Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels

Direct Sanger sequencing of a diploid template containing a heterozygous insertion or deletion results in a difficult-to-interpret mixed trace formed by two allelic traces superimposed onto each other. Existing computational methods for deconvolution of such traces require knowledge of a reference sequence or the availability of both direct and reverse mixed sequences of the same template. We describe a simple yet accurate method, which uses dynamic programming optimization to predict superimposed allelic sequences solely from a string of letters representing peaks within an individual mixed trace. We used the method to decode 104 human traces (mean length 294 bp) containing heterozygous indels 5 to 30 bp with a mean of 99.1% bases per allelic sequence reconstructed correctly and unambiguously. Simulations with artificial sequences have demonstrated that the method yields accurate reconstructions when (1) the allelic sequences forming the mixed trace are sufficiently similar, (2) the analyzed fragment is significantly longer than the indel, and (3) multiple indels, if present, are well-spaced. Because these conditions occur in most encountered DNA sequences, the method is widely applicable. It is available as a free Web application Indelligent at http://ctap.inhs.uiuc.edu/dmitriev/indel.asp

Genome Majority Vote Improves Gene Predictions

Recent studies have noted extensive inconsistencies in gene start sites among orthologous genes in related microbial genomes. Here we provide the first documented evidence that imposing gene start consistency improves the accuracy of gene start-site prediction. We applied an algorithm using a genome majority vote (GMV) scheme to increase the consistency of gene starts among orthologs. We used a set of validated Escherichia coli genes as a standard to quantify accuracy. Results showed that the GMV algorithm can correct hundreds of gene prediction errors in sets of five or ten genomes while introducing few errors. Using a conservative calculation, we project that GMV would resolve many inconsistencies and errors in publicly available microbial gene maps. Our simple and logical solution provides a notable advance toward accurate gene maps

The Genome of \u3ci\u3eLaccaria bicolor\u3c/i\u3e Provides Insights into Mycorrhizal Symbiosis

Mycorrhizal symbioses—the union of roots and soil fungi—are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains ~20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity

Skin Cancer Screening and Prevention in the Primary Care Setting National Ambulatory Medical Care Survey 1997

OBJECTIVE: To describe skin cancer prevention and screening activities in the primary care setting and to compare these findings to other cancer screening and prevention activities. DESIGN: Descriptive study. SETTING/PATIENTS: National Ambulatory Medical Care Survey 1997 data on office-based physician visits to family practitioners and internists. MEASUREMENTS AND MAIN RESULTS: Data were obtained on 784 primary care visits to 109 family practitioners and 61 internists. We observed that the frequency of skin cancer prevention and screening activities in the primary care setting was much lower than other cancer screening and prevention activities. Skin examination was reported at only 15.8% of all visits (17.4% for family practitioners vs 13.6% for internists, P > .1). For other cancer screening, the frequencies were as follows: breast examination, 30.3%; Papanicolaou test, 25.3%; pelvic examination, 27.6%; and rectal examination, 17.9%. Skin cancer prevention in the form of education and counseling was reported at 2.3% of these visits (2.9% for family practitioners vs 1.5% for internists, P > .1), while education on breast self-examination, diet and nutrition, tobacco use, and exercise was 13.0%, 25.3%, 5.7%, and 17.9%, respectively. CONCLUSIONS: The results of this study indicate that the proportion of primary care visits in which skin cancer screening and prevention occurs is low. Strategies to increase skin cancer prevention and screening by family practitioners and internists need to be considered

Urban Wellbeing in the Contemporary City

The concept of well-being in the contemporary city refers to people’s ability to live healthy, creative and fulfilling lives. In this chapter, the intent is to understand theoretical perspectives about well-being research, essentially objective and subjective health and well-being of individuals in modern urban society. The emphasis is given to “non-medical” factors to determine the term by complex interactions between social, cultural, physical environments and individual behaviours. The chapter further indicates the tools and techniques adopted by researchers for measuring well-being emphasising the capability approach by Amartya Sen and Luc Boltanski’s approach on critical capacity. As a conclusion, based on the views and measures, the chapter suggests that addition of citizen science methodologies have potential utility for bridging objective and subjective perspectives of health and well-being, and influencing urban planning and design