| 1. |
- Agliari, Elena, et al.
(författare)
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Anergy in self-directed B lymphocytes : A statistical mechanics perspective
- 2013
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Ingår i: Journal of Theoretical Biology. - : Elsevier. - 0022-5193 .- 1095-8541. ; 375, s. 21-31
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Tidskriftsartikel (refereegranskat)abstract
- Self-directed lymphocytes may evade clonal deletion at ontogenesis but still remain harmless due to a mechanism called clonal anergy. For B-lymphocytes, two major explanations for anergy developed over the last decades: according to Varela theory, anergy stems from a proper orchestration of the whole B-repertoire, such that self-reactive clones, due to intensive feed-back from other clones, display strong inertia when mounting a response. Conversely, according to the model of cognate response, self-reacting cells are not stimulated by helper lymphocytes and the absence of such signaling yields anergy. Through statistical mechanics we show that helpers do not prompt activation of a sub-group of B-cells: remarkably, the latter are just those broadly interacting in the idiotypic network. Hence Varela theory can finally be reabsorbed into the prevailing framework of the cognate response model. Further, we show how the B-repertoire architecture may emerge, where highly connected clones are self-directed as a natural consequence of ontogenetic learning.
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| 2. |
- Alger, Ingela, et al.
(författare)
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A generalization of Hamilton's rule-Love others how much?
- 2012
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 299, s. 42-54
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Tidskriftsartikel (refereegranskat)abstract
- According to Hamilton's (1964a, b) rule, a costly action will be undertaken if its fitness cost to the actor falls short of the discounted benefit to the recipient, where the discount factor is Wright's index of relatedness between the two. We propose a generalization of this rule, and show that if evolution operates at the level of behavior rules, rather than directly at the level of actions, evolution will select behavior rules that induce a degree of cooperation that may differ from that predicted by Hamilton's rule as applied to actions. In social dilemmas there will be less (more) cooperation than under Hamilton's rule if the actions are strategic substitutes (complements). Our approach is based on natural selection, defined in terms of personal (direct) fitness, and applies to a wide range of pairwise interactions.
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| 3. |
- Ali, Qasim, 1986, et al.
(författare)
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Adaptive damage retention mechanism enables healthier yeast population
- 2019
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 473, s. 52-66
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Tidskriftsartikel (refereegranskat)abstract
- During cytokinesis in budding yeast (Saccharomyces cerevisiae) damaged proteins are distributed asymmetrically between the daughter and the mother cell. Retention of damaged proteins is a crucial mechanism ensuring a healthy daughter cell with full replicative potential and an ageing mother cell. However, the protein quality control (PQC) system is tuned for optimal reproduction success which suggests optimal health and size of the population, rather than long-term survival of the mother cell. Modelling retention of damage as an adaptable mechanism, we propose two damage retention strategies to find an optimal way of decreasing damage retention efficiency to maximize population size and minimize the damage in the individual yeast cell. A pedigree model is used to investigate the impact of small variations in the strategies over the whole population. These impacts are based on the altruistic effects of damage retention mechanism and are measured by a cost function whose minimum value provides the optimal health and size of the population. We showed that fluctuations in the cost function allow yeast cell to continuously vary its strategy, suggesting that optimal reproduction success is a local minimum of the cost function. Our results suggest that a rapid decrease in the efficiency of damage retention, at the time when the mother cell is almost exhausted, produces fewer daughters with high levels of damaged proteins. In addition, retaining more damage during the early divisions increases the number of healthy daughters in the population. (C) 2019 Elsevier Ltd. All rights reserved.
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| 4. |
- Angus-Dunne, Sarah J., et al.
(författare)
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The Dissociation Constants of Diprotonated Chalcogenobispyridines : Transmission of Electronic Effects Across Chalcogen Bridges
- 2011
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Ingår i: Journal of Heterocyclic Chemistry. - : Wiley. - 0022-152X .- 1943-5193. ; 48:4, s. 868-871
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Tidskriftsartikel (refereegranskat)abstract
- The dissociation constants of the diprotonated chalcogenobispyridines have been determined using potentiometric titrations to establish a method for the measurement of the ability of a bridging ligand to relay electronic effects. The relationship between pK(a) and structure of the chalcogenobispyridines results from a balance between inductive, mesomeric, and steric effects. Delocalization of cationic charge onto the bridgehead increases the apparent electronegativity of the bridging atom, thereby relaying a strong base-weakening effect to the site of first deprotonation. Such delocalization was found to be a function of both the substitution site (4-X > 2-X >> 3-X) and orbital overlap requirements (S > O approximate to Se > Te).
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| 5. |
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| 6. |
- Asano, Masanari, et al.
(författare)
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Quantum-like model of diauxie in Escherichia coli : operational description of precultivation effect
- 2012
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 314, s. 130-137
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we apply the quantum-like (QL) approach to microbiology to present an operational description of the complex process of diauxie in Escherichia coil. We take as guaranteed that dynamics in cells is adaptive, i.e., it depends crucially on the microbiological context. This very general assumption is sufficient to appeal to quantum and more general QL probabilistic models. The next step is to find the operational representation - by operators in complex Hilbert space (as in quantum physics). To determine QL operators, we used the statistical data from Inada et al. (1996). To improve the QL-representation, we needed better experimental data. Corresponding experiments were recently done by two of the authors and in this paper we use these new data. In these data we found that biochemical context of precultivation of populations of E. coli plays a crucial role in E. coli preferences with respect to sugars. Hence, the form of the QL operator representing lactose operon activation also depends crucially on precultivation. One of our results is decomposition of the lactose operon activation operator to extract the factor determined by precultivation. The QL operational approach developed in this paper can be used not only for description of the process of diauxie in E. coli, but also other processes of gene expression. However, new experimental statistical data are demanded. (C) 2012 Elsevier Ltd. All rights reserved.
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| 7. |
- Bartoszek, Krzysztof, et al.
(författare)
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A consistent estimator of the evolutionary rate
- 2015
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 371, s. 69-78
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Tidskriftsartikel (refereegranskat)abstract
- We consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate 2, conditioned on the observed number of particles to be equal to n. Particles are assumed to move independently on the real line according to the Brownian motion with the local variance sigma(2). In this paper we treat n particles as a sample of related species. The spatial Brownian motion of a particle describes the development of a trait value of interest (e.g. log-body-size). We propose an unbiased estimator 4 of the evolutionary rate rho(2) - sigma(2)/lambda. The estimator R-n(2) is proportional to the sample variance S-n(2) computed from n trait values. We find an approximate formula for the standard error of R-n(2), based on a neat asymptotic relation for the variance of S-n(2). (C) 2015 Elsevier Ltd. All rights reserved.
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| 8. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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A consistent estimator of the evolutionary rate
- 2015
-
Ingår i: Journal of Theoretical Biology. - 0022-5193 .- 1095-8541. ; 371, s. 69-78
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Tidskriftsartikel (refereegranskat)abstract
- We consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate λ, conditioned on the observed number of particles to be equal to n. Particles are assumed to move independently on the real line according to the Brownian motion with the local variance σ2. In this paper we treat n particles as a sample of related species. The spatial Brownian motion of a particle describes the development of a trait value of interest (e.g. log-body-size). We propose an unbiased estimator Rn2 of the evolutionary rate ρ2=σ2/λ. The estimator Rn2 is proportional to the sample variance Sn2 computed from n trait values. We find an approximate formula for the standard error of Rn2 based on a neat asymptotic relation for the variance of Sn2.
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| 9. |
- Bartoszek, Krzysztof, 1984, et al.
(författare)
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A phylogenetic comparative method for studying multivariate adaptation
- 2012
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 314, s. 204-215
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic comparative methods have been limited in the way they model adaptation. Although some progress has been made, there are still no methods that can fully account for coadaptation between traits. Based on Ornstein–Uhlenbeck (OU) models of adaptive evolution, we present a method, with R implementation, in which multiple traits evolve both in response to each other and, as in previous OU models, to fixed or randomly evolving predictor variables. We present the interpretation of the model parameters in terms of evolutionary and optimal regressions enabling the study of allometric and adaptive relationships between traits. To illustrate the method we reanalyze a data set of antler and body-size evolution in deer (Cervidae).
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| 10. |
- Bartoszek, Krzysztof, 1984-
(författare)
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Phylogenetic effective sample size
- 2016
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 407, s. 371-386
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Tidskriftsartikel (refereegranskat)abstract
- In this paper I address the question—how large is a phylogenetic sample? I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein-Uhlenbeck processes-the regression effective sample size. I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AICc is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations.
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| 11. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Time to a single hybridization event in a group of species with unknown ancestral history
- 2013
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 322, s. 1-6
-
Tidskriftsartikel (refereegranskat)abstract
- We consider a stochastic process for the generation of species which combines a Yule process with a simple model for hybridization between pairs of co-existent species. We assume that the origin of the process, when there was one species, occurred at an unknown time in the past, and we condition the process on producing n species via the Yule process and a single hybridization event. We prove results about the distribution of the time of the hybridization event. In particular we calculate a formula for all moments, and show that under various conditions, the distribution tends to an exponential with rate twice that of the birth rate for the Yule process.
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| 12. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations
- 2017
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 429, s. 35-45
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Tidskriftsartikel (refereegranskat)abstract
- The Ornstein-Uhlenbeck (OU) process plays a major role in the analysis of the evolution of phenotypic traits along phylogenies. The standard OU process includes random perturbations and stabilizing selection and assumes that species evolve independently. However, evolving species may interact through various ecological process and also exchange genes especially in plants. This is particularly true if we want to study phenotypic evolution among diverging populations within species. In this work we present a straightforward statistical approach with analytical solutions that allows for the inclusion of adaptation and migration in a common phylogenetic framework, which can also be useful for studying local adaptation among populations within the same species. We furthermore present a detailed simulation study that clearly indicates the adverse effects of ignoring migration. Similarity between species due to migration could be misinterpreted as very strong convergent evolution without proper correction for these additional dependencies. Finally, we show that our model can be interpreted in terms of ecological interactions between species, providing a general framework for the evolution of traits between "interacting" species or populations.
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| 13. |
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| 14. |
- Björn, Lars Olof, et al.
(författare)
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Ecological importance of the thermal emissivity of avian eggshells
- 2012
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 301, s. 62-66
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Tidskriftsartikel (refereegranskat)abstract
- Breeding birds have to divide their time between egg incubation and foraging. Particularly in cases when only one parent incubates the eggs, and especially in cold climates, the cooling of the eggs during absence from the nest may be problematic. In the present study we find that the thermal emissivity of eggshells may be ecologically important, and that an evolutionary pressure towards lower emissivity for exposed eggs in cold climates exists. We plan to experimentally compare emissivities among species in a future study. (C) 2012 Elsevier Ltd. All rights reserved.
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| 15. |
- Brush, Eleanor, et al.
(författare)
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Indirect reciprocity with negative assortment and limited information can promote cooperation
- 2018
-
Ingår i: Journal of Theoretical Biology. - : Elsevier. - 0022-5193 .- 1095-8541. ; 443, s. 56-65
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Tidskriftsartikel (refereegranskat)abstract
- Cooperation is ubiquitous in biological and social systems, even though cooperative behavior is often costly and at risk of exploitation by non-cooperators. Several studies have demonstrated that indirect reciprocity, whereby some members of a group observe the behaviors of their peers and use this information to discriminate against previously uncooperative agents in the future, can promote prosocial behavior. Some studies have shown that differential propensities of interacting among and between different types of agents (interaction assortment) can increase the effectiveness of indirect reciprocity. No previous studies have, however, considered differential propensities of observing the behaviors of different types of agents (information assortment). Furthermore, most previous studies have assumed that discriminators possess perfect information about others and incur no costs for gathering and storing this information. Here, we (1) consider both interaction assortment and information assortment, (2) assume discriminators have limited information about others, and (3) introduce a cost for information gathering and storage, in order to understand how the ability of discriminators to stabilize cooperation is affected by these steps toward increased realism. We report the following findings. First, cooperation can persist when agents preferentially interact with agents of other types or when discriminators preferentially observe other discriminators, even when they have limited information. Second, contrary to intuition, increasing the amount of information available to discriminators can exacerbate defection. Third, introducing costs of gathering and storing information makes it more difficult for discriminators to stabilize cooperation. Our study is one of only a few studies to date that show how negative interaction assortment can promote cooperation and broadens the set of circumstances in which it is know that cooperation can be maintained.
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| 16. |
- Calleja-Rodriguez, Ainhoa, et al.
(författare)
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Analysis of phenotypic- and Estimated Breeding Values (EBV) to dissect the genetic architecture of complex traits in a Scots pine three-generation pedigree design
- 2019
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 462, s. 283-292
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Tidskriftsartikel (refereegranskat)abstract
- In forest tree breeding, family-based Quantitative Trait Loci (QTL) studies are valuable as methods to dissect the complexity of a trait and as a source of candidate genes. In the field of conifer research, our study contributes to the evaluation of phenotypic and predicted breeding values for the identification of QTL linked to complex traits in a three-generation pedigree population in Scots pine (Pinus sylvestris L.). A total of 11 470 open pollinated F-2-progeny trees established at three different locations, were measured for growth and adaptive traits. Breeding values were predicted for their 360 mothers, originating from a single cross of two grand-parents. A multilevel LASSO association analysis was conducted to detect QTL using genotypes of the mothers with the corresponding phenotypes and Estimated Breeding Values (EBV). Different levels of genotype-by-environment (G x E) effects among sites at different years, were detected for survival and height. Moderate-to-low narrow sense heritabilities and EBV accuracies were found for all traits and all sites. We identified 18 AFLPs and 12 SNPs to be associated with QTL for one or more traits. 62 QTL were significant with percentages of variance explained ranging from 1.7 to 18.9%. In those cases where the same marker was associated to a phenotypic or an ebvQTL, the ebvQTL always explained higher proportion of the variance, maybe due to the more accurate nature of Estimated Breeding Values (EBV). Two SNP-QTL showed pleiotropic effects for traits related with hardiness, seed, cone and flower production. Furthermore, we detected several QTL with significant effects across multiple ages, which could be considered as strong candidate loci for early selection. The lack of reproducibility of some QTL detected across sites may be due to environmental heterogeneity reflected by the genotype- and QTL-by-environment effects. (C) 2018 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license.
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| 17. |
- Cortés, Andrés J., 1989
(författare)
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On how role versatility boosts an STI
- 2018
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193. ; 440, s. 66-69
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 18. |
- de Borst, Karin, et al.
(författare)
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Structure-€“function relationships in hardwood : Insight from micromechanical modelling
- 2014
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 345, s. 78-91
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Tidskriftsartikel (refereegranskat)abstract
- Abstract A micromechanical model is presented that predicts the stiffness of wood tissues in their three principal anatomical directions, across various hardwood species. The wood polymers cellulose, hemicellulose, and lignin, common to all wood tissues, serve as the starting point. In seven homogenisation steps, the stiffnesses of these polymers are linked to the macroscopic stiffness. The good agreement of model predictions and corresponding experimental data for ten different European and tropical species confirms the functionality and accuracy of the model. The model enables investigating the influence of individual microstructural features on the overall stiffness. This is exploited to elucidate the mechanical effects of vessels and ray cells. Vessels are shown to reduce the stiffness of wood at constant overall density. This supports that a trade-off exists between the hydraulic efficiency and the mechanical support in relation to the anatomical design of wood. Ray cells are shown to act as reinforcing elements in the radial direction.
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| 19. |
- Diehl, Stefan, et al.
(författare)
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A one-dimensional moving-boundary model for tubulin-driven axonal growth.
- 2014
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 358:Online 21 June 2014, s. 194-207
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Tidskriftsartikel (refereegranskat)abstract
- A one-dimensional continuum-mechanical model of axonal elongation due to assembly of tubulin dimers in the growth cone is presented. The conservation of mass leads to a coupled system of three differential equations. A partial differential equation models the dynamic and the spatial behaviour of the concentration of tubulin that is transported along the axon from the soma to the growth cone. Two ordinary differential equations describe the time-variation of the concentration of free tubulin in the growth cone and the speed of elongation. All steady-state solutions of the model are categorized. Given a set of the biological parameter values, it is shown how one easily can infer whether there exist zero, one or two steady-state solutions and directly determine the possible steady-state lengths of the axon. Explicit expressions are given for each stationary concentration distribution. It is thereby easy to examine the influence of each biological parameter on a steady state. Numerical simulations indicate that when there exist two steady states, the one with shorter axon length is unstable and the longer is stable. Another result is that, for nominal parameter values extracted from the literature, in a large portion of a fully grown axon the concentration of free tubulin is lower than both concentrations in the soma and in the growth cone.
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| 20. |
- Ehn, Micael, et al.
(författare)
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Adaptive strategies for cumulative cultural learning
- 2012
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 301, s. 103-111
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Tidskriftsartikel (refereegranskat)abstract
- The demographic and ecological success of our species is frequently attributed to our capacity for cumulative culture. However, it is not yet known how humans combine social and asocial learning to generate effective strategies for learning in a cumulative cultural context. Here we explore how cumulative culture influences the relative merits of various pure and conditional learning strategies, including pure asocial and social learning, critical social learning, conditional social learning and individual refiner strategies. We replicate the Rogers' paradox in the cumulative setting. However, our analysis suggests that strategies that resolved Rogers' paradox in a non-cumulative setting may not necessarily evolve in a cumulative setting, thus different strategies will optimize cumulative and non-cumulative cultural learning.
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| 21. |
- Ellingsen, Tore, et al.
(författare)
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The evolution of parental investment: re-examining the anisogamy argument.
- 2012
-
Ingår i: Journal of Theoretical Biology. - : Elsevier. - 0022-5193. ; 299, s. 113-119
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Tidskriftsartikel (refereegranskat)abstract
- In most animals with internal fertilization, the early costs of parenting by necessity falls on the female, whereas male and female investments are closer substitutes later on. After Dawkins and Carlisle's (1976) critique of Trivers' (1972) anisogamy argument, the conventional wisdom has been that early investment costs as such are irrelevant for the allocation of subsequent parental investment. However, in a stylized evolutionary model with recurrent mutations, we show that if only one parent bears early costs, then the other parent should bear a substantial fraction of later costs. The result implies that the conventional wisdom has shaky logical foundations and that we have yet to understand the interaction between anisogamy and non-gamete parental investment.
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| 22. |
- Fagerlind, Magnus G., et al.
(författare)
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Dynamic modelling of cell death during biofilm development
- 2012
-
Ingår i: Journal of Theoretical Biology. - : Academic Press. - 0022-5193 .- 1095-8541. ; 295, s. 23-36
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Tidskriftsartikel (refereegranskat)abstract
- Biofilms are currently recognised as the predominant bacterial life-style and it has been suggested that biofilm development is influenced by a number of different processes such as adhesion, detachment, mass transport, quorum sensing, cell death and active dispersal. One of the least understood processes and its effects on biofilm development is cell death. However, experimental studies suggest that bacterial death is an important process during biofilm development and many studies show a relationship between cell death and dispersal in microbial biofilms. We present a model of the process of cell death during biofilm development, with a particular focus on the spatial localisation of cell death or cell damage. Three rules governing cell death or cell damage were evaluated which compared the effects of starvation, damage accumulation, and viability during biofilm development and were also used to design laboratory based experiments to test the model. Results from model simulations show that actively growing biofilms develop steep nutrient gradients within the interior of the biofilm that affect neighbouring microcolonies resulting in cell death and detachment. Two of the rules indicated that high substrate concentrations lead to accelerated cell death, in contrast to the third rule, based on the accumulation of damage, which predicted earlier cell death for biofilms grown with low substrate concentrations. Comparison of the modelling results with experimental results suggests that cell death is favoured under low nutrient conditions and that the accumulation of damage may be the main cause of cell death during biofilm development. (C) 2011 Elsevier Ltd. All rights reserved.
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| 23. |
- Fallqvist, Björn, 1985-, et al.
(författare)
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Constitutive modelling of composite biopolymer networks
- 2016
-
Ingår i: Journal of Theoretical Biology. - : Elsevier. - 0022-5193 .- 1095-8541. ; 395, s. 51-61
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Tidskriftsartikel (refereegranskat)abstract
- The mechanical behaviour of biopolymer networks is to a large extent determined at a microstructural level where the characteristics of individual filaments and the interactions between them determine the response at a macroscopic level. Phenomena such as viscoelasticity and strain-hardening followed by strain-softening are observed experimentally in these networks, often due to microstructural changes (such as filament sliding, rupture and cross-link debonding). Further, composite structures can also be formed with vastly different mechanical properties as compared to the indivudal networks. In this present paper, we present a constitutive model presented in a continuum framework aimed at capturing these effects. Special care is taken to formulate thermodynamically consistent evolution laws for dissipative effects. This model, incorporating possible anisotropic network properties, is based on a strain energy function, split into an isochoric and a volumetric part. Generalisation to three dimensions is performed by numerical integration over the unit sphere. Model predictions indicate that the constitutive model is well able to predict the elastic and viscoelastic response of biological networks, and to an extent also composite structures.
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| 24. |
- Fallqvist, B., et al.
(författare)
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Modelling of cross-linked actin networks : influence of network parameters and cross-link compliance
- 2014
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 350, s. 57-69
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Tidskriftsartikel (refereegranskat)abstract
- A major structural component of the cell is the actin cytoskeleton, in which actin subunits are polymerised into actin filaments. These networks can be cross-linked by various types of ABPs (Actin Binding Proteins), such as Filamin A. In this paper, the passive response of cross-linked actin filament networks is evaluated, by use of a numerical and continuum network model. For the numerical model, the influence of filament length, statistical dispersion, cross-link compliance (including that representative of Filamin A) and boundary conditions on the mechanical response is evaluated and compared to experimental results. It is found that the introduction of statistical dispersion of filament lengths has a significant influence on the computed results, reducing the network stiffness by several orders of magnitude. Actin networks have previously been shown to have a characteristic transition from an initial bending-dominated to a stretching-dominated regime at larger strains, and the cross-link compliance is shown to shift this transition. The continuum network model, a modified eight-chain polymer model, is evaluated and shown to predict experimental results reasonably well, although a single set of parameters cannot be found to predict the characteristic dependence of filament length for different types of cross-links. Given the vast diversity of cross-linking proteins, the dependence of mechanical response on cross-link compliance signifies the importance of incorporating it properly in models to understand the roles of different types of actin networks and their respective tasks in the cell.
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| 25. |
- Fallqvist, Björn, et al.
(författare)
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Modelling of cross-linked actin networks - Influence of geometrical parameters and cross-link compliance
- 2014
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 350, s. 57-69
-
Tidskriftsartikel (refereegranskat)abstract
- A major structural component of the cell is the actin cytoskeleton, in which actin subunits are polymerised into actin filaments. These networks can be cross-linked by various types of ABPs (Actin Binding Proteins), such as Filamin A. In this paper, the passive response of cross-linked actin filament networks is evaluated, by use of a numerical and continuum network model. For the numerical model, the influence of filament length, statistical dispersion, cross-link compliance (including that representative of Filamin A) and boundary conditions on the mechanical response is evaluated and compared to experimental results. It is found that the introduction of statistical dispersion of filament lengths has a significant influence on the computed results, reducing the network stiffness by several orders of magnitude. Actin networks have previously been shown to have a characteristic transition from an initial bending-dominated to a stretching-dominated regime at larger strains, and the cross-link compliance is shown to shift this transition. The continuum network model, a modified eight-chain polymer model, is evaluated and shown to predict experimental results reasonably well, although a single set of parameters cannot be found to predict the characteristic dependence of filament length for different types of cross-links. Given the vast diversity of cross-linking proteins, the dependence of mechanical response on cross-link compliance signifies the importance of incorporating it properly in models to understand the roles of different types of actin networks and their respective tasks in the cell.
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| 26. |
- Foster, David V., et al.
(författare)
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Dynamic landscapes : A model of context and contingency in evolution
- 2013
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 334, s. 162-172
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Tidskriftsartikel (refereegranskat)abstract
- Although the basic mechanics of evolution have been understood since Darwin, debate continues over whether macroevolutionary phenomena are driven by the fitness structure of genotype space or by ecological interaction. In this paper we propose a simple model capturing key features of fitness-landscape and ecological models of evolution. Our model describes evolutionary dynamics in a high-dimensional, structured genotype space with interspecies interaction. We find promising qualitative similarity with the empirical facts about macroevolution, including broadly distributed extinction sizes and realistic exploration of the genotype space. The abstraction of our model permits numerous applications beyond macroevolution, including protein and RNA evolution.
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| 27. |
- Ghachem, Montasser
(författare)
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The institution as a blunt instrument : Cooperation through imperfect observability
- 2016
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 396, s. 182-190
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Tidskriftsartikel (refereegranskat)abstract
- Observing others enables us to indirectly reciprocate their actions. In large societies, however, reliable individual observation is hard to achieve. Societies therefore rely on institutions to aid in observing cooperative behaviour and identifying those who cooperated. Institutions are integral part of modern societies. Here, we propose an evolutionary model in which an institution aims to label cooperators with a tag to verify their trustworthiness, as is the case for financial credit ratings or quality certificates. However, errors in assigning tags inevitably arise: the institution may accidentally leave some cooperators untagged or award tags to some defectors. Taking these two specific types of errors into account, we derive simple analytical conditions under which cooperation becomes stable and is favoured by selection. We find that these two institutional errors are not weighted equally in promoting cooperation: it is more detrimental to cooperation if tags are erroneously awarded to defectors than if they are mistakenly withheld from cooperators. Institutional tagging can lead to non-uniform interaction rates among cooperators and defectors, whereby cooperators benefit disproportionally by playing more games than defectors. This work sheds light on the significant role of institutions in promoting and maintaining societal cooperation.
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| 28. |
- Harding, Karin C., 1968, et al.
(författare)
-
Increased migration in host–pathogen metapopulations can cause host extinction
- 2012
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 298, s. 1-7
-
Tidskriftsartikel (refereegranskat)abstract
- There are at least two potentially counteracting effects of migration in host–pathogen metapopulations. On the one hand increased migration leads to increased colonization of empty habitats by healthy hosts; on the other hand migrants can carry infectious diseases to susceptible populations. Earlier metapopulation models have found that the beneficial effects of increasing migration (reduced infection) are likely to dominate, and a general recommendation for managers of endangered metapopulations has been to increase connectivity between habitat patches. We extend the model framework to simultaneously allow for (1) Allee effects in host colonization rate, (2) spillover of pathogens from a second host species, and (3) differential colonization success by infected and healthy hosts. We find that the dynamics of a host–pathogen system can be highly sensitive to increased migration rates. Allee effects make host populations vulnerable to spillover of pathogens from other hosts, and metapopulation extinction can emerge from seemingly stable situations of endemic coexistence. Increasing connectivity in endangered metapopulations can be a risky management action unless the details of the biology of the host–pathogen system are known.
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| 29. |
- Harish, Ajith, et al.
(författare)
-
Mitochondria are not captive bacteria
- 2017
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 434, s. 88-98
-
Tidskriftsartikel (refereegranskat)abstract
- Lynn Sagan's conjecture (1967) that three of the fundamental organelles observed in eukaryote cells, specifically mitochondria, plastids and flagella were once free-living primitive (prokaryotic) cells was accepted after considerable opposition. Even though the idea was swiftly refuted for the specific case of origins of flagella in eukaryotes, the symbiosis model in general was accepted for decades as a realistic hypothesis to describe the endosymbiotic origins of eukaryotes. However, a systematic analysis of the origins of the mitochondrial proteome based on empirical genome evolution models now indicates that 97% of modern mitochondrial protein domains as well their homologues in bacteria and archaea were present in the universal common ancestor (UCA) of the modern tree of life (ToL). These protein domains are universal modular building blocks of modern genes and genomes, each of which is identified by a unique tertiary structure and a specific biochemical function as well as a characteristic sequence profile. Further, phylogeny reconstructed from genome-scale evolution models reveals that Eukaryotes and Akaryotes (archaea and bacteria) descend independently from UCA. That is to say, Eukaryotes and Akaryotes are both primordial lineages that evolved in parallel. Finally, there is no indication of massive inter-lineage exchange of coding sequences during the descent of the two lineages. Accordingly, we suggest that the evolution of the mitochondrial proteome was autogenic (endogenic) and not endosymbiotic (exogenic).
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| 30. |
- Hartvig, Martin, et al.
(författare)
-
Food web framework for size-structured populations.
- 2011
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 272:1, s. 113-122
-
Tidskriftsartikel (refereegranskat)abstract
- We synthesise traditional unstructured food webs, allometric body size scaling, trait-based modelling, and physiologically structured modelling to provide a novel and ecologically relevant tool for size-structured food webs. The framework allows food web models to include ontogenetic growth and life-history omnivory at the individual level by resolving the population structure of each species as a size-spectrum. Each species is characterised by the trait 'size at maturation', and all model parameters are made species independent through scaling with individual body size and size at maturation. Parameter values are determined from cross-species analysis of fish communities as life-history omnivory is widespread in aquatic systems, but may be reparameterised for other systems. An ensemble of food webs is generated and the resulting communities are analysed at four levels of organisation: community level, species level, trait level, and individual level. The model may be solved analytically by assuming that the community spectrum follows a power law. The analytical solution provides a baseline expectation of the results of complex food web simulations, and agrees well with the predictions of the full model on (1) biomass distribution as a function of individual size, (2) biomass distribution as a function of size at maturation, and (3) relation between predator-prey mass ratio of preferred and eaten food. The full model additionally predicts the diversity distribution as a function of size at maturation.
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| 31. |
- Hauzy, Céline, et al.
(författare)
-
Density-dependent dispersal and relative dispersal affect the stability of predator-prey metacommunities
- 2010
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 266:3, s. 458-469
-
Tidskriftsartikel (refereegranskat)abstract
- Although density-dependent dispersal and relative dispersal (the difference in dispersal rates between species) have been documented in natural systems, their effects on the stability of metacommunities are poorly understood. Here we investigate the effects of intra- and interspecific density-dependent dispersal on the regional stability in a predator-prey metacommunity model. We show that, when the dynamics of the populations reach equilibrium, the stability of the metacommunity is not affected by density-dependent dispersal. However, the regional stability, measured as the regional variability or the persistence, can be modified by density-dependent dispersal when local populations fluctuate over time. Moreover these effects depend on the relative dispersal of the predator and the prey. Regional stability is modified through changes in spatial synchrony. Interspecific density-dependent dispersal always desynchronizses local dynamics, whereas intraspecific density-dependent dispersal may either synchronize or desynchronize it depending on dispersal rates. Moreover, intra- and interspecific density-dependent dispersal strengthen the top-down control of the prey by the predator at intermediate dispersal rates. As a consequence the regional stability of the metacommunity is increased at intermediate dispersal rates. Our results show that density-dependent dispersal and relative dispersal of species are keys to understanding the response of ecosystems to fragmentation.
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| 32. |
- Höhna, Sebastian
(författare)
-
The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events
- 2015
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 380, s. 321-331
-
Tidskriftsartikel (refereegranskat)abstract
- The homogeneous reconstructed evolutionary process is a birth-death process without observed extinct lineages. Each species evolves independently with the same diversification rate-speciation rate, lambda(t), and extinction rate, mu(t)-that may change over time. The process is commonly applied to model species diversification where the data are reconstructed phylogenies, e.g. trees estimated from present-day molecular data, and used to infer diversification rates. In the present paper I develop the general probability density of a reconstructed tree under any homogeneous, time-dependent birth-death process. I demonstrate how to adapt this probability density when conditioning on the survival of one or two initial lineages, or on the process realizing n species, and also how to transform between the probability density of a reconstructed tree and the probability density of the speciation times. I demonstrate the use of the general time-dependent probability density functions by deriving the probability density of a reconstructed tree under a birth-death-shift model with explicit mass-extinction events. I extend these functions to several special cases, including the pure-birth process, the pure-death process, the birth-death process, and the critical-branching process. Thus, I specify equations for the most commonly used birth-death models in a unified framework (e.g. same condition and same data) using a common notation.
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| 33. |
- Hössjer, Ola, et al.
(författare)
-
A monoecious and diploid Moran model of random mating
- 2016
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 394, s. 182-196
-
Tidskriftsartikel (refereegranskat)abstract
- An exact Markov chain is developed for a Moran model of random mating for monoecious diploid individuals with a given probability of self-fertilization. The model captures the dynamics of genetic variation at a biallelic locus. We compare the model with the corresponding diploid Wright-Fisher (WF) model. We also develop a novel diffusion approximation of both models, where the genotype frequency distribution dynamics is described by two partial differential equations, on different time scales. The first equation captures the more slowly varying allele frequencies, and it is the same for the Moran and WF models. The other equation captures departures of the fraction of heterozygous genotypes from a large population equilibrium curve that equals Hardy-Weinberg proportions in the absence of selfing. It is the distribution of a continuous time Ornstein-Uhlenbeck process for the Moran model and a discrete time autoregressive process for the WF model. One application of our results is to capture dynamics of the degree of non-random mating of both models, in terms of the fixation index f(IS). Although f(IS) has a stable fixed point that only depends on the degree of selfing, the normally distributed oscillations around this fixed point are stochastically larger for the Moran than for the WF model.
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| 34. |
- Jansson, Fredrik
(författare)
-
What games support the evolution of an ingroup bias?
- 2015
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 373, s. 100-110
-
Tidskriftsartikel (refereegranskat)abstract
- There is an increasing wealth of models trying to explain the evolution of group discrimination and an ingroup bias. This paper sets out to systematically investigate the most fundamental assumption in these models: in what kind of situations do the interactions take place? What strategic structures - games - support the evolution of an ingroup bias? More specifically, the aim here is to find the prerequisites for when a bias also with respect to minimal groups - arbitrarily defined groups void of group-specific qualities - is selected for, and which cannot be ascribed to kin selection.Through analyses and simulations of minimal models of two-person games, this paper indicates that only some games are conducive to the evolution of ingroup favouritism. In particular, this class does not contain the prisoners׳ dilemma, but it does contain anti-co-ordination and co-ordination games. Contrasting to the prisoners׳ dilemma, these are games where it is not a matter of whether to behave altruistically, but rather one of predicting what the other person will be doing, and where I would benefit from you knowing my intentions.In anti-co-ordination games, on average, not only will agents discriminate between groups, but also in such a way that their choices maximise the sum of the available payoffs towards the ingroup more often than towards the outgroup. And in co-ordination games, even if agents do manage to co-ordinate with the whole population, they are more likely to co-ordinate on the socially optimal equilibrium within their group. Simulations show that this occurs most often in games where there is a component of risk-taking, and thus trust, involved. A typical such game is the stag hunt or assurance game.
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| 35. |
- Jaworski, Jacek, et al.
(författare)
-
Sources of breathing pattern variability in the respiratory feedback control loop
- 2019
-
Ingår i: Journal of Theoretical Biology. - : Academic Press. - 0022-5193 .- 1095-8541. ; 469, s. 148-162
-
Tidskriftsartikel (refereegranskat)abstract
- The variability of the breath-to-breath breathing pattern, and its alterations in disease, may hold information of physiologic and/or diagnostic value. We hypothesized that this variability arises from the way that noise is processed within the respiratory feedback control loop, and that pathologic alterations to specific components within the system give rise to characteristic alterations in breathing pattern variability. We explored this hypothesis using a computational model of the respiratory control system that integrates mechanical factors, gas exchange processes, and chemoreceptor signals to simulate breathing patterns subject to the influences of random variability in each of the system components. We found that the greatest changes in the coefficient of variation (CV) of both breathing amplitude and timing were caused by increases in lung resistance and impairments in gas exchange, both common features of pulmonary disease. This suggests that breathing pattern variability may reflect discernible deterministic processes involved in the control of breathing. © 2019 Elsevier Ltd
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| 36. |
- Johansson, Anders, et al.
(författare)
-
Tuning positive feedback for signal detection in noisy dynamic environments
- 2012
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 309, s. 88-95
-
Tidskriftsartikel (refereegranskat)abstract
- Learning from previous actions is a key feature of decision-making. Diverse biological systems, from neuronal assemblies to insect societies, use a combination of positive feedback and forgetting of stored memories to process and respond to input signals. Here we look how these systems deal with a dynamic two-armed bandit problem of detecting a very weak signal in the presence of a high degree of noise. We show that by tuning the form of positive feedback and the decay rate to appropriate values, a single tracking variable can effectively detect dynamic inputs even in the presence of a large degree of noise. In particular, we show that when tuned appropriately a simple positive feedback algorithm is Fisher efficient, in that it can track changes in a signal on a time of order L(h)= (vertical bar h vertical bar/sigma)(-2), where vertical bar h vertical bar is the magnitude of the signal and sigma the magnitude of the noise.
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| 37. |
- Jonsson, Micael
(författare)
-
A solution to the accelerated-predator-satiety Lotka-Volterra predator-prey problem using Boubaker polynomial expansion scheme
- 2010
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 264, s. 154-160
-
Tidskriftsartikel (refereegranskat)abstract
- In this study, an analytical method is introduced for the identification of predator-prey populations time-dependent evolution in a Lotka-Volterra predator-prey model which takes into account the concept of accelerated-predator-satiety.Oppositely to most of the predator-prey problem models, the actual model does not suppose that the predation is strictly proportional to the prey density. In reference to some recent experimental results and particularly to the conclusions of May (1973) about predators which are 'never not hungry', an accelerated satiety function is matched with the initial conventional equations. Solutions are plotted and compared to some relevant ones. The obtained trends are in good agreement with many standard Lotka-Volterra solutions except for the asymptotic behaviour. (C) 2010 Elsevier Ltd. All rights reserved.
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| 38. |
- Khaji, Erfan, et al.
(författare)
-
3D protein structure prediction using Imperialist Competitive algorithm and half sphere exposure prediction
- 2016
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193. ; 391, s. 81-87
-
Tidskriftsartikel (refereegranskat)abstract
- Predicting the native structure of proteins based on half-sphere exposure and contact numbers has been studied deeply within recent years. Online predictors of these vectors and secondary structures of amino acids sequences have made it possible to design a function for the folding process. By choosing variant structures and directs for each secondary structure, a random conformation can be generated, and a potential function can then be assigned. Minimizing the potential function utilizing meta-heuristic algorithms is the final step of finding the native structure of a given amino acid sequence. In this work, Imperialist Competitive algorithm was used in order to accelerate the process of minimization. Moreover, we applied an adaptive procedure to apply revolutionary changes. Finally, we considered a more accurate tool for prediction of secondary structure. The results of the computational experiments on standard benchmark show the superiority of the new algorithm over the previous methods with similar potential function. © 2015 Elsevier Ltd.
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| 39. |
- Khayyeri, Hanifeh, et al.
(författare)
-
Primary cilia mechanics affects cell mechanosensation: A computational study.
- 2015
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 379, s. 38-46
-
Tidskriftsartikel (refereegranskat)abstract
- Primary cilia (PC) are mechanical cell structures linked to the cytoskeleton and are central to how cells sense biomechanical signals from their environment. However, it is unclear exactly how PC mechanics influences cell mechanosensation. In this study we investigate how the PC mechanical characteristics are involved in the mechanotransduction process whereby cilium deflection under fluid flow induces strains on the internal cell components that regulate the cell׳s mechanosensitive response. Our investigation employs a computational approach in which a finite element model of a cell consisting of a nucleus, cytoplasm, cortex, microtubules, actin bundles and a primary cilium was used together with a finite element representation of a flow chamber. Fluid-structure interaction analysis was performed by simulating perfusion flow of 1mm/s on the cell model. Simulations of cells with different PC mechanical characteristics, showed that the length and the stiffness of PC are responsible for the transmission of mechanical stimuli to the cytoskeleton. Fluid flow deflects the cilium, with the highest strains found at the base of the PC and in the cytoplasm. The PC deflection created further strains on the cell nucleus but did not influence microtubules and actin bundles significantly. Our results indicate that PC deflection under fluid flow stimulation transmits mechanical strain primarily to other essential organelles in the cytoplasm, such as the Golgi complex, that regulate cells' mechanoresponse. The simulations further suggest that cell mechanosensitivity can be altered by targeting PC length and rigidity.
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| 40. |
|
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| 41. |
- Konkoli, Zoran, 1966
(författare)
-
Modelling reaction noise with a desired accuracy by using the X level Approach Reaction Noise Estimator (XARNES) method
- 2012
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 305, s. 1-14
-
Tidskriftsartikel (refereegranskat)abstract
- A novel computational framework for modeling reaction noise characteristics has been suggested. The method can be classified as a moment closure method. The approach is based on the concept of correlation forms which are used for describing spatially extended many body problems where particle numbers change in space and time. In here, it was shown how the formalism of spatially extended correlation forms can be adapted to study well mixed reaction systems. Stochastic fluctuations in particle numbers are described by selectively capturing correlation effects up to the desired order, X. The method is referred to as the X-level Approximation Reaction Noise Estimator method (XARNES). For example, X=1 implies the mean field theory (first order effects), the X=2 case corresponds to the previously developed PARNES method (pair effects), etc. The main idea is that inclusion of higher order correlation effects should lead to better (more accurate) results. Three models were used to test the method, two versions of a simple complex formation model, and the Michaelis-Menten model of enzymatic kinetics. It was explicitly demonstrated that increase in X indeed improves accuracy. The approach has been implemented as automatic software using the Mathematica programming language.The user only needs to input reaction rates, stoichiometry coefficients, and the desired level of computation X.
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| 42. |
- Konkoli, Zoran, 1966
(författare)
-
Multiparticle reaction noise characteristics
- 2011
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 271:1, s. 78-86
-
Tidskriftsartikel (refereegranskat)abstract
- A simple multiparticle reaction model was studied where reactants A react with (a possibly large) stoichiometric coefficient k. Each reaction forms a product molecule P, and every product molecule can be split into k A particles through the back reaction. To study the fluctuations in particle numbers a novel approach has been developed; to be referred to as the Pair approach based Reaction Noise EStimator (PARNES) method. The PARNES method is based on the full Kirkwood superposition approximation implemented at the pair level. Kirkwood's method has been adapted to study stochastic properties of an arbitrary reaction network in a perfectly mixed reaction volume. PARNES works well for large particle numbers. It provides qualitative description when particle numbers are low. The PARNES method can easily augment mean field calculations. Extension of the method beyond the pair approach level is straightforward. Both stationary and non-stationary properties of the model were investigated, and the findings of this work point to two possible scenarios of intracellular noise control. When k is increased, the fluctuations in the number of product molecules become smaller (sub-Poissonian) in a stationary state, and relaxation to a stationary state becomes faster.
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| 43. |
- Konkoli, Zoran, 1966
(författare)
-
Spontaneous noise reduction in a strongly cooperative reaction model
- 2011
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 285:1, s. 96-102
-
Tidskriftsartikel (refereegranskat)abstract
- Noise characteristics of a simple multiparticle reaction model were investigated. The model can describe strongly cooperative reactions and is defined as follows. Particles A react in clusters of size k and each reaction forms a product molecule P. The back reaction is also allowed, and each cluster can dissociate into k reactants A. To describe a situation where the reaction is part of a pathway, the system is made open by assuming that particles A are injected and that particles P decay. This is a continuation study. The model is studied by using the same technique as employed previously, the pair approach reaction noise estimator (PARNES) method. Several new issues have been addressed. (i) In the previous work closeness to the Poisson distribution was used as a noise measure. In this work a more traditional noise measure, the ratio of the variance and the mean, was used to analyze stochastic features of the problem. (ii) The dependence of the new noise measure on k has been analyzed in detail, with an emphasis of investigating reactions with large k values. (iii) The previous study focused on understanding time-dependent issues, while this study focuses on describing the equilibrium state of the system. (iv) An exact solution (published elsewhere), available for closed system only, was used to re-investigate the validity of the PARNES method for describing reactions with large k. It was found that the PARNES method cannot describe fine details of the noise characteristics of such reactions.
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| 44. |
- Kroon, Martin
(författare)
-
Influence of dispersion in myosin filament orientation and anisotropic filament contractions in smooth muscle
- 2011
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 272:1, s. 72-82
-
Tidskriftsartikel (refereegranskat)abstract
- A new constitutive model for the biomechanical behaviour of smooth muscle tissue is proposed. The active muscle contraction is accomplished by the relative sliding between actin and myosin filaments, comprising contractile units in the smooth muscle cells. The orientation of the myosin filaments, and thereby the contractile units, are taken to exhibit a statistical dispersion around a preferred direction. The number of activated cross-bridges between the actin and myosin filaments governs the contractile force generated by the muscle and also the contraction speed. A strain-energy function is used to describe the mechanical behaviour of the smooth muscle tissue. Besides the active contractile apparatus, the mechanical model also incorporates a passive elastic part. The constitutive model was compared to histological and isometric tensile test results for smooth muscle tissue from swine carotid artery. In order to be able to predict the active stress at different muscle lengths, a filament dispersion significantly larger than the one observed experimentally was required. Furthermore, a comparison of the predicted active stress fora case of uniaxially oriented myosin filaments and a case of filaments with a dispersion based on the experimental histological data shows that the difference in generated stress is noticeable but limited. Thus, the results suggest that myosin filament dispersion alone cannot explain the increase in active muscle stress with increasing muscle stretch.
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| 45. |
- Kroon, Martin
(författare)
-
On the correlation between continuum mechanics entities and cell activity in biological soft tissues : Assessment of three possible criteria for cell-controlled fibre reorientation in collagen gels and collagenous tissues
- 2010
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 264:1, s. 66-76
-
Tidskriftsartikel (refereegranskat)abstract
- The biomechanical behaviour of biological cells is of great importance in many physiological processes. One such process is the maintenance of fibrous networks, such as collagenous tissues. The activity of the fibre-producing cells in this type of tissue is very important, and a comprehensive material description needs to incorporate the activity of the cells. In biomechanics, continuum mechanics is often employed to describe deforming solids, and modelling can be much simplified if continuum mechanics entities, such as stress and strain, can be correlated with cell activity. To investigate this, a continuum mechanics framework is employed in which remodelling of a collagen gel is modelled. The remodelling is accomplished by fibroblasts, and the activity of the fibroblasts is linked to the continuum mechanics theory. The constitutive model for the collagen fabric is formulated in terms of a strain energy function, which includes a density function describing the distribution of the collagen fibre orientation. This density function evolves according to an evolution law, where fibroblasts reorient fibres towards the direction of increasing Cauchy stress, elastic deformation, or stiffness. The theoretical framework is applied to experimental results from collagen gels, where gels have undergone remodelling under both biaxial and uniaxial constraint. The analyses indicated that criteria 1 and 2 (Cauchy stress and elastic deformations) are able to predict the collagen fibre distribution after remodelling, whereas criterion 3 (current stiffness) is not. This conclusion is, however, tentative and pertains, strictly speaking, only to fibre remodelling processes, and may not be valid for other types of cell activities.
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| 46. |
- Larson, Karen, et al.
(författare)
-
Data-driven selection and parameter estimation for DNA methylation mathematical models
- 2019
-
Ingår i: Journal of Theoretical Biology. - : Elsevier. - 0022-5193 .- 1095-8541. ; 467, s. 87-99
-
Tidskriftsartikel (refereegranskat)abstract
- Epigenetics is coming to the fore as a key process which underpins health. In particular emerging experimental evidence has associated alterations to DNA methylation status with healthspan and aging. Mammalian DNA methylation status is maintained by an intricate array of biochemical and molecular processes. It can be argued changes to these fundamental cellular processes ultimately drive the formation of aberrant DNA methylation patterns, which are a hallmark of diseases, such as cancer, Alzheimer’s disease and cardiovascular disease. In recent years mathematical models have been used as effective tools to help advance our understanding of the dynamics which underpin DNA methylation. In this paper we present linear and nonlinear models which encapsulate the dynamics of the molecular mechanisms which define DNA methylation. Applying a recently developed Bayesian algorithm for parameter estimation and model selection, we are able to estimate distributions of parameters which include nominal parameter values. Using limited noisy observations, the method also identified which methylation model the observations originated from, signaling that our method has practical applications in identifying what models best match the biological data for DNA methylation.
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| 47. |
- Larsson, Jan-Åke, et al.
(författare)
-
Modelling cell lineage using a meta-Boolean tree model with a relation to gene regulatory networks
- 2011
-
Ingår i: Journal of Theoretical Biology. - Amsterdam : Elsevier. - 0022-5193 .- 1095-8541. ; 268:1, s. 62-76
-
Tidskriftsartikel (refereegranskat)abstract
- A cell lineage is the ancestral relationship between a group of cells that originate from a single founder cell. For example, in the embryo of the nematode Caenorhabditis elegans an invariant cell lineage has been traced, and with this information at hand it is possible to theoretically model the emergence of different cell types in the lineage, starting from the single fertilized egg. In this report we outline a modelling technique for cell lineage trees, which can be used for the C. elegans embryonic cell lineage but also extended to other lineages. The model takes into account both cell-intrinsic (transcription factor-based) and -extrinsic (extracellular) factors as well as synergies within and between these two types of factors. The model can faithfully recapitulate the entire C. elegans cell lineage, but is also general, i.e., it can be applied to describe any cell lineage. We show that synergy between factors, as well as the use of extrinsic factors, drastically reduce the number of regulatory factors needed for recapitulating the lineage. The model gives indications regarding co-variation of factors, number of involved genes and where in the cell lineage tree that asymmetry might be controlled by external influence. Furthermore, the model is able to emulate other (Boolean, discrete and differential-equation-based) models. As an example, we show that the model can be translated to the language of a previous linear sigmoid-limited concentration-based model (Geard and Wiles, 2005). This means that this latter model also can exhibit synergy effects, and also that the cumbersome iterative technique for parameter estimation previously used is no longer needed. In conclusion, the proposed model is general and simple to use, can be mapped onto other models to extend and simplify their use, and can also be used to indicate where synergy and external influence would reduce the complexity of the regulatory process.
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| 48. |
- Leimar, Olof, et al.
(författare)
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Limiting similarity, species packing, and the shape of competition kernels
- 2013
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 339, s. 3-13
-
Tidskriftsartikel (refereegranskat)abstract
- A traditional question in community ecology is whether species' traits are distributed as more-or-less regularly spaced clusters. Interspecific competition has been suggested to play a role in such structuring of communities. The seminal theoretical work on limiting similarity and species packing, presented four decades ago by Robert MacArthur, Richard Levins and Robert May, has recently been extended. There is now a deeper understanding of how competitive interactions influence community structure, for instance, how the shape of competition kernels can determine the clustering of species' traits. Competition is typically weaker for greater phenotypic difference, and the shape of the dependence defines a competition kernel. The clustering tendencies of kernels interact with other effects, such as variation in resource availability along a niche axis, but the kernel shape can have a decisive influence on community structure. Here we review and further extend the recent developments and evaluate their importance.
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| 49. |
- Lundberg, Per
(författare)
-
On the evolutionary stability of partial migration.
- 2013
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 321, s. 36-39
-
Tidskriftsartikel (refereegranskat)abstract
- The evolution of partial migration in birds is typically assumed to be the result of an optimization process. The fitness rewards for individuals choosing to migrate are balanced against the rewards of remaining in the breeding area all year around. This balancing is often thought to result in an evolutionarily stable strategy (ESS) such that an optimal fraction of the population becomes migratory through adaptive evolution. Here I show that this solution can indeed be reached through adaptive evolution, but that the equilibrium is a neutral or "weak" ESS. The equilibrium fraction of migrants is more reminiscent of the Fisherian sex ratio. I also show that this individual-based evolutionary solution may deviate significantly from the optimal solution for the population (maximum population size), quite in line with previous findings. Finally, I show that partial migration is very unlikely without density- or frequency-dependent selection.
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| 50. |
- Ma, Qi, et al.
(författare)
-
A first principles derivation of animal group size distributions
- 2011
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 283:1, s. 35-43
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Tidskriftsartikel (refereegranskat)abstract
- Several empirical studies have shown that the animal group size distribution of many species can be well fit by power laws with exponential truncation. A striking empirical result due to Niwa is that the exponent in these power laws is one and the truncation is determined by the average group size experienced by an individual. This distribution is known as the logarithmic distribution. In this paper we provide first principles derivation of the logarithmic distribution and other truncated power laws using a site-based merge and split framework. In particular, we investigate two such models. Firstly, we look at a model in which groups merge whenever they meet but split with a constant probability per time step. This generates a distribution similar, but not identical to the logarithmic distribution. Secondly, we propose a model, based on preferential attachment, that produces the logarithmic distribution exactly. Our derivation helps explain why logarithmic distributions are so widely observed in nature. The derivation also allows us to link splitting and joining behavior to the exponent and truncation parameters in power laws.
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