Biomedical subjects

J Schein

Publications and source records attributed to J Schein.

At least 19 recordsLinked to original sources

PubMed2002

Resuspension of DNA sequencing reaction products in agarose increases sequence quality on an automated sequencer.

We are investigating approaches to increase DNA sequencing quality. Since a majorfactor in sequence generation is the cost of reagents and sample preparations, we have developed and optimized methods to sequence directly plasmid DNA isolated from alkaline lysis preparations. These methods remove the costly PCR and post-sequencing purification steps but can result in low sequence quality when using standard resuspension protocols on some sequencing platforms. This work outlines a simple, robust, and inexpensive resuspension protocol for DNA sequencing to correct this shortcoming. Resuspending the sequenced products in agarose before electrophoresis results in a substantial and reproducible increase in sequence quality and read length over resuspension in deionized water and has allowed us to use the aforementioned sample preparation methods to cut considerably the overall sequencing costs without sacrificing sequence quality. We demonstrate that resuspension of unpurified sequence products generated from template DNA isolated by a modified alkaline lysis technique in low concentrations of agarose yields a 384% improvement in sequence quality compared to resuspension in deionized water. Utilizing this protocol, we have produced more than 74,000 high-quality, long-read-length sequences from plasmid DNA template on the MegaBACET 1000 platform.

Cell Fractionation↗

PubMed2001

Cost of treatment for onychomycosis. Data from a 9-month observational study.

OBJECTIVES: To estimate component and total costs of treatment and to examine differences in cost and cost effectiveness between oral antifungal medication and local therapy for patients with toenail onychomycosis. DESIGN: Prospective, observational study of patients with onychomycosis who visited dermatologists and podiatrists in the US. Physicians provided data on clinical management, disease severity, nail improvement and resource utilisation. Patients completed questionnaires on resource utilisation and symptoms at base-line, 4 and 9 months. To estimate costs, reported utilisation was multiplied by unit costs expressed in 1997 US dollars ($US) and derived in 2 ways: first, using Medicare fees; and second, using standard physician fees. RESULTS: After adjustment for key demographic and clinical variables, participants receiving oral medication had higher total costs based on standard fees ($US794 vs $US575) and medication costs ($US564 vs $US109), lower procedure costs ($US0 vs $US122) and physician visit costs ($US200 vs $US330), and greater clinical effectiveness as measured by global improvement rating (86 vs 35%) and Toenail Symptom Index (94 vs 49%). For participants receiving oral medication, 90% of total costs were incurred during the first 4 months of follow-up, whereas for those receiving local therapy, costs were more evenly distributed throughout the study period. Incremental cost-effectiveness analysis showed $US304 to $US491 per additional case improved with oral medication over a 9-month timeframe. Extrapolation of these results using 2 time-points (months 4 and 9) suggested that cost equivalence would be reached 17 to 21 months following the initiation of treatment. CONCLUSIONS: During 9 months of follow-up in patients with toenail onychomycosis, the use of oral antifungal medication resulted in superior patient outcomes, but at higher total cost compared with local therapy.

Adult↗

PubMed2000

Conservation of sequence and function of the pag-3 genes from C. elegans and C. briggsae.

The Caenorhabditis briggsae homologue of the Caenorhabditis elegans pag-3 gene was cloned and sequenced. When transformed into a C. elegans pag-3 mutant, the C. briggsae pag-3 gene rescued the pag-3 reverse kinker and lethargic phenotypes. The C. elegans pag-3 gene fused to lacZ was expressed in the same pattern in C. elegans and C. briggsae. Unlike many gene homologues compared between C. elegans and C. briggsae, extensive sequence conservation was found in the non-coding regions upstream of the pag-3 exons, in several of the introns and in the downstream non-coding region. Furthermore, the splice acceptor and splice donor sites were conserved, and the size of the introns and exons was surprisingly similar. The predicted protein sequence of C. briggsae PAG-3 was 85% identical to the protein sequence of C. elegans PAG-3. Because so much of the non-coding region of pag-3 was conserved, the control of pag-3 may be quite complex, involving the binding of many trans-acting factors. These results suggest the evolutionary conservation of the pag-3 gene sequence, its expression and function.

Amino Acid Sequence↗

PubMed1999

zA map for sequence analysis of the Arabidopsis thaliana genome.

Arabidopsis thaliana has emerged as a model system for studies of plant genetics and development, and its genome has been targeted for sequencing by an international consortium (the Arabidopsis Genome Initiative; http://genome-www. stanford.edu/Arabidopsis/agi.html). To support the genome-sequencing effort, we fingerprinted more than 20,000 BACs (ref. 2) from two high-quality publicly available libraries, generating an estimated 17-fold redundant coverage of the genome, and used the fingerprints to nucleate assembly of the data by computer. Subsequent manual revision of the assemblies resulted in the incorporation of 19,661 fingerprinted BACs into 169 ordered sets of overlapping clones ('contigs'), each containing at least 3 clones. These contigs are ideal for parallel selection of BACs for large-scale sequencing and have supported the generation of more than 5.8 Mb of finished genome sequence submitted to GenBank; analysis of the sequence has confirmed the integrity of contigs constructed using this fingerprint data. Placement of contigs onto chromosomes can now be performed, and is being pursued by groups involved in both sequencing and positional cloning studies. To our knowledge, these data provide the first example of whole-genome random BAC fingerprint analysis of a eucaryote, and have provided a model essential to efforts aimed at generating similar databases of fingerprint contigs to support sequencing of other complex genomes, including that of human.

Arabidopsis↗

PubMed1999

Homologs of the Caenorhabditis elegans masculinizing gene her-1 in C. briggsae and the filarial parasite Brugia malayi.

The masculinizing gene her-1 in Caenorhabditis elegans (Ce-her-1) encodes a novel protein, HER-1A, which is required for male development. To identify conserved elements in her-1 we have cloned and characterized two homologous nematode genes: one by synteny from the closely related free-living species C. briggsae (Cb-her-1) and the other, starting with a fortuitously identified expressed sequence tag, from the distantly related parasite Brugia malayi (Bm-her-1). The overall sequence identities of the predicted gene products with Ce-HER-1A are only 57% for Cb-HER-1, which is considerably lower than has been found for most homologous briggsae genes, and 35% for Bm-HER-1. However, conserved residues are found throughout both proteins, and like Ce-HER-1A, both have putative N-terminal signal sequences. Ce-her-1 produces a larger masculinizing transcript (her-1a) and a smaller transcript of unknown function (her-1b); both are present essentially only in males. By contrast, Cb-her-1 appears to produce only one transcript, corresponding to her-1a; it is enriched in males but present also in hermaphrodites. Injection of dsRNA transcribed from Cb-her-1 into C. briggsae hermaphrodites (RNA interference) caused XO animals to develop into partially fertile hermaphrodites. Introducing a Cb-her-1 construct as a transgene under control of the C. elegans unc-54 myosin heavy chain promoter caused strong masculinization of both C. briggsae and C. elegans hermaphrodites. Introduction of a similar Bm-her-1 construct into C. elegans caused only very weak, if any, masculinization. We conclude that in spite of considerable divergence the Cb gene is likely to be a functional ortholog of Ce-her-1, while the function of the distantly related Bm gene remains uncertain.

Amino Acid Sequence↗

PubMed1998

Clinic visits and hospital admissions for care of acid-related upper gastrointestinal disorders in women using alendronate for osteoporosis.

CONTEXT: About 1 in 3 women taking alendronate for osteoporosis report gastrointestinal symptoms, a rate much higher than that found during clinical trials. OBJECTIVE: To establish the frequency of outpatient visits and hospital admissions for acid-related upper gastrointestinal disorder (ARD) among women taking alendronate and to identify potential risk factors. METHODS: A retrospective database analysis identified 812 women with osteoporosis who had filled one or more 10-mg alendronate prescriptions from October 1995 through October 1996. RESULTS: One hundred (12.3%) of the 812 women received healthcare for ARD, a clinical encounter rate of 28.5 per 100 person-years. A reference group of 362,109 women from the same health plan had 17.6 ARD encounters per 100 person-years. Excluding women who had ARDs before receiving alendronate, alendronate users were 1.6 (95% CI = 1.2, 2.7) times more likely to have an ARD encounter than nonusers. Risk of having ARD increased with age [users aged 70 years and older had a relative risk of 1.5 (95% confidence interval (CI) 1.0-2.30) compared with younger women] and with concurrent use of nonsteroidal anti-inflammatory drugs (NSAIDS) (relative risk 1.7, 95% CI 1.1-2.6). CONCLUSIONS: Elderly alendronate users or those concurrently taking NSAIDS should be carefully monitored because of their high risk of having ARD. Cost/benefit analyses of alendronate treatment for osteoporosis should include costs of treating ARD.

Aged↗

PubMed1998

Reducing clozapine-related morbidity and mortality: 5 years of experience with the Clozaril National Registry.

UNLABELLED: The Clozaril National Registry (CNR) was created to help protect patients from developing potentially fatal agranulocytosis secondary to treatment with the antipsychotic medicine clozapine. The CNR, designed and maintained by the manufacturer of the branded Clozaril (clozapine), has the principal goals of (1) prophylaxis-preventing inappropriate retreatment, and (2) quality assurance-overseeing adherence to a "no blood, no drug" policy. This article reviews the estimated impact of the CNR on clozapine-related morbidity and mortality over the first 5 years of commercial experience in the United States. METHOD: Complete data on leukopenia and agranulocytosis, gathered from the CNR database for the period of 1990-1994, were reviewed and compared with data from the pre-CNR period. RESULTS: Use of clozapine in 99,502 patients according to package labeling requirements (distribution of the medicine linked to mandated white blood cell count testing) was associated with a total of 382 cases of agranulocytosis (0.38%) versus an expected cumulative total of 995 cases (based on the pre-CNR rate of 1% to 2%). Based on the expected agranulocytosis rate, up to 149 deaths might have been anticipated. Instead, there were only 12 deaths attributed to complications of agranulocytosis. CONCLUSION: The CNR provides for universal rechallenge protection as well as controlled dispensing of clozapine. It also serves as an early warning system to promote the safe and effective use of clozapine. The CNR includes quality assurance mechanisms designed to enhance compliance. Despite the added logistic requirements this system places upon physician, pharmacist, and manufacturer, the CNR has helped to reduce substantially potential fatal outcomes. The CNR reinforces both patient and treatment system compliance. Based on this favorable experience concerning agranulocytosis and associated fatalities, the Neuropsychopharmacology Advisory Committee to the U.S. Food and Drug Administration has unanimously recommended a reduction in frequency of the white blood cell count testing requirement after 6 months to every 14 days, instead of weekly. Finally, the CNR database containing white blood cell count and demographic data on every patient in the United States who has received the medicine has served as a unique epidemiologic database.

Adverse Drug Reaction Reporting Systems↗

PubMed1997