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At least 685 records · Page 38Linked to original sources
PubMed2004

West Nile virus surveillance: A simple method for verifying the integrity of RNA in mosquito (Diptera: Culicidae) pools.

In a West Nile virus (WNV) -free ecosystem, it is essential to verify the integrity of RNA before concluding that RNA extracted from mosquito specimens is negative for WNV gene sequences. The primary objective of our study was to develop a rapid molecular assay to rapidly screen mosquitoes for the presence of 18S RNA and WNV gene sequences. Mosquitoes, collected from multiple sites on the island of O'ahu, were pooled into groups of 1-50 mosquitoes according to capture site, date, and species. Using primer design software and the GenBank database, generic oligonucleotide primer pairs were designed to amplify mosquito18S rRNA gene sequences from different species. RNA was extracted from mosquito pools, and reverse transcriptase-polymerase chain reaction (RT-PCR) was performed for the presence of mosquito18S rRNA and WNV gene sequences. Three of the seven primer pairs successfully detected 18S rRNA sequences for both Aedes and Culex by RT-PCR, and one primer pair successfully amplified 18S rRNA sequences for 15 different mosquito species. All 64 mosquito pools from 10 different sites on the island of Oahu, Hawaii, were negative for WNV nonstructural protein-5 gene sequences. This simple, one-step RT-PCR method for screening mosquito pools for arboviruses will become an increasingly valuable tool as WNV becomes endemic throughout the Americas.

Aedes↗
PubMed2004

Quantification of Enterococcus faecalis and Enterococcus faecium in different foods using rRNA-targeted oligonucleotide probes.

The abundance of Enterococcus faecalis and Enterococcus faecium in different Spanish foods was evaluated by using taxon-specific oligonucleotide probes targeted against extracted rRNA. Two satisfactory methods were developed for RNA extraction. Although the yield and purity of total RNA obtained largely depended on the type of food, method 1 should be recommended. The quantitative results obtained with the oligonucleotide probes DB6 for E. faecium and DB8 for E. faecalis showed that these two species accounted for less than 0.5% of the active microflora in all the food samples tested. These results suggest that enterococci form only a minor portion of the microflora of these products.

Animals↗
PubMed1992

Interleukin-6 in psoriasis: expression and mitogenicity studies.

Interleukin-6 (IL-6) is a multifunctional cytokine which has been suggested to function as an autocrine mitogen in psoriatic epidermis. We report here the results of several experiments designed to further examine this hypothesis. Blot hybridization was unable to detect 1.3 kb IL-6 transcripts in RNA extracted from normal or psoriatic epidermal (keratome) biopsies, suggesting that IL-6 expression is very low in normal and psoriatic epidermis. Therefore, qualitative and semiquantitative PCR/Southern blot analyses were performed on keratome-derived RNA, and revealed variable but significantly increased IL-6 mRNA levels in lesional psoriatic relative to normal tissue. To further examine the ability of normal human keratinocytes (NHK) to express IL-6, RNA was extracted from rapidly proliferating secondary NHK cultures. IL-6 transcripts were nearly undetectable by blotting in keratinocytes grown in low-calcium serum-free medium, but low levels could be induced by treatment with 1.8 mM CaCl2. IL-6 transcripts were strongly superinduced after cycloheximide treatment, suggesting that a labile protein regulates IL-6 mRNA levels in these cells. Finally, the mitogenic activity of IL-6 was examined in NHK under varying conditions of cell density and added growth factors. IL-6 did not stimulate high density keratinocyte growth in the presence or absence of other growth factors, but did stimulate clonal growth in epidermal growth factor (EGF)-deficient media at high concentrations (> or = 10 ng/ml). The proliferative effects of IL-6, but not of basic fibroblast growth factor, were abrogated by monoclonal antibodies directed against the EGF receptor.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1997

Poliovirus RNA recombination in cell-free extracts.

Poliovirus RNA has been shown to undergo homologous genetic recombination at a high frequency in infected human cells. Recently it has become possible to mimic the entire intracellular replicative cycle of poliovirus replication in cytoplasmic extracts prepared from HeLa cells, resulting in the generation of infectious poliovirions. The mechanism of poliovirus RNA recombination has been shown previously to be coupled to RNA replication, presumably by template switching during the replication of parental RNAs. Experiments were designed to test whether recombinant poliovirus RNA molecules are produced in a cell-free environment. Recombinant molecules generated bear marker sequences that can be detected physically by reverse transcription and PCR. We report here successful detection of poliovirus RNA recombination in a cell-free replication system. The frequency measured for cell-free RNA recombination between two polymorphic marker loci 656 nt apart was between 10(-2) and 10(-3) recombinants/genome, a frequency comparable to or slightly higher than that measured for RNA recombination in infected cells.

Antiviral Agents↗
PubMed1980

Further evidence for haploid gene expression during spermatogenesis: heterogeneous, poly(A)- containing RNA is synthesized post-meiotically.

Mouse testicular cells labelled in vivo with 3H-uridine for 1 hour were separated into enriched cell populations representing different stages of spermatogenesis by centrifugation in an Elutriator rotor. RNA extracted with phenol and chloroform was sized by electrophoresis on 2.4% acrylamide gels. The percentage of newly synthesized RNA which was not ribosomal RNA (or its precursors) and was not transfer RNA, was higher in early postmeiotic, as compared to late premeiotic, stages. RNA was also extracted from fractionated cells in the presence of guanidinium chloride and the proportion of total 3H-RNA-containing poly(A) sequences was determined by binding to an oligo-(dT)-cellulose column. RNA that bound in 0.5 NaCl was eluted with low salt buffer and reapplied twice more, after heating each time in DMSO to disaggregate any non-poly(A)-containing RNA. The percentage of newly synthesized RNA which contained poly(A) did not decrease in early postmeiotic, as compared to late premeiotic, stages. We suggest that at least some part of the 6-15S 3H-RNA and 3H-poly(A)-containing RNA represents mRNA(s) transcribed postmeiotically in haploid germ cells.

Animals↗
PubMed1999

Immuno-LCM: laser capture microdissection of immunostained frozen sections for mRNA analysis.

Microdissection of routinely stained or unstained frozen sections has been used successfully to obtain purified cell populations for the analysis of cell-specific gene expression patterns in primary tissues with a complex mixture of cell types. However, the precision and usefulness of microdissection is frequently limited by the difficulty to identify different cell types and structures by morphology alone. We therefore developed a rapid immunostaining procedure for frozen sections followed by laser capture microdissection (LCM) and RNA extraction, which allows targeted mRNA analysis of immunophenotypically defined cell populations. After fixation, frozen sections are immunostained under RNAse-free conditions using a rapid three-step streptavidin-biotin technique, dehydrated and immediately subjected to LCM. RNA is extracted from captured tissue, DNAse I treated, and reverse transcribed. Acetone-, methanol-, or ethanol/acetone-fixed sections give excellent immunostaining after 12 to 25 minutes total processing time. Specificity, precision, and speed of microdissection is markedly increased due to improved identification of desired (or undesired) cell types. The mRNA recovered from immunostained tissue is of high quality. Single-step PCR is able to amplify fragments of more than 600 bp from both housekeeping genes such as beta-actin as well as cell-specific messages such as CD4 or CD19, using cDNA derived from less than 500 immunostained, microdissected cells. Immuno-LCM allows specific mRNA analysis of cell populations isolated according to their immunophenotype or expression of function-related antigens and significantly expands our ability to investigate gene expression in heterogeneous tissues.

Cells↗
PubMed2004

Isolation of functional RNA from small amounts of different grape and apple tissues.

An efficient, simple, and small-scale procedure for isolating functional ribonucleic acid (RNA) was successfully applied to many different tissues of grape and apple. These woody plants are rich in polyphenolic compounds and polysaccharides that could impair the RNA extraction. The method chosen is based on the use of hot borate buffer at alkaline pH supplemented with several adjuvants and followed by selective precipitations. Starting with only 0.4 g of fresh tissue and working with small tubes (2 mL), we were able to obtain good yields of high-quality RNA suitable for further applications. The procedure can be proposed for many applications, and it is particularly highly recommended when isolating RNA from a large number of samples.

Chemical Precipitation↗
PubMedDate not supplied

Optimized blood cell profiling method for genomic biomarker discovery using high-density microarray.

High-quality biomarkers for disease progression, drug efficacy and toxicity liability are essential for improving the efficiency of drug discovery and development. The identification of drug-activity biomarkers is often limited by access to and the quantity of target tissue. Peripheral blood has increasingly become an attractive alternative to tissue samples from organs as source for biomarker discovery, especially during early clinical studies. However, given the heterogeneous blood cell population, possible artifacts from ex vivo activations, and technical difficulties associated with overall performance of the assay, it is challenging to profile peripheral blood cells directly for biomarker discovery. In the present study, Applied BioSystems' blood collection system was evaluated for its ability to isolate RNA suitable for use on the Affymetrix microarray platform. Blood was collected in a TEMPUS tube and RNA extracted using an ABI-6100 semi-automated workstation. Using human and rat whole blood samples, it was demonstrated that the RNA isolated using this approach was stable, of high quality and was suitable for Affymetrix microarray applications. The microarray data were statistically analysed and compared with other blood protocols. Minimal haemoglobin interference with RNA labelling efficiency and chip hybridization was found using the TEMPUS tube and extraction method. The RNA quality, stability and ease of handling requirement make the TEMPUS tube protocol an attractive approach for expression profiling of whole blood to support target and biomarker discovery.

Animals↗
PubMed2006

The RIN: an RNA integrity number for assigning integrity values to RNA measurements.

BACKGROUND: The integrity of RNA molecules is of paramount importance for experiments that try to reflect the snapshot of gene expression at the moment of RNA extraction. Until recently, there has been no reliable standard for estimating the integrity of RNA samples and the ratio of 28S:18S ribosomal RNA, the common measure for this purpose, has been shown to be inconsistent. The advent of microcapillary electrophoretic RNA separation provides the basis for an automated high-throughput approach, in order to estimate the integrity of RNA samples in an unambiguous way. METHODS: A method is introduced that automatically selects features from signal measurements and constructs regression models based on a Bayesian learning technique. Feature spaces of different dimensionality are compared in the Bayesian framework, which allows selecting a final feature combination corresponding to models with high posterior probability. RESULTS: This approach is applied to a large collection of electrophoretic RNA measurements recorded with an Agilent 2100 bioanalyzer to extract an algorithm that describes RNA integrity. The resulting algorithm is a user-independent, automated and reliable procedure for standardization of RNA quality control that allows the calculation of an RNA integrity number (RIN). CONCLUSION: Our results show the importance of taking characteristics of several regions of the recorded electropherogram into account in order to get a robust and reliable prediction of RNA integrity, especially if compared to traditional methods.

Algorithms↗
PubMed1989

The role of the various human peripheral blood mononuclear cells in the production of Sendai virus-induced interferon: IFN mRNA studies.

We have studied the relative contribution made to the production of interferon (IFN) in vitro in response to Sendai virus by the cells of different types present in human peripheral blood, with particular emphasis on the amounts of poly(A) plus RNA extractable from each subpopulation and its content of IFN mRNA. Peripheral blood cells were fractionated by conventional techniques, and the amounts of IFN made after induction with Sendai virus were measured. The proportion of IFN-producing cells in the various fractions was determined by immunofluorescent staining. Poly(A) plus RNA was extracted from each population and the content of IFN mRNA determined by microinjection into Xenopus laevis oocytes. Information obtained in these three ways was essentially concordant, and showed that monocytes and E rosette-negative lymphocytes predominantly contribute to IFN production.

Animals↗
PubMed2006

Integrated reverse transcription polymerase chain reaction systems for virus detection.

The current study reports on an integrated microreverse transcription polymerase chain reaction (RT-PCR) system for molecular diagnosis of microorganisms automatically. By using antibodies-conjugated superparamagnetic beads, the developed system can detect viruses with higher sensitivity and specificity when compared with traditional biological diagnosis methods using a ribonucleic acid (RNA) extraction kit. The target viruses were first captured by the conjugated antibodies on the magnetic beads, and were enriched using a magnetic field generated by micro-electromagnets or permanent magnets. With this approach, the virus can be purified and concentrated first, then the virus RNA was extracted and transcripted to complementary deoxyribonucleic acid (cDNA), followed by a nucleic acid amplification process using a micro-RT-PCR module. The integrated microfluidic chip can perform the whole process automatically with the aid of integrated micropumps and microvalves. This study successfully performs the specific detection of two different types of viruses, Dengue virus serotype 2 and enterovirus (EV) 71 using this developed integrated system. Comparable to a large-scale apparatus, the integrated microsystem can perform mixing, incubation, purification, transportation, and nucleic acid amplification of virus, possibly making it a crucial platform for future diagnosis applications.

Magnetics↗
PubMed1976

Investigation on the infection of cucumber mesophyll protoplasts with cucumber mosaic virus.

Isolated protoplasts from the first leaf mesophyll of cucumber plants have been successfully infected in vitro with cucumber mosaic virus (CMV). Virus instability before, during and after inoculation of the protoplasts resulted in low infectivities when extracts were assayed on cowpea; however, viral RNA extraction improved the bioassay technique. Attempts to optimize inoculation and incubation of protoplasts are outlined, incorporating the improved assay.

Culture Techniques↗
PubMed1991

Effect of tryptic or peptic digestion or mechanical isolation on the extraction of proteins, antigens, and ribonucleic acids from Sarcocystis muris bradyzoites.

Various methods have been used for the isolation of bradyzoites of Sarcocystis species. Using Sarcocystis muris as a model, the effect of 3 methods, trypsin digestion, pepsin digestion, and mechanical isolation, on the subsequent extraction of S. muris proteins, antigens, and RNA was examined. Although some quantitative differences were found among the proteins, antigens, and RNA extracted after the 3 isolation methods, qualitative differences were not evident. The overall isoelectric focusing protein profile showed approximately 30 bands in the pH range of 3-9 and was dominated by 5 bands with pI values of approximately 5.3, 6.3, 6.8, 7.0, and 7.4. In experimentally infected mice, antibodies were recorded from 35 days postinoculation (PI) until the end of examination (130 days PI). The S. muris RNA appeared to consist of at least 10 subunits in the range of 200-4,200 nucleotides. A Toxoplasma gondii DNA fragment specific for small subunit ribosomal RNA (rRNA) hybridized mainly to the S. muris 1,900-nucleotide subunit and a range of smaller subunits, and a probe specific for large subunit rRNA hybridized mainly to the 4,200-nucleotide subunit and a range of smaller subunits. All 3 methods of bradyzoite isolation gave good yields of intact messenger RNAs that showed similar in vitro translation curves.

Animals↗
PubMed2002

Induction of RNA interference in Caenorhabditis elegans by RNAs derived from plants exhibiting post-transcriptional gene silencing.

The term 'gene silencing' refers to transcriptional and post-transcriptional control of gene expression. Related processes are found across kingdoms in plants and animals. We intended to test whether particular RNA constituents of a silenced plant can induce silencing in an animal. We generated Nicotiana benthamiana lines that expressed green fluorescent protein (GFP) from a transgene. Plants in which GFP expression was spontaneously silenced showed siRNAs characteristic of post-transcriptional gene silencing (PTGS). RNA extracts prepared from silenced plants were injected into a GFP-expressing strain of Caenorhabditis elegans, where they induced RNA interference (RNAi). Extracts from non-silenced plants were inactive. This directly demonstrates a relationship and a mechanistic link between PTGS and RNAi. Controls confirmed that the silencing agent was an RNA. Size fractionation on denaturing gels revealed that an RNA of approximately 85 nt was most active in inducing silencing in the worm. Northern blot analysis of the region in question did not detect a prominent GFP-specific RNA of sense or antisense polarity, indicating that the RNA species which induced silencing was present only in low concentration or did not hybridize due to formation of an intramolecular double strand. In view of its high activity, it is possible that this agent is responsible for the systemic spread of silencing in plants and it might represent the aberrant RNA, a previously postulated inducer of silencing.

Animals↗
PubMed1991

The isolation and characterization of a Norwalk virus-specific cDNA.

Norwalk virus, an important cause of epidemic, acute, nonbacterial gastroenteritis in adults and children, has eluded adaptation to tissue culture, the development of an animal model, and molecular cloning. In this study, a portion of the Norwalk viral genome encoding an immunoreactive region was cloned from very small quantities of infected stool using sequence-independent single primer amplification. Six overlapping complementary DNA (cDNA) clones were isolated by immunologic screening. The expressed recombinant protein from a representative clone reacted with six of seven high titer. Norwalk-specific, postinfection sera but not with corresponding preinfection sera. Nucleic acid sequence for all clones defined a single open reading frame contiguous with the lambda gt11-expressed beta-galactosidase protein. Only oligonucleotide probes specific for the positive strand (defined by the open reading frame) hybridized to an RNaseA-sensitive, DNaseI-resistant nucleic acid sequence extracted from Norwalk-infected stool. Furthermore, RNA extracted from serial postinfection, but not preinfection, stools from three of five volunteers hybridized to a Norwalk virus cDNA probe. Clone-specific oligonucleotide probes hybridized with cesium chloride gradient fractions containing purified Norwalk virion. In conclusion, an antigenic, protein-coding region of the Norwalk virus genome has been identified. This epitope has potential utility in future sero- and molecular epidemiologic studies of Norwalk viral gastroenteritis.

Amino Acid Sequence↗
PubMed2000

Detection of micrometastasis by cytokeratin-20 (reverse transcription polymerase chain reaction) in lymph nodes of patients with endometrial cancer.

BACKGROUND: Cytokeratins are constituents of the intermediate filaments (IFs) of epithelial cells which are expressed in various combinations, depending on the type of epithelium and degree of differentiation. We have reported (R. Zemer, A. Fishman, J. Bernheim, S. Zimlichman, O. Markowitz, M. Altaras, and A. Klein, Gynecol Oncol 70:410-413, 1998) on the determination of cytokeratin-20 (CK-20) by reverse transcription polymerase chain reaction (RT-PCR) in the detection of endometrial cancer cells as a potential biomarker. In that study, we also found that by using immunocytochemistry, most carcinomas were found to be negative for CK-20. The sensitivity and specificity rates obtained by using the RT-PCR method were 94.4 and 91%, respectively. OBJECTIVE: The aim of this study is to investigate the feasibility and potential of the specific mRNA marker, CK-20, to detect endometrial cancer cells-micrometastases (MMs)-by RT-PCR in lymph node (LN) samplings of patients undergoing hysterectomy for endometrial carcinoma. METHOD: We used the RT-PCR method to determine the expression of CK-20 in the LNs of 20 patients [study group (SG)] who were being surgically staged and treated for endometrial carcinoma. The specificity of the mRNA CK-20 marker was examined in LNs obtained from five healthy patients [control group (CG)] who underwent abdominal hysterectomy and bilateral salpingo-oopherectomy for benign gynecologic conditions. The LNs obtained from the SG and CG patients were prepared together before mRNA extraction. RNA of the various cell pellets was extracted and RT-PCR was performed with CK-20 primers. RT-PCR products were analyzed by agarose gel electrophoresis and ethidium bromide staining against PCR size markers. Specificity of the RT-PCR products was examined by Southern blotting. RESULTS: Histopathologic examinations demonstrated the presence of metastases in two (10%) SG patients. These patients were also CK-20 positive. Of the remaining 18 patients with negative histopathologic results, 6 (33%) were CK-20 positive and 12 (67%) were negative. All the CG patients were CK-20 negative (specificity, 100%). CONCLUSIONS: The results obtained in this study suggest that RT-PCR of CK-20 is more sensitive than traditional histopathologic methods in the diagnosis of MMs in LNs of patients with endometrial cancer. Thus, due to the aforementioned characteristics of CK-20, it may be considered a powerful biomarker in the detection of MMs in LNs of patients with endometrial cancer.

Adenocarcinoma↗
PubMed2003

Evaluation of RNA messengers involved in lipid trafficking of human intestinal cells by reverse-transcription polymerase chain reaction with competimer technology and microchip electrophoresis.

We developed a semiquantitative reverse-transcription polymerase chain reaction (RT-PCR) procedure based on the combination of competimer technology with microchip electrophoresis. The approach was applied to total RNA extracts from the human colon carcinoma cell line CaCo-2 cultured for 22 days onto tissue plate inserts that allow the polarized cell growth. At time of experiment these cells were incubated for 2 h with lipid micelles containing either cholesterol or a mixture cholesterol/beta-sitosterol or serum-free Dulbecco's modified Eagle medium (DMEM) alone. Total RNA was extracted from cell pellets by silica membrane spin columns and reverse-transcribed by a genetically engineered M-MuLV enzyme and an oligo (dT)(15) primer. The cDNA underwent PCR amplification for the following genes: apolipoprotein A1 (ApoAI), apolipoprotein E (ApoE), ATP-binding cassette A1 (ABCA1), liver X receptor alpha (LXRalpha) and farnesoid X receptor (FXR). The beta-actin gene, used as an endogenous reference, was coamplified with mixtures of primer and competimer at a ratio leading to a reference band of intensity comparable to that of the gene under analysis. Amplification products were separated and quantitated by microchip electrophoresis in order to determine, for each gene, the optimum cycle numbers and primer to competimer ratios for the beta-actin therefore used for evaluating the relative variations of gene expressions in the different experiments. The incubation with cholesterol micelles stimulated both LXR and FXR expression that was accompanied by an increased expression of ABCA1 and ApoAI genes (1.4- and 1.5-fold, respectively) and halved the APOE expression. The effect on ABCA1 and ApoAI expression was even stronger (5.7- and 2.6-fold, respectively) with beta-sitosterol-containing micelles. Similar changes are in line with previous findings and suggest that the short incubation with beta-sitosterol-enriched micelles stimulates a specific mechanism that, via ABCA1 activation, can increase the cholesterol and phytosterol basolateral efflux.

Base Sequence↗
PubMed2001

Quantitation of TGF-beta1 mRNA in porcine mesangial cells by comparative kinetic RT/PCR: comparison with ribonuclease protection assay and in situ hybridization.

Gene expression can be examined with different techniques including ribonuclease protection assay (RPA), in situ hybridisation (ISH), and quantitative reverse transcription-polymerase chain reaction (RT/PCR). These methods differ considerably in their sensitivity and precision in detecting and quantifying low abundance mRNA. Although there is evidence that RT/PCR can be performed in a quantitative manner, the quantitative capacity of this method is generally underestimated. To demonstrate that the comparative kinetic RT/PCR strategy-which uses a housekeeping gene as internal standard-is a quantitative method to detect significant differences in mRNA levels between different samples, the inhibitory effect of heparin on phorbol 12-myristate 13-acetate (PMA)-induced-TGF-beta1 mRNA expression was evaluated by RT/PCR and RPA, the standard method of mRNA quantification, and the results were compared. The reproducibility of RT/PCR amplification was calculated by comparing the quantity of G3PDH and TGF-beta1 PCR products, generated during the exponential phases, estimated from two different RT/PCR (G3PDH, r = 0.968, P = 0.0000; TGF-beta1, r = 0.966, P = 0.0000). The quantitative capacity of comparative kinetic RT/PCR was demonstrated by comparing the results obtained from RPA and RT/PCR using linear regression analysis. Starting from the same RNA extraction, but using only 1% of the RNA for the RT/PCR compared to RPA, significant correlation was observed (r = 0.984, P = 0.0004). Moreover the morphometric analysis of ISH signal was applied for the semi-quantitative evaluation of the expression and localisation of TGF-beta1 mRNA in the entire cell population. Our results demonstrate the close similarity of the RT/PCR and RPA methods in giving quantitative information on mRNA expression and indicate the possibility to adopt the comparative kinetic RT/PCR as reliable quantitative method of mRNA analysis.

Animals↗