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Grigoryan EN, Markitantova YV. Tail and Spinal Cord Regeneration in Urodelean Amphibians. Life (Basel) 2024; 14:594. [PMID: 38792615 PMCID: PMC11122520 DOI: 10.3390/life14050594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/21/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Urodelean amphibians can regenerate the tail and the spinal cord (SC) and maintain this ability throughout their life. This clearly distinguishes these animals from mammals. The phenomenon of tail and SC regeneration is based on the capability of cells involved in regeneration to dedifferentiate, enter the cell cycle, and change their (or return to the pre-existing) phenotype during de novo organ formation. The second critical aspect of the successful tail and SC regeneration is the mutual molecular regulation by tissues, of which the SC and the apical wound epidermis are the leaders. Molecular regulatory systems include signaling pathways components, inflammatory factors, ECM molecules, ROS, hormones, neurotransmitters, HSPs, transcriptional and epigenetic factors, etc. The control, carried out by regulatory networks on the feedback principle, recruits the mechanisms used in embryogenesis and accompanies all stages of organ regeneration, from the moment of damage to the completion of morphogenesis and patterning of all its structures. The late regeneration stages and the effects of external factors on them have been poorly studied. A new model for addressing this issue is herein proposed. The data summarized in the review contribute to understanding a wide range of fundamentally important issues in the regenerative biology of tissues and organs in vertebrates including humans.
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Affiliation(s)
| | - Yuliya V. Markitantova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
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2
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Balagué N, Hristovski R, Almarcha M, Garcia-Retortillo S, Ivanov PC. Network Physiology of Exercise: Beyond Molecular and Omics Perspectives. SPORTS MEDICINE - OPEN 2022; 8:119. [PMID: 36138329 PMCID: PMC9500136 DOI: 10.1186/s40798-022-00512-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022]
Abstract
Molecular Exercise Physiology and Omics approaches represent an important step toward synthesis and integration, the original essence of Physiology. Despite the significant progress they have introduced in Exercise Physiology (EP), some of their theoretical and methodological assumptions are still limiting the understanding of the complexity of sport-related phenomena. Based on general principles of biological evolution and supported by complex network science, this paper aims to contrast theoretical and methodological aspects of molecular and network-based approaches to EP. After explaining the main EP challenges and why sport-related phenomena cannot be understood if reduced to the molecular level, the paper proposes some methodological research advances related to the type of studied variables and measures, the data acquisition techniques, the type of data analysis and the assumed relations among physiological levels. Inspired by Network Physiology, Network Physiology of Exercise provides a new paradigm and formalism to quantify cross-communication among diverse systems across levels and time scales to improve our understanding of exercise-related phenomena and opens new horizons for exercise testing in health and disease.
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3
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Xiao Z, Wang X, Hong L. Cellular reaction gene regulation network for swarm robots with pattern formation maneuvering control. Front Neurorobot 2022; 16:950572. [PMID: 36340329 PMCID: PMC9632853 DOI: 10.3389/fnbot.2022.950572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022] Open
Abstract
Self-organized pattern formation enables swarm robots to interact with local environments to self-organize into intricate structures generated by gene regulatory network (GRN) control methods without global knowledge. Previous studies have reported that it is challenging to maintain pattern formation stability during maneuvering in the environment due to local morphogenetic reaction rules. Motivated by the mechanism of the GRN in multi-cellular organisms, we propose a novel cellular reaction gene regulatory network (CR-GRN) for pattern formation maneuvering control. In CR-GRN, a cellular reaction network is creatively proposed to depict the robots, environment, virtual target pattern, and their interaction to generate emergent swarm behavior in multi-robot systems. A novel diffusion equation is proposed to simulate the process of morphogen diffusion among cells to ensure stable adaptive pattern generation. In addition, genes, proteins, and morphogens are used to define the internal and external states of cells and form a feedback regulation network. Simulation experiments are conducted to validate the proposed method. The results show that the CR-GRN can satisfy the requirements of turning curvature and maintain the robot's uniformity based on the proposed algorithm. This proves that robots using the CR-GRN can cooperate more effectively to cope in a complicated environment, and maintain a stable formation during maneuvering.
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4
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García CC. Bifurcations in a discontinuous Leslie-Gower model with harvesting and alternative food for predators and constant prey refuge at low density. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:14029-14055. [PMID: 36654078 DOI: 10.3934/mbe.2022653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Since environmental studies have shown that a constant quantity of prey become refuges from the predator at low densities and become accessible again for consumption when they reach a higher density, in this work we propose a discontinuous mathematical model, Lesli-Gower type, which describes the dynamics between prey and predators, interacting under the same environment, and whose predator functional response, of linear type, is altered by a refuge constant in the prey when below a critical value. Assuming that predators can be captured and have alternative food, the qualitative analysis of the proposed discontinuous model is performed by analyzing each of the vector fields that compose it, which serves as the basis for the calculation of the bifurcation curves of the discontinuous model, with respect to the threshold value of the prey and the harvest rate of predators. It is concluded that the perturbations of the parameters of the model leads either to the extinction of the predators or to a stabilization in the growth of both species, regardless of their initial conditions.
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Affiliation(s)
- Christian Cortés García
- Department of Mathematics, Universidad Carlos Ⅲ de Madrid, 30 University Avenue, Madrid, Spain
- Department of Systems Biology, Centro Nacional de Biotecnología, 3 Darwin Street, Madrid, Spain
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5
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Self-Organization of the Retina during Eye Development, Retinal Regeneration In Vivo, and in Retinal 3D Organoids In Vitro. Biomedicines 2022; 10:biomedicines10061458. [PMID: 35740479 PMCID: PMC9221005 DOI: 10.3390/biomedicines10061458] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/23/2022] Open
Abstract
Self-organization is a process that ensures histogenesis of the eye retina. This highly intricate phenomenon is not sufficiently studied due to its biological complexity and genetic heterogeneity. The review aims to summarize the existing central theories and ideas for a better understanding of retinal self-organization, as well as to address various practical problems of retinal biomedicine. The phenomenon of self-organization is discussed in the spatiotemporal context and illustrated by key findings during vertebrate retina development in vivo and retinal regeneration in amphibians in situ. Described also are histotypic 3D structures obtained from the disaggregated retinal progenitor cells of birds and retinal 3D organoids derived from the mouse and human pluripotent stem cells. The review highlights integral parts of retinal development in these conditions. On the cellular level, these include competence, differentiation, proliferation, apoptosis, cooperative movements, and migration. On the physical level, the focus is on the mechanical properties of cell- and cell layer-derived forces and on the molecular level on factors responsible for gene regulation, such as transcription factors, signaling molecules, and epigenetic changes. Finally, the self-organization phenomenon is discussed as a basis for the production of retinal organoids, a promising model for a wide range of basic scientific and medical applications.
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6
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Antonello PC, Varley TF, Beggs J, Porcionatto M, Sporns O, Faber J. Self-organization of in vitro neuronal assemblies drives to complex network topology. eLife 2022; 11:74921. [PMID: 35708741 PMCID: PMC9203058 DOI: 10.7554/elife.74921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 06/01/2022] [Indexed: 12/17/2022] Open
Abstract
Activity-dependent self-organization plays an important role in the formation of specific and stereotyped connectivity patterns in neural circuits. By combining neuronal cultures, and tools with approaches from network neuroscience and information theory, we can study how complex network topology emerges from local neuronal interactions. We constructed effective connectivity networks using a transfer entropy analysis of spike trains recorded from rat embryo dissociated hippocampal neuron cultures between 6 and 35 days in vitro to investigate how the topology evolves during maturation. The methodology for constructing the networks considered the synapse delay and addressed the influence of firing rate and population bursts as well as spurious effects on the inference of connections. We found that the number of links in the networks grew over the course of development, shifting from a segregated to a more integrated architecture. As part of this progression, three significant aspects of complex network topology emerged. In agreement with previous in silico and in vitro studies, a small-world architecture was detected, largely due to strong clustering among neurons. Additionally, the networks developed in a modular topology, with most modules comprising nearby neurons. Finally, highly active neurons acquired topological characteristics that made them important nodes to the network and integrators of modules. These findings leverage new insights into how neuronal effective network topology relates to neuronal assembly self-organization mechanisms.
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Affiliation(s)
- Priscila C Antonello
- Department of Biochemistry - Escola Paulista de Medicina - Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Thomas F Varley
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, United States.,Department of Informatics, Computing, and Engineering, Indiana University, Bloomington, United States
| | - John Beggs
- Department of Physics, Indiana University, Bloomington, United States
| | - Marimélia Porcionatto
- Department of Biochemistry - Escola Paulista de Medicina - Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Olaf Sporns
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, United States
| | - Jean Faber
- Department of Neurology and Neurosurgery - Escola Paulista de Medicina - Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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7
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8
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Mancinelli G, Galic M. Exploring the interdependence between self-organization and functional morphology in cellular systems. J Cell Sci 2020; 133:133/13/jcs242479. [PMID: 32620564 DOI: 10.1242/jcs.242479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All living matter is subject to continuous adaptation and functional optimization via natural selection. Consequentially, structures with close morphological resemblance repeatedly appear across the phylogenetic tree. How these designs emerge at the cellular level is not fully understood. Here, we explore core concepts of functional morphology and discuss its cause and consequences, with a specific focus on emerging properties of self-organizing systems as the potential driving force. We conclude with open questions and limitations that are present when studying shape-function interdependence in single cells and cellular ensembles.
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Affiliation(s)
- Gloria Mancinelli
- 'Cells in Motion' Interfaculty Centre, University of Muenster, 48149 Muenster, Germany.,Institute of Medical Physics and Biophysics, Medical Faculty, University of Muenster, 49149 Muenster, Germany.,CIM-IMRPS Graduate Program, 48149 Muenster, Germany
| | - Milos Galic
- 'Cells in Motion' Interfaculty Centre, University of Muenster, 48149 Muenster, Germany .,Institute of Medical Physics and Biophysics, Medical Faculty, University of Muenster, 49149 Muenster, Germany
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9
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Mondeel TDGA, Ivanov O, Westerhoff HV, Liebermeister W, Barberis M. Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs. NPJ Syst Biol Appl 2020; 6:8. [PMID: 32245958 PMCID: PMC7125140 DOI: 10.1038/s41540-020-0125-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/20/2020] [Indexed: 12/13/2022] Open
Abstract
Some biological networks exhibit oscillations in their components to convert stimuli to time-dependent responses. The eukaryotic cell cycle is such a case, being governed by waves of cyclin-dependent kinase (cyclin/Cdk) activities that rise and fall with specific timing and guarantee its timely occurrence. Disruption of cyclin/Cdk oscillations could result in dysfunction through reduced cell division. Therefore, it is of interest to capture properties of network designs that exhibit robust oscillations. Here we show that a minimal yeast cell cycle network is able to oscillate autonomously, and that cyclin/Cdk-mediated positive feedback loops (PFLs) and Clb3-centered regulations sustain cyclin/Cdk oscillations, in known and hypothetical network designs. We propose that Clb3-mediated coordination of cyclin/Cdk waves reconciles checkpoint and oscillatory cell cycle models. Considering the evolutionary conservation of the cyclin/Cdk network across eukaryotes, we hypothesize that functional ("healthy") phenotypes require the capacity to oscillate autonomously whereas dysfunctional (potentially "diseased") phenotypes may lack this capacity.
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Affiliation(s)
- Thierry D G A Mondeel
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK.,Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, UK.,Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Oleksandr Ivanov
- Theoretical Research in Evolutionary Life Sciences, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.,Systems, Control and Applied Analysis Group, Johan Bernoulli Institute for Mathematics and Computer Science, University of Groningen, Groningen, The Netherlands
| | - Hans V Westerhoff
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.,Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Wolfram Liebermeister
- Institute of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany.,Université Paris-Saclay, INRAE, MaIAGE, Jouy en Josas, France
| | - Matteo Barberis
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK. .,Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, UK. .,Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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10
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Metze K, Adam R, Florindo JB. The fractal dimension of chromatin - a potential molecular marker for carcinogenesis, tumor progression and prognosis. Expert Rev Mol Diagn 2019; 19:299-312. [DOI: 10.1080/14737159.2019.1597707] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Konradin Metze
- Department of Pathology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Randall Adam
- Department of Pathology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - João Batista Florindo
- Department of Applied Mathematics, Institute of Mathematics, Statistics and Scientific Computing, State University of Campinas, Campinas, Brazil
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11
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Nijhout HF, Best JA, Reed MC. Systems biology of robustness and homeostatic mechanisms. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1440. [DOI: 10.1002/wsbm.1440] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/30/2018] [Accepted: 09/21/2018] [Indexed: 12/30/2022]
Affiliation(s)
| | - Janet A. Best
- Department of Mathematics Ohio State University Columbus Ohio
| | - Michael C. Reed
- Department of Mathematics Duke University Durham North Carolina
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12
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Kruglova NN, Titova GE, Seldimirova OA. Callusogenesis as an in vitro Morphogenesis Pathway in Cereals. Russ J Dev Biol 2018. [DOI: 10.1134/s106236041805003x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Zhang W. A Supplement to Self-Organization Theory of Dreaming. Front Psychol 2016; 7:332. [PMID: 27014141 PMCID: PMC4782025 DOI: 10.3389/fpsyg.2016.00332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/22/2016] [Indexed: 12/04/2022] Open
Affiliation(s)
- Wei Zhang
- School of psychology, Nanjing Normal UniversityNanjing, China
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14
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Wang X, Hao M, Wang G. Numerical simulation of wrinkle morphology formation and the evolution of different Bacillus subtilis biofilms. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 73:527-534. [PMID: 26877034 DOI: 10.2166/wst.2015.486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Wrinkle morphology is a distinctive phenomenon observed in mature biofilms that are produced by a great number of bacteria. The wrinkle pattern depends on the mechanical properties of the agar substrate and the biofilm itself, governed by the extracellular matrix (ECM). Here we study the macroscopic structures and the evolution of Bacillus subtilis biofilm wrinkles using the commercial finite element software ABAQUS. A mechanical model and simulation are set up to analyze and evaluate bacteria biofilm's wrinkle characteristics. We uncover the wrinkle formation mechanism and enumerate the quantitative relationship between wrinkle structure and mechanical properties of biofilm and its substrate. Our work can be used to modify the wrinkle pattern and control the biofilm size.
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Affiliation(s)
- Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, China E-mail: ; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Mudong Hao
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, China E-mail:
| | - Guoqing Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, China E-mail:
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15
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Shin YJ, Mahrou B. Modeling collective & intelligent decision making of multi-cellular populations. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2015; 2014:334-7. [PMID: 25569965 DOI: 10.1109/embc.2014.6943597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In the presence of unpredictable disturbances and uncertainties, cells intelligently achieve their goals by sharing information via cell-cell communication and making collective decisions, which are more reliable compared to individual decisions. Inspired by adaptive sensor network algorithms studied in communication engineering, we propose that a multi-cellular adaptive network can convert unreliable decisions by individual cells into a more reliable cell-population decision. It is demonstrated using the effector T helper (a type of immune cell) population, which plays a critical role in initiating immune reactions in response to invading foreign agents (e.g., viruses, bacteria, etc.). While each individual cell follows a simple adaptation rule, it is the combined coordination among multiple cells that leads to the manifestation of "self-organizing" decision making via cell-cell communication.
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16
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Abstract
Fractal characteristics of chromatin, revealed by light or electron microscopy, have been reported during the last 20 years. Fractal features can easily be estimated in digitalized microscopic images and are helpful for diagnosis and prognosis of neoplasias. During carcinogenesis and tumor progression, an increase of the fractal dimension (FD) of stained nuclei has been shown in intraepithelial lesions of the uterine cervix and the anus, oral squamous cell carcinomas or adenocarcinomas of the pancreas. Furthermore, an increased FD of chromatin is an unfavorable prognostic factor in squamous cell carcinomas of the oral cavity and the larynx, melanomas and multiple myelomas. High goodness-of-fit of the regression line of the FD is a favorable prognostic factor in acute leukemias and multiple myelomas. The nucleus has fractal and power-law organization in several different levels, which might in part be interrelated. Some possible relations between modifications of the chromatin organization during carcinogenesis and tumor progression and an increase of the FD of stained chromatin are suggested. Furthermore, increased complexity of the chromatin structure, loss of heterochromatin and a less-perfect self-organization of the nucleus in aggressive neoplasias are discussed.
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Affiliation(s)
- Konradin Metze
- Department of Pathology, Faculty of Medical Sciences Research Group, 'Analytical Cellular Pathology' and National Institute of Photonics Applied to Cell Biology, University of Campinas, Campinas, Brazil +55 19 32893897 kmetze.at.fcm.unicamp.br
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17
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Isaeva VV, Kasyanov NV, Presnov EV. Topological singularities and symmetry breaking in development. Biosystems 2012; 109:280-98. [PMID: 22609746 DOI: 10.1016/j.biosystems.2012.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 05/10/2012] [Accepted: 05/10/2012] [Indexed: 11/18/2022]
Abstract
The review presents a topological interpretation of some morphogenetic events through the use of well-known mathematical concepts and theorems. Spatial organization of the biological fields is analyzable in topological terms. Topological singularities inevitably emerging in biological morphogenesis are retained and transformed during pattern formation. It is the topological language that can provide strict and adequate description of various phenomena in developmental and evolutionary transformations. The relationship between local and global orders in metazoan development, i.e., between local morphogenetic processes and integral developmental patterns, is established. A topological inevitability of some developmental events through the use of classical topological concepts is discussed. This methodology reveals a topological imperative as a certain set of topological rules that constrains and directs embryogenesis. A breaking of spatial symmetry of preexisting pattern plays a critical role in biological morphogenesis in development and evolution.
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Affiliation(s)
- Valeria V Isaeva
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Science, 119071 Moscow, Russia.
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