| 1. |
- Jagers, Peter, 1941, et al.
(författare)
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Random variation and concentration effects in PCR
- 2003
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Ingår i: J. Theoret. Biol. 224, 299-304 (2003). - 0022-5193 .- 1095-8541. ; 224, s. 299-304
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Tidskriftsartikel (refereegranskat)abstract
- Even though the efficiency of the PCR reaction decreases, analyses are made in terms of Galton-Watson processes, or simple deterministic models with constant replication probability (efficiency).Recently Schnell and Mendoza have suggested that the form of the efficiency can be derived from enzyme kinetics. This results in the sequence of molecules numbers forming a stochastic process with the properties of a branching process with population size dependence, which is supercritical, but has a mean reproductionnumber that approaches one. Such processes display ultimate linear growth, after an initial exponential phase, as is the case in PCR. It is also shown that the resulting stochastic process for a large Michaelis Menten constant behaves like the deterministic sequence x_n arising by iterations of the function f(x) = x+x/(1+x).
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| 2. |
- Borodich, A, et al.
(författare)
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Segregation of the photosystems in higher plant thylakoids and short- and long-term regulation by a mesoscopic approach
- 2003
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Ingår i: Journal of Theoretical Biology. - 0022-5193 .- 1095-8541. ; 225:4, s. 431-441
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we consider the relationship between the lateral segregation of photosystems I and II in the grana and characteristics of the short- and long-term regulation in thylakoids following the mesoscopic approach. Our study is thermodynamic; it is based on the Flory-Huggins theory for binary mixtures and the McMillan-Mayer theory of heterogeneous solutions. We demonstrate that state transitions promote rearrangement of photosystems by either favoring their mixing after LHCII phosphorylation or enhancing their segregation after LHCII dephosphorylation. This regulation influences the entire system properties locally. We also demonstrate that the variations of the photosystem ratio promote rearrangement of the photosystems preserving their segregation. This regulation influences the entire system properties globally. The studies presented are another indication of the importance of the segregation of the photosystems in the grana thylakoids of higher plants. Segregation of PSIs and PSIIs is a signature of the spinodal decomposition, which is a fine regulatory mechanism, related to both the short- and long-term adaptations of the photosynthetic apparatus in higher plant thylakoids. (C) 2003 Elsevier Ltd. All rights reserved.
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| 3. |
- Granlund, Gösta H.
(författare)
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The Use of Distribution Functions to Describe Integrated Density Profiles of Human Chromosomes
- 1973
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 40:3, s. 573-589
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Tidskriftsartikel (refereegranskat)abstract
- The advent of new stains for chromosomes has increased the possibilities that useful automated chromosome analysis can be implemented. The search for appropriate descriptors to use in this process is an important task. Data compression using integrated intensity and density profiles has already shown itself to be valuable. A method is proposed in this paper to describe these profiles as a sum of distribution functions. Every distribution function can be described by a triplet stating peak height, position, and width and it appears that these parameters are directly related to physical processes. The importance of such parameters in statistical chromosome analysis is emphasized. A classification experiment is described in which 240 chromosomes 1 to 22, X and Y have been classified with an accuracy of 96%.
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| 4. |
- 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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| 5. |
- Aikio, S, et al.
(författare)
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Seed bank in annuals: Competition between banker and non-banker morphs
- 2002
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 217:3, s. 341-349
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Tidskriftsartikel (refereegranskat)abstract
- Seed bank is a plant life history strategy against the unpredictability of the biotic and the abiotic environment. We simulated competition between a seed banking and a non-banking morph of an annual plant. A constant fraction of the banker morph seeds was allocated to the seed bank, where they had a constant mortality and germination rate. All surviving seeds of the non-banker morph germinated in the next generation. The seedlings of both morphs experienced similar density-dependent mortality. Whether one of the morphs wins or the morphs coexist was evaluated from parameter space plots and statistically with logistic regression analysis. All parameters of the model had a significant, nonlinear effect on the persistence of the morphs, supporting our approach of numerically covering a wide range of parameter values. The seed production of a focal morph increased its survival and decreased the survival of the other morph. Otherwise, the morphs showed opposite response to changes in the model parameters. The banker morph was usually the winning strategy when it had a higher seed production than the non-banker morph. The banker morph benefitted from high germination probability, while the non-banker benefitted from high allocation to seed bank and high seed mortality. The coexistence of the morphs was inhibited by high banker morph seed production and seed mortality and promoted by high values of all other parameters. The system showed complex dynamics when banking was the winning strategy or the morphs coexisted. In addition, a part of the parameter space where the non-banker morph wins showed complex dynamics. Our results suggest that seed banking is a beneficial strategy if seed number is increased consequently, e.g. due to a decreased seed size. If banking decreases seed number, the non-banker morph wins or the two morphs coexist. (C) 2002 Elsevier Science Ltd. All rights reserved.
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| 6. |
- Alerstam, Thomas
(författare)
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Detours in bird migration
- 2001
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 209:3, s. 319-331
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Tidskriftsartikel (refereegranskat)abstract
- Bird migration routes often follow detours where passages across ecological barriers are reduced in extent. This occurs in spite of the fact that long barrier crossings are within the birds' potential flight range capacity. Long-distance flights are associated with extra energy costs for transport of the heavy fuel loads required. This paper explores how important the fuel transport costs, estimated on the basis of flight mechanics, map be to explain detours for birds migrating by flapping flight, Maximum detours in relation to expanse of the barrier are predicted for cases where birds travel along the detour by numerous short flights and small fuel reserves, divide the detour into a limited number of flight steps, and where a reduced barrier passage is included in the detour. The principles for determining the optimum route, often involving a shortcut across part of the barrier, are derived. Furthermore, the effects of differences in fuel deposition rates and in transport costs for the profitability of detours are briefly considered. An evaluation of a number of observed and potential detours in relation to the general predictions of maximum detours, indicates that reduction of fuel transport costs may well be a factor of widespread importance for the evolution of detours in bird migration at wide ecological barriers. (C) 2001 Academic Press.
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| 7. |
- Alerstam, Thomas
(författare)
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Flight by night or day? Optimal daily timing of bird migration.
- 2009
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 258:4, s. 530-536
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Tidskriftsartikel (refereegranskat)abstract
- Many migratory bird species fly mainly during the night (nocturnal migrants), others during daytime (diurnal migrants) and still others during both night and day. Need to forage during the day, atmospheric structure, predator avoidance and orientation conditions have been proposed as explanations for the widespread occurrence of nocturnal migration. However, the general principles that determine the basic nocturnal-diurnal variation in flight habits are poorly known. In the present study optimal timing of migratory flights, giving the minimum total duration of the migratory journey, is evaluated in a schematic way in relation to ecological conditions for energy gain in foraging and for energy costs in flight. There exists a strong and fundamental advantage of flying by night because foraging time is maximized and energy deposition can take place on days immediately after and prior to the nocturnal flights. The increase in migration speed by nocturnal compared with diurnal migration will be largest for birds with low flight costs and high energy deposition rates. Diurnal migration will be optimal if it is associated with efficient energy gain immediately after a migratory flight because suitable stopover/foraging places have been located during the flight or if energy losses during flight are substantially reduced by thermal soaring and/or by fly-and-forage migration. A strategy of combined diurnal and nocturnal migration may be optimal when birds migrate across regions with relatively poor conditions for energy deposition (not only severe but also soft barriers). Predictions about variable timing of migratory flights depending on changing foraging and environmental conditions along the migration route may be tested for individual birds by analysing satellite tracking results with respect to daily travel routines in different regions. Documenting and understanding the adaptive variability in daily travel schedules among migrating animals constitute a fascinating challenge for future research.
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| 8. |
- 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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| 9. |
- 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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| 10. |
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| 11. |
- 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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| 12. |
- Bach, Lars, et al.
(författare)
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The evolution of n-player cooperation—threshold games and ESS bifurcations
- 2006
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 238:2, s. 426-434
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Tidskriftsartikel (refereegranskat)abstract
- An evolutionary game of individuals cooperating to obtain a collective benefit is here modelled as an n-player Prisoner's Dilemma game. With reference to biological situations, such as group foraging, we introduce a threshold condition in the number of cooperators required to obtain the collective benefit. In the simplest version, a three-player game, complex behaviour appears as the replicator dynamics exhibits a catastrophic event separating a parameter region allowing for coexistence of cooperators and defectors and a region of pure defection. Cooperation emerges through an ESS bifurcation, and cooperators only thrive beyond a critical point in cost-benefit space. Moreover, a repelling fixed point of the dynamics acts as a barrier to the introduction of cooperation in defecting populations. The results illustrate the qualitative difference between two-player games and multiple player games and thus the limitations to the generality of conclusions from two-player games. We present a procedure to find the evolutionarily stable strategies in any n-player game with cost and benefit depending on the number of cooperators. This was previously done by Motro [1991. Co-operation and defection: playing the field and the ESS. J. Theor. Biol. 151, 145–154] in the special cases of convex and concave benefit functions and constant cost.
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| 13. |
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| 14. |
- 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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| 15. |
- 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
-
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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| 16. |
- 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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| 17. |
- 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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| 18. |
- 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
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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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| 19. |
- 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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| 20. |
- Bengtsson, Bengt Olle
(författare)
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Modelling the evolution of genomes with integrated external and internal functions
- 2004
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 231:2, s. 271-278
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Tidskriftsartikel (refereegranskat)abstract
- The genomes that organisms transmit between generations contain information about different kinds of functions. The genome with the "best" mix and number of genes for these functions is the one that natural selection favours. Here I introduce a new way to model simple organisms with genes for external and internal functions, and use it to study the evolution of genome size. The external functions are exemplified by resource use and the internal functions by mutation control (repair). It is shown that even with a suitable proportion of genes for mutation control, the genomes in the organisms do not forever incorporate genes that increase resource use. Instead they evolve towards an optimal genome of limited size. The optimal proportion of genes for mutation control is shown to have an upper limit given by the ease with which transmission accuracy is improved by adding extra genes for this purpose to the genome. The model illustrates how natural selection on genomes integrates systems for the transmission of genetic information with systems relating to the external adaptation of the organism. It also opens Lip for other, more detailed theoretical investigations of genome functions.
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| 21. |
- Bengtsson, Bengt Olle, et al.
(författare)
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The effective size of bryophyte populations.
- 2009
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 258:Available online 8 January 2009, s. 121-126
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Tidskriftsartikel (refereegranskat)abstract
- Bryophytes with their dominant haploid stage conform poorly to the life cycles generally treated in population genetical models. Here we make a detailed analysis of what effective sizes bryophyte model populations have as a function of their breeding system. It is found that the effective size is rarely much smaller than the scored number of haploid gametophytic individuals, even when the limited number of diploids (sporophytes) formed is taken into account. The most severe decrease in effective size occurs when unisexual gametophytic females produce only a small number of fertile diploid sporophytes in male biased populations; this effect is due to the restricted sampling of male gametophytic individuals that then occurs. It is shown that the harmonic mean of diploid sporophytes formed per haploid gametophytic individuals is the relevant measure in these calculations and not the standard (and generally larger) arithmetic mean.
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| 22. |
- Bengtsson, Göran, et al.
(författare)
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Irregular walks and loops combines in small-scale movement of a soil insect : implications for dispersal biology
- 2004
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 231:2, s. 299-306
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Tidskriftsartikel (refereegranskat)abstract
- Analysis of small-scale movement patterns of animals we may help to understand and predict movement at a larger scale, such as dispersal, which is a key parameter in spatial population dynamics. We have chosen to study the movement of a soil-dwelling Collembola, Protaphorura armata, in an experimental system consisting of a clay surface with or without physical obstacles. A combination of video recordings, descriptive statistics, and walking simulations was used to evaluate the movement pattern. Individuals were found to link periods of irregular walk with those of looping in ahomogeneous environment as well as in one structured to heterogeneity by physical obstacles. The number of loops varied between 0 and 44 per hour from one individual to another and some individuals preferred to make loops by turning right and others by turning left. P. armata spent less time at the boundary of small obstacles compared to large, presumably because of a lower probability to track the steepness of the curvature as the individual walks along a highly curved surface. Food deprived P. armata had amore winding movement and made more circular loops than those that were well fed. The observed looping behaviour is interpreted in the context of systematic search strategies and compared with similar movement patterns found in other species.
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| 23. |
- Bengtsson, Hans-Uno, et al.
(författare)
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A simple model for the arterial system
- 2003
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Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 1095-8541 .- 0022-5193. ; 221:3, s. 437-443
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Tidskriftsartikel (refereegranskat)abstract
- We present a simple model for the arterial part of the cardiovascular system, based on Poiseuille flow constrained by the power dissipated into the cells lining the vessels. This, together with the assumption of a volume-filling network, leads to correct predictions for the evolution of vessel radii, vessel lengths and blood pressure in the human arterial system. The model can also be used to find exponents for allometric scaling, and gives good agreement with data on mammals.
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| 24. |
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| 25. |
- Björklund, Mats
(författare)
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Optimal choice in a neural network
- 2002
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Ingår i: Journal of Theoretical Biology. - 0022-5193 .- 1095-8541. ; 218, s. 149-154
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Tidskriftsartikel (refereegranskat)
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