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Visualization of DNA-containing structures in various species of Chlorophyta, Rhodophyta and Cyanophyta using SYBR Green I dye.

We developed an alternative method of staining cell nuclei and chloroplast nucleoids of algal cells using SYBR Green I (the fluorescent dye used commonly for detecting dsDNA in agarose and polyacrylamide gels as an alternative to highly mutagenic ethidium bromide and for DNA staining of viruses and bacteria followed by flow cytometry, digital image analysis or real-time PCR), which enabled routine staining in vivo. Cells do not need to be fixed or treated chemically or physically before staining, thus the shape, size and position of DNA-containing structures are not affected. The fluorescence signal is sharp and reproducible. Examples of application of the method are shown in color microphotographs for representatives of eukaryotic algae from the taxa Chlorophyta, Rhodophyta and the prokaryotic Cyanophyta. The method is also useful for studying progress of the cell cycle in algal cells dividing by multiple fission, as shown by observation of changes in nuclear number during the cell cycle of the green alga Chlamydomonas reinhardtii and Scenedesmus quadricauda. Staining with SYBR Green I can be recommended as a fast, safe and efficient method for the detection of DNA-containing structures in vivo.

Benzothiazoles↗

[Columbia University experience of detection of circulating cells by RT-PCR PSA in prostate cancer as a predictive factor of stage and biochemical recurrence].

OBJECTIVES: The Columbia University experience of RT-PCR PSA as a predictive factor of stage and biochemical recurrence is reviewed by trying to explain its differences. PATIENTS AND METHODS: 319 patients were included between January 1993 and March 1998. Radical prostatectomy was performed in all patients by the same surgeon. The RT-PCR protocol has been previously described (Katz et al., Urology, 1994). Biochemical recurrence was defined by a PSA greater than or equal to 0.2 ng/ml. RESULTS: Histological examination diagnosed 218 pT2 and 101 pT3 tumours. Thirty-four of the 218 pT2 patients (16%) had a positive RT-PCR versus 51 of the 101 pT3 patients (51%, p < 0.001). Analysis of Kaplan-Meier curves showed an 84% recurrence-free survival when RT-PER was negative versus 47% when RT-PCR was positive (Log-rank test, p = 0.0002). Multivariate analysis showed that independent predictive factors of biochemical recurrence were stage (p = 0.004), Gleason score estimated on the operative specimen (p = 0.010) and serum PSA (p = 0.047); RT-PCR (p = 0.075), strongly correlated with stage, was not an independent predictive factor. By exclusively comparing preoperative parameters, PSA (p = 0.004) and RT-PCR (p = 0.006) were found to be independent predictive factors compared to digital rectal examination (p = 0.371) and Gleason score on biopsies (p = 0.076). CONCLUSION: In this institution, RT-PCR PSA is a predictive parameter of stage and biochemical recurrence. No consensus has yet been reached in the literature concerning the reference protocol, as each team has developed its own RT-PCR technique applied to its own patient population. Comparison of results is therefore difficult.

Adult↗

Effect of prostate biopsy on the results of the PSA RT-PCR test.

OBJECTIVES: To evaluate the effect of prostate biopsy on the prostate-specific antigen (PSA) reverse transcriptase-polymerase chain reaction (RT-PCR) test. METHODS: Ninety men who were scheduled to undergo prostate biopsy because of an elevated PSA or abnormal digital rectal examination, or both, were recruited to have PSA RT-PCR performed on peripheral blood samples drawn before and at 30 minutes, 1 week, and 1 month after undergoing prostate biopsy. PSA RT-PCR was performed and all PCR products were blotted and hybridized with phosphorus-32 (32-P)-PSA cDNA probe (exon 3 to 5). RESULTS: Of 90 patients, 77 had a negative prebiopsy PSA RT-PCR result. Of these 77, 2 (2.6%) had a positive PSA RT-PCR result at some point after the biopsy procedure. Both of these patients had no evidence of malignancy on biopsy. The PSA RT-PCR test was positive at 30 minutes for 1 patient, but was negative at 1 week; the other was positive at 1 week but the patient did not return for the 1-month sample. CONCLUSIONS: Our study indicates that 2.6% of patients with an initially negative PSA RT-PCR will have a positive PSA RT-PCR test after biopsy has been performed. Although this is uncommon, it may have profound implications for those patients in whom it occurs. On the basis of our results, it appears that one should wait longer than 1 week after prostate biopsy before obtaining blood for PSA RT-PCR testing to decrease the likelihood of a spurious PSA RT-PCR result.

Aged↗

The use of RT-PCR for prostate-specific antigen assay to predict potential surgical failures before radical prostatectomy: molecular staging of prostate cancer.

OBJECTIVE: To assess the potential role of a recently developed reverse transcriptase-polymerase chain reaction (RT-PCR) assay for prostate-specific antigen (PSA), that detects circulating prostate cells in patients with prostate cancer, in the management of clinically localized cancer. PATIENTS AND METHODS: A total of 138 men (mean age 62.5 years, range 49-70) scheduled for radical retropubic prostatectomy had an RT-PCR assay before surgery. The results were compared with the final pathological stage of disease, the results from local imaging techniques, serum PSA levels, digital rectal examination (DRE) and Gleason score. RESULTS: Enhanced RT-PCR for PSA was the best predictor of potential surgical failures; 70% of patients with positive surgical margins or invasion into the seminal vesicle were identified pre-operatively by a positive RT-PCR assay (odds ratio = 12.0, positive predictive value = 64%, negative predictive value = 87%). RT-PCR was able to identify pre-operatively patients with adverse pathology, despite low serum PSA values (< 4.0 ng/mL). In patients with high PSA level (> 10 ng/mL), RT-PCR discriminated between potentially curable candidates and those with established extraprostatic disease. CONCLUSIONS: RT-PCR for PSA adds unique prognostic information when considering patients for radical surgery. The final role for the RT-PCR assay is as yet undefined; however, the ability to detect potential surgical failures pre-operatively using a molecular approach should have a significant impact on the management of patients with prostate cancer.

Aged↗

Dysregulation of annexin I protein expression in high-grade prostatic intraepithelial neoplasia and prostate cancer.

PURPOSE: To determine expression levels of annexin I (lipocortin I) in patient-matched benign prostatic epithelium (BPE), high-grade prostatic intraepithelial neoplasia (HGPIN), and prostate cancer (CaP). EXPERIMETNAL DESIGN: Annexin I protein expression was examined with a standard immunohistochemical protocol in 69 radical prostatectomy specimens, 45 of which also contained HGPIN. Immunostained sections were scored visually by a genitourinary pathologist and mean optical density was measured with digital image analysis. Real-time fluorescence quantitative PCR was used to measure expression levels of annexin I mRNA in patient-matched CaP and BPE from 14 snap-frozen, radical prostatectomy specimens. RESULTS: Annexin I protein expression was reduced in 91% (41/45) of HGPIN lesions and 94% (65/69) of invasive CaP compared with BPE in the same histological section when assessed visually. Mean absorbance was reduced significantly (P < 0.05) in 97.7% (44/45) of HGPIN lesions and 98.5% (68/69) of CaP glands compared with BPE. In 79% of cases (11/14; P < 0.05), mRNA expression was reduced in CaP as compared with patient-matched BPE. Annexin I mRNA and protein expression levels did not correlate with Gleason grade, pathological stage, or race. CONCLUSIONS: Down-regulation of annexin I protein expression is a common finding in HGPIN and CaP, suggesting that annexin I dysregulation may be an important early event in CaP initiation. Because mRNA levels are reduced in a high proportion of cases, one likely mechanism for annexin I dysregulation occurs at the level of gene transcription. Results of these studies support a valuable role for a molecular profiling approach to CaP research.

Annexin A1↗

A high-resolution polymerase chain reaction-sequence-specific primer HLA-B*27 typing set and its application in routine HLA-B27 testing.

We designed a set of 35 polymerase chain reaction sequence-specific primers (PCR-SSP) in 29 SSP mixtures to assign 29 HLA-B*27 4-digit level alleles (B*2701-B*2721 and B*2723-B*2730). This was used in conjunction with our 41 PCR-SSP primer mixture low-resolution HLA-B typing set to fully differentiate B*27 from all other HLA-B alleles. Successful typing set validation used 521 B*27 samples covering 13 (B*2701-B*2710 and B*2712, B*2717, B*2723) alleles. The distribution of B*27 alleles was determined in a random population of 4020 local blood donors and the use of PCR-SSP B*27 typing in our routine flow cytometry-based HLA-B27/B2708 typing strategy is described.

Alleles↗

DEPD, a high resolution gene expression profiling technique capable of identifying new drug targets in the central nervous system.

Digital expression pattern display (DEPD) is an open, automated, PCR-based system of gene expression profiling that is capable of resolving as many as 100,000 transcripts from a single brain tissue cDNA sample. It has a detection sensitivity of better than 1 in 750,000 and it can reliably detect differences in RNA expression levels of less than two-fold. Digital expression pattern display presently is the most sensitive and therefore the only expression profiling method available that is capable of monitoring, in a semi-quantitative fashion, the expression of even the rarest of transcripts found in human brain tissue. Biofrontera applies this proprietary technique, together with state-of-the-art bioinformatics, for the purposes of elucidating pathology pathways of major brain diseases, of analysing the target profiles of drugs presently applied or in development, and of identifying novel targets for drug action.

Animals↗

Competitive reverse transcription-polymerase chain reaction for quantitation of feline immunodeficiency virus.

A competitive reverse transcription-polymerase chain reaction (RT-PCR) was developed to quantify RNA of feline immunodeficiency virus (FIV) in cats. The assay uses in vitro synthesized RNA derived from the gag region of the FIV genome as a competitive internal control. The synthesized RNA has a 22-base deletion with respect to the wild-type sequence. PCR products were quantitated by densitometric analysis of a digitalized image of the ethidium bromide stained gel. The non-radioactive method was evaluated in reconstruction experiments. RNA synthesis in FIV-infected feline thymocytes correlated well with the amount of viral p24 antigen produced. Viral RNA concentrations in the plasma of two cats experimentally infected with FIV strain UT113 were followed for 32 weeks; peak copy numbers (2.3 x 10(4) and 1.3 x 10(4) per ml, respectively) were reached 11 weeks after subcutaneous injection of ten 50% cat infectious doses. With rising antibody titers against FIV-gag and FIV-env gene products, the amount of FIV RNA in plasma decreased. Nine asymptomatic cats that had been experimentally infected 3.5 to 4.5 years earlier had copy numbers between 5.6 x 10(3) and 4.3 x 10(4) per ml. This quantitative competitive RT-PCR will be useful to study the pathogenesis of the FIV infection, to evaluate the effectiveness of vaccines and to monitor antiviral and immunomodulating drugs.

Animals↗

[Quantification of feline immunodeficiency virus (FIV) RNA in the plasma of infected cats].

A competitive reverse transcription-polymerase chain reaction (RT-PCR) was used to quantify RNA of feline immunodeficiency virus (FIV) in cats. The assay uses in vitro synthesized RNA as a competitive internal control. The synthesized RNA has a 22-base deletion with respect to the wild-type sequence. PCR products were quantitated by densitometric analysis of a digitized image of the ethidium bromide stained gel. Viral RNA concentrations in the plasma of two cats experimentally infected with FIV strain UT113 were followed for 32 weeks; peak copy numbers (2.3 x 10(4) and 1.3 x 10(4) per ml, respectively) were reached 11 weeks after subcutaneous injection of ten 50% cat infectious doses. With rising antibody titers against FIV-gag and FIV-env gene products, the amount of FIV RNA in plasma decreased. Nine asymptomatic cats that had been experimentally infected 3.5 to 4.5 years earlier had copy numbers between 5.6 x 10(3) and 4.3 x 10(4) per ml. Cats treated for six weeks with 9-(2-phosphonylmethoxy-propyl)-2,6-diaminopurine [PMPDAP] (20 mg/kg body weight s.c. three times a week) showed a significant decrease of RNA copy numbers in plasma. This quantitative competitive RT-PCR will be useful to study the pathogenesis of the FIV infection, to evaluate the effectiveness of vaccines and to monitor antiviral and immunomodulating drugs.

Animals↗

Tumor size dependent changes in a murine fibrosarcoma: use of in vivo 31P NMR for non-invasive evaluation of tumor metabolic status.

Tumor tissue contains viable hypoxic regions that are radioresistant and often chemoresistant and may therefore be responsible for some treatment failures. A subject of general interest has been the development of non-invasive means of monitoring tissue oxygen. Pulse Fourier transform 31P NMR spectroscopy can be used to estimate intracellular nucleotide triphosphates (NTP), phosphocreatinine (PCr), inorganic phosphate (Pi) and pH. We have obtained 31P NMR spectra as an indirect estimate of tissue oxygen and metabolic status in a C3H mouse fibrosarcoma FSaII. Sequential spectra were studied during tumor growth in a cohort of animals and peak area ratios for several metabolites were computed digitally by computer. During growth, tumors showed a progressive loss of PCr with increasing Pi, and most tumors greater than 250 mm3 in volume had little or no measurable PCr. The smallest tumors (38 mm3 average volume) had PCr/Pi ratios of 1.03 +/- .24, whereas tumors 250 mm3 or more had an average PCr/Pi ratio of 0.15 +/- .04. Similarly derived NTP/Pi ratios decreased with tumor size, but this change was not significant (p = .17). Radiobiologic hypoxic cell fractions were estimated using the radiation dose required to control tumor in 50% of animals (TCD50) or by the lung colony technique. Tumors less than 100 mm3 had a hypoxic cell fraction of 4% (TCD50) while tumors 250 mm3 had a 40% hypoxic cell fraction (lung colony assay). These hypoxic fraction determinations correlated well with the depletion of PCr and decline in NTP/Pi ratios seen at 250 mm3 tumor volumes. Tumor spectral changes with acute ischemia were studied after ligation of the tumor bearing limb and were similar to changes seen with tumor growth. PCr was lost within 7 minutes, with concurrent increase in Pi and loss of NTP. Complete loss of all high energy phosphates occurred by 40 minutes of occlusion. In vivo tumor 31P NMR spectroscopy can be used to estimate tissue metabolic status and may be useful in non-invasive prediction of hypoxic cell fraction, reoxygenation, and radiation treatment response.

Animals↗

Comparison of gene expression in squamous cell carcinoma and adenocarcinoma of the uterine cervix.

OBJECTIVES: Microarray expression analysis of cervical tumors has revealed differential expression of genes that may be useful as markers or targets for treatment. We question the application of array findings across the major categories of cervical cancer. We sought to identify differences between normal squamous epithelium (NSQ) and glandular epithelium (NGL) of the uterine cervix and their malignant variants: squamous cell cancer (SCC) and adenocarcinoma (ACA). METHODS: Eight genes were selected: 12-lipoxygenase (12-LOX), keratin 4, trypsinogen 2 (TRY2), Rh glycoprotein C (RhGC), collagen type V alpha 2, integrin alpha 5, integrin alpha 6, and c-myc. Ten cases each of SCC and ACA of the cervix were selected from our tumor bank. NSQ and NGL epithelia were obtained from consecutive patients undergoing surgery for benign disease. RNA extraction, cDNA synthesis, and DNA amplification of all samples were performed according to an established protocol. Electrophoresis of the multiplexed polymerase chain reaction (PCR) products was performed under standard conditions, followed by digital image capture. A ratio of target to control gene (beta-actin) was obtained for each sample. Analysis of variance was applied to the mean ratios for each tissue to establish significant differences. Individual pairwise comparisons were made by Student t tests and verified with the Tukey-Kramer test. RESULTS: Clinically valid comparisons are NSQ to NGL, NSQ to SCC, NGL to ACA, and SCC to ACA. Various expression patterns were observed between the epithelia and their malignant phenotypes. Significant differences in gene expression were observed between benign squamous and glandular epithelium in four of the eight genes and between malignant squamous and glandular epithelium in three of the eight genes. Significant differences in gene expression between benign and malignant tissues were demonstrated in four of the eight genes. CONCLUSIONS: We have defined significant differential expression changes between the two principal cervical tumor types. Differences in genes are demonstrated and must be considered if array technology is applied to the study of the biologic behavior of these tumors as well as their screening and management. The observed differential expression should be a compelling argument to perform type-specific expression analysis for other tumors with histological variants.

Adenocarcinoma↗

Differentiating embryonic stem cells: GAPDH, but neither HPRT nor beta-tubulin is suitable as an internal standard for measuring RNA levels.

Embryonic stem (ES) cells are pluripotent cell lines that possess virtually unlimited self-renewal and differentiation capacity. Such characteristics make them potentially an invaluable cell source for diverse tissue-engineering applications. In vitro ES cell differentiation occurs spontaneously in three-dimensional structures termed "embryoid bodies" that mimic postimplantation embryonic tissue. HPRT, beta-tubulin, and GAPDH are commonly used as internal RNA standards in ES cell-derived gene transcription studies so that corrected sample mRNA levels can be obtained for (semi) quantitative gene expression data. However, if reliable data is to be obtained, it is essential that such housekeeping gene expression remains constant, and this has not been demonstrated for differentiating ES cell cultures, which represent a mixed and changing population of cells with time in culture. Therefore, in the present study, we tested the suitability of these housekeeping genes to act as true internal standards for differentiating murine ES cells cultured as embryoid bodies. PCR-amplified gene-specific products were quantified from digital images of ethidium bromide-stained gels using a computer software package. Both HPRT and beta-tubulin mRNA levels varied markedly in spontaneously differentiating and growth factor-supplemented (TGF-beta) ES cell cultures (p < 0.001, ANOVA), while GAPDH expression remained relatively constant (p > 0.2). Our results demonstrate the importance of fully validating housekeeping gene expression in in vitro ES cell gene transcription studies and suggest that GAPDH may be a suitable candidate to act as an internal RNA standard, while both HPRT and beta-tubulin appear to be inappropriate. Finally, we demonstrate enhanced mesodermal differentiation of ES cell-derived cultures by treatment with TGF-beta through significant upregulation of Brachyury T expression, with a concomitant decrease in expression of the undifferentiated ES cell marker Oct-4.

Animals↗

Microbial quantification in activated sludge: the hits and misses.

Since the implementation of the activated sludge process for treating wastewater, there has been a reliance on chemical and physical parameters to monitor the system. However, in biological nutrient removal (BNR) processes, the microorganisms responsible for some of the transformations should be used to monitor the processes with the overall goal to achieve better treatment performance. The development of in situ identification and rapid quantification techniques for key microorganisms involved in BNR are required to achieve this goal. This study explored the quantification of Nitrospira, a key organism in the oxidation of nitrite to nitrate in BNR. Two molecular genetic microbial quantification techniques were evaluated: real-time polymerase chain reaction (PCR) and fluorescence in situ hybridisation (FISH) followed by digital image analysis. A correlation between the Nitrospira quantitative data and the nitrate production rate, determined in batch tests, was attempted. The disadvantages and advantages of both methods will be discussed.

Bioreactors↗

Genotyping in contact investigations: a CDC perspective.

Genotyping of Mycobacterium tuberculosis isolates has been widely used to support investigations of outbreaks and as a tool for studying transmission dynamics and other aspects of tuberculosis epidemiology. Its applications to contact investigations are more limited. Targeted typing can be used to confirm or disprove suspected relationships among cases. Universal typing of isolates can be used to identify unsuspected transmission and broaden the scope of contact investigations. In order to properly use the results, one must understand the nature of the changes in the M. tuberculosis genome that produce the heterogeneity reflected in the genotypes, and understand the discriminatory power of the various methods. IS6110 fingerprinting provides the highest discriminatory power, but can be a slow process. Spoligotyping and MIRU-VNTR are PCR-based methods that provide faster turnaround and produce digital results that facilitate comparisons. Appropriately used, isolate genotyping can be a useful adjunct to standard contact investigations.

Centers for Disease Control and Prevention, U.S.↗

Digital DNA typing at a second hypervariable locus by minisatellite variant repeat mapping.

Minisatellite variant repeat unit mapping by PCR (MVR-PCR) assays the interspersion pattern of variant repeat units along minisatellite alleles. Mapping such internal variation in the highly polymorphic minisatellite MS31A (locus D7S21), reveals extreme levels of allelic variability, far in excess of that detectable by allele length analysis. Flanking base substitutional polymorphisms have enabled the 5' structure of large numbers of MS31A alleles to be derived from genomic DNA by allele-specific MVR-PCR. More than 100 alleles have now been mapped and all are different. Several alleles show related internal structures and some of these provide evidence of polarity in allelic variation reminiscent of that seen at two other hypervariable minisatellites, D1S8 (MS32) and D16S309 (MS205). We also describe the diploid digital coding of MS31A, including the simultaneous coding of MS31A and a second locus, MS32, by duplex MVR-PCR, which greatly enhances the potential forensic applications of this technique.

Alleles↗

Blood-based reverse transcriptase polymerase chain reaction assays for prostatic specific antigen: long term follow-up confirms the potential utility of this assay in identifying patients more likely to have biochemical recurrence (rising PSA) following radical prostatectomy.

Reverse transcriptase polymerase chain reaction (RT-PCR) assay is a sensitive technique to detect circulating cells expressing prostate-specific antigen (PSA) in blood or bone marrow from patients with prostate cancer. When applied to prostate cancer patients at our institution, this technique identifies those patients with a greater likelihood of extra-prostatic disease. We evaluated RT-PCR PSA as a predictor of PSA recurrence and compared it with pre-operative (serum PSA, digital rectal examination, Gleason score on biopsy) and post-operative parameters (pathological findings). Three hundred nineteen men scheduled for radical prostatectomy had an enhanced RT-PCR PSA assay before surgery. The enhanced RT-PCR PSA protocol has been previously described. PSA recurrence was defined as any serum PSA value above 0.2 microgram/l. Forty-six patients had PSA recurrence. The mean follow-up was 25.4 months. Recurrence free survival was 53% for patients with positive RT-PCR PSA vs. 84% if RT-PCR PSA was negative. By using multivariate analyses, RT-PCR PSA status was not an independent predictor of PSA recurrence compared to pathological stage pT3, Gleason score on prostate specimen and serum PSA. If only pre-operative parameters were studied, serum PSA and RT-PCR PSA status were 2 independent pre-operative predictors of PSA recurrence compared with Gleason score on biopsy and digital rectal examination. Int. J. Cancer (Pred. Oncol.) 84:360-364, 1999.

Disease-Free Survival↗

Internal controls as performance monitors and quantitative standards in the detection by polymerase chain reaction of herpes simplex virus and cytomegalovirus in clinical specimens.

Internal controls (IC) were produced and characterized for an HSV and a CMV PCR assay which serve both as test performance monitors and as quantitative standards. In each of the PCR assays the IC and native targets were amplified with equal efficiency and were detected with the same sensitivity, i.e. < 10 target copies. An algorithm was developed for the use of IC as a quantitative standard which entailed coamplifying a test specimen with four two-fold dilutions of the respective IC target (63-500 copies), followed by regression analysis of the relative yield of amplification products. This approach allowed the determination of both the initial virus genome copy number and the variability of the results, which provided a confidence index for the PCR assay. The relative yields of PCR products were determined by Southern blot and probe hybridization and by densitometry of digitized ethidium bromide-stained gels. Both methods produced estimations of the initial target copy numbers within +/- 40% of the expected value. Such a comprehensive analysis of an internal control for a PCR assay provides a rigorous control of test performance and permits reliable quantitative interpretation of a PCR assay result.

AIDS-Related Opportunistic Infections↗

A miniaturized DNA amplifier: its application in traditional Chinese medicine.

A Si-based miniaturized device for the polymerase chain reaction (PCR) has been developed. The device has Pt temperature sensors and heaters integrated on top of the reaction chamber for real-time accurate temperature sensing and control. Reaction temperature of the device is digitally controlled to achieve a temperature accuracy of +/-0.025 degrees C. The effects of PCR protocol optimization on the amplification performance of the surface-passivated chip reactor have been investigated in detail and quantitatively compared with that of the conventional thermal cycler. In this study, four traditional Chinese medicine genes including Fritillaria cirrhosa, Cartharmus tinctorius, Adenophora lobophilla, and Stephania tetrandra are used as model template. With appropriate chamber surface treatment (chlorotrimethylsilane/polyadenylic acid or SiO2 coatings), the device demonstrates amplification as efficient as that in the conventional thermal cycler at optimized MgCl2 concentration. The amplified DNA has concentration higher than 27 ng/microL, which is sufficient for subsequent on-chip analyses and detection. Experimental results reveal the importance of inclusion of BSA for an efficient amplification in the SiO2-passivated device and the excellent reusability of the device with a simple cleaning step.

DNA, Plant↗