Before the Endless Forms: Embodied Model of Transition from Single Cells to Aggregates to Ecosystem Engineering
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{"title"=>"Before the Endless Forms: Embodied Model of Transition from Single Cells to Aggregates to Ecosystem Engineering", "type"=>"journal", "authors"=>[{"first_name"=>"Ricard V.", "last_name"=>"Solé", "scopus_author_id"=>"7004381560"}, {"first_name"=>"Sergi", "last_name"=>"Valverde", "scopus_author_id"=>"7006393703"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"368726481", "sgr"=>"84876170005", "pmid"=>"23596506", "scopus"=>"2-s2.0-84876170005", "doi"=>"10.1371/journal.pone.0059664", "issn"=>"19326203"}, "id"=>"84499608-3c07-3a8b-81e4-4c5ca399710f", "abstract"=>"The emergence of complex multicellular systems and their associated developmental programs is one of the major problems of evolutionary biology. The advantages of cooperation over individuality seem well known but it is not clear yet how such increase of complexity emerged from unicellular life forms. Current multicellular systems display a complex cell-cell communication machinery, often tied to large-scale controls of body size or tissue homeostasis. Some unicellular life forms are simpler and involve groups of cells cooperating in a tissue-like fashion, as it occurs with biofilms. However, before true gene regulatory interactions were widespread and allowed for controlled changes in cell phenotypes, simple cellular colonies displaying adhesion and interacting with their environments were in place. In this context, models often ignore the physical embedding of evolving cells, thus leaving aside a key component. The potential for evolving pre-developmental patterns is a relevant issue: how far a colony of evolving cells can go? Here we study these pre-conditions for morphogenesis by using CHIMERA, a physically embodied computational model of evolving virtual organisms in a pre-Mendelian world. Starting from a population of identical, independent cells moving in a fluid, the system undergoes a series of changes, from spatial segregation, increased adhesion and the development of generalism. Eventually, a major transition occurs where a change in the flow of nutrients is triggered by a sub-population. This ecosystem engineering phenomenon leads to a subsequent separation of the ecological network into two well defined compartments. The relevance of these results for evodevo and its potential ecological triggers is discussed.", "link"=>"http://www.mendeley.com/research/before-endless-forms-embodied-model-transition-single-cells-aggregates-ecosystem-engineering", "reader_count"=>43, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Librarian"=>1, "Researcher"=>18, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Librarian"=>1, "Researcher"=>18, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Mathematics"=>1, "Agricultural and Biological Sciences"=>23, "Medicine and Dentistry"=>1, "Philosophy"=>1, "Physics and Astronomy"=>4, "Computer Science"=>5, "Earth and Planetary Sciences"=>1, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>4}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>23}, "Computer Science"=>{"Computer Science"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Mathematics"=>{"Mathematics"=>1}, "Environmental Science"=>{"Environmental Science"=>2}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"Vietnam"=>1, "United States"=>2, "Norway"=>1, "Switzerland"=>1, "Spain"=>2}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1023843"], "description"=>"<p>The system is confined within a rigid cube with a floor where particles fall and to which cells can attach. Five additional square boundaries are also present which cannot be crossed. The upper boundary allows a flow of nutrient particles (here small spheres) at a constant rate. Particles fall under gravity (a,b) and experience local turbulence as a random velocity field. As they reach the floor, they can keep moving under the same flow and also disappear as they degrade (c) into detritus particles. Cells can evolve adhesion among them (d) as well as with the substrate (e). Finally, cells and particles (f) ineract through collisions. If the cell is able to exploit that particular type of energy, the particle involved disappears and is transformed into cell's biomass (see text).</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Computational biology", "Ecosystem modeling", "systems biology", "developmental biology", "Evolutionary developmental biology", "ecology", "Evolutionary ecology", "Systems ecology", "theoretical ecology", "Molecular cell biology", "cell adhesion", "components", "chimera"], "article_id"=>681973, "categories"=>["Biological Sciences"], "users"=>["Ricard V. Solé", "Sergi Valverde"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059664.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Basic_scheme_of_the_components_of_the_CHIMERA_model_/681973", "title"=>"Basic scheme of the components of the CHIMERA model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-15 00:32:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023844"], "description"=>"<p>Here, and are the cell positions, is the offset vector, and are the cell radius, and is the interpenetration depth.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Computational biology", "Ecosystem modeling", "systems biology", "developmental biology", "Evolutionary developmental biology", "ecology", "Evolutionary ecology", "Systems ecology", "theoretical ecology", "Molecular cell biology", "cell adhesion", "geometry", "cell-cell"], "article_id"=>681974, "categories"=>["Biological Sciences"], "users"=>["Ricard V. Solé", "Sergi Valverde"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059664.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Simplified_geometry_of_cell_cell_collisions_/681974", "title"=>"Simplified geometry of cell-cell collisions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-15 00:32:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023845"], "description"=>"<p>(A) Bouncing collision takes place when the cell interpenetrates the nearest wall any distance along the unit normal vector of the wall. (B) Cell-wall adhesion occurs when cell-wall distance is below some threshold and according to adhesion probability (which depends on the cell genome, see text). In this case, a spring attaches the cell to a fixed point on the wall (see text).</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Computational biology", "Ecosystem modeling", "systems biology", "developmental biology", "Evolutionary developmental biology", "ecology", "Evolutionary ecology", "Systems ecology", "theoretical ecology", "Molecular cell biology", "cell adhesion", "interactions", "cells"], "article_id"=>681975, "categories"=>["Biological Sciences"], "users"=>["Ricard V. Solé", "Sergi Valverde"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059664.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Possible_interactions_between_cells_and_boundary_walls_/681975", "title"=>"Possible interactions between cells and boundary walls.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-15 00:32:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023847"], "description"=>"<p>Before the transition to the inverted population state (inset) cells grow and divide as they also evolve their characteristic parameters. At the beginning, the cell population grows by adapting to the variety of energy sources and we can see a thick layer of cells (a) plotted at After a while, an increase in the surface displayed by the population increases its efficiency to gather particles. Such increase is reached by evolving cell-substrate and cell-cell adhesion. The state shown in (b) is found at where we can appreciate a cluster of cells which appear to be climbing the surface of the cube. In (c) the cluster close to reaching the upper floor (here ) at this point the cell population does not experience further significant increase, but the number of particles decays to very low values. Here bright cells have high floor adhesion (where yellow indicates maximum adhesion) and darker colors correspond to cells with low adhesion or free-moving. Notice that adhesion evolves first in cells close to the wall boundaries. Here: particles per timestep, (see text).</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Computational biology", "Ecosystem modeling", "systems biology", "developmental biology", "Evolutionary developmental biology", "ecology", "Evolutionary ecology", "Systems ecology", "theoretical ecology", "Molecular cell biology", "cell adhesion", "cells", "particles"], "article_id"=>681977, "categories"=>["Biological Sciences"], "users"=>["Ricard V. Solé", "Sergi Valverde"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059664.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_time_evolution_of_cells_blue_and_particles_black_can_be_described_with_a_sequence_of_processes_/681977", "title"=>"The time evolution of cells (blue) and particles (black) can be described with a sequence of processes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-15 00:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023848"], "description"=>"<p>This transition is associated to the increasing height (inset) of the cell populations as further cells climb the walls towards the upper layer. Here the top floor is taken as the zero coordinate, whereas the bottom floor is taken as the (normalized) minimum (see text).</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Computational biology", "Ecosystem modeling", "systems biology", "developmental biology", "Evolutionary developmental biology", "ecology", "Evolutionary ecology", "Systems ecology", "theoretical ecology", "Molecular cell biology", "cell adhesion", "cell-floor"], "article_id"=>681978, "categories"=>["Biological Sciences"], "users"=>["Ricard V. Solé", "Sergi Valverde"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059664.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sharp_transition_in_the_time_evolution_of_average_cell_floor_adhesion_/681978", "title"=>"Sharp transition in the time evolution of average cell-floor adhesion.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-15 00:32:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023849"], "description"=>"<p>Here we have run CHIMERA using the same parameters of the previous figure but with different combinations of Four phases are found (a) including extinction (lower part), cellular monolayers as well as multilayered systems. Examples of each scenario are indicated with 3D snapshots where the adhesion strength between cells and the boundaries is color coded. A quantitative analysis of the transition from the EEN to the multilayer phase is indicated in (b), where has been used along with different levels of fluctuation. Ten replicas of each parameter combination were used and steps used to determine the final state. The standard deviation is also shown as error bars.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Computational biology", "Ecosystem modeling", "systems biology", "developmental biology", "Evolutionary developmental biology", "ecology", "Evolutionary ecology", "Systems ecology", "theoretical ecology", "Molecular cell biology", "cell adhesion", "intake", "fluctuations", "emergence"], "article_id"=>681979, "categories"=>["Biological Sciences"], "users"=>["Ricard V. Solé", "Sergi Valverde"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059664.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interplay_between_energy_intake_and_environmental_fluctuations_on_the_emergence_of_ecosystem_engineering_in_CHIMERA_s_model_/681979", "title"=>"Interplay between energy intake and environmental fluctuations on the emergence of ecosystem engineering in CHIMERA's model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-15 00:32:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023855"], "description"=>"<p>In (a) the increase in efficiency rate of detritus-grazing cells is shown. In (b) we display the population dynamics of both detritivores (number of cells exhibiting some level of detritus feeding behavior) and detritus particles. In (c–f) four snapshots of the evolved system are shown. Detritivores evolve initially at the corners between wall boundaries thanks to the increased concentration of residuals. Afterwards, detritivores spread along the bottom plane and consume residuals produced by the disintegration of generalist cells coming from above. Four snapshots are shown in (c-f) at different times in the evolution of detritivores. Hot colors indicate the relative detritivore efficiency. Here: particles per timestep, (see text).</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Computational biology", "Ecosystem modeling", "systems biology", "developmental biology", "Evolutionary developmental biology", "ecology", "Evolutionary ecology", "Systems ecology", "theoretical ecology", "Molecular cell biology", "cell adhesion", "detritus"], "article_id"=>681981, "categories"=>["Biological Sciences"], "users"=>["Ricard V. Solé", "Sergi Valverde"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059664.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dynamics_of_detritus_grazing_/681981", "title"=>"Dynamics of detritus grazing.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-15 00:33:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023856"], "description"=>"<p>(a) Flows in the initial food web, limited to a population of single-cell elements eating only one energy source () as defined by the CHIMERA model. The 1st nutrient is processed by the cells and transformed into cellular components high efficiency. At the end of the life cycle, the cell disintegrates into a number of residual particles. All molecules have similar degradation rates and get removed (right, lower box) from the system. After a while (b) an intermediate, diverse ecosystem is observed, with a large variety of cell exploiting different resources. This process proceeds until most cells become generalists, able to exploit all sources (c) whereas adhesion (indicated with smaller spheres) increases. Finally, once the population attached to the top floor has developed, another specialized population emerges at the bottom, fully composed by detritivores.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Computational biology", "Ecosystem modeling", "systems biology", "developmental biology", "Evolutionary developmental biology", "ecology", "Evolutionary ecology", "Systems ecology", "theoretical ecology", "Molecular cell biology", "cell adhesion"], "article_id"=>681982, "categories"=>["Biological Sciences"], "users"=>["Ricard V. Solé", "Sergi Valverde"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059664.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chimera_s_food_webs_/681982", "title"=>"Chimera's food webs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-15 00:33:02"}

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Relative Metric

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