Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior

A defining characteristic of living cells is the ability to respond dynamically to external stimuli while maintaining homeostasis under resting conditions. Capturing both of these features in a single kinetic model is difficult because the model must be able to reproduce both behaviors using the same set of molecular components. Here, we show how combining small, well-defined steady-state networks provides an efficient means of constructing large-scale kinetic models that exhibit realistic resting and dynamic behaviors. By requiring each kinetic module to be homeostatic (at steady state under resting conditions), the method proceeds by (i) computing steady-state solutions to a system of ordinary differential equations for each module, (ii) applying principal component analysis to each set of solutions to capture the steady-state solution space of each module network, and (iii) combining optimal search directions from all modules to form a global steady-state space that is searched for accurate simulation of the time-dependent behavior of the whole system upon perturbation. Importantly, this stepwise approach retains the nonlinear rate expressions that govern each reaction in the system and enforces constraints on the range of allowable concentration states for the full-scale model. These constraints not only reduce the computational cost of fitting experimental time-series data but can also provide insight into limitations on system concentrations and architecture. To demonstrate application of the method, we show how small kinetic perturbations in a modular model of platelet P2Y₁ signaling can cause widespread compensatory effects on cellular resting states.     

Mammal density and patterns of ectoparasite species richness and abundance

Patterns of species richness, prevalence and abundance of ectoparasites have rarely been investigated at both the levels of populations and species of hosts. Here, we investigated the effects in changes in small mammal density on species richness, abundance and prevalence of ectoparasitic fleas. The comparative analyses were conducted for different small mammal species and among several populations during a long-term survey. We tested the hypothesis that an increase in host density should be linked with an increase in parasite species richness both among host species and among populations within host species, as predicted by epidemiological models. We also used host species density data from literature. We found that host density has a major influence on the species richness of ectoparasite communities of small mammals among host populations. We found no relationship between data of host density from the literature and parasite species richness. In contrast with epidemiological hypotheses, we found no relationships between abundance, or prevalence, and host density, either among host species or among host populations. Moreover, a decrease in abundance of fleas in relation with an increase in host density was observed for two mammal species (Apodemus agrarius and A. flavicollis). The decrease or the lack of increase in flea abundance in relation with an increase in host density suggests anti-parasitic behavioural activities such as grooming.     

Patterns of parasite species richness of Western Palaeartic micro-mammals: island effects

We investigate the patterns of parasite species richness of small mammals of the Western Palaearctic, and the effects of insularity. We compiled 28 studies dealing with 16 species of mammals. There was a significant effect of area size on the total parasite species richness, controlling for host sample size. Four mammal species were sufficiently sampled. Two are associated with humans: Mus musculus, and Rattus rattus , and two are not associated with humans, Apodemus sylvaticus and Clethrionomys glaerolus. We show that there is an effect of insularity on parasite species richness of A. sylvaticus . Rodents associated with humans show no effect of insularity on parasite species richness. These rodents appear to reflect a more complex pattern of parasite species richness, probably because of their close association with humans. Host specificity of parasites significantly decreases on islands, with the exception of Rattus rattus . We use parasitological data in order to explore the geographical connections between host populations. We show that parasites may help to resolve these connections but we emphasise that parasites are better geographic than phylogenetic markers.     

Signs of deferasirox genotoxicity

Iron overload is a major health problem for patients who have to have continuous blood transfusions. It brings some metabolic problems together. Various iron chelating agents are being used for treatment of hemochromatosis which arises from excess iron accumulation. This study was conducted with the aim of determining whether deferasirox used as an iron chelator in patients with hemochromatosis has genotoxic effects. Commercial form of deferasirox, Exjade was used as test material. Test material showed a general mutagen character in mutant strains of Salmonella typhimurium. Deferasirox has also led to an increase in mutagenity-related polymorphic band count in random amplification of polymorphic DNA test done with bone marrow cells of rats. Similarly, test material has increased micronucleus formation in cultured in vitro human peripheral lymphocytes particularly in 48 h period. Consistently with the abovementioned findings, deferasirox reduced nuclear division index (NDI) compared to controls and some part of these reductions are statistically significant. NDI reductions were found at positive control levels at high concentrations.     

Mycobacterium tuberculosis Multidrug Resistant Strain M Induces an Altered Activation of Cytotoxic CD8+ T Cells

In human tuberculosis (TB), CD8⁺ T cells contribute to host defense by the release of Th1 cytokines and the direct killing of Mycobacterium tuberculosis (Mtb)-infected macrophages via granule exocytosis pathway or the engagement of receptors on target cells. Previously we demonstrated that strain M, the most prevalent multidrug-resistant (MDR) Mtb strain in Argentine, is a weak inducer of IFN-γ and elicits a remarkably low CD8-dependent cytotoxic T cell activity (CTL). In contrast, the closely related strain 410, which caused a unique case of MDR-TB, elicits a CTL response similar to H37Rv. In this work we extend our previous study investigating some parameters that can account for this discrepancy. We evaluated the expressions of the lytic molecules perforin, granzyme B and granulysin and the chemokine CCL5 in CD8⁺ T cells as well as activation markers CD69 and CD25 and IL-2 expression in CD4⁺ and CD8⁺ T cells stimulated with strains H37Rv, M and 410. Our results demonstrate that M-stimulated CD8⁺ T cells from purified protein derivative positive healthy donors show low intracellular expression of perforin, granzyme B, granulysin and CCL5 together with an impaired ability to form conjugates with autologous M-pulsed macrophages. Besides, M induces low CD69 and IL-2 expression in CD4⁺ and CD8⁺ T cells, being CD69 and IL-2 expression closely associated. Furthermore, IL-2 addition enhanced perforin and granulysin expression as well as the degranulation marker CD107 in M-stimulated CD8⁺ T cells, making no differences with cells stimulated with strains H37Rv or 410. Thus, our results highlight the role of IL-2 in M-induced CTL activity that drives the proper activation of CD8⁺ T cells as well as CD4⁺ T cells collaboration.     

Diffusion Kurtosis Imaging and High-Resolution MRI Demonstrate Structural Aberrations of Caudate Putamen and Amygdala after Chronic Mild Stress

The pathophysiology of major depressive disorder (MDD) and other stress related disorders has been associated with aberrations in the hippocampus and the frontal brain areas. More recently, other brain regions, such as the caudate nucleus, the putamen and the amygdala have also been suggested to play a role in the development of mood disorders. By exposing rats to a variety of stressors over a period of eight weeks, different phenotypes, i.e. stress susceptible (anhedonic-like) and stress resilient animals, can be discriminated based on the sucrose consumption test. The anhedonic-like animals are a well validated model for MDD. Previously, we reported that in vivo diffusion kurtosis imaging (DKI) of the hippocampus shows altered diffusion properties in chronically stressed rats independent of the hedonic state and that the shape of the right hippocampus is differing among the three groups, including unchallenged controls. In this study we evaluated diffusion properties in the prefrontal cortex, caudate putamen (CPu) and amygdala of anhedonic-like and resilient phenotypes and found that mean kurtosis in the CPu was significantly different between the anhedonic-like and resilient animals. In addition, axial diffusion and radial diffusion were increased in the stressed animal groups in the CPu and the amygdala, respectively. Furthermore, we found that the CPu/brain volume ratio was increased significantly in anhedonic-like animals as compared with control animals. Concurrently, our results indicate that the effects of chronic stress on the brain are not lateralized in these regions. These findings confirm the involvement of the CPu and the amygdala in stress related disorders and MDD. Additionally, we also show that DKI is a potentially important tool to promote the objective assessment of psychiatric disorders.     

Excessive use of nitrogen in Chinese agriculture results in high N2O/(N2O+N2) product ratio of denitrification,primarily due to acidification of the soils

China is the world's largest producer and consumer of fertilizer N, and decades of overuse has caused nitrate leaching and possibly soil acidification. We hypothesized that this would enhance the soils' propensity to emit N₂O from denitrification by reducing the expression of the enzyme N₂O reductase. We investigated this by standardized oxic/anoxic incubations of soils from five long‐term fertilization experiments in different regions of China. After adjusting the nitrate concentration to 2 mM, we measured oxic respiration (R), potential denitrification (D), substrate‐induced denitrification, and the denitrification product stoichiometry (NO, N₂O, N₂). Soils with a history of high fertilizer N levels had high N₂O/(N₂O+N₂) ratios, but only in those field experiments where soil pH had been lowered by N fertilization. By comparing all soils, we found a strong negative correlation between pH and the N₂O/(N₂O+N₂) product ratio (r² = 0.759, P < 0.001). In contrast, the potential denitrification (D) was found to be a linear function of oxic respiration (R), and the ratio D/R was largely unaffected by soil pH. The immediate effect of liming acidified soils was lowered N₂O/(N₂O+N₂) ratios. The results provide evidence that soil pH has a marginal direct effect on potential denitrification, but that it is the master variable controlling the percentage of denitrified N emitted as N₂O. It has been known for long that low pH may result in high N₂O/(N₂O+N₂) product ratios of denitrification, but our documentation of a pervasive pH‐control of this ratio across soil types and management practices is new. The results are in good agreement with new understanding of how pH may interfere with the expression of N₂O reductase. We argue that the management of soil pH should be high on the agenda for mitigating N₂O emissions in the future, particularly for countries where ongoing intensification of plant production is likely to acidify the soils.     

Influence of the ABCG2 gout risk 141?K allele on urate metabolism during a fructose challenge

Introduction

Both genetic variation in ATP-binding cassette sub-family G member 2 (ABCG2) and intake of fructose-containing beverages are major risk factors for hyperuricemia and gout. This study aimed to test the hypothesis that the ABCG2 gout risk allele 141 K promotes the hyperuricaemic response to fructose loading.

Methods

Healthy volunteers (n = 74) provided serum and urine samples immediately before and 30, 60, 120 and 180 minutes after ingesting a 64 g fructose solution. Data were analyzed based on the presence or absence of the ABCG2 141 K gout risk allele.

Results

The 141 K risk allele was present in 23 participants (31%). Overall, serum urate (SU) concentrations during the fructose load were similar in those with and without the 141 K allele (P_SNP = 0.15). However, the 141 K allele was associated with a smaller increase in SU following fructose intake (P_SNP <0.0001). Those with the 141 K allele also had a smaller increase in serum glucose following the fructose load (P_SNP = 0.002). Higher fractional excretion of uric acid (FEUA) at baseline and throughout the fructose load was observed in those with the 141 K risk allele (P_SNP <0.0001). However, the change in FEUA in response to fructose was not different in those with and without the 141 K risk allele (P_SNP = 0.39). The 141 K allele effects on serum urate and glucose were more pronounced in Polynesian participants and in those with a body mass index ≥25 kg/m².

Conclusions

In contrast to the predicted responses for a hyperuricemia/gout risk allele, the 141 K allele is associated with smaller increases in SU and higher FEUA following a fructose load. The results suggest that ABCG2 interacts with extra-renal metabolic pathways in a complex manner to regulate SU and gout risk.

Clinical Trials Registration

The study was registered by the Australian Clinical Trials Registry (ACTRN12610001036000).     

The seagrass Posidonia oceanica as indicator of coastal water quality: Experimental intercalibration of classification systems

The pervasive use of ecological indices is increasingly requiring actions of harmonisation. Specifically, within the EU Water Framework Directive, an important effort in methods intercalibration is being done. However, a significant limitation in comparability assessment arises from the datasets used, which have different geographic origins. The purpose of our study was to perform an experimental intercalibration, where data were collected specifically on a set of common sites and following all the requirements of the methods being assessed. Three indices based on the marine angiosperm Posidonia oceanica, the POMI, the BiPo and the PoSte, were applied to sites in three different geographical areas of the western Mediterranean: Catalonia, Corsica and Southern Italy (Ischia), distant between hundreds and more than thousands of kilometers. Two indices, POMI and BiPo, showed not only a very good relationship with human pressures (measured on a common scale for all sites) but also a high comparability, in all aspects investigated. The differences found for the third one (PoSte) are hypothesised as being due to a different rationale used to define reference conditions, the different metrics used in the index, and in particular to a different definition of ecological status in relation to the time scale of the response to anthropogenic pressures. Our study demonstrates that indices with very different approaches can provide fully reliable and comparable results.