The metabolic network of Clostridium acetobutylicum: Comparison of the approximate Bayesian computation via sequential Monte Carlo (ABC-SMC) and profile likelihood estimation (PLE) methods for determinability analysis

Modeling the temporal periodicity of growth increments based on harmonic functions

Age estimation methods based on hard structures require a process of validation to confirm the periodical pattern of growth marks. Among such processes, one of the most used is the marginal increment ratio (MIR), which was stated to follow a sinusoidal cycle in a population. Despite its utility, in most cases, its implementation has lacked robust statistical analysis. Accordingly, we propose a modeling approach for the temporal periodicity of growth increments based on single and second order harmonic functions. For illustrative purposes, the MIR periodicities for two geoduck species (Panopea generosa and Panopea globosa) were modeled to identify the periodical pattern of growth increments in the shell. This model identified an annual periodicity for both species but described different temporal patterns. The proposed procedure can be broadly used to objectively define the timing of the peak, the degree of symmetry, and therefore, the synchrony of band deposition of different species on the basis of MIR data.

Modelling the role of CtfA/B in reverse shift continuous culture experiments of Clostridium acetobutylicum

In continuous phosphate-limited conditions, under pH control from high pH (pH ≳ 5.2) to low pH (pH ≲ 5.2), the metabolism of the Gram-positive bacterium Clostridium acetobutylicum,switches from acid to solvent production. Three main enzymes are responsible for the shift, acetoacetate decarboxylase (Adc), alcohol dehydrogenase (AdhE1/2) and a CoA-transferase (CtfA/B), which are produced in increased quantities during solventogenesis. A two-population model, Millat et al. (2013) and fitted to such 'forward'-shift data, can explain this, as well as observed changes in optical density immediately following the shift: an acidogenic subpopulation is washed out and a solventogenic subpopulation grows in its place, each with distinct physiologies and proteomes. We fit this model to a 'reverse'-shift experiment, where the pH is increased from solventogenic to acidogenic conditions. We find corresponding changes in reaction rates, with AdhE1 and Adc production falling, as in the 'forward' experiments; however, for CtfA/B, the best fit surprisingly arises from the same level of production in both conditions. We propose experiments that would test whether this is a model artefact or accurately reflects cultures shifted in this reverse direction, and, if true, may suggest that over-expressing CtfA/B in both solventogenic and acidogenic conditions could improve the efficiency of fermentation.