To generate amounts of nucleic acids sufficient for use in standard cloning strategies, we have devised a method for producing amplified heterogeneous populations of RNA from limited quantities of cDNA. Whole cerebellar RNA was primed with a synthetic oligonucleotide containing the T7 RNA polymerase promoter sequence 5' to a polythymidylate region. After second-strand cDNA synthesis, T7 RNA polymerase was used to generate amplified antisense RNA (aRNA). Up to 80-fold molar amplification has been achieved from nanogram quantities of cDNA. The amplified material is similar in size distribution to the parent cDNA and shows sequence heterogeneity as assessed by Southern and Northern blot analysis. Specific messages for moderate-abundance mRNAs for actin and guanine nucleotide-binding protein (G-protein) alpha subunits have been detected in the amplified material. By using in situ transcription to generate cDNA, sequences for cyclophilin have been detected in aRNA derived from single cerebellar tissue sections. cDNA derived from a single cerebellar Purkinje cell also has been amplified and yields material that hybridizes to cognate whole RNA and mRNA but not to Escherichia coli RNA.

Actins↗
PubMed2000

Determinants of the quantity of hepatitis C virus RNA.

To test the hypothesis that person-to-person variability in blood levels of hepatitis C virus (HCV) RNA can be explained, the quantity of HCV RNA was assessed in 969 persons who acquired HCV infection in the context of injection drug use. Serum HCV RNA levels ranged from 200,000 to >120 million equivalents/mL (the linear range of the assay). The median log10 HCV RNA level was 0.46 higher in 468 human immunodeficiency virus (HIV)-positive persons than in 501 HIV-negative persons (P<.001). In addition, among HIV-negative persons, lower HCV RNA levels were independently associated with younger age (P<.001), ongoing hepatitis B infection (P=.005), and the absence of needle sharing (P=.02). However, >90% of the person-to-person HCV RNA level variability was not explained by these sociodemographic, environmental, and virologic factors. Additional research is necessary to ascertain what determines the level of HCV RNA in blood.

Adult↗
PubMed1979

Replication cycle of Newcastle disease virus in three host cells of different permissiveness.

Various degrees of permissiveness for NDV have been described in different cell lines. In the present work three systems were investigated: bovine kidney (MDBK) cells, chick embryo (CE) cells and mouse L cells producing 50 to 100 p.f.u., 2 to 10 p.f.u. and less than 0.1 p.f.u./cell, respectively. Analysis of the radioactive virus messenger RNAs (vmRNAs) accumulating in actinomycin D-treated cells throughout the infection cycle revealed that, except for the absence of one 18S vmRNA species in L cells, all vmRNA components were formed in the three cell types, although variations occurred in their total and relative amounts from one cell type to another. Kinetic studies of vmRNA synthesis confirmed the absence of one 18S vmRNA species in L cells and also showed that the labelling rate of this vmRNA component is higher in CE cells. Virus proteins synthesized in the infected cells were labelled with 14C-amino acids and analysed by polyacrylamide gel electrophoresis. All the major NDV polypeptides were formed as expected in both CE and MDBK cells but only traces were detected in L cells. In contrast in a cell-free translation system from wheat germ, all of the NDV major proteins were synthesized using RNA extracted from the three infected cell types. Moreover, the total radioactivity incorporated into NDV proteins was twice as great with CE cell RNA and five times as great with L cell RNA than with equivalent quantities of RNA from MDBK cells.

Animals↗