Towards a model of non-equilibrium binding of metal ions in biological systems

We have used a systems biology approach to address the hitherto insoluble problem of the quantitative analysis of non-equilibrium binding of aqueous metal ions by competitive ligands in heterogeneous media. To-date, the relative proportions of different metal complexes in aqueous media has only been modelled at chemical equilibrium and there are no quantitative analyses of the approach to equilibrium. While these models have improved our understanding of how metals are used in biological systems they cannot account for the influence of kinetic factors in metal binding, transport and fate. Here we have modelled the binding of aluminium, Al(III), in blood serum by the iron transport protein transferrin (Tf) as it is widely accepted that the biological fate of this non-essential metal is not adequately described by experiments, invitro and insilico, which have consistently demonstrated that at equilibrium 90% of serum Al(III) is bound by Tf. We have coined this paradox ‘the blood-aluminium problem’ and herein applied a systems biology approach which utilised well-found assumptions to pare away the complexities of the problem such that it was defined by a comparatively simple set of computational rules and, importantly, its solution assumed significant predictive capabilities. Here we show that our novel computational model successfully described the binding of Al(III) by Tf both at equilibrium and as equilibrium for Al_Tf was approached. The model predicted significant non-equilibrium binding of Al by ligands in competition with Tf and, thereby, provided an explanation of why the distribution of Al(III) in the body cannot be adequately described by its binding and transport by Tf alone. Generically the model highlighted the significance of kinetic in addition to thermodynamic constraints in defining the fate of metal ions in biological systems.     

Nitrosation-modulating effect of ascorbate in a model dynamic system of coexisting nitric oxide and superoxide

Abstract

The coexistence of nitric oxide and superoxide leads to complex oxidative and nitrosative chemistry, which has been implicated in many pathophysiological conditions. The present study investigated the role of ascorbate in affecting the kinetics of nitrosative chemistry in a model dynamic snystem of coexisting nitric oxide and superoxide. SIN-1 (3-morpholinosydnonimine) was used to elicit various degrees of nitroxidative stress in a reaction buffer and DAN (2,3-diaminonaphthalene) was used as a probe for N-nitrosation reaction. The nitrosation kinetics in the absence and presence of ascorbate was followed by measuring the formation of the fluorescent product over time. Computational modelling was used to provide quantitative or semi-quantitative insights into the studied system. The results show that ascorbate effectively quenches N-nitrosation reaction, which could be partially attributed to the free radical scavenging and repairing effect of ascorbate. Computational modelling reveals an interesting temporal distribution of superoxide, nitric oxide and peroxynitrite. The model predicts that peroxynitrite is the most predominant species in the SIN-1 system. Furthermore, ascorbate might alter the system dynamics by removing superoxide and, thereby, increasing the availability of nitric oxide.     

Duplication of <Emphasis Type="Italic">AP1</Emphasis> within the <Emphasis Type="Italic">Spinacia oleracea</Emphasis> L. <Emphasis Type="Italic">AP1/FUL</Emphasis> clade is followed by rapid amino acid and regulatory evolution

The AP1/FUL clade of MADS box genes have undergone multiple duplication events among angiosperm species. While initially identified as having floral meristem identity and floral organ identity function in Arabidopsis, the role of AP1 homologs does not appear to be universally conserved even among eudicots. In comparison, the role of FRUITFULL has not been extensively explored in non-model species. We report on the isolation of three AP1/FUL genes from cultivated spinach, Spinacia oleracea L. Two genes, designated SpAPETALA1-1 (SpAP1-1) and SpAPETALA1-2 (SpAP1-2), cluster as paralogous genes within the Caryophyllales AP1 clade. They are highly differentiated in the 3′, carboxyl-end encoding region of the gene following the third amphipathic alpha-helix region, while still retaining some elements of a signature AP1 carboxyl motifs. In situ hybridization studies also demonstrate that the two paralogs have evolved different temporal and spatial expression patterns, and that neither gene is expressed in the developing sepal whorl, suggesting that the AP1 floral organ identity function is not conserved in spinach. The spinach FRUITFULL homolog, SpFRUITFULL (SpFUL), has retained the conserved motif and groups with Caryophyllales FRUITFULL homologs. SpFUL is expressed in leaf as well as in floral tissue, and shows strong expression late in flower development, particularly in the tapetal layer in males, and in the endothecium layer and stigma, in the females. The combined evidence of high rates of non-synonymous substitutions and differential expression patterns supports a scenario in which the AP1 homologs in the spinach AP1/FUL gene family have experienced rapid evolution following duplication. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Modeling and experimental studies on intermittent starch feeding and citrate addition in simultaneous saccharification and fermentation of starch to flavor compounds

Simultaneous saccharification and fermentation (SSF) is a combined process of saccharification of a renewable bioresource and fermentation process to produce products, such as lactic acid and ethanol. Recently, SSF has been extensively used to convert various sources of cellulose and starch into fermentative products. Here, we present a study on production of buttery flavors, namely diacetyl and acetoin, by growing Lactobacillus rhamnosus on a starch medium containing the enzyme glucoamylase. We further develop a structured kinetics for the SSF process, which includes enzyme and growth kinetics. The model was used to simulate the effect of pH and temperature on the SSF process so as to obtain optimum operating conditions. The model was experimentally verified by conducting SSF using an initial starch concentration of 100 g/L. The study demonstrated that the developed kinetic was able to suggest strategies for improved productivities. The developed model was able to accurately predict the enhanced productivity of flavors in a three stage process with intermittent addition of starch. Experimental and simulations demonstrated that citrate addition can also lead to enhanced productivity of flavors. The developed optimal model for SSF was able to capture the dynamics of SSF in batch mode as well as in a three stage process. The structured kinetics was also able to quantify the effect of multiple substrates present in the medium. The study demonstrated that structured kinetic models can be used in the future for design and optimization of SSF as a batch or a fed-batch process. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The habitat and conduit functions of roads in the spread of three invasive plant species

Nonnative plant species commonly occur along roadsides, and populations are often assumed to invade by spread along the road axis. To distinguish between the function of roadsides as movement corridors and as habitat, nonnative plant species were surveyed along roads in deciduous forest sites in southeastern Ohio, USA. The importance of road proximity was tested by comparing nonnative species abundance in 100 m transects along roads with transects in undisturbed forest. Nonnative species were most abundant and most frequently observed in roadside sites in valleys. Three common species were chosen for closer scrutiny. In a seed sowing experiment roads and open sites proved to be better locations for the germination and growth of Microstegium vimineum than non-roadside and closed-canopy sites. Tussilago farfara and Rosa multiflora occurred in a small number of disjunct patches suggesting infrequent arrival in the sampled transects. Both species were strongly clustered at scales consistent with diffusive spread by vegetative growth and short-range seed dispersal. Comparisons of distributions parallel and perpendicular to roads showed no evidence for enhanced dispersal along the road axis. Microstegium distributions were correlated with local light availability implying site saturation. Microstegium micro-distributions suggested that spread along the road axis was facilitated by movement of dormant seeds in road maintenance. Thus, roadsides appear to function as both habitat and a conduit for population expansion, with the rate of spread dependent on the life history of the individual species. These results suggest a hierarchical process of regional invasion, with different dispersal mechanisms functioning at different spatial scales.     

Modeling the Evolution of Insect Phenology

Climate change is likely to disrupt the timing of developmental events (phenology) in insect populations in which development time is largely determined by temperature. Shifting phenology puts insects at risk of being exposed to seasonal weather extremes during sensitive life stages and losing synchrony with biotic resources. Additionally, warming may result in loss of developmental synchronization within a population making it difficult to find mates or mount mass attacks against well-defended resources at low population densities. It is unknown whether genetic evolution of development time can occur rapidly enough to moderate these effects. We present a novel approach to modeling the evolution of phenology by allowing the parameters of a phenology model to evolve in response to selection on emergence time and density. We use the Laplace method to find asymptotic approximations for the temporal variation in mean phenotype and phenotypic variance arising in the evolution model that are used to characterize invariant distributions of the model under periodic temperatures at leading order. At these steady distributions the mean phenotype allows for parents and offspring to be oviposited at the same time of year in consecutive years. Numerical simulations show that populations evolve to these steady distributions under periodic temperatures. We consider an example of how the evolution model predicts populations will evolve in response to warming temperatures and shifting resource phenology.     

Concentration dependent growth/non-growth linked kinetics of endosulfan biodegradation by <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis>

The rates of biodegradation of endosulfan by P. aeruginosa were determined with different initial endosulfan concentrations (10, 50, 100, 150, 200 and 250 mg l⁻¹) and different growth linked kinetic models were fitted at these concentrations. At 10 mg endosulfan l⁻¹, Monod no growth model was well fitted. Monod with growth model described the biodegradation pattern at an initial concentration of 50, 100 and 150 mg endosulfan l⁻¹. Significant increases of P. aeruginosa MN2B14 density in broth culture during incubation further support this result. Conversely, zero order kinetic model was well fitted into the biodegradation data if initial endosulfan concentration was ≥200 mg endosulfan l⁻¹. The kinetics of endosulfan biodegradation by P. aeruginosa MN2B14 in liquid broth was highly dependent upon its initial concentration. The results of this study could be employed for predicting the persistence of endosulfan in water environment containing P. aeruginosa as an endosulfan degrading bacterium.     

Tree growth and competition in a post-logging Quercus mongolica forest on Mt. Sobaek, South Korea

Secondary woodlands in South Korea cover most mountains from low to middle elevations. While general patterns of forest succession are well understood, little is known about mechanisms of stand recovery after disturbance. We examined the spatio-temporal variations in establishment, growth, size inequality, and mode of competition among trees in a 50-year-old post-logging Quercus mongolica-dominated stand. We further compared the growth and stem allometry of single trees, presumably of seed origin, with multi-stemmed trees resprouting from stumps. Q. mongolica formed the upper canopy 16–22 m tall, 88.3% of total stand basal area, and 36.2% of total stem density, with most trees established during the first post-logging decade (51.2% were resprouts). During the first three decades, the Q. mongolica recruits grew exponentially, and disproportionately more in diameter than few older reserved trees left after the last cutting. This substantially decreased size inequality. The reverse trend was observed from 1994 to 2004: larger trees grow more, indicating an increasing asymmetry of competition for light. Neighborhood analysis revealed that when target trees had more or larger neighbors, their exponential phase of growth was reduced and maximum size was decreased. After the 50 years of stand development, more than 70% of Q. mongolica showed growth decline as a result of competitive stress, and mortality was about 30%, concentrated in smaller size classes. Compared to single stems, resprouts within clones do not seem to compete less asymmetric as might be expected based on studies of clonal herbaceous plants and physiological integration within genets. As Q. mongolica was also negatively affected by competition from woody species currently prevailing in the lower tree stratum (Tilia amurensis, Acer mono, Fraxinus rhynchophylla, Acer pseudosieboldianum), we predict the stand will become increasingly dominated by these more shade-tolerant trees.