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At least 1,531 records · Page 85Linked to original sources
PubMed2006

ADAM28 is overexpressed in human non-small cell lung carcinomas and correlates with cell proliferation and lymph node metastasis.

ADAM (a disintegrin and metalloproteinases) are a recently discovered gene family of proteins with sequence similarity to the reprolysin family of snake venom metalloproteinases, and about one-third of the family members have the catalytic site consensus sequence in their metalloproteinase domains. We screened the mRNA expression of 11 different ADAM species with putative metalloproteinase activity in human non-small cell lung carcinomas by RT-PCR, and found that prototype membrane-anchored ADAM28 (ADAM28m) and secreted ADAM28 (ADAM28s) are predominantly expressed in the carcinoma tissues. Real-time quantitative PCR demonstrated that the expression levels of ADAM28m and ADAM28s are significantly 16.8-fold and 9.0-fold higher in the carcinomas than in the non-carcinoma tissues, respectively. In addition, the expression levels of ADAM28m and ADAM28s were significantly higher in the carcinomas with >30 mm in diameter than in those < or =30 mm. The expression levels were also significantly higher in the carcinomas with lymph node metastasis than in those without metastasis. MIB1-positive cell index of the carcinomas had a direct correlation with the expression levels of ADAM28m and ADAM28s (r = 0.667, p < 0.001 and r = 0.535, p < 0.01, respectively). In situ hybridization and immunohistochemistry demonstrated that ADAM28 is expressed predominantly in the carcinoma cells. Immunoblot analysis showed the activated form of ADAM28 in the carcinoma tissues. These data demonstrate for the first time that ADAM28 is overexpressed and activated in human non-small cell lung carcinomas, and suggest the possibility that ADAM28 plays a role in cell proliferation and progression of the human lung carcinomas.

ADAM Proteins↗
PubMed2003

Comparative evaluation of measles virus-specific RT-PCR methods through an international collaborative study.

Comparison of RT-PCR assays established in house at various places revealed that laboratories could differ in sensitivity by as much as 1,000-fold in terms of the ability to detect measles virus sequences in clinical samples. The study indicates that PCR findings, positive or negative, are questionable if they are not supported by the associated data demonstrating the overall sensitivity of the assay applied. Measles virus-specific RT-PCR-based assays need to be validated using standard virus preparation or nucleic acid-based target templates. A correlation between real-time quantitative PCR and the conventional PCR for measles virus is highly desirable.

DNA Primers↗
PubMed2001

Quantification of minimal residual disease in T-lineage acute lymphoblastic leukemia with the TAL-1 deletion using a standardized real-time PCR assay.

Hematologic relapse remains the greatest obstacle to the cure of children with acute lymphoblastic leukemia (ALL). Recent studies have shown that patients with increased risk of relapse can be identified by measuring residual leukemic cells, called minimal residual disease (MRD), during clinical remission. Current PCR methods, however, for measuring MRD are cumbersome and time-consuming. To improve and simplify MRD assessment, we developed a real-time quantitative PCR (RQ-PCR) assay for detection of leukemic cells that harbor the TAL-1 deletion. We studied serial dilutions of leukemic DNA and found the assay had a sensitivity of detection of one leukemic cell among 100,000 normal cells. We then investigated 23 samples from eight children with ALL in clinical remission. We quantified residual leukemic cells by using the TAL-1 RQ-PCR assay and by using limiting dilution analysis. In 17 samples, both methods detected MRD levels > or =0.001%. The percentages of leukemic cells measured by the two methods correlated well (r2 = 0.926). In the remaining six samples, both methods detected fewer than 0.001% leukemic cells. We conclude the TAL-1 RQ-PCR assay can be used for rapid, sensitive and accurate assessment of MRD in T-lineage ALL with the TAL-1 deletion.

Basic Helix-Loop-Helix Proteins↗
PubMed2005

Bacillus clausii effect on gene expression pattern in small bowel mucosa using DNA microarray analysis.

BACKGROUND: Probiotics are widely used for the cure or prevention of several clinical conditions. However, clinical decisions need to be substantiated by an analysis of the complex bacteria-host interplay in the intestinal lumen. AIMS: To identify the gene expression pattern induced by Bacillus clausii in the intestinal mucosa of healthy individuals. METHODS: Six male patients (mean age 38+/-5 years) affected by endoscopically confirmed mild oesophagitis were treated for one month with esomeprazole, and were randomly selected to receive or not B. clausii (groups I and II, respectively). Duodenal biopsies were taken pre and post-treatment to identify the modification of gene expression, using the GeneChip Human U133A array. To validate the microarray analysis, real-time reverse transcriptase-polymerase chain reaction (PCR) of five target genes was performed. RESULTS: After B. clausii administration, a total of 158 and 265 genes were up and downregulated, respectively. Quantitative PCR confirmed the microarray data. B. clausii mainly affected the expression of genes involved in immune response and inflammation, apoptosis and cell growth, cell differentiation, cell-cell signalling, cell adhesion, signal transcription and transduction. CONCLUSIONS: Our data represent the first global analysis of B. clausii effects on the gene expression profile in normal intestine, and provide the basis to identify the mechanisms by which these agents interact with the host and exert their beneficial effects. Future studies are needed to clarify the B. clausii-induced gene pattern in the clinical disorders in which probiotics have proved to be effective.

Adult↗
PubMed1999

New advances in the diagnosis of congenital cytomegalovirus infection.

With the advances in anticytomegalovirus (anti-CMV) serology, the new recombinant IgM tests seem likely to become the screening tests for pregnant women whose prepregnancy serological status for CMV is unknown. When a woman is found to be IgM-positive, further diagnostic evaluation focused on determining whether this is due to a primary infection should be carried out. Maternal primary infections that were difficult to determine until a few years ago unless documented by seroconversion can now be readily diagnosed from the presence of low-avidity anti-CMV antibody which persists for approximately 20 weeks after primary infection. In primarily infected mothers prenatal diagnosis can be performed between 21 and 23 weeks of gestation, and the amniotic fluid (AF) represents the pathological material of choice to determine intrauterine virus transmission. In AF, the virus can be detected by culture and/or PCR. Both procedures differentiate uninfected from infected fetuses, but cannot predict fetal outcome. The determination of the viral load in AF carried out by quantitative PCR is more promising and could represent an important starting point for preemptive fetal therapy.

Amniotic Fluid↗
PubMed2001

All trans-retinoic acid selectively down-regulates matrix metalloproteinase-9 (MMP-9) and up-regulates tissue inhibitor of metalloproteinase-1 (TIMP-1) in human bronchoalveolar lavage cells.

BACKGROUND: The balance between proteinases and antiproteinases plays an important role in tissue destruction and remodelling. In chronic obstructive pulmonary disease (COPD) and emphysema, an imbalance between matrix metalloproteinases (MMPs) and inhibitors of tissue metalloproteinase (TIMPs) has been reported. Alveolar macrophages are considered to be the main source of MMPs. We therefore have analyzed the effects of free and liposomal all trans-retinoic acid (ATRA) on the expression of MMP-9 and TIMP-1 in bronchoalveolar lavage (BAL) cells from patients with COPD and patients with other lung diseases. MATERIAL AND METHODS: BAL cells were incubated 1-3 day with either liposomal or free ATRA. Supernatants were tested for MMP-9 and TIMP-1 protein in specific ELISA systems; mRNA analysis was performed by semi-quantitative RT-PCR and by quantitative LightCycler PCR. RESULTS: We demonstrate that either liposomal or free ATRA selectively down-regulates MMP-9 and up-regulates TIMP-1. At the protein level, MMP-9 is decreased 3-fold and TIMP-1 is increased 3.5-fold compared to the base line with empty liposomes or untreated cells. The ratio of MMP-9 and its inhibitor TIMP-1, which may be crucial to the overall proteolytic potential decreased by factor 8. That this countercurrent effect of ATRA is not due to an altered protein stability but to transcriptional regulation could be demonstrated by RT-PCR. Quantitative LightCycler analysis revealed a 2.5-fold decrease of MMP-9 mRNA and a 4.5 fold increase of TIMP- 1 mRNA. CONCLUSIONS: These data suggest that ATRA treatment via its impact on the proteinase/antiproteinase ratio may become a new therapeutic strategy for patients with inflammatory destructive lung diseases.

Antineoplastic Agents↗
PubMed2002

[Expression of human G6PD gene in K562 cells mediated by retroviral vector].

OBJECTIVE: This study aimed to investigate the feasibility of gene therapy for severe G6PD deficiency. METHODS: The recombinant retroviral vector bearing normal human G6PD cDNA was constructed and transferred into the erythroleukemia cell line K562. Author identified the integration of NeoR gene in the targeted cellular DNA by means of specific PCR. Quantitative method was used to measure the expression of G6PD in the targeted cells. RESULTS: Construction of the recombinant retroviral vector was successfully established. PCR indicated the integration of NeoR gene in the targeted genomic DNA of the cells. The vector was also shown to be capable of expressing the foreign gene compared to the control (P<0.01). CONCLUSIONS: The recombinant retroviral vector is competent for transferring and expressing the G6PD gene.

Gene Expression↗
PubMed2003

Development of an Alu-based, real-time PCR method for quantitation of human DNA in forensic samples.

Determining the amount of human DNA extracted from a crime scene sample is an important step in DNA profiling. The forensic community relies almost entirely upon a technique (slot blot) to quantitate human DNA that is imprecise, time consuming, and labor intensive. We have previously described a method for quantitation of human DNA based on PCR amplification of a repetitive Alu sequence that uses a fluorescence plate reader. This manuscript describes and validates a variation of this assay using real-time PCR and SYBR Green I for quantitation. The advantages of the real-time assay over the plate reader assay are: reduced hands-on time, lower assay cost, and a greater dynamic range. The main disadvantage is the cost of the real-time instrument. However, for those forensic laboratories with access to a real-time instrument, this Alu-based assay has a dynamic range of 16 ng to 1 pg, is sensitive, specific, fast, quantitative, and uses only 2 microL of sample.

Alu Elements↗
PubMed1995

Band 3, the anion transporter, is conserved during evolution: implications for aging and vertebrate evolution.

A cDNA fragment corresponding to a highly evolutionarily conserved region of the major anion transport protein band 3 was cloned from lamprey mRNA using PCR homology probing. This is the first report providing evidence for a band-3 like transporter in the lowest vertebrates, the agnathostomes. Semi-quantitative PCR showed expression similar to that of higher vertebrates. Lamprey serum contains antibody-like molecules that bind to synthetic peptides of band 3 comprising senescent cell antigen, an aging antigen that terminates the life of cells. The high degree of homology found in nucleic acid and derived proteins sequence and the reaction of "antibodies" in lamprey serum with senescent cell antigen peptides of band 3 suggests that lamprey band 3 plays a role comparable to that in higher vertebrates.

Aging↗
PubMed2004

Real-time PCR monitoring of fungal development in Arabidopsis thaliana infected by Alternaria brassicicola and Botrytis cinerea.

Reliable methods for disease severity assessment are of crucial importance in the study of plant pathogen interactions, either for disease diagnostic on the field or to assess phenotypical differences in plants or pathogen strains. Currently, most of the assays used in fungal disease diagnostic rely on visual assessment of the symptoms, lesion diameter measurement or spore counting. However, these tests are tedious and often cannot discriminate between slightly different levels of resistance. Besides, they are not well suited to assess fungal development in the early phases of the infection, before macroscopical symptoms are visible or before sporulation. We describe here a pathogenicity assay based on the relative quantification of fungal and plant DNA in infected Arabidopsis thaliana leaves by means of real-time quantitative PCR. We show that it allows to monitor quantitatively the growth of the fungi Alternaria brassicicola and Botrytis cinerea in a sensitive and reliable way. Although highly sensitive, this test also exhibits a high robustness, which is crucial to significantly discriminate between lines displaying slightly different levels of resistance. Therefore, it allows to assess fungal development from the very first stages of infection and provides a fast and very practical alternative to currently described assays for phenotyping either plant mutant lines or fungal strains.

Alternaria↗
PubMed2000

Relative quantitative RT-PCR protocol for TrkB expression in neuroblastoma using GAPD as an internal control.

An RT-PCR protocol for the relative quantitative measurement of TrkB transcripts using glyceraldehyde-3-phosphate-dehydrogenase (GAPD) transcripts as an internal control is described. Both TrkB and GAPD sequences were co-amplified in the exponential phase of amplification using 5'-biotinylated primers. The PCR products were subjected to PAGE, electro-transferred to nylon membrane and detected by a chemiluminescent procedure using alkaline phosphatase conjugated with avidin. Signals detected on X-ray film were analyzed by densitometry. The ratio between TrkB and GAPD expression levels was determined to normalize the expression levels of TrkB transcripts. Initially, strong signals of GAPD transcripts led to overexposure of X-ray film compared to those of TrkB, which causes difficulties in the accurate determination of the TrkB/GAPD ratio. To circumvent this problem, uniformly biotinylated GAPD primers were replaced with a mixture of biotinylated and non-biotinylated GAPD primers of the same sequence and concentration. GAPD signals detected on X-ray film were proportionally decreased as the amount of biotin-labeled primers was reduced in the total GAPD primers. This modification enabled both GAPD and TrkB signals to be analyzed within the linear range of X-ray film detection without affecting the amplification efficiency of TrkB sequence. Use of composite primers may have a wide range of applicability in quantitative analysis of nucleic acids.

Biotinylation↗
PubMed2002

Rapid detection and quantification of CMV DNA in urine using LightCycler-based real-time PCR.

A real-time quantitative PCR-hybridisation assay was developed for the detection of human cytomegalovirus DNA in clinical material. The assay is based on a LightCycler (LC) and provides both rapid results (<1 h) and quantification over a broad dynamic range (2 x 10(3)-5 x 10(8) CMV DNA copies/ml). Given that the assay showed a 3-fold increase in sensitivity compared to detection of early antigen fluorescent foci (DEAFF) testing of urine samples, we investigated the practicality of testing surveillance such specimens from immunocompromised patients at risk of CMV disease. Over a 12-month period, CMV DNA was detected in 81 (7%) of 1154 urine samples examined. A total of 28 patients tested positive; urine viral loads were higher in 13 infants being investigated for suspected congenital infection (median 1.6 x 10(5) copies/ml) compared with 15 transplant recipients (median 9 x 10(3) copies/ml). Urine samples could be tested directly without processing such that results were available in <1h. Real-time PCR provided information on the quantification of CMV DNA in urine and proved a reliable method for the surveillance of immunocompromised patients at risk of CMV disease. This approach should facilitate a better understanding of the epidemiology and natural history of CMV disease. Moreover, LC-based quantitative PCR is a potentially valuable tool for the management of CMV disease; assisting with the prompt initiation of treatment and assessing therapeutic response.

Cytomegalovirus↗
PubMed2004

Quantification of C13orf19/P38IP mRNA expression by quantitative real-time PCR in patients with urological malignancies.

Quantitative real-time PCR was performed for C13orf19, a gene located on chromosome 13q and previously described to be down-regulated in prostate carcinoma, on different cancer cell lines, on matched prostate tissues from 61 patients with prostate carcinoma and on matched kidney tissues from 23 patients with renal clear cell carcinoma. All data were normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH), porphobilinogen deaminase (PBGD) and hypoxanthine guanine phosphoribosyl transferase (HPRT) mRNA expression. A C13orf19 quantitative PCR (QPCR) showed the mRNA to be down-regulated in matched prostate tissues (P=0.007 and lower, paired Student's t-test). However, an at least 1.5-fold C13orf19 mRNA downregulation was observed in samples from 28 patients (46%) and an at least 1.5-fold upregulation was observed in samples from 17 patients (28%). In contrast, C13orf19 mRNA alterations in expression seemed to be random events in kidney cancers.

Adenocarcinoma, Clear Cell↗
PubMed1998

Human herpesvirus type 7 in Hodgkin's disease.

Several lines of evidence have pointed to the involvement of a viral agent in the pathogenesis of Hodgkin's disease (HD). Therefore we investigated the presence of human herpesvirus type 7 (HHV-7) in 53 cases of HD by polymerase chain reaction (PCR), DNA in situ hybridization (ISH) and immunohistochemistry. HHV-7 DNA was frequently detected (68% of the cases) in HD biopsies by PCR independently of the histological type, whereas only 32% (P<0.05) of positive cases were found in 19 reactive lymph nodes. However, by applying the quantitative PCR technique, the majority of the samples showed a low level of viral load. Moreover, ISH for HHV-7 DNA was positive in a low number of small T lymphocytes and consistently negative in Hodgkin and Reed-Sternberg (HRS) cells, which appeared negative for HHV-7 also at immunohistochemistry. These results indicate that the high frequency of HHV-7 infection in HD: (i) is probably non-productive, (ii) mainly involves small lymphocytes belonging to the T-lineage, and (iii) is probably due to the recruitment of non-malignant reactive cells in HD tissue.

DNA, Viral↗
PubMed2002

Characterization of KLK4 expression and detection of KLK4-specific antibody in prostate cancer patient sera.

The ability to identify prostate tumor or prostate tissue specific genes that are expressed at high levels and use their protein products as targets could greatly aid in the diagnosis and treatment of prostate cancer. Using a polymerase chain reaction (PCR)-based subtraction technique, we have recovered the recently described KLK4 (prostase) gene from human prostate cDNA. In this study, KLK4 gene expression in human prostate tumors was further characterized using cDNA quantitative PCR and immunohistochemistry, demonstrating that the gene is specifically expressed at both the mRNA and protein levels in normal human prostate tissue, and in both primary and metastatic prostate tumor samples. Quantitative mRNA analysis also demonstrated low level expression including adrenal gland, salivary gland and thyroid. Finally, it was demonstrated that prostate cancer patient sera contain antibodies that bind specifically to recombinant KLK4 protein. This antibody has been used to detect KLK4-specific peptides in epitope mapping experiments. The relatively specific expression profile and elevated level of KLK4 mRNA and protein in both tumor and normal prostate tissues, in addition to detectable KLK4-specific antibody in cancer patient sera, supports additional efforts to determine if KLK4 can play a role in the diagnosis of prostate cancer, the monitoring of residual disease, or act as a target for immunotherapy.

Antibodies↗
PubMed2003

Quantification of common carp (Cyprinus carpio) IGF-I and IGF-II mRNA by real-time PCR: differential regulation of expression by GH.

IGFs are potent mitogens for many different cell types and play important roles in growth and development. A multitude of regulatory factors modulate the expression of IGFs. In some teleosts, liver IGF-I expression has been demonstrated to depend on the presence of GH. However, the GH dependence of IGF-II expression in teleosts is controversial. Moreover, most IGF expression studies in bony fish have been focused on the liver, and information on extrahepatic tIssues are conflicting and inconsistent. This is partly due to the fact that the traditional methods of mRNA measurement such as Northern blot and RT-PCR are not sensitive enough to detect changes in IGF levels in extrahepatic tIssues because of the low levels of IGFs in these tIssues. In addition, there have been few studies on the IGF system of non-salmonid teleosts. Our laboratory has thus begun such studies on a local tropical fast-growing fish, the common carp (Cyprinus carpio). In this study, real-time quantitative PCR assays were developed for the accurate measurement of IGF-I and IGF-II mRNA levels in common carp tIssues. This quantitative method was based on the measurement of a fluorescent labeled probe, which was cleaved by Taq polymerase during PCR by the 5'-->3' nuclease activity. The signal generated was directly proportional to the starting copy number of the target molecules in the sample. Hence, it was possible to detect and quantify the mRNA levels of both IGF-I and IGF-II reliably in very small amounts of tIssues obtained from juvenile common carp. Using these assays, the expression pattern of IGF-I and IGF-II in various common carp tIssues was studied, and their differential response to GH stimulation was also investigated.

Animals↗
PubMed2005

Crop-to-crop gene flow using farm scale sites of oilseed rape (Brassica napus) in the UK.

From 2000-2003 a range of Farm Scale Evaluation (FSE) trials were established in the UK to assess the effect of the release and management of herbicide tolerant (HT) crops on the abundance and diversity of farmland wildlife compared with their conventionally managed non-GM-equivalents. The objective of this research project was to investigate gene flow within the winter (WOSR) and spring oilseed rape (SOSR) FSE trials and to develop a statistical model for the prediction of cross-pollination frequency that can be used to evaluate current separation distance guidelines. Seed samples were collected from the non-GM half of the trial sites and were tested for evidence of cross-pollination from the GM HT halves using a quantitative PCR assay specific to the HT (bar) gene. Rates of cross-pollination were found to decrease rapidly with increasing distance from the GM source. The quantitative data were subjected to statistical analysis and a two-step model was found to provide the best fit for the data. Significant differences were found between the results for WOSR, SOSR and varietal association (VA) crops. The model predicted that the %GM content (including upper 95% confidence limits) of a sample taken at a distance of 50 m away from the GM source would be 0.04% (0.84%) for WOSR, 0.02% (0.39%) for SOSR, 0.77% (21.72%) for WOSR VA and 0.37% (5.18%) for SOSR VA. The data and models presented here are discussed in the context of necessary separation distances to meet various possible thresholds for adventitious presence of GM in OSR.

Agriculture↗
PubMed2005

The elevated level of CXCR4 is correlated with nodal metastasis of human breast cancer.

CXCR4, the receptor for stromal cell-derived factor-1(SDF-1), belongs to the chemokine receptor family and has been shown to play an important role in regulating the directional migration of breast cancer cells to sites of metastasis. In the present study, we evaluated the expression of CXCR4 and its association with pathological features and clinical outcome in human breast cancer. Expression of CXCR4 in eight breast cancer cell lines and breast cancer tissues was investigated using conventional PCR. Levels of CXCR4 transcript and protein were examined in human breast cancer tissues (n=120) and corresponding normal tissues (n=32) using real-time quantitative PCR and immunohistochemistry, respectively. The level of CXCR4 expression was analyzed against tumour types, grade, nodal status, recurrence, metastasis, and survival over a median 120 month follow-up period. The expression of CXCR4 was detected in all breast cancer cell lines examined, as well as in breast cancer tissues and breast normal tissues. Breast cancer tissues highly expressed CXCR4 compared with corresponding normal tissues (P=0.029). The level of CXCR4 expression showed a significant difference between node-positive group and node-negative group (19+/-13 vs. 49.7+/-9, respectively, P=0.03). The level of CXCR4 expression was marginal, yet statistically insignificant, higher in tumours from patients with metastatic disease compared with those who remained disease free. No correlation was seen between levels of CXCR4 and the overall survival, although at higher levels of CXCR4 linked to shorter disease free survival (113.0 vs. 136.7 months in patients with low CXCR4, P=0.14, Cox proportional test). The level of CXCR4 expression is significantly correlated with lymph node metastasis. The elevated levels of CXCR4 suggest that the patient has high possibility of lymph node metastasis. CXCR4 may be a useful prognostic indicator and a potential therapeutic target in cancer therapies in patients with breast cancer.

Axilla↗