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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/29792876/temperature-dependent-sex-determination-realized-by-hormonal-dynamics-with-enzymatic-reactions-sensitive-to-ambient-temperature
#1
Sachi Yamaguchi, Yoh Iwasa
Temperature-dependent sex determination (TSD) is adopted by many animal taxa, including reptiles and fishes. In some species, the eggs develop into females under a low hatching temperature, whereas they will develop into males under a high hatching temperature (called the FM-pattern). In other species, the eggs develop into males (or females) under a low (or high) hatching temperature (MF-pattern). Still, in other species, the eggs develop into females, males, or females, respectively, when under a low, intermediate, or high hatching temperature (FMF-pattern)...
May 21, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29792875/modelling-the-skip-and-resurgence-of-japanese-encephalitis-epidemics-in-hong-kong
#2
Shi Zhao, Yijun Lou, Alice P Y Chiu, Daihai He
Japanese encephalitis virus (JEV) is a zoonotic mosquito-borne virus, persisting in pigs, Ardeid birds and Culex mosquitoes. It is endemic to China and Southeastern Asia. The case-fatality ratio (CFR) or the rate of permanent psychiatric sequelae is 30% among symptomatic patients. There were no reported local JEV human cases between 2006 to 2010 in Hong Kong, but it was followed by a resurgence of cases from 2011 to 2017. The mechanism behind this "skip-and-resurgence" patterns is unclear. This work aims to reveal the mechanism behind the "skip-and-resurgence" patterns using mathematical modelling and likelihood-based inference techniques...
May 21, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29787747/spatially-explicit-approach-to-estimation-of-total-population-abundance-in-field-surveys
#3
Nao Takashina, Buntarou Kusumoto, Maria Beger, Suren Rathnayake, Hugh P Possingham
Population abundance is fundamental in ecology and conservation biology, and provides essential information for predicting population dynamics and implementing conservation actions. While a range of approaches have been proposed to estimate population abundance based on existing data, data deficiency is ubiquitous. When information is deficient, a population estimation will rely on labor intensive field surveys. Typically, time is one of the critical constraints in conservation, and management decisions must often be made quickly under a data deficient situation...
May 19, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29782932/resin-flow-in-conifers
#4
Paulo Cabrita
Resins are plant exudates of economic importance used by plants as defence. They flow out of resin ducts, open and long tube-like intercellular spaces lined by a layer of specialized parenchyma cells, called the epithelium, which secrete resin into the duct lumen. A model that describes resin flow in conifers is presented to investigate how duct structure, resin loading, crystallization, and viscosity affect flow and could explain differences between species. Considering resin viscosity, the structure of resin ducts, and a pressure-driven resin loading through the duct wall, the unsteady Stokes equation was applied...
May 18, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29782931/optimal-gut-size-of-small-birds-and-its-dependence-on-environmental-and-physiological-parameters
#5
Adnane Ez-Zizi, John M McNamara, Gaurav Malhotra, Alasdair I Houston
Most optimal foraging models assume that the foraging behaviour of small birds depends on a single state variable, their energy reserves in the form of stored fat. Here, we include a second state variable-the contents of the bird's gut-to investigate how a bird should optimise its gut size to minimise its long-term mortality, depending on the availability of food, the size of meal and the bird's digestive constraints. Our results show that (1) the current level of fat is never less important than gut contents in determining the bird's survival; (2) there exists a unique optimal gut size, which is determined by a trade-off between the energetic gains and costs of maintaining a large digestive system; (3) the optimal gut size increases as the bird's digestive cycle becomes slower, allowing the bird to store undigested food; (4) the critical environmental factor for determining the optimal gut size is the mass of food found in a successful foraging effort ("meal size")...
May 18, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29782930/all-atom-four-body-knowledge-based-statistical-potential-to-distinguish-native-tertiary-rna-structures-from-nonnative-folds
#6
Majid Masso
Scientific breakthroughs in recent decades have uncovered the capability of RNA molecules to fulfill a wide array of structural, functional, and regulatory roles in living cells, leading to a concomitantly significant increase in both the number and diversity of experimentally determined RNA three-dimensional (3D) structures. Atomic coordinates from a representative training set of solved RNA structures, displaying low sequence and structure similarity, facilitate derivation of knowledge-based energy functions...
May 18, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29782929/coated-platelets-introduce-significant-delay-in-onset-of-peak-thrombin-production-theoretical-predictions
#7
M Susree, Mikhail A Panteleev, M Anand
Platelets play a crucial role in the initiation, progress, termination as well as regulation of blood coagulation. Recent studies have confirmed that not all but only a small percentage of thrombin-activated platelets ("coated" platelets) exhibit procoagulant properties (namely the expression of phosphatidylserine binding sites) required for the acceleration and progress of coagulation. A mechanistic model is developed for in vitro coagulation whose key features are distinct equations for coated platelets, thrombin dose-dependence for coated platelets, and competitive binding of coagulation factors to platelet membrane...
May 18, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29782928/a-mathematical-approach-to-effects-of-ctls-on-cancer-virotherapy-in-the-second-injection-of-virus
#8
A Ashyani, O RabieiMotlagh, H M Mohammadinezhad
This paper proposes a planar delay differential equation for cancer virotherapy. The model simulates the situation in which an oncolytic virus is injected for the second time, and the immune system suppresses the viral infection with a time delay. Our purpose is to provide theoretical conditions so that the therapy can be continued successfully. With the help of the characteristic equation, we examine the singularities and their local stability. Hopf bifurcation is also investigated around the endemic singularity...
May 18, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29782927/modeling-the-odor-landscape-resulting-from-the-pumping-behavior-of-bivalve-clams-in-the-presence-of-predators
#9
A Alvarez
Motivated by experimental findings, a computational fluid dynamics (CFD) model was used to investigate whether the clam Mercenaria mercenaria may alter its cue downstream variability by an exhalant random pumping behavior. This behavior was hypothesized to occur in the presence of predator chemical signals in order to prevent successful tracking by the predator. Simulated downstream flow and mixing conditions derived from the random nature of the clam exhalant jet in a crossflow were analyzed by computing an intermittency factor, determining the field of finite-time Lyapunov exponents (FTLEs) and identifying the resulting Lagrangian coherent structures (LCSs)...
May 18, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29778649/fermentation-of-saccharomyces-cerevisiae-combining-kinetic-modeling-and-optimization-techniques-points-out-avenues-to-effective-process-design
#10
Johannes Scheiblauer, Stefan Scheiner, Martin Joksch, Barbara Kavsek
A combined experimental/theoretical approach is presented, for improving the predictability of Saccharomyces cerevisiae fermentations. In particular, a mathematical model was developed explicitly taking into account the main mechanisms of the fermentation process, allowing for continuous computation of key process variables, including the biomass concentration and the respiratory quotient (RQ). For model calibration and experimental validation, batch and fed-batch fermentations were carried out. Comparison of the model-predicted biomass concentrations and RQ developments with the corresponding experimentally recorded values shows a remarkably good agreement for both batch and fed-batch processes, confirming the adequacy of the model...
May 17, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29775683/viscoelastic-modeling-of-the-fusion-of-multicellular-tumor-spheroids-in-growth-phase
#11
Guillaume Dechristé, Jérôme Fehrenbach, Elena Griseti, Valérie Lobjois, Clair Poignard
BACKGROUND: Since several decades, the experiments have highlighted the analogy of fusing cell aggregates with liquid droplets. The physical macroscopic models have been derived under incompressible assumptions. The aim of this paper is to provide a 3D model of growing spheroids, which is more relevant regarding embryo cell aggregates or tumor cell spheroids. METHODS: We extend the past approach to a compressible 3D framework in order to account for the tumor spheroid growth...
May 15, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29775682/some-implications-of-an-epigenetic-based-omnigenic-model-of-psychiatric-disorders
#12
LETTER
Jacob Peedicayil, Dennis R Grayson
No abstract text is available yet for this article.
May 15, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29775681/asymmetric-evolutionary-game-dynamics-based-on-individuals-own-volition
#13
Qiao-Qiao He, Tian-Jiao Feng, Yi Tao, Boyu Zhang, Ting Ji
For the pairwise interactions, the evolution of individual behavior should involve two major factors: one is what you will do in an interaction with a given opponent, and another is what type of opponents you prefer to interact with. In this study, we developed a two-phenotype iterated bimatrix replicator dynamics model based on individuals' own volition, where, different from the classic iterated game model, we assume that (i) for all interaction pairs, the maximum expected interaction time is same and it is limited even if two individuals in an interaction pair would like to keep their interaction; and (ii) all individuals are able to unilaterally break off the interactions with their opponents according to their own volition...
May 15, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29775680/assessing-the-effects-of-daily-commuting-in-two-patch-dengue-dynamics-a-case-study-of-cali-colombia
#14
Edwin Barrios, Sunmi Lee, Olga Vasilieva
There are many infectious diseases that can be spread by daily commuting of people and dengue fever is one of them. The absence of vaccine and irregularities in ongoing vector control programs make this disease the most frequent and persistent in many tropical and subtropical regions of the world. This paper targets to access the effects of daily commuting on dengue transmission dynamics by using a deterministic two-patch model fitted to observed data gathered in Cali, Colombia where dengue fever is highly persistent and exhibits endemo-epidemic patterns...
May 15, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29763610/sequential-interactions-in-which-one-player-plays-first-and-another-responds-promote-cooperation-in-evolutionary-dynamical-simulations-of-single-shot-prisoner-s-dilemma-and-snowdrift-games
#15
Robert A Laird
Cooperation is a central topic in evolutionary biology because (a) it is difficult to reconcile why individuals would act in a way that benefits others if such action is costly to themselves, and (b) it underpins many of the 'major transitions of evolution', making it essential for explaining the origins of successively higher levels of biological organization. Within evolutionary game theory, the Prisoner's Dilemma and Snowdrift games are the main theoretical constructs used to study the evolution of cooperation in dyadic interactions...
May 12, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29753757/dpp-pseaac-a-dna-binding-protein-prediction-model-using-chou-s-general-pseaac
#16
M Saifur Rahman, Swakkhar Shatabda, Sanjay Saha, M Kaykobad, M Sohel Rahman
A DNA-binding protein (DNA-BP) is a protein that can bind and interact with a DNA. Identification of DNA-BPs using experimental methods is expensive as well as time consuming. As such, fast and accurate computational methods are sought for predicting whether a protein can bind with a DNA or not. In this paper, we focus on building a new computational model to identify DNA-BPs in an efficient and accurate way. Our model extracts meaningful information directly from the protein sequences, without any dependence on functional domain or structural information...
May 10, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29752953/do-cells-sense-time-by-number-of-divisions
#17
Z Schuss, K Tor, D Holcman
Can the cell's perception of time be expressed through the length of the shortest telomere? To address this question, we analyze an asymmetric random walk that models telomere length for each division that can decrease by a fixed length a or, if recognized by a polymerase, it increases by a fixed length b ≫ a. Our analysis of the model reveals two phases, first, a determinist drift of the length toward a quasi-equilibrium state, and second, persistence of the length near an attracting state for the majority of divisions...
May 9, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29752952/will-forest-size-structure-follow-the-2-power-law-distribution-under-ideal-demographic-equilibrium-state
#18
Jian Zhou, Guanghui Lin
Scaling relations formed in forest development processes are fairly important for understanding and predicting forest dynamics. During self-thinning of a relatively even-sized forest, tree abundance will decrease with an increase in average tree size, forming the size-abundance relation (SAR); while for a size-structured forest under the demographic equilibrium state, the frequency of trees also varies with size classes in a similar pattern, manifesting as the size-frequency distribution (SFD). In the metabolic scaling theory (MST), the two scaling relations are considered to be consistent...
May 9, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29752951/the-start-of-the-abiogenesis-preservation-of-homochirality-in-proteins-as-a-necessary-and-sufficient-condition-for-the-establishment-of-the-metabolism
#19
Søren Toxvaerd
Biosystems contain an almost infinite amount of vital important details, which together ensure their life. There are, however, some common structures and reactions in the systems: the homochirality of carbohydrates and proteins, the metabolism and the genetics. The Abiogenesis, or the origin of life, is probably not a result of a series of single events, but rather the result of a gradual process with increasing complexity of molecules and chemical reactions, and the prebiotic synthesis of molecules might not have left a trace of the establishment of structures and reactions at the beginning of the evolution...
May 9, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29750999/modeling-triple-negative-breast-cancer-heterogeneity-effects-of-stromal-macrophages-fibroblasts-and-tumor-vasculature
#20
Kerri-Ann Norton, Kideok Jin, Aleksander S Popel
A hallmark of breast tumors is its spatial heterogeneity that includes its distribution of cancer stem cells and progenitor cells, but also heterogeneity in the tumor microenvironment. In this study we focus on the contributions of stromal cells, specifically macrophages, fibroblasts, and endothelial cells on tumor progression. We develop a computational model of triple-negative breast cancer based on our previous work and expand it to include macrophage infiltration, fibroblasts, and angiogenesis. In vitro studies have shown that the secretomes of tumor-educated macrophages and fibroblasts increase both the migration and proliferation rates of triple-negative breast cancer cells...
May 8, 2018: Journal of Theoretical Biology
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