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Seo Y, Bang S, Son J, Kim D, Jeong Y, Kim P, Yang J, Eom JH, Choi N, Kim HN. Brain physiome: A concept bridging in vitro 3D brain models and in silico models for predicting drug toxicity in the brain. Bioact Mater 2022; 13:135-148. [PMID: 35224297 PMCID: PMC8843968 DOI: 10.1016/j.bioactmat.2021.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 12/12/2022] Open
Abstract
In the last few decades, adverse reactions to pharmaceuticals have been evaluated using 2D in vitro models and animal models. However, with increasing computational power, and as the key drivers of cellular behavior have been identified, in silico models have emerged. These models are time-efficient and cost-effective, but the prediction of adverse reactions to unknown drugs using these models requires relevant experimental input. Accordingly, the physiome concept has emerged to bridge experimental datasets with in silico models. The brain physiome describes the systemic interactions of its components, which are organized into a multilevel hierarchy. Because of the limitations in obtaining experimental data corresponding to each physiome component from 2D in vitro models and animal models, 3D in vitro brain models, including brain organoids and brain-on-a-chip, have been developed. In this review, we present the concept of the brain physiome and its hierarchical organization, including cell- and tissue-level organizations. We also summarize recently developed 3D in vitro brain models and link them with the elements of the brain physiome as a guideline for dataset collection. The connection between in vitro 3D brain models and in silico modeling will lead to the establishment of cost-effective and time-efficient in silico models for the prediction of the safety of unknown drugs.
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Affiliation(s)
- Yoojin Seo
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Seokyoung Bang
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Jeongtae Son
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Dongsup Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Yong Jeong
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Pilnam Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jihun Yang
- Next&Bio Inc., Seoul, 02841, Republic of Korea
| | - Joon-Ho Eom
- Medical Device Research Division, National Institute of Food and Drug Safety Evaluation, Cheongju, 28159, Republic of Korea
| | - Nakwon Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea
| | - Hong Nam Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Republic of Korea
- School of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
- Yonsei-KIST Convergence Research Institute, Yonsei University, Seoul, 03722, Republic of Korea
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2
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Laskowski KL, Seebacher F, Habedank M, Meka J, Bierbach D. Two Locomotor Traits Show Different Patterns of Developmental Plasticity Between Closely Related Clonal and Sexual Fish. Front Physiol 2021; 12:740604. [PMID: 34712149 PMCID: PMC8546259 DOI: 10.3389/fphys.2021.740604] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/22/2021] [Indexed: 12/11/2022] Open
Abstract
The capacity to compensate for environmental change determines population persistence and biogeography. In ectothermic organisms, performance at different temperatures can be strongly affected by temperatures experienced during early development. Such developmental plasticity is mediated through epigenetic mechanisms that induce phenotypic changes within the animal's lifetime. However, epigenetic modifiers themselves are encoded by DNA so that developmental plasticity could itself be contingent on genetic diversity. In this study, we test the hypothesis that the capacity for developmental plasticity depends on a species' among-individual genetic diversity. To test this, we exploited a unique species complex that contains both the clonal, genetically identical Amazon molly (Poecilia formosa), and the sexual, genetically diverse Atlantic molly (Poecilia mexicana). We predicted that the greater among-individual genetic diversity in the Atlantic molly may increase their capacity for developmental plasticity. We raised both clonal and sexual mollies at either warm (28°C) or cool (22°C) temperatures and then measured locomotor capacity (critical sustained swimming performance) and unforced movement in an open field across a temperature gradient that simulated environmental conditions often experienced by these species in the wild. In the clonal Amazon molly, differences in the developmental environment led to a shift in the thermal performance curve of unforced movement patterns, but much less so in maximal locomotor capacity. In contrast, the sexual Atlantic mollies exhibited the opposite pattern: developmental plasticity was present in maximal locomotor capacity, but not in unforced movement. Thus our data show that developmental plasticity in clones and their sexual, genetically more diverse sister species is trait dependent. This points toward mechanistic differences in how genetic diversity mediates plastic responses exhibited in different traits.
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Affiliation(s)
- Kate L Laskowski
- Department of Biology and Ecology of Fishes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Department of Evolution and Ecology, University of California, Davis, Davis, CA, United States
| | - Frank Seebacher
- School of Life and Environmental Sciences A08, The University of Sydney, Sydney, NSW, Australia
| | - Marie Habedank
- Department of Biology and Ecology of Fishes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Johannes Meka
- Department of Biology and Ecology of Fishes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - David Bierbach
- Department of Biology and Ecology of Fishes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University of Berlin, Berlin, Germany.,Cluster of Excellence "Science of Intelligence," Technische Universität Berlin, Berlin, Germany
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Mathema VB, Nakeesathit S, White NJ, Dondorp AM, Imwong M. Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi. Parasite 2020; 27:34. [PMID: 32410726 PMCID: PMC7227371 DOI: 10.1051/parasite/2020034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/30/2020] [Indexed: 12/16/2022] Open
Abstract
Microsatellites can be utilized to explore genotypes, population structure, and other genomic features of eukaryotes. Systematic characterization of microsatellites has not been a focus for several species of Plasmodium, including P. malariae and P. ovale, as the majority of malaria elimination programs are focused on P. falciparum and to a lesser extent P. vivax. Here, five human malaria species (P. falciparum, P. vivax, P. malariae, P. ovale curtisi, and P. knowlesi) were investigated with the aim of conducting in-depth categorization of microsatellites for P. malariae and P. ovale curtisi. Investigation of reference genomes for microsatellites with unit motifs of 1-10 base pairs indicates high diversity among the five Plasmodium species. Plasmodium malariae, with the largest genome size, displays the second highest microsatellite density (1421 No./Mbp; 5% coverage) next to P. falciparum (3634 No./Mbp; 12% coverage). The lowest microsatellite density was observed in P. vivax (773 No./Mbp; 2% coverage). A, AT, and AAT are the most commonly repeated motifs in the Plasmodium species. For P. malariae and P. ovale curtisi, microsatellite-related sequences are observed in approximately 18-29% of coding sequences (CDS). Lysine, asparagine, and glutamic acids are most frequently coded by microsatellite-related CDS. The majority of these CDS could be related to the gene ontology terms "cell parts," "binding," "developmental processes," and "metabolic processes." The present study provides a comprehensive overview of microsatellite distribution and can assist in the planning and development of potentially useful genetic tools for further investigation of P. malariae and P. ovale curtisi epidemiology.
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Affiliation(s)
- Vivek Bhakta Mathema
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University 10400 Bangkok Thailand
| | - Supatchara Nakeesathit
- Mahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University 10400 Bangkok Thailand
| | - Nicholas J. White
- Mahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University 10400 Bangkok Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford OX1 2JD Oxford United Kingdom
| | - Arjen M. Dondorp
- Mahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University 10400 Bangkok Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford OX1 2JD Oxford United Kingdom
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University 10400 Bangkok Thailand
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Jørgensen PS, Folke C, Carroll SP. Evolution in the Anthropocene: Informing Governance and Policy. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110218-024621] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Anthropocene biosphere constitutes an unprecedented phase in the evolution of life on Earth with one species, humans, exerting extensive control. The increasing intensity of anthropogenic forces in the twenty-first century has widespread implications for attempts to govern both human-dominated ecosystems and the last remaining wild ecosystems. Here, we review how evolutionary biology can inform governance and policies in the Anthropocene, focusing on five governance challenges that span biodiversity, environmental management, food and other biomass production, and human health. The five challenges are: ( a) evolutionary feedbacks, ( b) maintaining resilience, ( c) alleviating constraints, ( d) coevolutionary disruption, and ( e) biotechnology. Strategies for governing these dynamics will themselves have to be coevolutionary, as eco-evolutionary and social dynamics change in response to each other.
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Affiliation(s)
- Peter Søgaard Jørgensen
- Global Economic Dynamics and the Biosphere, Royal Swedish Academy of Sciences, SE104-05 Stockholm, Sweden;,
- Stockholm Resilience Centre, Stockholm University, SE106-91 Stockholm, Sweden
| | - Carl Folke
- Global Economic Dynamics and the Biosphere, Royal Swedish Academy of Sciences, SE104-05 Stockholm, Sweden;,
- Stockholm Resilience Centre, Stockholm University, SE106-91 Stockholm, Sweden
- Beijer Institute of Ecological Economics, Royal Swedish Academy of Sciences, SE104-05 Stockholm, Sweden
| | - Scott P. Carroll
- Institute for Contemporary Evolution, Davis, California 95616, USA
- Department of Entomology and Nematology, University of California, Davis, California 95616, USA
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5
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Fuentes M. Biological novelty in the anthropocene. J Theor Biol 2018; 437:137-140. [PMID: 29106992 DOI: 10.1016/j.jtbi.2017.10.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 09/06/2017] [Accepted: 10/23/2017] [Indexed: 11/24/2022]
Abstract
It is well known that humans are creating new variants of organisms, ecosystems and landscapes. Here I argue that the degree of biological novelty generated by humans goes deeper than that. We use property rules to create exclusivity in cooperation among humans, and between humans and other biological entities, thus overcoming social dilemmas and breaking barriers to cooperation. This is leading to novel forms of cooperation. One of them is the human control, modification and replication of whole ecosystems. For the first time, there exist ecosystems with functional design, division of labor and unlimited heredity. We use mental representation and language as new mechanisms of inheritance and modification that apply to an increasing variety of biological and non-biological entities. As a result, the speed, depth and scale of biological innovation are unprecedented in the history of life.
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Affiliation(s)
- Marcelino Fuentes
- Facultade de Ciencias, Universidade da Coruña, A Coruña, 15071 Spain.
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Frías-Lasserre D, Villagra CA. The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution. Front Microbiol 2017; 8:2483. [PMID: 29312192 PMCID: PMC5744636 DOI: 10.3389/fmicb.2017.02483] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/29/2017] [Indexed: 12/12/2022] Open
Abstract
Neo-Darwinian explanations of organic evolution have settled on mutation as the principal factor in producing evolutionary novelty. Mechanistic characterizations have been also biased by the classic dogma of molecular biology, where only proteins regulate gene expression. This together with the rearrangement of genetic information, in terms of genes and chromosomes, was considered the cornerstone of evolution at the level of natural populations. This predominant view excluded both alternative explanations and phenomenologies that did not fit its paradigm. With the discovery of non-coding RNAs (ncRNAs) and their role in the control of genetic expression, new mechanisms arose providing heuristic power to complementary explanations to evolutionary processes overwhelmed by mainstream genocentric views. Viruses, epimutation, paramutation, splicing, and RNA editing have been revealed as paramount functions in genetic variations, phenotypic plasticity, and diversity. This article discusses how current epigenetic advances on ncRNAs have changed the vision of the mechanisms that generate variation, how organism-environment interaction can no longer be underestimated as a driver of organic evolution, and how it is now part of the transgenerational inheritance and evolution of species.
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Affiliation(s)
- Daniel Frías-Lasserre
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile
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Seebacher F, Webster MM, James RS, Tallis J, Ward AJW. Morphological differences between habitats are associated with physiological and behavioural trade-offs in stickleback (Gasterosteus aculeatus). ROYAL SOCIETY OPEN SCIENCE 2016; 3:160316. [PMID: 27429785 PMCID: PMC4929920 DOI: 10.1098/rsos.160316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 05/24/2016] [Indexed: 06/06/2023]
Abstract
Local specialization can be advantageous for individuals and may increase the resilience of the species to environmental change. However, there may be trade-offs between morphological responses and physiological performance and behaviour. Our aim was to test whether habitat-specific morphology of stickleback (Gasterosteus aculeatus) interacts with physiological performance and behaviour at different salinities. We rejected the hypothesis that deeper body shape of fish from habitats with high predation pressure led to decreases in locomotor performance. However, there was a trade-off between deeper body shape and muscle quality. Muscle of deeper-bodied fish produced less force than that of shallow-bodied saltmarsh fish. Nonetheless, saltmarsh fish had lower swimming performance, presumably because of lower muscle mass overall coupled with smaller caudal peduncles and larger heads. Saltmarsh fish performed better in saline water (20 ppt) relative to freshwater and relative to fish from freshwater habitats. However, exposure to salinity affected shoaling behaviour of fish from all habitats and shoals moved faster and closer together compared with freshwater. We show that habitat modification can alter phenotypes of native species, but local morphological specialization is associated with trade-offs that may reduce its benefits.
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Affiliation(s)
- Frank Seebacher
- School of Life and Environmental Sciences A08, University of Sydney, New South Wales 2006, Australia
| | | | - Rob S. James
- Centre for Applied Biological and Exercise Sciences, Coventry University, Coventry CV1 5FB, UK
| | - Jason Tallis
- Centre for Applied Biological and Exercise Sciences, Coventry University, Coventry CV1 5FB, UK
| | - Ashley J. W. Ward
- School of Life and Environmental Sciences A08, University of Sydney, New South Wales 2006, Australia
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8
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Gillings MR, Hilbert M, Kemp DJ. Information in the Biosphere: Biological and Digital Worlds. Trends Ecol Evol 2016; 31:180-189. [PMID: 26777788 DOI: 10.1016/j.tree.2015.12.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 01/12/2023]
Abstract
Evolution has transformed life through key innovations in information storage and replication, including RNA, DNA, multicellularity, and culture and language. We argue that the carbon-based biosphere has generated a cognitive system (humans) capable of creating technology that will result in a comparable evolutionary transition. Digital information has reached a similar magnitude to information in the biosphere. It increases exponentially, exhibits high-fidelity replication, evolves through differential fitness, is expressed through artificial intelligence (AI), and has facility for virtually limitless recombination. Like previous evolutionary transitions, the potential symbiosis between biological and digital information will reach a critical point where these codes could compete via natural selection. Alternatively, this fusion could create a higher-level superorganism employing a low-conflict division of labor in performing informational tasks.
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Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2019, Australia.
| | - Martin Hilbert
- Department of Communication, University of California, Davis, Davis, CA 95616, USA
| | - Darrell J Kemp
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2019, Australia
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Gillings MR, Paulsen IT, Tetu SG. Ecology and Evolution of the Human Microbiota: Fire, Farming and Antibiotics. Genes (Basel) 2015; 6:841-57. [PMID: 26371047 PMCID: PMC4584332 DOI: 10.3390/genes6030841] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/26/2015] [Accepted: 08/31/2015] [Indexed: 01/15/2023] Open
Abstract
Human activities significantly affect all ecosystems on the planet, including the assemblages that comprise our own microbiota. Over the last five million years, various evolutionary and ecological drivers have altered the composition of the human microbiota, including the use of fire, the invention of agriculture, and the increasing availability of processed foods after the Industrial Revolution. However, no factor has had a faster or more direct effect than antimicrobial agents. Biocides, disinfectants and antibiotics select for individual cells that carry resistance genes, immediately reducing both overall microbial diversity and within-species genetic diversity. Treated individuals may never recover their original diversity, and repeated treatments lead to a series of genetic bottlenecks. The sequential introduction of diverse antimicrobial agents has selected for increasingly complex DNA elements that carry multiple resistance genes, and has fostered their spread through the human microbiota. Practices that interfere with microbial colonization, such as sanitation, Caesarian births and bottle-feeding, exacerbate the effects of antimicrobials, generating species-poor and less resilient microbial assemblages in the developed world. More and more evidence is accumulating that these perturbations to our internal ecosystems lie at the heart of many diseases whose frequency has shown a dramatic increase over the last half century.
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Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Sasha G Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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