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Journal of Theoretical Biology

Mike Steel, Vahab Pourfaraj, Abhishek Chaudhary, Arne Mooers
The extinction of species at the present leads to the loss of 'phylogenetic diversity' (PD) from the evolutionary tree in which these species lie. Prior to extinction, the total PD present can be divided up among the species in various ways using measures of evolutionary isolation (such as 'fair proportion' and 'equal splits'). However, the loss of PD when certain combinations of species become extinct can be either larger or smaller than the cumulative loss of the isolation values associated with the extinct species...
November 13, 2017: Journal of Theoretical Biology
Paul David Williams, Stephanie Jill Kamel
Much of evolutionary epidemiology theory is derived from a perspective in which all hosts, and all parasites, are epidemiologically equivalent. This stands in contrast to the well-documented existence of the numerous processes generating heterogeneity among hosts and parasites that can profoundly influence evolutionary/epidemiological dynamics. Age-related immunological changes, inequities in nutritional status, and interactions between parasites via coinfection are just a few of the many factors that generate heterogeneity among hosts in the ways they express susceptibility to, and respond to infection by, a focal pathogen...
November 10, 2017: Journal of Theoretical Biology
Wei Liu, Yaolin Jiang
In this paper, a Gause predator-prey model with gestation delay and Michaelis-Menten type harvesting of prey is proposed and analyzed by considering Holling type III functional response. We first consider the local stability of the interior equilibrium by investigating the corresponding characteristic equation. In succession, we derive some sufficient conditions on the occurrence of the stability switches of the positive steady state by taking the gestation delay as a bifurcation parameter. It is shown that the delay can induce instability and small amplitude oscillations of population densities via Hopf bifurcations...
November 9, 2017: Journal of Theoretical Biology
M Jabed A Choudhury, Philip M J Trevelyan, Graeme P Boswell
Fungi have a well-established role in nutrient cycling and are widely used as agents in biological control and in the remediation of polluted landscapes. Competition for resources between different fungal communities is common in these contexts and its outcome impacts on the success of such biotechnological applications. In this investigation a mathematical model is constructed to represent competition between two fungal colonies that have access to different resources. It is shown that the model equations display a multitude of travelling wave solutions and that the outcome of competition between two fungal biomasses can be controlled through the simple manipulation of the nutrient resources available to each...
November 9, 2017: Journal of Theoretical Biology
Ernesto Estrada, Grant Ross
Complex networks can be used to represent complex systems which originate in the real world. Here we study a transformation of these complex networks into simplicial complexes, where cliques represent the simplices of the complex. We extend the concept of node centrality to that of simplicial centrality and study several mathematical properties of degree, closeness, betweenness, eigenvector, Katz, and subgraph centrality for simplicial complexes. We study the degree distributions of these centralities at the different levels...
November 8, 2017: Journal of Theoretical Biology
Mike Steel, Stuart Kauffman
A variety of evolutionary processes in biology can be viewed as settings where organisms 'catalyse' the formation of new types of organisms. One example, relevant to the origin of life, is where transient biological colonies (e.g. prokaryotes or protocells) give rise to new colonies via lateral gene transfer. In this short note, we describe and analyse a simple random process which models such settings. By applying theory from general birth-death processes, we describe how the survival of a population under catalytic diversification depends on interplay of the catalysis rate and the initial population size...
November 3, 2017: Journal of Theoretical Biology
O Angulo, O Gandrillon, F Crauste
Production of red blood cells involves growth-factor mediated regulation of erythroid progenitor apoptosis and self-renewal. During severe anemia, characterized by a strong fall of the hematocrit followed by a recovery phase, these controls allow a fast recovery of the hematocrit and survival of the organism. Using a mathematical model of stress erythropoiesis and an ad hoc numerical method, we investigate the respective roles of anemia-inducing phenylhydrazine injections and physiological regulation on the organism's recovery...
November 2, 2017: Journal of Theoretical Biology
Atsushi Hashimoto, Atsuki Nagao, Satoru Okuda
Vertex models are generally powerful tools for exploring biological insights into multicellular dynamics. In these models, a multicellular structure is represented by a network, which is dynamically rearranged using topological operations. Remarkably, the topological dynamics of the network are important in guaranteeing the results from the models and their biological implications. However, it remains unclear whether the entire pattern of multicellular topological dynamics can be accurately expressed by a set of operators in the models...
November 2, 2017: Journal of Theoretical Biology
Alexander P Browning, Scott W McCue, Rachelle N Binny, Michael J Plank, Esha T Shah, Matthew J Simpson
Collective cell spreading takes place in spatially continuous environments, yet it is often modelled using discrete lattice-based approaches. Here, we use data from a series of cell proliferation assays, with a prostate cancer cell line, to calibrate a spatially continuous individual based model (IBM) of collective cell migration and proliferation. The IBM explicitly accounts for crowding effects by modifying the rate of movement, direction of movement, and the rate of proliferation by accounting for pair-wise interactions...
November 1, 2017: Journal of Theoretical Biology
Noble J Malunguza, Senelani D Hove-Musekwa, Zindoga Mukandavire
Whereas penile vaginal intercourse (VI) is thought to be the dominant mode of HIV transmission in sub-Saharan Africa, cross-sectional studies in the region indicate the preponderance of heterosexual anal intercourse (AI) among high activity groups. A dynamic, heterosexual core group model with risk of infection through both vaginal and anal pathways is formulated and comprehensively analysed. The model is coupled to a general population model and fitted to HIV prevalence data for Zimbabwe in order to explore the parameter space related to heterosexual AI...
November 1, 2017: Journal of Theoretical Biology
Shengli Zhang, Xin Duan
Predicting protein subcellular location with support vector machine has been a popular research area recently because of the dramatic explosion of bioinformation. Though substantial achievements have been obtained, few researchers considered the problem of data imbalance before classification, which will lead to low accuracy for some categories. So in this work, we combined oversampling method with SVM to deal with the protein subcellular localization of unbalanced data sets. To capture valuable information of a protein, a PseAAC (Pseudo Amino Acid Composition) has been extracted from PSSM(Position-Specific Scoring Matrix) as a feature vector, and then be selected by principal component analysis (PCA)...
October 31, 2017: Journal of Theoretical Biology
Kevin J Painter, William Ho, Denis J Headon
The orderly formation of the avian feather array is a classic example of periodic pattern formation during embryonic development. Various mathematical models have been developed to describe this process, including Turing/activator-inhibitor type reaction-diffusion systems and chemotaxis/mechanical-based models based on cell movement and tissue interactions. In this paper we formulate a mathematical model founded on experimental findings, a set of interactions between the key cellular (dermal and epidermal cell populations) and molecular (fibroblast growth factor, FGF, and bone morphogenetic protein, BMP) players and a medially progressing priming wave that acts as the trigger to initiate patterning...
October 31, 2017: Journal of Theoretical Biology
Ashish Kumar Agrahari, Amit Kumar, Siva R, Hatem Zayed, George Priya Doss C
X-linked Charcot-Marie-Tooth type 1 X (CMTX1) disease is a subtype of Charcot-Marie-Tooth (CMT), which is mainly caused by mutations in the GJB1 gene. It is also known as connexin 32 (Cx32) that leads to Schwann cell abnormalities and peripheral neuropathy. CMTX1 is considered as the second most common form of CMT disease. The aim of this study is to computationally predict the potential impact of different single amino acid substitutions at position 75 of Cx32, from arginine (R) to proline (P), glutamine (Q) and tryptophan (W)...
October 28, 2017: Journal of Theoretical Biology
Yukio Yasui, Jin Yoshimura
The origin and maintenance of polyandry is one of the key unresolved questions in evolutionary biology. In particular, extra-pair paternity (EPP) due to polyandry is observed in most (socially-) monogamous female birds and the frequency of EPP is surprisingly high (up to 72% in a clutch on average in some species). Many case-by-case hypotheses have been presented to explain this phenomenon but a ubiquitous explanation is still lacking. One possible general explanation is bet-hedging, which is a strategy to avoid the risk associated to mating with a single unsuitable male and thus to minimize the chances of complete reproductive failure by the female...
October 28, 2017: Journal of Theoretical Biology
Jiayu Wu, Hong Yuan, Longyuan Li, Kunjie Fan, Shanguang Qian, Bing Li
Owing to its viscoelastic nature, tendon exhibits stress rate-dependent breaking and stiffness function. A Kelvin-Voigt viscoelastic shear lag model is proposed to illustrate the micromechanical behavior of the tendon under dynamic tensile conditions. Theoretical closed-form expressions are derived to predict the deformation and stress transfer between fibrils and interfibrillar matrix while tendon is dynamically stretched. The results from the analytical solutions demonstrate that how the fibril overlap length and fibril volume fraction affect the stress transfer and mechanical properties of tendon...
October 27, 2017: Journal of Theoretical Biology
Marcelino Fuentes
It is well known that humans are creating new variants of organisms, ecosystems and landscapes. Here I argue that the degree of biological novelty generated by humans goes deeper than that. We use property rules to create exclusivity in cooperation among humans, and between humans and other biological entities, thus overcoming social dilemmas and breaking barriers to cooperation. This is leading to novel forms of cooperation. One of them is the human control, modification and replication of whole ecosystems...
October 26, 2017: Journal of Theoretical Biology
A Jalilvand, B Akbari, F Zare Mirakabad
The functional linkage network (FLN) construction is a primary and important step in drug discovery and disease gene prioritization methods. In order to construct FLN, several methods have been introduced based on integration of various biological data. Although, there are impressive ideas behind these methods, they suffer from low quality of the biological data. In this paper, a hierarchical sequence-based approach is proposed to construct FLN. The proposed approach, denoted as S-FLN (Sequence-based Functional Linkage Network), uses the sequence of proteins as the primary data in three main steps...
October 26, 2017: Journal of Theoretical Biology
Emilene Pliego Pliego, Jorge Velázquez-Castro, Markus P Eichhorn, Andrés Fraguela Collar
Dengue fever is increasing in geographical range, spread by invasion of its vector mosquitoes. The trade in second-hand tires has been implicated as a factor in this process because they act as mobile reservoirs of mosquito eggs and larvae. Regional transportation of tires can create linkages between rural areas with dengue and disease-free urban areas, potentially giving rise to outbreaks even in areas with strong local control measures. In this work we sought to model the dynamics of mosquito transportation via the tire trade, in particular to predict its role in causing unexpected dengue outbreaks through vertical transmission of the virus across generations of mosquitoes...
October 25, 2017: Journal of Theoretical Biology
Dan E Ganz, Briana Sexton-Stallone, Emily L Brackett, Neil S Forbes
A method to predict the effect of tissue transport on the scheduling of chemotherapeutic treatment could increase efficacy. Many drugs with desirable pharmacokinetic properties fail in vivo due to poor transport through tissue. To predict the effect of treatment schedule on drug efficacy we developed an in silico method that integrates diffusion through tissue and cell binding into a pharmacokinetic model. The model was evaluated with an array of theoretical drugs that had different rates of diffusivity, binding, and clearance...
October 21, 2017: Journal of Theoretical Biology
Simone Cenci, Ana Montero-Castaño, Serguei Saavedra
A major challenge in community ecology is to understand how species respond to environmental changes. Previous studies have shown that the reorganization of interactions among co-occurring species can modulate their chances to adapt to novel environmental conditions. Moreover, empirical evidence has shown that these ecological dynamics typically facilitate the persistence of groups of species rather than entire communities. However, so far, we have no systematic methodology to identify those groups of species with the highest or lowest chances to adapt to new environments through a reorganization of their interactions...
October 21, 2017: Journal of Theoretical Biology
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