Rapid quantification of drug resistance gene expression in Candida albicans by reverse transcriptase LightCycler PCR and fluorescent probe hybridization.

We developed a rapid, sensitive, and reproducible assay to quantify Candida albicans ACT1, CDR1, CDR2, ERG11, and MDR1 mRNA using a two-step reverse transcription and LightCycler real-time PCR (RT-LightCycler PCR) method with sequence-specific hybridization probes. We compared RT-LightCycler PCR with Northern hybridization for quantitative analysis of gene expression in isolates with various fluconazole susceptibilities. Specificity of each LightCycler PCR was verified by LightCycler melting curve analysis and agarose gel electrophoresis of amplified products. Correlation of quantification results between RT-LightCycler PCR and Northern hybridization yielded correlation coefficients of > or = 0.91 for all genes except MDR1 (0.74). In this case, reduced correlation was due to the inability of Northern hybridization to accurately quantify the high MDR1 expression in a susceptible dose-dependent isolate which was shown by RT-LightCycler PCR to overexpress MDR1 >200-fold relative to the other isolates tested. In four isolates, low levels of CDR2 mRNA were detected by RT-LightCycler PCR but were undetectable by Northern hybridization. mRNA quantification by RT-LightCycler PCR correlates with Northern hybridization and offers additional advantages, including increased sensitivity and speed of analysis, along with lower RNA concentration requirements and an increased dynamic range of signal detection.

Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment.

BACKGROUND: To cancel experimental variations, microarray data must be normalized prior to analysis. Where an appropriate model for statistical data distribution is available, a parametric method can normalize a group of data sets that have common distributions. Although such models have been proposed for microarray data, they have not always fit the distribution of real data and thus have been inappropriate for normalization. Consequently, microarray data in most cases have been normalized with non-parametric methods that adjust data in a pair-wise manner. However, data analysis and the integration of resultant knowledge among experiments have been difficult, since such normalization concepts lack a universal standard. RESULTS: A three-parameter lognormal distribution model was tested on over 300 sets of microarray data. The model treats the hybridization background, which is difficult to identify from images of hybridization, as one of the parameters. A rigorous coincidence of the model to data sets was found, proving the model's appropriateness for microarray data. In fact, a closer fitting to Northern analysis was obtained. The model showed inconsistency only at very strong or weak data intensities. Measurement of z-scores as well as calculated ratios was reproducible only among data in the model-consistent intensity range; also, the ratios were independent of signal intensity at the corresponding range. CONCLUSION: The model could provide a universal standard for data, simplifying data analysis and knowledge integration. It was deduced that the ranges of inconsistency were caused by experimental errors or additive noise in the data; therefore, excluding the data corresponding to those marginal ranges will prevent misleading analytical conclusions.

Comparative analysis of gene-expression patterns in human and African great ape cultured fibroblasts.

Although much is known about genetic variation in human and African great ape (chimpanzee, bonobo, and gorilla) genomes, substantially less is known about variation in gene-expression profiles within and among these species. This information is necessary for defining transcriptional regulatory networks that contribute to complex phenotypes unique to humans or the African great apes. We took a systematic approach to this problem by investigating gene-expression profiles in well-defined cell populations from humans, bonobos, and gorillas. By comparing these profiles from 18 human and 21 African great ape primary fibroblast cell lines, we found that gene-expression patterns could predict the species, but not the age, of the fibroblast donor. Several differentially expressed genes among human and African great ape fibroblasts involved the extracellular matrix, metabolic pathways, signal transduction, stress responses, as well as inherited overgrowth and neurological disorders. These gene-expression patterns could represent molecular adaptations that influenced the development of species-specific traits in humans and the African great apes.

The role of lipogenesis in the development of uremic hyperlipidemia.

BACKGROUND: It is well documented that hypertriglyceridemia in renal failure mostly is a result of impaired plasma triglyceride (TG) removal. However, the role of TG production in its development is obscure. Therefore, our attention was given to the gene expression of lipogenic enzymes participating in TG biosynthesis. METHODS: We measured some lipogenic enzyme activities, protein abundance (Western blot analysis), and messenger RNA level (Northern blot analysis) in liver and epididymal white adipose tissue (WAT) of rats with surgically induced renal failure (two-stage subtotal nephrectomy). Simultaneously, plasma TG and very low-density lipoprotein (VLDL) concentrations in uremic animals were determined. RESULTS: An increase in plasma TG and VLDL concentrations in rats with renal failure was observed. It was associated with an increase in fatty acid synthase and adenosine triphosphate-citrate lyase (ACL) gene expression in liver and WAT. Moreover, increased activities of malic enzyme, glucose-6-phosphate dehydrogenase, and 6-phosphogluconate dehydrogenase were found. CONCLUSION: Results of the present study provide some evidence that the accumulation of TG-rich lipoproteins in renal insufficiency could be related in part to increased lipogenic enzyme gene expression and, consequently, TG overproduction.

Northern blot and in situ hybridization analyses of MARCKS mRNA expression in the cerebral cortex of the macaque monkey.

Myristoylated alanine-rich C-kinase substrate (MARCKS) is a major substrate for protein kinase C, and is involved in synaptic plasticity. Using both Northern blot and in situ hybridization techniques, we investigated whether MARCKS expression varied according to the cerebral region, including the hippocampal formation, or according to the type of neuron. Northern blot analysis showed that the MARCKS mRNA level was higher in the association areas than in the primary sensory and motor areas of the cerebral neocortex. MARCKS mRNA levels in the hippocampus and the amygdala were as high as those in the association areas. The in situ hybridization experiments confirmed the Northern blot results and showed the distribution and characteristics of MARCKS mRNA-positive neurons. In the association areas of the neocortex, prominent signals were observed in neurons in layers II-VI. In the primary areas, prominent signals were restricted to neurons in layers IV-VI. In the hippocampus, the most intense hybridization signals were observed in neurons in the granule cell layer of the dentate gyrus. The observed region-specific expression might reflect functional specialization for plasticity in individual regions of the monkey cerebral cortex.

Effect of endogenous and exogenous prostaglandin E(2) on interleukin-1 beta-induced cyclooxygenase-2 expression in human airway smooth-muscle cells.

We studied the effect of endogenous and exogenous prostaglandin E(2) (PGE(2)), a metabolite of arachidonic acid through the cyclooxygenase (COX) pathway, on interleukin (IL)-1 beta-induced COX-2 expression, using primary cultures of human bronchial smooth-muscle cells (HBSMC). Treatment with exogenous PGE(2) resulted in enhanced expression of IL-1 beta-induced COX-2 protein and messenger RNA (mRNA) as compared with the effect of the cytokine per se. Inhibition of PGE(2) production with a nonselective COX inhibitor (flurbiprofen, 10 microM) resulted in a significant reduction in IL-1 beta- induced COX-2 expression, supporting a role of endogenous COX metabolites in the modulation of COX-2 expression. None of the experimental conditions used in the study affected the expression of constitutive cyclooxygenase (COX-1). Treatment with cycloheximide to inhibit translation, and with dexamethasone or actinomycin D to inhibit transcription, linked the effect of PGE(2) to the transcriptional level of COX-2 mRNA rather than to a potential effect on protein and/or mRNA stabilization. PGE(2) increased adenylate cyclase activity in a concentration dependent manner, and forskolin, a direct activator of adenylate cyclase, caused a marked increase in IL-1 beta-dependent COX-2, suggesting the existence of a causal relationship between the two events. The same results were observed with salbutamol, a bronchodilator that acts by increasing cyclic adenosine monophosphate. The effect of PGE(2) on COX-2 expression may contribute to the hypothesized antiinflammatory role of PGE(2) in human airways, providing a self-amplifying loop leading to increased biosynthesis of PGE(2) during an inflammatory event.

Chronic phosphorus supplementation decreases the expression of renal PTH/PTHrP receptor mRNA in rats.

Dietary intake of high levels of phosphorus is known to increase serum levels of parathyroid hormone (PTH); however, how this increased serum PTH affects the action of PTH in major target tissues, particularly by kidney, remains unknown. In the present study, we therefore undertook to clarify this point in intact animals fed a high-P diet by examining various parameters of PTH action. Twelve weanling Wistar male rats were assigned randomly to two groups: a control group with dietary Ca:P = 1:1 and a high-P group (Ca:P = 1:3) fed the standard AIN-76 diet supplemented with P (0.5 and 1.5 g/100 g of diet). After 3 weeks of feeding, in the high-P diet group, we observed that serum Ca was lowered, without a difference in serum P, when compared to the control group. Excretion of urinary cAMP, an index of renal PTH action, was also decreased, with higher excretion of urinary P in those rats fed the high-P diet. In agreement with the decreased cAMP excretion, a clear reduction in PTH/PTH-related protein (PTHrP) receptor gene expression as estimated by Northern blotting was observed in the kidney, despite increased levels of serum PTH. Thus, the present study indicated that a high-P diet reduces PTH action in the kidney, though the serum PTH is increased.

Comparison of the stress response after laparoscopic and open cholecystectomy.

BACKGROUND: We designed a prospective controlled animal study to compare the stress response induced after laparoscopic and open cholecystectomy. METHODS: Twelve female pigs (20-25 kg body weight) were anesthetized with ketamine, pentobarbital, and fentanyl. The animals were randomized into the following four groups: control (C), pneumoperitoneum with CO(2) at 14-15 mmHg (P), laparoscopic cholecystectomy (LC), and open cholecystectomy (OC). The average duration of the procedure in each group was 35 min. RESULTS: Central venous pressure, mean arterial pressure, pulmonary capillary wedge pressure, and cardiac output were monitored. Measurements were recorded when animals were anesthetized (baseline), immediately before and after surgery, and thereafter every 30 min for a maximum of 3 h. White blood cell count (WBC) was determined from blood samples taken before and after 3 h of surgery. Ultrasound-guided liver biopsies were done preoperatively and after 3 h of surgery. Total RNA was isolated from the liver biopsy specimens. Steady-state mRNA levels of beta-fibrinogen (beta-fib), alpha 1-chymotrypsin inhibitor (alpha1-CTI), metallothionein (MT), heat shock protein 70 (Hsp70), and polyubiquitin (Ub) were detected by Northern blot/hybridization. There were no statistical differences in the hemodynamic parameters among the groups. The number of circulating neutrophils and monocytes decreased only after LC. Expression of Hsp70 was not induced after any surgical procedure, and the mRNA levels of Ub did not change after surgery. The expression of alpha1-CTI and beta-fib (acute phase genes) were similarly increased after LC and OC. Steady-state mRNA levels of MT were slightly increased after P and LC but not after OC. CONCLUSION: These data indicate that there are no significant differences between LC and OC in terms of induction of the stress response.

EGF and TGF-beta1 gene expression in chronically rejecting small bowel transplants.

Long-term survival of small bowel transplants is hampered by chronic rejection. Epidermal growth factor (EGF) and transforming growth factor beta (TGF-beta) have opposing, regulatory roles in normal intestinal physiology and may be involved in the pathogenesis of chronic intestinal rejection. Our aim was to investigate the expression of EGF and TGF-beta1 in chronically rejecting small bowel transplants. Orthotopic small bowel transplantation was performed in the allogeneic DA-to-AS rat combination; Cyclosporin was administered temporarily to prevent acute rejection. Controls were DA isografts and normal DA rats. PreproEGF and TGF-beta1 gene expression was evaluated by northern blot analysis of the ileum RNA and standardized against glyceraldehyde-3-phosphate-dehydrogenase expression. Allografts demonstrated functional impairment and histological features of chronic rejection, whereas isografts appeared normal. Allografts demonstrated a significant reduction of EGF mRNA when compared to DA isografts. No significant changes were detected in TGF-beta1 expression in either allogeneic or syngeneic grafts. In conclusion, this study demonstrates reduced preproEGF and preserved TGF-beta1 gene expression in chronically rejecting small bowel transplants.

Expression of TGF-beta isoforms and their receptors during mineralized nodule formation by rat periodontal ligament cells in vitro.

Transforming growth factor-betas (TGF-beta s) and bone morphogenetic proteins (BMPs), members of a TGF-beta superfamily, are known to play an important role in osteogenic cell differentiation and consequently bone formation. We have reported previously that periodontal ligament (PDL) cells differentiate and form mineralized nodules when cultured in the presence of dexamethasone (Dex), beta-glycerophosphate (GP) and ascorbic acid (AA). To understand the roles of TGF-beta isoforms (TGF-beta 1, 2 and 3) and TGF-beta type I receptors (activin receptor-like kinase (ALK)-2, -3, -5 and -6) in PDL cell differentiation, their expression was investigated using Northern blot analysis. Rat PDL cells, derived from coagulum in the tooth socket, were cultured in the presence of Dex (5 microM), GP (10 mM) and AA (50 micrograms/ml) for up to 21 d. Total RNA was isolated from PDL cells after 0, 7, 14 and 21 d and used for northern blot analysis of mRNAs for matrix proteins, TGF-beta isoforms and their receptors using 32P-labeled cDNAs as probes. Four stages showing distinct morphological characteristics and matrix expression during development of mineralized nodules were identified. Type I collagen (Col I) and SPARC (secreted protein, acidic and rich in cysteine) mRNAs were expressed at the confluent stage, but decreased during the mineralization stage. Osteopontin (OPN) and alkaline phosphatase (ALP) transcripts were initially observed at multilayer stage, while bone sialoprotein (BSP) and osteocalcin (OC) at the nodule stage and all 4 were expressed thereafter. TGF-beta 1 mRNA expression increased with the progression of PDL cell differentiation, while a relatively high level of TGF-beta 3 transcript decreased slightly during their differentiation. TGF-beta 2 mRNA was not expressed. The expression of TGF beta-RI mRNA decreased, whereas that of TGF beta-RIII increased dramatically with PDL cell differentiation. TGF beta-RII gene activities remained high throughout all stages. ALK-2, ALK-3 and ALK-6 mRNA expression increased with the progression of PDL cell differentiation, suggesting that these receptors may play important roles in Dex-induced PDL cell differentiation and mineralized nodule formation.

Sensitive northern blot hybridization using digoxigenin RNA probes for the mRNA detection of two glucose transporter isoforms.

Diseases involving glucose metabolism disorders are more and more prevalent. Therefore the question of glucose transporter gene expression is being addressed in experimental and clinical studies. Radioactive probes are generally used to assess glucose transporter mRNA levels, but these probes are short-lived, costly and harmful to the environment. Alternative methods that do not present these disadvantages, for example digoxigenin (DIG) labelled probes, might prove to be very interesting for the study of glucose transporter mRNA. The aim of the present work was to compare DIG-labelled cRNA probes to 32P-labelled cRNA probes in order to see whether or not the non-radioactive method can be used to assess glucose transporter gene expression. This work shows that DIG-labelled glucose transporter (GLUT1 and GLUT4) cRNAs are suitable probes for the assessment of these gene expressions. We have found that the DIG system offers a much higher sensitivity than the 32P system for both GLUT1 and GLUT4 mRNA detection. This represents a decisive advantage in human studies where tissue quantity is a limiting factor. In addition, stability, safety, time saving and cost reduction are other considerations that make DIG-labelled GLUT1 and GLUT4 cRNAs very attractive.

Abnormal expression of plasminogen activators in aortic aneurysmal and occlusive disease.

PURPOSE AND METHODS: Aortic aneurysms are characterized by the destruction of the extracellular matrix of the media, whereas occlusive disease involves excess matrix accumulation within the intima. Plasmin degrades extracellular matrix directly and indirectly by activation of latent metalloenzymes. To determine the expression of tissue- and urokinase-type plasminogen activators, immunoassay, fibrin autography, Northern analysis, and immunohistochemistry were performed on specimens of aneurysmal (n = 12), occlusive (n = 8), and healthy (n = 6) aorta. RESULTS: Immunoassay of tissue-type plasminogen activator revealed 8.7 +/- 0.9 ng tissue-type plasminogen activator/mg extracted protein in aneurysmal aorta, 5.7 +/- 0.3 ng/mg in normal aorta, and 2.5 +/- 0.3 ng/mg in occlusive aorta (p < 0.05 for comparisons between all groups). No urokinase-type plasminogen activator antigen was detected by urokinase-type plasminogen activator immunoassay. Fibrin autography exhibited lytic activity at 64 kDa and 54 kDa attributable to tissue-type plasminogen activator and urokinase-type plasminogen activator. The vast majority of fibrinolysis was secondary to free tissue-type plasminogen activator and was greatest in aneurysmal disease and least in occlusive disease. There was only a small amount of lysis secondary to urokinase-type plasminogen activator. Expression of tissue-type plasminogen activator and urokinase-type plasminogen activators mRNA was comparable in aneurysmal and occlusive aortas. In contrast to occlusive disease, aneurysms had an inflammatory cell infiltrate characterized by the expression of urokinase-type plasminogen activator by specific mononuclear cells. Tissue-type plasminogen activator expression was evident in the intima of normal and diseased aorta and in the media of diseased aorta. CONCLUSION: Differential expression of plasminogen activators within the arterial wall may contribute to the unique pathogenesis of aneurysmal and occlusive aortic disease.