Hybrid dynamic/static method for large-scale simulation of metabolism

BACKGROUND: Many computer studies have employed either dynamic simulation or metabolic flux analysis (MFA) to predict the behaviour of biochemical pathways. Dynamic simulation determines the time evolution of pathway properties in response to environmental changes, whereas MFA provides only a snapshot of pathway properties within a particular set of environmental conditions. However, owing to the large amount of kinetic data required for dynamic simulation, MFA, which requires less information, has been used to manipulate large-scale pathways to determine metabolic outcomes. RESULTS: Here we describe a simulation method based on cooperation between kinetics-based dynamic models and MFA-based static models. This hybrid method enables quasi-dynamic simulations of large-scale metabolic pathways, while drastically reducing the number of kinetics assays needed for dynamic simulations. The dynamic behaviour of metabolic pathways predicted by our method is almost identical to that determined by dynamic kinetic simulation. CONCLUSION: The discrepancies between the dynamic and the hybrid models were sufficiently small to prove that an MFA-based static module is capable of performing dynamic simulations as accurately as kinetic models. Our hybrid method reduces the number of biochemical experiments required for dynamic models of large-scale metabolic pathways by replacing suitable enzyme reactions with a static module

Surface Marker-Defined Head Kidney Granulocytes and B Lymphocytes of Rainbow Trout Express Benzo[a]pyrene-Inducible Cytochrome P4501A Protein

Polycyclic aromatic hydrocarbons (PAHs) such as benzo[a]pyrene (BaP) are immunotoxic to fish. Metabolism of PAHs in immune cells has been implicated in PAH immunotoxicity in mammals, but for fish the presence of metabolic enzymes in immune cells is less clear. The objective of this study was to examine localization and induction of the BaP-metabolizing biotransformation enzyme, cytochrome P4501A (CYP1A), in head kidney immune cells of rainbow trout (Oncorhynchus mykiss). In the first step, we measured induction of CYP1A-dependent 7-ethoxyresorufin-O-deethylase (EROD) activity and CYP1A protein in head kidney of rainbow trout treated with a single intraperitoneal (ip) injection of 25 mg BaP/kg body weight. From days 3 to 10 postinjection, the BaP treatment led to a significant elevation of EROD and CYP1A protein in head kidney and liver, with CYP1A expression levels in the head kidney being much lower than in the liver. Next, we examined the cellular localization of CYP1A protein in the head kidney cell types: vascular endothelial, endocrine and lymphoid cells. CYP1A immunoreactivity was detectable only in BaP-treated trout, where it was localized in endothelial and lymphoid cells. Finally, we aimed to clarify which of the hematopoietic cell types possess CYP1A protein. Using double immunostaining for CYP1A and surface markers of rainbow trout immune cells, we identified B lymphocytes and granulocytes expressing inducible CYP1A protein and being the likely sites of BaP metabolism in the head kidne

A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles

BACKGROUND: In order to improve understanding of metabolic systems there have been attempts to construct S-system models from time courses. Conventionally, non-linear curve-fitting algorithms have been used for modelling, because of the non-linear properties of parameter estimation from time series. However, the huge iterative calculations required have hindered the development of large-scale metabolic pathway models. To solve this problem we propose a novel method involving power-law modelling of metabolic pathways from the Jacobian of the targeted system and the steady-state flux profiles by linearization of S-systems. RESULTS: The results of two case studies modelling a straight and a branched pathway, respectively, showed that our method reduced the number of unknown parameters needing to be estimated. The time-courses simulated by conventional kinetic models and those described by our method behaved similarly under a wide range of perturbations of metabolite concentrations. CONCLUSION: The proposed method reduces calculation complexity and facilitates the construction of large-scale S-system models of metabolic pathways, realizing a practical application of reverse engineering of dynamic simulation models from the Jacobian of the targeted system and steady-state flux profiles

Surface Marker-Defined Head Kidney Granulocytes and B Lymphocytes of Rainbow Trout Express Benzo[a]pyrene-Inducible Cytochrome P4501A Protein

Polycyclic aromatic hydrocarbons (PAHs) such as benzo[a]pyrene (BaP) are immunotoxic to fish. Metabolism of PAHs in immune cells has been implicated in PAH immunotoxicity in mammals, but for fish the presence of metabolic enzymes in immune cells is less clear. The objective of this study was to examine localization and induction of the BaP-metabolizing biotransformation enzyme, cytochrome P4501A (CYP1A), in head kidney immune cells of rainbow trout (Oncorhynchus mykiss). In the first step, we measured induction of CYP1A-dependent 7-ethoxyresorufin-O-deethylase (EROD) activity and CYP1A protein in head kidney of rainbow trout treated with a single intraperitoneal (ip) injection of 25 mg BaP/kg body weight. From days 3 to 10 postinjection, the BaP treatment led to a significant elevation of EROD and CYP1A protein in head kidney and liver, with CYP1A expression levels in the head kidney being much lower than in the liver. Next, we examined the cellular localization of CYP1A protein in the head kidney cell types: vascular endothelial, endocrine and lymphoid cells. CYP1A immunoreactivity was detectable only in BaP-treated trout, where it was localized in endothelial and lymphoid cells. Finally, we aimed to clarify which of the hematopoietic cell types possess CYP1A protein. Using double immunostaining for CYP1A and surface markers of rainbow trout immune cells, we identified B lymphocytes and granulocytes expressing inducible CYP1A protein and being the likely sites of BaP metabolism in the head kidney

Morphological and Biochemical Changes During Aging and Photoaging of the Skin of C57BL/6J Mice

The differences between the dorsal skin of 11- and 16-week-old C57BL/6J mice were examined morphologically and biochemically. The dermis of the 16-week-old mice was thinner than that of the 11-week-old mice due to decreases in the amounts of soluble collagen and elastin. Next, the changes in dorsal skin exposed to UVA irradiation for 8 weeks (576 J/cm2) were examined in 3 (younger)- and 8 (older)-week-old C57BL/6J mice. The thickness of the dermis was not significantly different between the UVA-irradiated and control mice in either the younger or older group. The increase in the amount of collagen was related to the increase in the level of soluble collagen in the younger mice. In contrast, it was related to the increase in the level of insoluble collagen in the older mice. In the UVA-irradiated older mice, the activity of the latent form of MMP-13 was significantly higher than that in the control mice. These results suggest that aging and UVA-induced photoaging in the skin are histologically and biochemically different phenomena

Immunotoxic effects of environmental toxicants in fish — how to assess them?

Numerous environmental chemicals, both long-known toxicants such as persistent organic pollutants as well as emerging contaminants such as pharmaceuticals, are known to modulate immune parameters of wildlife species, what can have adverse consequences for the fitness of individuals including their capability to resist pathogen infections. Despite frequent field observations of impaired immunocompetence and increased disease incidence in contaminant-exposed wildlife populations, the potential relevance of immunotoxic effects for the ecological impact of chemicals is rarely considered in ecotoxicological risk assessment. A limiting factor in the assessment of immunotoxic effects might be the complexity of the immune system what makes it difficult (1) to select appropriate exposure and effect parameters out of the many immune parameters which could be measured, and (2) to evaluate the significance of the selected parameters for the overall fitness and immunocompetence of the organism. Here, we present — on the example of teleost fishes — a brief discussion of how to assess chemical impact on the immune system using parameters at different levels of complexity and integration: immune mediators, humoral immune effectors, cellular immune defenses, macroscopical and microscopical responses of lymphoid tissues and organs, and host resistance to pathogens. Importantly, adverse effects of chemicals on immunocompetence may be detectable only after immune system activation, e.g., after pathogen challenge, but not in the resting immune system of non-infected fish. Current limitations to further development and implementation of immunotoxicity assays and parameters in ecotoxicological risk assessment are not primarily due to technological constraints, but are related from insufficient knowledge of (1) possible modes of action in the immune system, (2) the importance of intra- and inter-species immune system variability for the response against chemical stressors, and (3) deficits in conceptual and mechanistic assessment of combination effects of chemicals and pathogen

Factors influencing healthcare-seeking behaviour among Muslims from Southeast Asian countries (Indonesia and Malaysia) living in Japan: an exploratory qualitative study

[Objectives] To identify factors influencing healthcare-seeking behaviours and to explore issues with healthcare experiences of Muslims from Southeast Asian countries (Indonesia and Malaysia) living in Japan. [Design] Qualitative study. [Setting] Kansai area of Japan (Kyoto, Osaka, Hyogo and Nara prefectures). [Participants] Forty-five Muslims in Japan from Southeast Asian countries (Indonesia and Malaysia). [Methods] Semistructured interviews were conducted by trained interviewers who are Muslims living in Japan. Interviews were conducted in Indonesian and Malaysian languages and transcribed and translated into English. The data were thematically analysed. [Results] Four themes were identified: (1) trying to comply with the recommendations of Islam, (2) confusion about healthcare system, (3) improvising an informal support system and (4) language barrier problems. [Conclusion] Muslims in Japan have some issues when obtaining healthcare services mainly because of communication issues besides the conflicts to meet their religious obligations. Education and awareness building for the Muslim patients in Japan as well as Japanese healthcare providers are needed to allow smooth communication between Japanese healthcare providers and Muslim patients in Japan