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Jager T, Salaberria I, Hansen BH. Capturing the life history of the marine copepod Calanus sinicus into a generic bioenergetics framework. Ecol Modell 2015. [DOI: 10.1016/j.ecolmodel.2014.12.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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53
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Overjordet IB, Altin D, Berg T, Jenssen BM, Gabrielsen GW, Hansen BH. Acute and sub-lethal response to mercury in Arctic and boreal calanoid copepods. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 155:160-165. [PMID: 25036619 DOI: 10.1016/j.aquatox.2014.06.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 06/17/2014] [Accepted: 06/25/2014] [Indexed: 06/03/2023]
Abstract
Acute lethal toxicity, expressed as LC50 values, is a widely used parameter in risk assessment of chemicals, and has been proposed as a tool to assess differences in species sensitivities to chemicals between climatic regions. Arctic Calanus glacialis and boreal Calanus finmarchicus were exposed to mercury (Hg(2+)) under natural environmental conditions including sea temperatures of 2° and 10°C, respectively. Acute lethal toxicity (96 h LC50) and sub-lethal molecular response (GST expression; in this article gene expression is used as a synonym of gene transcription, although it is acknowledged that gene expression is also regulated, e.g., at translation and protein stability level) were studied. The acute lethal toxicity was monitored for 96 h using seven different Hg concentrations. The sub-lethal experiment was set up on the basis of nominal LC50 values for each species using concentrations equivalent to 50, 5 and 0.5% of their 96 h LC50 value. No significant differences were found in acute lethal toxicity between the two species. The sub-lethal molecular response revealed large differences both in response time and the fold induction of GST, where the Arctic species responded both faster and with higher mRNA levels of GST after 48 h exposure. Under the natural exposure conditions applied in the present study, the Arctic species C. glacialis may potentially be more susceptible to mercury exposure on the sub-lethal level.
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Affiliation(s)
- Ida Beathe Overjordet
- Norwegian University of Science and Technology, Department of Biology, N-7491 Trondheim, Norway; SINTEF Materials and Chemistry, Environmental Technology, N-7465 Trondheim, Norway.
| | | | - Torunn Berg
- Norwegian University of Science and Technology, Department of Chemistry, N-7491 Trondheim, Norway
| | - Bjørn Munro Jenssen
- Norwegian University of Science and Technology, Department of Biology, N-7491 Trondheim, Norway
| | | | - Bjørn Henrik Hansen
- SINTEF Materials and Chemistry, Environmental Technology, N-7465 Trondheim, Norway
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54
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Appling AP, Heffernan JB. Nutrient Limitation and Physiology Mediate the Fine-Scale (De)coupling of Biogeochemical Cycles. Am Nat 2014; 184:384-406. [DOI: 10.1086/677282] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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55
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Barsi A, Jager T, Collinet M, Lagadic L, Ducrot V. Considerations for test design to accommodate energy-budget models in ecotoxicology: a case study for acetone in the pond snail Lymnaea stagnalis. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2014; 33:1466-1475. [PMID: 24395114 DOI: 10.1002/etc.2399] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 08/27/2013] [Accepted: 09/11/2013] [Indexed: 06/03/2023]
Abstract
Toxicokinetic-toxicodynamic (TKTD) modeling offers many advantages in the analysis of ecotoxicity test data. Calibration of TKTD models, however, places different demands on test design compared with classical concentration-response approaches. In the present study, useful complementary information is provided regarding test design for TKTD modeling. A case study is presented for the pond snail Lymnaea stagnalis exposed to the narcotic compound acetone, in which the data on all endpoints were analyzed together using a relatively simple TKTD model called DEBkiss. Furthermore, the influence of the data used for calibration on accuracy and precision of model parameters is discussed. The DEBkiss model described toxic effects on survival, growth, and reproduction over time well, within a single integrated analysis. Regarding the parameter estimates (e.g., no-effect concentration), precision rather than accuracy was affected depending on which data set was used for model calibration. In addition, the present study shows that the intrinsic sensitivity of snails to acetone stays the same across different life stages, including the embryonic stage. In fact, the data on egg development allowed for selection of a unique metabolic mode of action for the toxicant. Practical and theoretical considerations for test design to accommodate TKTD modeling are discussed in the hope that this information will aid other researchers to make the best possible use of their test animals.
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Affiliation(s)
- Alpar Barsi
- INRA, UMR 0985, Ecologie et Santé des Ecosystèmes, Equipe Ecotoxicologie et Qualité des Milieux Aquatiques, Rennes, France
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56
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Jager T, Barsi A, Hamda NT, Martin BT, Zimmer EI, Ducrot V. Dynamic energy budgets in population ecotoxicology: Applications and outlook. Ecol Modell 2014. [DOI: 10.1016/j.ecolmodel.2013.06.024] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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57
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Gergs A, Jager T. Body size-mediated starvation resistance in an insect predator. J Anim Ecol 2014; 83:758-68. [DOI: 10.1111/1365-2656.12195] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 12/14/2013] [Indexed: 11/27/2022]
Affiliation(s)
- André Gergs
- Department of Environmental, Social and Spatial Change; Roskilde University; Universitetsvej 3 DK-4000 Roskilde Denmark
- Institute for Environmental Research; RWTH Aachen University; Worringer Weg 1 D-52074 Aachen Germany
| | - Tjalling Jager
- Department of Theoretical Biology; VU University; de Boelelaan 1085 NL-1081 HV Amsterdam the Netherlands
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58
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Jeon J, Kretschmann A, Escher BI, Hollender J. Characterization of acetylcholinesterase inhibition and energy allocation in Daphnia magna exposed to carbaryl. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2013; 98:28-35. [PMID: 24139064 DOI: 10.1016/j.ecoenv.2013.09.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/21/2013] [Accepted: 09/25/2013] [Indexed: 06/02/2023]
Abstract
The inhibition of acetylcholinesterase (AChE) activity and energy allocation in the freshwater organism Daphnia magna exposed to carbaryl and potential recovery from the effects was examined. The binding of carbaryl-AChE was characterized through in vitro assays. To evaluate the recovery from inhibition and the alteration in energy budget, in vivo exposure and recovery regime tests were conducted. In comparison to diazoxon, the active metabolite of the insecticide diazinon, the stability of enzyme-carbaryl complex was fifteen times lower and the reactivity toward the active site was two times lower, resulting in approximately 30 times lower overall inhibition rate than for diazoxon. The in vitro reactivation rate constant of the inhibited enzyme and the in vivo recovery rate constant of AChE activity were 1.9 h⁻¹ and 0.12 h⁻¹ for carbaryl, respectively, which are much higher than the corresponding rate constants for diazoxon. The lower AChE inhibition and greater reactivation/recovery rates are in accordance with the lower toxicity of carbaryl compared to diazinon. Carbaryl exposure also altered the profile of the energy reserve: the decrease in lipid and glycogen and the increase in protein content resulted in the reduction of the total energy budget by about 45 mJ/g(ww). This corresponds to 26 percent of the available energy, which might allocate for external stressors. The mechanistic model of AChE inhibition is helpful to get an insight into (eco-)toxicological effects of AChE inhibitors on freshwater crustaceans under environmentally realistic conditions.
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Affiliation(s)
- Junho Jeon
- Swiss Federal Institute of Aquatic Science and Technology (Eewag), Überlandstrasse 133, 8600 Dübendorf, Switzerland.
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59
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Martínez-Jerónimo F, Arzate-Cárdenas M, Ortiz-Butrón R. Linking sub-individual and population level toxicity effects in Daphnia schoedleri (Cladocera: Anomopoda) exposed to sublethal concentrations of the pesticide α-cypermethrin. ECOTOXICOLOGY (LONDON, ENGLAND) 2013; 22:985-995. [PMID: 23661095 DOI: 10.1007/s10646-013-1077-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/28/2013] [Indexed: 06/02/2023]
Abstract
Synthetic pyrethroids are classified as moderately toxic to mammals and birds; nevertheless, they are highly toxic to non-target aquatic organisms such as fish and zooplankters. Chemical pollutants produce different effects in exposed organisms, ranging from biochemical to population responses. Cladocerans can modify the energy content of their offspring according to the surrounding medium as a way to improve their odds in case they have to cope with stressful conditions at birth. In this study, the effect of a synthetic pesticide on two levels of response in a Daphnia species different from those traditionally used as test organisms was evaluated. With this aim, Daphnia schoedleri neonates (<24 h) were exposed for 21 days to three sublethal concentrations of α-cypermethrin, 0.54, 5.4, and 54 ng L(-1), which correspond to 48-h EC1/100, EC1/10, and EC1, respectively. Effects were measured through a life table analysis for fecundity and survivorship. For effects on progeny, protein, carbohydrates, and lipids were determined and then transformed to caloric content. Biomarkers (BM) were expected to be the most sensitive evaluated response; nevertheless, population parameters such as survivorship and net reproductive rate (R0) were more sensitive since they presented significant differences with respect to controls at the lowest tested concentration. Neonates' caloric content varied during the reproductive period assessed and was negatively correlated to fecundity: as more neonates were born, less energy was provided by the adult females. Macromolecules concentration and caloric content values in cypermethrin-exposed adults were not different from those recorded in the control at the end of exposure time. The results herein presented suggest that stressed daphnids allocate more energy reserves to their offspring, although this strategy can vary depending on the number of reproductive events during the lifecycle, and on the toxicant's concentration. Sub-individual approaches to assess toxicant effects should be accompanied by demographic studies, which support population effect predictions inferred from BMs assessment.
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Affiliation(s)
- Fernando Martínez-Jerónimo
- Laboratorio de Hidrobiología Experimental, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Col. Santo Tomás, 11340, Mexico, DF, Mexico.
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60
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Whitehead A. Interactions between oil-spill pollutants and natural stressors can compound ecotoxicological effects. Integr Comp Biol 2013; 53:635-47. [PMID: 23842611 DOI: 10.1093/icb/ict080] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coastal estuaries are among the most biologically productive habitats on earth, yet are at risk from human activities including marine oil spills. The 2010 Deepwater Horizon oil spill contaminated hundreds of kilometers of coastal habitat, particularly in Louisiana's delta. Coastal estuaries are naturally dynamic habitats where periodic and stochastic fluctuations, for example in temperature, salinity, nutrients, and hypoxia, are common. Such environmental variability regularly imposes suboptimal conditions for which resident species must continually compensate by drawing on diverse physiological abilities. However, exposures to oil, in addition to their direct toxic effects, may interfere with functions that normally enable physiological compensation for suboptimal conditions. This review summarizes the panoply of naturally-encountered stressors that may interact with oil, including salinity, hypoxia, pathogens, and competition, and the mechanisms that may underlie these interactions. Combined effects of these stressors can amplify the costs of oil-exposures to organisms in the real world, and contribute to impacts on fitness, populations, and communities, that may not have been predicted from direct toxicity of hydrocarbons alone. These interactions pose challenges for accurate and realistic assessment of risks and of actual damage. To meet these challenges, environmental scientists and managers must capitalize on the latest understanding of the complexities of chemical effects of natural stressors on organisms, and adopt integrative and holistic measures of effect from the molecular to whole-animal levels, in order to anticipate, characterize, diagnose, and solve, ecotoxicological problems.
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Affiliation(s)
- Andrew Whitehead
- Department of Environmental Toxicology, University of California Davis, Davis, One Shields Avenue, Davis, CA 95616, USA
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61
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Jager T, Martin BT, Zimmer EI. DEBkiss or the quest for the simplest generic model of animal life history. J Theor Biol 2013; 328:9-18. [DOI: 10.1016/j.jtbi.2013.03.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 02/11/2013] [Accepted: 03/11/2013] [Indexed: 11/15/2022]
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62
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Holden PA, Nisbet RM, Lenihan HS, Miller RJ, Cherr GN, Schimel JP, Gardea-Torresdey JL. Ecological nanotoxicology: integrating nanomaterial hazard considerations across the subcellular, population, community, and ecosystems levels. Acc Chem Res 2013; 46:813-22. [PMID: 23039211 DOI: 10.1021/ar300069t] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Research into the health and environmental safety of nanotechnology has seriously lagged behind its emergence in industry. While humans have often adopted synthetic chemicals without considering ancillary consequences, the lessons learned from worldwide pollution should motivate making nanotechnology compatible with environmental concerns. Researchers and policymakers need to understand exposure and harm of engineered nanomaterials (ENMs), currently nanotechnology's main products, to influence the ENM industry toward sustainable growth. Yet, how should research proceed? Standard toxicity testing anchored in single-organism, dose-response characterizations does not adequately represent real-world exposure and receptor scenarios and their complexities. Our approach is different: it derives from ecology, the study of organisms' interactions with each other and their environments. Our approach involves the characterization of ENMs and the mechanistic assessment of their property-based effects. Using high throughput/content screening (HTS/HCS) with cells or environmentally-relevant organisms, we measure the effects of ENMs on a subcellular or population level. We then relate those effects to mechanisms within dynamic energy budget (DEB) models of growth and reproduction. We reconcile DEB model predictions with experimental data on organism and population responses. Finally, we use microcosm studies to measure the potential for community- or ecosystem-level effects by ENMs that are likely to be produced in large quantities and for which either HTS/HCS or DEB modeling suggest their potential to harm populations and ecosystems. Our approach accounts for ecological interactions across scales, from within organisms to whole ecosystems. Organismal ENM effects, if propagated through populations, can alter communities comprising multiple populations (e.g., plant, fish, bacteria) within food webs. Altered communities can change ecosystem services: processes that cycle carbon, nutrients, and energy, and regulate Earth's waters and atmosphere. We have shown ENM effects on populations, communities, and ecosystems, including transfer and concentration of ENMs through food chains, for a range of exposure scenarios; in many cases, we have identified subcellular ENM effects mechanisms. To keep pace with ENM development, rapid assessment of the mechanisms of ENM effects and modeling are needed. DEB models provide a method for mathematically representing effects such as the generation of reactive oxygen species and their associated damage. These models account for organism-level effects on metabolism and reproduction and can predict outcomes of ENM-organism combinations on populations; those predictions can then suggest ENM characteristics to be avoided. HTS/HCS provides a rapid assessment tool of the ENM chemical characteristics that affect biological systems; such results guide and expand DEB model expressions of hazard. Our approach addresses ecological processes in both natural and managed ecosystems (agriculture) and has the potential to deliver timely and meaningful understanding towards environmentally sustainable nanotechnology.
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Affiliation(s)
- Patricia A. Holden
- UC Center for the Environmental Implications of Nanotechnology (UC CEIN)
- Bren School of Environmental Science and Management
- Earth Research Institute, and
| | - Roger M. Nisbet
- UC Center for the Environmental Implications of Nanotechnology (UC CEIN)
- Earth Research Institute, and
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, United States
| | - Hunter S. Lenihan
- UC Center for the Environmental Implications of Nanotechnology (UC CEIN)
- Bren School of Environmental Science and Management
- Earth Research Institute, and
| | - Robert J. Miller
- UC Center for the Environmental Implications of Nanotechnology (UC CEIN)
- Bren School of Environmental Science and Management
- Earth Research Institute, and
| | - Gary N. Cherr
- UC Center for the Environmental Implications of Nanotechnology (UC CEIN)
- Departments of Environmental Toxicology and Nutrition, Bodega Marine Laboratory, University of California, Davis, Bodega Bay, California, United States
| | - Joshua P. Schimel
- UC Center for the Environmental Implications of Nanotechnology (UC CEIN)
- Earth Research Institute, and
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, United States
| | - Jorge L. Gardea-Torresdey
- UC Center for the Environmental Implications of Nanotechnology (UC CEIN)
- Department of Chemistry, The University of Texas at El Paso, El Paso, Texas, United States
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63
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Jager T, Barsi A, Ducrot V. Hormesis on life-history traits: is there such thing as a free lunch? ECOTOXICOLOGY (LONDON, ENGLAND) 2013; 22:263-270. [PMID: 23179410 DOI: 10.1007/s10646-012-1022-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/15/2012] [Indexed: 05/26/2023]
Abstract
The term "hormesis" is used to describe dose-response relationships where the response is reversed between low and high doses of a stressor (generally, stimulation at low doses and inhibition at high ones). A mechanistic explanation is needed to interpret the relevance of such responses, but there does not appear to be a single universal mechanism underlying hormesis. When the endpoint is a life-history trait such as growth or reproduction, a stimulation of the response comes with costs in terms of resources. Organisms have to obey the conservation laws for mass and energy; there is no such thing as a free lunch. Based on the principles of Dynamic Energy Budget theory, we introduce three categories of explanations for hormesis that obey the conservation laws: acquisition (i.e., increasing the input of energy into the individual), allocation (i.e., rearranging the energy flows over various traits) and medication (e.g., the stressor is an essential element or acts as a cure for a disease or infection). In this discussion paper, we illustrate these explanations with cases where they might apply, and elaborate on the potential consequences for field populations.
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Affiliation(s)
- Tjalling Jager
- Department of Theoretical Biology, VU University Amsterdam, Amsterdam, the Netherlands.
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64
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Kooijman SALM. Waste to hurry: dynamic energy budgets explain the need of wasting to fully exploit blooming resources. OIKOS 2013. [DOI: 10.1111/j.1600-0706.2012.00098.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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65
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Padmanabha H, Correa F, Legros M, Nijhout HF, Lord C, Lounibos LP. An eco-physiological model of the impact of temperature on Aedes aegypti life history traits. JOURNAL OF INSECT PHYSIOLOGY 2012; 58:1597-1608. [PMID: 23068992 DOI: 10.1016/j.jinsphys.2012.09.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 09/25/2012] [Accepted: 09/27/2012] [Indexed: 06/01/2023]
Abstract
Physiological processes mediate the impact of ecological conditions on the life histories of insect vectors. For the dengue/chikungunya mosquito, Aedes aegypti, three life history traits that are critical to urban population dynamics and control are: size, development rate and starvation mortality. In this paper we make use of prior laboratory experiments on each of these traits at 2°C intervals between 20 and 30°C, in conjunction with eco-evolutionary theory and studies on A.aegypti physiology, in order to develop a conceptual and mathematical framework that can predict their thermal sensitivity. Our model of reserve dependent growth (RDG), which considers a potential tradeoff between the accumulation of reserves and structural biomass, was able to robustly predict laboratory observations, providing a qualitative improvement over the approach most commonly used in other A.aegypti models. RDG predictions of reduced size at higher temperatures, but increased reserves relative to size, are supported by the available evidence in Aedes spp. We offer the potentially general hypothesis that temperature-size patterns in mosquitoes are driven by a net benefit of finishing the growing stage with proportionally greater reserves relative to structure at warmer temperatures. By relating basic energy flows to three fundamental life history traits, we provide a mechanistic framework for A.aegypti development to which ecological complexity can be added. Ultimately, this could provide a framework for developing and field testing hypotheses on how processes such as climate variation, density dependent regulation, human behavior or control strategies may influence A.aegypti population dynamics and disease risk.
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Affiliation(s)
- Harish Padmanabha
- Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St., New Haven, CT 06520, USA.
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66
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Examination of the role of detritus food quality, phytoplankton intracellular storage capacity, and zooplankton stoichiometry on planktonic dynamics. ECOL INFORM 2012. [DOI: 10.1016/j.ecoinf.2012.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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67
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Nisbet RM, Jusup M, Klanjscek T, Pecquerie L. Integrating dynamic energy budget (DEB) theory with traditional bioenergetic models. J Exp Biol 2012; 215:892-902. [DOI: 10.1242/jeb.059675] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Summary
Dynamic energy budget (DEB) theory offers a systematic, though abstract, way to describe how an organism acquires and uses energy and essential elements for physiological processes, in addition to how physiological performance is influenced by environmental variables such as food density and temperature. A ‘standard’ DEB model describes the performance (growth, development, reproduction, respiration, etc.) of all life stages of an animal (embryo to adult), and predicts both intraspecific and interspecific variation in physiological rates. This approach contrasts with a long tradition of more phenomenological and parameter-rich bioenergetic models that are used to make predictions from species-specific rate measurements. These less abstract models are widely used in fisheries studies; they are more readily interpretable than DEB models, but lack the generality of DEB models. We review the interconnections between the two approaches and present formulae relating the state variables and fluxes in the standard DEB model to measured bioenergetic rate processes. We illustrate this synthesis for two large fishes: Pacific bluefin tuna (Thunnus orientalis) and Pacific salmon (Oncorhynchus spp.). For each, we have a parameter-sparse, full-life-cycle DEB model that requires adding only a few species-specific features to the standard model. Both models allow powerful integration of knowledge derived from data restricted to certain life stages, processes and environments.
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Affiliation(s)
- Roger M. Nisbet
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106-9610, USA
| | - Marko Jusup
- Rudjer Boskovic Institute, Department for Marine and Environmental Research, Bijenicka cesta 54, POB 180, HR-10002 Zagreb, Croatia
- Faculty of Environment and Information Sciences, Yokohama National University, 79-7, Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan
| | - Tin Klanjscek
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106-9610, USA
- Rudjer Boskovic Institute, Department for Marine and Environmental Research, Bijenicka cesta 54, POB 180, HR-10002 Zagreb, Croatia
| | - Laure Pecquerie
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106-9610, USA
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68
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Martin BT, Zimmer EI, Grimm V, Jager T. Dynamic Energy Budget theory meets individual-based modelling: a generic and accessible implementation. Methods Ecol Evol 2011. [DOI: 10.1111/j.2041-210x.2011.00168.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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69
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Franklin O, Hall EK, Kaiser C, Battin TJ, Richter A. Optimization of biomass composition explains microbial growth-stoichiometry relationships. Am Nat 2011; 177:E29-42. [PMID: 21460549 DOI: 10.1086/657684] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Integrating microbial physiology and biomass stoichiometry opens far-reaching possibilities for linking microbial dynamics to ecosystem processes. For example, the growth-rate hypothesis (GRH) predicts positive correlations among growth rate, RNA content, and biomass phosphorus (P) content. Such relationships have been used to infer patterns of microbial activity, resource availability, and nutrient recycling in ecosystems. However, for microorganisms it is unclear under which resource conditions the GRH applies. We developed a model to test whether the response of microbial biomass stoichiometry to variable resource stoichiometry can be explained by a trade-off among cellular components that maximizes growth. The results show mechanistically why the GRH is valid under P limitation but not under N limitation. We also show why variability of growth rate-biomass stoichiometry relationships is lower under P limitation than under N or C limitation. These theoretical results are supported by experimental data on macromolecular composition (RNA, DNA, and protein) and biomass stoichiometry from two different bacteria. In addition, compared to a model with strictly homeostatic biomass, the optimization mechanism we suggest results in increased microbial N and P mineralization during organic-matter decomposition. Therefore, this mechanism may also have important implications for our understanding of nutrient cycling in ecosystems.
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Affiliation(s)
- Oskar Franklin
- International Institute for Applied Systems Analysis, A-2361 Laxenburg, Austria.
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70
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A dynamic energy budget (DEB) model for the energy usage and reproduction of the Icelandic capelin (Mallotus villosus). J Theor Biol 2011; 281:1-8. [DOI: 10.1016/j.jtbi.2011.03.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 03/18/2011] [Accepted: 03/24/2011] [Indexed: 11/17/2022]
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71
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Benchmarks in organism performance and their use in comparative analyses. Oecologia 2011; 167:379-90. [DOI: 10.1007/s00442-011-2004-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 04/11/2011] [Indexed: 10/18/2022]
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72
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Augustine S, Gagnaire B, Floriani M, Adam-Guillermin C, Kooijman SALM. Developmental energetics of zebrafish, Danio rerio. Comp Biochem Physiol A Mol Integr Physiol 2011; 159:275-83. [PMID: 21440658 DOI: 10.1016/j.cbpa.2011.03.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 03/21/2011] [Accepted: 03/22/2011] [Indexed: 10/18/2022]
Abstract
Using zebrafish (Danio rerio) as a case study, we show that the maturity concept of Dynamic Energy Budget (DEB) theory is a useful metric for developmental state. Maturity does not depend on food or temperature contrary to age and to some extent length. We compile the maturity levels for each developmental milestone recorded in staging atlases. The analysis of feeding, growth, reproduction and aging patterns throughout the embryo, juvenile and adult life stages are well-captured by a simple extension of the standard DEB model and reveals that embryo development is slow relative to adults. A threefold acceleration of development occurs during the larval period. Moreover we demonstrate that growth and reproduction depend on food in predictable ways and their simultaneous observation is necessary to estimate parameters. We used data on diverse aspects of the energy budget simultaneously for parameter estimation using the covariation method. The lowest mean food intake level to initiate reproduction was found to be as high as 0.6 times the maximum level. The digestion efficiency for Tetramin™ was around 0.5, growth efficiency was just 0.7 and the value for the allocation fraction to soma (0.44) was close to the one that maximizes ultimate reproduction.
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Affiliation(s)
- S Augustine
- Laboratory of Radioecology and Ecotoxicology, DEI/SECRE/LRE, Institute of Radioprotection and Nuclear Safety (IRSN), Caradache, Building 186, BP3, 13115 St-Paul-lez-Durance Cedex, France.
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73
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Wren JF, Kille P, Spurgeon DJ, Swain S, Sturzenbaum SR, Jager T. Application of physiologically based modelling and transcriptomics to probe the systems toxicology of aldicarb for Caenorhabditis elegans (Maupas 1900). ECOTOXICOLOGY (LONDON, ENGLAND) 2011; 20:397-408. [PMID: 21253838 PMCID: PMC3037492 DOI: 10.1007/s10646-010-0591-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/28/2010] [Indexed: 05/02/2023]
Abstract
The toxicity of aldicarb on movement, life cycle, population growth rate and resource allocation, and the gene expression changes underpinning these effects, were investigated for Caenorhabditis elegans. A clear effect of aldicarb on nematode movement was found suggesting that this pesticide acts as a neurotoxicant. Aldicarb also had an effect on life cycle traits including low concentration life-span extension; high concentration brood size reduction and a high concentration extension of time to first egg. All life-cycle and growth data were integrated into a biology-based model (DEBtox) to characterise aldicarb effects on life-history traits, resource allocation and population growth rate within a single modelling framework. The DEBtox fits described concentration dependent effects on individual traits and population growth rate and indicated that the most probable mechanism of action of the pesticide was an increase in energy demands for somatic and reproductive tissue maintenance. Transcriptomic profiling indicated that aldicarb was associated with changes in amino acid metabolism, DNA structure, fatty acid metabolism and cytochrome P450 mediated xenobiotic metabolism. The changes in the amino acid and fatty acid pathways suggest an effect of aldicarb on protein integrity; while effects on DNA suggests that aldicarb influence DNA morphology or replication. Both these effects have the potential to incur increased costs for structural maintenance of macromolecules. These effects, coupled to the effect on biotransformation enzymes also seen, represent the materialisation of the maintenance costs indicated by DEBtox modelling.
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Affiliation(s)
- Jodie F. Wren
- School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3TL UK
- Centre for Ecology and Hydrology, Monks Wood, Abbots Ripton, Huntingdon, Cambridgeshire PE27 2LS UK
| | - Peter Kille
- School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3TL UK
| | - David J. Spurgeon
- Centre for Ecology and Hydrology, Monks Wood, Abbots Ripton, Huntingdon, Cambridgeshire PE27 2LS UK
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire OX10 8BB UK
| | - Suresh Swain
- Pharmaceutical Science Division, King’s College London, 150 Stamford Street, London, SE1 9NH UK
| | - Stephen R. Sturzenbaum
- Pharmaceutical Science Division, King’s College London, 150 Stamford Street, London, SE1 9NH UK
| | - Tjalling Jager
- Department of Theoretical Biology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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74
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Abstract
Biogeochemical cycles in the ocean are mediated by complex and diverse microbial communities. Over the past decade, marine ecosystem and biogeochemistry models have begun to address some of this diversity by resolving several groups of (mostly autotrophic) plankton, differentiated by biogeochemical function. Here, we review recent model approaches that are rooted in the notion that an even richer diversity is fundamental to the organization of marine microbial communities. These models begin to resolve, and address the significance of, diversity within functional groups. Seeded with diverse populations spanning prescribed regions of trait space, these simulations self-select community structure according to relative fitness in the virtual environment. Such models are suited to considering ecological questions, such as the regulation of patterns of biodiversity, and to simulating the response to changing environments. A key issue for all such models is the constraint of viable trait space and trade-offs. Size-structuring and mechanistic descriptions of energy and resource allocation at the individual level can rationalize these constraints.
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Affiliation(s)
- Michael J Follows
- Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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75
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Sousa T, Domingos T, Poggiale JC, Kooijman SALM. Dynamic energy budget theory restores coherence in biology. Philos Trans R Soc Lond B Biol Sci 2010; 365:3413-28. [PMID: 20921042 PMCID: PMC2981977 DOI: 10.1098/rstb.2010.0166] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We present the state of the art of the development of dynamic energy budget theory, and its expected developments in the near future within the molecular, physiological and ecological domains. The degree of formalization in the set-up of the theory, with its roots in chemistry, physics, thermodynamics, evolution and the consistent application of Occam's razor, is discussed. We place the various contributions in the theme issue within this theoretical setting, and sketch the scope of actual and potential applications.
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Affiliation(s)
- Tânia Sousa
- Environment and Energy Section, DEM, Instituto Superior Técnico. Av. Rovisco Pais, 1, 1049-001 Lisboa, Portugal.
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Peeters F, Li J, Straile D, Rothhaupt KO, Vijverberg J. Influence of low and decreasing food levels on Daphnia-algal interactions: Numerical experiments with a new dynamic energy budget model. Ecol Modell 2010. [DOI: 10.1016/j.ecolmodel.2010.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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77
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Baas J, Jager T, Kooijman B. A review of DEB theory in assessing toxic effects of mixtures. THE SCIENCE OF THE TOTAL ENVIRONMENT 2010; 408:3740-5. [PMID: 19850324 DOI: 10.1016/j.scitotenv.2009.09.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 09/17/2009] [Accepted: 09/22/2009] [Indexed: 05/14/2023]
Abstract
In this manuscript we review the use of mechanistic models to interpret effects of mixtures of compounds within the framework of the Dynamic Energy Budget (DEB) theory. Within this approach the effect of a mixture is built up from the effects of the individual components making up the mixture. Understanding effects of mixtures is essential as it is impossible to assess effects of all possible mixtures experimentally. In contrast to the more classical way of interpreting effects of mixtures with concentration addition or effect addition models, DEB theory offers a single consistent framework to understand effects of mixtures on growth, reproduction and survival in an integrated, way. It systematically incorporates exposure time and biology of the organisms, including the natural links between the processes of feeding, maintenance, growth, development and reproduction. We also give directions for an experimental setup to interpret the results within the DEB framework. The DEB framework was successfully applied to assess effects of complex mixtures on survival and binary mixtures on sub-lethal endpoints. It gives the possibility to explain observed interactions by the underlying biological mechanisms or pinpoint interactions. We expect this approach to help in identifying key mechanisms and enable to focus further research in cooperation with modelers and experimentalists to improve our understanding of the mechanisms underlying mixture toxicity.
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Affiliation(s)
- Jan Baas
- Vrije Universiteit of Amsterdam, Department of Theoretical Biology, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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78
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Swain S, Wren JF, Stürzenbaum SR, Kille P, Morgan AJ, Jager T, Jonker MJ, Hankard PK, Svendsen C, Owen J, Hedley BA, Blaxter M, Spurgeon DJ. Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans. BMC SYSTEMS BIOLOGY 2010; 4:32. [PMID: 20331876 PMCID: PMC2857823 DOI: 10.1186/1752-0509-4-32] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Accepted: 03/23/2010] [Indexed: 02/02/2023]
Abstract
Background Physiologically based modelling using DEBtox (dynamic energy budget in toxicology) and transcriptional profiling were used in Caenorhabditis elegans to identify how physiological modes of action, as indicated by effects on system level resource allocation were associated with changes in gene expression following exposure to three toxic chemicals: cadmium, fluoranthene (FA) and atrazine (AZ). Results For Cd, the physiological mode of action as indicated by DEBtox model fitting was an effect on energy assimilation from food, suggesting that the transcriptional response to exposure should be dominated by changes in the expression of transcripts associated with energy metabolism and the mitochondria. While evidence for effect on genes associated with energy production were seen, an ontological analysis also indicated an effect of Cd exposure on DNA integrity and transcriptional activity. DEBtox modelling showed an effect of FA on costs for growth and reproduction (i.e. for production of new and differentiated biomass). The microarray analysis supported this effect, showing an effect of FA on protein integrity and turnover that would be expected to have consequences for rates of somatic growth. For AZ, the physiological mode of action predicted by DEBtox was increased cost for maintenance. The transcriptional analysis demonstrated that this increase resulted from effects on DNA integrity as indicated by changes in the expression of genes chromosomal repair. Conclusions Our results have established that outputs from process based models and transcriptomics analyses can help to link mechanisms of action of toxic chemicals with resulting demographic effects. Such complimentary analyses can assist in the categorisation of chemicals for risk assessment purposes.
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Affiliation(s)
- Suresh Swain
- King's College London, Department of Biochemistry, Pharmaceutical Sciences Research Division, 150 Stamford Street, London, UK
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Jager T, Vandenbrouck T, Baas J, De Coen WM, Kooijman SALM. A biology-based approach for mixture toxicity of multiple endpoints over the life cycle. ECOTOXICOLOGY (LONDON, ENGLAND) 2010; 19:351-61. [PMID: 19771510 PMCID: PMC2811243 DOI: 10.1007/s10646-009-0417-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/11/2009] [Indexed: 05/18/2023]
Abstract
Typical approaches for analyzing mixture ecotoxicity data only provide a description of the data; they cannot explain observed interactions, nor explain why mixture effects can change in time and differ between endpoints. To improve our understanding of mixture toxicity we need to explore biology-based models. In this paper, we present an integrated approach to deal with the toxic effects of mixtures on growth, reproduction and survival, over the life cycle. Toxicokinetics is addressed with a one-compartment model, accounting for effects of growth. Each component of the mixture has its own toxicokinetics model, but all compounds share the effect of body size on uptake kinetics. The toxicodynamic component of the method is formed by an implementation of dynamic energy budget theory; a set of simple rules for metabolic organization that ensures conservation of mass and energy. Toxicant effects are treated as a disruption of regular metabolic processes such as an increase in maintenance costs. The various metabolic processes interact, which means that mixtures of compounds with certain mechanisms of action have to produce a response surface that deviates from standard models (such as 'concentration addition'). Only by separating these physiological interactions from the chemical interactions between mixture components can we hope to achieve generality and a better understanding of mixture effects. For example, a biology-based approach allows for educated extrapolations to other mixtures, other species, and other exposure situations. We illustrate our method with the interpretation of partial life-cycle data for two polycyclic aromatic hydrocarbons in Daphnia magna.
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Affiliation(s)
- Tjalling Jager
- FALW/Department of Theoretical Biology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
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80
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Muller EB, Osenberg CW, Schmitt RJ, Holbrook SJ, Nisbet RM. Sublethal toxicant effects with dynamic energy budget theory: application to mussel outplants. ECOTOXICOLOGY (LONDON, ENGLAND) 2010; 19:38-47. [PMID: 19629682 PMCID: PMC2797407 DOI: 10.1007/s10646-009-0384-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 07/03/2009] [Indexed: 05/02/2023]
Abstract
We investigate the effectiveness of a sublethal toxic effect model embedded in Dynamic Energy Budget (DEB) theory for the analysis of field data. We analyze the performance of two species of mussels, Mytilus galloprovincialis and M. californianus, near a diffuser discharging produced water in the Southern California Bight, California. Produced water is a byproduct of oil production consisting of fossil water together with compounds added during the extraction process, and generally contains highly elevated levels of pollutants relative to sea water. Produced water negatively affects the production of somatic and reproductive biomass in both mussel species; we show that these negative effects can be quantified with our DEB-based modeling framework through the estimation of toxic effect scaling parameters. Our analyses reveal that the toxic impact of produced water on growth and reproduction of M. californianus is substantially higher than for M. galloprovincialis. Projections of the expected lifetime production of gonad biomass indicate that the environmental impact of produced water can be as large as 100%, whereas short-term assessment without the use of DEB theory projects a maximum effect of only 30%.
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Affiliation(s)
- Erik B Muller
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA.
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81
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Muller EB, Nisbet RM, Berkley HA. Sublethal toxicant effects with dynamic energy budget theory: model formulation. ECOTOXICOLOGY (LONDON, ENGLAND) 2010; 19:48-60. [PMID: 19633955 PMCID: PMC2797403 DOI: 10.1007/s10646-009-0385-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/03/2009] [Indexed: 05/02/2023]
Abstract
We develop and test a general modeling framework to describe the sublethal effects of pollutants by adding toxicity modules to an established dynamic energy budget (DEB) model. The DEB model describes the rates of energy acquisition and expenditure by individual organisms; the toxicity modules describe how toxicants affect these rates by changing the value of one or more DEB parameters, notably the parameters quantifying the rates of feeding and maintenance. We investigate four toxicity modules that assume: (1) effects on feeding only; (2) effects on maintenance only; (3) effects on feeding and maintenance with similar values for the toxicity parameters; and (4) effects on feeding and maintenance with different values for the toxicity parameters. We test the toxicity modules by fitting each to published data on feeding, respiration, growth and reproduction. Among the pollutants tested are metals (mercury and copper) and various organic compounds (chlorophenols, toluene, polycyclic aromatic hydrocarbons, tetradifon and pyridine); organisms include mussels, oysters, earthworms, water fleas and zebrafish. In most cases, the data sets could be adequately described with any of the toxicity modules, and no single module gave superior fits to all data sets. We therefore propose that for many applications, it is reasonable to use the most general and parameter sparse module, i.e. module 3 that assumes similar effects on feeding and maintenance, as a default. For one example (water fleas), we use parameter estimates to calculate the impact of food availability and toxicant levels on the long term population growth rate.
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Affiliation(s)
- Erik B Muller
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA.
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82
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de Graaf AA, Freidig AP, De Roos B, Jamshidi N, Heinemann M, Rullmann JAC, Hall KD, Adiels M, van Ommen B. Nutritional systems biology modeling: from molecular mechanisms to physiology. PLoS Comput Biol 2009; 5:e1000554. [PMID: 19956660 PMCID: PMC2777333 DOI: 10.1371/journal.pcbi.1000554] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the consideration and interpretation of experimental data at widely differing scales of space and time. In this review, we discuss a selection of available modeling approaches and applications relevant for nutrition. We then put these models into perspective by categorizing them according to their space and time domain. Through this categorization process, we identified a dearth of models that consider processes occurring between the microscopic and macroscopic scale. We propose a "middle-out" strategy to develop the required full-scale, multilevel computational models. Exhaustive and accurate phenotyping, the use of the virtual patient concept, and the development of biomarkers from "-omics" signatures are identified as key elements of a successful systems biology modeling approach in nutrition research--one that integrates physiological mechanisms and data at multiple space and time scales.
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83
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84
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Muller EB, Kooijman SALM, Edmunds PJ, Doyle FJ, Nisbet RM. Dynamic energy budgets in syntrophic symbiotic relationships between heterotrophic hosts and photoautotrophic symbionts. J Theor Biol 2009; 259:44-57. [PMID: 19285512 DOI: 10.1016/j.jtbi.2009.03.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 02/13/2009] [Accepted: 03/03/2009] [Indexed: 11/30/2022]
Abstract
In this paper we develop and investigate a dynamic energy budget (DEB) model describing the syntrophic symbiotic relationship between a heterotrophic host and an internal photoautotrophic symbiont. The model specifies the flows of matter and energy among host, symbiont and environment with minimal complexity and uses the concept of synthesizing units to describe smoothly the assimilation of multiple limiting factors, in particular inorganic carbon and nitrogen, and irradiance. The model has two passive regulation mechanisms: the symbiont shares only photosynthate that it cannot use itself, and the host delivers only excess nutrients to the symbiont. With parameter values plausible for scleractinian corals, we show that these two regulation mechanisms suffice to obtain a stable symbiotic relationship under constant ambient conditions, provided those conditions support sustenance of host and symbiont. Furthermore, the symbiont density in the host varies relatively little as a function of ambient food density, inorganic nitrogen and irradiance. This symbiont density tends to increase with light deprivation or nitrogen enrichment, either directly or via food. We also investigate the relative benefit each partner derives from the relationship and conclude that this relationship may shift from mutualism to parasitism as environmental conditions change.
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Affiliation(s)
- Erik B Muller
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA.
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85
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86
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Kooijman SALM, Sousa T, Pecquerie L, Van Der Meer J, Jager T. From food-dependent statistics to metabolic parameters, a practical guide to the use of dynamic energy budget theory. Biol Rev Camb Philos Soc 2008; 83:533-52. [DOI: 10.1111/j.1469-185x.2008.00053.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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87
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Sousa T, Domingos T, Kooijman S. From empirical patterns to theory: a formal metabolic theory of life. Philos Trans R Soc Lond B Biol Sci 2008; 363:2453-64. [PMID: 18331988 PMCID: PMC2606805 DOI: 10.1098/rstb.2007.2230] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 11/20/2007] [Indexed: 11/12/2022] Open
Abstract
The diversity of life on Earth raises the question of whether it is possible to have a single theoretical description of the quantitative aspects of the organization of metabolism for all organisms. However, similarities between organisms, such as von Bertalanffy's growth curve and Kleiber's law on metabolic rate, suggest that mechanisms that control the uptake and use of metabolites are common to all organisms. These and other widespread empirical patterns in biology should be the ultimate test for any metabolic theory that hopes for generality. The present study (i) collects empirical evidence on growth, stoichiometry, feeding, respiration and energy dissipation and exhibits it as stylized biological facts; (ii) formalizes assumptions and propositions in a metabolic theory that is fully consistent with the Dynamic Energy Budget theory; and (iii) proves that these assumptions and propositions are consistent with the stylized facts.
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Affiliation(s)
- Tânia Sousa
- Environment and Energy Section, Instituto Superior Técnico1049-001 Lisboa, Portugal
| | - Tiago Domingos
- Environment and Energy Section, Instituto Superior Técnico1049-001 Lisboa, Portugal
| | - S.A.L.M Kooijman
- Department of Theoretical Biology, Vrije Universiteit1081 HV Amsterdam, The Netherlands
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Temperature is the key factor explaining interannual variability of Daphnia development in spring: a modelling study. Oecologia 2008; 157:531-43. [DOI: 10.1007/s00442-008-1081-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Accepted: 05/06/2008] [Indexed: 10/21/2022]
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89
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Rinke K, Hülsmann S, Mooij WM. Energetic costs, underlying resource allocation patterns, and adaptive value of predator-induced life-history shifts. OIKOS 2007. [DOI: 10.1111/j.2007.0030-1299.16099.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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90
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Kooijman SALM, Baas J, Bontje D, Broerse M, Jager T, Van Gestel CAM, Van Hattum B. Scaling relationships based on partition coefficients and body sizes have similarities and interactions. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2007; 18:315-30. [PMID: 17514573 DOI: 10.1080/10629360701304196] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The LC(50) of compounds with a similar biological effect, at a given exposure period, is frequently plotted log-log against the octanol-water partition coefficient and a straight line is fitted for interpolation purposes. This is also frequently done for physiological properties, such as the weight-specific respiration rate, as function of the body weight of individuals. This paper focuses on the remarkable observation that theoretical explanations for these relationships also have strong similarities. Both can be understood as result of the covariation of the values of parameters of models of a particular type for the underlying processes, while this covariation follows logically from the model structure. The one-compartment model for the uptake and elimination of compounds by organisms is basic to the BioConcentration Factor (BCF), or the partition coefficient; the standard Dynamic Energy Budget model is basic to the (ultimate) body size. The BCF is the ratio of the uptake and the elimination rates; the maximum body length is the ratio of the assimilation (i.e. uptake of resources) and the maintenance (i.e. use of resources) rates. This paper discusses some shortcomings of descriptive approaches and conceptual aspects of theoretical explanations. The strength of the theory is in the combination of why metabolic transformation depends both on the BCF and the body size. We illustrate the application of the theory with several data sets from the literature.
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Affiliation(s)
- S A L M Kooijman
- Faculty Earth & Life Sciences, Vrije Universiteit, 1081 HV, Amsterdam, The Netherlands.
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92
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Kooijman SALM, Troost TA. Quantitative steps in the evolution of metabolic organisation as specified by the Dynamic Energy Budget theory. Biol Rev Camb Philos Soc 2007; 82:113-42. [PMID: 17313526 DOI: 10.1111/j.1469-185x.2006.00006.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Dynamic Energy Budget (DEB) theory quantifies the metabolic organisation of organisms on the basis of mechanistically inspired assumptions. We here sketch a scenario for how its various modules, such as maintenance, storage dynamics, development, differentiation and life stages could have evolved since the beginning of life. We argue that the combination of homeostasis and maintenance induced the development of reserves and that subsequent increases in the maintenance costs came with increases of the reserve capacity. Life evolved from a multiple reserves - single structure system (prokaryotes, many protoctists) to systems with multiple reserves and two structures (plants) or single reserve and single structure (animals). This had profound consequences for the possible effects of temperature on rates. We present an alternative explanation for what became known as the down-regulation of maintenance at high growth rates in microorganisms; the density of the limiting reserve increases with the growth rate, and reserves do not require maintenance while structure-specific maintenance costs are independent of the growth rate. This is also the mechanism behind the variation of the respiration rate with body size among species. The DEB theory specifies reserve dynamics on the basis of the requirements of weak homeostasis and partitionability. We here present a new and simple mechanism for this dynamics which accounts for the rejection of mobilised reserve by busy maintenance/growth machinery. This module, like quite a few other modules of DEB theory, uses the theory of Synthesising Units; we review recent progress in this field. The plasticity of membranes that evolved in early eukaryotes is a major step forward in metabolic evolution; we discuss quantitative aspects of the efficiency of phagocytosis relative to the excretion of digestive enzymes to illustrate its importance. Some processes of adaptation and gene expression can be understood in terms of allocation linked to the relative workload of metabolic modules in (unicellular) prokaryotes and organs in (multicellular) eukaryotes. We argue that the evolution of demand systems can only be understood in the light of that of supply systems. We illustrate some important points with data from the literature.
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Affiliation(s)
- S A L M Kooijman
- Department of Theoretical Biology Vrije Universiteit, de Boelelaan 1087, 1081 HV Amsterdam, The Netherlands.
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93
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Sousa T, Mota R, Domingos T, Kooijman SALM. Thermodynamics of organisms in the context of dynamic energy budget theory. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 74:051901. [PMID: 17279933 DOI: 10.1103/physreve.74.051901] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Revised: 08/10/2006] [Indexed: 05/13/2023]
Abstract
We carry out a thermodynamic analysis to an organism. It is applicable to any type of organism because (1) it is based on a thermodynamic formalism applicable to all open thermodynamic systems and (2) uses a general model to describe the internal structure of the organism--the dynamic energy budget (DEB) model. Our results on the thermodynamics of DEB organisms are the following. (1) Thermodynamic constraints for the following types of organisms: (a) aerobic and exothermic, (b) anaerobic and exothermic, and (c) anaerobic and endothermic; showing that anaerobic organisms have a higher thermodynamic flexibility. (2) A way to compute the changes in the enthalpy and in the entropy of living biomass that accompany changes in growth rate solving the problem of evaluating the thermodynamic properties of biomass as a function of the amount of reserves. (3) Two expressions for Thornton's coefficient that explain its experimental variability and theoretically underpin its use in metabolic studies. (4) A mechanism that organisms in non-steady-state use to rid themselves of internal entropy production: "dilution of entropy production by growth." To demonstrate the practical applicability of DEB theory to quantify thermodynamic changes in organisms we use published data on Klebsiella aerogenes growing aerobically in a continuous culture. We obtain different values for molar entropies of the reserve and the structure of Klebsiella aerogenes proving that the reserve density concept of DEB theory is essential in discussions concerning (a) the relationship between organization and entropy and (b) the mechanism of storing entropy in new biomass. Additionally, our results suggest that the entropy of dead biomass is significantly different from the entropy of living biomass.
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Affiliation(s)
- Tânia Sousa
- Environment and Energy Section, DEM, Instituto Superior Técnico, Avenida Rovisco Pais, 1. 1049-001 Lisbon, Portugal.
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94
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Jager T, Heugens EHW, Kooijman SALM. Making sense of ecotoxicological test results: towards application of process-based models. ECOTOXICOLOGY (LONDON, ENGLAND) 2006; 15:305-14. [PMID: 16739032 DOI: 10.1007/s10646-006-0060-x] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/06/2006] [Indexed: 05/09/2023]
Abstract
The environmental risk of chemicals is routinely assessed by comparing predicted exposure levels to predicted no-effect levels for ecosystems. Although process-based models are commonly used in exposure assessment, the assessment of effects usually comprises purely descriptive models and rules-of-thumb. The problems with this approach start with the analysis of laboratory ecotoxicity tests, because only a limited amount of information is extracted. Standard summary statistics (NOEC, ECx, LC50) are of limited use in part because they change with exposure duration in a manner that varies with the tested species and the toxicant. As an alternative, process-based models are available. These models allow for toxicity measures that are independent of exposure time, make efficient use of the available data from routine toxicity tests, and are better suited for educated extrapolations (e.g., from individual to population, and from continuous to pulse exposure). These capabilities can be used to improve regulatory decisions and allow for a more efficient assessment of effects, which ultimately will reduce the need for animal testing. Process-based modeling also can help to achieve the goals laid out in REACH, the new strategy of the European Commission in dealing with chemicals. This discussion is illustrated with effects data for Daphnia magna, analyzed by the DEBtox model.
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Affiliation(s)
- Tjalling Jager
- FALW/Department of Theoretical Biology, Vrije Universiteit Amsterdam, De Boelelaan 1085, NL-1081 HV, Amsterdam, The Netherlands.
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95
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Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE. Mimivirus and the emerging concept of "giant" virus. Virus Res 2006; 117:133-44. [PMID: 16469402 DOI: 10.1016/j.virusres.2006.01.008] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Revised: 01/06/2006] [Accepted: 01/09/2006] [Indexed: 11/15/2022]
Abstract
The recently discovered Acanthamoeba polyphaga Mimivirus is the largest known DNA virus. Its particle size (750 nm), genome length (1.2 million bp) and large gene repertoire (911 protein coding genes) blur the established boundaries between viruses and parasitic cellular organisms. In addition, the analysis of its genome sequence identified many types of genes never before encountered in a virus, including aminoacyl-tRNA synthetases and other central components of the translation machinery previously thought to be the signature of cellular organisms. In this article, we examine how the finding of such a giant virus might durably influence the way we look at microbial biodiversity, and lead us to revise the classification of microbial domains and life forms. We propose to introduce the word "girus" to recognize the intermediate status of these giant DNA viruses, the genome complexity of which makes them closer to small parasitic prokaryotes than to regular viruses.
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Affiliation(s)
- Jean-Michel Claverie
- Information Génomique et Structurale, CNRS UPR 2589, IBSM, Parc Scientifique de Luminy, 163 Avenue de Luminy, Case 934, 13288 Marseille Cedex 9, France.
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96
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Hölker F, Breckling B. A spatiotemporal individual-based fish model to investigate emergent properties at the organismal and the population level. Ecol Modell 2005. [DOI: 10.1016/j.ecolmodel.2005.02.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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97
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Custer AV. Stoichiometric estimates of the biochemical conversion efficiencies in tsetse metabolism. BMC Ecol 2005; 5:6. [PMID: 16083496 PMCID: PMC1215481 DOI: 10.1186/1472-6785-5-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Accepted: 08/05/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The time varying flows of biomass and energy in tsetse (Glossina) can be examined through the construction of a dynamic mass-energy budget specific to these flies but such a budget depends on efficiencies of metabolic conversion which are unknown. These efficiencies of conversion determine the overall yields when food or storage tissue is converted into body tissue or into metabolic energy. A biochemical approach to the estimation of these efficiencies uses stoichiometry and a simplified description of tsetse metabolism to derive estimates of the yields, for a given amount of each substrate, of conversion product, by-products, and exchanged gases. This biochemical approach improves on estimates obtained through calorimetry because the stoichiometric calculations explicitly include the inefficiencies and costs of the reactions of conversion. However, the biochemical approach still overestimates the actual conversion efficiency because the approach ignores all the biological inefficiencies and costs such as the inefficiencies of leaky membranes and the costs of molecular transport, enzyme production, and cell growth. RESULTS This paper presents estimates of the net amounts of ATP, fat, or protein obtained by tsetse from a starting milligram of blood, and provides estimates of the net amounts of ATP formed from the catabolism of a milligram of fat along two separate pathways, one used for resting metabolism and one for flight. These estimates are derived from stoichiometric calculations constructed based on a detailed quantification of the composition of food and body tissue and on a description of the major metabolic pathways in tsetse simplified to single reaction sequences between substrates and products. The estimates include the expected amounts of uric acid formed, oxygen required, and carbon dioxide released during each conversion. The calculated estimates of uric acid egestion and of oxygen use compare favorably to published experimental measurements. CONCLUSION This biochemical analysis provides reasonable first estimates of the conversion efficiencies for the major pathways used by tsetse metabolism. These results now enable a deeper analysis of tsetse ecology based on the construction of a dynamic mass-energy budget for tsetse and their populations.
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Affiliation(s)
- Adrian V Custer
- Department of Environmental Science, Policy and Management, 201 Wellman Hall #3112, University of California, Berkeley 94720, USA.
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98
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Rinke K, Vijverberg J. A model approach to evaluate the effect of temperature and food concentration on individual life-history and population dynamics of Daphnia. Ecol Modell 2005. [DOI: 10.1016/j.ecolmodel.2005.01.031] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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99
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ALVAREZ OALDA, JAGER T, KOOIJMAN SALM, KAMMENGA JE. Responses to stress of Caenorhabditis elegans populations with different reproductive strategies. Funct Ecol 2005. [DOI: 10.1111/j.1365-2435.2005.01012.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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100
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Baillieul M, Smolders R, Blust R. The effect of environmental stress on absolute and mass-specific scope for growth in Daphnia magna Strauss. Comp Biochem Physiol C Toxicol Pharmacol 2005; 140:364-73. [PMID: 15893503 DOI: 10.1016/j.cca.2005.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2004] [Revised: 03/24/2005] [Accepted: 03/30/2005] [Indexed: 11/26/2022]
Abstract
Daphnids were reared for 2 weeks in different concentrations of food or cadmium, and growth and reproduction were measured as endpoints. At the end of the 14-day experimental period, scope for growth (SFG) was measured and expressed per individual (mJ/ind/h=absolute SFG) and per mg dry weight (mJ/mg/h=mass-specific SFG). Both food deprivation and cadmium stress decreased body size, and absolute SFG decreased with decreasing body size in both exposure scenarios. Also mass-specific SFG decreased with decreasing body size under cadmium exposure, but an increase in mass-specific SFG was observed in the food ration experiment. This suggested that cadmium stress, apart from decreasing energy assimilation, also disturbs energy metabolism. Changes in both absolute and mass-specific SFG were mainly determined by changes in energy uptake, whereas energy loss varied little in response to both environmental stressors. With the cadmium-stressed daphnids, reproduction correlated positively with both absolute and mass-specific SFG. With the food-stressed daphnids however, reproduction correlated positively with absolute SFG but negatively with mass-specific SFG. Mass-corrected SFG still decreased with increasing cadmium stress, but did not differ between ration groups. Thus, mass-corrected SFG provides an indication of metabolic functioning, but appears less suited as an indicator of reproduction.
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Affiliation(s)
- Marc Baillieul
- University of Antwerp, Ecophysiology, Biochemistry, and Toxicology Group, Department of Biology, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
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