Global organization of metabolic fluxes in the bacterium, Escherichia coli

Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological organization of individual reactions into metabolic networks is increasingly well understood, the principles governing their global functional utilization under different growth conditions pose many open questions. We implement a flux balance analysis of the E. coli MG1655 metabolism, finding that the network utilization is highly uneven: while most metabolic reactions have small fluxes, the metabolism's activity is dominated by several reactions with very high fluxes. E. coli responds to changes in growth conditions by reorganizing the rates of selected fluxes predominantly within this high flux backbone. The identified behavior likely represents a universal feature of metabolic activity in all cells, with potential implications to metabolic engineering.Comment: 15 pages 4 figure

The rise of the quasi-public space and its consequences for cities and culture

This article argues that whilst appearing new, quasi-public spaces have emerged from a process of investment restructuring over the last 50 years. The profound change that is set in motion is a loss of control of public space and its cultural uses in cities. The tensions set up in this transformation are illustrated by the cultural fortunes of the largest such space in London, Granary Square; and, that of the City of London that has little, if any, public space

Using nexus thinking to identify opportunities for mangrove management in the Klang Islands, Malaysia

Despite wide recognition of the multiple ecosystem services provided by mangroves, they continue to experience decline and degradation especially in the face of urbanization. Given the interplay between multiple resources and stakeholders in the fate of mangroves, mangrove management can be framed as a nexus challenge and nexus thinking used to identify potential solutions. Using the Klang Islands, Malaysia, as a case study site, this paper characterizes the mangrove nexus and stakeholders visions for the future to identify potential options for future management. Through a series of stakeholder workshops and focus group discussions conducted over two years results show that local communities can identify benefits from mangroves beyond the provisioning of goods and significant impacts to their lives from mangrove loss. While better protected and managed mangroves remained a central part of participants' visions for the islands, participants foresaw a limited future for fishing around the islands, preferring instead alternative livelihood opportunities such as eco-tourism. The network of influencers of the Klang Islands’ mangroves extends far beyond the local communities and many of these actors were part of the visions put forward. Stakeholders with a high interest in the mangroves typically have a low influence over their management and many high influence stakeholders (e.g. private sector actors) were missing from the engagement. Future nexus action should focus on integrating stakeholders and include deliberate and concerted engagement with high influence stakeholders while at the same time ensuring a platform for high interest/low influence groups. Fortifying existing plans to include mangroves more explicitly will also be essential. Lessons learnt from this study are highly relevant for coastal mangrove systems elsewhere in the Southeast Asian region

Mathematizing Darwin

Ernst Mayr called the first part of the evolutionary synthesis the ‘Fisherian synthesis’ on account of the dominant role played by R.A. Fisher in forging a mathematical theory of natural selection together with J.B.S. Haldane and Sewall Wright in the decade 1922–1932. It is here argued that Fisher’s contribution relied on a close reading of Darwin’s work to a much greater extent than did the contributions of Haldane and Wright, that it was synthetic in contrast to their analytic approach and that it was greatly influenced by his friendship with the Darwin family, particularly with Charles’s son Leonard

Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum

BACKGROUND: Quantification of the metabolic network of an organism offers insights into possible ways of developing mutant strain for better productivity of an extracellular metabolite. The first step in this quantification is the enumeration of stoichiometries of all reactions occurring in a metabolic network. The structural details of the network in combination with experimentally observed accumulation rates of external metabolites can yield flux distribution at steady state. One such methodology for quantification is the use of elementary modes, which are minimal set of enzymes connecting external metabolites. Here, we have used a linear objective function subject to elementary modes as constraint to determine the fluxes in the metabolic network of Corynebacterium glutamicum. The feasible phenotypic space was evaluated at various combinations of oxygen and ammonia uptake rates. RESULTS: Quantification of the fluxes of the elementary modes in the metabolism of C. glutamicum was formulated as linear programming. The analysis demonstrated that the solution was dependent on the criteria of objective function when less than four accumulation rates of the external metabolites were considered. The analysis yielded feasible ranges of fluxes of elementary modes that satisfy the experimental accumulation rates. In C. glutamicum, the elementary modes relating to biomass synthesis through glycolysis and TCA cycle were predominantly operational in the initial growth phase. At a later time, the elementary modes contributing to lysine synthesis became active. The oxygen and ammonia uptake rates were shown to be bounded in the phenotypic space due to the stoichiometric constraint of the elementary modes. CONCLUSION: We have demonstrated the use of elementary modes and the linear programming to quantify a metabolic network. We have used the methodology to quantify the network of C. glutamicum, which evaluates the set of operational elementary modes at different phases of fermentation. The methodology was also used to determine the feasible solution space for a given set of substrate uptake rates under specific optimization criteria. Such an approach can be used to determine the optimality of the accumulation rates of any metabolite in a given network

A survey of medical students to assess their exposure to and knowledge of renal transplantation

BACKGROUND: Within the field of renal transplantation there is a lack of qualified and trainee surgeons and a shortage of donated organs. Any steps to tackle these issues should, in part, be aimed at future doctors. METHODS: A questionnaire was distributed to final year students at a single medical school in the UK to assess their exposure to and knowledge of renal transplantation. RESULTS: Although 46% of responding students had examined a transplant recipient, only 14% had ever witnessed the surgery. Worryingly, 9% of students believed that xenotransplantation commonly occurs in the UK and 35% were unable to name a single drug that a recipient may need to take. CONCLUSIONS: This survey demonstrates a lack of exposure to, and knowledge of, the field of renal transplantation. Recommendations to address the problems with the recruitment of surgeons and donation of organs, by targeting medical students are made

Maximising response to postal questionnaires – A systematic review of randomised trials in health research

Background Postal self-completion questionnaires offer one of the least expensive modes of collecting patient based outcomes in health care research. The purpose of this review is to assess the efficacy of methods of increasing response to postal questionnaires in health care studies on patient populations. Methods The following databases were searched: Medline, Embase, CENTRAL, CDSR, PsycINFO, NRR and ZETOC. Reference lists of relevant reviews and relevant journals were hand searched. Inclusion criteria were randomised trials of strategies to improve questionnaire response in health care research on patient populations. Response rate was defined as the percentage of questionnaires returned after all follow-up efforts. Study quality was assessed by two independent reviewers. The Mantel-Haenszel method was used to calculate the pooled odds ratios. Results Thirteen studies reporting fifteen trials were included. Implementation of reminder letters and telephone contact had the most significant effect on response rates (odds ratio 3.7, 95% confidence interval 2.30 to 5.97 p = <0.00001). Shorter questionnaires also improved response rates to a lesser degree (odds ratio 1.4, 95% confidence interval 1.19 to 1.54). No evidence was found that incentives, re-ordering of questions or including an information brochure with the questionnaire confer any additional advantage. Conclusion Implementing repeat mailing strategies and/or telephone reminders may improve response to postal questionnaires in health care research. Making the questionnaire shorter may also improve response rates. There is a lack of evidence to suggest that incentives are useful. In the context of health care research all strategies to improve response to postal questionnaires require further evaluation

Arduous implementation: Does the Normalisation Process Model explain why it's so difficult to embed decision support technologies for patients in routine clinical practice

Background: decision support technologies (DSTs, also known as decision aids) help patients and professionals take part in collaborative decision-making processes. Trials have shown favorable impacts on patient knowledge, satisfaction, decisional conflict and confidence. However, they have not become routinely embedded in health care settings. Few studies have approached this issue using a theoretical framework. We explained problems of implementing DSTs using the Normalization Process Model, a conceptual model that focuses attention on how complex interventions become routinely embedded in practice.Methods: the Normalization Process Model was used as the basis of conceptual analysis of the outcomes of previous primary research and reviews. Using a virtual working environment we applied the model and its main concepts to examine: the 'workability' of DSTs in professional-patient interactions; how DSTs affect knowledge relations between their users; how DSTs impact on users' skills and performance; and the impact of DSTs on the allocation of organizational resources.Results: conceptual analysis using the Normalization Process Model provided insight on implementation problems for DSTs in routine settings. Current research focuses mainly on the interactional workability of these technologies, but factors related to divisions of labor and health care, and the organizational contexts in which DSTs are used, are poorly described and understood.Conclusion: the model successfully provided a framework for helping to identify factors that promote and inhibit the implementation of DSTs in healthcare and gave us insights into factors influencing the introduction of new technologies into contexts where negotiations are characterized by asymmetries of power and knowledge. Future research and development on the deployment of DSTs needs to take a more holistic approach and give emphasis to the structural conditions and social norms in which these technologies are enacte