| 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. |
- Lundberg, Sigfrid, et al.
(författare)
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Intra-specific competition in the sex communication channel : a selective force in the evolution of moth pheromones?
- 1987
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Ingår i: Journal of Theoretical Biology. - 0022-5193. ; 125:1, s. 15-24
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Tidskriftsartikel (refereegranskat)abstract
- A model for mate competition in moths sexually signalling with pheromones is presented. The model has four variables. N is the number of individuals of each sex per area unit. r is the length of the female odour plume as detected by a responding male. ε is a parameter increasing with male ability to discriminate between concentrations. r-ε becomes the competitive part of the female pheromone plume, i.e. the distance at which an upwind female is able to distract males from downwind plumes. Assuming a random distribution of males and females the number of matings in a generation can be calculated. Introducing a fourth parameter, B = surviving offspring of each sex from a mating, the population dynamics of the population can be described. Two special cases are analysed; (1) ε = r, and (2) ε = 0. In case (1) mating success increases with population density towards unity. In case (2) interference between the pheromone plumes of different females will lower the mating success at higher population densities. The stability of the communicating population decreases with increasing ε and B. We conclude that there should be a strong selection pressure for male ability to discriminate between odour plumes under natural circumstances and for individually distinguishable pheromone plumes.
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| 3. |
- 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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| 4. |
- 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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| 5. |
- 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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| 6. |
- 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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| 7. |
- 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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| 8. |
- 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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| 9. |
- 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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| 10. |
- 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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