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Results for “Reverse Transcriptase Polymerase Chain Reaction”

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At least 433 records · Page 24Linked to original sources
PubMed2000

Molecular evolution of the neuropeptide Y (NPY) family of peptides: cloning of three NPY-related peptides from the sea bass (Dicentrarchus labrax).

Neuropeptide Y (NPY) is a 36-amino-acid peptide that is widely and abundantly expressed in the central nervous system of all vertebrates investigated. Related peptides have been found in various vertebrate groups: peptide YY (PYY) is present in gut endocrine cells of many species and pancreatic polypeptide (PP) is made in the pancreas of all tetrapods. In addition, a fish pancreatic peptide called PY has been reported in three species of fishes. The evolutionary relationships of fish PY have been unclear and it has been proposed to be the orthologue (species homologue) of each of the three tetrapod peptides. We demonstrate here with molecular cloning techniques that the sea bass (Dicentrarchus labrax), an acanthomorph fish, has orthologues of both NPY and PYY as well as a separate PY peptide. Sequence comparisons suggest that PY arose as a copy of the PYY gene, presumably in a duplication event separate from the one that generated PP from PYY in tetrapods. PY sequences from four species of fish indicate that, similar to PP, PY evolves much more rapidly than NPY and PYY. The physiological role of PY is unknown, but we demonstrate here that sea bass PY, like NPY and PYY but in contrast to the tetrapod PP, is expressed in brain.

Amino Acid Sequence↗
PubMed2001

The expression of genes induced in melanocytes by exposure to 365-nm UVA: study by cDNA arrays and real-time quantitative RT-PCR.

Ultraviolet A radiation (UVA; 320-400 nm) constitutes more than 90% of the terrestrial UV solar energy. This type of radiation generates reactive oxygen species and consequently induces DNA damage. UVA irradiation is now considered to be an important carcinogen agent especially in the development of melanoma. UVA radiation is known to activate several pathways in mammalian cells. We have used cDNA arrays to analyze differential gene expression in primary cultures of human melanocytes in response to 365-nm UVA. Among 588 genes studied, 11 were overexpressed. These genes included genes involved in cell cycle regulation (GADD45, CIP1/WAF1), in stress response (HSP70, HSP40, HSP86), in apoptosis (GADD153, tristetraproline) and genes encoding transcription factors (EGR-1, ETR-101, c-JUN, ATF4). This coordinate gene regulation was confirmed by real-time quantitative RT-PCR.

Cell Differentiation↗
PubMed2003

In vivo transcription of bovine leukemia virus and bovine immunodeficiency-like virus.

Cellular tropism and transcription of bovine leukemia virus (BLV) and bovine immunodeficiency-like virus (BIV) were investigated using peripheral blood mononuclear cells (PBMC) collected from a cow infected with both viruses. Each PBMC subset, purified by magnetic cell sorting, was subjected to PCR and RT-PCR for detection of their integrated proviruses and transcript mRNAs. Both BLV and BIV genomes were detected by nested PCR in CD3(+), CD4(+), CD8(+) and gammadelta T cells, B cells and monocytes. However, BLV tax transcription was only detected in B cells, and only B cells also formed BLV syncytia in CC81 cells. On the other hand, BIV transcript was detected in each subpopulation of PBMC. These results indicated that BLV can infect T cells and monocytes as well as B cells, but can be expressed by transcription only in B cells. In contrast, BIV can express its transcripts in all infected cells.

Animals↗
PubMed2001

Expression of Wnt genes in human colon cancers.

A polymerase chain reaction-based approach was used to study the expression of Wnt genes in human colon carcinoma tissue and normal colon mucosa. In a number of cases Wnts 2, 4, 5a, 6 and/or 7a were found to be more highly expressed in colon carcinoma tissue compared to surrounding normal-appearing mucosa from the same patients. Wnts 4, 5a, 6 and 7a, but not 2, were also found to be expressed in colon cancer cell lines. The increased levels of expression of these Wnt genes in tumor tissue may indicate their possible involvement in human colon tumorigenesis.

Cell Line↗
PubMed2002

Induced transcriptional expression of calcium-binding protein S100A1 and S100A10 genes in human renal cell carcinoma.

Expression of 16 S100 family calcium-binding protein genes was evaluated by PCR in ten human tissue cDNA libraries. Six to 12 S100 genes were expressed in a tissue-specific manner. Then, the expression in the surgically resected renal cell carcinoma (RCC) and a cultured RCC cell line was studied by RT-PCR. Although eight to nine S100 genes were transcribed in the normal kidney library and non-cancerous part of resected kidney tumors, S100A1 and S100A10 genes were not expressed. However, these genes were newly expressed in the RCC lesions (n=7) and the RCC cell line, indicating that expression of S100A1 and S100A10 genes is accompanied by RCC.

Annexin A2↗
PubMed2003

Differential increase in the expression of heat shock protein family members during sleep deprivation and during sleep.

Although sleep is thought to be restorative from prior wakeful activities, it is not clear what is being restored. To determine whether the synthesis of macromolecules is increased in the cerebral cortex during sleep, we subjected C57BL/6 mice to 6 hours of sleep deprivation and then screened the expression of 1176 genes of known function by using cDNA arrays. The expression of the heat shock proteins (HSP), endoplasmic reticulum protein (ERp72) and glucose-regulated protein (GRp78), was among the genes whose expression was significantly elevated in the cortex during sleep deprivation, whereas GRp78 and GRp94 mRNAs were elevated in the cortex during recovery sleep after sleep deprivation, as confirmed by conventional and quantitative real-time polymerase chain reaction and/or Northern analyses. A systematic evaluation of the expression of six heat shock protein family members (ERP72, GRp78, GRp94, HSP27, HSP70-1, and HSP84) in seven brain regions revealed increased mRNA levels in cortex, basal forebrain, hypothalamus, cerebellum and medulla during sleep deprivation, whereas increased mRNA levels during recovery sleep were limited to the cortex and medulla. Immunohistochemical studies identified increased numbers of GRp78-, GRp94-, and ERp72-immunoreactive cells in the dorsal and lateral cortex during sleep deprivation but, during recovery sleep, elevated numbers of these cells were found only in the lateral cortex. In the medulla, increased numbers of GRp94-immunoreactive cells were observed in nucleus tractus solitarius, dorsal motor nucleus of the vagus and the rostroventrolateral medulla during recovery sleep. The widespread increase of heat shock protein family mRNAs in brain during sleep deprivation may be a neuroprotective response to prolonged wakefulness. In contrast, the relatively limited heat shock protein family mRNA expression during recovery sleep may be related to the role of heat shock proteins in protein biogenesis and thus to the restorative function of sleep.

Animals↗
PubMed1999

The detection of viral genomes by polymerase chain reaction in the myocardium of pediatric patients with advanced HIV disease.

OBJECTIVES: The aim of this study was to investigate the frequency of viral nucleic acid detection in the myocardium of human immunodeficiency virus (HIV)-infected children to determine whether an association exists with the development of heart disease. BACKGROUND: As improved medical interventions increase the life expectancy of HIV-infected patients, increased incidences of myocarditis and dilated cardiomyopathy (DCM) are becoming more apparent, even in patients without clinical symptoms. METHODS: Myocardial samples were obtained from the postmortem hearts of 32 HIV-infected children and from 32 age-matched controls consisting of patients with structural congenital heart disease and no myocardial inflammation and no cardiac or systemic viral infection. The hearts were examined histologically and analyzed for the presence of viral sequences by polymerase chain reaction (PCR) or reverse transcription-PCR. RESULTS: Myocarditis was detected histologically in 11 of the 32 HIV-infected patients, and borderline myocarditis was diagnosed in another 13 cases. Infiltrates were confined to the epicardium in two additional hearts. Virus sequences were detected by PCR in 11 of these 26 cases (42.3%); adenovirus in 6, CMV in 3 and both adenovirus and CMV in 2. Two cases without infiltrates were also positive for adenovirus: one had congestive heart failure (CHF) and the other adenoviral pneumonia. No other viruses were detected by PCR, including HIV proviral DNA. All control samples were negative for all viruses tested. CONCLUSIONS: These data suggest that the presence of viral nucleic acid in the myocardium is common in HIV-infected children, and may relate to the development of myocarditis, DCM or CHF and may contribute to the rapid progression of HIV disease.

Base Sequence↗
PubMed2002

A high-throughput induction gene trap approach defines C4ST as a target of BMP signaling.

Here we describe a novel gene trap protocol to screen for target genes that are regulated during inductive events in undifferentiated and differentiated mouse embryonic stem cells. This approach integrates several features that allows in vitro screening of large numbers of gene trap clones prior to generating lines of mutant mice. Moreover, targets of spatially and temporally restricted signaling pathways can be analyzed by screening undifferentiated ES cells versus ES cells differentiated into embryoid bodies. We employed this protocol to screen 1920 gene trap lines to identify targets and mediators of signaling through three growth factors of the TGFbeta superfamily--BMP2, activin and nodal. We identified two genes that are induced by BMP2 in a differentiation-dependent manner. One of the genes encodes for Chondroitin-4-sulfotransferase and displays a highly specific temporal and spatial expression pattern during mouse embryogenesis. These results demonstrate the feasibility of a high-throughput gene trap approach as a means to identify mediators and targets of multiple growth factor signaling pathways that function during different stages of development.

Animals↗
PubMed2003

Steroidogenesis during in vitro maturation of bovine cumulus oocyte complexes and possible effects of tri-butyltin on granulosa cells.

Steroids are known as important factors on the route of oocytes development and cumulus oocyte complexes (COC) as well as follicular granulosa cells (GC) are suggested to be themselves involved in steroidogenesis. The aim of this study was to characterize such a local sex steroidogenic system during in vitro maturation (IVM) of bovine COCs according to the production of estradiol (E), testosterone (T) and progesterone (P). The expression of two steroid-converting key-enzymes was measured in parallel by quantitative RT-PCR. Furthermore, possible effects of the environmental pollutant tri-butyltin (TBT) were elucidated for the first time on bovine COC and GC in vitro concerning that steroidogenic system. During IVM of bovine COCs concentrations of P increased continuously, corresponding with steady-state levels of 3-beta-hydroxy-steroid-dehydrogenase (HSD) transcripts. In contrast, E together with P450 aromatase mRNA (ARO) increased in the first hours of IVM but declining thereafter, whereas T reached almost balanced levels. However, TBT showed only slight effects during IVM of COC. In cultured GC, LH caused highest P- and E-production within 24h and treatment with 50pM TBT induced a significant decrease of E in contrast to 100pM TBT and the control. These results indicate, that (1) COCs were able to modulate their steroidogenic environment in vitro and that (2) TBT may possibly influence or disturb steroidogenesis in the cows reproductive tract shown here for GC.

Animals↗
PubMed2002

A digestive beta-glucosidase from the salivary glands of the termite, Neotermes koshunensis (Shiraki): distribution, characterization and isolation of its precursor cDNA by 5'- and 3'-RACE amplifications with degenerate primers.

beta-Glucosidase activity [EC 3.2.1.21] was measured in the salivary glands and the gut of wood-eating termite, Neotermes koshunensis (Shiraki). 75% of the activity was detected in the salivary glands, whereas 15% of the activity was present in the hindgut, where numerous symbiotic flagellates reside. The salivary beta-glucosidase was partially purified by ion-exchange and gel filtration chromatography. The molecular weight of the salivary beta-glucosidase was 60 kDa, and the K(m) value on cellobiose was 2.5 mM. Its optimal pH was 5.6 and the activity was stable from 20 degrees C up to 45 degrees C. In addition to cellobiose, p-nitrophenyl-beta-D-fucopyranoside and laminaribiose were efficiently hydrolyzed by the salivary beta-glucosidase. Degenerate PCR using primers designed from N-terminal amino acid sequences of the salivary beta-glucosidase resulted in a cDNA fragment of 1730 bp, encoding 498 amino acids and with sequence similarity to glycosyl hydrolase family 1. Reverse-transcription (RT)-PCR showed that this beta-glucosidase is produced only in the salivary glands.

3' Untranslated Regions↗
PubMed2003

Genomic dissection for characterization of cancerous oral epithelium tissues using transcription profiling.

Genome-wide and high-throughput functional genomic tools offer the potential of identifying disease-associated genes and dissecting disease regulatory patterns. There is a need for a set of systematic bioinformatic tools that handles efficiently a large number of variables for extracting biological meaning from experimental outputs. We present well-characterized statistical tools to discover genes that are differentially expressed between malignant oral epithelial and normal tissues in microarray experiments and to construct a robust classifier using the identified discriminatory genes. Those tools include Wilks' lambda score, error rate estimated from leave-one out cross-validation (LOOCV) and Fisher Discriminant Analysis (FDA). High Density DNA microarrays and Real Time Quantitative PCR were employed for the generation and validation of the transcription profile of the oral cancer and normal samples. We identified 45 genes that are strongly correlated with malignancy. Of the 45 genes identified, six have been previously implicated in the disease, and two are uncharacterized clones.

Gene Expression Profiling↗
PubMed2003

Rapid detection of influenza A and B viruses in clinical specimens by Light Cycler real time RT-PCR.

BACKGROUND: the influenza viruses cause morbidity and mortality annually among children and elderly. Surveillance and rapid diagnosis is imperative in the reference laboratory, as clinical symptoms are insufficient for proper diagnosis. OBJECTIVES: this study involved the design of a rapid detection method for influenza A and B viruses using real time RT-PCR from clinical specimens. Methods were specifically designed for use on the Light Cycler. The sensitivity and specificity were also to be determined. STUDY DESIGN: the identification and discrimination of influenza A and B viruses employs two dual probe systems based on fluorescence resonance energy transfer (FRET) technology. Following submission by physicians participating in the Florida sentinel influenza network, 58 specimens were chosen for testing using both tissue culture and Light Cycler methods. RESULTS: of the 35 identified positive for influenza virus via tissue culture isolation, the Light Cycler results matched identification and typing with 100% agreement. However, the Light Cycler recognized 16 additional specimens that were positive for the presence of the virus. RT-PCR and nucleotide sequencing confirmed the presence of influenza A virus in these specimens. Using tenfold serial dilutions, the sensitivity of the Light Cycler method was determined to be 0.01 TCID50. The lower limit of RNA detection was determined as 1.6 x 10(-7) microg for influenza A virus, and 1.2 x 10(-7) microg for influenza B virus. Specificity of the Light Cycler method was determined by testing specimens containing adenovirus, parainfluenza virus and echovirus, all of which yielded negative results with no discernible background. CONCLUSIONS: overall, this newly developed method of simultaneous detection and typing of influenza types A and B using the Light Cycler proves to be more sensitive than tissue culture isolation, with corresponding specificity. This technique may be valuable for surveillance and rapid identification of influenza for early diagnosis.

Humans↗
PubMed2000

Biotechnical use of polymerase chain reaction for microbiological analysis of biological samples.

Since its introduction in the mid-80s, polymerase chain reaction (PCR) technology has been recognised as a rapid, sensitive and specific molecular diagnostic tool for the analysis of micro-organisms in clinical, environmental and food samples. Although this technique can be extremely effective with pure solutions of nucleic acids, it's sensitivity may be reduced dramatically when applied directly to biological samples. This review describes PCR technology as a microbial detection method, PCR inhibitors in biological samples and various sample preparation techniques that can be used to facilitate PCR detection, by either separating the micro-organisms from PCR inhibitors and/or by concentrating the micro-organisms to detectable concentrations. Parts of this review are updated and based on a doctoral thesis by Lantz [1] and on a review discussing methods to overcome PCR inhibition in foods [2].

Animals↗
PubMed2003

Genomic structure and expression of a gene coding for a new fatty acid binding protein from Echinococcus granulosus.

This work describes a new gene coding for a fatty acid binding protein (FABP) in the parasite Echinococcus granulosus, named EgFABP2. The complete gene structure, including the promoter sequence, is reported. The genomic coding domain organisation of the previously reported E. granulosus FABP gene (EgFABP1) has been also determined. The corresponding polypeptide chains share 76% of identical residues and an overall 96% of similarity. The two EgFABPs present the highest amino acid homologies with the mammalian FABP subfamily containing heart-FABPs (H-FABPs). The coding sequences of both genes are interrupted by a single intron located in the position of the third intron reported for vertebrate FABP genes. Both genes are expressed in the protoscolex stage of the parasite. The promoter region of EgFABP2 presents several consensus putative cis-acting elements found in other members of the family, suggesting interesting possible mechanisms involved in the host-parasite adaptation.

Amino Acid Sequence↗
PubMed2004

Early detection and identification of commonly encountered Candida species from simulated blood cultures by using a real-time PCR-based assay.

In a recent study, Candida species in clinical blood samples were detected using a real-time PCR-based method (Maaroufi et al, J Clin Microbiol 2003, 41:3293-3298). For the present study, we evaluated the efficiency of this method as an adjunct to the BACTEC blood culture system to early detection of positivity and negativity of simulated low candidemias. We first established an in vitro correlation between the inoculum of the most frequently encountered Candida species and the time to positivity of these microorganisms. Then, aliquots from blood culture bottles infected with a final average candidal inoculum of 3.18 colony-forming units (CFU)/culture bottle (range, 1 to 6 CFU) were collected at increasing incubation times, and DNA was extracted and submitted to the TaqMan-based PCR assay. To optimize this assay, we evaluated the effect of adding 0.5% bovine serum albumin (BSA) to DNA extracts and found that it decreased the effects of inhibitors. Using specific probes for the tested Candida species, the PCR assay was positive on blood culture aliquots collected from the BACTEC system after a minimum culture turnaround time (TAT) of 3.11 +/- 1.24 hours. Addition of BSA to PCR reaction mixtures improves the TAT (1.84 +/- 0.41 hours). Hence, the combination of DNA "amplification" in the culture bottles by normal growth with an additional DNA amplification by PCR might be a reliable tool facilitating the early diagnosis of low candidemias.

Animals↗
PubMed2004

Measurement of relative copy number of CDKN2A/ARF and CDKN2B in bladder cancer by real-time quantitative PCR and multiplex ligation-dependent probe amplification.

Many tumors have large homozygous deletions of the CDKN2A locus (encoding p14(ARF) and p16) and of CDKN2B (p15). Our aim was to determine which gene is the major target in bladder cancer. We used quantitative real-time PCR (RTQ-PCR) to determine copy number of p15, of p14(ARF) exon 1beta, and p16 exon 2 in 22 tumor cell lines and 83 bladder tumors, some of which had been assessed previously by duplex PCR. Titration experiments showed that homozygous deletion could be detected in the presence of up to 30% normal DNA. Results for cell lines were compatible with previous cytogenetic analyses. Ten cell lines and 32 tumors (38.5%) had homozygous deletion of at least one target. Thirteen tumors (15.7%) had deletion of all three targets. Two tumors had deletion of p14(ARF) exon 1beta alone and four of p16 exon 2 alone. RTQ-PCR detected more homozygous deletions than duplex PCR. Finally we used a multiplex ligation-dependent probe amplification kit to provide independent confirmation of results. We conclude that with appropriate controls RTQ-PCR is a sensitive and robust method to detect copy number changes in tumors even in the presence of contaminating normal cell DNA.

Cell Cycle Proteins↗
PubMed2004

Expression analysis of the Candida albicans lipase gene family during experimental infections and in patient samples.

Secreted lipases of Candida albicans are encoded by a gene family with at least 10 members (LIP1-LIP10). The expression pattern of this multigene family was investigated using reverse transcription polymerase chain reaction in experimental infections and in samples of patients suffering from oral candidosis. The findings illustrate that individual lipase genes are differentially regulated in a mouse model of systemic candidosis with some members showing sustained expression and others being transiently expressed or even silent. The lipase gene expression profile depended on the stage of infection rather than on the organ localization. This temporal regulation of lipase gene expression was also detected in an experimental model of oral candidosis. Furthermore, the expression of candidal lipase genes in human specimens is shown for the first time.

Animals↗