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Jackson TK, Rhode C. Comparative genomics of dusky kob (Argyrosomus japonicus, Sciaenidae) conspecifics: Evidence for speciation and the genetic mechanisms underlying traits. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38885946 DOI: 10.1111/jfb.15844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/17/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024]
Abstract
Dusky kob (Argyrosomus japonicus) is a commercially important finfish, indigenous to South Africa, Australia, and China. Previous studies highlighted differences in genetic composition, life history, and morphology of the species across geographic regions. A draft genome sequence of 0.742 Gb (N50 = 5.49 Mb; BUSCO completeness = 97.8%) and 22,438 predicted protein-coding genes was generated for the South African (SA) conspecific. A comparison with the Chinese (CN) conspecific revealed a core set of 32,068 orthologous protein clusters across both genomes. The SA genome exhibited 440 unique clusters compared to 1928 unique clusters in the CN genome. Transportation and immune response processes were overrepresented among the SA accessory genome, whereas the CN accessory genome was enriched for immune response, DNA transposition, and sensory detection (FDR-adjusted p < 0.01). These unique clusters may represent an adaptive component of the species' pangenome that could explain population divergence due to differential environmental specialisation. Furthermore, 700 single-copy orthologues (SCOs) displayed evidence of positive selection between the SA and CN genomes, and globally these genomes shared only 92% similarity, suggesting they might be distinct species. These genes primarily play roles in metabolism and digestion, illustrating the evolutionary pathways that differentiate the species. Understanding these genomic mechanisms underlying adaptation and evolution within and between species provides valuable insights into growth and maturation of kob, traits that are particularly relevant to commercial aquaculture.
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Affiliation(s)
- Tassin Kim Jackson
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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Henson SA, Cael BB, Allen SR, Dutkiewicz S. Future phytoplankton diversity in a changing climate. Nat Commun 2021; 12:5372. [PMID: 34508102 PMCID: PMC8433162 DOI: 10.1038/s41467-021-25699-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 08/24/2021] [Indexed: 11/08/2022] Open
Abstract
The future response of marine ecosystem diversity to continued anthropogenic forcing is poorly constrained. Phytoplankton are a diverse set of organisms that form the base of the marine ecosystem. Currently, ocean biogeochemistry and ecosystem models used for climate change projections typically include only 2-3 phytoplankton types and are, therefore, too simple to adequately assess the potential for changes in plankton community structure. Here, we analyse a complex ecosystem model with 35 phytoplankton types to evaluate the changes in phytoplankton community composition, turnover and size structure over the 21st century. We find that the rate of turnover in the phytoplankton community becomes faster during this century, that is, the community structure becomes increasingly unstable in response to climate change. Combined with alterations to phytoplankton diversity, our results imply a loss of ecological resilience with likely knock-on effects on the productivity and functioning of the marine environment.
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Affiliation(s)
| | - B B Cael
- National Oceanography Centre, European Way, Southampton, UK
| | - Stephanie R Allen
- National Oceanography Centre, European Way, Southampton, UK
- School of Ocean and Earth Sciences, University of Southampton, Waterfront Campus, European Way, Southampton, UK
- Plymouth Marine Laboratory, Prospect Place, Plymouth, UK
| | - Stephanie Dutkiewicz
- Center for Global Change Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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Han C, Kim HJ, Lee JS, Sakakura Y, Hagiwara A. Species-specific effects of iron on temperate and tropical marine rotifers in reproduction, lipid and ROS metabolisms. CHEMOSPHERE 2021; 277:130317. [PMID: 33780671 DOI: 10.1016/j.chemosphere.2021.130317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/07/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
Two euryhaline rotifers, the temperate species Brachionus plicatilis and tropical species Brachionus rotundiformis, were used to investigate the effects of iron (FeSO4·7H2O), an essential trace metal, on reproductive patterns and lifetables, including the metabolism of lipid and reactive oxygen species (ROS). B. plicatilis was more sensitive to iron with regard to sexual reproduction. While iron had no significant effect on the population growth at 0-48 μg/mL, it caused a decrease in the resting egg production. B. plicatilis exposed to 6 and 12 μg/mL of iron showed an increase in the intracellular ROS levels and a decrease in the neutral lipid content in sexual organs, accompanied by downregulation of antioxidant components CuZnSOD and two cytochromes (CYP clan 2&3). These patterns suggested that iron-induced oxidative stress was not neutralized by its antioxidant defense system, thus negatively affecting the fecundity of fertilized mictic females. However, B. rotundiformis showed a dose-dependent increase in population growth with extended lifespan and positive sexual reproduction in response to 0-24 μg/mL iron. Furthermore, compared to Fe-exposed B. plicatilis, B. rotundiformis showed better antioxidant mechanism, whereas genes involved in lipid synthesis (citrate lyase, mitochondrial CYP) and reproduction (vasa, sirtuin-2) were significantly upregulated compared to the control, implying that B. rotundiformis was likely to have higher resilience in response to iron-induced oxidative stress. These findings suggest that iron is likely to cause interspecific interactions in the B. plicatilis species complex, whereas the tropical species B. rotundiformis may have evolved an effective defense mechanism against iron-induced stress.
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Affiliation(s)
- Chengyan Han
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, 852-8521, Japan.
| | - Hee-Jin Kim
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, 852-8521, Japan.
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea.
| | - Yoshitaka Sakakura
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, 852-8521, Japan; Organization for Marine Science and Technology, Nagasaki University, Bunkyo 1-14, Nagasaki, 852-8521, Japan.
| | - Atsushi Hagiwara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, 852-8521, Japan; Organization for Marine Science and Technology, Nagasaki University, Bunkyo 1-14, Nagasaki, 852-8521, Japan.
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Gergs A, Baden CU. A Dynamic Energy Budget Approach for the Prediction of Development Times and Variability in Spodoptera frugiperda Rearing. INSECTS 2021; 12:insects12040300. [PMID: 33805418 PMCID: PMC8067041 DOI: 10.3390/insects12040300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022]
Abstract
A major challenge in insect rearing is the need to provide certain life cycle stages at a given time for the initiation of experimental trials. The timing of delivery, organism quality, and variability directly affect the outcome of such trials. Development times and intraspecific variability are directly linked to the availability of food and to the ambient temperature. Varying temperature regimes is an approach to adapt development times to fulfill experimental needs without impairment of larval quality. However, current practices of temperature setting may lead to increased variability in terms of development times and the frequency of particular life stages at a given point in time. In this study, we analyzed how resource availability and ambient temperature may affect the larval development of the economically important noctuid species Spodoptera frugiperda by means of dynamic energy budget modeling. More specifically, we analyzed how rearing practices such as raising of temperatures may affect the variability in larval development. Overall, the presented modeling approach provides a support system for decisions that must be made for the timely delivery of larvae and reduction of variability.
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Cattaneo S, Verlengia G, Marino P, Simonato M, Bettegazzi B. NPY and Gene Therapy for Epilepsy: How, When,... and Y. Front Mol Neurosci 2021; 13:608001. [PMID: 33551745 PMCID: PMC7862707 DOI: 10.3389/fnmol.2020.608001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
Neuropeptide Y (NPY) is a neuropeptide abundantly expressed in the mammalian central and peripheral nervous system. NPY is a pleiotropic molecule, which influences cell proliferation, cardiovascular and metabolic function, pain and neuronal excitability. In the central nervous system, NPY acts as a neuromodulator, affecting pathways that range from cellular (excitability, neurogenesis) to circuit level (food intake, stress response, pain perception). NPY has a broad repertoire of receptor subtypes, each activating specific signaling pathways in different tissues and cellular sub-regions. In the context of epilepsy, NPY is thought to act as an endogenous anticonvulsant that performs its action through Y2 and Y5 receptors. In fact, its overexpression in the brain with the aid of viral vectors can suppress seizures in animal models of epilepsy. Therefore, NPY-based gene therapy may represent a novel approach for the treatment of epilepsy patients, particularly for pharmaco-resistant and genetic forms of the disease. Nonetheless, considering all the aforementioned aspects of NPY signaling, the study of possible NPY applications as a therapeutic molecule is not devoid of critical aspects. The present review will summarize data related to NPY biology, focusing on its anti-epileptic effects, with a critical appraisal of key elements that could be exploited to improve the already existing NPY-based gene therapy approaches for epilepsy.
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Affiliation(s)
- Stefano Cattaneo
- Vita-Salute San Raffaele University, Milan, Italy.,San Raffaele Scientific Institute, Milan, Italy
| | - Gianluca Verlengia
- San Raffaele Scientific Institute, Milan, Italy.,Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Ferrara, Italy
| | - Pietro Marino
- Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Ferrara, Italy.,Department of Medical Sciences, Section of Pediatrics, University of Ferrara, Ferrara, Italy
| | - Michele Simonato
- Vita-Salute San Raffaele University, Milan, Italy.,San Raffaele Scientific Institute, Milan, Italy.,Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Ferrara, Italy
| | - Barbara Bettegazzi
- Vita-Salute San Raffaele University, Milan, Italy.,San Raffaele Scientific Institute, Milan, Italy
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Yoon DS, Lee Y, Park JC, Lee MC, Lee JS. Alleviation of tributyltin-induced toxicity by diet and microplastics in the marine rotifer Brachionus koreanus. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:123739. [PMID: 33254767 DOI: 10.1016/j.jhazmat.2020.123739] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 06/12/2023]
Abstract
To determine the effects of tributyltin (TBT) upon multiple exposures of diet and microplastic in rotifer, in vivo life parameters were measured. In 10 μg/L TBT-exposed rotifer, the 1 and 0.5 x diet groups resulted in reproduction reduction. However, 10 x diet treatment showed no significant changes in the total fecundity, despite a decrease in daily reproduction. Besides, differences in the lifespan were observed in response to different diet regimens. TBT and/or MP-exposed parental rotifer (F0) showed a significant delay in the pre-reproductive day under 0.5 x diet regimen. In all dietary regimens, exposure to TBT and MP induced an increase in reactive oxygen species, but antioxidant activities were perturbed. To further verify the carryover effect of TBT toxicity, progeny rotifer (F1) obtained from 24 h TBT and/or MP-exposed F0 was used. Interestingly, the faster hatching rate was observed only in F1 obtained from 1 x diet regimen-exposed F0. However, in the 0.5 x diet, the total fecundity was reduced and the pattern of the daily reproduction was collapsed. Thus, the toxicity of TBT can be alleviated by MP and nutrition status, but TBT-induced toxicity and its carryover effect are inevitable.
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Affiliation(s)
- Deok-Seo Yoon
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Yoseop Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Chul Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Han J, Lee KW. Influence of salinity on population growth, oxidative stress and antioxidant defense system in the marine monogonont rotifer Brachionus plicatilis. Comp Biochem Physiol B Biochem Mol Biol 2020; 250:110487. [DOI: 10.1016/j.cbpb.2020.110487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/20/2020] [Accepted: 08/02/2020] [Indexed: 11/26/2022]
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Han J, Lee JS, Park JC, Hagiwara A, Lee KW, Lee JS. Effects of temperature changes on life parameters, oxidative stress, and antioxidant defense system in the monogonont marine rotifer Brachionus plicatilis. MARINE POLLUTION BULLETIN 2020; 155:111062. [PMID: 32469753 DOI: 10.1016/j.marpolbul.2020.111062] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 06/11/2023]
Abstract
Global warming is a big concern for all organisms and many efforts have been made to reveal the potential effects of temperature elevation on aquatic organisms. However, limited studies on molecular mechanistic approaches on physiological effects due to temperature changes are available. Here, we investigated the effects of temperature changes on life parameters (e.g., population growth [total number of rotifers], and lifespan), oxidative stress levels and antioxidant activities (e.g., glutathione S-transferase [GST], catalase [CAT], superoxide dismutase [SOD]) with expression levels in the monogonont marine rotifer Brachionus plicatilis. The changes in temperatures led to significant reduction (P < 0.05) in lifespan, possibly due to significant decrease (P < 0.05) in antioxidant activities, reducing the potential to cope with significant elevation in the temperature-induced oxidative stress in B. plicatilis. To further assess the actual induction and clearance of reactive oxygen species (ROS), N-acetyl-L-cysteine was used to examine whether the temperature-induced oxidative stress could be successfully scavenged. Furthermore, expression patterns of the antioxidant-related genes (GSTs, SODs, and CATs) were down- or upregulated (P < 0.05) in response to different temperatures in B. plicatilis. Overall, these findings indicate that ROS-mediated oxidative stress led to cellular damage and antioxidant defense system, resulting in deleterious effects on life parameters in rotifer.
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Affiliation(s)
- Jeonghoon Han
- Department of Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea; Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jin-Sol Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Chul Park
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Atsushi Hagiwara
- Institute of Integrated Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan; Organization for Marine Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan
| | - Kyun-Woo Lee
- Department of Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, South Korea.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Munns R, Day DA, Fricke W, Watt M, Arsova B, Barkla BJ, Bose J, Byrt CS, Chen ZH, Foster KJ, Gilliham M, Henderson SW, Jenkins CLD, Kronzucker HJ, Miklavcic SJ, Plett D, Roy SJ, Shabala S, Shelden MC, Soole KL, Taylor NL, Tester M, Wege S, Wegner LH, Tyerman SD. Energy costs of salt tolerance in crop plants. THE NEW PHYTOLOGIST 2020; 225:1072-1090. [PMID: 31004496 DOI: 10.1111/nph.15864] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/25/2019] [Indexed: 05/21/2023]
Abstract
Agriculture is expanding into regions that are affected by salinity. This review considers the energetic costs of salinity tolerance in crop plants and provides a framework for a quantitative assessment of costs. Different sources of energy, and modifications of root system architecture that would maximize water vs ion uptake are addressed. Energy requirements for transport of salt (NaCl) to leaf vacuoles for osmotic adjustment could be small if there are no substantial leaks back across plasma membrane and tonoplast in root and leaf. The coupling ratio of the H+ -ATPase also is a critical component. One proposed leak, that of Na+ influx across the plasma membrane through certain aquaporin channels, might be coupled to water flow, thus conserving energy. For the tonoplast, control of two types of cation channels is required for energy efficiency. Transporters controlling the Na+ and Cl- concentrations in mitochondria and chloroplasts are largely unknown and could be a major energy cost. The complexity of the system will require a sophisticated modelling approach to identify critical transporters, apoplastic barriers and root structures. This modelling approach will inform experimentation and allow a quantitative assessment of the energy costs of NaCl tolerance to guide breeding and engineering of molecular components.
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Affiliation(s)
- Rana Munns
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, and School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - David A Day
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia, 5001, Australia
| | - Wieland Fricke
- School of Biology and Environmental Sciences, University College Dublin (UCD), Dublin, 4, Ireland
| | - Michelle Watt
- Plant Sciences, Institute of Bio and Geosciences, Forschungszentrum Juelich, Helmholtz Association, 52425, Juelich, Germany
| | - Borjana Arsova
- Plant Sciences, Institute of Bio and Geosciences, Forschungszentrum Juelich, Helmholtz Association, 52425, Juelich, Germany
| | - Bronwyn J Barkla
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2481, Australia
| | - Jayakumar Bose
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Caitlin S Byrt
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Zhong-Hua Chen
- School of Science and Health, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Kylie J Foster
- Phenomics and Bioinformatics Research Centre, School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Matthew Gilliham
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Sam W Henderson
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Urrbrae, SA, 5064, Australia
| | - Colin L D Jenkins
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia, 5001, Australia
| | - Herbert J Kronzucker
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Stanley J Miklavcic
- Phenomics and Bioinformatics Research Centre, School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Darren Plett
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Stuart J Roy
- Australian Research Council (ARC) Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Sergey Shabala
- Tasmanian Institute for Agriculture, University of Tasmania, Private Bag 54, Hobart, Tas., 7001, Australia
- International Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
| | - Megan C Shelden
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Kathleen L Soole
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia, 5001, Australia
| | - Nicolas L Taylor
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Molecular Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Mark Tester
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Stefanie Wege
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Lars H Wegner
- Karlsruhe Institute of Technology, Institute for Pulsed Power and Microwave Technology (IHM), D-76344, Eggenstein-Leopoldshafen, Germany
| | - Stephen D Tyerman
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
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Muller EB, Lika K, Nisbet RM, Schultz IR, Casas J, Gergs A, Murphy CA, Nacci D, Watanabe KH. REGULATION OF REPRODUCTIVE PROCESSES WITH DYNAMIC ENERGY BUDGETS. Funct Ecol 2019; 33:819-832. [PMID: 32038063 PMCID: PMC7006839 DOI: 10.1111/1365-2435.13298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/03/2019] [Indexed: 12/17/2022]
Abstract
1. The simple bioenergetic models in the family of Dynamic Energy Budget (DEB) consist of a small number of state equations quantifying universal processes, such as feeding, maintenance, development, reproduction and growth. Linking these organismal level processes to underlying suborganismal mechanisms at the molecular, cellular and organ level constitutes a major challenge for predictive ecological risk assessments. 2. Motivated by the need for process-based models to evaluate the impact of endocrine disruptors on ecologically relevant endpoints, this paper develops and evaluates two general modeling modules describing demand-driven feedback mechanisms exerted by gonads on the allocation of resources to production of reproductive matter within the DEB modeling framework. 3. These modules describe iteroparous, semelparous and batch-mode reproductive strategies. The modules have a generic form with both positive and negative feedback components; species and sex specific attributes of endocrine regulation can be added without changing the core of the modules. 4. We demonstrate that these modules successfully describe time-resolved measurements of wet weight of body, ovaries and liver, egg diameter and plasma content of vitellogenin and estradiol in rainbow trout (Oncorynchus mykiss) by fitting these models to published and new data, which require the estimation of less than two parameters per data type. 5. We illustrate the general applicability of the concept of demand-driven allocation of resources to reproduction as worked out in this paper by evaluating one of the modules with data on growth and seed production of an annual plant, the common bean (Phaseolis vulgaris).
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Affiliation(s)
- Erik B. Muller
- Department of Biology. Norwegian University of Science and Technology, Trondheim, Norway
- Marine Science Institute, University of California, Santa Barbara, CA, USA
| | - Konstadia Lika
- Department of Biology, University of Crete, Heraklion, Greece
| | - Roger M. Nisbet
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Irvin R. Schultz
- Pacific Northwest National Laboratory, Marine Sciences Laboratory, Sequim, WA, USA
| | - Jérôme Casas
- Institute de Recherche sur la Biologie de l’Insecte, Université de Tours, Tours, France
| | - André Gergs
- gaiac - Research Institute for Ecosystem Analysis and Assessment, Aachen, Germany
| | - Cheryl A. Murphy
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Diane Nacci
- US Environmental Protection Agency, Office of Research and Development, Narragansett, RI, USA
| | - Karen H. Watanabe
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ, USA
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13
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Ockleford C, Adriaanse P, Berny P, Brock T, Duquesne S, Grilli S, Hernandez-Jerez AF, Bennekou SH, Klein M, Kuhl T, Laskowski R, Machera K, Pelkonen O, Pieper S, Smith RH, Stemmer M, Sundh I, Tiktak A, Topping CJ, Wolterink G, Cedergreen N, Charles S, Focks A, Reed M, Arena M, Ippolito A, Byers H, Teodorovic I. Scientific Opinion on the state of the art of Toxicokinetic/Toxicodynamic (TKTD) effect models for regulatory risk assessment of pesticides for aquatic organisms. EFSA J 2018; 16:e05377. [PMID: 32626020 PMCID: PMC7009662 DOI: 10.2903/j.efsa.2018.5377] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Following a request from EFSA, the Panel on Plant Protection Products and their Residues (PPR) developed an opinion on the state of the art of Toxicokinetic/Toxicodynamic (TKTD) models and their use in prospective environmental risk assessment (ERA) for pesticides and aquatic organisms. TKTD models are species‐ and compound‐specific and can be used to predict (sub)lethal effects of pesticides under untested (time‐variable) exposure conditions. Three different types of TKTD models are described, viz., (i) the ‘General Unified Threshold models of Survival’ (GUTS), (ii) those based on the Dynamic Energy Budget theory (DEBtox models), and (iii) models for primary producers. All these TKTD models follow the principle that the processes influencing internal exposure of an organism, (TK), are separated from the processes that lead to damage and effects/mortality (TD). GUTS models can be used to predict survival rate under untested exposure conditions. DEBtox models explore the effects on growth and reproduction of toxicants over time, even over the entire life cycle. TKTD model for primary producers and pesticides have been developed for algae, Lemna and Myriophyllum. For all TKTD model calibration, both toxicity data on standard test species and/or additional species can be used. For validation, substance and species‐specific data sets from independent refined‐exposure experiments are required. Based on the current state of the art (e.g. lack of documented and evaluated examples), the DEBtox modelling approach is currently limited to research applications. However, its great potential for future use in prospective ERA for pesticides is recognised. The GUTS model and the Lemna model are considered ready to be used in risk assessment.
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Han J, Lee MC, Park JC, Kim S, Lee JS. Effects of temperature shifts on life parameters and expression of fatty acid synthesis and heat shock protein genes in temperate and Antarctic copepods Tigriopus japonicus and Tigriopus kingsejongensis. Polar Biol 2018. [DOI: 10.1007/s00300-018-2382-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Salguero‐Gómez R, Violle C, Gimenez O, Childs D, Fox C. Delivering the promises of trait-based approaches to the needs of demographic approaches, and vice versa. Funct Ecol 2018; 32:1424-1435. [PMID: 30034074 PMCID: PMC6049886 DOI: 10.1111/1365-2435.13148] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/22/2018] [Indexed: 11/28/2022]
Abstract
Few facets of biology vary more than functional traits and life-history traits. To explore this vast variation, functional ecologists and population ecologists have developed independent approaches that identify the mechanisms behind and consequences of trait variation.Collaborative research between researchers using trait-based and demographic approaches remains scarce. We argue that this is a missed opportunity, as the strengths of both approaches could help boost the research agendas of functional ecology and population ecology.This special feature, which spans three journals of the British Ecological Society due to its interdisciplinary nature, showcases state-of-the-art research applying trait-based and demographic approaches to examine relationships between organismal function, life history strategies and population performance across multiple kingdoms. Examples include the exploration of how functional trait × environment interactions affect vital rates and thus explain population trends and species occurrence; the coordination of seed traits and dispersal ability with the pace of life in plants; the incorporation of functional traits in dynamic energy budget models; or the discovery of linkages between microbial functional traits and the fast-slow continuum.Despite their historical isolation, collaborative work between functional ecologists and population ecologists could unlock novel research pathways. We call for an integrative research agenda to evaluate which and when traits are functional, as well as their ability to describe and predict life history strategies and population dynamics. We highlight promising, complementary research avenues to overcome current limitations. These include a more explicit linkage of selection gradients in the context of functional trait-vital rate relationships, and the implementation of standardised protocols to track changes in traits and vital rates over time at the same location and individuals, thus allowing for the explicit incorporation of trade-offs in analyses of covariation of functional traits and life-history traits.
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Affiliation(s)
- Roberto Salguero‐Gómez
- Department of ZoologyUniversity of OxfordOxfordUK
- Evolutionary Biodemography LaboratoryMax Planck Institute for Demographic ResearchRostockGermany
- Centre for Biodiversity and Conservation ScienceUniversity of QueenslandSt LuciaQldAustralia
| | - Cyrille Violle
- CEFE, CNRSUniv MontpellierUniv Paul Valéry Montpellier 3, EPHE, IRDMontpellierFrance
| | - Olivier Gimenez
- CEFE, CNRSUniv MontpellierUniv Paul Valéry Montpellier 3, EPHE, IRDMontpellierFrance
| | - Dylan Childs
- Department of Animal & Plant SciencesThe University of SheffieldSheffieldUK
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Lee MC, Park JC, Yoon DS, Han J, Kang S, Kamizono S, Om AS, Shin KH, Hagiwara A, Lee JS. Aging extension and modifications of lipid metabolism in the monogonont rotifer Brachionus koreanus under chronic caloric restriction. Sci Rep 2018; 8:1741. [PMID: 29379054 PMCID: PMC5789037 DOI: 10.1038/s41598-018-20108-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/12/2018] [Indexed: 12/11/2022] Open
Abstract
To examine the interrelationship of aging extension and modification of lipid metabolism under chronic caloric restriction (CCR; reduced concentration of the green algae Tetraselmis suecica) in the monogonont rotifer Brachionus koreanus, we assessed life cycle parameters, fatty acid composition, and expression of sirtuin and genes related to lipid metabolism. B. koreanus in the 5% T. suecica group showed an increased life span but decreased reproduction. Based on this finding, we chose 5% T. suecica for further experiments and compared the data with those for 100% T. suecica. Upregulation of sirtuin gene expression was observed under CCR. In addition, despite the reduction in the amount of total fatty acid (FA) and the area of triacylglycerol, increases in the ratios of saturated fatty acid and monounsaturated fatty acid (MUFA) to total FA in 5%-exposed B. koreanus were observed. Furthermore, mRNA expression analysis confirmed that CCR promoted the synthesis of MUFA through Δ9 desaturase. Moreover, expression of the docosahexaenoic acid (DHA) synthesizing gene Δ4 desaturase was also upregulated, together with DHA content. These data suggest that CCR modified protein acetylation and lipid metabolism, leading to a decrease in reproduction and consequently resulting in life span extension.
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Affiliation(s)
- Min-Chul Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jun Chul Park
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Deok-Seo Yoon
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Sujin Kang
- Department of Marine Sciences and Convergent Technology, Hanyang University, Ansan, 15588, South Korea
| | - Shohei Kamizono
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Ae-Son Om
- Department of Food and Nutrition, College of Human Ecology, Hanyang University, Seoul, 04763, South Korea
| | - Kyung-Hoon Shin
- Department of Marine Sciences and Convergent Technology, Hanyang University, Ansan, 15588, South Korea
| | - Atsushi Hagiwara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea.
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Lee MC, Park JC, Kim DH, Kang S, Shin KH, Park HG, Han J, Lee JS. Interrelationship of salinity shift with oxidative stress and lipid metabolism in the monogonont rotifer Brachionus koreanus. Comp Biochem Physiol A Mol Integr Physiol 2017; 214:79-84. [DOI: 10.1016/j.cbpa.2017.09.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 10/18/2022]
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Grossowicz M, Marques GM, van Voorn GA. A dynamic energy budget (DEB) model to describe population dynamics of the marine cyanobacterium Prochlorococcus marinus. Ecol Modell 2017. [DOI: 10.1016/j.ecolmodel.2017.06.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Marn N, Kooijman SALM, Jusup M, Legović T, Klanjšček T. Inferring physiological energetics of loggerhead turtle (Caretta caretta) from existing data using a general metabolic theory. MARINE ENVIRONMENTAL RESEARCH 2017; 126:14-25. [PMID: 28219019 DOI: 10.1016/j.marenvres.2017.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 01/18/2017] [Accepted: 01/19/2017] [Indexed: 05/14/2023]
Abstract
Loggerhead turtle is an endangered sea turtle species with a migratory lifestyle and worldwide distribution, experiencing markedly different habitats throughout its lifetime. Environmental conditions, especially food availability and temperature, constrain the acquisition and the use of available energy, thus affecting physiological processes such as growth, maturation, and reproduction. These physiological processes at the population level determine survival, fecundity, and ultimately the population growth rate-a key indicator of the success of conservation efforts. As a first step towards the comprehensive understanding of how environment shapes the physiology and the life cycle of a loggerhead turtle, we constructed a full life cycle model based on the principles of energy acquisition and utilization embedded in the Dynamic Energy Budget (DEB) theory. We adapted the standard DEB model using data from published and unpublished sources to obtain parameter estimates and model predictions that could be compared with data. The outcome was a successful mathematical description of ontogeny and life history traits of the loggerhead turtle. Some deviations between the model and the data existed (such as an earlier age at sexual maturity and faster growth of the post-hatchlings), yet probable causes for these deviations were found informative and discussed in great detail. Physiological traits such as the capacity to withstand starvation, trade-offs between reproduction and growth, and changes in the energy budget throughout the ontogeny were inferred from the model. The results offer new insights into physiology and ecology of loggerhead turtle with the potential to lead to novel approaches in conservation of this endangered species.
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Affiliation(s)
- Nina Marn
- Ruđer Bošković Institute, Bijenička cesta 54, HR-10002 Zagreb, Croatia.
| | - S A L M Kooijman
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Marko Jusup
- Center of Mathematics for Social Creativity, Hokkaido University, 12-7 Kita Ward, 060-0812 Sapporo, Japan.
| | - Tarzan Legović
- Ruđer Bošković Institute, Bijenička cesta 54, HR-10002 Zagreb, Croatia
| | - Tin Klanjšček
- Ruđer Bošković Institute, Bijenička cesta 54, HR-10002 Zagreb, Croatia
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The universality and the future prospects of physiological energetics. Phys Life Rev 2017; 20:78-84. [DOI: 10.1016/j.plrev.2017.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 12/23/2022]
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Kooijman SA. Homeostasis and the fuelling of metabolism. Phys Life Rev 2017; 20:60-62. [DOI: 10.1016/j.plrev.2016.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 11/15/2016] [Indexed: 11/26/2022]
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Giacomini HC, Shuter BJ. Adaptive responses of energy storage and fish life histories to climatic gradients. J Theor Biol 2013; 339:100-11. [DOI: 10.1016/j.jtbi.2013.08.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 08/20/2013] [Accepted: 08/21/2013] [Indexed: 11/29/2022]
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Maino JL, Kearney MR, Nisbet RM, Kooijman SALM. Reconciling theories for metabolic scaling. J Anim Ecol 2013; 83:20-9. [DOI: 10.1111/1365-2656.12085] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 03/16/2013] [Indexed: 11/30/2022]
Affiliation(s)
- James L. Maino
- Department of Zoology; The University of Melbourne; Melbourne Vic. 3010 Australia
| | - Michael R. Kearney
- Department of Zoology; The University of Melbourne; Melbourne Vic. 3010 Australia
| | - Roger M. Nisbet
- Department of Ecology, Evolution and Marine Biology; University of California; Santa Barbara CA 93106-9620 USA
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Palos Ladeiro M, Bigot A, Aubert D, Hohweyer J, Favennec L, Villena I, Geffard A. Protozoa interaction with aquatic invertebrate: interest for watercourses biomonitoring. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:778-789. [PMID: 23001759 DOI: 10.1007/s11356-012-1189-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 09/06/2012] [Indexed: 06/01/2023]
Abstract
Toxoplasma gondii, Cryptosporidium parvum, and Giardia duodenalis are human waterborne protozoa. These worldwide parasites had been detected in various watercourses as recreational, surface, drinking, river, and seawater. As of today, water protozoa detection was based on large water filtration and on sample concentration. Another tool like aquatic invertebrate parasitism could be used for sanitary and environmental biomonitoring. In fact, organisms like filter feeders could already filtrate and concentrate protozoa directly in their tissues in proportion to ambient concentration. So molluscan shellfish can be used as a bioindicator of protozoa contamination level in a site since they were sedentary. Nevertheless, only a few researches had focused on nonspecific parasitism like protozoa infection on aquatic invertebrates. Objectives of this review are twofold: Firstly, an overview of protozoa in worldwide water was presented. Secondly, current knowledge of protozoa parasitism on aquatic invertebrates was detailed and the lack of data of their biological impact was pointed out.
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Affiliation(s)
- M Palos Ladeiro
- Unité Interactions Animal-Environnement, EA 4689, UFR Sciences Exactes et Naturelles, Université de Reims Champagne Ardenne, Campus du Moulin de la Housse, 51100, Reims, France
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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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Yolky eggs prepare for metabolic acceleration. J Math Biol 2012; 66:795-805. [PMID: 23053538 DOI: 10.1007/s00285-012-0597-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 09/12/2012] [Indexed: 10/27/2022]
Abstract
Embryos convert some of their reserve into structure during development. At birth, enough must be left for further maturation, which implicitly defines the minimum amount of initial reserve. The maximum amount occurs if the mother is well-fed. Yolkiness is defined as the ratio of the maximum and the minimum amounts of initial reserve of an animal egg. Embryo development is frequently slower than can be expected on the basis of late juvenile and adult development. So development accelerates during the early juvenile stage, quantified as the ratio of the lengths at metamorphosis and at birth; during acceleration maximum specific assimilation and energy conductance increase with length. Parameters of the standard DEB model have now been estimated for some 165 species, and the goodness of fit with data is typically very good. These parameters have been used to quantify yolkiness and metabolic acceleration and a clear proportionality relationship resulted. I present some suggestions for explanations in the context of life histories.
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Vinga S, Neves AR, Santos H, Brandt BW, Kooijman SALM. Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories. Philos Trans R Soc Lond B Biol Sci 2011; 365:3429-42. [PMID: 20921043 DOI: 10.1098/rstb.2010.0156] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The dynamic modelling of metabolic networks aims to describe the temporal evolution of metabolite concentrations in cells. This area has attracted increasing attention in recent years owing to the availability of high-throughput data and the general development of systems biology as a promising approach to study living organisms. Biochemical Systems Theory (BST) provides an accurate formalism to describe biological dynamic phenomena. However, knowledge about the molecular organization level, used in these models, is not enough to explain phenomena such as the driving forces of these metabolic networks. Dynamic Energy Budget (DEB) theory captures the quantitative aspects of the organization of metabolism at the organism level in a way that is non-species-specific. This imposes constraints on the sub-organismal organization that are not present in the bottom-up approach of systems biology. We use in vivo data of lactic acid bacteria under various conditions to compare some aspects of BST and DEB approaches. Due to the large number of parameters to be estimated in the BST model, we applied powerful parameter identification techniques. Both models fitted equally well, but the BST model employs more parameters. The DEB model uses similarities of processes under growth and no-growth conditions and under aerobic and anaerobic conditions, which reduce the number of parameters. This paper discusses some future directions for the integration of knowledge from these two rich and promising areas, working top-down and bottom-up simultaneously. This middle-out approach is expected to bring new ideas and insights to both areas in terms of describing how living organisms operate.
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Affiliation(s)
- S Vinga
- Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento, R Alves Redol 9, 1000-029 Lisboa, Portugal.
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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: 135] [Impact Index Per Article: 9.6] [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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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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Bioengineering plant resistance to abiotic stresses by the global calcium signal system. Biotechnol Adv 2008; 26:503-10. [DOI: 10.1016/j.biotechadv.2008.04.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Revised: 04/07/2008] [Accepted: 04/07/2008] [Indexed: 12/21/2022]
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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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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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Kooijman SALM, Grasman J, Kooi BW. A new class of non-linear stochastic population models with mass conservation. Math Biosci 2007; 210:378-94. [PMID: 17659307 DOI: 10.1016/j.mbs.2007.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 05/15/2007] [Accepted: 05/18/2007] [Indexed: 11/28/2022]
Abstract
We study the effects of random feeding, growing and dying in a closed nutrient-limited producer/consumer system, in which nutrient is fully conserved, not only in the mean, but, most importantly, also across random events. More specifically, we relate these random effects to the closest deterministic models, and evaluate the importance of the various times scales that are involved. These stochastic models differ from deterministic ones not only in stochasticity, but they also have more details that involve shorter times scales. We tried to separate the effects of more detail from that of stochasticity. The producers have (nutrient) reserve and (body) structure, and so a variable chemical composition. The consumers have only structure, so a constant chemical composition. The conversion efficiency from producer to consumer, therefore, varies. The consumers use reserve and structure of the producers as complementary compounds, following the rules of Dynamic Energy Budget theory. Consumers die at constant specific rate and decompose instantaneously. Stochasticity is incorporated in the behaviour of the consumers, where the switches to handling and searching, as well as dying are Poissonian point events. We show that the stochastic model has one parameter more than the deterministic formulation without time scale separation for conversions between searching and handling consumers, which itself has one parameter more than the deterministic formulation with time scale separation for these conversions. These extra parameters are the contributions of a single individual producer and consumer to their densities, and the ratio of the two, respectively. The tendency to oscillate increases with the number of parameters. The focus bifurcation point has more relevance for the asymptotic behaviour of the stochastic model than the Hopf bifurcation point, since a randomly perturbed damped oscillation exhibits a behaviour similar to that of the stochastic limit cycle particularly near this bifurcation point. For total nutrient values below the focus bifurcation point, the system gradually becomes more confined to the direct neighbourhood of the isocline for which the producers do not change.
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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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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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Tolla C, Kooijman SALM, Poggiale JC. A kinetic inhibition mechanism for maintenance. J Theor Biol 2007; 244:576-87. [PMID: 17069860 DOI: 10.1016/j.jtbi.2006.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Revised: 08/09/2006] [Accepted: 09/06/2006] [Indexed: 11/25/2022]
Abstract
To fulfil their maintenance costs, most species use mobile pools of metabolites (reserve) in favourable conditions, but can also use less mobile pools (structure) under food-limiting conditions. While some empirical models always pay maintenance costs from structure, the presence of reserve inhibits the use of structure for maintenance purposes. The standard dynamic energy budgets (DEB) model captures this by simply supplementing all costs that could not be paid from reserve with structure. This is less realistic at the biochemical level, and involves a sudden use of structure that can complicate the analysis of the model properties. We here propose a new inhibition formulation for the preferential use of reserve above structure in maintenance that avoids sudden changes in the metabolites use. It is based on the application of the theory for synthesizing units, which can easily become rather complex for demand processes, such as the maintenance. We found, however, a simple explicit expression for the use of reserve and structure for maintenance purposes and compared the numerical behaviour with that of a classical model in oscillating conditions, by using parameters values from a fit of the models to data on yeasts in a batch culture. We conclude that our model can better handle variable environments. This new inhibition formulation has a wide applicability in modelling metabolic processes.
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Affiliation(s)
- Caroline Tolla
- Laboratoire de Microbiologie Géochimie et d'Ecologie Marine, UMR 6117-Centre d'Océanologie de Marseille, Case 901, Campus de Luminy, 13 288 Marseille Cedex 9, France.
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