1
|
Zhao Y, Wytock TP, Reynolds KA, Motter AE. Irreversibility in bacterial regulatory networks. SCIENCE ADVANCES 2024; 10:eado3232. [PMID: 39196926 PMCID: PMC11352831 DOI: 10.1126/sciadv.ado3232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 07/19/2024] [Indexed: 08/30/2024]
Abstract
Irreversibility, in which a transient perturbation leaves a system in a new state, is an emergent property in systems of interacting entities. This property has well-established implications in statistical physics but remains underexplored in biological networks, especially for bacteria and other prokaryotes whose regulation of gene expression occurs predominantly at the transcriptional level. Focusing on the reconstructed regulatory network of Escherichia coli, we examine network responses to transient single-gene perturbations. We predict irreversibility in numerous cases and find that the incidence of irreversibility increases with the proximity of the perturbed gene to positive circuits in the network. Comparison with experimental data suggests a connection between the predicted irreversibility to transient perturbations and the evolutionary response to permanent perturbations.
Collapse
Affiliation(s)
- Yi Zhao
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
- Center for Network Dynamics, Northwestern University, Evanston, IL 60208, USA
| | - Thomas P. Wytock
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
- Center for Network Dynamics, Northwestern University, Evanston, IL 60208, USA
| | - Kimberly A. Reynolds
- The Green Center for Systems Biology–Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adilson E. Motter
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
- Center for Network Dynamics, Northwestern University, Evanston, IL 60208, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
- National Institute for Theory and Mathematics in Biology, Evanston, IL 60208, USA
| |
Collapse
|
2
|
Di Patti F, Ugartechea Chirino Y, Arbel-Goren R, Sharon T, Castillo A, Alvarez–Buylla E, Fanelli D, Stavans J. Stochastic Turing patterns of trichomes in Arabidopsis leaves. Proc Natl Acad Sci U S A 2023; 120:e2309616120. [PMID: 37824528 PMCID: PMC10589648 DOI: 10.1073/pnas.2309616120] [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: 06/09/2023] [Accepted: 09/03/2023] [Indexed: 10/14/2023] Open
Abstract
Biological patterns that emerge during the morphogenesis of multicellular organisms can display high precision at large scales, while at cellular scales, cells exhibit large fluctuations stemming from cell-cell differences in molecular copy numbers also called demographic noise. We study the conflicting interplay between high precision and demographic noise in trichome patterns on the epidermis of wild-type Arabidopsis thaliana leaves, as a two-dimensional model system. We carry out a statistical characterization of these patterns and show that their power spectra display fat tails-a signature compatible with noise-driven stochastic Turing patterns-which are absent in power spectra of patterns driven by deterministic instabilities. We then present a theoretical model that includes demographic noise stemming from birth-death processes of genetic regulators which we study analytically and by stochastic simulations. The model captures the observed experimental features of trichome patterns.
Collapse
Affiliation(s)
- Francesca Di Patti
- Dipartimento di Matematica e Informatica, Universitá degli Studi di Perugia, Perugia06123, Italia
- Istituto Nazionale di Fisica Nucleare - Sezione di Perugia, Perugia06123, Italia
| | - Yamel Ugartechea Chirino
- Instituto de Ecología, Universidad Nacional Autónoma de México Ciudad, Universitaria 3er Circuito Interior Coyoacán, Ciudad de México04510, México
| | - Rinat Arbel-Goren
- Faculty of Physics, Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot76100, Israel
| | - Tom Sharon
- Faculty of Physics, Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot76100, Israel
| | - Aaron Castillo
- Instituto de Ecología, Universidad Nacional Autónoma de México Ciudad, Universitaria 3er Circuito Interior Coyoacán, Ciudad de México04510, México
| | - Elena Alvarez–Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México Ciudad, Universitaria 3er Circuito Interior Coyoacán, Ciudad de México04510, México
| | - Duccio Fanelli
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, Sesto Fiorentino, Firenze50019, Italia
- Centro Interdipartimentale per lo Studio delle Dinamiche Complesse and Istituto Nazionale di Fisica Nucleare Sezione di Firenze, Sesto Fiorentino, Firenze50019, Italia
| | - Joel Stavans
- Faculty of Physics, Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot76100, Israel
| |
Collapse
|
3
|
Avila-Ponce de León U, Vázquez-Jiménez A, Padilla-Longoria P, Resendis-Antonio O. Uncoding the interdependency of tumor microenvironment and macrophage polarization: insights from a continuous network approach. Front Immunol 2023; 14:1150890. [PMID: 37283734 PMCID: PMC10240616 DOI: 10.3389/fimmu.2023.1150890] [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: 01/26/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
The balance between pro- and anti-inflammatory immune system responses is crucial to preventing complex diseases like cancer. Macrophages are essential immune cells that contribute to this balance constrained by the local signaling profile of the tumor microenvironment. To understand how pro- and anti-inflammatory unbalance emerges in cancer, we developed a theoretical analysis of macrophage differentiation that is derived from activated monocytes circulating in the blood. Once recruited to the site of inflammation, monocytes can be polarized based on the specific interleukins and chemokines in the microenvironment. To quantify this process, we used a previous regulatory network reconstructed by our group and transformed Boolean Network attractors of macrophage polarization to an ODE scheme, it enables us to quantify the activation of their genes in a continuous fashion. The transformation was developed using the interaction rules with a fuzzy logic approach. By implementing this approach, we analyzed different aspects that cannot be visualized in the Boolean setting. For example, this approach allows us to explore the dynamic behavior at different concentrations of cytokines and transcription factors in the microenvironment. One important aspect to assess is the evaluation of the transitions between phenotypes, some of them characterized by an abrupt or a gradual transition depending on specific concentrations of exogenous cytokines in the tumor microenvironment. For instance, IL-10 can induce a hybrid state that transits between an M2c and an M2b macrophage. Interferon- γ can induce a hybrid between M1 and M1a macrophage. We further demonstrated the plasticity of macrophages based on a combination of cytokines and the existence of hybrid phenotypes or partial polarization. This mathematical model allows us to unravel the patterns of macrophage differentiation based on the competition of expression of transcriptional factors. Finally, we survey how macrophages may respond to a continuously changing immunological response in a tumor microenvironment.
Collapse
Affiliation(s)
- Ugo Avila-Ponce de León
- Programa de Doctorado en Ciencias Biológicas, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico, Mexico
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de Mexico, Mexico
| | - Aarón Vázquez-Jiménez
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de Mexico, Mexico
| | - Pablo Padilla-Longoria
- Institute for Applied Mathematics (IIMAS), Universidad Nacional Autónoma de Mexico, Ciudad de Mexico, Mexico
| | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de Mexico, Mexico
- Coordinación de la Investigación Científica - Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México (UNAM), Ciudad de Mexico, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de Mexico, Ciudad de Mexico, Mexico
| |
Collapse
|
4
|
Subbaroyan A, Sil P, Martin OC, Samal A. Leveraging developmental landscapes for model selection in Boolean gene regulatory networks. Brief Bioinform 2023; 24:7145905. [PMID: 37114653 DOI: 10.1093/bib/bbad160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/26/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Boolean models are a well-established framework to model developmental gene regulatory networks (DGRNs) for acquisition of cellular identities. During the reconstruction of Boolean DGRNs, even if the network structure is given, there is generally a large number of combinations of Boolean functions that will reproduce the different cell fates (biological attractors). Here we leverage the developmental landscape to enable model selection on such ensembles using the relative stability of the attractors. First we show that previously proposed measures of relative stability are strongly correlated and we stress the usefulness of the one that captures best the cell state transitions via the mean first passage time (MFPT) as it also allows the construction of a cellular lineage tree. A property of great computational importance is the insensitivity of the different stability measures to changes in noise intensities. That allows us to use stochastic approaches to estimate the MFPT and thereby scale up the computations to large networks. Given this methodology, we revisit different Boolean models of Arabidopsis thaliana root development, showing that a most recent one does not respect the biologically expected hierarchy of cell states based on relative stabilities. We therefore developed an iterative greedy algorithm that searches for models which satisfy the expected hierarchy of cell states and found that its application to the root development model yields many models that meet this expectation. Our methodology thus provides new tools that can enable reconstruction of more realistic and accurate Boolean models of DGRNs.
Collapse
Affiliation(s)
- Ajay Subbaroyan
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | - Priyotosh Sil
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | - Olivier C Martin
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| |
Collapse
|
5
|
Martínez-Méndez D, Huerta L, Villarreal C. Modeling the effect of environmental cytokines, nutrient conditions and hypoxia on CD4+ T cell differentiation. Front Immunol 2022; 13:962175. [PMID: 36211418 PMCID: PMC9539201 DOI: 10.3389/fimmu.2022.962175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Upon antigen stimulation and co-stimulation, CD4+ T lymphocytes produce soluble factors that promote the activity of other immune cells against pathogens or modified tissues; this task must be performed in presence of a variety of environmental cytokines, nutrient, and oxygen conditions, which necessarily impact T cell function. The complexity of the early intracellular processes taking place upon lymphocyte stimulation is addressed by means of a mathematical model based on a network that integrates variable microenvironmental conditions with intracellular activating, regulatory, and metabolic signals. Besides the phenotype subsets considered in previous works (Th1, Th2, Th17, and Treg) the model includes the main early events in differentiation to the TFH phenotype. The model describes how cytokines, nutrients and oxygen availability regulate the differentiation of naïve CD4+ T cells into distinct subsets. Particularly, it shows that elevated amounts of an all-type mixture of effector cytokines under optimal nutrient and oxygen availability conduces the system towards a highly-polarized Th1 or Th2 state, while reduced cytokine levels allow the expression of the Th17, Treg or TFH subsets, or even hybrid phenotypes. On the other hand, optimal levels of an all-type cytokine mixture in combination with glutamine or tryptophan restriction implies a shift from Th1 to Th2 expression, while decreased levels of the Th2-inducing cytokine IL-4 leads to the rupture of the Th1-Th2 axis, allowing the manifestation of different (or hybrid) subsets. Modeling proposes that, even under reduced levels of pro-inflammatory cytokines, the sole action of hypoxia boost Th17 expression.
Collapse
Affiliation(s)
| | - Leonor Huerta
- Instituto de Investigaciones Biomédicas, Departamento de Inmunología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Carlos Villarreal, ; Leonor Huerta,
| | - Carlos Villarreal
- Instituto de Física, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Carlos Villarreal, ; Leonor Huerta,
| |
Collapse
|
6
|
Chávez-Hernández EC, Quiroz S, García-Ponce B, Álvarez-Buylla ER. The flowering transition pathways converge into a complex gene regulatory network that underlies the phase changes of the shoot apical meristem in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:852047. [PMID: 36017258 PMCID: PMC9396034 DOI: 10.3389/fpls.2022.852047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/04/2022] [Indexed: 05/08/2023]
Abstract
Post-embryonic plant development is characterized by a period of vegetative growth during which a combination of intrinsic and extrinsic signals triggers the transition to the reproductive phase. To understand how different flowering inducing and repressing signals are associated with phase transitions of the Shoot Apical Meristem (SAM), we incorporated available data into a dynamic gene regulatory network model for Arabidopsis thaliana. This Flowering Transition Gene Regulatory Network (FT-GRN) formally constitutes a dynamic system-level mechanism based on more than three decades of experimental data on flowering. We provide novel experimental data on the regulatory interactions of one of its twenty-three components: a MADS-box transcription factor XAANTAL2 (XAL2). These data complement the information regarding flowering transition under short days and provides an example of the type of questions that can be addressed by the FT-GRN. The resulting FT-GRN is highly connected and integrates developmental, hormonal, and environmental signals that affect developmental transitions at the SAM. The FT-GRN is a dynamic multi-stable Boolean system, with 223 possible initial states, yet it converges into only 32 attractors. The latter are coherent with the expression profiles of the FT-GRN components that have been experimentally described for the developmental stages of the SAM. Furthermore, the attractors are also highly robust to initial states and to simulated perturbations of the interaction functions. The model recovered the meristem phenotypes of previously described single mutants. We also analyzed the attractors landscape that emerges from the postulated FT-GRN, uncovering which set of signals or components are critical for reproductive competence and the time-order transitions observed in the SAM. Finally, in the context of such GRN, the role of XAL2 under short-day conditions could be understood. Therefore, this model constitutes a robust biological module and the first multi-stable, dynamical systems biology mechanism that integrates the genetic flowering pathways to explain SAM phase transitions.
Collapse
Affiliation(s)
- Elva C. Chávez-Hernández
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stella Quiroz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Berenice García-Ponce,
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Elena R. Álvarez-Buylla,
| |
Collapse
|
7
|
Martínez-Méndez D, Mendoza L, Villarreal C, Huerta L. Continuous Modeling of T CD4 Lymphocyte Activation and Function. Front Immunol 2021; 12:743559. [PMID: 34804023 PMCID: PMC8602102 DOI: 10.3389/fimmu.2021.743559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
T CD4+ cells are central to the adaptive immune response against pathogens. Their activation is induced by the engagement of the T-cell receptor by antigens, and of co-stimulatory receptors by molecules also expressed on antigen presenting cells. Then, a complex network of intracellular events reinforce, diversify and regulate the initial signals, including dynamic metabolic processes that strongly influence both the activation state and the differentiation to effector cell phenotypes. The regulation of cell metabolism is controlled by the nutrient sensor adenosine monophosphate-activated protein kinase (AMPK), which drives the balance between oxidative phosphorylation (OXPHOS) and glycolysis. Herein, we put forward a 51-node continuous mathematical model that describes the temporal evolution of the early events of activation, integrating a circuit of metabolic regulation into the main routes of signaling. The model simulates the induction of anergy due to defective co-stimulation, the CTLA-4 checkpoint blockade, and the differentiation to effector phenotypes induced by external cytokines. It also describes the adjustment of the OXPHOS-glycolysis equilibrium by the action of AMPK as the effector function of the T cell develops. The development of a transient phase of increased OXPHOS before induction of a sustained glycolytic phase during differentiation to the Th1, Th2 and Th17 phenotypes is shown. In contrast, during Treg differentiation, glycolysis is subsequently reduced as cell metabolism is predominantly polarized towards OXPHOS. These observations are in agreement with experimental data suggesting that OXPHOS produces an ATP reservoir before glycolysis boosts the production of metabolites needed for protein synthesis, cell function, and growth.
Collapse
Affiliation(s)
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos Villarreal
- Instituto de Física, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Leonor Huerta
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
8
|
Díaz J, Álvarez-Buylla ER. Spatio-Temporal Dynamics of the Patterning of Arabidopsis Flower Meristem. FRONTIERS IN PLANT SCIENCE 2021; 12:585139. [PMID: 33659013 PMCID: PMC7917056 DOI: 10.3389/fpls.2021.585139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
The qualitative model presented in this work recovers the onset of the four fields that correspond to those of each floral organ whorl of Arabidopsis flower, suggesting a mechanism for the generation of the positional information required for the differential expression of the A, B, and C identity genes according to the ABC model for organ determination during early stages of flower development. Our model integrates a previous model for the emergence of WUS pattern in the floral meristem, and shows that this pre-pattern is a necessary but not sufficient condition for the posterior information of the four fields predicted by the ABC model. Furthermore, our model predicts that LFY diffusion along the L1 layer of cells is not a necessary condition for the patterning of the floral meristem.
Collapse
Affiliation(s)
- José Díaz
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| |
Collapse
|
9
|
Ladin ZS, Ferrell B, Dums JT, Moore RM, Levia DF, Shriver WG, D'Amico V, Trammell TLE, Setubal JC, Wommack KE. Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems. Sci Rep 2021; 11:1629. [PMID: 33452291 PMCID: PMC7811025 DOI: 10.1038/s41598-020-80602-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023] Open
Abstract
We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.
Collapse
Affiliation(s)
- Zachary S Ladin
- Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA.
| | - Barbra Ferrell
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA
| | - Jacob T Dums
- Biotechnology Program, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ryan M Moore
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA
| | - Delphis F Levia
- Department of Entomology and Wildlife Ecology, University of Delaware, 250 Townsend Hall, Newark, DE, 19716, USA
| | - W Gregory Shriver
- Departments of Geography and Spatial Sciences and Plant and Soil Sciences, University of Delaware, 216C Pearson Hall, Newark, DE, 19716, USA
| | - Vincent D'Amico
- US Forest Service, Northern Research Station, Newark, DE, USA
| | - Tara L E Trammell
- Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA
| | - João Carlos Setubal
- Instituto de Química, University of Sao Paulo, São Paulo, SP, 05508-000, Brazil
| | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA
| |
Collapse
|
10
|
Enciso J, Mendoza L, Álvarez-Buylla ER, Pelayo R. Dynamical modeling predicts an inflammation-inducible CXCR7+ B cell precursor with potential implications in lymphoid blockage pathologies. PeerJ 2020; 8:e9902. [PMID: 33062419 PMCID: PMC7531334 DOI: 10.7717/peerj.9902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/18/2020] [Indexed: 12/16/2022] Open
Abstract
Background The blockage at the early B lymphoid cell development pathway within the bone marrow is tightly associated with hematopoietic and immune diseases, where the disruption of basal regulatory networks prevents the continuous replenishment of functional B cells. Dynamic computational models may be instrumental for the comprehensive understanding of mechanisms underlying complex differentiation processes and provide novel prediction/intervention platforms to reinvigorate the system. Methods By reconstructing a three-module regulatory network including genetic transcription, intracellular transduction, and microenvironment communication, we have investigated the early B lineage cell fate decisions in normal and pathological settings. The early B cell differentiation network was simulated as a Boolean model and then transformed, using fuzzy logic, to a continuous model. We tested null and overexpression mutants to analyze the emergent behavior of the network. Due to its importance in inflammation, we investigated the effect of NFkB induction at different early B cell differentiation stages. Results While the exhaustive synchronous and asynchronous simulation of the early B cell regulatory network (eBCRN) reproduced the configurations of the hematopoietic progenitors and early B lymphoid precursors of the pathway, its simulation as a continuous model with fuzzy logics suggested a transient IL-7R+ ProB-to-Pre-B subset expressing pre-BCR and a series of dominant B-cell transcriptional factors. This conspicuous differentiating cell population up-regulated CXCR7 and reduced CXCR4 and FoxO1 expression levels. Strikingly, constant but intermediate NFkB signaling at specific B cell differentiation stages allowed stabilization of an aberrant CXCR7+ pre-B like phenotype with apparent affinity to proliferative signals, while under constitutive overactivation of NFkB, such cell phenotype was aberrantly exacerbated from the earliest stage of common lymphoid progenitors. Our mutant models revealed an abnormal delay in the BCR assembly upon NFkB activation, concomitant to sustained Flt3 signaling, down-regulation of Ebf1, Irf4 and Pax5 genes transcription, and reduced Ig recombination, pointing to a potential lineage commitment blockage. Discussion For the first time, an inducible CXCR7hi B cell precursor endowed with the potential capability of shifting central lymphoid niches, is inferred by computational modeling. Its phenotype is compatible with that of leukemia-initiating cells and might be the foundation that bridges inflammation with blockage-related malignancies and a wide range of immunological diseases. Besides the predicted differentiation impairment, inflammation-inducible phenotypes open the possibility of newly formed niches colonized by the reported precursor. Thus, emergent bone marrow ecosystems are predicted following a pro-inflammatory induction, that may lead to hematopoietic instability associated to blockage pathologies.
Collapse
Affiliation(s)
- Jennifer Enciso
- Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Metepec, Puebla, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, México.,Programa de Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, México
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, México
| | | | - Rosana Pelayo
- Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Metepec, Puebla, Mexico
| |
Collapse
|
11
|
Barrera M, Hiriart M, Cocho G, Villarreal C. Type 2 diabetes progression: A regulatory network approach. CHAOS (WOODBURY, N.Y.) 2020; 30:093132. [PMID: 33003944 DOI: 10.1063/5.0011125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
In order to elucidate central elements underlying type 2 diabetes, we constructed a regulatory network model involving 37 components (molecules, receptors, processes, etc.) associated to signaling pathways of pancreatic beta-cells. In a first approximation, the network topology was described by Boolean rules whose interacting dynamics predicted stationary patterns broadly classified as health, metabolic syndrome, and diabetes stages. A subsequent approximation based on a continuous logic analysis allowed us to characterize the progression of the disease as transitions between these states associated to alterations of cell homeostasis due to exhaustion or exacerbation of specific regulatory signals. The method allowed the identification of key transcription factors involved in metabolic stress as essential for the progression of the disease. Integration of the present analysis with existent mathematical models designed to yield accurate account of experimental data in human or animal essays leads to reliable predictions for beta-cell mass, insulinemia, glycemia, and glycosylated hemoglobin in diabetic fatty rats.
Collapse
Affiliation(s)
- M Barrera
- Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - M Hiriart
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - G Cocho
- Instituto de Física, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - C Villarreal
- Instituto de Física, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| |
Collapse
|
12
|
A system-level mechanistic explanation for asymmetric stem cell fates: Arabidopsis thaliana root niche as a study system. Sci Rep 2020; 10:3525. [PMID: 32103059 PMCID: PMC7044435 DOI: 10.1038/s41598-020-60251-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/23/2019] [Indexed: 11/09/2022] Open
Abstract
Asymmetric divisions maintain long-term stem cell populations while producing new cells that proliferate and then differentiate. Recent reports in animal systems show that divisions of stem cells can be uncoupled from their progeny differentiation, and the outcome of a division could be influenced by microenvironmental signals. But the underlying system-level mechanisms, and whether this dynamics also occur in plant stem cell niches (SCN), remain elusive. This article presents a cell fate regulatory network model that contributes to understanding such mechanism and identify critical cues for cell fate transitions in the root SCN. Novel computational and experimental results show that the transcriptional regulator SHR is critical for the most frequent asymmetric division previously described for quiescent centre stem cells. A multi-scale model of the root tip that simulated each cell's intracellular regulatory network, and the dynamics of SHR intercellular transport as a cell-cell coupling mechanism, was developed. It revealed that quiescent centre cell divisions produce two identical cells, that may acquire different fates depending on the feedback between SHR's availability and the state of the regulatory network. Novel experimental data presented here validates our model, which in turn, constitutes the first proposed systemic mechanism for uncoupled SCN cell division and differentiation.
Collapse
|
13
|
Enciso J, Pelayo R, Villarreal C. From Discrete to Continuous Modeling of Lymphocyte Development and Plasticity in Chronic Diseases. Front Immunol 2019; 10:1927. [PMID: 31481957 PMCID: PMC6710364 DOI: 10.3389/fimmu.2019.01927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 07/30/2019] [Indexed: 12/12/2022] Open
Abstract
The molecular events leading to differentiation, development, and plasticity of lymphoid cells have been subject of intense research due to their key roles in multiple pathologies, such as lymphoproliferative disorders, tumor growth maintenance and chronic diseases. The emergent roles of lymphoid cells and the use of high-throughput technologies have led to an extensive accumulation of experimental data allowing the reconstruction of gene regulatory networks (GRN) by integrating biochemical signals provided by the microenvironment with transcriptional modules of lineage-specific genes. Computational modeling of GRN has been useful for the identification of molecular switches involved in lymphoid specification, prediction of microenvironment-dependent cell plasticity, and analyses of signaling events occurring downstream the activation of antigen recognition receptors. Among most common modeling strategies to analyze the dynamical behavior of GRN, discrete dynamic models are widely used for their capacity to capture molecular interactions when a limited knowledge of kinetic parameters is present. However, they are less powerful when modeling complex systems sensitive to biochemical gradients. To compensate it, discrete models may be transformed into regulatory networks that includes state variables and parameters varying within a continuous range. This approach is based on a system of differential equations dynamics with regulatory interactions described by fuzzy logic propositions. Here, we discuss the applicability of this method on modeling of development and plasticity processes of adaptive lymphocytes, and its potential implications in the study of pathological landscapes associated to chronic diseases.
Collapse
Affiliation(s)
- Jennifer Enciso
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rosana Pelayo
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Carlos Villarreal
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Física Cuántica y Fotónica, Instituto de Física, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
14
|
Álvarez-Buylla Roces ME, Martínez-García JC, Dávila-Velderrain J, Domínguez-Hüttinger E, Martínez-Sánchez ME. Medical Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1069:1-33. [PMID: 30076565 DOI: 10.1007/978-3-319-89354-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The aim of this volume is to encourage the use of systems-level methodologies to contribute to the improvement of human-health . We intend to motivate biomedical researchers to complement their current theoretical and empirical practice with up-to-date systems biology conceptual approaches. Our perspective is based on the deep understanding of the key biomolecular regulatory mechanisms that underlie health, as well as the emergence and progression of human-disease . We strongly believe that the contemporary systems biology perspective opens the door to the effective development of novel methodologies to the improvement of prevention . This requires a deeper and integrative understanding of the involved underlying systems-level mechanisms. In order to explain our proposal in a simple way, in this chapter we privilege the conceptual exposition of our chosen framework over formal considerations. The formal exposition of our proposal will be expanded and discussed later in the next chapters.
Collapse
|
15
|
Martinez-Sanchez ME, Huerta L, Alvarez-Buylla ER, Villarreal Luján C. Role of Cytokine Combinations on CD4+ T Cell Differentiation, Partial Polarization, and Plasticity: Continuous Network Modeling Approach. Front Physiol 2018; 9:877. [PMID: 30127748 PMCID: PMC6089340 DOI: 10.3389/fphys.2018.00877] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 06/19/2018] [Indexed: 12/16/2022] Open
Abstract
Purpose: We put forward a theoretical and dynamical approach for the semi-quantitative analysis of CD4+ T cell differentiation, the process by which cells with different functions are derived from activated CD4+ T naïve lymphocytes in the presence of particular cytokine microenvironments. We explore the system-level mechanisms that underlie CD4+ T plasticity-the conversion of polarized cells to phenotypes different from those originally induced. Methods: In this paper, we extend a previous study based on a Boolean network to a continuous framework. The network includes transcription factors, signaling pathways, as well as autocrine and exogenous cytokines, with interaction rules derived using fuzzy logic. Results: This approach allows us to assess the effect of relative differences in the concentrations and combinations of exogenous and endogenous cytokines, as well as of the expression levels of diverse transcription factors. We found either abrupt or gradual differentiation patterns between observed phenotypes depending on critical concentrations of single or multiple environmental cytokines. Plastic changes induced by environmental cytokines were observed in conditions of partial phenotype polarization in the T helper 1 to T helper 2 transition. On the other hand, the T helper 17 to induced regulatory T-cells transition was highly dependent on cytokine concentrations, with TGFβ playing a prime role. Conclusion: The present approach is useful to further understand the system-level mechanisms underlying observed patterns of CD4+ T differentiation and response to changing immunological challenges.
Collapse
Affiliation(s)
- Mariana E. Martinez-Sanchez
- Laboratorio Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Leonor Huerta
- Laboratorio B108, Departmento de Immunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Elena R. Alvarez-Buylla
- Laboratorio Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos Villarreal Luján
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Física Cuántica y Fotónica, Instituto de Física, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
16
|
Espinosa-Soto C. On the role of sparseness in the evolution of modularity in gene regulatory networks. PLoS Comput Biol 2018; 14:e1006172. [PMID: 29775459 PMCID: PMC5979046 DOI: 10.1371/journal.pcbi.1006172] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/31/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology. One hypothesis for the evolution of modules suggests that interactions between some sets of genes become maladaptive when selection favours additional gene activity patterns. The removal of such interactions by selection would result in the formation of modules. A second hypothesis suggests that modularity evolves in response to sparseness, the scarcity of interactions within a system. Here I simulate the evolution of gene regulatory networks and analyse diverse experimentally sustained networks to study the relationship between sparseness and modularity. My results suggest that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, sparseness amplifies the effects of forms of selection that, like selection for additional gene activity patterns, already produce an increase in modularity. That evolution of new gene activity patterns is frequent across evolution also supports that it is a major factor in the evolution of modularity. That sparseness is widespread across gene regulatory networks indicates that it may have facilitated the evolution of modules in a wide variety of cases. Modular systems have performance and design advantages over non-modular systems. Thus, modularity is very important for the development of a wide range of new technological or clinical applications. Moreover, modularity is paramount to evolutionary biology since it allows adjusting one organismal function without disturbing other previously evolved functions. But how does modularity itself evolve? Here I analyse the structure of regulatory networks and follow simulations of network evolution to study two hypotheses for the origin of modules in gene regulatory networks. The first hypothesis considers that sparseness, a low number of interactions among the network genes, could be responsible for the evolution of modular networks. The second, that modules evolve when selection favours the production of additional gene activity patterns. I found that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, it enhances the effects of selection for multiple gene activity patterns. While selection for multiple patterns may be decisive in the evolution of modularity, that sparseness is widespread across gene regulatory networks suggests that its contributions should not be neglected.
Collapse
Affiliation(s)
- Carlos Espinosa-Soto
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Universitaria, San Luis Potosí, Mexico
- * E-mail:
| |
Collapse
|
17
|
Hernández-Hernández V, Barrio RA, Benítez M, Nakayama N, Romero-Arias JR, Villarreal C. A physico-genetic module for the polarisation of auxin efflux carriers PIN-FORMED (PIN). Phys Biol 2018; 15:036002. [PMID: 29393068 DOI: 10.1088/1478-3975/aaac99] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Intracellular polarisation of auxin efflux carriers is crucial for understanding how auxin gradients form in plants. The polarisation dynamics of auxin efflux carriers PIN-FORMED (PIN) depends on both biomechanical forces as well as chemical, molecular and genetic factors. Biomechanical forces have shown to affect the localisation of PIN transporters to the plasma membrane. We propose a physico-genetic module of PIN polarisation that integrates biomechanical, molecular, and cellular processes as well as their non-linear interactions. The module was implemented as a discrete Boolean model and then approximated to a continuous dynamic system, in order to explore the relative contribution of the factors mediating PIN polarisation at the scale of single cell. Our models recovered qualitative behaviours that have been experimentally observed and enable us to predict that, in the context of PIN polarisation, the effects of the mechanical forces can predominate over the activity of molecular factors such as the GTPase ROP6 and the ROP-INTERACTIVE CRIB MOTIF-CONTAINING PROTEIN RIC1.
Collapse
Affiliation(s)
- Valeria Hernández-Hernández
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico. Current Address: Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France. Author to whom any correspondence should be addressed
| | | | | | | | | | | |
Collapse
|
18
|
Arias Del Angel JA, Escalante AE, Martínez-Castilla LP, Benítez M. Cell-fate determination inMyxococcus xanthusdevelopment: Network dynamics and novel predictions. Dev Growth Differ 2018; 60:121-129. [DOI: 10.1111/dgd.12424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/27/2017] [Accepted: 11/16/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Juan A. Arias Del Angel
- National Laboratory for Sustainability Sciences (LANCIS); Institute of Ecology; National Autonomous University of Mexico; Mexico City Mexico
- Center for Complexity Sciences; National Autonomous University of Mexico; Mexico City Mexico
- Graduate Program in Biomedical Sciences; National Autonomous University of Mexico; Mexico City Mexico
| | - Ana E. Escalante
- National Laboratory for Sustainability Sciences (LANCIS); Institute of Ecology; National Autonomous University of Mexico; Mexico City Mexico
| | - León Patricio Martínez-Castilla
- Department of Biochemistry; Faculty of Chemistry; National Autonomous University of Mexico; Mexico City Mexico
- Center for Complexity Sciences; National Autonomous University of Mexico; Mexico City Mexico
| | - Mariana Benítez
- National Laboratory for Sustainability Sciences (LANCIS); Institute of Ecology; National Autonomous University of Mexico; Mexico City Mexico
- Center for Complexity Sciences; National Autonomous University of Mexico; Mexico City Mexico
| |
Collapse
|
19
|
Case Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1069:135-209. [DOI: 10.1007/978-3-319-89354-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
20
|
|
21
|
Álvarez-Buylla ER, Dávila-Velderrain J, Martínez-García JC. Systems Biology Approaches to Development beyond Bioinformatics: Nonlinear Mechanistic Models Using Plant Systems. Bioscience 2016. [DOI: 10.1093/biosci/biw027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
22
|
Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER. Dynamic network modelling to understand flowering transition and floral patterning. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2565-72. [PMID: 27025221 DOI: 10.1093/jxb/erw123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Differentiation and morphogenetic processes during plant development are particularly robust. At the cellular level, however, plants also show great plasticity in response to environmental conditions, and can even reverse apparently terminal differentiated states with remarkable ease. Can we understand and predict both robust and plastic systemic responses as a general consequence of the non-trivial interplay between intracellular regulatory networks, extrinsic environmental signalling, and tissue-level mechanical constraints? Flower development has become an ideal model system to study these general questions of developmental biology, which are especially relevant to understanding stem cell patterning in plants, animals, and human disease. Decades of detailed study of molecular developmental genetics, as well as novel experimental techniques for in vivo assays in both wild-type and mutant plants, enable the postulation and testing of experimentally grounded mathematical and computational network dynamical models. Research in our group aims to explain the emergence of robust transitions that occur at the shoot apical meristem, as well as flower development, as the result of the collective action of key molecular components in regulatory networks subjected to intra-organismal signalling and extracellular constraints. Here we present a brief overview of recent work from our group, and that of others, focusing on the use of simple dynamical models to address cell-fate specification and cell-state stochastic dynamics during flowering transition and cell-state transitions at the shoot apical meristem of Arabidopsis thaliana. We also focus on how our work fits within the general field of plant developmental modelling, which is being developed by many others.
Collapse
Affiliation(s)
- J Davila-Velderrain
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Cd Universitaria, México, DF 04510, México
| | - J C Martinez-Garcia
- Departamento de Control Autómatico, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, AP 14-740, 07300 México, DF, México
| | - E R Alvarez-Buylla
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Cd Universitaria, México, DF 04510, México Instituto de Ecología, Universidad Nacional Autónoma de México, Cd Universitaria, México, DF 04510, México
| |
Collapse
|
23
|
Zhou JX, Samal A, d'Hérouël AF, Price ND, Huang S. Relative stability of network states in Boolean network models of gene regulation in development. Biosystems 2016; 142-143:15-24. [PMID: 26965665 DOI: 10.1016/j.biosystems.2016.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/27/2016] [Accepted: 03/02/2016] [Indexed: 01/06/2023]
Abstract
Progress in cell type reprogramming has revived the interest in Waddington's concept of the epigenetic landscape. Recently researchers developed the quasi-potential theory to represent the Waddington's landscape. The Quasi-potential U(x), derived from interactions in the gene regulatory network (GRN) of a cell, quantifies the relative stability of network states, which determine the effort required for state transitions in a multi-stable dynamical system. However, quasi-potential landscapes, originally developed for continuous systems, are not suitable for discrete-valued networks which are important tools to study complex systems. In this paper, we provide a framework to quantify the landscape for discrete Boolean networks (BNs). We apply our framework to study pancreas cell differentiation where an ensemble of BN models is considered based on the structure of a minimal GRN for pancreas development. We impose biologically motivated structural constraints (corresponding to specific type of Boolean functions) and dynamical constraints (corresponding to stable attractor states) to limit the space of BN models for pancreas development. In addition, we enforce a novel functional constraint corresponding to the relative ordering of attractor states in BN models to restrict the space of BN models to the biological relevant class. We find that BNs with canalyzing/sign-compatible Boolean functions best capture the dynamics of pancreas cell differentiation. This framework can also determine the genes' influence on cell state transitions, and thus can facilitate the rational design of cell reprogramming protocols.
Collapse
Affiliation(s)
- Joseph Xu Zhou
- Institute for Systems Biology, Seattle, WA, USA; Kavli Institute for Theoretical Physics, UC Santa Barbara, CA, USA
| | - Areejit Samal
- Institute for Systems Biology, Seattle, WA, USA; The Institute of Mathematical Sciences, Chennai, India; The Abdus Salam International Centre for Theoretical Physics, Trieste, Italy
| | - Aymeric Fouquier d'Hérouël
- Institute for Systems Biology, Seattle, WA, USA; Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette, Luxembourg
| | | | - Sui Huang
- Institute for Systems Biology, Seattle, WA, USA.
| |
Collapse
|
24
|
Martinez-Sanchez ME, Mendoza L, Villarreal C, Alvarez-Buylla ER. A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity. PLoS Comput Biol 2015; 11:e1004324. [PMID: 26090929 PMCID: PMC4475012 DOI: 10.1371/journal.pcbi.1004324] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 05/07/2015] [Indexed: 12/24/2022] Open
Abstract
CD4+ T cells orchestrate the adaptive immune response in vertebrates. While both experimental and modeling work has been conducted to understand the molecular genetic mechanisms involved in CD4+ T cell responses and fate attainment, the dynamic role of intrinsic (produced by CD4+ T lymphocytes) versus extrinsic (produced by other cells) components remains unclear, and the mechanistic and dynamic understanding of the plastic responses of these cells remains incomplete. In this work, we studied a regulatory network for the core transcription factors involved in CD4+ T cell-fate attainment. We first show that this core is not sufficient to recover common CD4+ T phenotypes. We thus postulate a minimal Boolean regulatory network model derived from a larger and more comprehensive network that is based on experimental data. The minimal network integrates transcriptional regulation, signaling pathways and the micro-environment. This network model recovers reported configurations of most of the characterized cell types (Th0, Th1, Th2, Th17, Tfh, Th9, iTreg, and Foxp3-independent T regulatory cells). This transcriptional-signaling regulatory network is robust and recovers mutant configurations that have been reported experimentally. Additionally, this model recovers many of the plasticity patterns documented for different T CD4+ cell types, as summarized in a cell-fate map. We tested the effects of various micro-environments and transient perturbations on such transitions among CD4+ T cell types. Interestingly, most cell-fate transitions were induced by transient activations, with the opposite behavior associated with transient inhibitions. Finally, we used a novel methodology was used to establish that T-bet, TGF-β and suppressors of cytokine signaling proteins are keys to recovering observed CD4+ T cell plastic responses. In conclusion, the observed CD4+ T cell-types and transition patterns emerge from the feedback between the intrinsic or intracellular regulatory core and the micro-environment. We discuss the broader use of this approach for other plastic systems and possible therapeutic interventions.
Collapse
Affiliation(s)
- Mariana Esther Martinez-Sanchez
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, México Distrito Federal, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán, México Distrito Federal, México
| | - Luis Mendoza
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México Distrito Federal, México
| | - Carlos Villarreal
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán, México Distrito Federal, México
- Departamento de Física Teórica, Instituto de Física, Universidad Nacional Autónoma de México, México Distrito Federal, México
| | - Elena R. Alvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, México Distrito Federal, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán, México Distrito Federal, México
- * E-mail:
| |
Collapse
|
25
|
Davila-Velderrain J, Villarreal C, Alvarez-Buylla ER. Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates. BMC SYSTEMS BIOLOGY 2015; 9:20. [PMID: 25967891 PMCID: PMC4438470 DOI: 10.1186/s12918-015-0166-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/22/2015] [Indexed: 12/17/2022]
Abstract
BACKGROUND Gene regulatory network (GRN) dynamical models are standard systems biology tools for the mechanistic understanding of developmental processes and are enabling the formalization of the epigenetic landscape (EL) model. METHODS In this work we propose a modeling framework which integrates standard mathematical analyses to extend the simple GRN Boolean model in order to address questions regarding the impact of gene specific perturbations in cell-fate decisions during development. RESULTS We systematically tested the propensity of individual genes to produce qualitative changes to the EL induced by modification of gene characteristic decay rates reflecting the temporal dynamics of differentiation stimuli. By applying this approach to the flower specification GRN (FOS-GRN) we uncovered differences in the functional (dynamical) role of their genes. The observed dynamical behavior correlates with biological observables. We found a relationship between the propensity of undergoing attractor transitions between attraction basins in the EL and the direction of differentiation during early flower development - being less likely to induce up-stream attractor transitions as the course of development progresses. Our model also uncovered a potential mechanism at play during the transition from EL basins defining inflorescence meristem to those associated to flower organs meristem. Additionally, our analysis provided a mechanistic interpretation of the homeotic property of the ABC genes, being more likely to produce both an induced inter-attractor transition and to specify a novel attractor. Finally, we found that there is a close relationship between a gene's topological features and its propensity to produce attractor transitions. CONCLUSIONS The study of how the state-space associated with a dynamical model of a GRN can be restructured by modulation of genes' characteristic expression times is an important aid for understanding underlying mechanisms occurring during development. Our contribution offers a simple framework to approach such problem, as exemplified here by the case of flower development. Different GRN models and the effect of diverse inductive signals can be explored within the same framework. We speculate that the dynamical role of specific genes within a GRN, as uncovered here, might give information about which genes are more likely to link a module to other regulatory circuits and signaling transduction pathways.
Collapse
Affiliation(s)
- Jose Davila-Velderrain
- Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. Universitaria, México, 04510, D.F., México.
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Cd. Universitaria, México, 04510, D.F., México.
| | - Carlos Villarreal
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Cd. Universitaria, México, 04510, D.F., México.
- Instituto de Física, Universidad Nacional Autónoma de México, Cd. Universitaria, México, 04510, D.F., México.
| | - Elena R Alvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. Universitaria, México, 04510, D.F., México.
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Cd. Universitaria, México, 04510, D.F., México.
| |
Collapse
|
26
|
Pérez-Ruiz RV, García-Ponce B, Marsch-Martínez N, Ugartechea-Chirino Y, Villajuana-Bonequi M, de Folter S, Azpeitia E, Dávila-Velderrain J, Cruz-Sánchez D, Garay-Arroyo A, Sánchez MDLP, Estévez-Palmas JM, Álvarez-Buylla ER. XAANTAL2 (AGL14) Is an Important Component of the Complex Gene Regulatory Network that Underlies Arabidopsis Shoot Apical Meristem Transitions. MOLECULAR PLANT 2015; 8:796-813. [PMID: 25636918 DOI: 10.1016/j.molp.2015.01.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 12/10/2014] [Accepted: 01/05/2015] [Indexed: 05/21/2023]
Abstract
In Arabidopsis thaliana, multiple genes involved in shoot apical meristem (SAM) transitions have been characterized, but the mechanisms required for the dynamic attainment of vegetative, inflorescence, and floral meristem (VM, IM, FM) cell fates during SAM transitions are not well understood. Here we show that a MADS-box gene, XAANTAL2 (XAL2/AGL14), is necessary and sufficient to induce flowering, and its regulation is important in FM maintenance and determinacy. xal2 mutants are late flowering, particularly under short-day (SD) condition, while XAL2 overexpressing plants are early flowering, but their flowers have vegetative traits. Interestingly, inflorescences of the latter plants have higher expression levels of LFY, AP1, and TFL1 than wild-type plants. In addition we found that XAL2 is able to bind the TFL1 regulatory regions. On the other hand, the basipetal carpels of the 35S::XAL2 lines lose determinacy and maintain high levels of WUS expression under SD condition. To provide a mechanistic explanation for the complex roles of XAL2 in SAM transitions and the apparently paradoxical phenotypes of XAL2 and other MADS-box (SOC1, AGL24) overexpressors, we conducted dynamic gene regulatory network (GRN) and epigenetic landscape modeling. We uncovered a GRN module that underlies VM, IM, and FM gene configurations and transition patterns in wild-type plants as well as loss and gain of function lines characterized here and previously. Our approach thus provides a novel mechanistic framework for understanding the complex basis of SAM development.
Collapse
Affiliation(s)
- Rigoberto V Pérez-Ruiz
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Berenice García-Ponce
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico.
| | - Nayelli Marsch-Martínez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Yamel Ugartechea-Chirino
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Mitzi Villajuana-Bonequi
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Carretera Irapuato - León, AP 629, 36821 Irapuato, Guanajuato, Mexico
| | - Eugenio Azpeitia
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - José Dávila-Velderrain
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - David Cruz-Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Adriana Garay-Arroyo
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - María de la Paz Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Juan M Estévez-Palmas
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Elena R Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico; University of California, 431 Koshland Hall, Berkeley, CA 94720, USA.
| |
Collapse
|
27
|
Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER. Modeling the epigenetic attractors landscape: toward a post-genomic mechanistic understanding of development. Front Genet 2015; 6:160. [PMID: 25954305 PMCID: PMC4407578 DOI: 10.3389/fgene.2015.00160] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 04/08/2015] [Indexed: 12/18/2022] Open
Abstract
Robust temporal and spatial patterns of cell types emerge in the course of normal development in multicellular organisms. The onset of degenerative diseases may result from altered cell fate decisions that give rise to pathological phenotypes. Complex networks of genetic and non-genetic components underlie such normal and altered morphogenetic patterns. Here we focus on the networks of regulatory interactions involved in cell-fate decisions. Such networks modeled as dynamical non-linear systems attain particular stable configurations on gene activity that have been interpreted as cell-fate states. The network structure also restricts the most probable transition patterns among such states. The so-called Epigenetic Landscape (EL), originally proposed by C. H. Waddington, was an early attempt to conceptually explain the emergence of developmental choices as the result of intrinsic constraints (regulatory interactions) shaped during evolution. Thanks to the wealth of molecular genetic and genomic studies, we are now able to postulate gene regulatory networks (GRN) grounded on experimental data, and to derive EL models for specific cases. This, in turn, has motivated several mathematical and computational modeling approaches inspired by the EL concept, that may be useful tools to understand and predict cell-fate decisions and emerging patterns. In order to distinguish between the classical metaphorical EL proposal of Waddington, we refer to the Epigenetic Attractors Landscape (EAL), a proposal that is formally framed in the context of GRNs and dynamical systems theory. In this review we discuss recent EAL modeling strategies, their conceptual basis and their application in studying the emergence of both normal and pathological developmental processes. In addition, we discuss how model predictions can shed light into rational strategies for cell fate regulation, and we point to challenges ahead.
Collapse
Affiliation(s)
- Jose Davila-Velderrain
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de MéxicoMexico City, Mexico
| | - Juan C. Martinez-Garcia
- Departamento de Control Automático, Cinvestav-Instituto Politécnico NacionalMexico City, Mexico
| | - Elena R. Alvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de MéxicoMexico City, Mexico
| |
Collapse
|
28
|
Networks and Hierarchies: Approaching Complexity in Evolutionary Theory. INTERDISCIPLINARY EVOLUTION RESEARCH 2015. [DOI: 10.1007/978-3-319-15045-1_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
29
|
Benso A, Di Carlo S, Politano G, Savino A, Vasciaveo A. An extended gene protein/products Boolean network model including post-transcriptional regulation. Theor Biol Med Model 2014; 11 Suppl 1:S5. [PMID: 25080304 PMCID: PMC4108923 DOI: 10.1186/1742-4682-11-s1-s5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Networks Biology allows the study of complex interactions between biological systems using formal, well structured, and computationally friendly models. Several different network models can be created, depending on the type of interactions that need to be investigated. Gene Regulatory Networks (GRN) are an effective model commonly used to study the complex regulatory mechanisms of a cell. Unfortunately, given their intrinsic complexity and non discrete nature, the computational study of realistic-sized complex GRNs requires some abstractions. Boolean Networks (BNs), for example, are a reliable model that can be used to represent networks where the possible state of a node is a boolean value (0 or 1). Despite this strong simplification, BNs have been used to study both structural and dynamic properties of real as well as randomly generated GRNs. Results In this paper we show how it is possible to include the post-transcriptional regulation mechanism (a key process mediated by small non-coding RNA molecules like the miRNAs) into the BN model of a GRN. The enhanced BN model is implemented in a software toolkit (EBNT) that allows to analyze boolean GRNs from both a structural and a dynamic point of view. The open-source toolkit is compatible with available visualization tools like Cytoscape and allows to run detailed analysis of the network topology as well as of its attractors, trajectories, and state-space. In the paper, a small GRN built around the mTOR gene is used to demonstrate the main capabilities of the toolkit. Conclusions The extended model proposed in this paper opens new opportunities in the study of gene regulation. Several of the successful researches done with the support of BN to understand high-level characteristics of regulatory networks, can now be improved to better understand the role of post-transcriptional regulation for example as a network-wide noise-reduction or stabilization mechanisms.
Collapse
|
30
|
The topology of robustness and evolvability in evolutionary systems with genotype-phenotype map. J Theor Biol 2014; 356:144-62. [PMID: 24793533 DOI: 10.1016/j.jtbi.2014.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 03/26/2014] [Accepted: 04/14/2014] [Indexed: 11/21/2022]
Abstract
In this paper we formulate a topological definition of the concepts of robustness and evolvability. We start our investigation by formulating a multiscale model of the evolutionary dynamics of a population of cells. Our cells are characterised by a genotype-phenotype map: their chances of survival under selective pressure are determined by their phenotypes, whereas the latter are determined their genotypes. According to our multiscale dynamics, the population dynamics generates the evolution of a genotype-phenotype network. Our representation of the genotype-phenotype network is similar to previously described ones, but has a novel element, namely, our network contains two types of nodes: genotype and phenotype nodes. This network representation allows us to characterise robustness and evolvability in terms of its topological properties: phenotypic robustness by means of the clustering coefficient of the phenotype nodes, and evolvability as the emergence of giant connected component which allows navigation between phenotypes. This topological definition of evolvability allows us to characterise the so-called robustness of evolvability, which is defined in terms of the robustness against attack (i.e. edge removal) of the giant connected component. An investigation of the factors that affect the robustness of evolvability shows that phenotypic robustness and the cryptic genetic variation are key to the integrity of the ability to innovate. These results fit within the framework of a number of models which point out that robustness favours rather than hindering evolvability. We further show that the corresponding phenotype network, defined as the one-component projection of the whole genotype-phenotype network, exhibits the small-world phenomenon, which implies that in this type of evolutionary system the rate of adaptability is enhanced.
Collapse
|
31
|
Gao B, Li L, Peng H, Kurths J, Zhang W, Yang Y. Principle for performing attractor transits with single control in Boolean networks. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:062706. [PMID: 24483485 DOI: 10.1103/physreve.88.062706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 09/12/2013] [Indexed: 06/03/2023]
Abstract
We present an algebraic approach to reveal attractor transitions in Boolean networks under single control based on the recently developed matrix semitensor product theory. In this setting, the reachability of attractors is estimated by the state transition matrices. We then propose procedures that compute the shortest control sequence and the result of each step of input (control) exactly. The general derivation is exemplified by numerical simulations for two kinds of gene regulation networks, the protein-nucleic acid interactions network and the cAMP receptor of Dictyostelium discoideum network.
Collapse
Affiliation(s)
- Bo Gao
- School of Computer and Information Technology, Beijing Jiaotong University, Beijing 100044, China and Information Security Center, State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing 100876, China and School of Computer Information management, Inner Mongolia University of Finance and Economics, Hohhot 010051, China
| | - Lixiang Li
- Information Security Center, State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Haipeng Peng
- Information Security Center, State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Jürgen Kurths
- Potsdam Institute for Climate Impact Research, Potsdam D-14473, Germany
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yixian Yang
- School of Computer and Information Technology, Beijing Jiaotong University, Beijing 100044, China and Information Security Center, State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing 100876, China
| |
Collapse
|
32
|
Davila-Velderrain J, Servin-Marquez A, Alvarez-Buylla ER. Molecular evolution constraints in the floral organ specification gene regulatory network module across 18 angiosperm genomes. Mol Biol Evol 2013; 31:560-73. [PMID: 24273325 DOI: 10.1093/molbev/mst223] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The gene regulatory network of floral organ cell fate specification of Arabidopsis thaliana is a robust developmental regulatory module. Although such finding was proposed to explain the overall conservation of floral organ types and organization among angiosperms, it has not been confirmed that the network components are conserved at the molecular level among flowering plants. Using the genomic data that have accumulated, we address the conservation of the genes involved in this network and the forces that have shaped its evolution during the divergence of angiosperms. We recovered the network gene homologs for 18 species of flowering plants spanning nine families. We found that all the genes are highly conserved with no evidence of positive selection. We studied the sequence conservation features of the genes in the context of their known biological function and the strength of the purifying selection acting upon them in relation to their placement within the network. Our results suggest an association between protein length and sequence conservation, evolutionary rates, and functional category. On the other hand, we found no significant correlation between the strength of purifying selection and gene placement. Our results confirm that the studied robust developmental regulatory module has been subjected to strong functional constraints. However, unlike previous studies, our results do not support the notion that network topology plays a major role in constraining evolutionary rates. We speculate that the dynamical functional role of genes within the network and not just its connectivity could play an important role in constraining evolution.
Collapse
|
33
|
Wang G, Zhu X, Hood L, Ao P. From Phage lambda to human cancer: endogenous molecular-cellular network hypothesis. QUANTITATIVE BIOLOGY 2013. [DOI: 10.1007/s40484-013-0007-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|