Molecular sequence accuracy and the analysis of protein coding regions.

Molecular sequences, like all experimental data, have finite error rates. The impact of errors on the information content of molecular sequence data is dependent on the analytic paradigm used to interpret the data. We studied the impact of nucleic acid sequence errors on the ability to align predicted amino acid sequences with the sequences of related proteins. We found that with a simultaneous translation and alignment algorithm, identification of sequence homologies is resilient to the introduction of random errors. Proteins with greater than 30% sequence identity can be reliably recognized even in the presence of 1% frameshifting (insertion or deletion) error rates and 5% base substitution rates. Incorporation of prior knowledge about the location and characteristics of errors improves tolerance to error of amino acid sequence alignments. Similarly, inclusion of prior knowledge of biased codon utilization by yeast (Saccharomyces cerevisiae) allows reliable detection of correct reading frames in yeast sequences even in the presence of 5% substitution and 1% frameshift errors.     

Expression of human cytochrome P450 1A1 in DNA repair deficient and proficient human fibroblasts stably transformed with an inducible expression vector

Cytochromes P450 catalyze the bioactivation of many carcinogens.In particular, cytochrome P450 1A1 (CYP1A1) catalyzes the conversionof polycyclic aromatic hydrocarbons, such as benzo[a]pyrene,into potent mutagenic agents. Human skin fibroblasts, both DNArepair deficient (xeroderma pigmentosum group A: XPA) and DNArepair normal have been co-transformed with a chimeric geneconstruct containing human CYP1A1 coding sequences controlledby the cadmium (Cd) ion inducible mouse metallothionein-I promoterand pRSV-NEO, a dominant selectable marker for G418 resistance.Individual G418 resistant colonies were cloned and analyzedfor Cd inducible CYP1A1 activity. Six clones of DNA repair deficientcells and five clones of DNA repair proficient cells have beenisolated which express Cd inducible CYP1A1. Benzo[a]pyrene-Aww-7,8-diol (BPD) is cytotoxic in Cd induced CYP1A1 expressing cells.The cytotoxkity can be inhibited by 10 µM     

Pheochromocytoma and the normal adrenal medulla: improved visualization with I-123 MIBG scintigraphy

The radiopharmaceutical iodine 131 metaiodobenzylguanidine (I-131 MIBG) has been shown to locate pheochromocytomas scintigraphically with a false-negative rate of approximately 13%. To improve image quality and reduce the false-negative rate, I-123 was examined as a radioactive label for MIBG, as it has many advantages over I-131, including superior dosimetry and better detection efficiency. Diagnostic doses of 0.5 mCi (18.5 MBq) I-131 MIBG and 10.0 mCi (370.0 MBq) I-123 MIBG with nearly equivalent radiation dosimetries were compared in 18 patients with known or suspected pheochromocytomas. Images of superior quality were obtained with I-123 MIBG in 18 of 18 patients, and in eight cases lesions not visualized on I-131 MIBG scintigraphy were portrayed. A further advantage of I-123 MIBG is that it permits single photon emission computed tomography (SPECT). This was performed in six cases and provided additional information in three cases. The adrenal medullae were definitely visualized using I-123 scintigraphy in eight of 14 patients still possessing adrenal glands, whereas I-131 MIBG images portrayed the adrenal medulla in only one of 14 cases. Five remaining patients had multiple abdominal tumor deposits that were difficult to differentiate from normal adrenal medullae.     

Pitfalls in MR imaging of the knee

Discrepancies between the findings of magnetic resonance (MR) imaging and those of arthroscopy were reviewed retrospectively in 52 knee examinations. Some of the discrepancies between MR imaging and arthroscopy were caused by errors in interpretation of MR images due to normal structures that mimicked meniscal tears. The transverse ligament and the lateral inferior genicular artery can produce the appearance of tears in the anterior horns of the medial and lateral menisci, respectively. The popliteus tendon may be mistaken for a tear in the posterior horn of the lateral meniscus. The normal concavity at the outer edge of the meniscus can create a volume-averaging artifact, which mimics a horizontal tear in the meniscus. Tears of the meniscus and separations of the meniscus from the joint capsule were not seen or were underestimated when the tears were oriented parallel to the plane of the image. An awareness of these pitfalls may improve the accuracy of the interpretation of MR images of the knee.     

Nitrate, coliforms, and Cryptosporidium spp. as indicators of stream water quality in western Pennsylvania

Surface-water treatment plants provide water to approximately 67 percent of the residents of Pennsylvania. Industrial activities and agricultural practices significantly contribute to the chemical and microbiological load of surface-water systems. For the study reported here, surface water from three sites along Two Lick Creek in Indiana County in Pennsylvania were sampled and analyzed for nitrate, iron, total and fecal coliforms, and Cryptosporidium oocysts. Mean nitrate concentrations were 2.88, 3.15, and 3.83 mg/L for Site 1, Site 2, and Site 3, respectively, while mean total-coliform counts ranged from 6.89 x 10(2) to 22.40 x 10(2) CFUs per 100 mL, and fecal coliform counts ranged from 0.30 x 10(2) to 11.1 x 10(2) CFUs per 100 mL. Cryptosporidium oocysts ranged from a low of <46 to a high of 91 per 100 L depending on sample turbidity. The recovery rates of oocysts from spiked samples ranged from 22 percent (low-turbidity samples) to a low of 0.76 percent (high-turbidity samples). This paper discusses the impact of environmental factors on nitrate concentration, coliforms, and Cryptosporidium, as well as the health significance of these water quality indicators.