The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks

The dynamic behavior of metabolic networks is governed by numerous regulatory mechanisms, such as reversible phosphorylation, binding of allosteric effectors or temporal gene expression, by which the activity of the participating enzymes can be adjusted to the functional requirements of the cell. For most of the cellular enzymes, such regulatory mechanisms are at best qualitatively known, whereas detailed enzyme-kinetic models are lacking. To explore the possible dynamic behavior of metabolic networks in cases of lacking or incomplete enzyme-kinetic information, we present a computational approach based on structural kinetic modeling. We derive statistical measures for the relative impact of enzyme-kinetic parameters on dynamic properties (such as local stability) and apply our approach to the metabolism of human erythrocytes. Our findings show that allosteric enzyme regulation significantly enhances the stability of the network and extends its potential dynamic behavior. Moreover, our approach allows to differentiate quantitatively between metabolic states related to senescence and metabolic collapse of the human erythrocyte. We think that the proposed method represents an important intermediate step on the long way from topological network analysis to detailed kinetic modeling of complex metabolic networks

Delayed prescribing of antibiotics for acute respiratory infections by GP registrars: a qualitative study

Background: Antibiotic prescribing for acute self-limiting respiratory tract infections (ARTIs) in Australia is higher than international benchmarks. Antibiotics have little or no efficacy in these conditions, and unnecessary use contributes to antibiotic resistance. Delayed prescribing has been shown to reduce antibiotic use. GP registrars are at a career-stage when long-term prescribing patterns are being established. Aim: To explore experiences, perceptions and attitudes of GP registrars and supervisors to delayed antibiotic prescribing for ARTIs. Design and setting: A qualitative study of Australian GP registrars and supervisors using a thematic analysis approach. Method: GP registrars and supervisors were recruited across three Australian states/territories, using maximum variation sampling. Telephone interviews explored participants’ experience and perceptions of delayed prescribing of antibiotics in ARTIs. Data collection and analysis were concurrent and iterative. Results: A total of 12 registrars and 10 supervisors were interviewed. Key themes included the use of delayed prescribing as a safety-net in cases of diagnostic uncertainty or when clinical review was logistically difficult. Delayed prescribing was viewed as a method of educating and empowering patients, and building trust and the doctor–patient relationship. Conversely, it was also seen as a loss of control over management decisions. Supervisors, more so than registrars, appreciated the psychosocial complexity of ARTI consultations and the importance of delayed antibiotic prescribing in this context. Conclusion: Better awareness and understanding by GP registrars of the evidence for delayed antibiotic prescription may be a means of reducing antibiotic prescribing. Understanding both registrar and supervisor usage, uncertainties and attitudes should inform educational approaches on this topic

The Roles of Children's Literature in the English Program in Primary Schools: Reading the texts of our lives?

This study explores the possible roles children's literature plays in the contemporary primary English classroom. How teachers perceive literature is directly linked to the relationship they see between the reader, the 'read' and the practice of reading. Such perceptions are derived from many influences, both ideological and pedagogical. All, in some way, are driven by a Foucauldian perspective of power where many competing discourses of English education organise meaning differently and establish their own positions of power. The research for this study adopts a multimethodological approach that draws on ethnographic and quasi-experimental research, together with conceptual, discursive research. It is organised in a metaphorical framework of research in three broad categories of 'lab', 'field' and 'library' research. The context for the study involves two New South Wales sites: primary schools and a regional university. Through surveys of two hundred and eighty-nine teacher education students and interviews with eight classroom teachers, the study examines how preservice and practising teachers recognise and develop their own expertise in the areas of reading and literature. It explores their attitudes to literature and their knowledge of literary theory and of children's literature, and the roles they see literature playing in English education in the primary school. In keeping with the postcritical thinking of this research, the study has followed Romm's suggestion (1997) that claiming multiple realities offers sound arguments that will stimulate discussion in society and enhance the Discourse of the primary English classroom

Incorporating expression data in metabolic modeling: a case study of lactate dehydrogenase

Integrating biological information from different sources to understand cellular processes is an important problem in systems biology. We use data from mRNA expression arrays and chemical kinetics to formulate a metabolic model relevant to K562 erythroleukemia cells. MAP kinase pathway activation alters the expression of metabolic enzymes in K562 cells. Our array data show changes in expression of lactate dehydrogenase (LDH) isoforms after treatment with phorbol 12-myristate 13-acetate (PMA), which activates MAP kinase signaling. We model the change in lactate production which occurs when the MAP kinase pathway is activated, using a non-equilibrium, chemical-kinetic model of homolactic fermentation. In particular, we examine the role of LDH isoforms, which catalyze the conversion of pyruvate to lactate. Changes in the isoform ratio are not the primary determinant of the production of lactate. Rather, the total concentration of LDH controls the lactate concentration.Comment: In press, Journal of Theoretical Biology. 27 pages, 9 figure

Determination of Rapid-Equilibrium Kinetic Parameters of Ordered and Random Enzyme-Catalyzed Reaction A + B = P + Q

This article deals with the rapid-equilibrium kinetics of the forward and reverse reactions together for the ordered and random enzyme-catalyzed A + B = P + Q and emphasizes the importance of reporting the values of the full set of equilibrium constants. Equilibrium constants that are not in the rate equation can be calculated for random mechanisms using thermodynamic cycles. This treatment is based on the use of a computer to derive rate equations for three mechanisms and to estimate the kinetic parameters with the minimum number of velocity measurements. The most general of these three programs is the one to use first when the mechanism for A + B = P + Q is studied for the first time. This article shows the effects of experimental errors in velocity measurements on the values of the kinetic parameters and on the apparent equilibrium constant calculated using the Haldane relation

Immediate and delayed antibiotic prescribing strategies used by Australian early-career GP: A cross-sectional analysis

BACKGROUND: Antibiotics are overused for non-pneumonia acute respiratory tract infections (ARTIs). AIM: To establish prevalence and explore associations of delayed and immediate antibiotic prescribing strategies of Australian early-career GPs (specialist GP vocational trainees, also known as GP registrars) for non-pneumonia ARTIs. DESIGN AND SETTING: Cross-sectional analysis of data collected between September 2016 and December 2017 from the Registrar Clinical Encounters in Training cohort (ReCEnT) study, an ongoing cohort study of GP registrars’ in-practice clinical experiences in four Australian states and territories. METHOD: Multinomial logistic regression with outcome antibiotic prescribing (no prescribing, immediate prescribing, and delayed prescribing). RESULTS: Of 7156 new ARTI diagnoses, no antibiotics were prescribed for 4892 (68%); antibiotics were prescribed for immediate use for 1614 diagnoses (23%) and delayed antibiotics were used for 650 diagnoses (9%). Delayed prescribing was used in 22% of otitis media, 16% of sinusitis, 13% of sore throat, 11% of acute bronchitis/bronchiolitis, and 5% of upper respiratory tract infection (URTI) diagnoses. Delayed prescribing was used for 29% of all prescriptions written. Delayed prescribing and immediate prescribing were associated with markers of clinical concern. Delayed prescribing was associated with longer duration of consultation and with fewer diagnoses/problems dealt with in the consultation. CONCLUSION: Australian early-career GPs use no prescribing for ARTIs substantially more than established GPs; however, except where URTIs are concerned, they still prescribe antibiotics in excess of validated benchmarks. Australian early-career GPs may use delayed prescribing more often than European established GPs, and may use it to manage diagnostic uncertainty and, possibly, conflicting influences on prescribing behaviour. The use of delayed prescribing may enable a transition to an environment of more-rational antibiotic prescribing for ARTIs

Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters

The aspartate-derived amino-acid pathway from plants is well suited for analysing the function of the allosteric network of interactions in branched pathways. For this purpose, a detailed kinetic model of the system in the plant model Arabidopsis was constructed on the basis of in vitro kinetic measurements. The data, assembled into a mathematical model, reproduce in vivo measurements and also provide non-intuitive predictions. A crucial result is the identification of allosteric interactions whose function is not to couple demand and supply but to maintain a high independence between fluxes in competing pathways. In addition, the model shows that enzyme isoforms are not functionally redundant, because they contribute unequally to the flux and its regulation. Another result is the identification of the threonine concentration as the most sensitive variable in the system, suggesting a regulatory role for threonine at a higher level of integration

Changing the antibiotic prescribing of general practice registrars: The ChAP study protocol for a prospective controlled study of a multimodal educational intervention

Background: Australian General Practitioners (GPs) are generous prescribers of antibiotics, prompting concerns including increasing antimicrobial resistance in the community. Recent data show that GPs in vocational training have prescribing patterns comparable with the high prescribing rate of their established GP supervisors. Evidence-based guidelines consistently advise that antibiotics are not indicated for uncomplicated upper respiratory tract infections (URTI) and are rarely indicated for acute bronchitis. A number of interventions have been trialled to promote rational antibiotic prescribing by established GPs (with variable effectiveness), but the impact of such interventions in a training setting is unclear. We hypothesise that intervening while early-career GPs are still developing their practice patterns and prescribing habits will result in better adherence to evidence-based guidelines as manifested by lower antibiotic prescribing rates for URTIs and acute bronchitis. Methods/design: The intervention consists of two online modules, a face-to-face workshop for GP trainees, a face-to-face workshop for their supervisors and encouragement for the trainee-supervisor dyad to include a case-based discussion of evidence-based antibiotic prescribing in their weekly one-on-one teaching meetings. We will use a non-randomised, non-equivalent control group design to assess the impact on antibiotic prescribing for acute upper respiratory infections and acute bronchitis by GP trainees in vocational training. Discussion: Early-career GPs who are still developing their clinical practice and prescribing habits are an underutilized target-group for interventions to curb the growth of antimicrobial resistance in the community. Interventions that are embedded into existing training programs or are linked to continuing professional development have potential to increase the impact of existing interventions at limited additional cost. Trial registration: Australian New Zealand Clinical Trials Registry, ACTRN12614001209684 (registered 17/11/2014)

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

BackgroundThe mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question.ResultsIn this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations.ConclusionsOverall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches