The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases

Background: Large molecular sequence databases are fundamental resources for modern\ud bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often\ud advantageous to maintain smaller sequence databases. However, this is usually not an easy task for\ud the average bench scientist.\ud \ud Results: We present the Personal Sequence Database (PSD), a suite of tools to create and\ud maintain small- to medium-sized web-accessible sequence databases. All interactions with PSD\ud tools occur via the internet with a web browser. Users may define sequence groups within their\ud database that can be maintained privately or published to the web for public use. A sequence group\ud can be downloaded, browsed, searched by keyword or searched for sequence similarities using\ud BLAST. Publishing a sequence group extends these capabilities to colleagues and collaborators. In\ud addition to being able to manage their own sequence databases, users can enroll sequences in\ud BLASTAgent, a BLAST hit tracking system, to monitor NCBI databases for new entries displaying\ud a specified level of nucleotide or amino acid similarity.\ud \ud Conclusion: The PSD offers a valuable set of resources unavailable elsewhere. In addition to\ud managing sequence data and BLAST search results, it facilitates data sharing with colleagues,\ud collaborators and public users. The PSD is hosted by the authors and is available at http://\ud bioinfo.cgrb.oregonstate.edu/psd/

CSF omeprazole concentration and albumin quotient following high dose intravenous omeprazole in dogs.

peer reviewedClinical signs of syringomyelia and hydrocephalus occur secondary to cerebrospinal fluid (CSF) accumulation within the central nervous system. Omeprazole is recommended to treat these conditions despite little evidence of its capacity to decrease CSF production in the dog. Studies into new treatments are hampered by difficulties in measuring CSF production. The albumin quotient (QAlb), the ratio between CSF and serum albumin concentrations, may reflect CSF production and any decrease in CSF production should be associated with an increase in QAlb. The primary objective of this study was to determine CSF omeprazole concentration after administration of a high intravenous dose of omeprazole and to evaluate its impact on QAlb in the dog. The second aim was to validate QAlb as a surrogate marker of CSF production. Eighteen dogs were included in this prospective crossover placebo-controlled study. Each dog received omeprazole (10 mg/kg), acetazolamide (50 mg/kg) combined with furosemide (1 mg/kg) and saline. Blood and CSF samples were obtained on day 0 and then every 7 days, one hour after drug administration. Omeprazole concentrations (2.0 ± 0.4 μmol/L) reached in CSF after high dose omeprazole were lower than the concentrations previously described as decreasing CSF production in dogs. There was no significant increase in QAlb following administration of acetazolamide/furosemide, prohibiting validation of QAlb as a surrogate marker for CSF production. Several dogs presented transient mild side effects after injection of acetazolamide/furosemide. High dose omeprazole was well tolerated in all dogs

Effects of round bale feeding sites on soil fecal bacteria and nutrient concentrations

An experiment was conducted over seven months (January to July 2003) to evaluate fecal bacteria and nutrient concentrations in soil surrounding round bale feeders at winter feeding sites. Six-inch soil samples were taken each month from a total of ten feeding sites, at distances of 10, 40, 70, and 100 feet from each feeder. Soil samples were taken before (January) livestock access to the sites, during (February, March, and April) the feeding period, and after (May, June, and July) cattle had been removed from the sites. Results indicate that fecal bacteria concentrations increased over the duration of feeding period and were greatest at close proximity to round bale feeders. The data suggest that environmental contamination due to fecal bacteria in the soil can occur up to 100 feet from the feeding site. For soil nutrients, the greatest increase generally occurred at 10 feet from the feeders, with few differences thereafter