GEM-based computational modeling for exploring metabolic interactions in a microbial community.

Microbial communities play fundamental roles in every complex ecosystem, such as soil, sea and the human body. The stability and diversity of the microbial community depend precisely on the composition of the microbiota. Any change in the composition of these communities affects microbial functions. An important goal of studying the interactions between species is to understand the behavior of microbes and their responses to perturbations. These interactions among species are mediated by the exchange of metabolites within microbial communities. We developed a computational model for the microbial community that has a separate compartment for exchanging metabolites. This model can predict possible metabolites that cause competition, commensalism, and mutual interactions between species within a microbial community. Our constraint-based community metabolic modeling approach provides insights to elucidate the pattern of metabolic interactions for each common metabolite between two microbes. To validate our approach, we used a toy model and a syntrophic co-culture of Desulfovibrio vulgaris and Methanococcus maripaludis, as well as another in co-culture between Geobacter sulfurreducens and Rhodoferax ferrireducens. For a more general evaluation, we applied our algorithm to the honeybee gut microbiome, composed of seven species, and the epiphyte strain Pantoea eucalypti 299R. The epiphyte strain Pe299R has been previously studied and cultured with six different phyllosphere bacteria. Our algorithm successfully predicts metabolites, which imply mutualistic, competitive, or commensal interactions. In contrast to OptCom, MRO, and MICOM algorithms, our COMMA algorithm shows that the potential for competitive interactions between an epiphytic species and Pe299R is not significant. These results are consistent with the experimental measurements of population density and reproductive success of the Pe299R strain.

SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks.

BACKGROUND: High-throughput omics technologies have enabled the comprehensive reconstructions of genome-scale metabolic networks for many organisms. However, only a subset of reactions is active in each cell which differs from tissue to tissue or from patient to patient. Reconstructing a subnetwork of the generic metabolic network from a provided set of context-specific active reactions is a demanding computational task. RESULTS: We propose SWIFTCC and SWIFTCORE as effective methods for flux consistency checking and the context-specific reconstruction of genome-scale metabolic networks which consistently outperform the previous approaches. CONCLUSIONS: We have derived an approximate greedy algorithm which efficiently scales to increasingly large metabolic networks. SWIFTCORE is freely available for non-commercial use in the GitHub repository at https://mtefagh.github.io/swiftcore/.

Quantitative flux coupling analysis.

Flux coupling analysis (FCA) aims to describe the functional dependencies among reactions in a metabolic network. Currently studied coupling relations are qualitative in the sense that they identify pairs of reactions for which the activity of one reaction necessitates the activity of the other one, but without giving any numerical bounds relating the possible activity rates. The potential applications of FCA are heavily investigated, however apart from some trivial cases there is no clue of what bottleneck in the metabolic network causes each dependency. In this article, we introduce a quantitative approach to the same flux coupling problem named quantitative flux coupling analysis (QFCA). It generalizes the current concepts as we show that all the qualitative information provided by FCA is readily available in the quantitative flux coupling equations of QFCA, without the need for any additional analysis. Moreover, we design a simple algorithm to efficiently identify these flux coupling equations which scales up to the genome-scale metabolic networks with thousands of reactions and metabolites in an effective way. Furthermore, this framework enables us to quantify the "strength" of the flux coupling relations. We also provide different biologically meaningful interpretations, including one which gives an intuitive certificate of precisely which metabolites in the network enforce each flux coupling relation. Eventually, we conclude by suggesting the probable application of QFCA to the metabolic gap-filling problem, which we only begin to address here and is left for future research to further investigate.

A mathematical approach to emergent properties of metabolic networks: partial coupling relations, hyperarcs and flux ratios.

Emergent properties in systems biology are those which arise only when the biological system passes a certain level of complexity. In this study, we introduce some of the emergent properties which appear in the constraint-based analysis of metabolic networks. These properties generally appear as a result of existence of hfdeyperarcs and irreversible reactions in networks. Here, we present examples of metabolic networks in which there exist at least two reactions whose fluxes cannot be written as products and/or ratios of the stoichiometric coefficients of the network. We show that any such network contains at least one hyperarc. Additionally, we prove that partial coupling cannot appear in consistent metabolic networks with less than four reactions, or with less than three irreversible reactions, or without hyperarc(s).

Built-in wavelet-induced smoothness to reduce plan complexity in intensity modulated radiation therapy (IMRT).

Objective.Reducing plan complexity in intensity modulated radiation therapy (IMRT) to ensure dosimetric accuracy and delivery efficiency of the radiation treatment plans. We propose a novel approach by representing the beamlet intensities using an incomplete wavelet basis that explicitly excludes fluctuating intensity maps from the decision space (explicit hard constraint). This technique provides a built-in wavelet-induced smoothness that improves both dosimetric plan quality and delivery efficiency.Approach.The beamlet intensity maps need to be especially smooth in the leaf travel direction (referred to as theX-direction). We treat the intensity map of each beam as a 2D image and represent it using the wavelets corresponding to low-frequency changes in theX-direction (i.e. approximation and horizontal). The absence of wavelets corresponding to high-frequency changes (i.e. vertical and diagonal) induces built-in smoothness. We still utilize a regularization term in the objective function to promote smoothness in theY-direction (perpendicular to theX-direction) and further possible smoothness in theX-direction. This technique has been tested on three patient cases of different disease sites (paraspinal, lung, prostate) and all final evaluations and comparisons have been performed on an FDA-approved commercial treatment planning system (Varian EclipseTM).Main results.Wavelet-induced smoothness reduced monitor units by about 10%, 45%, and 14% for paraspinal, lung, and prostate cases, respectively. It also improved organ at risk sparing, especially on the complex paraspinal case where it resulted in about 7%, 13%, and 14% less mean dose to esophagus, lung, and cord, respectively. Moreover, built-in wavelet-induced smoothness desensitizes the results to changing the weight associated to the regularization term, and thereby mitigates the weight fine-tuning difficulty.Significance.Fluence smoothness is often achieved by smoothing the beamlet intensity maps using a proper regularization term in the objective function aiming at disincentivizing fluctuation in the beamlet intensities (implicit soft constraint). This work reports a novel application of wavelets in imposing an explicit smoothness hard constraint in the search space using an incomplete wavelet basis. This idea has been successfully applied to exclude complex and clinically irrelevant radiation plans from the search space. The code and pertained models along with a sample dataset are released on our LowDimRT GitHub (https://github.com/PortPy-Project/LowDimRT).