Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology

Utilization of Papanicolaou Smears by South Asian Women Living in the United States

OBJECTIVES: Papanicolaou (Pap) smears are an underutilized screening modality among racial and ethnic minorities. However, no data exist on Pap smear utilization among South Asians, a rapidly growing population in the United States, whose country of origin includes India, Pakistan, Bangladesh, and Sri Lanka. We determined rates and identified variables associated with Pap smear receipt by South Asians. DESIGN: A self-administered survey instrument was mailed to a random sample of South Asians nationwide over a 3-month time period. South Asian households were identified by surnames that were used to search white pages in telephone directories, Department of Motor Vehicle records, and voter registries. Questions regarding Pap smear receipt were taken from the 1999 National Health Interview Survey. Sociodemographic information and measures of acculturation were obtained. PARTICIPANTS: A nationwide nonprobability sample of South Asian women. INTERVENTION: Cross-sectional observational study. MEASUREMENTS AND MAIN RESULTS: The overall response rate was 42%. In this sample, South Asians belonged to a high socioeconomic strata (SES), with 45% having a household income of >$80,000 and 42% having a master's degree. Three quarters of the respondents (73%) reported having a Pap smear in the last 3 years. In multivariate logistic regression analysis, South Asian women had greater odds of having had a Pap smear if they were married (P < .001), more educated (P = .004), had a usual source of care (P = .002), and were more acculturated (P = .004). CONCLUSIONS: Despite the high SES of South Asian women, their rates of Pap smear receipt were lower than national recommendations. Marital status, socioeconomic status, and acculturation are all associated with Pap smear receipt. South Asian communities should be targeted for outreach to promote Pap smear utilization