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Journal of Theoretical Biology

A G Dimitrov
The membrane transporters (pumps and co-transporters) are the main players in maintaining the cell homeostasis. Models of various types, each with their own drawbacks, describe transporter behavior. The aim of this study is to find the link between the biophysically based and empirical models to face and solve their specific problems. Instead of decreasing the number of states and using few complex rate constants as is usually done, we use the number of states as great as possible. Then, each transition in the cycle can represent an elementary process and we can apply the mass action law, according to which if rate constants depend on concentrations the dependence is linear...
October 17, 2016: Journal of Theoretical Biology
Eric Hermand, François J Lhuissier, Nicolas Voituron, Jean-Paul Richalet
We evaluated the mechanisms responsible for the instability of ventilation control system under simultaneous metabolic (exercise) and environmental (hypoxia) stresses, promoting the genesis of periodic breathing. A model following the main concepts of ventilatory control has been tested, including cardiovascular and respiratory parameters, characteristics of peripheral and central chemoreceptors, at mild exercise in hypoxia (FIO2=0.145). Interaction between O2 and CO2 sensing was introduced following three different modalities...
October 12, 2016: Journal of Theoretical Biology
Sylvain Billiard, Pierre Collet, Régis Ferrière, Sylvie Méléard, Viet Chi Tran
Horizontal transfer (HT) of heritable information or 'traits' (carried by genetic elements, plasmids, endosymbionts, or culture) is widespread among living organisms. Yet current ecological and evolutionary theory addressing HT is scant. We present a modeling framework for the dynamics of two populations that compete for resources and horizontally exchange (transfer) an otherwise vertically inherited trait. Competition infuences individual demographics, thereby affecting population size, which feeds back on the dynamics of transfer...
October 11, 2016: Journal of Theoretical Biology
Sophie Lèbre, Olivier Gascuel
Overlapping genes exist in all domains of life and are much more abundant than expected upon their first discovery in the late 1970s. Assuming that the reference gene is read in frame +0, an overlapping gene can be encoded in two reading frames in the sense strand, denoted by +1 and +2, and in three reading frames in the opposite strand, denoted by -0, -1, and -2. This motivated numerous researchers to study the constraints induced by the genetic code on the various overlapping frames, mostly based on information theory...
October 10, 2016: Journal of Theoretical Biology
Marek Ingr, Eva Kutálková, Josef Hrnčiřík, Reinhard Lange
High pressure methods have become a useful tool for studying protein structure and stability. Using them, various physico-chemical processes including protein unfolding, aggregation, oligomer dissociation or enzyme-activity decrease were studied on many different proteins. Oligomeric protein dissociation is a process that can perfectly utilize the potential of high-pressure techniques, as the high pressure shifts the equilibria to higher concentrations making them better observable by spectroscopic methods...
October 4, 2016: Journal of Theoretical Biology
Ezhilarasi Krishnamoorthy, Sameer Hassan, Luke Elizabeth Hanna, Indira Padmalayam, Rama Rajaram, Vijay Viswanathan
Lipoic acid synthase (LIAS) is an iron-sulfur cluster mitochondrial enzyme which catalyzes the final step in the de novo pathway for the biosynthesis of lipoic acid, a potent antioxidant. Recently there has been significant interest in its role in metabolic diseases and its deficiency in LIAS expression has been linked to conditions such as diabetes, atherosclerosis and neonatal-onset epilepsy, suggesting a strong inverse correlation between LIAS reduction and disease status. In this study we use a bioinformatics approach to predict its structure, which would be helpful to understanding its role...
October 4, 2016: Journal of Theoretical Biology
Xia Wang, Sanyi Tang, Robert A Cheke
An outbreak of dengue fever in Guangdong province in 2014 was the most serious outbreak ever recorded in China. Given the known positive correlation between the abundance of mosquitoes and the number of dengue fever cases, a stage structured mosquito model was developed to investigate the cause of the large abundance of mosquitoes in 2014 and its implications for outbreaks of the disease. Data on the Breteau index (number of containers positive for larvae per 100 premises investigated), temperature and precipitation were used for model fitting...
September 28, 2016: Journal of Theoretical Biology
Sunmi Lee, Gerardo Chowell
The impact of optimal control strategies in the context of seasonally varying infectious disease transmission remains a wide open area of research. We investigate optimal control strategies for flu-like epidemics using an SIR (susceptible-infectious-recovered) type epidemic model where the transmission rate varies seasonally together with treatment and vaccination strategies. Specifically, we explore optimal control strategies using time-dependent treatment and vaccination as control functions alone or in combination...
September 27, 2016: Journal of Theoretical Biology
Michael H Cortez
A species exhibits a hydra effect when, counter-intuitively, increased mortality of the species causes an increase in its abundance. Hydra effects have been studied in many continuous time (differential equation) multispecies models, but only rarely have hydra effects been observed in or studied with discrete time (difference equation) multispecies models. In addition most discrete time theory focuses on single-species models. Thus, it is unclear what unifying characteristics determine when hydra effects arise in discrete time models...
September 27, 2016: Journal of Theoretical Biology
Kelvin J Richards
Viruses are known to impact blooms of phytoplankton in the ocean, in some cases causing the bloom to crash. Here, using a population model that includes viral infection, we investigate the conditions under which the presence of a virus significantly impacts the population dynamics. A major focus is how spatial variability influences the spread of an epidemic in a stirring and mixing field. The combination of viral infection and diffusion can cause waves of the epidemic to sweep through the domain, with the epidemic lasting much longer than in the homogeneous case...
September 27, 2016: Journal of Theoretical Biology
Dhrubajyoti Gogoi, Vishwa Jyoti Baruah, Amrita Kashyap Chaliha, Bibhuti Bhushan Kakoti, Diganta Sarma, Alak Kumar Buragohain
Human epidermal growth factor receptor 2 (HER2) is one of the four members of the epidermal growth factor receptor (EGFR) family and is expressed to facilitate cellular proliferation across various tissue types. Therapies targeting HER2, which is a transmembrane glycoprotein with tyrosine kinase activity, offer promising prospects especially in breast and gastric/gastroesophageal cancer patients. Persistence of both primary and acquired resistance to various routine drugs/antibodies is a disappointing outcome in the treatment of many HER2 positive cancer patients and is a challenge that requires formulation of new and improved strategies to overcome the same...
September 27, 2016: Journal of Theoretical Biology
Guillaume Bassil, Manuel Zarzoso, Sami F Noujaim
Variations in body mass impose constraints on the structure and function of mammalian species, including those of the cardiovascular system. Numerous biological processes, including cardiovascular parameters, have been shown to scale with body mass (BM) according to the law of allometric scaling: Y = Y =a∙BM(b) (Y, biological process; a, normalization constant; b, scaling exponent, which in many instances is a multiple of ¼). These parameters include heart and breathing rates, intervals and subintervals of the electrocardiogram (ECG), action potential duration (APD), metabolic rate, and temporal properties of ventricular fibrillation...
September 26, 2016: Journal of Theoretical Biology
Katarzyna Jesionek, Aleksandra Slapik, Marcin Kostur
The influence of hypertension on low-density lipoproteins intake into the arterial wall is an important factor for understanding mechanisms of atherosclerosis. It has been experimentally observed that the increased pressure leads to the higher level of the LDL inside the wall. In this paper we attempt to construct a model of the LDL transport which reproduces quantitatively experimental outcomes. We supplement the well known four-layer arterial wall model to include two pressure induced effects: the compression of the intima tissue and the increase of the fraction of leaky junctions...
September 26, 2016: Journal of Theoretical Biology
Loïc Chaumont, Valéry Malécot, Richard Pymar, Chaker Sbai
Data obtained from ISSR amplification may readily be extracted but only allows us to know, for each gene, if a specific allele is present or not. From this partial information we provide a probabilistic method to reconstruct the pedigree corresponding to some families of diploid cultivars. This method consists in determining for each individual what is the most likely couple of parent pair amongst all older individuals, according to some probability measure. The construction of this measure bears on the fact that the probability to observe the specific alleles in the child, given the status of the parents does not depend on the generation and is the same for each gene...
September 24, 2016: Journal of Theoretical Biology
Su Do Yi, Seung Ki Baek, Jung-Kyoo Choi
One of the most important questions in game theory concerns how mutual cooperation can be achieved and maintained in a social dilemma. In Axelrod's tournaments of the iterated prisoner's dilemma, Tit-for-Tat (TFT) demonstrated the role of reciprocity in the emergence of cooperation. However, the stability of TFT does not hold in the presence of implementation error, and a TFT population is prone to neutral drift to unconditional cooperation, which eventually invites defectors. We argue that a combination of TFT and anti-TFT (ATFT) overcomes these difficulties in a noisy environment, provided that ATFT is defined as choosing the opposite to the opponent's last move...
September 23, 2016: Journal of Theoretical Biology
Javad Salimi Sartakhti, Mohammad Hossein Manshaei, Mehdi Sadeghi
One of the main step in solid cancers to invade surrounding tissues is degradation of tissue barriers in the extracellular matrix. This operation that leads to initiate, angiogenesis and metastasis to other organs, is essentially consequence of collapsing dynamic balance between matrix metalloproteinases (MMP) and tissue inhibitors of metalloproteinases (TIMP). In this work, we model the MMP-TIMP interaction in both normal tissue and invasive cancer using evolutionary game theory. Our model explains how invasive cancer cells get the upper hand in MMP-TIMP imbalance scenarios...
September 23, 2016: Journal of Theoretical Biology
Biao Tang, Yanni Xiao, Sanyi Tang, Jianhong Wu
We develop a mathematical model to closely mimic the integrated program of impulsive vector control (every Friday afternoon since the initiation of the program) and continuous patient treatment and isolation implemented in the Guangdong Province of China during its 2014 dengue outbreak. We fitted the data of accumulated infections and used the parameterized model to carry out a retrospective analysis to estimate the basic reproduction number 1.7425 (95% CI 1.4443-2.0408), the control reproduction number 0.1709, and the mosquito-killing ratios 0...
September 17, 2016: Journal of Theoretical Biology
Satoshi Yamashita, Tatsuo Michiue
Planar cell polarity is an important property of epithelial tissue. The boundary propagation model was proposed as the mechanism of PCP induction, while it has been doubted whether it can induce PCP on wide tissue. Using simulation, a set of proteins can be shown to induce PCP, but it does not explain why and how the set can induce PCP. In this study, we made theoretical model and simulation model to explore when and how the boundary propagation induce PCP. We incorporated multipolar cell in our model. Intracellular interactions have been thought to amplify polarity of a cell, but we propose instead that they are to keep a cell-cell interface polarized, and bipolarity of cell is obtained as a result...
September 16, 2016: Journal of Theoretical Biology
W D Comper, L M Russo, J Vuchkova
In order to understand the mechanism of albuminuria we have explored how other plasma proteins are processed by the kidney as compared to inert molecules like Ficolls. When fractional clearances are plotted versus protein radius there is a remarkable parallelism between protein (molecular weight range 30-150kDa) clearance in healthy controls, in Dent's disease, in nephrotic states and the clearance of Ficolls. Although there are significant differences in the levels of fractional clearances in these states...
September 16, 2016: Journal of Theoretical Biology
Masoud Amiri, Mahmood Amiri, Soheila Nazari, Karim Faez
Hyper-synchronous neural oscillations are the character of several neurological diseases such as epilepsy. On the other hand, glial cells and particularly astrocytes can influence neural synchronization. Therefore, based on the recent researches, a new bio-inspired stimulator is proposed which basically is a dynamical model of the astrocyte biophysical model. The performance of the new stimulator is investigated on a large-scale, cortical network. Both excitatory and inhibitory synapses are also considered in the simulated spiking neural network...
September 13, 2016: Journal of Theoretical Biology
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