David Andrew Fell

Oxford Brookes University · Department of Biological and Medical Sciences

The increasing global demand for vegetable oils will only be met if there are significant improvements in the productivity of the major oil crops, such as oilseed rape. Metabolic engineering offers the prospect of further gains in yield beyond that already achieved by breeding and selection but requires guidance as to the changes that need to be ma...

Exploiting biological processes to recycle renewable carbon into high value platform chemicals provides a sustainable and greener alternative to current reliance on petrochemicals. In this regard Cupriavidus necator H16 represents a particularly promising microbial chassis due to its ability to grow on a wide range of low-cost feedstocks, including...

The regulation of lipid metabolism in oil seeds is still not fully understood and increasing our knowledge in this regard is of great economic, as well as intellectual, importance. Oilseed rape (Brassica napus) is a major global oil crop where increases in triacylglycerol (TAG) accumulation have been achieved by overexpression of relevant biosynthe...

Metabolic control analysis is a theoretical, systems biology framework for understanding how changes in the activity of one or more enzymes affect metabolic rates and concentrations. This chapter begins with a brief account of some of its terms and equations relevant to characterizing the responses of metabolic networks to modulation of enzymes, wi...

Diatoms are photoautotrophic unicellular algae and are among the most abundant, adaptable, and diverse marine phytoplankton. They are extremely interesting not only for their ecological role but also as potential feedstocks for sustainable biofuels and high-value commodities such as omega fatty acids, because of their capacity to accumulate lipids....

Lysophosphatidate acyltransferase (LPAAT) catalyses the second step of the Kennedy pathway for triacylglycerol (TAG) synthesis. In this study we expressed Trapaeolum majus LPAAT in Brassica napus (B. napus) cv 12075 to evaluate the effects on lipid synthesis and estimate the flux control coefficient for LPAAT. We estimated the flux control coeffici...

Mitochondrial respiratory states and rates MitoEAGLE Task Group

Clostridium autoethanogenum is an industrial microbe used for the commercial-scale production of ethanol from carbon monoxide. While significant progress has been made in the attempted diversification of this bioprocess, further improvements are desirable, particularly in the formation of the high-value platform chemicals, such as 2,3-butanediol. A...

Metabolic Control Analysis defines the relationships between the change in activity of an enzyme and the resulting impacts on metabolic fluxes and metabolite concentrations at steady state. In many biotechnological applications of metabolic engineering, however, the goal is to alter the product yield. In this case, although metabolism may be at a p...

Analysis of the impact of photorespiration on plant metabolism is usually based on manual inspection of small network diagrams. Here we create a structural metabolic model that contains the reactions that participate in photorespiration in the plastid, peroxisome, mitochondrion and cytosol and the metabolite exchanges between them. This model was s...

The article "Evidence that the metabolite repair enzyme NAD(P)HX epimerase has a moonlighting function" in this issue illustrates a number of the problems that still arise when attempting to translate genotypes to phenotypes, such as for interpreting mutant phenotypes or building genome-scale metabolic models. In this case, the mutation concerned a...

Biologically-derived hydrocarbons are considered to have great potential as next-generation biofuels owing to the similarity of their chemical properties to contemporary diesel and jet fuels. However, the low yield of these hydrocarbons in biotechnological production is a major obstacle for commercialization. Several genetic and process engineering...

The non-conventional yeast Kluyveromyces marxianus is an emerging industrial producer for many biotechnological processes. Here, we show the application of a biomass-linked stoichiometric model of central metabolism that is experimentally validated, and mass and charge balanced for assessing the carbon conversion efficiency of wild type and modifie...

Rice straw is a major crop residue which is burnt in many countries, creating significant air pollution. Thus, alternative routes for disposal of rice straw are needed. Biotechnological treatment of rice straw hydrolysate has potential to convert this agriculture waste into valuable biofuel(s) and platform chemicals. Geobacillus thermoglucosidasius...

Marine diatoms have potential as a biotechnological production platform, especially for lipid-derived products, including biofuels. Here we introduce some features of diatom metabolism, particularly with respect to photosynthesis, photorespiration and lipid synthesis and their differences relative to other photosynthetic eukaryotes. Since structura...

Previously we have used a genome scale model of rice metabolism to describe how metabolism reconfigures at different light intensities in an expanding leaf of rice. Although this established that the metabolism of the leaf was adequately represented, in the model, the scenario was not that of the typical function of the leaf—to provide material for...

Produce rich in phytochemicals may alter postprandial glucose and insulin responses by interacting with the pathways that regulate glucose uptake and insulin secretion in humans. The aims of the present study were to assess the phytochemical constituents of red beetroot juice and to measure the postprandial glucose and insulin responses elicited by...

Salmonella enterica serovar Typhimurium is an established model organism for Gram-negative, intracellular pathogens. Owing to the rapid spread of resistance to antibiotics among this group of pathogens, new approaches to identify suitable target proteins are required. Based on the genome sequence of Salmonella Typhimurium and associated databases,...

Although leaves have to accommodate markedly different metabolic flux patterns in the light and the dark, models of leaf metabolism based on flux balance analysis (FBA) have so far been confined to consideration of the network under continuous light. A new FBA framework is presented that solves the two phases of the diel cycle as a single optimisat...

Mathematical modeling of metabolism is essential for rational metabolic engineering. The present work focuses on several types of modeling approach to quantitative understanding of central metabolic network and energetics in the bioethanol-producing bacterium Zymomonas mobilis. Combined use of Flux Balance, Elementary Flux Mode, and thermodynamic a...

Zymomonas mobilis, an ethanol-producing bacterium, possesses the Entner-Doudoroff (E-D) pathway, pyruvate decarboxylase and two alcohol dehydrogenase isoenzymes for the fermentative production of ethanol and carbon dioxide from glucose. Using available kinetic parameters, we have developed a kinetic model that incorporates the enzymatic reactions o...

Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC Ionizing radiation exposure induces DNA double strand breaks in mammalian cells. In response, cells activate repair mechanisms which involve cell cycle arrest at discrete transition points of the cell cycle. The results in an accumulation of cells in S and G2 phase in an i...

Flux-balance models of metabolism generally utilise synthesis of biomass as the main determinant of intracellular fluxes. However, the biomass constraint alone is not sufficient to predict realistic fluxes in central heterotrophic metabolism of plant cells because of the major demand on the energy budget from transport costs and cell maintenance. T...

We describe the construction and analysis of a genome-scale metabolic model representing a developing leaf cell of rice, Oryza sativa, primarily derived from the annotations in the RiceCyc database. We used Flux Balance Analysis to determine that the model represents a network capable of producing biomass precursors (amino-acids, nucleotides, lipid...

The active, yet energetically inefficient electron transport chain of the ethanologenic bacterium Zymomonas mobilis could be used in metabolic engineering for redox-balancing purposes during synthesis of certain products. Although several reconstructions of Z. mobilis metabolism have been published, important aspects of redox balance and aerobic ca...

The discovery of synergistic combinations of standard-of-care drugs or new chemical or biological entities shows much promise in the treatment of cancer, and there is much interest in this strategy. However, the increasing number of possible combinations makes the task of selecting the best regimens particularly difficult. As a response to this pro...

s: AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics--Nov 12-16, 2011; San Francisco, CA Physiomics and pharmacometrics have collaborated to design a new database of anti-cancer drugs and therapeutic treatment information aimed at researchers in oncology and clinicians. This database, accessible through the web, of...

There is currently a great deal of interest in determining synergistic drug combinations, however, it is not easy to determine which schedules should be tested, since the number of different possible schedules increases combinatorially when more than one drug is considered. We have therefore developed a predictive PK-PD “Virtual Tumor” model that a...

New approaches are currently being investigated in drug development to improve the large failure rate seen in many clinical trials. Systems biology is one area which shows promise for changing the way we think about disease and drug development. Over the last decade, several biotechnology companies have been set up with the aim of incorporating sys...

In recent years there has been great interest in determining synergistic drug combinations. A difficulty, however, is that the number of different possible schedules increases combinatorically when more than one drug is considered, so it is very hard to know what schedules should be tested. Physiomics, a computational biology company based in Oxfor...

Since the early 1960s, drug combination therapy has been used to treat cancer, because of the limited number of malignancies that could respond to single-agent chemotherapy. Combination chemotherapy regimens have been designed on the basis of mechanism of action of the drugs, tumor cell specificity, balance between effectiveness and toxicity, and s...

Protoplasmic streaming (cyclosis) in plant cells has long been presented as a purely qualitative exercise in microscopy. Using simple formulae, it is possible to determine the energetics of this process (in terms of ATP hydrolysis) and its relation to the total energy expenditure of the plant cell. This exercise can provide a valuable integration o...

Reconstructing a model of the metabolic network of an organism from its annotated genome sequence would seem, at first sight, to be one of the most straightforward tasks in functional genomics, even if the various data sources required were never designed with this application in mind. The number of genome-scale metabolic models is, however, laggin...

Organisms share a common core to their metabolic networks. But what determined this: chance, chemical necessity, or evolutionary optimization? In this issue of Molecular Cell, Noor et al. (2010) provide new evidence for selection of a network with optimal features from a broader set of possibilities.

Flux is a key measure of the metabolic phenotype. Recently, complete (genome-scale) metabolic network models have been established for Arabidopsis (Arabidopsis thaliana), and flux distributions have been predicted using constraints-based modeling and optimization algorithms such as linear programming. While these models are useful for investigating...

Systems biology takes an interdisciplinary approach to the systematic study of complex interactions in biological systems. This approach seeks to decipher the emergent behaviors of complex systems rather than focusing only on their constituent properties. As an increasing number of examples illustrate the value of systems biology approaches to unde...

s: AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics--Nov 15-19, 2009; Boston, MA Nocodazole is an anti‐neoplastic agent which reversibly impairs tubulin assembly, resulting in blocking cells in mitosis. At high concentration, nocodazole rapidly depolymerises microtubules in vivo, preventing cells from progressing...

We describe the construction and analysis of a genome-scale metabolic model of Arabidopsis (Arabidopsis thaliana) primarily derived from the annotations in the Aracyc database. We used techniques based on linear programming to demonstrate the following: (1) that the model is capable of producing biomass components (amino acids, nucleotides, lipid,...

The following report selects and summarises some of the conclusions and recommendations generated throughout a series of workshops and discussions that have lead to the publication of the Science Policy Briefing (SPB) Nr. 35, published by the European Science Foundation. (Large parts of the present text are directly based on the ESF SPB. Detailed r...

MOTIVATION: In recent years, several methods have been proposed for determining metabolic pathways in an automated way based on network topology. The aim of this work is to analyse these methods by tackling a concrete example relevant in biochemistry. It concerns the question whether even-chain fatty acids, being the most important constituents of...

A decrease in retinoic acid levels due to alcohol consumption has been proposed as a contributor to such conditions as fetal alcohol spectrum diseases and ethanol-induced cancers. One molecular mechanism, competitive inhibition by ethanol of the catalytic activity of human alcohol dehydrogenase (EC 1.1.1.1) (ADH) on all-trans-retinol oxidation has...

Motivation: In recent years, several methods have been proposed for determining metabolic pathways in an automated way based on network topology. The aim of this work is to analyse these methods by tackling a concrete example relevant in biochemistry. It concerns the question whether even-chain fatty acids, being the most important constituents of...

Enzymes and other proteins coded by nuclear genes are targeted towards various compartments in the plant cell. Here, we describe a method by which localisation of enzymes in a plant cell may be predicted based on their transcription profile in conjunction with analysis of the structure of the metabolic network. This method uses reaction correlation...

Metabolic modelling provides a mathematically rigorous basis for system-level analysis of biochemical networks. However, the growing sizes of metabolic models can lead to serious problems in their construction and validation. In this work, we describe a relatively poorly investigated type of modelling error, called stoichiometric inconsistencies. T...

Stoichiometric analysis of metabolic networks allows the calculation of possible metabolic flux distributions in the absence of kinetic data. In order to predict which of the possible fluxes are present under certain conditions, additional constraints and optimization principles can be applied. One approach of calculating unknown fluxes (frequently...

Research into plant metabolism has a long history, and analytical approaches of ever-increasing breadth and sophistication have been brought to bear. We now have access to vast repositories of data concerning enzymology and regulatory features of enzymes, as well as large-scale datasets containing profiling information of transcripts, protein and m...

We describe a method by which the reactions in a metabolic system may be grouped hierarchically into sets of modules to form a metabolic reaction tree. In contrast to previous approaches, the method described here takes into account the fact that, in a viable network, reactions must be capable of sustaining a steady-state flux. In order to achieve...

The chapter discusses metabolism as an example of a complex biological system, where the explanations that are given for how the properties and activities of the components account for the function at the system level have been changing. It is argued that the difficulties in arriving at satisfactory explanations that contribute to understanding ari...

The 4th EMBO Workshop on Nuclear Organization took place between 12 and 15 October 2006 in Gosau, Austria, and was organized by D. Jackson, R. van Driel, H. Lipps and H. Westerhoff. ![][1] It is clear that DNA sequence and transcription factor availability alone are not sufficient for effective gene regulation in eukaryotes. Epigenetic factors a...

In the post-genomic era, the biochemical information for individual compounds, enzymes, reactions to be found within named organisms has become readily available. The well-known KEGG and BioCyc databases provide a comprehensive catalogue for this information and have thereby substantially aided the scientific community. Using these databases, the c...

Systems biology needs to show practical relevance to commercial biological challenges such as those of pharmaceutical development. The aim of this work is to design and validate some applications in anti-cancer therapeutic development. The test system was a group of novel cyclin-dependent kinase (CDK) inhibitors synthesised by Cyclacel Ltd. The mea...

For both, cardioplegia (CP) and ischemic preconditioning (IP), increased ischemic tolerance with reduction in infarct size is well documented. These cardioprotective effects are related to a limitation of high energy phosphate (HEP) depletion. As CP and IP have to be assumed to act by different mechanisms, their effects on myocardial HEP metabolism...

IntroductionMethods ResultsDiscussion

IntroductionControl Coefficients and ElasticitiesTop-Down Control AnalysisSupply and DemandMultisite Modulation and Proportional ActivationConclusion

Metabolic Control Analysis (MCA) is a theoretical framework for investigating and understanding control and regulation of metabolism. In particular, it relates the properties of metabolic systems to the kinetic characteristics of the component enzymes. However, not all of the properties of enzymes strongly influence the be-haviour of metabolic syst...

Aspects of metabolic control theory and experiments from metabolic biochemistry are reviewed in order to deduce the circumstances in which experimental studies involving metabolomics have the greatest chance of success. It is concluded that metabolic changes effected mainly through a single enzyme are those most likely to lead to large changes in m...

In this article we address the question of how, given information about the reaction fluxes of a system, flux values can be assigned to the elementary modes of that system. Having described a method by which this may be accomplished, we first illustrate its application to a hypothetical, in silico system, and then apply it to fermentation data from...

In this paper some of the general concepts underpinning the computer modelling of metabolic systems are introduced. The difference between kinetic and structural modelling is emphasized, and the more important techniques from both, along with the physiological implications, are described. These approaches are then illustrated by descriptions of oth...

Despite dramatic increases in glucose influx during the transition from fasting to fed states, plasma glucose concentration remains tightly controlled. This constancy is in large part due to the capacity of skeletal muscle to absorb excess glucose and store it as glycogen. The magnitude of this capacity is controlled by insulin by way of regulated...

The enzymatic activities of threonine pathway in Escherichia coli are sensitive to pollutants such as cadmium, copper and mercury, which, even at low concentration, can substantially decrease or even block the pathway at several steps. Our aim was to investigate the complex effects on a metabolic pathway of such general enzyme inhibitors with sever...

Metabolic pathways are a central paradigm in biology. Historically, they have been defined on the basis of their step-by-step discovery. However, the genome-scale metabolic networks now being reconstructed from annotation of genome sequences demand new network-based definitions of pathways to facilitate analysis of their capabilities and functions,...

We briefly review the metabolism of the chloroplast stroma, and describe the structural modelling technique of elementary modes analysis. The technique is applied to a model of chloroplast metabolism to investigate viable pathways in the light, in the dark, and in the dark with the addition of sedoheptulose-1,7-bisphosphatase (normally inactive in...

The effect of externally applied L-cysteine and glutathione (GSH) on ATP sulphurylase and adenosine 5'-phosphosulphate reductase (APR), two key enzymes of assimilatory sulphate reduction, was examined in Arabidopsis thaliana root cultures. Addition of increasing L-cysteine to the nutrient solution increased internal cysteine, gamma-glutamylcysteine...

Elementary flux modes (direct reaction routes) are minimal sets of enzymes that can operate at steady state, with all irreversible reactions used in the appropriate direction. They can be interpreted as component pathways of a (bio)chemical reaction network. Here, two different definitions of elementary modes are given and their equivalence is prov...

Exact adjustment of the Embden-Meyerhof pathway (EMP) is an important issue in ischemic preconditioning (IP) because an attenuated ischemic lactate accumulation contributes to myocardial protection. However, precise mechanisms of glycolytic flux and its regulation in IP remain to be elucidated. In open chest pigs, IP was achieved by two cycles of 1...

Elementary mode analysis has been used to study a metabolic pathway model of a recombinant Saccharomyces cerevisiae system that was genetically engineered to produce the bacterial storage compound poly-beta-hydroxybutyrate (PHB). The model includes biochemical reactions from the intermediary metabolism and takes into account cellular compartmentali...

Myocardial hibernation represents an adaptation to sustained ischemia to maintain tissue vitality during severe supply-demand imbalance which is characterized by an increased glucose uptake. To elucidate this adaptive protective mechanism, the regulation of anaerobic glycolysis was investigated using human biopsies. In hibernating myocardium showin...

Both experimental and theoretical studies of metabolism are likely to relate to a segment that has been isolated for analytical purposes. In practice, it will be embedded in the whole of cellular metabolism. Thus, it is necessary to consider how conclusions about the control of an isolated pathway may be modified in this wider context where the inp...

The added value obtained by combining genomic analysis with proteomic analysis and supplementary information on mechanisms of interaction has been well illustrated in a recent paper by Ideker et al. This gives a far more meaningful interpretation of metabolic responses to a mutation or change in environment than could be obtained from correlation o...

The metabolic network of the catabolic, energy and biosynthetic metabolism of Escherichia coli is a paradigmatic case for the large genetic and metabolic networks that functional genomics efforts are beginning to elucidate. To analyse the structure of previously unknown networks involving hundreds or thousands of components by simple visual inspect...

We have determined the kinetic parameters of the individual steps of the threonine pathway from aspartate in Escherichia coli under a single set of experimental conditions chosen to be physiologically relevant. Our aim was to summarize the kinetic behaviour of each enzyme in a single tractable equation that takes into account the effect of the prod...

We have developed an experimental model of the whole threonine pathway that allows us to study the production of threonine from aspartate under different conditions. The model consisted of a desalted crude extract of Escherichia coli to which we added the substrates and necessary cofactors of the pathway: aspartate, ATP and NADPH. In this experimen...

A computer simulation of the threonine-synthesis pathway in Escherichia coli Tir-8 has been developed based on our previous measurements of the kinetics of the pathway enzymes under near-physiological conditions. The model successfully simulates the main features of the time courses of threonine synthesis previously observed in a cell-free extract...