Multiscale metabolic modeling of C4 plants: connecting nonlinear genome-scale models to leaf-scale metabolism in developing maize leaves

C4 plants, such as maize, concentrate carbon dioxide in a specialized compartment surrounding the veins of their leaves to improve the efficiency of carbon dioxide assimilation. Nonlinear relationships between carbon dioxide and oxygen levels and reaction rates are key to their physiology but cannot be handled with standard techniques of constraint-based metabolic modeling. We demonstrate that incorporating these relationships as constraints on reaction rates and solving the resulting nonlinear optimization problem yields realistic predictions of the response of C4 systems to environmental and biochemical perturbations. Using a new genome-scale reconstruction of maize metabolism, we build an 18000-reaction, nonlinearly constrained model describing mesophyll and bundle sheath cells in 15 segments of the developing maize leaf, interacting via metabolite exchange, and use RNA-seq and enzyme activity measurements to predict spatial variation in metabolic state by a novel method that optimizes correlation between fluxes and expression data. Though such correlations are known to be weak in general, here the predicted fluxes achieve high correlation with the data, successfully capture the experimentally observed base-to-tip transition between carbon-importing tissue and carbon-exporting tissue, and include a nonzero growth rate, in contrast to prior results from similar methods in other systems. We suggest that developmental gradients may be particularly suited to the inference of metabolic fluxes from expression data.Comment: 57 pages, 14 figures; submitted to PLoS Computational Biology; source code available at http://github.com/ebogart/fluxtools and http://github.com/ebogart/multiscale_c4_sourc

Small Chvatal rank

We propose a variant of the Chvatal-Gomory procedure that will produce a sufficient set of facet normals for the integer hulls of all polyhedra {xx : Ax <= b} as b varies. The number of steps needed is called the small Chvatal rank (SCR) of A. We characterize matrices for which SCR is zero via the notion of supernormality which generalizes unimodularity. SCR is studied in the context of the stable set problem in a graph, and we show that many of the well-known facet normals of the stable set polytope appear in at most two rounds of our procedure. Our results reveal a uniform hypercyclic structure behind the normals of many complicated facet inequalities in the literature for the stable set polytope. Lower bounds for SCR are derived both in general and for polytopes in the unit cube.Comment: 24 pages, 3 figures, v3. Major revision: additional author, new application to stable-set polytopes, reorganization of sections. Accepted for publication in Mathematical Programmin

Ages of D/d,n/He sup 3 and T/d,n/He sup 4 neutrons in water and tungsten-water mixtures

Ages for D-D and D-T neutrons in water and tungsten-water mixture

Plasma enhanced chemical vapor deposition of SiO_2 using novel alkoxysilane precursors

This communication describes our results using these novel alkoxysilane precursors for PECVD of SiO_2 films in an inductively coupled rf plasma reactor. The effects of deposition time, rf power, and organosilane pressure on the films’ characteristics are described

Investigating the role of model-based reasoning while troubleshooting an electric circuit

We explore the overlap of two nationally-recognized learning outcomes for physics lab courses, namely, the ability to model experimental systems and the ability to troubleshoot a malfunctioning apparatus. Modeling and troubleshooting are both nonlinear, recursive processes that involve using models to inform revisions to an apparatus. To probe the overlap of modeling and troubleshooting, we collected audiovisual data from think-aloud activities in which eight pairs of students from two institutions attempted to diagnose and repair a malfunctioning electrical circuit. We characterize the cognitive tasks and model-based reasoning that students employed during this activity. In doing so, we demonstrate that troubleshooting engages students in the core scientific practice of modeling.Comment: 20 pages, 6 figures, 4 tables; Submitted to Physical Review PE

Process Evaluation of a Peer-Driven, HIV Stigma Reduction and HIV Testing Intervention in Latino and African American Churches.

Purpose: Faith-based organizations may be effective in addressing HIV-related disparities, but few interventions have been implemented across diverse churches. The Facilitating Awareness to Increase Testing for HIV (FAITH) intervention harnessed peer leadership to decrease HIV stigma and promote HIV testing in African American and Latino congregations. A pilot study found more consistent effects among Latino congregations. This process evaluation evaluates implementation of FAITH to better understand the pilot study's findings. Methods: Data sources included HIV education and peer leader workshop evaluation forms, participant views of the community's perspective of HIV, and peer leader follow-up interviews. Data were triangulated with systematic observation notes and analyzed using process-related themes of recruitment, reach, context, implementation, dose-delivered, and fidelity. Results: At the Latino churches (compared to the African American church), facilitators spent more time addressing community-based misconceptions about HIV. The peer leader model was well received, especially among Latino participants, and most said that after the workshop they felt comfortable speaking with others about HIV-related topics. Latino peer leaders reported speaking with up to 20 people within their social networks (particularly with family members); African Americans reported up to 4. Implementation challenges at the African American church may have contributed to the limited intervention effects. Nevertheless, we found the peer motivator model feasible and acceptable across diverse faith settings. Conclusion: Peer-based models within faith settings are promising for addressing HIV. However, differences among groups in HIV knowledge, social network characteristics and norms, and church preferences may influence overall effectiveness