Generation, Annotation and Analysis of First Large-Scale Expressed Sequence Tags from Developing Fiber of Gossypium barbadense L

BACKGROUND: Cotton fiber is the world's leading natural fiber used in the manufacture of textiles. Gossypium is also the model plant in the study of polyploidization, evolution, cell elongation, cell wall development, and cellulose biosynthesis. G. barbadense L. is an ideal candidate for providing new genetic variations useful to improve fiber quality for its superior properties. However, little is known about fiber development mechanisms of G. barbadense and only a few molecular resources are available in GenBank. METHODOLOGY AND PRINCIPAL FINDINGS: In total, 10,979 high-quality expressed sequence tags (ESTs) were generated from a normalized fiber cDNA library of G. barbadense. The ESTs were clustered and assembled into 5852 unigenes, consisting of 1492 contigs and 4360 singletons. The blastx result showed 2165 unigenes with significant similarity to known genes and 2687 unigenes with significant similarity to genes of predicted proteins. Functional classification revealed that unigenes were abundant in the functions of binding, catalytic activity, and metabolic pathways of carbohydrate, amino acid, energy, and lipids. The function motif/domain-related cytoskeleton and redox homeostasis were enriched. Among the 5852 unigenes, 282 and 736 unigenes were identified as potential cell wall biosynthesis and transcription factors, respectively. Furthermore, the relationships among cotton species or between cotton and other model plant systems were analyzed. Some putative species-specific unigenes of G. barbadense were highlighted. CONCLUSIONS/SIGNIFICANCE: The ESTs generated in this study are from the first large-scale EST project for G. barbadense and significantly enhance the number of G. barbadense ESTs in public databases. This knowledge will contribute to cotton improvements by studying fiber development mechanisms of G. barbadense, establishing a breeding program using marker-assisted selection, and discovering candidate genes related to important agronomic traits of cotton through oligonucleotide array. Our work will also provide important resources for comparative genomics, polyploidization, and genome evolution among Gossypium species

Barriers to the Treatment of Hepatitis C: Patient, Provider, and System Factors

BACKGROUND: Hepatitis C virus (HCV) infection is both prevalent and undertreated. OBJECTIVE: To identify barriers to HCV treatment in primary care practice. DESIGN: Cross-sectional study. SETTING AND PARTICIPANTS: A cohort of 208 HCV-infected patients under the care of a primary care physician (PCP) between December 2001 and April 2004 at a single academically affiliated community health center. MEASUREMENTS: Data were collected from the electronic medical record (EMR), the hospital clinical data repository, and interviews with PCPs. MAIN RESULTS: Our cohort consisted of 208 viremic patients with HCV infection. The mean age was 47.6 (±9.7) years, 56% were male, and 79% were white. Fifty-seven patients (27.4% of the cohort) had undergone HCV treatment. Independent predictors of not being treated included: unmarried status (adjusted odds ratio [aOR] for treatment 0.36, P=.02), female gender (aOR 0.31, P=.01), current alcohol abuse (aOR 0.08, P=.0008), and a higher ratio of no-shows to total visits (aOR 0.005 per change of 1.0 in the ratio of no-shows to total visits, P=.002). The major PCP-identified reasons not to treat included: substance abuse (22.5%), patient preference (16%), psychiatric comorbidity (15%), and a delay in specialist input (12%). For 13% of the untreated patients, no reason was identified. CONCLUSIONS: HCV treatment was infrequent in our cohort of outpatients. Barriers to treatment included patient factors (patient preference, alcohol use, missed appointments), provider factors (reluctance to treat past substance abusers), and system factors (referral-associated delays). Multimodal interventions may be required to increase HCV treatment rates