Detection of point mutations in KRAS oncogene by real-time PCR-based genotyping assay in GIT diseases.

OBJECTIVES: The determination of gene mutations is important for the diagnosis and prognosis of various gastrointestinal cancers. The aim of our study was to develop a new procedure for the analysis of KRAS gene mutation by application of the real-time PCR method. BACKGROUND: The detection process requires discriminate trace amount of mutant allele in a large excess of wild-type DNA in various samples. METHODS: The real-time PCR based technique using hybridization probes for five most frequently KRAS codon 12 mutations and WT specific peptide nucleic acid (PNA) was performed. Our multiplex detection system was tested in various DNA samples (tissue, bile, pancreatic juice) of patients with different diagnoses of gastrointestinal tract disease obtained by endoscopy and ERCP. RESULTS: We designed and optimized the real-time PCR conditions and tested various amount of PNA in PCR reaction to suppress amplification of the wild-type DNA. We determined the interassay variability of the melting temperatures and the results of mutation testing were confirmed by DNA sequencing with the 100 % accuracy. Incidence of searched mutations was 67.5 % in cohort of 40 patients; for KRASG12D it was in 44.4 %, KRASG12V in 22.2 %, KRASG12S in 14.8 %, KRASG12A in 14.8 % and KRASG12C in 3.8 %. The sensitivity of the assays is 1x10-5. CONCLUSIONS: Advantages of this technique are rapidity, accuracy and it is generally easy to perform. This method can be adapted for synchronic detection of multiple mutations and after readjustment by other type mutation of KRAS gene may serve as useful clinical tool for analyzing point mutations in various clinical samples (Tab. 3, Fig. 3, Ref. 42).

Assay design and optimization of mutant-enriched PCR based method for detection of K-ras gene mutations in pancreatic carcinoma.

The aim of our work was to develop a fast, reliable and sensitive PCR method to detect K-ras mutations in various clinical samples. There is a need for an unimpeachable method for early diagnosis and/or screening of pancreatic cancer (PC). We optimized and subsequently analyzed four methods based on mutant-enriched PCR for the sensitivity, cost and time expense. Using the selected optimal method we examined codon 12 K- ras mutations in a study population of 59 patients with upper GIT malignancies. Reliability of the genotyping was confirmed by sequencing. By using the best of our modified mutant-enriched PCR methods we achieved sensitivity of 1:1 x 10(5). Further studies are necessary to determine the optimal biological material sampling in PC.

Resistance of corynebacterial strains to infection and lysis by corynephage BFK 20.

AIMS: Defence mechanisms of the corynebacterial strains against corynephage BFK 20, which causes lysis of Brevibacterium flavum CCM 251. METHODS AND RESULTS: We tested adsorption of the phage BFK 20 to the corynebacterial cell surface. We observed strong adsorption ranging from ca 79 to 93% on the cells of B. flavum ATCC strains, but only ca 76% for B. flavum CCM 251. Minor adsorption for Brevibacterium lactofermentum BLOB (ca 13%) and no adsorption for Corynebacterium glutamicum RM3 were determined. BFK 20 infection had no significant effect on growth and viability of C. glutamicum and B. lactofermentum, but significantly influenced growth and viability of B. flavum ATCC 21127, 21128 and 21474. Cell growth stopped in short time after infection but with no lysis. Brevibacterium flavum CCM 251 cell growth was arrested too and lysis occurred. The Southern hybridization confirmed the presence of significant amount of BFK 20 DNA in samples from B. flavum CCM 251 and B. flavum ATCC strains after BFK 20 infection. Only weak hybridization signal was detected for DNA from infected cells of B. lactofermentum BLOB and no signal for C. glutamicum RM3. CONCLUSIONS: Based on the above results we suggest presence of a mechanism leading to abortive infection in B. flavum ATCC 21127, 21128 and 21474. In B. lactofermentum BLOB and C. glutamicum RM3 the adsorption barrier is more likely. SIGNIFICANCE AND IMPACT OF THE STUDY: This study increases the knowledge on defence mechanisms of corynebacteria against bacteriophages.

Small proteoglycans in human diabetic nephropathy: discrepancy between glomerular expression and protein accumulation of decorin, biglycan, lumican, and fibromodulin.

Small leucine-rich proteoglycans (SLRPs), for example, decorin, biglycan, fibromodulin, and lumican, are extracellular matrix organizers and binding partners of TGF-b. Decorin is also involved in growth control and angiogenesis. Hence, these proteoglycans are likely of importance in the pathogenesis of diabetic glomerulosclerosis. In normal kidney, SLRPs were preferentially expressed in the tubulointerstitium. Weak expression occurred in the mesangial matrix. Biglycan was expressed by glomerular endothelial cells and, together with fibromodulin, by distal tubular cells and in collecting ducts. In all stages of diabetic nephropathy, there was a marked up-regulation of the proteoglycans in tubulointerstitium and glomeruli. Decorin and lumican became expressed in tubuli. However, in glomeruli, overexpression was not mirrored by local proteoglycan accumulation except in advanced nephropathy. In severe glomerulosclerosis, increased decorin concentrations were found in plasma and urine, and urinary TGF-b/decorin complexes could be demonstrated indirectly. The failure to detect an increased glomerular proteoglycan quantity during the development of nephropathy could be explained by assuming that they are secreted into the mesangial matrix, but cleared via the vasculature or the urinary tract, in part as complexes with TGF-b. They could thereby counteract the vicious circle being characterized by increased TGF-b production and increased matrix deposition in diabetic nephropathy.

Small proteoglycans of normal adult human kidney: distinct expression patterns of decorin, biglycan, fibromodulin, and lumican.

BACKGROUND: Among the members of the small leucine-rich proteoglycan family, decorin, biglycan, and fibromodulin have been proposed to be potent modulators of transforming growth factor-beta (TGF-beta) activity, thereby playing an important role in the pathogenesis of fibrotic kidney diseases. Furthermore, decorin expression influences the expression of p21WAF1/CIP1, which has been related to kidney hypertrophy and hyperplasia. However, none of the members of this proteoglycan family have been investigated in normal adult human kidney cortex, thus making it impossible to correlate disease-mediated alterations of their expression with the normal situation in vivo. METHODS: The chondroitin/dermatan sulfate proteoglycans, decorin and biglycan, and the keratan sulfate proteoglycans, fibromodulin and lumican, were investigated in normal human adult renal cortex by immunohistochemistry on the light and electron microscopic level and by in situ hybridization. Northern blot and reverse transcription-polymerase chain reaction (RT-PCR) methods were used to get an estimate of their expression in isolated glomeruli. Decorin excretion with the urine was measured by Western blotting. RESULTS: Two bands of decorin and a single band of biglycan mRNA were identified in Northern blots of isolated glomeruli. Amplification by RT-PCR was required to detect the signals for fibromodulin and lumican. All four proteoglycans were preferentially expressed in the renal interstitium with accumulations around tubules. Weak expression was found in the mesangial matrix. Biglycan was expressed by glomerular endothelial cells and, together with fibromodulin, was synthesized and deposited in distal tubular cells and collecting ducts. Immunogold labeling indicated the presence of the proteoglycans in the glomerular basement membrane, which was interpreted as a result of glomerular filtration. Indirect evidence suggested tubular reuptake of decorin after glomerular filtration. CONCLUSION: The data indicate that the different cells of the adult human kidney are characterized by a distinct expression pattern of the four small proteoglycans. It is suggested that these proteoglycans may have distinct pathophysiological roles depending upon whether they are expressed by mesangial cells, endothelial cells, epithelial cells, or cells of the tubulointerstitium.

Construction of promoter-probe shuttle vectors for Escherichia coli and corynebacteria on the basis of promoterless alpha-amylase gene.

We constructed new promoter-probe vectors for E. coli and corynebacteria based on the promoterless alpha-amylase gene originating from Bacillus subtilis. Vectors pJUPAE1 and pJUPAE2 are suitable for isolation of transcriptionally active fragments from plasmids, phages or genomic DNA. alpha-Amylase activity can be easily visually detected on agar plates containing a chromogenic substrate, or by direct measurement of alpha-amylase activity.

Decorin, biglycan and their endocytosis receptor in rat renal cortex.

BACKGROUND: Among the small proteoglycans, biglycan and decorin have been proposed to be potent modulators of TGF-beta-mediated inflammatory kidney diseases. They were considered to become induced during glomerulonephritis and to subsequently inactivate the cytokine. METHODS: Decorin and biglycan as well as their endocytosis receptor were investigated in normal rat renal cortex, in anti-Thy-1 glomerulonephritis, in polycystic kidneys, in the remnant kidney following 5/6-nephrectomy, and in kidneys from the Milan normotensive strain by immunohistochemistry and in situ hybridization. Northern blots were used for the detection of mRNA expression for decorin and biglycan in isolated glomeruli. Functional aspects of the endocytosis of decorin and biglycan were studied in cultured mesangial cells. RESULTS: In the normal adult rat kidney decorin was expressed preferentially by Bowman's capsule and by interstitial connective tissue cells, but only in trace amounts by mesangial cells. In contrast, biglycan was found in tubular epithelial cells, in association with glomerular capillaries, podocytes and occasionally in the mesangium. In the tubulointerstitium of diseased kidneys (polycystic kidneys, 5/6-nephrectomy, kidneys from the Milan normotensive strain) there was a general up-regulation of decorin expression, while biglycan was localized only in distinct foci of fibrotic lesions. Glomerulosclerosis (5/6-nephrectomy, Milan normotensive strain) was associated with an increased staining for both decorin and biglycan within glomeruli. However, even in the anti-Thy-1 model of an acute mesangioproliferative glomerulonephritis where the greatest accumulation of decorin was found there was only a slight enhancement of decorin mRNA in isolated glomeruli. Decorin and biglycan become degraded upon receptor-mediated endocytosis. Immunohistochemical investigations indicated that the pattern of expression of the receptor protein correlated well with the immunolocalization of both decorin and biglycan. In vitro experiments with cultured mesangial cells provided direct evidence for the expression of the receptor and for the cell's capability to endocytose decorin as well as biglycan. CONCLUSIONS: Decorin and biglycan are characterized by a distinct expression pattern in the normal rat kidney, whereas the presence of their endocytosis receptor protein correlates with the expression of both proteoglycans. Decorin is almost completely absent in the normal mesangium. Both proteoglycans become up-regulated in various models of renal disease. The mesangial accumulation of decorin in the anti-Thy-1 glomerulonephritis that is observed in spite of the only slightly enhanced mRNA expression could result from decreased decorin turnover and/or increased mesangial retention.

Construction and characterization of new corynebacterial plasmids carrying the alpha-amylase gene.

Novel corynebacterial plasmids carrying alpha-amylase gene from Bacillus have been constructed. The level of alpha-amylase expression depends on the size of the vector. The highest expression levels were measured in brevibacteria harboring pA61 plasmid.

Characterization and sequence analysis of the F2 promoter from corynephage BFK20.

F2 promoter from corynephage BFK20 was isolated and characterized. It was functional in Escherichia coli and Corynebacterium glutamicum. Cloning of the F2 promoter into the pJUP05 promoter probe vector caused an increase of the neomycin phosphotransferase II specific activity. According to the Northern blot hybridization the nptII gene was expressed from the cloned F2 promoter. The apparent transcription start point in E. coli and C. glutamicum was determined. The -35 region of F2 promoter showed high similarity to that of E. coli promoter consensus sequence, but its -10 region was G+C rich and had no significant homology to that.

Characterization of bacteriophage BFK20 from Brevibacterium flavum.

Bacteriophage BFK20 was isolated from a Brevibacterium flavum strain that had become contaminated during industrial fermentation. BFK20 has a polyhedral head 50 nm wide and a non-contractile tail 200 nm long and 10 nm in diameter. The genome of this bacteriophage consists of a linear double stranded DNA molecule of 44-45 kb with cohesive ends. The capsid of phage BFK20 contains nine polypeptides with molecular masses from 22.0-108.0 kDa. BFK20 DNA was used as a donor for fragments carrying promoters and transcription-terminators.