Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors

Accurate measurements of metabolic fluxes in living cells are central to metabolism research and metabolic engineering. The gold standard method is model-based metabolic flux analysis (MFA), where fluxes are estimated indirectly from mass isotopomer data with the use of a mathematical model of the metabolic network. A critical step in MFA is model selection: choosing what compartments, metabolites, and reactions to include in the metabolic network model. Model selection is often done informally during the modelling process, based on the same data that is used for model fitting (estimation data). This can lead to either overly complex models (overfitting) or too simple ones (underfitting), in both cases resulting in poor flux estimates. Here, we propose a method for model selection based on independent validation data. We demonstrate in simulation studies that this method consistently chooses the correct model in a way that is independent on errors in measurement uncertainty. This independence is beneficial, since estimating the true magnitude of these errors can be difficult. In contrast, commonly used model selection methods based on the χ²-test choose different model structures depending on the believed measurement uncertainty; this can lead to errors in flux estimates, especially when the magnitude of the error is substantially off. We present a new approach for quantification of prediction uncertainty of mass isotopomer distributions in other labelling experiments, to check for problems with too much or too little novelty in the validation data. Finally, in an isotope tracing study on human mammary epithelial cells, the validation-based model selection method identified pyruvate carboxylase as a key model component. Our results argue that validation-based model selection should be an integral part of MFA model development.     

Parrotfish sex ratios recover rapidly in Bermuda following a fishing ban

Parrotfishes are an ecologically and commercially important teleost group whose grazing contributes to maintaining coral-dominated states on hermatypic reefs. However, overfishing has skewed sex ratios of Atlantic parrotfishes because fishing has disproportionate impacts on larger individuals, and males are generally larger than females. Whether protection from fishing may allow sex ratios to return to equilibrium is unknown, as fishing can induce irreversible ecological and/or evolutionary shifts. Bermuda banned trap fishing in 1990, creating a unique opportunity to analyse long-term responses of Atlantic parrotfishes to release from fishing. We found that sex ratios of four common parrotfishes were initially skewed, with male proportions ranging from 0.04 to 0.18. However, male proportions rebounded within 3–4 yr, equilibrating at values ranging from 0.36 to 0.54, similar to those reported at unfished sites in the region. Our results are encouraging for regional efforts to recover lost grazing function by restoring overfished herbivore populations.     

Long-term use of high-efficiency vacuum cleaners and residential airborne fungal-spore exposure

Exposure to fungal allergens is an important contributor to allergic respiratory disease, but information on the efficacy of residential fungal allergen-avoidance in allergic-disease management is lacking. Using vacuum cleaners with high-efficiency exhaust filtration is one method recommended for reducing residential allergen exposure levels, but their use to reduce fungal-spore exposure levels has not been evaluated. To evaluate the effectiveness of high-efficiency vacuuming to control airborne fungal-spore levels, fungal bioaerosols were repeatedly assessed over the course of 10 months in homes randomly assigned to groups using either conventionally filtered (control) or high-efficiency-filtered vacuum cleaners for routine vacuum cleaning. Air samples were analyzed for three fungal-spore categories representing taxa with predominantly outdoor sources and one representing taxa that commonly have indoor sources. In a two-way analysis of variance, sampling period had a significant effect on mean levels of all fungal-spore categories. Vacuum cleaner type had a marginally significant effect on the indoor spore category, with one high-efficiency vacuum group mean (of three) significantly lower than one control mean. No effect was observed of vacuum cleaner type on outdoor spore categories. Including home-environment variables in analysis of covariance models strengthened the effect of the vacuum-type treatment on the indoor spore category, with no effect on the three outdoor spore categories. Decreased indoor spore levels vs. controls were only observed in high-efficiency vacuum groups during the last sampling period, at the end of the heating season. The results suggest that using a vacuum with high-efficiency filtered exhaust could have some modest effectiveness in controlling airborne fungal-spore exposure in homes when infiltration of outdoor air is very limited.     

Metabolic Basis for the Self-Referential Genetic Code

An investigation of the biosynthesis pathways producing glycine and serine was necessary to clarify an apparent inconsistency between the self-referential model (SRM) for the formation of the genetic code and the model of coevolution of encodings and of amino acid biosynthesis routes. According to the SRM proposal, glycine was the first amino acid encoded, followed by serine. The coevolution model does not state precisely which the first encodings were, only presenting a list of about ten early assignments including the derivation of glycine from serine—this being derived from the glycolysis intermediate glycerate, which reverses the order proposed by the self-referential model. Our search identified the glycine-serine pathway of syntheses based on one-carbon sources, involving activities of the glycine decarboxylase complex and its associated serine hydroxymethyltransferase, which is consistent with the order proposed by the self-referential model and supports its rationale for the origin of the genetic code: protein synthesis was developed inside an early metabolic system, serving the function of a sink of amino acids; the first peptides were glycine-rich and fit for the function of building the early ribonucleoproteins; glycine consumption in proteins drove the fixation of the glycine-serine pathway.