Genomic stuff: Governing the (im)matter of life

Emphasizing the context of what has often been referred to as “scarce natural resources”, in particular forests, meadows, and fishing stocks, Elinor Ostrom’s important work Governing the commons (1990) presents an institutional framework for discussing the development and use of collective action with respect to environmental problems. In this article we discuss extensions of Ostrom’s approach to genes and genomes and explore its limits and usefulness. With the new genetics, we suggest, the biological gaze has not only been turned inward to the management and mining of the human body, also the very notion of the “biological” has been destabilized. This shift and destabilization, we argue, which is the result of human refashioning and appropriation of “life itself”, raises important questions about the relevance and applicability of Ostrom’s institutional framework in the context of what we call “genomic stuff”, genomic material, data, and information

Associations of iron status with dietary and other factors in 6-year-old children

To access publisher full text version of this article. Please click on the hyperlink in Additional Links fieldOBJECTIVE: To investigate the associations of iron status at 6 years of age with dietary and other factors. DESIGN: In a cross-sectional study, children's dietary intakes (3-day weighed food record) were recorded, body size was measured and blood samples were taken near their sixth birthday. SUBJECTS: A sample of 188 children, from two previous studies (cohorts 1 and 2), was contacted, and 139 (74%) agreed to participate. RESULTS: Multiple regression analyses with dietary and other factors showed that meat and fish consumption, multivitamin/mineral supplement intake (both positively) and cow's milk product consumption (negatively) were associated with log serum ferritin (SF) (adjusted R (2)=0.125; P=0.028; n=129), and juices and residence (rural>urban) with haemoglobin (Hb) (adjusted R (2)=0.085; P=0.034; n=127). Of 21 multivitamin/mineral consumers, none had depleted iron stores compared to 21 iron-depleted of 108 non-consumers (P=0.024). Children living in rural areas (10,000 inhabitants) (82.1+/-3.2 fl; n=103) (P=0.048). Multiple regression analyses with dietary and other factors and growth showed in cohort 1 that residence (rural>urban), weight gain 0-1years (negatively), and meat and fish intake (positively) were associated with Hb (adjusted R (2)=0.323; P=0.030; n=51), meat and fish (positively) with both log SF (adjusted R (2)=0.069; P=0.035; n=52) and MCV (adjusted R (2)=0.064; P=0.035; n=52), and in cohort 2 cow's milk product consumption (negatively) was associated with log SF (adjusted R (2)=0.119; P=0.017; n=41) and residence (rural>urban) with MCV (adjusted R (2)=0.102; P=0.025; n=41). CONCLUSIONS: Consumption of meat and fish and possibly also juices, as well as multivitamin/mineral intake might affect iron status in 6-year-old children positively, whereas cow's milk product consumption might affect iron status negatively. Slower growth in the first year of life and rural residence are positively related to iron status of 6-year-olds

The Regularizing Capacity of Metabolic Networks

Despite their topological complexity almost all functional properties of metabolic networks can be derived from steady-state dynamics. Indeed, many theoretical investigations (like flux-balance analysis) rely on extracting function from steady states. This leads to the interesting question, how metabolic networks avoid complex dynamics and maintain a steady-state behavior. Here, we expose metabolic network topologies to binary dynamics generated by simple local rules. We find that the networks' response is highly specific: Complex dynamics are systematically reduced on metabolic networks compared to randomized networks with identical degree sequences. Already small topological modifications substantially enhance the capacity of a network to host complex dynamic behavior and thus reduce its regularizing potential. This exceptionally pronounced regularization of dynamics encoded in the topology may explain, why steady-state behavior is ubiquitous in metabolism.Comment: 6 pages, 4 figure

Flux networks in metabolic graphs

A metabolic model can be represented as bipartite graph comprising linked reaction and metabolite nodes. Here it is shown how a network of conserved fluxes can be assigned to the edges of such a graph by combining the reaction fluxes with a conserved metabolite property such as molecular weight. A similar flux network can be constructed by combining the primal and dual solutions to the linear programming problem that typically arises in constraint-based modelling. Such constructions may help with the visualisation of flux distributions in complex metabolic networks. The analysis also explains the strong correlation observed between metabolite shadow prices (the dual linear programming variables) and conserved metabolite properties. The methods were applied to recent metabolic models for Escherichia coli, Saccharomyces cerevisiae, and Methanosarcina barkeri. Detailed results are reported for E. coli; similar results were found for the other organisms.Comment: 9 pages, 4 figures, RevTeX 4.0, supplementary data available (excel

Duality, thermodynamics, and the linear programming problem in constraint-based models of metabolism

It is shown that the dual to the linear programming problem that arises in constraint-based models of metabolism can be given a thermodynamic interpretation in which the shadow prices are chemical potential analogues, and the objective is to minimise free energy consumption given a free energy drain corresponding to growth. The interpretation is distinct from conventional non-equilibrium thermodynamics, although it does satisfy a minimum entropy production principle. It can be used to motivate extensions of constraint-based modelling, for example to microbial ecosystems.Comment: 4 pages, 2 figures, 1 table, RevTeX 4, final accepted versio

Structural Kinetic Modeling of Metabolic Networks

To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit kinetic modeling based on differential equations is still often severely hampered by inadequate knowledge of the enzyme-kinetic rate laws and their associated parameter values. Here we propose a method that aims to give a detailed and quantitative account of the dynamical capabilities of metabolic systems, without requiring any explicit information about the particular functional form of the rate equations. Our approach is based on constructing a local linear model at each point in parameter space, such that each element of the model is either directly experimentally accessible, or amenable to a straightforward biochemical interpretation. This ensemble of local linear models, encompassing all possible explicit kinetic models, then allows for a systematic statistical exploration of the comprehensive parameter space. The method is applied to two paradigmatic examples: The glycolytic pathway of yeast and a realistic-scale representation of the photosynthetic Calvin cycle.Comment: 14 pages, 8 figures (color

Comparison of aneroid and oscillometric blood pressure measurements in children.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access.Limited data exist on the comparison of blood pressure (BP) measurements using aneroid and oscillometric devices. The purpose of the study was to investigate the difference in BP obtained using oscillometric and aneroid BP monitors in 9- to 10-year-old children. A total of 979 children were divided into group O, which underwent two oscillometric BP readings followed by two aneroid readings, and group A, which had BP measured in the reverse order. No significant difference was found between the mean (±standard deviation) of the two systolic BP readings obtained using the oscillometric and aneroid devices (111.5±8.6 vs 111.3±8.1 mm Hg; P=.39), whereas the mean diastolic BP was lower with the oscillometric monitor (61.5±8.0 vs 64.5±6.8 mm Hg; P<.001). A significant downward trend in BP was observed with each consecutive measurement, and agreement between the two monitors was limited. Multiple BP measurements are, therefore, recommended before the diagnosis of elevated BP or hypertension is made with either method.Landspitali - The National University Hospital of Iceland Research Fun