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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/28633970/unified-neural-field-theory-of-brain-dynamics-underlying-oscillations-in-parkinson-s-disease-and-generalized-epilepsies
#1
E J Müller, S J van Albada, J W Kim, P A Robinson
The mechanisms underlying pathologically synchronized neural oscillations in Parkinson's disease (PD) and generalized epilepsies are explored in parallel via a physiologically-based neural field model of the corticothalamic-basal ganglia (CTBG) system. The basal ganglia (BG) are approximated as a single effective population and their roles in the modulation of oscillatory dynamics of the corticothalamic (CT) system and vice versa are analyzed. In addition to normal EEG rhythms, enhanced activity around 4 Hz and 20 Hz exists in the model, consistent with the characteristic frequencies observed in PD...
June 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28625476/feedback-loops-interlocked-at-competitive-binding-sites-amplify-and-facilitate-genetic-oscillations
#2
Koichiro Uriu, Hajime Tei
Positive and negative feedback loops are often present in regulatory networks for genetic oscillations. Relative time scales and integration of these feedback loops are key to robust oscillations in expression levels. Using examples from the circadian clock and synthetic genetic oscillators, we study positive and negative feedback loops interlocked at competitive binding sites. In the mammalian circadian clock, a key clock gene Bmal1 is regulated by the activator ROR and the repressor REV-ERB. Conversely, Bmal1 activates both of them, forming interlocked feedback loops...
June 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28625475/prediction-of-protein-protein-interactions-by-label-propagation-with-protein-evolutionary-and-chemical-information-derived-from-heterogeneous-network
#3
Yu-Ting Wen, Hai-Jun Lei, Zhu-Hong You, Bai-Ying Lei, Xing Chen, Li-Ping Li
Prediction of protein-protein interactions (PPIs) is of great significance. To achieve this, we propose a novel computational method for PPIs prediction based on a similarity network fusion (SNF) model for integrating the physical and chemical properties of proteins. Specifically, the physical and chemical properties of protein are the protein amino acid mutation rate and its hydrophobicity, respectively. The amino acid mutation rate is extracted using a BLOSUM62 matrix, which puts the protein sequence into block substitution matrix...
June 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28625474/identifying-circumstances-under-which-high-insecticide-dose-increases-or-decreases-resistance-selection
#4
J C Helps, N D Paveley, F van den Bosch
Insect management strategies for agricultural crop pests must reduce selection for insecticide resistant mutants while providing effective control of the insect pest. One management strategy that has long been advocated is the application of insecticides at the maximum permitted dose. This has been found, under some circumstances, to be able to prevent the resistance allele frequency from increasing. However this approach may, under different circumstances, lead to rapid selection for resistance to the insecticide...
June 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28624394/reduced-foraging-investment-as-an-adaptation-to-patchy-food-sources-a-phasic-army-ant-simulation
#5
Serafino Teseo, Francesco Delloro
Colonies of several ant species within the subfamily Dorylinae alternate stereotypical discrete phases of foraging and reproduction. Such phasic cycles are thought to be adaptive because they minimize the amount of foraging and the related costs, and at the same time enhance the colony-level ability to rely on patchily distributed food sources. In order to investigate these hypotheses, we use here a simple computational approach to study the population dynamics of two species of virtual ant colonies that differ quantitatively in their foraging investment...
June 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28624393/endosymbiosis-the-feeling-is-not-mutual
#6
Patrick J Keeling, John P McCutcheon
Endosymbiosis is an idea that provided a remarkable amount of explanatory power about the origins of eukaryotic organelles. But it also promoted a number of assumptions that have also been influential, but are less well-examined. Here we look at two of these to see whether or not they fit current evidence. The assumption we first address is that endosymbiotic relationships such as nutritional symbioses and eukaryotic organelles are mutualisms. We argue instead that they are more one-sided associations that can be regarded as context-dependent power struggles like any other ecological interaction...
June 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28596112/aggregation-of-biological-particles-under-radial-directional-guidance
#7
Ion Bica, Thomas Hillen, Kevin J Painter
Many biological environments display an almost radially-symmetric structure, allowing proteins, cells or animals to move in an oriented fashion. Motivated by specific examples of cell movement in tissues, pigment protein movement in pigment cells and animal movement near watering holes, we consider a class of radially-symmetric anisotropic diffusion problems, which we call the star problem. The corresponding diffusion tensor D(x) is radially symmetric with isotropic diffusion at the origin. We show that the anisotropic geometry of the environment can lead to strong aggregations and blow-up at the origin...
June 13, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28619246/using-the-ornstein-uhlenbeck-process-to-model-the-evolution-of-interacting-populations
#8
Krzysztof Bartoszek, Sylvain Glémin, Ingemar Kaj, Martin Lascoux
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...
June 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28610834/the-evolution-of-ecosystem-ascendency-in-a-complex-systems-based-model
#9
Katharina Brinck, Henrik Jeldtoft Jensen
General patterns in ecosystem development can shed light on driving forces behind ecosystem formation and recovery and have been of long interest. In recent years, the need for integrative and process oriented approaches to capture ecosystem growth, development and organisation, as well as the scope of information theory as a descriptive tool has been addressed from various sides. However data collection of ecological network flows is difficult and tedious and comprehensive models are lacking. We use a hierarchical version of the Tangled Nature Model of evolutionary ecology to study the relationship between structure, flow and organisation in model ecosystems, their development over evolutionary time scales and their relation to ecosystem stability...
June 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28606751/risk-stratification-in-compartmental-epidemic-models-where-to-draw-the-line
#10
Sze-Chuan Suen, Jeremy D Goldhaber-Fiebert, Margaret L Brandeau
Economic evaluations of infectious disease control interventions frequently use dynamic compartmental epidemic models. Such models capture heterogeneity in risk of infection by stratifying the population into discrete risk groups, thus approximating what is typically continuous variation in risk. An important open question is whether and how different risk stratification choices influence model predictions of intervention effects. We develop equivalent Susceptible-Infected-Susceptible (SIS) dynamic transmission models: an unstratified model, a model stratified into a high-risk and low-risk group, and a model with an arbitrary number of risk groups...
June 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28606750/error-thresholds-for-rna-replication-in-the-presence-of-both-point-mutations-and-premature-termination-errors
#11
Andrew S Tupper, Paul G Higgs
We consider a spatial model of replication in the RNA World in which polymerase ribozymes use neighbouring strands as templates. Point mutation errors create parasites that have the same replication rate as the polymerase. We have shown previously that spatial clustering allows survival of the polymerases as long as the error rate is below a critical error threshold. Here, we additionally consider errors where a polymerase prematurely terminates replication before reaching the end of the template, creating shorter parasites that are replicated faster than the functional polymerase...
June 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28596113/evolution-of-delayed-dispersal-and-subsequent-emergence-of-helping-with-implications-for-cooperative-breeding
#12
Geoff Wild, Judith Korb
Cooperative breeding occurs when individuals help raise the offspring of others. It is widely accepted that help displayed by cooperative breeders emerged only after individuals' tendency to delay dispersal had become established. We use this idea as a basis for two inclusive-fitness models: one for the evolution of delayed dispersal, and a second for the subsequent emergence of helpful behavior exhibited by non-breeding individuals. We focus on a territorial species in a saturated environment, and allow territories to be inherited by non-breeding individuals who have delayed dispersal...
June 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28601427/games-of-corruption-in-preventing-the-overuse-of-common-pool-resources
#13
Joung-Hun Lee, Marko Jusup, Yoh Iwasa
Maintaining human cooperation in the context of common-pool resource management is extremely important because otherwise we risk overuse and corruption. To analyse the interplay between economic and ecological factors leading to corruption, we couple the resource dynamics and the evolutionary dynamics of strategic decision making into a powerful analytical framework. The traits of this framework are: (i) an arbitrary number of harvesters share the responsibility to sustainably exploit a specific part of an ecosystem, (ii) harvesters face three strategic choices for exploiting the resource, (iii) a delegated enforcement system is available if called upon, (iv) enforcers are either honest or corrupt, and (v) the resource abundance reflects the choice of harvesting strategies...
June 7, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28587744/mathematical-comparison-of-memory-functions-between-mutual-activation-and-repression-networks-in-a-stochastic-environment
#14
A B M Shamim Ul Hasan, Hiroyuki Kurata
Biological memory is a ubiquitous function that can generate a sustained response to a transient inductive stimulus. To better understand this function, we must consider the mechanisms by which different structures of genetic networks achieve memory. Here, we investigated two competitive gene regulatory network models: the regulated mutual activation network (MAN) and the regulated mutual repression network (MRN). Stochasticity deteriorated the persistence of memory of both the MAN and the MRN. Mathematical comparison by simulation and theoretical analysis identified functional differences in the stochastic memory between the competitive models: specifically, the MAN provided much more robust, persistent memory than the MRN...
June 3, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28587743/a-novel-alignment-free-vector-method-to-cluster-protein-sequences
#15
Lily He, Yongkun Li, Rong Lucy He, Stephen S-T Yau
Classification of protein are crucial topics in biology. The number of protein sequences stored in databases increases sharply in the past decade. Traditionally, comparison of protein sequences is usually carried out through multiple sequence alignment methods. However, these methods may be unsuitable for clustering of protein sequences when gene rearrangements occur such as in viral genomes. The computation is also very time-consuming for large datasets with long genomes. In this paper, based on three important biochemical properties of amino acids: the hydropathy index, polar requirement and chemical composition of the side chain, we propose a 24 dimensional feature vector describing the composition of amino acids in protein sequences...
June 3, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28579427/infections-of-wolbachia-may-destabilize-mosquito-population-dynamics
#16
Arndt Telschow, Florian Grziwotz, Philip Crain, Takeshi Miki, James W Mains, George Sugihara, Stephen L Dobson, Chih-Hao Hsieh
Recent efforts in controlling mosquito-borne diseases focus on biocontrol strategies that incapacitate pathogens inside mosquitoes by altering the mosquito's microbiome. A case in point is the introduction of Wolbachia into natural mosquito populations in order to eliminate Dengue virus. However, whether this strategy can successfully control vector-borne diseases is debated; particularly, how artificial infection affects population dynamics of hosts remains unclear. Here, we show that natural Wolbachia infections are associated with unstable mosquito population dynamics by contrasting Wolbachia-infected versus uninfected cage populations of the Asian tiger mosquito (Aedes albopictus)...
June 1, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28571669/fetal-programming-and-eating-disorder-risk
#17
REVIEW
Candace Jones, Brad Pearce, Ingrid Barrera, Amanda Mummert
Fetal programming describes the process by which environmental stimuli impact fetal development to influence disease development later in life. Our analysis summarizes evidence for the role of fetal programming in eating disorder etiology through review of studies demonstrating specific obstetric complications and later eating risk of anorexia or bulimia. Using Pubmed, we found thirteen studies investigating obstetric factors and eating disorder risk published between 1999 and 2016. We then discuss modifiable maternal risk factors, including nutrition and stress, that influence anorexia or bulimia risk of their offspring...
May 29, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28571668/thermodynamic-stability-of-biomolecules-and-evolution
#18
Ashim K Chakravarty
The thermodynamic stability of biomolecules in the perspective of evolution is a complex issue and needs discussion. Intra molecular bonds maintain the structure and the state of internal energy (E) of a biomolecule at "local minima". In this communication, possibility of loss in internal energy level of a biomolecule through the changes in the bonds has been discussed, that might earn more thermodynamic stability for the molecule. In the process variations in structure and functions of the molecule could occur...
May 29, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28554611/a-mathematical-model-of-embodied-consciousness
#19
David Rudrauf, Daniel Bennequin, Isabela Granic, Gregory Landini, Karl Friston, Kenneth Williford
We introduce a mathematical model of embodied consciousness, the Projective Consciousness Model (PCM), which is based on the hypothesis that the spatial field of consciousness (FoC) is structured by a projective geometry and under the control of a process of active inference. The FoC in the PCM combines multisensory evidence with prior beliefs in memory, and frames them by selecting points of view and perspectives according to preferences. The choice of projective frames governs how expectations are transformed by consciousness...
May 26, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28554610/reverse-allostasis-in-biological-systems-minimal-conditions-and-implications
#20
Nasrollah Rezaei-Ghaleh, Davood Bakhtiari, Armin Rashidi
Biological control systems regulate the behavior of biological systems in a constantly changing environment. Homeostasis is the most widely studied outcome of biological control systems. Homeostatic systems maintain the system in its desired state despite variations in system parameters or the externally-determined input rates of their constituents, i.e. they have zero or near zero steady state error. On the other hand, allostatic systems are not resistant against environmental changes and the steady state level of their controlled variables responds positively to the changes in their input rates...
May 26, 2017: Journal of Theoretical Biology
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