Overview of Seafood Research at Ashtown Food Research Centre (1990 - 2007)

End of project reportIn recent years, the Irish seafood industry has faced stringent quotas and dwindling fish stocks. The introduction of fish farming added a new dimension but falling prices also created difficulties for this sector. However, the recent report of the Seafood Industry Strategy Group on ‘Steering a New Course’ and the Sea Change Programme of the Marine Institute will add new impetus to the industry. The current report summarises R&D on seafood conducted at Ashtown Food Research Centre (AFRC) in the period 1990-2007 and represents a major portion of seafood R&D conducted nationally during that period.Thanks are also extended to the European Union (and especially the SEAFOODplus project), Bord Iascaigh Mhara, Marine Institute, Enterprise Ireland and various seafood companies for their support and part-funding of elements of this research

Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration

Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to mimic this forcing. We provide a general formulation to force an arbitrary large kinetic model in a manner that is still consistent with the existence of a non-equilibrium steady state. We can guarantee the existence of a non-equilibrium steady state assuming only two conditions; that every reaction is mass balanced and that continuous kinetic reaction rate laws never lead to a negative molecule concentration. These conditions can be verified in polynomial time and are flexible enough to permit one to force a system away from equilibrium. In an expository biochemical example we show how a reversible, mass balanced perpetual reaction, with thermodynamically infeasible kinetic parameters, can be used to perpetually force a kinetic model of anaerobic glycolysis in a manner consistent with the existence of a steady state. Easily testable existence conditions are foundational for efforts to reliably compute non-equilibrium steady states in genome-scale biochemical kinetic models.Comment: 11 pages, 2 figures (v2 is now placed in proper context of the excellent 1962 paper by James Wei entitled "Axiomatic treatment of chemical reaction systems". In addition, section 4, on "Utility of steady state existence theorem" has been expanded.

Adding Value To Under utilised Fish Species

End of project reportTightening fish quotas and supply shortages for conventional species are causing major difficulties for both fishermen and seafood processors. There is a need, therefore, to explore the potential of underutilised fish species both as fillets or portions and as added-value products. The current project at Ashtown Food Research Centre (AFRC) addressed this issue for a number of underutilised species via (a) sous vide processing (with savoury sauces),(b)marinating (salt- and sugar-based marinades) and (c) via a combination of freeze-chilling and modified atmosphere packaging (MAP).A range of physico-chemical and sensory tests was conducted on the products and their shelf-life status was also determined.National Development Plan (NDP

MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models

Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. Through this work, which consists of a protocol, a toolbox, and tutorials of two use cases, we make our methods available to the broader scientific community. The protocol describes, in a step-wise manner, the workflow of data integration and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorials explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, this protocol constitutes a comprehensive guide to the intra-model analysis of extracellular metabolomic data and a resource offering a broad set of computational analysis tools for a wide biomedical and non-biomedical research community

Conditions for duality between fluxes and concentrations in biochemical networks

Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective equivalent to the other? Mathematical duality translates concepts, theorems or mathematical structures into other concepts, theorems or structures, in a one-to-one manner. We present a novel stoichiometric condition that is necessary and sufficient for duality between unidirectional fluxes and concentrations. Our numerical experiments, with computational models derived from a range of genome-scale biochemical networks, suggest that this flux-concentration duality is a pervasive property of biochemical networks. We also provide a combinatorial characterisation that is sufficient to ensure flux-concentration duality. That is, for every two disjoint sets of molecular species, there is at least one reaction complex that involves species from only one of the two sets. When unidirectional fluxes and molecular species concentrations are dual vectors, this implies that the behaviour of the corresponding biochemical network can be described entirely in terms of either concentrations or unidirectional fluxes

Acrylamide formation in potato products

End of Project ReportAcrylamide, a substance classified as a potential carcinogen, occurs in heated starchy foods at concentrations many times in excess of levels permitted in drinking water. Early surveys indicated that levels of acrylamide in potato products such as French fries and potato crisps were the highest of the foodstuffs investigated. The present project addressed this issue by determining levels of acrylamide precursors (asparagine and reducing sugars) in raw potatoes and levels of acrylamide in (i) potato products from different storage regimes, (ii) spot-sampled potatoes purchased from a local supermarket, (iii) samples that received pre-treatments and were fried at different temperatures and (iv) French fries reheated in different ovens.A risk assessment of the estimated acrylamide intake from potato products for various cohorts of the Irish population was also conducted

Developing Sous Vide/Freezing Systems for Ready-Meal omponents

End of project reportSous vide cooking involves sealing raw or par-cooked food in a vacuumised laminated plastic pouch or container, cooking by controlled heating, rapid chilling and then re-heating for consumption. The chilled storage period is up to 21 days at 0 to 3oC. The recommended thermal process for sous vide products is 90oC for 10min or its time-temperature equivalent. Concerns about the safety of sous vide products, mainly due to the potential for temperature abuse in the chill chain, has prevented the widespread use of this technology. The role of the current project, therefore, was to investigate sous vide cooking followed by freezing, as a safe alternative to sous vide/chilling for 10 ready-meal components i.e. carbohydrates (potatoes, pasta, rice), vegetables (carrots, broccoli) and muscle foods (salmon, cod, chicken, beef and lamb).National Development Plan (NDP