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Lenart P, Bienertová-Vašků J, Berec L. Learning mitigates genetic drift. Sci Rep 2022; 12:20403. [PMID: 36437294 PMCID: PMC9701794 DOI: 10.1038/s41598-022-24748-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Genetic drift is a basic evolutionary principle describing random changes in allelic frequencies, with far-reaching consequences in various topics ranging from species conservation efforts to speciation. The conventional approach assumes that genetic drift has the same effect on all populations undergoing the same changes in size, regardless of different non-reproductive behaviors and history of the populations. However, here we reason that processes leading to a systematic increase of individuals` chances of survival, such as learning or immunological memory, can mitigate loss of genetic diversity caused by genetic drift even if the overall mortality rate in the population does not change. We further test this notion in an agent-based model with overlapping generations, monitoring allele numbers in a population of prey, either able or not able to learn from successfully escaping predators' attacks. Importantly, both these populations start with the same effective size and have the same and constant overall mortality rates. Our results demonstrate that even under these conditions, learning can mitigate loss of genetic diversity caused by drift, by creating a pool of harder-to-die individuals that protect alleles they carry from extinction. Furthermore, this effect holds regardless if the population is haploid or diploid or whether it reproduces sexually or asexually. These findings may be of importance not only for basic evolutionary theory but also for other fields using the concept of genetic drift.
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Affiliation(s)
- Peter Lenart
- grid.10267.320000 0001 2194 0956Faculty of Science, Research Centre for Toxic Compounds in the Environment, Masaryk University, Kamenice 5, Building A29, 62500 Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic ,grid.5734.50000 0001 0726 5157Faculty of Science, Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Julie Bienertová-Vašků
- grid.10267.320000 0001 2194 0956Faculty of Science, Research Centre for Toxic Compounds in the Environment, Masaryk University, Kamenice 5, Building A29, 62500 Brno, Czech Republic
| | - Luděk Berec
- grid.14509.390000 0001 2166 4904Department of Mathematics, Faculty of Science, Centre for Mathematical Biology, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic ,grid.418095.10000 0001 1015 3316Department of Ecology, Biology Centre, Institute of Entomology, The Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
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Price EJ, Vitale CM, Miller GW, David A, Barouki R, Audouze K, Walker DI, Antignac JP, Coumoul X, Bessonneau V, Klánová J. Merging the exposome into an integrated framework for “omics” sciences. iScience 2022; 25:103976. [PMID: 35310334 PMCID: PMC8924626 DOI: 10.1016/j.isci.2022.103976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The exposome concept encourages holistic consideration of the non-genetic factors (environmental exposures including lifestyle) that influence an individual’s health over their life course. However, disconnect between the concept and practical application has promoted divergent interpretations of the exposome across disciplines and reinforced separation of the environmental (emphasizing exposures) and biological (emphasizing responses) research communities. In particular, while knowledge of biological responses can help to distinguish actual (i.e. experienced) from potential exposures, the inclusion of endogenous processes has generated confusion about the position of the exposome in a multi-omics systems biology context. We propose a reattribution of “exposome” to exclusively represent the totality of contact with external factors that a biological entity experiences, and introduce the term “functional exposomics” to denote the systematic study of exposure-phenotype interaction. This reoriented definition of the exposome allows a more readily integrable dataset for multi-omics and systems biology research. Reattribution of exposome concept to exclusively represent environmental exposures Generalized the exposome concept for all levels of biological organization Functional exposome presented as the totality of exposure-phenotype interaction
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Pan Y, Lei X, Zhang Y. Association predictions of genomics, proteinomics, transcriptomics, microbiome, metabolomics, pathomics, radiomics, drug, symptoms, environment factor, and disease networks: A comprehensive approach. Med Res Rev 2021; 42:441-461. [PMID: 34346083 DOI: 10.1002/med.21847] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 05/22/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022]
Abstract
Currently, the research of multi-omics, such as genomics, proteinomics, transcriptomics, microbiome, metabolomics, pathomics, and radiomics, are hot spots. The relationship between multi-omics data, drugs, and diseases has received extensive attention from researchers. At the same time, multi-omics can effectively predict the diagnosis, prognosis, and treatment of diseases. In essence, these research entities, such as genes, RNAs, proteins, microbes, metabolites, pathways as well as pathological and medical imaging data, can all be represented by the network at different levels. And some computer and biology scholars have tried to use computational methods to explore the potential relationships between biological entities. We summary a comprehensive research strategy, that is to build a multi-omics heterogeneous network, covering multimodal data, and use the current popular computational methods to make predictions. In this study, we first introduce the calculation method of the similarity of biological entities at the data level, second discuss multimodal data fusion and methods of feature extraction. Finally, the challenges and opportunities at this stage are summarized. Some scholars have used such a framework to calculate and predict. We also summarize them and discuss the challenges. We hope that our review could help scholars who are interested in the field of bioinformatics, biomedical image, and computer research.
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Affiliation(s)
- Yi Pan
- Faculty of Computer Science and Control Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Yuchen Zhang
- School of Computer Science, Shaanxi Normal University, Xi'an, China
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Sholl J. Can aging research generate a theory of health? HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2021; 43:45. [PMID: 33768353 DOI: 10.1007/s40656-021-00402-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 03/12/2021] [Indexed: 05/21/2023]
Abstract
While aging research and policy aim to promote 'health' at all ages, there remains no convincing explanation of what this 'health' is. In this paper, I investigate whether we can find, implicit within the sciences of aging, a way to know what health is and how to measure it, i.e. a theory of health. To answer this, I start from scientific descriptions of aging and its modulators and then try to develop some generalizations about 'health' implicit within this research. After discussing some of the core aspects of aging and the ways in which certain models describe spatial and temporal features specific to both aging and healthy phenotypes, I then extract, explicate, and evaluate one potential construct of health in these models. This suggests a theory of health based on the landscape of optimized phenotypic trajectories. I conclude by considering why it matters for more candidate theories to be proposed and evaluated by philosophers and scientists alike.
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Affiliation(s)
- Jonathan Sholl
- University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 33000, Bordeaux, France.
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Bienertova-Vasku J, Lenart P, Scheringer M. Eustress and Distress: Neither Good Nor Bad, but Rather the Same? Bioessays 2020; 42:e1900238. [PMID: 32302008 DOI: 10.1002/bies.201900238] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/18/2020] [Indexed: 11/07/2022]
Abstract
The terms "eustress" and "distress" are widely used throughout the scientific literature. As of February 2020, 203 items in the Web of Science show up in a search for "eustress," however, there are almost 16 400 items found in a search for the term "distress." Based on the reasoning in this article, however, it is believed there is no such thing as eustress or distress. The adaptation reaction of an organism under stress is not intrinsically good or bad, and its effect on health or performance depends on a plethora of other interactions of the body with the environment as well as on the history of such interactions. The vagueness of the terms "eustress/distress" has historically led to vast differences in the perception and application of the terms across disciplines. While psychology or sociology perceive eustress as something inextricably linked to positive perception and enhanced cognition, biomedicine perceives eustress as generally associated with better survival, health, or increased longevity, no matter how the event is perceived. In this paper, the authors review the current understanding of the term "eustress" in different fields, discuss possible implications of its misleading use, and suggest that the term may be replaced by "stress" only.
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Affiliation(s)
- Julie Bienertova-Vasku
- Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, building A29, 625 00, Brno, Czech Republic
| | - Peter Lenart
- Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, building A29, 625 00, Brno, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Martin Scheringer
- Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, building A29, 625 00, Brno, Czech Republic.,Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Universitätstrasse 16, 8092, Zürich, Switzerland
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