Non-radioactive detection of K-ras mutations by nested allele specific PCR and oligonucleotide hybridization

PURPOSE: The aim of the study was to evaluate prospectively urinary alpha 1-microglobulin as a marker of proximal tubular damage following acute pyelonephritis and outflow disease of the upper urinary tract in a urological population with minimal exclusion criteria. We also measured the urinary gamma-glutamyltransferase activity, urinary albumin, urinary and serum creatinine, serum IgA and serum alpha 1-microglobulin. PATIENTS AND METHODS: We studied 483 urological patients (age: 1 to 92 years, 297 men, 186 women) excluding patients receiving nephrotoxic drugs, or suffering from type 1 diabetes or renal diseases. There were 141 patients with urinary tract infection but no fever, 36 patients with high fever of non-renal origin, 51 patients with acute pyelonephritis and 156 patients with outflow disease of the upper tract, and 99 patients were included in the reference population. RESULTS: For acute pyelonephritis, vesico-ureteral reflux, and ureteral obstruction, urinary alpha 1-microglobulin had a sensitivity of 94%, 90% and 63% respectively and a specificity of 67%, 77% and 76%. The area under the curve of the receiver operator characteristic curve was significantly (p < 0.001) higher for urinary alpha 1-microglobulin than for albumin or gamma-glutamyltransferase activity. Unexpected positive results were found in acute prostatitis. The urinary alpha 1-microglobulin was the only parameter which differentiated between acute prostatitis and pyelonephritis (p < 0.001). Creatinine clearance or age had little and gender had no influence on the urinary excretion of alpha 1-microglobulin. Urine production rate significantly increases the urinary alpha 1-microglobulin/creatinine ratio. CONCLUSION: Our results suggest that the urinary alpha 1-microglobulin/creatinine ratio is a diagnostically useful marker of tubular damage in acute pyelonephritis and vesico-ureteral reflux in the urological population. Following renal colic and chronic ureteral obstruction, a significant increase in urinary alpha 1-microglobulin excretion was observed.     

Detection of Dekkera-Brettanomyces strains in sherry by a nested PCR method

Brettanomyces sp. and its ascosporogenous sexual state, Dekkera sp., have been well documented as spoilage microorganisms, usually associated with barrel-aged red wines. In this report, we describe the genetic characterization, on the basis of DNA content per cell, electrophoretic karyotyping, and mitochondrial DNA restriction patterns, of a Dekkera yeast strain isolated from sherries and of a number of other Brettanomyces and Dekkera strains. By using a genomic DNA fragment of the isolated Dekkera strain, we developed a two-step PCR method which directs the specific amplification of target DNA from this strain and from other Brettanomyces-Dekkera strains. The method efficiently amplified the target DNA from intact cells, obviating DNA isolation, and yielded a detection limit of fewer than 10 yeast cells in contaminated samples of sherry.     

Primary, pure, large-cell neuroendocrine carcinoma of the urinary bladder

We report what to our knowledge is the first case in the English-language literature of a primary, pure, undifferentiated large-cell neuroendocrine carcinoma of the urinary bladder. To date, only one case of a large-cell neuroendocrine carcinoma was reported, and it was associated with an adenocarcinoma most likely of urachal origin. On the other hand, slightly more than 100 cases of undifferentiated small-cell carcinoma of the urinary bladder were reported, approximately one-half of which were associated with poorly differentiated transitional-cell carcinoma of the conventional type. The patient in our case was a 73-year-old man with a history of prostatic cancer treated with radiation therapy. He presented with hematuria, leading to the discovery of a solitary tumor on the dorsal wall of the urinary bladder. A diagnosis of large-cell neuroendocrine carcinoma was made, supported by immunohistochemical reactivity for chromogranin, neuron-specific enolase, and synaptophysin; a variety of other hormonal markers of neuroendocrine tumors were negative. The radical cystoprostatectomy and bilateral pelvic lymphadenectomy specimen showed a transmurally invasive tumor, without regional lymph node metastases. The patient died 2 months after surgery, and the autopsy revealed disseminated metastases histologically identical to the urinary bladder neoplasm. Awareness of the occurrence of large-cell neuroendocrine carcinoma of the urinary bladder seems to be important because of the possible aggressive outcome associated with this tumor and because of differential diagnostic considerations, which include malignant lymphoma and metastasis from another primary, especially in tumors occurring in a pure form.     

Rapid and specific detection of Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans by PCR

Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans are two of the most important bacteria in heap bioleaching processes of copper sulphide at common operating temperatures (18–24 °C). In this paper, both microorganisms were detected in solutions and ores coming from processes in 2 days, using specific amplification of 16S rDNA sequences by PCR. The technique was first validated using template DNA from pure cultures of the microorganisms. Then it was applied to samples of solutions and ores from bioleaching processes. Results were confirmed using tRFLP (terminal Restriction Fragment Length Polymorphism) with universal primers and by identification of isolated bacteria by means of culture. This methodology is more rapid and specific than the identification by tRFLP or by culture, which require from 1 to three weeks to positively detect the bacteria. The detection limit of this technique is 10⁵ cells per ml.     

Primary mucinous carcinoma of the skin. Report of case

The authors report a case of a primary mucinous carcinoma of the skin. This is a rare adnexial tumor arising from the eccrine secretory coils. The histologic characteristic finding of this lesion is the heap of abundant mucinous material (sialomucin) in the dermis in which rare epithelial islands are free-floating. In this study we also value the importance of a correct diagnosis for an appropriate therapy.     

Undifferentiated carcinoma of the liver with neuroendocrine features: a case report

The authors present an account on their first experience with treatment of central serous chorioretinopathy (CSCHR) by beta-blocking agents. In 21 patients with CSCHR Trimepranol (metipranololum) a beta non-selective blocker, 2 x 10 mg/day for two to three months was used. In 30 patients with CSCHR Vasocardin (Metoprololi tartas) was used i.e. a beta-1 selective blocking agent, 2 x 50 mg/day for two to three months. In all patients remission of the disease occurred, on average 4.5 to 4.8 weeks after the onset of treatment. During treatment of CSCHR by beta-blocking agents no significant difference was found in the action of beta selective and non-selective blockers regardless of the duration of the disease before onset of treatment and the number of relapses.     

Application of nested PCR and mass spectrometry for DNA-based virus detection: HBV-DNA detected in the majority of isolated anti-HBc positive sera

DNA preparations from three different groups of serum samples were examined for HBV-DNA via a nested polymerase chain reaction assay (lower detection limit: 10 viral genomes in 100 microliters serum): Group I consisted of 11 uninfected control sera, group II consisted of sera obtained from 11 HBV infected patients and group III consisted of 21 isolated anti-HBc positive samples. The 21 samples from group III were HBV-DNA negative according to a conventional non-nested PCR assay and hybridization with a 32P-labelled probe. Using nested PCR and mass spectrometry, HBV-DNA was detected in none of group I and in all of group II samples. In 11 out of 21 (52%) of the isolated anti-HBc positive sera from group III, HBV-DNA was detected. No correlation was observed between HBV-DNA positivity and anti-HBc titers. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry provided a fast, sensitive and non-radioactive assay for the detection of PCR products without the need for gel electrophoresis or hybridization with labelled probes.     

The early detection of prostate carcinoma with prostate specific antigen: the Washington University experience

BACKGROUND: It is not yet known whether screening for the detection of early prostate carcinoma will reduce mortality rates. However, data are available to assess intermediate outcomes from screening, including the performance characteristics of the screening tests and shifts in disease stage. METHODS: Approximately 30,000 community volunteers (mean age 60 years; <5% nonwhite) were enrolled in 1 of 3 screening studies. Volunteers were screened with PSA or PSA in combination with digital rectal examination at 6-month intervals, and prostatic biopsy was recommended for those with results suspicious for cancer. Based on a first-time screen, the current study reports screening test results, the proportion of men recommended to undergo biopsy, the proportion who actually underwent biopsy, and the carcinoma detection rates for each study, stratified by initial PSA level. The authors also report the pathologic features of screen-detected carcinomas for a subset of men who underwent radical prostatectomy and for whom complete embedding and microscopic examination of the surgical specimen was performed. RESULTS: Approximately 10% of the volunteers had PSA levels >4.0 ng/mL and 3-10% had digital rectal examination results suspicious for cancer. Overall, 9-20% of volunteers were recommended to undergo biopsy and 8-13% actually underwent the procedure. The positive predictive value for carcinoma detection ranged from 25-33% across studies. In the subset of men for whom surgical specimens were completely embedded, the majority of tumors detected had the clinicopathologic features of significant carcinoma (<10% possibly harmless). CONCLUSIONS: The intermediate outcomes for screening with PSA and/or PSA in combination with digital rectal examination are encouraging. In community volunteers these screening tests demonstrated reasonable positive predictive value and detected carcinomas at an earlier stage. The majority of screen-detected tumors had the pathologic characteristics of medically significant carcinoma.     

PCR amplification of the fimA gene sequence of Salmonella typhimurium, a specific method for detection of Salmonella spp

The goal of this study was to evaluate the suitability of the fimA gene amplification by PCR as a specific method for detection of Salmonella strains. Salmonella typhimurium and other pathogenic members of the family Enterobacteriaceae produce morphologically and antigenically related, thin, aggregative, type 1 fimbriae. A single gene, fimA, encodes the major fimbrial unit. In order to obtain higher specificity, we have selected a series of primers internal to the fimA gene sequence and have developed a PCR method for detecting Salmonella strains. A collection of 376 strains of Salmonella comprising over 80 serovars, isolated from animals and humans in Canada, have been used to evaluate this PCR method. Forty non-Salmonella strains were also tested by the same procedure. Cultures were screened by inoculating a single colony of bacteria directly into a PCR mixture containing a pair of primers specific for the fimA gene. The specific PCR product is an 85-bp fragment which was visualized by polyacrylamide gel electrophoresis and ethidium bromide staining. All Salmonella strains gave positive results by the PCR. Feed and milk samples contaminated by Salmonella strains were also detected by this procedure. The detection of all Salmonella strains tested and the failure to amplify the fragment from non-Salmonella strains confirm that the fimA gene contains sequences unique to Salmonella strains and demonstrate that this gene is a suitable PCR target for detection of Salmonella strains in food samples.     

Identification of H. pylori in saliva by a nested PCR assay derived from a newly cloned DNA probe

A novel probe was developed from genomic DNA of Helicobacter pylori ATCC type strain 43629. It hybridized with all 73 H. pylori clinical isolates tested but not with any of 183 non-H. pylori DNAs in dot blot hybridization. Typing tests revealed 41 different HaeIII-digestion patterns from 57 H. pylori strains tested. Based on the sequence of the probe, a nested PCR was developed that detected as little as 2 fg of H. pylori DNA or approximately equivalent to one cell. No PCR products were amplified from any of 21 non-H. pylori strains tested. Using this nested PCR, H. pylori DNA was detected in 33 of 45 (73%) saliva samples collected from patients with gastric H. pylori infection. These data suggest that the probe is useful for typing H. pylori and that the nested PCR is a valuable tool for detecting H. pylori DNA in saliva.     

Identification of putative sequence specific PCR primers for detection of the toxigenic fungal species Stachybotrys chartarum

The nucleotide sequence of a c 936 bp segment of the nuclear rRNA gene operon was determined for the toxigenic fungal species Stachybotrys chartarum and for other species of Stachybotrys and the related genus Memnoniella. This information was used to infer the phylogenetic relationships of these organisms and to search for sequence specific polymerase chain reaction (PCR) primers for S. chartarum in the internal transcribed spacer (ITS) regions. Searches for candidate primers were performed both by computer using the commercially available Oligo(R) v5.0 primer analysis software package and by manual inspection of the aligned sequences. Primers identified in both types of searches were evaluated for their specificities using a priming efficiency analysis algorithm available in the Oligo(R) 5.0 software. The automated computer searches were unsuccessful in finding S. chartarum-specific primers but did identify a group-specific reverse primer (designated as StacR4) for a phylogenetically related cluster of species that included S. chartarum. Manual searches led to the identification of a reverse primer (designated as StacR3) that was predicted to be specific for only S. chartarum and one other species of Stachybotrys. Experimental PCR analyses using these primers in conjunction with a universal forward primer indicated that the computer-generated amplification efficiency predictions were correct in most instances. A notable exception was the finding that StacR3 was specific only for S. chartarum. The relative merits of different PCR strategies for the detection of S. chartarum employing either one or both of the primers identified in this study are discussed.     

Primary linitis plastica carcinoma of the colon: a case report

Primary linitis plastica carcinoma of the colon is rare. Most lesions are located on the left side of the colon and these tumors often involve the lymph nodes, peritoneum, and ovaries. We report a case of primary linitis plastica of the sigmoid colon in a 32-year-old Chinese woman who presented with a 7-month history of constipation and associated abdominal pain and tenesmus. Colonoscopy and barium-enema studies showed a stricture at the sigmoid colon. The patient underwent radical surgical resection and received adjuvant radiation therapy and chemotherapy. She died 12 months after the initial diagnosis. The poor prognosis seen with this tumor is due largely to a delay in diagnosis. With increasing familiarity with this tumor, it is hoped that earlier diagnosis and curative surgery will be possible, leading to improvement in survival.     

Multiplex PCR for TCR delta rearrangements: a rapid and specific approach for the detection and identification of immature and mature rearrangements in ALL

The preferential occurrence of immature T-cell receptor (TCR) delta rearrangements (i.e. incomplete Ddelta2-Ddelta3 and Vdelta2-Ddelta3) in B-cell precursor acute lymphoblastic leukaemia (BCP ALL) and of predominantly mature rearrangements (incomplete Ddelta2-Jdelta1, complete Vdelta1, Vdelta2, Vdelta3 to Jdelta1) in T-lineage ALL prompted us to establish two separate multiplex PCR systems for the identification of clonal TCRdelta rearrangements. PCR products of the expected size for the specific rearrangements were detectable from a dilution of 100-1000 clonal cells in 150000 polyclonal cells. Both multiplex PCR systems were used to analyse samples from 86 childhood BCPALLs and 30 T-lineage ALLs. The results of the multiplex PCRs were controlled by standard PCR analyses for the individual rearrangements and Southern blots, which were identical. Only immature TCRdelta rearrangements were detected in BCP ALL (59%), whereas no rearrangement was found in the remaining BCP leukaemias, thus confirming the exclusive presence of immature TCRdelta rearrangements in B-lineage cells. 50% of the T-lineage ALLs contained mature rearrangements, but no immature rearrangements were found. These two multiplex PCR techniques appear to be reliable and fast aids in the analysis of clonal TCRdelta rearrangements in ALL.     

Primary mucoepidermoid carcinoma of the thyroid: diagnosis by fine-needle aspiration biopsy

Fine-needle aspiration biopsy (FNAB) has been recognized as a safe and reliable procedure in the evaluation of thyroid nodules. We herein report a case of a low-grade mucoepidermoid carcinoma of the thyroid that was diagnosed with this technique. Examination of an intra-operative FNAB showed cohesive clusters of polygonal squamoid cells with distinct cellular borders, uniform round nuclei, distinct nucleoli, and homogeneous amphophilic to cyanophilic cytoplasm. Focal keratin "pearl" formation was apparent, along with extracellular, lightly basophilic mucin deposits mantled by squamoid cells. These cytologic features are characteristic of low-grade mucoepidermoid carcinoma, as seen in other anatomic sites. This impression was confirmed by examination of paraffin sections. Previous reports have indicated that mucoepidermoid thyroid carcinoma is an indolent, locally recurring lesion. However, in spite of low-grade histology in our case, the neoplasm presented with distant metastases to bones, pleura, and lung.     

Rapid detection of species of the opportunistic yeast Trichosporon by PCR

Trichosporon species are opportunistic pathogens, associated with a high mortality rate in immunocompromised patients. Oligonucleotide primers were used to amplify a 170-bp fragment of small-subunit ribosomal DNA of all species in the genus Trichosporon by PCR. The primers amplify DNAs of all species in the genus Trichosporon, including six causative agents of trichosporonosis. DNAs of other medically important yeasts, such as Candida albicans and Cryptococcus neoformans, are not amplified by this detection system.     

Fine-needle sampling of a case of carcinoma of the breast with neuroendocrine differentiation

Biochemical and pharmacological characterization of small synaptic vesicle (SSV) membrane proteins and genetic studies of yeast secretion mutants led to the identification of an exocytotic fusion complex. The S?llner-Rothman SNARE hypothesis has led to remarkable progresses in the understanding of the molecular mechanisms of neurotransmitter release, endocrine and exocrine cell secretion.