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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/28089874/mathematical-modelling-of-cell-layer-growth-in-a-hollow-fibre-bioreactor
#1
Lloyd A C Chapman, Jonathan P Whiteley, Helen M Byrne, Sarah L Waters, Rebecca J Shipley
Generating autologous tissue grafts of a clinically useful volume requires efficient and controlled expansion of cell populations harvested from patients. Hollow fibre bioreactors show promise as cell expansion devices, owing to their potential for scale-up. However, further research is required to establish how to specify appropriate hollow fibre bioreactor operating conditions for expanding different cell types. In this study we develop a simple model for the growth of a cell layer seeded on the outer surface of a single fibre in a perfused hollow fibre bioreactor...
January 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28088357/joint-genome-wide-prediction-in-several-populations-accounting-for-randomness-of-genotypes-a-hierarchical-bayes-approach-ii-multivariate-spike-and-slab-priors-for-marker-effects-and-derivation-of-approximate-bayes-and-fractional-bayes-factors-for-the-complete
#2
Carlos Alberto Martínez, Kshitij Khare, Arunava Banerjee, Mauricio A Elzo
This study corresponds to the second part of a companion paper devoted to the development of Bayesian multiple regression models accounting for randomness of genotypes in across population genome-wide prediction. This family of models considers heterogeneous and correlated marker effects and allelic frequencies across populations, and has the ability of considering records from non-genotyped individuals and individuals with missing genotypes in any subset of loci without the need for previous imputation, taking into account uncertainty about imputed genotypes...
January 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28088356/advancing-the-prediction-accuracy-of-protein-protein-interactions-by-utilizing-evolutionary-information-from-position-specific-scoring-matrix-and-ensemble-classifier
#3
Lei Wang, Zhu-Hong You, Shi-Xiong Xia, Feng Liu, Xing Chen, Xin Yan, Yong Zhou
Protein-Protein Interactions (PPIs) are essential to most biological processes and play a critical role in most cellular functions. With the development of high-throughput biological techniques and in silico methods, a large number of PPI data have been generated for various organisms, but many problems remain unsolved. These factors promoted the development of the in silico methods based on machine learning to predict PPIs. In this study, we propose a novel method by combining ensemble Rotation Forest (RF) classifier and Discrete Cosine Transform (DCT) algorithm to predict the interactions among proteins...
January 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28087422/nano-qsar-in-cell-biology-model-of-cell-viability-as-a-mathematical-function-of-available-eclectic-data
#4
Alla P Toropova, Andrey A Toropov
The prediction of biochemical endpoints is an important task of the modern medicinal chemistry, cell biology, and nanotechnology. Simplified molecular input-line entry system (SMILES) is a tool for representation of the molecular structure. In particular, SMILES can be used to build up the quantitative structure - property / activity relationships (QSPRs/QSARs). The QSPR/QSAR is a tool to predict an endpoint for a new substance, which has not been examined in experiment. Quasi-SMILES are representation of eclectic data related to an endpoint...
January 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28087421/physiology-anaerobes-and-the-origin-of-mitosing-cells-50-years-on
#5
William F Martin
Endosymbiotic theory posits that some organelles or structures of eukaryotic cells stem from free-living prokaryotes that became endosymbionts within a host cell. Endosymbiosis has a long and turbulent history of controversy and debate going back over 100 years. The 1967 paper by Lynn Sagan (later Lynn Margulis) forced a reluctant field to take endosymbiotic theory seriously and to incorporate it into the fabric of evolutionary thinking. Margulis envisaged three cellular partners associating in series at eukaryotic origin: the host (an engulfing bacterium), the mitochondrion (a respiring bacterium), and the flagellum (a spirochaete), with lineages descended from that flagellated eukaryote subsequently acquiring plastids from cyanobacteria, but on multiple different occasions in her 1967 account...
January 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28087420/on-the-quirks-of-maximum-parsimony-and-likelihood-on-phylogenetic-networks
#6
Christopher Bryant, Mareike Fischer, Simone Linz, Charles Semple
Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogenetic networks, which can display such events, are becoming of more and more interest in phylogenetic research...
January 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28082128/individual-based-energetic-model-suggests-bottom-up-mechanisms-for-the-impact-of-coastal-hypoxia-on-pacific-harbor-seal-phoca-vitulina-richardii-foraging-behavior
#7
Sheanna Steingass, Markus Horning
Wind-driven coastal hypoxia represents an environmental stressor that has the potential to drive redistribution of gilled marine organisms, and thereby indirectly affect the foraging characteristics of air-breathing upper trophic-level predators. We used a conceptual individual-based model to simulate effects of coastal hypoxia on the spatial foraging behavior and efficiency of a marine mammal, the Pacific harbor seal (Phoca vitulina richardii) on the Oregon coast. Habitat compression of fish was simulated at varying intensities of hypoxia...
January 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28077336/predicting-protein-submitochondrial-locations-by-incorporating-the-positional-specific-physicochemical-properties-into-chou-s-general-pseudo-amino-acid-compositions
#8
Ya-Sen Jiao, Pu-Feng Du
Predicting protein submitochondrial locations has been studied for about ten years. A dozen of methods were developed in this regard. Although a mitochondrion has four submitochondrial compartments, all existing studies considered only three of them. The mitochondrial intermembrane space proteins were always excluded in these studies. However, there are over 50 mitochondrial intermembrane space proteins in the recent release of UniProt database. We think it is time to incorporate these proteins in predicting protein submitochondrial locations...
January 8, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28077290/hidden-symmetries-of-dna-molecule
#9
Alexander A Tulub, Vassily E Stefanov
Despite the fact that DNA molecule is studied up and down, we know very little about the role of DNA triplets in coding amino acids and stop-codons. The paper aims to fill this gap through attracting spintronic ideas and carrying out QM/MM computations on a full-turn DNA fragment. The computations reveal two hidden symmetries: the spin splitting (the Rashba effect), confined within each triplet, and the quantum "phase" link between the triplet nature (in total, 64 triplets) and the corresponding amino acid and three stop-codons...
January 7, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28069450/micromechanical-modeling-of-rate-dependent-behavior-of-connective-tissues
#10
A Fallah, M T Ahmadian, K Firozbakhsh, M M Aghdam
In this paper, a constitutive and micromechanical model for prediction of rate-dependent behavior of connective tissues (CTs) is presented. Connective tissues are considered as nonlinear viscoelastic material. The rate-dependent behavior of CTs is incorporated into model using the well-known quasi-linear viscoelasticity (QLV) theory. A planar wavy representative volume element (RVE) is considered based on the tissue microstructure histological evidences. The presented model parameters are identified based on the available experiments in the literature...
January 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28069449/a-model-of-ovulatory-regulation-examining-the-effects-of-insulin-mediated-testosterone-production-on-ovulatory-function
#11
Erica J Graham, James F Selgrade
Polycystic ovary syndrome (PCOS), a common cause of infertility in women, is often accompanied by abnormal reproductive and metabolic hormone levels. Specifically, androgens such as testosterone are elevated in many PCOS women, and the syndrome itself is frequently associated with insulin resistance, which leads to hyperinsulinemia, i.e., elevated insulin. Although the precise role of insulin in ovulatory function is unclear, its role in ovulatory dysfunction is often linked to the effects of increased ovarian androgen production...
January 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28069448/interaction-times-change-evolutionary-outcomes-two-player-matrix-games
#12
Vlastimil Křivan, Ross Cressman
Two most influential models of evolutionary game theory are the Hawk-Dove and Prisoner's dilemma models. The Hawk-Dove model explains evolution of aggressiveness, predicting individuals should be aggressive when the cost of fighting is lower than its benefit. As the cost of aggressiveness increases and outweighs benefits, aggressiveness in the population should decrease. Similarly, the Prisoner's dilemma models evolution of cooperation. It predicts that individuals should never cooperate despite cooperation leading to a higher collective fitness than defection...
January 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28069447/limiting-fitness-distributions-in-evolutionary-dynamics
#13
Matteo Smerlak, Ahmed Youssef
Natural selection works on variation in fitness, but how should we measure "variation" to predict the rate of future evolution? Fisher's fundamental theorem of natural selection provides the short-run answer: the instantaneous rate of growth of a population's mean fitness is its variance in fitness. This identity captures an important feature of the evolutionary process, but, because it does not specify how the variance itself evolves in time, it cannot be used to predict evolutionary dynamics in the long run...
January 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28065783/mathematical-modeling-of-mutant-transferrin-crm107-molecular-conjugates-for-cancer-therapy
#14
Dennis J Yoon, Kevin Y Chen, André M Lopes, April A Pan, Joseph Shiloach, Anne B Mason, Daniel T Kamei
The transferrin (Tf) trafficking pathway is a promising mechanism for use in targeted cancer therapy due to the overexpression of transferrin receptors (TfRs) on cancerous cells. We have previously developed a mathematical model of the Tf/TfR trafficking pathway to improve the efficiency of Tf as a drug carrier. By using diphtheria toxin (DT) as a model toxin, we found that mutating the Tf protein to change its iron release rate improves cellular association and efficacy of the drug. Though this is an improvement upon using wild-type Tf as the targeting ligand, conjugated toxins like DT are unfortunately still highly cytotoxic at off-target sites...
January 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28063843/partial-differential-equation-techniques-for-analysing-animal-movement-a-comparison-of-different-methods
#15
Yi-Shan Wang, Jonathan R Potts
Recent advances in animal tracking have allowed us to uncover the drivers of movement in unprecedented detail. This has enabled modellers to construct ever more realistic models of animal movement, which aid in uncovering detailed patterns of space use in animal populations. Partial differential equations (PDEs) provide a popular tool for mathematically analysing such models. However, their construction often relies on simplifying assumptions which may greatly affect the model outcomes. Here, we analyse the effect of various PDE approximations on the analysis of some simple movement models, including a biased random walk, central-place foraging processes and movement in heterogeneous landscapes...
January 5, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28048970/partner-selection-and-emergence-of-the-merit-based-equity-norm
#16
Hirofumi Takesue
The merit-based equity norm is a widely observed principle of fairness in resource distribution, in which the resources acquired by each individual are expected to be proportional to the contribution. Despite the empirical significance of this principle, theoretical progress in evolutionary explanations of the fairness norm has been limited to an egalitarian norm. In this study, we examined the effect of partner selection on the evolution of the merit-based equity norm in a simple bargaining game. Our agent-based model demonstrates that the merit-based equity norm emerges when the agent can choose to continue the current partnership based on the bargaining result, whereas the egalitarian norm arises in a random matching situation...
December 31, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28048969/on-the-developmental-self-regulatory-dynamics-and-evolution-of-individuated-multicellular-organisms
#17
Felipe A Veloso
Changes in gene expression are thought to regulate the cell differentiation process intrinsically through complex epigenetic mechanisms. In fundamental terms, however, this assumed regulation refers only to the intricate propagation of changes in gene expression or else leads to non-explanatory regresses. The developmental self-regulatory dynamics and evolution of individuated multicellular organisms also lack a unified and falsifiable description. To fill this gap, I computationally analyzed publicly available high-throughput data of histone H3 post-translational modifications and mRNA abundance for different Homo sapiens, Mus musculus, and Drosophila melanogaster cell-type/developmental-period samples...
December 31, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28043818/molecular-noise-can-minimize-the-collective-sensitivity-of-a-clonal-heterogeneous-cell-population
#18
Marzo Forment, Guillermo Rodrigo
It is now widely accepted that molecular noise, rather than be always detrimental, introduces in many circumstances the required boost to reach fundamental cellular activities or strategies otherwise unattainable. In threshold-like genetic systems, molecular noise serves to generate heterogeneous responses in a clonal population, also in a tissue, due to cell-to-cell variability. Here, we derived a mathematical framework from which we could study in detail this effect. We focused on a minimal decision-making gene circuit implemented as a transcriptional positive-feedback loop...
December 31, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28043819/joint-genome-wide-prediction-in-several-populations-accounting-for-randomness-of-genotypes-a-hierarchical-bayes-approach-i-multivariate-gaussian-priors-for-marker-effects-and-derivation-of-the-joint-probability-mass-function-of-genotypes
#19
Carlos Alberto Martínez, Kshitij Khare, Arunava Banerjee, Mauricio A Elzo
It is important to consider heterogeneity of marker effects and allelic frequencies in across population genome-wide prediction studies. Moreover, all regression models used in genome-wide prediction overlook randomness of genotypes. In this study, a family of hierarchical Bayesian models to perform across population genome-wide prediction modeling genotypes as random variables and allowing population-specific effects for each marker was developed. Models shared a common structure and differed in the priors used and the assumption about residual variances (homogeneous or heterogeneous)...
December 30, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28041891/on-the-definition-and-measurement-of-fitness-in-finite-populations
#20
Thomas F Hansen
I argue that some standard accounts of fitness in finite populations are both inaccurate and conceptually misleading. I show that the usual population-genetics conceptualization of fitness as the ratio between amounts of a type after selection and before selection works just as well in finite as in infinite populations. Fitness then becomes a random variable, and selection can be conceptualized as any difference in the distribution of this variable while genetic drift can be conceptualized through realized variation in the variable...
December 29, 2016: Journal of Theoretical Biology
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