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PubMed1997

Viral replication in patients with concomitant hepatitis B and C virus infections.

The aim of this study was to assess the implications of dual infection with hepatitis B virus (HBV) and hepatitis C virus (HCV). The HBV and HCV status in 100 patients with chronic hepatitis was analysed. HBV DNA was studied using liquid hybridization and the polymerase chain reaction (PCR). HCV viremia was measured using qualitative and quantitative PCR. The HCV genotype was determined by PCR. Patients were divided into three groups according to their HCV-RNA and HBsAg status: group I consisted of 40 patients with chronic hepatitis caused by HBV; group II, 40 patients with chronic hepatitis caused by HCV; and group III, 20 patients infected with both viruses. The HBV-DNA level was higher in group I than in group III (66.4 vs. 11.5 pg/ml; p < 0.05). Quantification of HCV viremia revealed mean values of 36.9 copies x 10(5)/ml in group II and 5.5 copies/ml x 10(5) in group III (p < 0.05). The mean aminotransferase level and histological activity were higher in group III. HCV genotype lb was the predominant type. The data suggest that there is reciprocal inhibition of viral replication in patients with dual HBV and HCV infection. Liver disease appears to be more severe in patients with chronic hepatitis B and C.

Adolescent↗
PubMed1996

A polymerase chain reaction to detect a spliced late transcript of human cytomegalovirus in the blood of bone marrow transplant recipients.

A reverse transcription (RT) nested polymerase chain reaction (PCR) procedure is described for detecting RNA to a spliced late gene (SLG) of human cytomegalovirus (CMV), the product of which (175 bp) is easily differentiated in agarose gels from the product when the target is unspliced viral RNA or DNA (258 bp). The SLG-RT-PCR has been compared against a semi-quantitative PCR for CMV DNA in buffy-coat specimens collected weekly after bone marrow transplantation from 3 patients and against the results of culturing these specimens for CMV both by conventional virus isolation, based on the detection of cytopathic effect, and by the early detection of infected cells by staining with virus-specific monoclonal antibodies. The detection of CMV RNA by SLG-RT-PCR correlated well with the detection of infective virus but only when the results of both culture methods were combined, in that neither culture method alone was as sensitive as the SLG-RT-PCR. The presence of SLG RNA in the circulation is of value as a marker of active CMV infection.

Base Sequence↗
PubMed2005

Serum amyloid A production by chicken fibroblast-like synoviocytes.

In brown chicken with chronic inflammatory processes of the joints amyloid arthropathy easily develops. The amyloid has been shown to be of the AA type which is derived from serum amyloid A (SAA). The aim of the present study was to investigate whether fibroblast-like synoviocytes (FLS) originating from brown chicken and other chicken breeds express SAA mRNA and produce SAA protein. FLS were isolated from the knee joint synovium of healthy brown chickens, white chickens, and broilers. The absence of macrophages in FLS cultures was confirmed by assessment of the phagocytic capability and by immunohistochemistry. Additionally, cultured cells were identified by electron microscopy and immunohistochemical staining. Expression of SAA mRNA in normal and lipopolysaccharide (LPS)-stimulated cells was assessed by in situ hybridization, Northern blot analysis, reverse transcriptase-polymerase chain reaction (RT-PCR), Southern blot analysis and real-time quantitative PCR. SAA protein production was analyzed by Western blotting and ELISA. SAA mRNA was detected in unstimulated FLS isolated from the three different chicken breeds and more abundantly in those stimulated with LPS. However, SAA protein production was only detected in culture medium and cell lysate of LPS-stimulated FLS. Furthermore, FLS produced SAA in a concentration-dependent manner after stimulation with different amounts of LPS. The data suggest that during infection and inflammation chicken FLS may act as a source of articular SAA. This process may enhance development of amyloid from SAA in the joint.

Amyloidosis↗
PubMed2003

Amplification efficiency of thermostable DNA polymerases.

The amplification efficiencies of several polymerase chain reaction (PCR) enzymes were compared using real-time quantitative PCR with SYBR Green I detection. Amplification data collected during the exponential phase of PCR are highly reproducible, and PCR enzyme performance comparisons based upon efficiency measurements are considerably more accurate than those based on endpoint analysis. DNA polymerase efficiencies were determined under identical conditions using five different amplicon templates that varied in length or percentage GC content. Pfu- and Taq-based formulations showed similar efficiencies when amplifying shorter targets (<900 bp) with 45 to 56% GC content. However, when amplicon length or GC content was increased, Pfu formulations with dUTPase exhibited significantly higher efficiencies than Taq, Pfu, and other archaeal DNA polymerases. We discuss the implications of these results.

Base Sequence↗
PubMed2000

Relationship between IgM antibody to human cytomegalovirus, virus load, donor and recipient serostatus, and administration of methylprednisolone as risk factors for cytomegalovirus disease after liver transplantation.

A retrospective study was performed on a selected cohort of 40 liver transplant recipients derived from the previous prospective follow-up of 162 liver transplant patients. The criterion for selection of this cohort was the presence of human cytomegalovirus (HCMV) DNAemia after transplantation, as determined by qualitative polymerase chain reaction (PCR). These 40 patients were followed longitudinally by quantitative PCR and by the new recombinant antigen-based AxSYM immunoassay for IgM to HCMV. The detection of IgM to CMV after transplantation was significantly associated with the development of HCMV disease in patients who had evidence of active HCMV replication in the blood by PCR (P=.01). On the basis of multivariate logistic regression analyses, the maximum titer of IgM detected after transplantation was a risk factor that was independent of augmented methylprednisolone and donor seropositivity. However, in multivariate analyses, elevated virus load continued to be the predominant risk factor for progression to HCMV disease.

Anti-Inflammatory Agents↗
PubMed2002

Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces.

For the detection and identification of predominant bacteria in human feces, 16S rRNA-gene-targeted group-specific primers for the Bacteroides fragilis group, Bifidobacterium, the Clostridium coccoides group, and Prevotella were designed and evaluated. The specificity of these primers was confirmed by using DNA extracted from 90 species that are commonly found in the human intestinal microflora. The group-specific primers were then used for identification of 300 isolates from feces of six healthy volunteers. The isolates were clearly identified as 117 isolates of the B. fragilis group, 22 isolates of Bifidobacterium, 65 isolates of the C. coccoides group, and 17 isolates of Prevotella, indicating that 74% of the isolates were identified with the four pairs of primers. The remaining 79 isolates were identified by 16S ribosomal DNA sequence analysis and consisted of 40 isolates of Collinsella, 24 isolates of the Clostridium leptum subgroup, and 15 isolates of disparate clusters. In addition, qualitative detection of these bacterial groups was accomplished without cultivation by using DNA extracted from the fecal samples. The goal for this specific PCR technique is to develop a procedure for quantitative detection of these bacterial groups, and a real-time quantitative PCR for detection of Bifidobacterium is now being investigated (T. Requena, J. Burton, T. Matsuki, K. Munro, M. A. Simon, R. Tanaka, K. Watanabe, and G. W. Tannock, Appl. Environ. Microbiol. 68:2420-2427, 2002). Therefore, the approaches used to detect and identify predominant bacteria with the group-specific primers described here should contribute to future studies of the composition and dynamics of the intestinal microflora.

Bacteria↗
PubMed1994

Didanosine resistance in HIV-infected patients switched from zidovudine to didanosine monotherapy.

OBJECTIVE: To determine the frequency and pattern of development of specific drug resistance mutations for human immunodeficiency virus (HIV) reverse transcriptase in patients switched from zidovudine to didanosine therapy and to examine the relation of the didanosine resistance mutation at codon 74 of the HIV reverse-transcriptase gene to CD4+ T-cell changes and virus burden. DESIGN: Retrospective analysis of all patients enrolled at Stanford University in protocols where patients were switched from zidovudine to didanosine monotherapy. SETTING: A university hospital. PATIENTS: 64 patients infected with HIV who were switched from zidovudine to didanosine monotherapy. Patients had the acquired immunodeficiency syndrome (AIDS), AIDS-related complex, or were asymptomatic (mean [+/- SD] starting CD4+ T-cell count of 129 +/- 88 cells/mm3). MEASUREMENTS: Serial serum specimens were tested for the didanosine resistance mutation at codon 74 of the HIV reverse-transcriptase gene and for a zidovudine resistance mutation at codon 215 using selective polymerase chain reactions (PCR). Serum HIV RNA levels were determined by quantitative PCR. CD4+ T-cell counts were determined at serial time points. RESULTS: By 24 weeks of didanosine therapy, the proportion of patients with the didanosine resistance mutation at codon 74 increased from 0% to 56% (36 of 64). In contrast, the proportion of patients with the zidovudine resistance mutation at codon 215 decreased from 84% at the start to 59% after 24 weeks of didanosine therapy (a 25% decrease, 95% lower CI, 15%; P < 0.0001). Patients who developed the codon 74 mutation had a greater decrease in CD4+ T cells after the development of the mutation than did patients without the mutation (P < 0.001). In addition, after 24 weeks of didanosine, patients who developed the codon 74 mutation had a greater serum HIV RNA burden than patients who remained wild type (did not have the mutation) at codon 74 (225,000 compared with 82,400 HIV RNA copies/mL serum; P = 0.01). CONCLUSIONS: Among patients infected with HIV who had advanced disease and were switched from zidovudine to didanosine therapy, more than one half developed the didanosine resistance mutation at codon 74 by 24 weeks of didanosine therapy. Patients who developed the codon 74 mutation had a greater decline in CD4+ T cells after the development of the mutation and had a greater serum virus burden than did patients without the codon 74 mutation.

CD4-Positive T-Lymphocytes↗
PubMed2004

[Relationship between podocyte molecule's distribution and expression, foot process morphology and proteinuria].

OBJECTIVE: To investigate the association between nephrin, podocin and alpha-actinin of the glomerular podocyte molecules, the morphometric change of podocyte foot process and the development of proteinuria. METHODS: Puromycin aminonucleoside (PAN) nephrosis was established. Immunofluorescence staining, image analysis and real time quantitative PCR were employed to study the distribution and quantitation of glomerular expression of nephrin, podocin and alpha-actinin. Morphometric methods were applied to evaluate the morphology change of podocyte foot processes under electron microscopy. RESULTS: (1) Before the onset of proteinuria, 2 days after PAN injection, the podocyte foot process became swollen nephrin and podocin staining were changed into discontinuous pattern accompanied by the decrease of podocin staining intensity. The foot process became more swollen on day 5,and podocin intensity continued to decrease. Meanwhile, nephrin decreased significantly both in protein intensity and at mRNA level. (2) When heavy proteinuria [(130.8+/-30.7) mg/d, P=0.02] occurred, complete effacement of podocyte foot processes was revealed; both podocin and nephrin staining intensity decreased dramatically(P<0.01), and no linear staining could be observed; nephrin and podocin mRNA gained back. (3) During the recovery of proteinuria, the foot process morphology recovered stepwise; both the intensity of nephrin and podocin increased. When proteinuria disappeared, the podocyte foot process reappeared; podocin immunofluorescence intensity recovered whereas nephrin did not; the intensity of alpha-actinin increased significantly and the distribution changed too. (4) Podocyte foot process volume density correlated negatively with nephrin(r(nephrin)=-0.78, P=0.000 1) and podocin immunofluorescence intensity(r(podocin)=-0.76, P=0.000 1), respectively. CONCLUSION: Before the onset of proteinuria, the first response of podocyte is the swollen foot process, the distribution change of nephrin and podocin and the decreased podocin intensity. There was close relationship between nephrin, podocin protein level and distribution pattern with the development of proteinuria and podocyte foot process effacement, whereas no major role was found for mRNA of nephrin and podocin. Our results suggest that proteinuria might occur after series of events of nephrin and podocin distribution change, their protein and mRNA expression level decrease, and morphology change of podocyte foot process.

Actinin↗
PubMed2003

Experiences and perspectives for the use of a Paenibacillus strain as a plant protectant.

A study on the microbial ecology in an active slow sand filter, used for disinfecting the circulating plant nutrient solutions, showed that spore-forming plant-associated bacteria belonging to the Bacillus-Paenibacillus complex are well adapted for transmission in the solutions and passage through the filter. Therefore, strains from this bacterial group were suitable candidates for biological control in irrigated and closed plant growth systems. The spore-forming Paenibacillus polymyxa strain PpDGB was selected in in vitro tests as a potent pathogen-antagonist and was tested as a prophylactic protection agent in the plant rhizosphere, especially for cultures stages that are highly susceptible to stress and disease. Plant cuttings, in vitro plants and seeds of different plant types were bacterized and planted in their typical disease-conducive environment where nutrient solutions or water irrigation was applied and further plant development was monitored. Observed plant parameters were plant survival, weight, chlorophyll concentration in the leaf mesophyl, root health and root hair formation. The PpDGB treatment initially induced stress in the plants, which was observed as a transient stop in plant transpiration. This effect caused some necrosis in the most stress-sensitive in vitro plant species. In the other plants this stress period was followed by a significant enhancement in plant growth. In case of seed treatment, more seeds germinated and seedling growth was faster. In the tested formulation, PpDGB enhanced growth but not disease resistance, probably due to simultaneous activation of the residual plant pathogens. Therefore variant formulations have to be tested. The influence of PpDGB on the composition of the bacterial communities in the rhizosphere was assessed by DGGE profiling. In soilless plant cultures, PpDGB-driven profile changes could be observed from the 5th day after the initial treatment. P. polymyxa bacteria were shown to be widely present in association with plants and specific PpDGB detection in plant and rhizosphere was only possible with newly developed strain-specific PCR primers based on Nif H gene sequences. Quantitative PCR based on SYBR Green fluorescence enabled detection of low PpDGB concentrations in the plant rhizosphere.

Araceae↗
PubMed2006

[Dynamic analysis of the heat shock protein 60 and its gene expression in Thermoanaerobacter tengcongensis induced by temperature increase].

Heat shock protein 60 (HSP60) is one of the important chaperonins, which can assist proper protein folding and configuration,and can prevent denaturation and degradation of proteins as well. It was found that HSP60 in Thermoanaerobacter tengcongensis (T. tengcongensis) was typically temperature-dependent with the highest protein expression at 80 degrees C. To understand the molecular mechanisms of thermophiles in their responding to heat stress, further investigation was conducted to examine the dynamic expression of HSP60 gene induced by higher temperature. The T. tengcongensis cells cultured at optimal temperature (75 degrees C) were transferred to 80 degrees C followed by taking the aliquots at different time intervals. To monitor the expression levels of HSP60 mRNA and protein, these bacterial gene products were analyzed by two-dimensional electrophoresis, MALDI-TOF, HPLC-MS/MS, Western blot and quantitative PCR. The experimental data were calculated statistically and quantitatively, which indicate that the HSP60 protein increases steadily and significantly within 4h period after temperature raised, but its mRNA level is shown as a peak shape change within 1h. Obviously, the expression response of HSP60 protein to heat stress is significantly slower than that of its mRNA expression. Additionally, the expression extent of HSP60 mRNA and protein induced by raised-temperature is very different. In E. coli strains, the expression of HSP60 is usually regulated by the sigma32 factor, which disassociates with DnaK immediately when the environmental temperature elevated. Since the genome of T. tengcongensis contains two sigma32 genes, thus, it is likely that both bacteria share the similar mechanisms which regulate HSP60 transcription responding to the changes of temperature. Interestingly, the mRNA of HSP60 drops down about 70% within 30m responding to heat shock, but goes to the increased expression after then. Although this phenomenon is hard to explain based upon the current theory, it is plausible that the transcription in T. tengcongensis is temporally inhibited due to the culture temperature sharply raised.

Bacterial Proteins↗
PubMed1994

PCR-based analysis of herpes simplex virus type 1 latency in the rat trigeminal ganglion established with a ribonucleotide reductase-deficient mutant.

Competitive quantitative PCR and reverse transcriptase-PCR were used to quantitate DNA and RNA from an attenuated ribonucleotide reductase-deleted herpes simplex virus type 1 (HSV-1) mutant in the rat trigeminal ganglion after peripheral inoculation following corneal scarification. Amplification of ganglionic DNA with oligonucleotide primers specific for the HSV-1 glycoprotein B (gB) gene and for the latency-associated transcript (LAT) gene indicated that there were approximately 2 x 10(5) genome equivalents per ganglion at 2 days, 7 days, and 8 weeks after inoculation. Amplification of ganglionic RNA with primers specific for HSV-1 LAT indicated that the amount of LAT RNA was also stable over 8 weeks, with 10(7) LAT molecules per ganglion at 2 days and at 7 days postinoculation and 1.4 x 10(7) LAT molecules per ganglion at 8 weeks. In situ hybridization with a digoxigenin-labeled riboprobe specific for LAT detected an average of one to two LAT-positive cells in each positive 6-microns section of trigeminal ganglion. In situ PCR detection of HSV-1 genomes in similar sections, using digoxigenin-labeled nucleotides with primers specific for HSV-1 gB, identified as many as 120 genome-positive cells per section. These results indicate that there are approximately 50 LAT molecules per latent HSV-1 genome in the trigeminal ganglion, compared with 15 LAT molecules per latent HSV-1 genome in the central nervous system (R. Ramakrishnan, D. J. Fink, G. Jiang, P. Desai, J. C. Glorioso, and M. Levine, J. Virol. 68:1864-1873, 1994), but that cells with detectable LATs by in situ hybridization represent only a small proportion of those ganglionic neurons containing HSV-1 genomes. The presence of latent HSV-1 genomes in a large number of neurons suggests that HSV-1 may be more efficient in establishing the latent state than would be anticipated from previous reports.

Animals↗
PubMed2005

Development of a real-time QPCR assay for the detection of RV2 lineage-specific rhadinoviruses in macaques and baboons.

BACKGROUND: Two distinct lineages of rhadinoviruses related to Kaposi's sarcoma-associated herpesvirus (KSHV/HHV8) have been identified in macaques and other Old World non-human primates. We have developed a real-time quantitative PCR (QPCR) assay using a TaqMan probe to differentially detect and quantitate members of the rhadinovirus-2 (RV2) lineage. PCR primers were derived from sequences within ORF 60 and the adjacent ORF 59/60 intergenic region which were highly conserved between the macaque RV2 rhadinoviruses, rhesus rhadinovirus (RRV) and Macaca nemestrina rhadinovirus-2 (MneRV2). These primers showed little similarity to the corresponding sequences of the macaque RV1 rhadinoviruses, retroperitoneal fibromatosis herpesvirus Macaca nemestrina (RFHVMn) and Macaca mulatta (RFHVMm). To determine viral loads per cell, an additional TaqMan QPCR assay was developed to detect the single copy cellular oncostatin M gene. RESULTS: We show that the RV2 QPCR assay is linear from less than 2 to more than 300,000 copies using MneRV2 DNA, and is non-reactive with RFHVMn DNA up to 1 billion DNA templates per reaction. RV2 loads ranging from 6 to 2,300 viral genome equivalent copies per 10(6) cells were detected in PBMC from randomly sampled macaques from the Washington National Primate Research Center. Screening tissue from other primate species, including another macaque, Macaca fascicularis, and a baboon, Papio cynocephalus, revealed the presence of novel rhadinoviruses, MfaRV2 and PcyRV2, respectively. Sequence comparison and phylogenetic analysis confirmed their inclusion within the RV2 lineage of KSHV-like rhadinoviruses. CONCLUSIONS: We describe a QPCR assay which provides a quick and sensitive method for quantitating rhadinoviruses belonging to the RV2 lineage of KSHV-like rhadinoviruses found in a variety of macaque species commonly used for biomedical research. While this assay broadly detects different RV2 rhadinovirus species, it is unreactive with RV1 rhadinovirus species which commonly co-infect the same primate hosts. We also show that this QPCR assay can be used to identify novel RV2 rhadinoviruses in different primate species.

Animals↗
PubMed2005

Fibroblast differentiation of bone marrow-derived cells during wound repair.

To examine the ontogeny of the wound fibroblast, bone marrow transplantation was performed to wild-type recipients from transgenic donors that express both the luciferase and beta-galactosidase reporter genes under transcriptional control of the promoter/enhancer for the alpha2 chain of type I collagen. Polyvinyl alcohol sponges were implanted to elicit a naïve granulation tissue response, removed at defined time points, and processed for nucleic acids and histochemistry. Quantitative PCR for the luciferase transgene demonstrated that donor-derived cells were present during inflammation, declined, and rebounded during later stages of tissue remodeling. Furthermore, quantitative RT-PCR revealed that bone marrow-derived collagen transcripts contributed significantly to the total collagen I alpha2 promoter activation during later stages of repair. beta-galactosidase staining revealed that indeed those cells which expressed the transgene exhibited a fibroblastic phenotype, co-localized with sites of active collagen deposition, and expressed fibroblast specific protein-1. These data strongly support the concept that the adult bone marrow compartment houses progenitors with the potential to migrate to sites of tissue damage, and participate in repair beyond inflammation as fibroblasts. Moreover, that bone marrow-derived fibroblasts make a substantial contribution to the formation of new connective tissue, including type I collagen, during wound repair.

Animals↗
PubMed2005

Diagnosis of Pelizaeus-Merzbacher disease: detection of proteolipid protein gene copy number by real-time PCR.

Duplication of the proteolipid protein gene (PLP1) is the most frequent cause of Pelizaeus-Merzbacher disease (PMD), a severe X-linked myelination disorder. We developed an assay for the detection of the PLP1 gene dosage by real-time quantitative PCR using the ABI Prism 7700 Sequence Detection System and the TaqMan chemistry. Copy number of the PLP1 gene was determined by the standard curve method using GAPDH as the reference gene. The assay was tested both on 50 normal controls and on 20 subjects whose PLP1 gene copy number was previously determined by quantitative fluorescent multiplex PCR. The procedure confirmed the expected results both on the male and female normal controls as well as on the 20 subjects previously tested. Ratios corresponding to the presence of one, two or three PLP1 gene copies, distributed in three non-overlapping ranges, were obtained by real-time PCR analysis. Subsequently, 29 DNA samples of putative PMD patients and possible female carriers, with unknown PLP1 gene dosage, were analysed. Five affected males carrying the PLP1 gene duplication and four female heterozygotes carrying three PLP1 gene copies were identified among them. The method is suitable for the identification of affected male patients and female carriers. Specific ranges are widely spaced, ensuring a correct assignment of the PLP1 gene copy number.

Female↗
PubMed2001

Dual-label detection of amplified products in quantitative RT-PCR assay using lanthanide-labeled probes.

Quantitative RT-PCR (QRT-PCR) enables the sensitive and specific detection of mRNA with a small copy number. We used the QRT-PCR method and dual-label analysis of amplification products for the detection of prostate-specific antigen (PSA) mRNA. The QRT-PCR assay employed a PSA-like internal standard (IS) mRNA, which was used to quantify the PSA mRNA copies and to control the variations during the whole assay procedure from the RNA extraction to the detection of QRT-PCR amplification products by hybridization assay. After co-amplification, the PSA and IS products were detected in a microplate using Eu3+ chelate-labeled PSA and Tb3+ chelate-labeled IS hybridization probes. The detection probes allowed the simultaneous and dual-label detection of PSA and IS products in the same microtiter well. Compared to the single-label assay, the dual-label detection improved the within- and between-assay CV% from 21.7 to 7.5 and from 36.0 to 30.3, respectively. The between- and within-assay variation of the dual-label assay was further studied using PSA-producing LNCaP cells. The cells were found to express 980 +/- 170 (mean +/- SD) copies of PSA-mRNA with the within-assay CV% of 17.7 and 890 +/- 220 (mean +/- SD) copies of PSA-mRNA with the between-assay CV% of 25.0. The methodology developed may help in future studies to obtain reliable quantification of PSA mRNA generated by circulating prostate cancer cells.

Animals↗
PubMed2006

Antiprimer quenching-based real-time PCR and its application to the analysis of clinical cancer samples.

BACKGROUND: Nucleic acid amplification plays an increasingly important role in genetic analysis of clinical samples, medical diagnostics, and drug discovery. We present a novel quantitative PCR technology that combines the advantages of existing methods and allows versatile and flexible nucleic acid target quantification in clinical samples of widely different origin and quality. METHODS: We modified one of the 2 PCR primers by use of an oligonucleotide "tail" fluorescently labeled at the 5' end. An oligonucleotide complementary to this tail, carrying a 3' quenching molecule (antiprimer), was included in the reaction along with 2 primers. After primer extension, the reaction temperature was lowered such that the antiprimer hybridizes and quenches the fluorescence of the free primer but not the fluorescence of the double-stranded PCR product. The latter provides real-time fluorescent product quantification. This antiprimer-based quantitative real-time PCR method (aQRT-PCR) was used to amplify and quantify minute amounts of input DNA for genes important to cancer. RESULTS: Simplex and multiplex aQRT-PCR demonstrated linear correlation (r(2) >0.995) down to a DNA input equivalent to 20 cells. Multiplex aQRT-PCR reliably identified the HER-2 gene in microdissected breast cancer samples; in formalin-fixed, paraffin-embedded specimens; and in plasma circulating DNA from cancer patients. Adaptation to multiplex single-nucleotide polymorphism detection via allele-specific aQRT-PCR allowed correct identification of apolipoprotein B polymorphisms in 51 of 51 human specimens. CONCLUSION: The simplicity, versatility, reliability, and low cost of aQRT-PCR make it suitable for genetic analysis of clinical specimens.

Apolipoproteins B↗
PubMed2004

Expression and functional significance of CDC25B in human pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer-related deaths. Deregulation of cell-cycle control is thought to be a crucial event in malignant transformation, and CDC25 phosphatases are a family of cyclin-dependent kinase activators, which act at different points of the cell cycle, including G1-S and G2-M transition. Here, we investigated the expression and functional significance of CDC25s in PDAC. CDC25B mRNA expression levels in human pancreatic tissue samples were analysed by cDNA array, quantitative PCR and Northern blotting. Immunohistochemistry was carried out to localize and quantify CDC25B expression. Two specific CDC25B inhibitors were utilized to determine the functional relevance of CDC25B. By quantitative RT-PCR, CDC25B mRNA was overexpressed in pancreatic cancer (7.5-fold) in comparison to the normal pancreas. Strong nuclear CDC25B immunoreactivity was present in both pancreatic and metastatic cancer samples, and there was a marked increase of the percentage of positive cells in primary cancer (48.6+/-16.3%) and metastatic tissues (71.7+/-3.1%) compared to normal samples (8.3+/-1.8%). Two CDC25B inhibitors reduced the growth of pancreatic cancer cell lines, resulting in the accumulation of phosphorylated CDC2 and G2/M arrest. These findings demonstrate an important role of CDC25B in cell-cycle progression, raising the possibility that inhibition of CDC25B may have therapeutic potential in pancreatic cancer.

Adenocarcinoma↗
PubMed2005

Nuclear gene expression changes due to mitochondrial dysfunction in ARPE-19 cells: implications for age-related macular degeneration.

PURPOSE: To measure changes in nuclear gene expression resulting from mitochondrial dysfunction in retinal pigment epithelial cells. METHODS: ARPE-19 retinal pigment epithelial cells were depleted of their mitochondrial (mt)DNA by passaging in a low concentration of ethidium bromide. Loss of mitochondrial DNA was determined by uridine auxotrophy and quantitative real-time polymerase chain reaction of isolated DNA. Loss of mitochondrial membrane potential was estimated by uptake of JC-1. Changes in nuclear gene expression were determined by quantitative real-time reverse transcription-polymerase chain reaction of isolated total RNA from ethidium-bromide-treated and untreated cells. Morphologic and phenotypic changes were determined by phase-contrast microscopy, sensitivity to the oxidant tert-butyl hydroperoxide (tBH), and invasion assay. RESULTS: ARPE-19 cells became auxotrophic for growth on uridine after eight passages in 50 ng/mL ethidium bromide. Quantitative PCR revealed almost complete loss of mitochondrial DNA (rho(0) cells). Uptake of JC-1 was reduced in the rho(0) cells, indicating reduction of mitochondrial membrane potential. Quantitative RT-PCR measured increased expression of genes coding for drusen components, lipid transport, extracellular matrix components, and responses to inflammation in the rho(0) cells. The rho(0) cells also exhibited an increased sensitivity to killing by tBH and increased migration and invasion through solubulized basement membrane-coated tissue culture inserts. CONCLUSIONS: ARPE-19 cells respond to loss of mitochondrial function by changes in nuclear gene expression that resemble changes observed in age-related macular degeneration. The results lead to the hypothesis that loss of mitochondrial function with age and resultant changes in nuclear gene expression may explain some of the changes in the macula that are associated with the known clinical manifestations of age-related macular degeneration.

Benzimidazoles↗