1
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Theorell A, Jadebeck JF, Wiechert W, McFadden J, Nöh K. Rethinking 13C-metabolic flux analysis - The Bayesian way of flux inference. Metab Eng 2024; 83:137-149. [PMID: 38582144 DOI: 10.1016/j.ymben.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/08/2024]
Abstract
Metabolic reaction rates (fluxes) play a crucial role in comprehending cellular phenotypes and are essential in areas such as metabolic engineering, biotechnology, and biomedical research. The state-of-the-art technique for estimating fluxes is metabolic flux analysis using isotopic labelling (13C-MFA), which uses a dataset-model combination to determine the fluxes. Bayesian statistical methods are gaining popularity in the field of life sciences, but the use of 13C-MFA is still dominated by conventional best-fit approaches. The slow take-up of Bayesian approaches is, at least partly, due to the unfamiliarity of Bayesian methods to metabolic engineering researchers. To address this unfamiliarity, we here outline similarities and differences between the two approaches and highlight particular advantages of the Bayesian way of flux analysis. With a real-life example, re-analysing a moderately informative labelling dataset of E. coli, we identify situations in which Bayesian methods are advantageous and more informative, pointing to potential pitfalls of current 13C-MFA evaluation approaches. We propose the use of Bayesian model averaging (BMA) for flux inference as a means of overcoming the problem of model uncertainty through its tendency to assign low probabilities to both, models that are unsupported by data, and models that are overly complex. In this capacity, BMA resembles a tempered Ockham's razor. With the tempered razor as a guide, BMA-based 13C-MFA alleviates the problem of model selection uncertainty and is thereby capable of becoming a game changer for metabolic engineering by uncovering new insights and inspiring novel approaches.
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Affiliation(s)
- Axel Theorell
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Johann F Jadebeck
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52062 Aachen, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52062 Aachen, Germany
| | - Johnjoe McFadden
- Department of Microbial and Cellular Sciences, University of Surrey, GU2 7XH Guildford, United Kingdom
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
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2
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McFadden J. Razor sharp: The role of Occam's razor in science. Ann N Y Acad Sci 2023; 1530:8-17. [PMID: 38018886 PMCID: PMC10952609 DOI: 10.1111/nyas.15086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Occam's razor-the principle of simplicity-has recently been attacked as a cultural bias without rational foundation. Increasingly, belief in pseudoscience and mysticism is growing. I argue that inclusion of Occam's razor is an essential factor that distinguishes science from superstition and pseudoscience. I also describe how the razor is embedded in Bayesian inference and argue that science is primarily the means to discover the simplest descriptions of our world.
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Affiliation(s)
- Johnjoe McFadden
- Leverhulme Quantum Biology Doctoral Training CentreUniversity of SurreyGuildfordUK
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3
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Lauber N, Flamm C, Ruiz-Mirazo K. "Minimal metabolism": A key concept to investigate the origins and nature of biological systems. Bioessays 2021; 43:e2100103. [PMID: 34426986 DOI: 10.1002/bies.202100103] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 11/07/2022]
Abstract
The systems view on life and its emergence from complex chemistry has remarkably increased the scientific attention on metabolism in the last two decades. However, during this time there has not been much theoretical discussion on what constitutes a metabolism and what role it actually played in biogenesis. A critical and updated review on the topic is here offered, including some references to classical models from last century, but focusing more on current and future research. Metabolism is considered as intrinsically related to the living but not necessarily equivalent to it. More precisely, the idea of "minimal metabolism", in contrast to previous, top-down conceptions, is formulated as a heuristic construct, halfway between chemistry and biology. Thus, rather than providing a complete or final characterization of metabolism, our aim is to encourage further investigations on it, particularly in the context of life's origin, for which some concrete methodological suggestions are provided. Also see the video abstract here: https://youtu.be/DP7VMKk2qpA.
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Affiliation(s)
- Nino Lauber
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain.,Department of Philosophy, University of the Basque Country, Leioa, Spain
| | - Christoph Flamm
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain.,Department of Philosophy, University of the Basque Country, Leioa, Spain
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4
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Kolisis N, Kolisis F. Synthetic Biology: Old and New Dilemmas—The Case of Artificial Life. BIOTECH 2021; 10:biotech10030016. [PMID: 35822770 PMCID: PMC9245477 DOI: 10.3390/biotech10030016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/30/2021] [Accepted: 07/14/2021] [Indexed: 11/16/2022] Open
Abstract
This article aims to examine some of the ethical questions emerging from the use of already existing biotechnological tools and the issues which might occur by synthetic biology’s potential future possibilities. In the first part, the essence of synthetic biology and its relation to the contemporary biotechnological research is analyzed. In the second part, the article examines whether the new biotechnological inventions pose new or revive old moral questions about the ethics of science, engineering, and technology in general. After briefly addressing some of the various issues which are raised by experts, philosophers, but also the general public, concerning synthetic biology in general, it focuses on the topic of “artificial life creation” and presents moral reasons which may or may not allow it. The topic is approached by referring to consequentialist, deontological, but also, virtue theory arguments for and against it and the possibility of a partial permission of “artificial life” experiments, asking whether the benefits outweigh the risks and moral implications is explored. Finally, it proposes an argument in favor of the future exploration of biological innovation, underlying the need for a more balanced access to its beneficial results.
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Affiliation(s)
- Nikolaos Kolisis
- School of Law, National and Kapodistrian University of Athens, Solonos 57, 10679 Athens, Greece
- Correspondence: ; Tel.: +30-698-285-2587
| | - Fragiskos Kolisis
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Zografou Campus, 9, Iroon Polytechniou str, 15780 Athens, Greece;
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5
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Tretter F, Wolkenhauer O, Meyer-Hermann M, Dietrich JW, Green S, Marcum J, Weckwerth W. The Quest for System-Theoretical Medicine in the COVID-19 Era. Front Med (Lausanne) 2021; 8:640974. [PMID: 33855036 PMCID: PMC8039135 DOI: 10.3389/fmed.2021.640974] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/17/2021] [Indexed: 12/15/2022] Open
Abstract
Precision medicine and molecular systems medicine (MSM) are highly utilized and successful approaches to improve understanding, diagnosis, and treatment of many diseases from bench-to-bedside. Especially in the COVID-19 pandemic, molecular techniques and biotechnological innovation have proven to be of utmost importance for rapid developments in disease diagnostics and treatment, including DNA and RNA sequencing technology, treatment with drugs and natural products and vaccine development. The COVID-19 crisis, however, has also demonstrated the need for systemic thinking and transdisciplinarity and the limits of MSM: the neglect of the bio-psycho-social systemic nature of humans and their context as the object of individual therapeutic and population-oriented interventions. COVID-19 illustrates how a medical problem requires a transdisciplinary approach in epidemiology, pathology, internal medicine, public health, environmental medicine, and socio-economic modeling. Regarding the need for conceptual integration of these different kinds of knowledge we suggest the application of general system theory (GST). This approach endorses an organism-centered view on health and disease, which according to Ludwig von Bertalanffy who was the founder of GST, we call Organismal Systems Medicine (OSM). We argue that systems science offers wider applications in the field of pathology and can contribute to an integrative systems medicine by (i) integration of evidence across functional and structural differentially scaled subsystems, (ii) conceptualization of complex multilevel systems, and (iii) suggesting mechanisms and non-linear relationships underlying the observed phenomena. We underline these points with a proposal on multi-level systems pathology including neurophysiology, endocrinology, immune system, genetics, and general metabolism. An integration of these areas is necessary to understand excess mortality rates and polypharmacological treatments. In the pandemic era this multi-level systems pathology is most important to assess potential vaccines, their effectiveness, short-, and long-time adverse effects. We further argue that these conceptual frameworks are not only valid in the COVID-19 era but also important to be integrated in a medicinal curriculum.
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Affiliation(s)
- Felix Tretter
- Bertalanffy Center for the Study of Systems Science, Vienna, Austria
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Johannes W Dietrich
- Endocrine Research, Medical Hospital I, Bergmannsheil University Hospitals, Ruhr University of Bochum, Bochum, Germany.,Ruhr Center for Rare Diseases (CeSER), Ruhr University of Bochum, Witten/Herdecke University, Bochum, Germany
| | - Sara Green
- Section for History and Philosophy of Science, Department of Science Education, University of Copenhagen, Copenhagen, Denmark
| | - James Marcum
- Department of Philosophy, Baylor University, Waco, TX, United States
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
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6
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Gruden K, Lidoy J, Petek M, Podpečan V, Flors V, Papadopoulou KK, Pappas ML, Martinez-Medina A, Bejarano E, Biere A, Pozo MJ. Ménage à Trois: Unraveling the Mechanisms Regulating Plant-Microbe-Arthropod Interactions. TRENDS IN PLANT SCIENCE 2020; 25:1215-1226. [PMID: 32828689 DOI: 10.1016/j.tplants.2020.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Plant-microbe-arthropod (PMA) three-way interactions have important implications for plant health. However, our poor understanding of the underlying regulatory mechanisms hampers their biotechnological applications. To this end, we searched for potential common patterns in plant responses regarding taxonomic groups or lifestyles. We found that most signaling modules regulating two-way interactions also operate in three-way interactions. Furthermore, the relative contribution of signaling modules to the final plant response cannot be directly inferred from two-way interactions. Moreover, our analyses show that three-way interactions often result in the activation of additional pathways, as well as in changes in the speed or intensity of defense activation. Thus, detailed, basic knowledge of plant-microbe-arthropod regulation will be essential for the design of environmentally friendly crop management strategies.
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Affiliation(s)
- Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
| | - Javier Lidoy
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Vid Podpečan
- Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Victor Flors
- Metabolic Integration and Cell Signaling Laboratory, Department of Ciencias Agrarias y del Medio Natural, Universitat Jaume I; Unidad Asociada al Consejo Superior de Investigaciones Científicas (EEZ-CSIC)-Universitat Jaume I, Castellón, Spain
| | - Kalliopi K Papadopoulou
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Biopolis, Larissa, Greece
| | - Maria L Pappas
- Department of Agricultural Development, Faculty of Agricultural Sciences and Forestry, Democritus University of Thrace, Orestiada, Greece
| | - Ainhoa Martinez-Medina
- Plant-Microbe Interaction, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
| | - Eduardo Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Department Biología Celular, Genética y Fisiología, Universidad de Málaga, Málaga, Spain
| | - Arjen Biere
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Maria J Pozo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, Spain.
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7
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Brun-Usan M, Thies C, Watson RA. How to fit in: The learning principles of cell differentiation. PLoS Comput Biol 2020; 16:e1006811. [PMID: 32282832 PMCID: PMC7179933 DOI: 10.1371/journal.pcbi.1006811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/23/2020] [Accepted: 02/20/2020] [Indexed: 11/18/2022] Open
Abstract
Cell differentiation in multicellular organisms requires cells to respond to complex combinations of extracellular cues, such as morphogen concentrations. Some models of phenotypic plasticity conceptualise the response as a relatively simple function of a single environmental cues (e.g. a linear function of one cue), which facilitates rigorous analysis. Conversely, more mechanistic models such those implementing GRNs allows for a more general class of response functions but makes analysis more difficult. Therefore, a general theory describing how cells integrate multi-dimensional signals is lacking. In this work, we propose a theoretical framework for understanding the relationships between environmental cues (inputs) and phenotypic responses (outputs) underlying cell plasticity. We describe the relationship between environment and cell phenotype using logical functions, making the evolution of cell plasticity equivalent to a simple categorisation learning task. This abstraction allows us to apply principles derived from learning theory to understand the evolution of multi-dimensional plasticity. Our results show that natural selection is capable of discovering adaptive forms of cell plasticity associated with complex logical functions. However, developmental dynamics cause simpler functions to evolve more readily than complex ones. By using conceptual tools derived from learning theory we show that this developmental bias can be interpreted as a learning bias in the acquisition of plasticity functions. Because of that bias, the evolution of plasticity enables cells, under some circumstances, to display appropriate plastic responses to environmental conditions that they have not experienced in their evolutionary past. This is possible when the selective environment mirrors the bias of the developmental dynamics favouring the acquisition of simple plasticity functions–an example of the necessary conditions for generalisation in learning systems. These results illustrate the functional parallelisms between learning in neural networks and the action of natural selection on environmentally sensitive gene regulatory networks. This offers a theoretical framework for the evolution of plastic responses that integrate information from multiple cues, a phenomenon that underpins the evolution of multicellularity and developmental robustness. In organisms composed of many cell types, the differentiation of cells relies on their ability to respond to complex extracellular cues, such as morphogen concentrations, a phenomenon known as cell plasticity. Although cell plasticity plays a crucial role in development and evolution, it is not clear how, and if, cell plasticity can enhance adaptation to a novel environment and/or facilitate robust developmental processes. In some models, the relationships between the environmental cues (inputs) and the phenotypic responses (outputs) are conceptualised as one-to-one (i.e. simple ‘reaction norms’); whereas the phenotype of plastic cells commonly depends on several simultaneous inputs (i.e. many-to-one, multi-dimensional reaction norms). One alternative is the use of a gene-regulatory network (GRN) models that allow for much more general responses; but this can make analysis difficult. In this work we use a theoretical framework based on logical functions and learning theory to characterize such multi-dimensional reaction norms produced by GRNs. This allows us to reveal a strong and previously unnoticed bias towards the acquisition of simple forms of cell plasticity, which increases their ability to adapt to novel environments. Recognising this bias helps us to understand when the evolution of cell plasticity will increase the ability of plastic cells to adapt to novel environments, to respond appropriately to complex extracellular cues and to enhance developmental robustness. Since this set of properties are required for the evolution of multicellularity, our approach can also contribute to our understanding of this evolutionary transition.
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Affiliation(s)
- Miguel Brun-Usan
- Institute for Life Sciences/Electronics and Computer Sciences, University of Southampton, Southampton, (United Kingdom)
| | - Christoph Thies
- Institute for Life Sciences/Electronics and Computer Sciences, University of Southampton, Southampton, (United Kingdom)
| | - Richard A. Watson
- Institute for Life Sciences/Electronics and Computer Sciences, University of Southampton, Southampton, (United Kingdom)
- * E-mail:
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8
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Tibocha-Bonilla JD, Zuñiga C, Godoy-Silva RD, Zengler K. Advances in metabolic modeling of oleaginous microalgae. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:241. [PMID: 30202436 PMCID: PMC6124020 DOI: 10.1186/s13068-018-1244-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
Production of biofuels and bioenergy precursors by phototrophic microorganisms, such as microalgae and cyanobacteria, is a promising alternative to conventional fuels obtained from non-renewable resources. Several species of microalgae have been investigated as potential candidates for the production of biofuels, for the most part due to their exceptional metabolic capability to accumulate large quantities of lipids. Constraint-based modeling, a systems biology approach that accurately predicts the metabolic phenotype of phototrophs, has been deployed to identify suitable culture conditions as well as to explore genetic enhancement strategies for bioproduction. Core metabolic models were employed to gain insight into the central carbon metabolism in photosynthetic microorganisms. More recently, comprehensive genome-scale models, including organelle-specific information at high resolution, have been developed to gain new insight into the metabolism of phototrophic cell factories. Here, we review the current state of the art of constraint-based modeling and computational method development and discuss how advanced models led to increased prediction accuracy and thus improved lipid production in microalgae.
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Affiliation(s)
- Juan D. Tibocha-Bonilla
- Grupo de Investigación en Procesos Químicos y Bioquímicos, Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Av. Carrera 30 No. 45-03, Bogotá, D.C. Colombia
| | - Cristal Zuñiga
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760 USA
| | - Rubén D. Godoy-Silva
- Grupo de Investigación en Procesos Químicos y Bioquímicos, Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Av. Carrera 30 No. 45-03, Bogotá, D.C. Colombia
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760 USA
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412 USA
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0436 USA
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9
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Berlin R, Gruen R, Best J. Systems Medicine Disease: Disease Classification and Scalability Beyond Networks and Boundary Conditions. Front Bioeng Biotechnol 2018; 6:112. [PMID: 30131956 PMCID: PMC6090066 DOI: 10.3389/fbioe.2018.00112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/18/2018] [Indexed: 12/26/2022] Open
Abstract
In order to accommodate the forthcoming wealth of health and disease related information, from genome to body sensors to population and the environment, the approach to disease description and definition demands re-examination. Traditional classification methods remain trapped by history; to provide the descriptive features that are required for a comprehensive description of disease, systems science, which realizes dynamic processes, adaptive response, and asynchronous communication channels, must be applied (Wolkenhauer et al., 2013). When Disease is viewed beyond the thresholds of lines and threshold boundaries, disease definition is not only the result of reductionist, mechanistic categories which reluctantly face re-composition. Disease is process and synergy as the characteristics of Systems Biology and Systems Medicine are included. To capture the wealth of information and contribute meaningfully to medical practice and biology research, Disease classification goes beyond a single spatial biologic level or static time assignment to include the interface of Disease process and organism response (Bechtel, 2017a; Green et al., 2017).
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Affiliation(s)
- Richard Berlin
- Department of Computer Science, University of Illinois, Urbana, IL, United States
| | - Russell Gruen
- Department of Surgery, Nanyang Institute of Technology in Health and Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - James Best
- Lee Kong China School of Medicine, Nanyang Technological University, Singapore, Singapore
- Imperial College, London, United Kingdom
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10
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Albright MBN, Johansen R, Lopez D, Gallegos-Graves LV, Steven B, Kuske CR, Dunbar J. Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil. Appl Environ Microbiol 2018; 84:e00598-18. [PMID: 29802185 PMCID: PMC6052259 DOI: 10.1128/aem.00598-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/15/2018] [Indexed: 01/05/2023] Open
Abstract
Numerous studies have examined the long-term effect of experimental nitrogen (N) deposition in terrestrial ecosystems; however, N-specific mechanistic markers are difficult to disentangle from responses to other environmental changes. The strongest picture of N-responsive mechanistic markers is likely to arise from measurements over a short (hours to days) time scale immediately after inorganic N deposition. Therefore, we assessed the short-term (3-day) transcriptional response of microbial communities in two soil strata from a pine forest to a high dose of N fertilization (ca. 1 mg/g of soil material) in laboratory microcosms. We hypothesized that N fertilization would repress the expression of fungal and bacterial genes linked to N mining from plant litter. However, despite N suppression of microbial respiration, the most pronounced differences in functional gene expression were between strata rather than in response to the N addition. Overall, ∼4% of metabolic genes changed in expression with N addition, while three times as many (∼12%) were significantly different across the different soil strata in the microcosms. In particular, we found little evidence of N changing expression levels of metabolic genes associated with complex carbohydrate degradation (CAZymes) or inorganic N utilization. This suggests that direct N repression of microbial functional gene expression is not the principle mechanism for reduced soil respiration immediately after N deposition. Instead, changes in expression with N addition occurred primarily in general cell maintenance areas, for example, in ribosome-related transcripts. Transcriptional changes in functional gene abundance in response to N addition observed in longer-term field studies likely result from changes in microbial composition.IMPORTANCE Ecosystems are receiving increased nitrogen (N) from anthropogenic sources, including fertilizers and emissions from factories and automobiles. High levels of N change ecosystem functioning. For example, high inorganic N decreases the microbial decomposition of plant litter, potentially reducing nutrient recycling for plant growth. Understanding how N regulates microbial decomposition can improve the prediction of ecosystem functioning over extended time scales. We found little support for the conventional view that high N supply represses the expression of genes involved in decomposition or alters the expression of bacterial genes for inorganic N cycling. Instead, our study of pine forest soil 3 days after N addition showed changes in microbial gene expression related to cell maintenance and stress response. This highlights the challenge of establishing predictive links between microbial gene expression levels and measures of ecosystem function.
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Affiliation(s)
| | - Renee Johansen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Deanna Lopez
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | | | - Blaire Steven
- Department of Environmental Sciences, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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11
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Roosterman D, Meyerhof W, Cottrell GS. Proton Transport Chains in Glucose Metabolism: Mind the Proton. Front Neurosci 2018; 12:404. [PMID: 29962930 PMCID: PMC6014028 DOI: 10.3389/fnins.2018.00404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/25/2018] [Indexed: 01/11/2023] Open
Abstract
The Embden-Meyerhof-Parnas (EMP) pathway comprises eleven cytosolic enzymes interacting to metabolize glucose to lactic acid [CH3CH(OH)COOH]. Glycolysis is largely considered as the conversion of glucose to pyruvate (CH3COCOO-). We consider glycolysis to be a cellular process and as such, transporters mediating glucose uptake and lactic acid release and enable the flow of metabolites through the cell, must be considered as part of the EMP pathway. In this review, we consider the flow of metabolites to be coupled to a flow of energy that is irreversible and sufficient to form ordered structures. This latter principle is highlighted by discussing that lactate dehydrogenase (LDH) complexes irreversibly reduce pyruvate/H+ to lactate [CH3CH(OH)COO-], or irreversibly catalyze the opposite reaction, oxidation of lactate to pyruvate/H+. However, both LDH complexes are considered to be driven by postulated proton transport chains. Metabolism of glucose to two lactic acids is introduced as a unidirectional, continuously flowing pathway. In an organism, cell membrane-located proton-linked monocarboxylate transporters catalyze the final step of glycolysis, the release of lactic acid. Consequently, both pyruvate and lactate are discussed as intermediate products of glycolysis and substrates of regulated crosscuts of the glycolytic flow.
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Affiliation(s)
| | - Wolfgang Meyerhof
- Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
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12
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Oh SJ, Choi YK, Shin OS. Systems Biology-Based Platforms to Accelerate Research of Emerging Infectious Diseases. Yonsei Med J 2018; 59:176-186. [PMID: 29436184 PMCID: PMC5823818 DOI: 10.3349/ymj.2018.59.2.176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Indexed: 12/29/2022] Open
Abstract
Emerging infectious diseases (EIDs) pose a major threat to public health and security. Given the dynamic nature and significant impact of EIDs, the most effective way to prevent and protect against them is to develop vaccines in advance. Systems biology approaches provide an integrative way to understand the complex immune response to pathogens. They can lead to a greater understanding of EID pathogenesis and facilitate the evaluation of newly developed vaccine-induced immunity in a timely manner. In recent years, advances in high throughput technologies have enabled researchers to successfully apply systems biology methods to analyze immune responses to a variety of pathogens and vaccines. Despite recent advances, computational and biological challenges impede wider application of systems biology approaches. This review highlights recent advances in the fields of systems immunology and vaccinology, and presents ways that systems biology-based platforms can be applied to accelerate a deeper understanding of the molecular mechanisms of immunity against EIDs.
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Affiliation(s)
- Soo Jin Oh
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Young Ki Choi
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea
| | - Ok Sarah Shin
- Department of Biomedical Sciences, College of Medicine, Korea University Guro Hospital, Seoul, Korea.
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Dobreva A, Paus R, Cogan NG. Analysing the dynamics of a model for alopecia areata as an autoimmune disorder of hair follicle cycling. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2017; 35:387-407. [DOI: 10.1093/imammb/dqx009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 06/26/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Atanaska Dobreva
- Department of Mathematics, Florida State University, Tallahassee, FL, USA
| | - Ralf Paus
- Centre for Dermatology Research, University of Manchester, and NIHR Manchester Biomedical Research Centre, Manchester, UK
| | - N G Cogan
- Department of Mathematics, Florida State University, Tallahassee, FL, USA
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14
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Serrano-Bermúdez LM, González Barrios AF, Maranas CD, Montoya D. Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol. BMC SYSTEMS BIOLOGY 2017; 11:58. [PMID: 28571567 PMCID: PMC5455137 DOI: 10.1186/s12918-017-0434-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 05/16/2017] [Indexed: 01/15/2023]
Abstract
BACKGROUND The increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like Clostridium butyricum. However, despite the increasing role of Clostridium butyricum as a bio-production platform, its metabolism remains poorly modeled. RESULTS We reconstructed iCbu641, the first genome-scale metabolic (GSM) model of a PDO producer Clostridium strain, which included 641 genes, 365 enzymes, 891 reactions, and 701 metabolites. We found an enzyme expression prediction of nearly 84% after comparison of proteomic data with flux distribution estimation using flux balance analysis (FBA). The remaining 16% corresponded to enzymes directionally coupled to growth, according to flux coupling findings (FCF). The fermentation data validation also revealed different phenotype states that depended on culture media conditions; for example, Clostridium maximizes its biomass yield per enzyme usage under glycerol limitation. By contrast, under glycerol excess conditions, Clostridium grows sub-optimally, maximizing biomass yield while minimizing both enzyme usage and ATP production. We further evaluated perturbations in the GSM model through enzyme deletions and variations in biomass composition. The GSM predictions showed no significant increase in PDO production, suggesting a robustness to perturbations in the GSM model. We used the experimental results to predict that co-fermentation was a better alternative than iCbu641 perturbations for improving PDO yields. CONCLUSIONS The agreement between the predicted and experimental values allows the use of the GSM model constructed for the PDO-producing Clostridium strain to propose new scenarios for PDO production, such as dynamic simulations, thereby reducing the time and costs associated with experimentation.
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Affiliation(s)
- Luis Miguel Serrano-Bermúdez
- Bioprocesses and Bioprospecting Group, Universidad Nacional de Colombia. Ciudad Universitaria, Carrera 30 No. 45-03, Bogotá, D.C Colombia
| | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería Química, Universidad de los Andes, Carrera 1 N.° 18A – 12, Bogotá, Colombia
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802 USA
| | - Dolly Montoya
- Bioprocesses and Bioprospecting Group, Universidad Nacional de Colombia. Ciudad Universitaria, Carrera 30 No. 45-03, Bogotá, D.C Colombia
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15
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Jahan N, Maeda K, Matsuoka Y, Sugimoto Y, Kurata H. Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli. Microb Cell Fact 2016; 15:112. [PMID: 27329289 PMCID: PMC4915146 DOI: 10.1186/s12934-016-0511-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/08/2016] [Indexed: 01/17/2023] Open
Abstract
Background A kinetic model provides insights into the dynamic response of biological systems and predicts how their complex metabolic and gene regulatory networks generate particular functions. Of many biological systems, Escherichia coli metabolic pathways have been modeled extensively at the enzymatic and genetic levels, but existing models cannot accurately reproduce experimental behaviors in a batch culture, due to the inadequate estimation of a specific cell growth rate and a large number of unmeasured parameters. Results In this study, we developed a detailed kinetic model for the central carbon metabolism of E. coli in a batch culture, which includes the glycolytic pathway, tricarboxylic acid cycle, pentose phosphate pathway, Entner-Doudoroff pathway, anaplerotic pathway, glyoxylate shunt, oxidative phosphorylation, phosphotransferase system (Pts), non-Pts and metabolic gene regulations by four protein transcription factors: cAMP receptor, catabolite repressor/activator, pyruvate dehydrogenase complex repressor and isocitrate lyase regulator. The kinetic parameters were estimated by a constrained optimization method on a supercomputer. The model estimated a specific growth rate based on reaction kinetics and accurately reproduced the dynamics of wild-type E. coli and multiple genetic mutants in a batch culture. Conclusions This model overcame the intrinsic limitations of existing kinetic models in a batch culture, predicted the effects of multilayer regulations (allosteric effectors and gene expression) on central carbon metabolism and proposed rationally designed fast-growing cells based on understandings of molecular processes. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0511-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nusrat Jahan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Kazuhiro Maeda
- Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu, Fukuoka, 804-8550, Japan.,Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Yu Matsuoka
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Yurie Sugimoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan. .,Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan.
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16
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González-Cabaleiro R, Ofiţeru ID, Lema JM, Rodríguez J. Microbial catabolic activities are naturally selected by metabolic energy harvest rate. ISME JOURNAL 2015; 9:2630-41. [PMID: 26161636 DOI: 10.1038/ismej.2015.69] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 03/18/2015] [Accepted: 03/25/2015] [Indexed: 01/06/2023]
Abstract
The fundamental trade-off between yield and rate of energy harvest per unit of substrate has been largely discussed as a main characteristic for microbial established cooperation or competition. In this study, this point is addressed by developing a generalized model that simulates competition between existing and not experimentally reported microbial catabolic activities defined only based on well-known biochemical pathways. No specific microbial physiological adaptations are considered, growth yield is calculated coupled to catabolism energetics and a common maximum biomass-specific catabolism rate (expressed as electron transfer rate) is assumed for all microbial groups. Under this approach, successful microbial metabolisms are predicted in line with experimental observations under the hypothesis of maximum energy harvest rate. Two microbial ecosystems, typically found in wastewater treatment plants, are simulated, namely: (i) the anaerobic fermentation of glucose and (ii) the oxidation and reduction of nitrogen under aerobic autotrophic (nitrification) and anoxic heterotrophic and autotrophic (denitrification) conditions. The experimentally observed cross feeding in glucose fermentation, through multiple intermediate fermentation pathways, towards ultimately methane and carbon dioxide is predicted. Analogously, two-stage nitrification (by ammonium and nitrite oxidizers) is predicted as prevailing over nitrification in one stage. Conversely, denitrification is predicted in one stage (by denitrifiers) as well as anammox (anaerobic ammonium oxidation). The model results suggest that these observations are a direct consequence of the different energy yields per electron transferred at the different steps of the pathways. Overall, our results theoretically support the hypothesis that successful microbial catabolic activities are selected by an overall maximum energy harvest rate.
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Affiliation(s)
- Rebeca González-Cabaleiro
- Institute Centre for Water and Environment (iWATER), Department of Chemical and Environmental Engineering (CEE), Masdar Institute of Science and Technology, Abu Dhabi, UAE.,Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Irina D Ofiţeru
- Institute Centre for Water and Environment (iWATER), Department of Chemical and Environmental Engineering (CEE), Masdar Institute of Science and Technology, Abu Dhabi, UAE
| | - Juan M Lema
- Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Jorge Rodríguez
- Institute Centre for Water and Environment (iWATER), Department of Chemical and Environmental Engineering (CEE), Masdar Institute of Science and Technology, Abu Dhabi, UAE
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17
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Tanevski J, Todorovski L, Kalaidzidis Y, Džeroski S. Domain-specific model selection for structural identification of the Rab5-Rab7 dynamics in endocytosis. BMC SYSTEMS BIOLOGY 2015; 9:31. [PMID: 26112042 PMCID: PMC4482292 DOI: 10.1186/s12918-015-0175-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 06/02/2015] [Indexed: 12/22/2022]
Abstract
Background Given its recent rapid development and the central role that modeling plays in the discipline, systems biology clearly needs methods for automated modeling of dynamical systems. Process-based modeling focuses on explanatory models of dynamical systems; it constructs such models from measured time-course data and formalized modeling knowledge. In this paper, we apply process-based modeling to the practically relevant task of modeling the Rab5-Rab7 conversion switch in endocytosis. The task is difficult due to the limited observability of the system variables and the noisy measurements, which pose serious challenges to the process of model selection. To address these issues, we propose a domain-specific model selection criteria that take into account knowledge about the necessary properties of the simulated model behavior. Results In a series of modeling experiments, we compare the results of process-based modeling obtained with different model selection criteria. The first is the standard maximum likelihood criterion based solely on least-squares model error. The second one is a parsimony-based criterion that also takes into account model complexity. We also introduce three domain-specific criteria based on domain expert expectations about the simulated behavior of an endocytosis model. According to the first criterion, 90 of the candidate models are indistinguishable. Furthermore, taking into account the complexity of the model does not lead to better model selection. However, the use of domain-specific criteria results in a remarkable improvement over the other two model selection criteria. Conclusions We demonstrate the applicability of process-based modeling to the task of modeling the Rab5-Rab7 dynamics in endocytosis. Our experiments show that the domain-specific criteria outperform the standard domain-independent criteria for model selection. We also find that some of the model structures discarded as implausible in previous studies lead to the expected Rab5-Rab7 switch behavior. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0175-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jovan Tanevski
- Jožef Stefan Institute, Jamova cesta 39, Ljubljana, 1000, Slovenia. .,Jožef Stefan International Postgraduate School, Jamova cesta 39, Ljubljana, 1000, Slovenia.
| | - Ljupčo Todorovski
- University of Ljubljana, Gosarjeva ulica 5, Ljubljana, 1000, Slovenia.
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauer Straße 108, Dresden, 01308, Germany.
| | - Sašo Džeroski
- Jožef Stefan Institute, Jamova cesta 39, Ljubljana, 1000, Slovenia.
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18
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Abstract
The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these different areas of research and identify common and complementary aspects of each one. We focus on systems biology, a discipline that is greatly facilitating the classical top-down and bottom-up approaches toward minimal cells. In addition, we also review the so-called middle-out approach and its contributions to the field with mathematical and computational models. Owing to the advances in genomics technologies, much of the work in this area has been centered on minimal genomes, or rather minimal gene sets, required to sustain life. Nevertheless, a fundamental expansion has been taking place in the last few years wherein the minimal gene set is viewed as a backbone of a more complex system. Complementing genomics, progress is being made in understanding the system-wide properties at the levels of the transcriptome, proteome, and metabolome. Network modeling approaches are enabling the integration of these different omics data sets toward an understanding of the complex molecular pathways connecting genotype to phenotype. We review key concepts central to the mapping and modeling of this complexity, which is at the heart of research on minimal cells. Finally, we discuss the distinction between minimizing the number of cellular components and minimizing cellular complexity, toward an improved understanding and utilization of minimal and simpler cells.
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19
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Stanford NJ, Millard P, Swainston N. RobOKoD: microbial strain design for (over)production of target compounds. Front Cell Dev Biol 2015; 3:17. [PMID: 25853130 PMCID: PMC4371745 DOI: 10.3389/fcell.2015.00017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/25/2015] [Indexed: 11/16/2022] Open
Abstract
Sustainable production of target compounds such as biofuels and high-value chemicals for pharmaceutical, agrochemical, and chemical industries is becoming an increasing priority given their current dependency upon diminishing petrochemical resources. Designing these strains is difficult, with current methods focusing primarily on knocking-out genes, dismissing other vital steps of strain design including the overexpression and dampening of genes. The design predictions from current methods also do not translate well-into successful strains in the laboratory. Here, we introduce RobOKoD (Robust, Overexpression, Knockout and Dampening), a method for predicting strain designs for overproduction of targets. The method uses flux variability analysis to profile each reaction within the system under differing production percentages of target-compound and biomass. Using these profiles, reactions are identified as potential knockout, overexpression, or dampening targets. The identified reactions are ranked according to their suitability, providing flexibility in strain design for users. The software was tested by designing a butanol-producing Escherichia coli strain, and was compared against the popular OptKnock and RobustKnock methods. RobOKoD shows favorable design predictions, when predictions from these methods are compared to a successful butanol-producing experimentally-validated strain. Overall RobOKoD provides users with rankings of predicted beneficial genetic interventions with which to support optimized strain design.
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Affiliation(s)
- Natalie J Stanford
- Manchester Institute of Biotechnology, University of Manchester Manchester, UK ; School of Computer Science, University of Manchester Manchester, UK
| | - Pierre Millard
- Manchester Institute of Biotechnology, University of Manchester Manchester, UK ; School of Computer Science, University of Manchester Manchester, UK ; INSA, UPS, INP, LISBP, Université de Toulouse Toulouse, France ; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés Toulouse, France ; Centre National de la Recherche Scientifique, UMR5504 Toulouse, France
| | - Neil Swainston
- Manchester Institute of Biotechnology, University of Manchester Manchester, UK ; School of Computer Science, University of Manchester Manchester, UK
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20
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Kleessen S, Irgang S, Klie S, Giavalisco P, Nikoloski Z. Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:822-35. [PMID: 25600836 DOI: 10.1111/tpj.12763] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/19/2014] [Indexed: 05/19/2023]
Abstract
Flux phenotypes predicted by constraint-based methods can be refined by the inclusion of heterogeneous data. While recent advances facilitate the integration of transcriptomics and proteomics data, purely stoichiometry-based approaches for the prediction of flux phenotypes by considering metabolomics data are lacking. Here we propose a constraint-based method, termed TREM-Flux, for integrating time-resolved metabolomics and transcriptomics data. We demonstrate the applicability of TREM-Flux in the dissection of the metabolic response of Chlamydomonas reinhardtii to rapamycin treatment by integrating the expression levels of 982 genes and the content of 45 metabolites obtained from two growth conditions. The findings pinpoint cysteine and methionine metabolism to be most affected by the rapamycin treatment. Our study shows that the integration of time-resolved unlabeled metabolomics data in addition to transcriptomics data can specify the metabolic pathways involved in the system's response to a studied treatment.
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21
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Gomez-Cabrero D, Lluch-Ariet M, Tegnér J, Cascante M, Miralles F, Roca J. Synergy-COPD: a systems approach for understanding and managing chronic diseases. J Transl Med 2014; 12 Suppl 2:S2. [PMID: 25472826 PMCID: PMC4255903 DOI: 10.1186/1479-5876-12-s2-s2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chronic diseases (CD) are generating a dramatic societal burden worldwide that is expected to persist over the next decades. The challenges posed by the epidemics of CD have triggered a novel health paradigm with major consequences on the traditional concept of disease and with a profound impact on key aspects of healthcare systems. We hypothesized that the development of a systems approach to understand CD together with the generation of an ecosystem to transfer the acquired knowledge into the novel healthcare scenario may contribute to a cost-effective enhancement of health outcomes. To this end, we designed the Synergy-COPD project wherein the heterogeneity of chronic obstructive pulmonary disease (COPD) was addressed as a use case representative of CD. The current manuscript describes main features of the project design and the strategies put in place for its development, as well the expected outcomes during the project life-span. Moreover, the manuscript serves as introductory and unifying chapter of the different papers associated to the Supplement describing the characteristics, tools and the objectives of Synergy-COPD.
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Affiliation(s)
- David Gomez-Cabrero
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Magi Lluch-Ariet
- Department of eHealth, Barcelona Digital, 08017 Barcelona, Catalunya, Spain
| | - Jesper Tegnér
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Marta Cascante
- Hospital Clinic - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS). Universitat de Barcelona, 08036 Barcelona, Spain
- Departament de Bioquimica i Biologia Molecular i IBUB, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Felip Miralles
- Department of eHealth, Barcelona Digital, 08017 Barcelona, Catalunya, Spain
| | - Josep Roca
- Hospital Clinic - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS). Universitat de Barcelona, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Bunyola, Balearic Islands
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22
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Lankelma J, Kooi B, Krab K, Dorsman JC, Joenje H, Westerhoff HV. A reason for intermittent fasting to suppress the awakening of dormant breast tumors. Biosystems 2014; 127:1-6. [PMID: 25448890 DOI: 10.1016/j.biosystems.2014.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/25/2014] [Accepted: 11/01/2014] [Indexed: 12/21/2022]
Abstract
For their growth, dormant tumors, which lack angiogenesis may critically depend on gradients of nutrients and oxygen from the nearest blood vessel. Because for oxygen depletion the distance from the nearest blood vessel to depletion will generally be shorter than for glucose depletion, such tumors will contain anoxic living tumor cells. These cells are dangerous, because they are capable of inducing angiogenesis, which will "wake up" the tumor. Anoxic cells are dependent on anaerobic glucose breakdown for ATP generation. The local extracellular glucose concentration gradient is determined by the blood glucose concentration and by consumption by cells closer to the nearest blood vessel. The blood glucose concentration can be lowered by 20-40% during fasting. We calculated that glucose supply to the potentially hazardous anoxic cells can thereby be reduced significantly, resulting in cell death specifically of the anoxic tumor cells. We hypothesize that intermittent fasting will help to reduce the incidence of tumor relapse via reducing the number of anoxic tumor cells and tumor awakening.
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Affiliation(s)
- Jan Lankelma
- Department of Molecular Cell Physiology, VU University, De Boelelaan 1085, Room G-226a, 1081 HV Amsterdam, The Netherlands.
| | - Bob Kooi
- Department of Theoretical Biology, VU University, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Klaas Krab
- Department of Molecular Cell Physiology, VU University, De Boelelaan 1085, Room G-226a, 1081 HV Amsterdam, The Netherlands
| | - Josephine C Dorsman
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Hans Joenje
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Hans V Westerhoff
- Department of Molecular Cell Physiology, VU University, De Boelelaan 1085, Room G-226a, 1081 HV Amsterdam, The Netherlands; Synthetic Systems Biology, SILS, University of Amsterdam and Manchester Centre for Integrative Systems Biology, The University of Manchester, UK
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23
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Kell DB, Oliver SG. How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion. Front Pharmacol 2014; 5:231. [PMID: 25400580 PMCID: PMC4215795 DOI: 10.3389/fphar.2014.00231] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/29/2014] [Indexed: 12/12/2022] Open
Abstract
One approach to experimental science involves creating hypotheses, then testing them by varying one or more independent variables, and assessing the effects of this variation on the processes of interest. We use this strategy to compare the intellectual status and available evidence for two models or views of mechanisms of transmembrane drug transport into intact biological cells. One (BDII) asserts that lipoidal phospholipid Bilayer Diffusion Is Important, while a second (PBIN) proposes that in normal intact cells Phospholipid Bilayer diffusion Is Negligible (i.e., may be neglected quantitatively), because evolution selected against it, and with transmembrane drug transport being effected by genetically encoded proteinaceous carriers or pores, whose “natural” biological roles, and substrates are based in intermediary metabolism. Despite a recent review elsewhere, we can find no evidence able to support BDII as we can find no experiments in intact cells in which phospholipid bilayer diffusion was either varied independently or measured directly (although there are many papers where it was inferred by seeing a covariation of other dependent variables). By contrast, we find an abundance of evidence showing cases in which changes in the activities of named and genetically identified transporters led to measurable changes in the rate or extent of drug uptake. PBIN also has considerable predictive power, and accounts readily for the large differences in drug uptake between tissues, cells and species, in accounting for the metabolite-likeness of marketed drugs, in pharmacogenomics, and in providing a straightforward explanation for the late-stage appearance of toxicity and of lack of efficacy during drug discovery programmes despite macroscopically adequate pharmacokinetics. Consequently, the view that Phospholipid Bilayer diffusion Is Negligible (PBIN) provides a starting hypothesis for assessing cellular drug uptake that is much better supported by the available evidence, and is both more productive and more predictive.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry, The University of Manchester Manchester, UK ; Manchester Institute of Biotechnology, The University of Manchester Manchester, UK
| | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge Cambridge, UK ; Cambridge Systems Biology Centre, University of Cambridge Cambridge, UK
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24
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Kaldma A, Klepinin A, Chekulayev V, Mado K, Shevchuk I, Timohhina N, Tepp K, Kandashvili M, Varikmaa M, Koit A, Planken M, Heck K, Truu L, Planken A, Valvere V, Rebane E, Kaambre T. An in situ study of bioenergetic properties of human colorectal cancer: the regulation of mitochondrial respiration and distribution of flux control among the components of ATP synthasome. Int J Biochem Cell Biol 2014; 55:171-86. [PMID: 25218857 DOI: 10.1016/j.biocel.2014.09.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 08/12/2014] [Accepted: 09/02/2014] [Indexed: 11/25/2022]
Abstract
The aim of this study is to characterize the function of mitochondria and main energy fluxes in human colorectal cancer (HCC) cells. We have performed quantitative analysis of cellular respiration in post-operative tissue samples collected from 42 cancer patients. Permeabilized tumor tissue in combination with high resolution respirometry was used. Our results indicate that HCC is not a pure glycolytic tumor and the oxidative phosphorylation (OXPHOS) system may be the main provider of ATP in these tumor cells. The apparent Michaelis-Menten constant (Km) for ADP and maximal respiratory rate (Vm) values were calculated for the characterization of the affinity of mitochondria for exogenous ADP: normal colon tissue displayed low affinity (Km = 260 ± 55 μM) whereas the affinity of tumor mitochondria was significantly higher (Km = 126 ± 17 μM). But concurrently the Vm value of the tumor samples was 60-80% higher than that in control tissue. The reason for this change is related to the increased number of mitochondria. Our data suggest that in both HCC and normal intestinal cells tubulin β-II isoform probably does not play a role in the regulation of permeability of the MOM for adenine nucleotides. The mitochondrial creatine kinase energy transfer system is not functional in HCC and our experiments showed that adenylate kinase reactions could play an important role in the maintenance of energy homeostasis in colorectal carcinomas instead of creatine kinase. Immunofluorescent studies showed that hexokinase 2 (HK-2) was associated with mitochondria in HCC cells, but during carcinogenesis the total activity of HK did not change. Furthermore, only minor alterations in the expression of HK-1 and HK-2 isoforms have been observed. Metabolic Control analysis showed that the distribution of the control over electron transport chain and ATP synthasome complexes seemed to be similar in both tumor and control tissues. High flux control coefficients point to the possibility that the mitochondrial respiratory chain is reorganized in some way or assembled into large supercomplexes in both tissues.
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Affiliation(s)
- Andrus Kaldma
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Aleksandr Klepinin
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Vladimir Chekulayev
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Kati Mado
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Igor Shevchuk
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Natalja Timohhina
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Kersti Tepp
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | | | - Minna Varikmaa
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Andre Koit
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | | | | | - Laura Truu
- Tallinn University of Technology, Tallinn, Estonia
| | - Anu Planken
- Cancer Research Competence Center, Tallinn, Estonia
| | | | - Egle Rebane
- Cancer Research Competence Center, Tallinn, Estonia
| | - Tuuli Kaambre
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia; Tallinn University, Tallinn, Estonia.
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25
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Kurata H, Maeda K, Matsuoka Y. Dynamic Modeling of Metabolic and Gene Regulatory Systems toward Developing Virtual Microbes. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2014. [DOI: 10.1252/jcej.13we152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
- Biomedical Informatics R&D Center, Kyushu Institute of Technology
| | - Kazuhiro Maeda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
| | - Yu Matsuoka
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
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MacLeod M, Nersessian NJ. Coupling simulation and experiment: The bimodal strategy in integrative systems biology. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:572-84. [PMID: 23932563 DOI: 10.1016/j.shpsc.2013.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 07/01/2013] [Accepted: 07/02/2013] [Indexed: 05/15/2023]
Abstract
The importation of computational methods into biology is generating novel methodological strategies for managing complexity which philosophers are only just starting to explore and elaborate. This paper aims to enrich our understanding of methodology in integrative systems biology, which is developing novel epistemic and cognitive strategies for managing complex problem-solving tasks. We illustrate this through developing a case study of a bimodal researcher from our ethnographic investigation of two systems biology research labs. The researcher constructed models of metabolic and cell-signaling pathways by conducting her own wet-lab experimentation while building simulation models. We show how this coupling of experiment and simulation enabled her to build and validate her models and also triangulate and localize errors and uncertainties in them. This method can be contrasted with the unimodal modeling strategy in systems biology which relies more on mathematical or algorithmic methods to reduce complexity. We discuss the relative affordances and limitations of these strategies, which represent distinct opinions in the field about how to handle the investigation of complex biological systems.
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Affiliation(s)
- Miles MacLeod
- School of Interactive Computing, Georgia Institute of Technology, Suite 221B, 85 West 5th Street, Atlanta, GA 30308, USA.
| | - Nancy J Nersessian
- School of Interactive Computing, Georgia Institute of Technology, Suite 221B, 85 West 5th Street, Atlanta, GA 30308, USA.
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van Heeswijk WC, Westerhoff HV, Boogerd FC. Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiol Mol Biol Rev 2013; 77:628-95. [PMID: 24296575 PMCID: PMC3973380 DOI: 10.1128/mmbr.00025-13] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now.
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Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JEG, Paton NW, Westerhoff HV, Kell DB, Mendes P. A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Lett 2013; 587:2832-41. [PMID: 23831062 PMCID: PMC3764422 DOI: 10.1016/j.febslet.2013.06.043] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/24/2013] [Accepted: 06/25/2013] [Indexed: 11/17/2022]
Abstract
We present an experimental and computational pipeline for the generation of kinetic models of metabolism, and demonstrate its application to glycolysis in Saccharomyces cerevisiae. Starting from an approximate mathematical model, we employ a “cycle of knowledge” strategy, identifying the steps with most control over flux. Kinetic parameters of the individual isoenzymes within these steps are measured experimentally under a standardised set of conditions. Experimental strategies are applied to establish a set of in vivo concentrations for isoenzymes and metabolites. The data are integrated into a mathematical model that is used to predict a new set of metabolite concentrations and reevaluate the control properties of the system. This bottom-up modelling study reveals that control over the metabolic network most directly involved in yeast glycolysis is more widely distributed than previously thought.
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Affiliation(s)
- Kieran Smallbone
- Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK
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Towards systems biology of mycotoxin regulation. Toxins (Basel) 2013; 5:675-82. [PMID: 23598563 PMCID: PMC3705286 DOI: 10.3390/toxins5040675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 03/22/2013] [Accepted: 04/10/2013] [Indexed: 11/16/2022] Open
Abstract
Systems biology is a scientific approach that integrates many scientific disciplines to develop a comprehensive understanding of biological phenomena, thus allowing the prediction and accurate simulation of complex biological behaviors. It may be presumptuous to write about toxin regulation at the level of systems biology, but the last decade of research is leading us closer than ever to this approach. Past research has delineated multiple levels of regulation in the pathways leading to the biosynthesis of secondary metabolites, including mycotoxins. At the top of this hierarchy, the global or master transcriptional regulators perceive various environmental cues such as climatic conditions, the availability of nutrients, and the developmental stages of the organism. Information accumulated from various inputs is integrated through a complex web of signalling networks to generate the eventual outcome. This review will focus on adapting techniques such as chemical and other genetic tools available in the model system Saccharomyces cerevisiae, to disentangle the various biological networks involved in the biosynthesis of mycotoxins in the Fusarium spp.
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Kolodkin A, Simeonidis E, Westerhoff HV. Computing life: Add logos to biology and bios to physics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 111:69-74. [DOI: 10.1016/j.pbiomolbio.2012.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 10/16/2012] [Accepted: 10/16/2012] [Indexed: 11/28/2022]
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Medina MÁ. Systems biology for molecular life sciences and its impact in biomedicine. Cell Mol Life Sci 2013; 70:1035-53. [PMID: 22903296 PMCID: PMC11113420 DOI: 10.1007/s00018-012-1109-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/24/2012] [Accepted: 07/25/2012] [Indexed: 01/02/2023]
Abstract
Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.
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Affiliation(s)
- Miguel Ángel Medina
- Department of Molecular Biology and Biochemistry, University of Málaga, Malaga, Spain.
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Matsuoka Y, Shimizu K. Importance of understanding the main metabolic regulation in response to the specific pathway mutation for metabolic engineering of Escherichia coli. Comput Struct Biotechnol J 2013; 3:e201210018. [PMID: 24688678 PMCID: PMC3962149 DOI: 10.5936/csbj.201210018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 12/27/2012] [Accepted: 01/02/2013] [Indexed: 01/05/2023] Open
Abstract
Recent metabolic engineering practice was briefly reviewed in particular for the useful metabolite production such as natural products and biofuel productions. With the emphasis on systems biology approach, the metabolic regulation of the main metabolic pathways in E. coli was discussed from the points of view of enzyme level (allosteric and phosphorylation/ dephosphorylation) regulation, and gene level (transcriptional) regulation. Then the effects of the specific pathway gene knockout such as pts, pgi, zwf, gnd, pyk, ppc, pckA, lpdA, pfl gene knockout on the metabolism in E. coli were overviewed from the systems biology point of view with possible application for strain improvement point.
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Affiliation(s)
- Yu Matsuoka
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Kazuyuki Shimizu
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan ; Institute of Advanced Bioscience, Keio University, Tsuruoka, Yamagata 997-0017, Japan
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Cruz LAB, Hebly M, Duong GH, Wahl SA, Pronk JT, Heijnen JJ, Daran-Lapujade P, van Gulik WM. Similar temperature dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics? BMC SYSTEMS BIOLOGY 2012; 6:151. [PMID: 23216813 PMCID: PMC3554419 DOI: 10.1186/1752-0509-6-151] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 11/06/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND Temperature strongly affects microbial growth, and many microorganisms have to deal with temperature fluctuations in their natural environment. To understand regulation strategies that underlie microbial temperature responses and adaptation, we studied glycolytic pathway kinetics in Saccharomyces cerevisiae during temperature changes. RESULTS Saccharomyces cerevisiae was grown under different temperature regimes and glucose availability conditions. These included glucose-excess batch cultures at different temperatures and glucose-limited chemostat cultures, subjected to fast linear temperature shifts and circadian sinoidal temperature cycles. An observed temperature-independent relation between intracellular levels of glycolytic metabolites and residual glucose concentration for all experimental conditions revealed that it is the substrate availability rather than temperature that determines intracellular metabolite profiles. This observation corresponded with predictions generated in silico with a kinetic model of yeast glycolysis, when the catalytic capacities of all glycolytic enzymes were set to share the same normalized temperature dependency. CONCLUSIONS From an evolutionary perspective, such similar temperature dependencies allow cells to adapt more rapidly to temperature changes, because they result in minimal perturbations of intracellular metabolite levels, thus circumventing the need for extensive modification of enzyme levels.
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Affiliation(s)
- Luisa Ana B Cruz
- Department of Biotechnology, Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, Delft, The Netherlands
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García-Contreras R, Vos P, Westerhoff HV, Boogerd FC. Why in vivo may not equal in vitro - new effectors revealed by measurement of enzymatic activities under the same in vivo-like assay conditions. FEBS J 2012; 279:4145-59. [PMID: 22978366 DOI: 10.1111/febs.12007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/09/2012] [Accepted: 09/10/2012] [Indexed: 01/10/2023]
Abstract
Does the understanding of the dynamics of biochemical networks in vivo, in terms of the properties of their components determined in vitro, require the latter to be determined all under the same conditions? An in vivo-like assay medium for enzyme activity determination was designed based on the concentrations of the major ionic constituents of the Escherichia coli cytosol: K(+), Na(+), Mg(2+), phosphate, glutamate, sulfate and Cl(-). The maximum capacities (V(max)) of the extracted enzymes of two pathways were determined using both this in vivo-like assay medium and the assay medium specific for each enzyme. The enzyme activities differed between the two assay conditions. Most of the differences could be attributed to unsuspected, pleiotropic effects of K(+) and phosphate. K(+) activated some enzymes (aldolase, enolase and glutamate dehydrogenase) and inhibited others (phosphoglucose isomerase, phosphofructokinase, triosephosphate isomerase, glyceraldehyde 3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase), whereas phosphate inhibited all glycolytic enzymes and glutamine synthetase but only activated glutamine 2-oxoglutarate amidotransferase. Neither a high glutamate concentration, nor macromolecular crowding affected the glycolytic or nitrogen assimilation enzymes, other than through the product inhibition of glutamate dehydrogenase by glutamate. This strategy of assessing all pathway enzymes kinetically under the same conditions may be necessary to avoid inadvertent differences between in vivo and in vitro biochemistry. It may also serve to reveal otherwise unnoticed pleiotropic regulation, such as that demonstrated in the present study by K(+) and phosphate.
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Affiliation(s)
- Rodolfo García-Contreras
- Section of Molecular Cell Physiology, Netherlands Institute for Systems Biology, VU University Amsterdam, The Netherlands
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35
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Verma M, Zakhartsev M, Reuss M, Westerhoff HV. 'Domino' systems biology and the 'A' of ATP. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:19-29. [PMID: 23031542 DOI: 10.1016/j.bbabio.2012.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/17/2012] [Accepted: 09/23/2012] [Indexed: 11/30/2022]
Abstract
We develop a strategic 'domino' approach that starts with one key feature of cell function and the main process providing for it, and then adds additional processes and components only as necessary to explain provoked experimental observations. The approach is here applied to the energy metabolism of yeast in a glucose limited chemostat, subjected to a sudden increase in glucose. The puzzles addressed include (i) the lack of increase in adenosine triphosphate (ATP) upon glucose addition, (ii) the lack of increase in adenosine diphosphate (ADP) when ATP is hydrolyzed, and (iii) the rapid disappearance of the 'A' (adenine) moiety of ATP. Neither the incorporation of nucleotides into new biomass, nor steady de novo synthesis of adenosine monophosphate (AMP) explains. Cycling of the 'A' moiety accelerates when the cell's energy state is endangered, another essential domino among the seven required for understanding of the experimental observations. This new domino analysis shows how strategic experimental design and observations in tandem with theory and modeling may identify and resolve important paradoxes. It also highlights the hitherto unexpected role of the 'A' component of ATP.
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Affiliation(s)
- Malkhey Verma
- Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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36
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Rehman S, Day PJR, Bayat A, Westerhoff HV. Understanding Dupuytren's Disease Using Systems Biology: A Move Away from Reductionism. Front Physiol 2012; 3:316. [PMID: 22934066 PMCID: PMC3429086 DOI: 10.3389/fphys.2012.00316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/18/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Samrina Rehman
- Manchester Centre for Integrative Systems Biology, University of Manchester Manchester, UK
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37
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Kaambre T, Chekulayev V, Shevchuk I, Karu-Varikmaa M, Timohhina N, Tepp K, Bogovskaja J, Kütner R, Valvere V, Saks V. Metabolic control analysis of cellular respiration in situ in intraoperational samples of human breast cancer. J Bioenerg Biomembr 2012; 44:539-58. [PMID: 22836527 DOI: 10.1007/s10863-012-9457-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 06/21/2012] [Indexed: 12/19/2022]
Abstract
The aim of this study was to analyze quantitatively cellular respiration in intraoperational tissue samples taken from human breast cancer (BC) patients. We used oxygraphy and the permeabilized cell techniques in combination with Metabolic Control Analysis (MCA) to measure a corresponding flux control coefficient (FCC). The activity of all components of ATP synthasome, and respiratory chain complexes was found to be significantly increased in human BC cells in situ as compared to the adjacent control tissue. FCC(s) were determined upon direct activation of respiration with exogenously-added ADP and by titrating the complexes with their specific inhibitors to stepwise decrease their activity. MCA showed very high sensitivity of all complexes and carriers studied in human BC cells to inhibition as compared to mitochondria in normal oxidative tissues. The sum of FCC(s) for all ATP synthasome and respiratory chain components was found to be around 4, and the value exceeded significantly that for normal tissue (close to 1). In BC cells, the key sites of the regulation of respiration are Complex IV (FCC = 0.74), ATP synthase (FCC = 0.61), and phosphate carrier (FCC = 0.60); these FCC(s) exceed considerably (~10-fold) those for normal oxidative tissues. In human BC cells, the outer mitochondrial membrane is characterized by an increased permeability towards adenine nucleotides, the mean value of the apparent K(m) for ADP being equal to 114.8 ± 13.6 μM. Our data support the two-compartment hypothesis of tumor metabolism, the high sum of FCC(s) showing structural and functional organization of mitochondrial respiratory chain and ATP synthasome as supercomplexes in human BC.
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Affiliation(s)
- Tuuli Kaambre
- Laboratory of Bioenergetics, National Institute of Chemical Physics and Biophysics, Estonia.
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Kolodkin A, Simeonidis E, Balling R, Westerhoff HV. Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence. Front Physiol 2012; 3:291. [PMID: 22934043 PMCID: PMC3429063 DOI: 10.3389/fphys.2012.00291] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 07/04/2012] [Indexed: 02/03/2023] Open
Abstract
Healthy functioning is an emergent property of the network of interacting biomolecules that comprise an organism. It follows that disease (a network shift that causes malfunction) is also an emergent property, emerging from a perturbation of the network. On the one hand, the biomolecular network of every individual is unique and this is evident when similar disease-producing agents cause different individual pathologies. Consequently, a personalized model and approach for every patient may be required for therapies to become effective across mankind. On the other hand, diverse combinations of internal and external perturbation factors may cause a similar shift in network functioning. We offer this as an explanation for the multi-factorial nature of most diseases: they are "systems biology diseases," or "network diseases." Here we use neurodegenerative diseases, like Parkinson's disease (PD), as an example to show that due to the inherent complexity of these networks, it is difficult to understand multi-factorial diseases with simply our "naked brain." When describing interactions between biomolecules through mathematical equations and integrating those equations into a mathematical model, we try to reconstruct the emergent properties of the system in silico. The reconstruction of emergence from interactions between huge numbers of macromolecules is one of the aims of systems biology. Systems biology approaches enable us to break through the limitation of the human brain to perceive the extraordinarily large number of interactions, but this also means that we delegate the understanding of reality to the computer. We no longer recognize all those essences in the system's design crucial for important physiological behavior (the so-called "design principles" of the system). In this paper we review evidence that by using more abstract approaches and by experimenting in silico, one may still be able to discover and understand the design principles that govern behavioral emergence.
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Affiliation(s)
- Alexey Kolodkin
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
- Institute for Systems Biology, SeattleWA, USA
| | - Evangelos Simeonidis
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
- Institute for Systems Biology, SeattleWA, USA
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Hans V. Westerhoff
- Department of Molecular Cell Physiology, VU UniversityAmsterdam, Netherlands
- Manchester Centre for Integrative Systems Biology, FALW, NISB, The University of ManchesterUK
- Synthetic Systems Biology, SILS, NISB, University of AmsterdamNetherlands
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Adamczyk M, Westerhoff HV. Engineering of self-sustaining systems: substituting the yeast glucose transporter plus hexokinase for the Lactococcus lactis phosphotransferase system in a Lactococcus lactis network in silico. Biotechnol J 2012; 7:877-83. [PMID: 22700394 DOI: 10.1002/biot.201100314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 05/10/2012] [Accepted: 05/22/2012] [Indexed: 11/09/2022]
Abstract
The success rate of introducing new functions into a living species is still rather unsatisfactory. Much of this is due to the very essence of the living state, i.e. its robustness towards perturbations. Living cells are bound to notice that metabolic engineering is being effected, through changes in metabolite concentrations. In this study, we asked whether one could engage in such engineering without changing metabolite concentrations. We have illustrated that, in silico, one can do so in principle. We have done this for the case of substituting the yeast glucose transporter plus hexokinase for the Lactococcus lactis phosphotransferase system, in an L. lactis network, this engineering is 'silent' in terms of metabolite concentrations and almost all fluxes.
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Affiliation(s)
- Malgorzata Adamczyk
- Manchester Centre for Integrative Systems Biology, University of Manchester, MIB, Manchester, UK
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40
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Oldham P, Hall S, Burton G. Synthetic biology: mapping the scientific landscape. PLoS One 2012; 7:e34368. [PMID: 22539946 PMCID: PMC3335118 DOI: 10.1371/journal.pone.0034368] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Accepted: 02/27/2012] [Indexed: 12/18/2022] Open
Abstract
This article uses data from Thomson Reuters Web of Science to map and analyse the scientific landscape for synthetic biology. The article draws on recent advances in data visualisation and analytics with the aim of informing upcoming international policy debates on the governance of synthetic biology by the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) of the United Nations Convention on Biological Diversity. We use mapping techniques to identify how synthetic biology can best be understood and the range of institutions, researchers and funding agencies involved. Debates under the Convention are likely to focus on a possible moratorium on the field release of synthetic organisms, cells or genomes. Based on the empirical evidence we propose that guidance could be provided to funding agencies to respect the letter and spirit of the Convention on Biological Diversity in making research investments. Building on the recommendations of the United States Presidential Commission for the Study of Bioethical Issues we demonstrate that it is possible to promote independent and transparent monitoring of developments in synthetic biology using modern information tools. In particular, public and policy understanding and engagement with synthetic biology can be enhanced through the use of online interactive tools. As a step forward in this process we make existing data on the scientific literature on synthetic biology available in an online interactive workbook so that researchers, policy makers and civil society can explore the data and draw conclusions for themselves.
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Affiliation(s)
- Paul Oldham
- ESRC Centre for Economic and Social Aspects of Genomics, Lancaster University, Lancaster, United Kingdom.
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41
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Synthetic Biology of secondary metabolite biosynthesis in actinomycetes: Engineering precursor supply as a way to optimize antibiotic production. FEBS Lett 2012; 586:2171-6. [DOI: 10.1016/j.febslet.2012.04.025] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/13/2012] [Accepted: 04/13/2012] [Indexed: 01/12/2023]
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42
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Rodríguez-Enríquez S, Pacheco-Velázquez SC, Gallardo-Pérez JC, Marín-Hernández A, Aguilar-Ponce JL, Ruiz-García E, Ruizgodoy-Rivera LM, Meneses-García A, Moreno-Sánchez R. Multi-biomarker pattern for tumor identification and prognosis. J Cell Biochem 2012; 112:2703-15. [PMID: 21678471 DOI: 10.1002/jcb.23224] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In last decades, the basic, clinical, and translational research efforts have been directed to the identification of standard biomarkers associated with the degree of malignancy. There is an increasingly public health concern for earlier detection of cancer development at stages in which successful treatments can be achieved. To meet this urgent clinical demand, early stage cancer biomarkers supported by reliable and robust experimental data that can be readily applicable in the clinical practice, are required. In the current standard protocols, when one or two of the canonical proliferating index biomarkers are analyzed, contradictory results are frequently reached leading to incorrect cancer diagnostic and unsuccessful therapies. Therefore, the identification of other cellular characteristics or signatures present in the tumor cells either alone or in combination with the well-established proliferation markers emerge as an alternative strategy in the improvement of cancer diagnosis and treatment. Because it is well known that several pathways and processes are altered in tumor cells, the concept of "single marker" in cancer results incorrect. Therefore, this review aims to analyze and discuss the proposal that the molecular profile of different genes or proteins in different altered tumor pathways must be established to provide a better global clinical pattern for cancer detection and prognosis.
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Hendriks MM, Eeuwijk FA, Jellema RH, Westerhuis JA, Reijmers TH, Hoefsloot HC, Smilde AK. Data-processing strategies for metabolomics studies. Trends Analyt Chem 2011. [DOI: 10.1016/j.trac.2011.04.019] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Fundamental properties of Ca2+ signals. Biochim Biophys Acta Gen Subj 2011; 1820:1185-94. [PMID: 22040723 DOI: 10.1016/j.bbagen.2011.10.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 10/16/2011] [Accepted: 10/17/2011] [Indexed: 11/21/2022]
Abstract
BACKGROUND Ca2+ is a ubiquitous and versatile second messenger that transmits information through changes of the cytosolic Ca2+ concentration. Recent investigations changed basic ideas on the dynamic character of Ca2+ signals and challenge traditional ideas on information transmission. SCOPE OF REVIEW We present recent findings on key characteristics of the cytosolic Ca2+ dynamics and theoretical concepts that explain the wide range of experimentally observed Ca2+ signals. Further, we relate properties of the dynamical regulation of the cytosolic Ca2+ concentration to ideas about information transmission by stochastic signals. MAJOR CONCLUSIONS We demonstrate the importance of the hierarchal arrangement of Ca2+ release sites on the emergence of cellular Ca2+ spikes. Stochastic Ca2+ signals are functionally robust and adaptive to changing environmental conditions. Fluctuations of interspike intervals (ISIs) and the moment relation derived from ISI distributions contain information on the channel cluster open probability and on pathway properties. GENERAL SIGNIFICANCE Robust and reliable signal transduction pathways that entail Ca2+ dynamics are essential for eukaryotic organisms. Moreover, we expect that the design of a stochastic mechanism which provides robustness and adaptivity will be found also in other biological systems. Ca2+ dynamics demonstrate that the fluctuations of cellular signals contain information on molecular behavior. This article is part of a Special Issue entitled Biochemical, biophysical and genetic approaches to intracellular calcium signaling.
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Winder CL, Dunn WB, Goodacre R. TARDIS-based microbial metabolomics: time and relative differences in systems. Trends Microbiol 2011; 19:315-22. [DOI: 10.1016/j.tim.2011.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 05/09/2011] [Indexed: 01/30/2023]
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Emergence of the silicon human and network targeting drugs. Eur J Pharm Sci 2011; 46:190-7. [PMID: 21704158 DOI: 10.1016/j.ejps.2011.06.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 06/07/2011] [Indexed: 01/09/2023]
Abstract
The development of disease may be characterized as a pathological shift of homeostasis; the main goal of contemporary drug treatment is, therefore, to return the pathological homeostasis back to the normal physiological range. From the view point of systems biology, homeostasis emerges from the interactions within the network of biomolecules (e.g. DNA, mRNA, proteins), and, hence, understanding how drugs impact upon the entire network should improve their efficacy at returning the network (body) to physiological homeostasis. Large, mechanism-based computer models, such as the anticipated human whole body models (silicon or virtual human), may help in the development of such network-targeting drugs. Using the philosophical concept of weak and strong emergence, we shall here take a more general look at the paradigm of network-targeting drugs, and propose our approaches to scale the strength of strong emergence. We apply these approaches to several biological examples and demonstrate their utility to reveal principles of bio-modeling. We discuss this in the perspective of building the silicon human.
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Miquel PA. Extended physics as a theoretical framework for systems biology? PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 106:348-52. [PMID: 21463648 DOI: 10.1016/j.pbiomolbio.2011.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this essay we examine whether a theoretical and conceptual framework for systems biology could be built from the Bailly and Longo (2008, 2009) proposal. These authors aim to understand life as a coherent critical structure, and propose to develop an extended physical approach of evolution, as a diffusion of biomass in a space of complexity. Their attempt leads to a simple mathematical reconstruction of Gould's assumption (1989) concerning the bacterial world as a "left wall of least complexity" that we will examine. Extended physical systems are characterized by their constructive properties. Time is acting and new properties emerge by their history that can open the list of their initial properties. This conceptual and theoretical framework is nothing more than a philosophical assumption, but as such it provides a new and exciting approach concerning the evolution of life, and the transition between physics and biology.
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Abstract
Systems biology is all about networks. A recent trend has been to associate systems biology exclusively with the study of gene regulatory or protein-interaction networks. However, systems biology approaches can be applied at many other scales, from the subatomic to the ecosystem scales. In this review, we describe studies at the sub-cellular, tissue, whole plant and crop scales and highlight how these studies can be related to systems biology. We discuss the properties of system approaches at each scale as well as their current limits, and pinpoint in each case advances unique to the considered scale but representing potential for the other scales. We conclude by examining plant models bridging different scales and considering the future prospects of plant systems biology.
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Affiliation(s)
- Mikaël Lucas
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, UK.
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Pritchard L, Birch P. A systems biology perspective on plant-microbe interactions: biochemical and structural targets of pathogen effectors. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 180:584-603. [PMID: 21421407 DOI: 10.1016/j.plantsci.2010.12.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 12/13/2010] [Accepted: 12/15/2010] [Indexed: 05/22/2023]
Abstract
Plants have biochemical defences against stresses from predators, parasites and pathogens. In this review we discuss the interaction of plant defences with microbial pathogens such as bacteria, fungi and oomycetes, and viruses. We examine principles of complex dynamic networks that allow identification of network components that are differentially and predictably sensitive to perturbation, thus making them likely effector targets. We relate these principles to recent developments in our understanding of known effector targets in plant-pathogen systems, and propose a systems-level framework for the interpretation and modelling of host-microbe interactions mediated by effectors. We describe this framework briefly, and conclude by discussing useful experimental approaches for populating this framework.
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Affiliation(s)
- Leighton Pritchard
- Plant Pathology Programme, SCRI, Errol Road, Invergowrie, Dundee, Scotland DD25DA, UK.
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Abstract
Advances in biological techniques have led to the availability of genome-scale metabolic reconstructions for yeast. The size and complexity of such networks impose limits on what types of analyses one can perform. Constraint-based modelling overcomes some of these restrictions by using physicochemical constraints to describe the potential behaviour of an organism. FBA (flux balance analysis) highlights flux patterns through a network that serves to achieve a particular objective and requires a minimal amount of data to make quantitative inferences about network behaviour. Even though FBA is a powerful tool for system predictions, its general formulation sometimes results in unrealistic flux patterns. A typical example is fermentation in yeast: ethanol is produced during aerobic growth in excess glucose, but this pattern is not present in a typical FBA solution. In the present paper, we examine the issue of yeast fermentation against respiration during growth. We have studied a number of hypotheses from the modelling perspective, and novel formulations of the FBA approach have been tested. By making the observation that more respiration requires the synthesis of more mitochondria, an energy cost related to mitochondrial synthesis is added to the FBA formulation. Results, although still approximate, are closer to experimental observations than earlier FBA analyses, at least on the issue of fermentation.
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