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Journal of Theoretical Biology

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https://read.qxmd.com/read/30776388/maximization-of-fertility-transfers-from-rangeland-to-cropland-the-contribution-of-control-theory
#1
Anne Bisson, Céline Casenave, Simon Boudsocq, Tanguy Daufresne
In traditional mixed farming systems, soil fertility in cropland relies on the transfer of fertility from rangeland through the transfer of manure produced by livestock that grazes in rangeland. In this work, we introduce a simple meta-ecosystem model in which the mixed farming system is represented by a cropland sub-system connected to a rangeland sub-system by nutrient fluxes. The livestock plays the role of nutrient-pump from the rangeland sub-system to the cropland sub-system. We use this model to study how spatial organization and practices of livestock management such as the control of grazing pressure and night corralling can help optimize both nutrient transfers and crop production...
February 15, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30772340/methods-for-approximating-stochastic-evolutionary-dynamics-on-graphs
#2
Christopher E Overton, Mark Broom, Christoforos Hadjichrysanthou, Kieran J Sharkey
Population structure can have a significant effect on evolution. For some systems with sufficient symmetry, analytic results can be derived within the mathematical framework of evolutionary graph theory which relate to the outcome of the evolutionary process. However, for more complicated heterogeneous structures, computationally intensive methods are required such as individual-based stochastic simulations. By adapting methods from statistical physics, including moment closure techniques, we first show how to derive existing homogenised pair approximation models and the exact neutral drift model...
February 14, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30768975/sprenylc-pseaac-a-sequence-based-model-developed-via-chou-s-5-steps-rule-and-general-pseaac-for-identifying-s-prenylation-sites-in-proteins
#3
Waqar Hussain, Yaser Daanial Khan, Nouman Rasool, Sher Afzal Khan, Kuo-Chen Chou
The protein prenylation (or S-prenylation) is one of the most essential modifications, required for the association of membrane of a plethora of signalling proteins with the key biological process such as protein trafficking, cell growth, proliferation and differentiation. Due to the ubiquitous nature of S-prenylation and its role in cellular functions, any defect in the biosynthesis or regulation of the isoprenoid leads to the occurrence of a variety of diseases including neurodegenerative disorders, metabolic issues, cardiovascular diseases and one of the most fatal diseases, cancer...
February 12, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30768974/an-efficient-genomic-signature-ranking-method-for-genomic-island-prediction-from-a-single-genome
#4
Jin Tao, Xiaoqing Liu, Siqian Yang, Chaohui Bao, Pingan He, Qi Dai
Genomic islands that are associated with microbial adaptations and carry genomic signatures different from that of the host, and thus many methods have been proposed to select the informative genomic signatures from a range of organisms and discriminate genomic islands from the rest of the genome in terms of these signature bias. However, they are of limited use when closely related genomes are unavailable. In the present work, we proposed a kurtosis-based ranking method to select the informative genomic signatures from a single genome...
February 12, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30753839/spatial-stochastic-modelling-of-synthetic-gene-regulatory-networks
#5
Cicely K Macnamara, Elaine I Mitchell, Mark A J Chaplain
Transcription factors are important molecules which control the levels of mRNA and proteins within cells by modulating the process of transcription (the mechanism by which mRNA is produced within cells) and hence translation (the mechanism by which proteins are produced within cells). Transcription factors are part of a wider family of molecular interaction networks known as gene regulatory networks (GRNs) which play an important role in key cellular processes such as cell division and apoptosis (e.g. the p53-Mdm2, NFκB pathways)...
February 9, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30742837/memory-in-plants-boolean-modeling-of-the-learning-and-store-recall-memory-functions-in-response-to-environmental-stimuli
#6
Jacques Demongeot, Hana Hasgui, Michel Thellier
-This paper presents a new model of memory functions in plants, which improves the previous approaches done by René Thomas and colleagues. We have decomposed the plant memory processing into three main functions: learning, storing and recalling. We propose as main mechanism for these three functions the occurrence of a calcium wave consecutive to an environmental stimulus, followed by the activation of specific genes and proteins changing their phosphorylated state. Feedback is ensured by Calcium Dependent Protein Kinases and oxidative phosphorylation...
February 8, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30742836/managing-yield-and-resilience-in-a-harvested-tritrophic-food-chain-model
#7
Tapan Kumar Kar, Debprasad Pal, Bapan Ghosh
In this article, we compare the two ecological services known as yield and resilience, for a tritrophic food chain model consisting of a prey, an intermediate predator and a top predator. For this comparison process, we use both analytical and numerical techniques. It is shown that a variety of patterns are possible based on the intensity of efforts distributed among different trophic levels. Thus we may suggest that fishing down the food chain, as suggested by Pauly et al. (1998) is not bound to happen. Our analysis also shows that balancing the harvest between prey, intermediate predator and top predator could give more yield and stabilizing the ecosystem, than the selective harvesting of any one species...
February 8, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30738052/equilibrium-properties-of-the-spatial-sis-model-as-a-point-pattern-dynamics-how-is-infection-distributed-over-space
#8
Miki Hamada, Fugo Takasu
We revisit the classical epidemiological SIS model as a stochastic point pattern dynamics with special focus on its spatial distribution at equilibrium. In this model, each point on a continuous space is either susceptible S or infectious I, and infection occurs with an infection kernel as a function of distance from I to S. This stochastic process has been mathematically described by the hierarchical dynamics of the probabilities that a point, a pair made by two points, and a triplet made by three points, etc...
February 6, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30738051/dynamics-in-schizo-obsessive-spectrum-disorders-a-computational-approach
#9
Krisztina Szalisznyó, David Silverstein, János Tóth
The co-morbidity of obsessive-compulsive disorder (OCD) and schizophrenia is higher than what would be expected by chance and the common underlying neuropathophysiology is not well understood. Repetitive stereotypes and routines can be caused by perseverative thoughts and motor sequences in both of these disorders. We extended a previously published computational model to investigate cortico-striatal network dynamics. Given the considerable overlap in symptom phenomenology and the high degree of co-morbidity between OCD and schizophrenia, we examined the dynamical consequences of functional connectivity variations in the overlapping network...
February 6, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30738050/can-evolution-paths-be-explained-by-chance-alone
#10
Rinaldo B Schinazi
We propose a purely probabilistic model to explain the evolution path of a population maximum fitness. We show that after n births in the population there are about ln n upwards jumps. This is true for any mutation probability and any fitness distribution and therefore suggests a general law for the number of upwards jumps. Simulations of our model show that a typical evolution path has first a steep rise followed by long plateaux. Moreover, independent runs show parallel paths. This is consistent with what was observed by Lenski and Travisano (1994) in their bacteria experiments...
February 6, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30738049/formalizing-and-enriching-phenotype-signatures-using-boolean-networks
#11
Méline Wery, Olivier Dameron, Jacques Nicolas, Lisabeth Remy, Anne Siegel
In order to predict the behavior of a biological system, one common approach is to perform a simulation on a dynamic model. Boolean networks allow to analyze the qualitative aspects of the model by identifying its steady states and attractors. Each of them, when possible, is associated with a phenotype which conveys a biological interpretation. Phenotypes are characterized by their signatures, provided by domain experts. The number of steady states tends to increase with the network size and the number of simulation conditions, which makes the biological interpretation difficult...
February 6, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30738048/effects-of-gene-duplication-epistasis-recombination-and-gene-conversion-on-the-fixation-time-of-compensatory-mutations
#12
Junko Kusumi, Motoshi Ichinose, Masaru Iizuka
Gene duplication is one of the major mechanisms of molecular evolution. Gene duplication enables copies of a gene to accumulate mutations through functional redundancy. If a gene encodes a specific protein that interacts with other proteins, RNA, or DNA, the relaxation of selective constraints caused by gene duplication might contribute to the fixation of compensatory mutations that occur at the interacting sites. In this study, we investigate the effect of gene duplication, epistasis among the duplicated copies and gene conversion on the fixation time of compensatory mutations by extending the original model of compensatory evolution proposed by Kimura in 1985...
February 6, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30735738/assessing-the-effects-of-modeling-the-spectrum-of-clinical-symptoms-on-the-dynamics-and-control-of-ebola
#13
Joan Ponce, Yiqiang Zheng, Guang Lin, Zhilan Feng
Mathematical modelers have attempted to capture the dynamics of Ebola transmission and to evaluate the effectiveness of control measures, as well as to make predictions about ongoing outbreaks. Many of their models consider only infections with typical symptoms, but Ebola presents clinically in a more complicated way. Even the most common symptom, fever, is not experienced by 13% of patients. This suggests that infected individuals could be asymptomatic or have moderately symptomatic infections as reported during previous Ebola outbreaks...
February 5, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30735737/risk-management-signal-processing-and-econometrics-a-new-tool-for-forecasting-the-risk-of-disease-outbreaks
#14
Hossein Hassani, Mohammad Reza Yeganegi, Emmanuel Silva, Fatemeh Ghodsi
This paper takes a novel approach for forecasting the risk of disease emergence by combining risk management, signal processing and econometrics to develop a new forecasting approach. We propose quantifying risk using the Value at Risk criterion and then propose a two staged model based on Multivariate Singular Spectrum Analysis and Quantile Regression (MSSA-QR model). The proposed risk measure (PLVaR) and forecasting model (MASS-QR) is used to forecast the worst cases of waterborne disease outbreaks in 22 European and North American countries based on socio-economic and environmental indicators...
February 5, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30735736/foraging-decisions-as-multi-armed-bandit-problems-applying-reinforcement-learning-algorithms-to-foraging-data
#15
Juliano Morimoto
Finding resources is crucial for animals to survive and reproduce, but the understanding of the decision-making underlying foraging decisions to explore new resources and exploit old resources remains lacking. Theory predicts an 'exploration-exploitation trade-off' where animals must balance their effort into either stay and exploit a seemingly good resource or move and explore the environment. To date, however, it has been challenging to generate flexible yet tractable statistical models that can capture this trade-off, and our understanding of foraging decisions is limited...
February 5, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30716332/the-heart-function-as-a-motor-brake-system
#16
Ivan Colorado Cervantes, Vittorio Sansalone, Luciano Teresi
The controversy between passive and active ventricular filling has been debated for decades and the question about the existence of an active diastole remains open. In this work, we advocate the model of active diastole by considering the heart as a suction pump and we add some more clues to support this point of view by the analysis of the pressure-volume (PV) loops of the left heart, comprising of the left ventricle (LV) and atrium (LA). Our working hypothesis is based on the dichotomy motor-brake: the cardiac muscle can act as a motor, when shortening against a load, or as a brake, when lengthening to a load...
February 1, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30711456/sub-or-supercritical-transmissibilities-in-a-finite-disease-outbreak-symmetry-in-outbreak-properties-of-a-disease-conditioned-on-extinction
#17
David Waxman, Pierre Nouvellet
This work is concerned with the transmissibility of a disease, on observation of an outbreak of limited size. When such an outbreak occurs, an accurate estimate of the transmissibility of the responsible pathogen is essential for an appropriate response to future outbreaks. Transmissibility is usually characterised in terms of the reproduction number, R, which is the mean number of new cases of infection produced by a single infectious individual. A subcritical reproduction number (R<1) guarantees that an outbreak will eventually die out of its own accord...
January 31, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30711455/a-neutral-evolution-test-derived-from-a-theoretical-amino-acid-substitution-model
#18
Gabriel S Zamudio, Francisco Prosdocimi, Sávio Torres de Farias, Marco V José
A neutral evolution model that explicitly considers codons, amino acids, and the degeneracy of the genetic code is developed. The model is built from nucleotides up to amino acids, and it represents a refinement of the neutral theory of molecular evolution. The model is based on a stochastic process that leads to a stationary probability distribution of amino acids. The latter is used as a neutral test of evolution. We provide some examples for assessing the neutrality test for a small set of protein sequences...
January 31, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30711454/population-dynamics-of-chemotrophs-in-anaerobic-conditions-where-the-metabolic-energy-acquisition-per-redox-reaction-is-limited
#19
Mayumi Seto, Yoh Iwasa
We present a new model of microbial population growth that focuses on the acquisition of metabolic energy through chemosynthesis and how this depends on the concentration of resources and byproducts. Due to entropy effects, organisms extract the greater energy (i.e., they produce the greater amount of adenosine triphosphate) when they use resources that are abundant and generates byproducts that are rare. This effect, which we call the "abundant resource premium," has been neglected in traditional models of microbial growth because the total metabolic energy acquisition is generally far greater than this premium...
January 31, 2019: Journal of Theoretical Biology
https://read.qxmd.com/read/30711453/ensembles-dynamics-and-cell-types-revisiting-the-statistical-mechanics-perspective-on-cellular-regulation
#20
Stefan Bornholdt, Stuart Kauffman
Genetic regulatory networks control ontogeny. For fifty years Boolean networks have served as models of such systems, ranging from ensembles of random Boolean networks as models for generic properties of gene regulation to working dynamical models of a growing number of sub-networks of real cells. At the same time, their statistical mechanics has been thoroughly studied. Here we recapitulate their original motivation in the context of current theoretical and empirical research. We discuss ensembles of random Boolean networks whose dynamical attractors model cell types...
January 31, 2019: Journal of Theoretical Biology
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