Quantitative stove use and ventilation guidance for behavior change strategies.

Achieving World Health Organization air quality targets and aspirational fuel savings targets through clean cooking solutions will require high usage rates of high-performing products and low usage rates of traditional stoves. Catalyzing this shift is challenging as fuel and stove use practices associated with new technologies generally differ from those used with traditional technologies. Accompanying this shift with ventilation improvements can help further reduce exposure to emissions of health damaging pollutants. Behavior change strategies will be central to these efforts to move users to new technologies and minimize exposure to emissions. In this article, the authors show how behavior change can be linked to quantitative guidance on stove usage, household ventilation rates, and performance. The guidance provided here can help behavior change efforts in the household energy sector set and achieve quantitative goals for usage and ventilation rates.

Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.

The evolution of enzymes affects how well a species can adapt to new environmental conditions. During enzyme evolution, certain aspects of molecular function are conserved while other aspects can vary. Aspects of function that are more difficult to change or that need to be reused in multiple contexts are often conserved, while those that vary may indicate functions that are more easily changed or that are no longer required. In analogy to the study of conservation patterns in enzyme sequences and structures, we have examined the patterns of conservation and variation in enzyme function by analyzing graph isomorphisms among enzyme substrates of a large number of enzyme superfamilies. This systematic analysis of substrate substructures establishes the conservation patterns that typify individual superfamilies. Specifically, we determined the chemical substructures that are conserved among all known substrates of a superfamily and the substructures that are reacting in these substrates and then examined the relationship between the two. Across the 42 superfamilies that were analyzed, substantial variation was found in how much of the conserved substructure is reacting, suggesting that superfamilies may not be easily grouped into discrete and separable categories. Instead, our results suggest that many superfamilies may need to be treated individually for analyses of evolution, function prediction, and guiding enzyme engineering strategies. Annotating superfamilies with these conserved and reacting substructure patterns provides information that is orthogonal to information provided by studies of conservation in superfamily sequences and structures, thereby improving the precision with which we can predict the functions of enzymes of unknown function and direct studies in enzyme engineering. Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized and uncharacterized enzyme superfamilies.

Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily.

Understanding how proteins evolve to provide both exquisite specificity and proficient activity is a fundamental problem in biology that has implications for protein function prediction and protein engineering. To study this problem, we analyzed the evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase (OSBS/NAAAR) family, part of the mechanistically diverse enolase superfamily. Although all characterized members of the family catalyze the OSBS reaction, this family is extraordinarily divergent, with some members sharing <15% identity. In addition, a member of this family, Amycolatopsis OSBS/NAAAR, is promiscuous, catalyzing both dehydration and racemization. Although the OSBS/NAAAR family appears to have a single evolutionary origin, no sequence or structural motifs unique to this family could be identified; all residues conserved in the family are also found in enolase superfamily members that have different functions. Based on their species distribution, several uncharacterized proteins similar to Amycolatopsis OSBS/NAAAR appear to have been transmitted by lateral gene transfer. Like Amycolatopsis OSBS/NAAAR, these might have additional or alternative functions to OSBS because many are from organisms lacking the pathway in which OSBS is an intermediate. In addition to functional differences, the OSBS/NAAAR family exhibits surprising structural variations, including large differences in orientation between the two domains. These results offer several insights into protein evolution. First, orthologous proteins can exhibit significant structural variation, and specificity can be maintained with little conservation of ligand-contacting residues. Second, the discovery of a set of proteins similar to Amycolatopsis OSBS/NAAAR supports the hypothesis that new protein functions evolve through promiscuous intermediates. Finally, a combination of evolutionary, structural, and sequence analyses identified characteristics that might prime proteins, such as Amycolatopsis OSBS/NAAAR, for the evolution of new activities.

The Structure Superposition Database.

The need for new tools for investigating biological systems on a large scale is becoming acute, particularly with respect to computationally intensive analyses such as comparisons of many three-dimensional protein structures. Structure superposition is a valuable approach for understanding evolutionary relationships and for the prediction of function. But while available tools are adequate for generating and viewing superpositions of single pairs of protein structures, these tools are generally too cumbersome and time-consuming for examining multiple superpositions. To address this need, we have created the Structure Superposition Database (SSD) for accessing, viewing and understanding large sets of structure superposition data. The initial implementation of the SSD contains the results of pairwise, all-by-all superpositions of a representative set of 115 (beta/alpha)8 barrel structures (TIM barrels). Future plans call for extending the database to include representative structure superpositions for many additional folds. The SSD can be browsed with a user interface module developed as an extension to Chimera, an extensible molecular modeling program. Features of the user interface module facilitate viewing multiple superpositions together. The SSD interface module can be downloaded from http://ssd.rbvi.ucsf.edu.

Quantitative Guidance for Stove Usage and Performance to Achieve Health and Environmental Targets.

BACKGROUND: Displacing the use of polluting and inefficient cookstoves in developing countries is necessary to achieve the potential health and environmental benefits sought through clean cooking solutions. Yet little quantitative context has been provided on how much displacement of traditional technologies is needed to achieve targets for household air pollutant concentrations or fuel savings. OBJECTIVES: This paper provides instructive guidance on the usage of cooking technologies required to achieve health and environmental improvements. METHODS: We evaluated different scenarios of displacement of traditional stoves with use of higher performing technologies. The air quality and fuel consumption impacts were estimated for these scenarios using a single-zone box model of indoor air quality and ratios of thermal efficiency. RESULTS: Stove performance and usage should be considered together, as lower performing stoves can result in similar or greater benefits than a higher performing stove if the lower performing stove has considerably higher displacement of the baseline stove. Based on the indoor air quality model, there are multiple performance-usage scenarios for achieving modest indoor air quality improvements. To meet World Health Organization guidance levels, however, three-stone fire and basic charcoal stove usage must be nearly eliminated to achieve the particulate matter target (< 1-3 hr/week), and substantially limited to meet the carbon monoxide guideline (< 7-9 hr/week). CONCLUSIONS: Moderate health gains may be achieved with various performance-usage scenarios. The greatest benefits are estimated to be achieved by near-complete displacement of traditional stoves with clean technologies, emphasizing the need to shift in the long term to near exclusive use of clean fuels and stoves. The performance-usage scenarios are also provided as a tool to guide technology selection and prioritize behavior change opportunities to maximize impact.