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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/27916703/oogenesis_pred-a-sequence-based-method-for-predicting-oogenesis-proteins-by-six-different-modes-of-chou-s-pseudo-amino-acid-composition
#1
Maryam Rahimi, Mohammad Reza Bakhtiarizadeh, Abdollah Mohammadi-Sangcheshmeh
Regarding to critical roles of oogenesis in formation of ova or unfertilized eggs from the oogonia by mitotic division and subsequent differentiation, the identification of oogenesis-related proteins is of great interest. However, the experimental determination of proteins involved in oogenesis is expensive, time consuming and labor-intensive. Therefore, a new powerful discriminating model is indispensable for classifying oogenesis/non-oogenesis-related proteins with high accuracy and precision. Hereby, for the first time we developed a support vector machine based oogenesis protein prediction method which differentiates oogenesis from non-oogenesis proteins...
December 1, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27915074/evolutionary-stability-for-matrix-games-under-time-constraints
#2
József Garay, Villő Csiszár, Tamás F Móri
Game theory focuses on payoffs and typically ignores time constraints that play an important role in evolutionary processes where the repetition of games can depend on the strategies, too. We introduce a matrix game under time constraints, where each pairwise interaction has two consequences: both players receive a payoff and they cannot play the next game for a specified time duration. Thus our model is defined by two matrices: a payoff matrix and an average time duration matrix. Maynard Smith's concept of evolutionary stability is extended to this class of games...
November 30, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27915073/a-mathematical-model-of-reward-and-executive-circuitry-in-obsessive-compulsive-disorder
#3
Anca Raˇdulescu, Rachel Marra
The neuronal circuit that controls obsessive and compulsive behaviors involves a complex network of brain regions (some with known involvement in reward processing). Among these are cortical regions, the striatum and the thalamus (which compose the CSTC pathway), limbic areas such as the amygdala and the hippocampus, and well as dopamine pathways. Abnormal dynamic behavior in this brain network is a hallmark feature of patients with increased anxiety and motor activity, like the ones affected by OCD. There is currently no clear understanding of precisely what mechanisms generate these behaviors...
November 30, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27908705/a-novel-method-for-in-silico-identification-of-regulatory-snps-in-human-genome
#4
Rong Li, Dexing Zhong, Ruiling Liu, Hongqiang Lv, Xinman Zhang, Jun Liu, Jiuqiang Han
Regulatory single nucleotide polymorphisms (rSNPs), kind of functional noncoding genetic variants, can affect gene expression in a regulatory way, and they are thought to be associated with increased susceptibilities to complex diseases. Here a novel computational approach to identify potential rSNPs is presented. Different from most other rSNPs finding methods which based on hypothesis that SNPs causing large allele-specific changes in transcription factor binding affinities are more likely to play regulatory functions, we use a set of documented experimentally verified rSNPs and nonfunctional background SNPs to train classifiers, so the discriminating features are found...
November 28, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27908704/on-the-relationship-between-cell-cycle-analysis-with-ergodic-principles-and-age-structured-cell-population-models
#5
K Kuritz, D Stöhr, N Pollak, F Allgöwer
Cyclic processes, in particular the cell cycle, are of great importance in cell biology. Continued improvement in cell population analysis methods like fluorescence microscopy, flow cytometry, CyTOF or single-cell omics made mathematical methods based on ergodic principles a powerful tool in studying these processes. In this paper, we establish the relationship between cell cycle analysis with ergodic principles and age structured population models. To this end, we describe the progression of a single cell through the cell cycle by a stochastic differential equation on a one dimensional manifold in the high dimensional dataspace of cell cycle markers...
November 28, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27899286/natural-mitochondrial-proteolysis-confirms-transcription-systematically-exchanging-deleting-nucleotides-peptides-coded-by-expanded-codons
#6
Hervé Seligmann
Protein sequences have higher linguistic complexities than human languages. This indicates undeciphered multilayered, overprinted information/genetic codes. Some superimposed genetic information is revealed by detections of transcripts systematically (a) exchanging nucleotides (nine symmetric, e.g. A<->C, fourteen asymmetric, e.g. A->C->G->A, swinger RNAs) translated according to tri-, tetra- and pentacodons, and (b) deleting mono-, dinucleotides after each trinucleotide (delRNAs). Here analyses of two independent proteomic datasets considering natural proteolysis confirm independently translation of these non-canonical RNAs, also along tetra- and pentacodons, increasing coverage of putative, cryptically encoded proteins...
November 27, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27899285/a-model-of-processive-movement-of-dimeric-kinesin
#7
Si-Kao Guo, Peng-Ye Wang, Ping Xie
Dimeric kinesin can move processively on microtubule filaments by hydrolyzing ATP. Diverse aspects of its movement dynamics have been studied extensively by using various experimental methods. However, the detailed molecular mechanism of the processive movement is still undetermined and a model that can provide a consistent and quantitative explanation of the diverse experimental data is still lacking. Here, we present such a model, with which we study the movement dynamics of the dimer under variations of solution viscosity, external load, ATP concentration, neck linker length, effect of neck linker docking, effect of a large-size particle attached to one kinesin head, etc...
November 27, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27890574/modeling-the-role-of-information-and-limited-optimal-treatment-on-disease-prevalence
#8
Anuj Kumar, Prashant K Srivastava, Yasuhiro Takeuchi
Disease outbreaks induce behavioural changes in healthy individuals to avoid contracting infection. We first propose a compartmental model which accounts for the effect of individual's behavioural response due to information of the disease prevalence. It is assumed that the information is growing as a function of infective population density that saturates at higher density of infective population and depends on active educational and social programmes. Model analysis has been performed and the global stability of equilibrium points is established...
November 25, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27890575/3d-hybrid-modelling-of-vascular-network-formation
#9
Holger Perfahl, Barry D Hughes, Tomás Alarcón, Philip K Maini, Mark C Lloyd, Matthias Reuss, Helen M Byrne
We develop an off-lattice, agent-based model to describe vasculogenesis, the de novo formation of blood vessels from endothelial progenitor cells during development. The endothelial cells that comprise our vessel network are viewed as linearly elastic spheres that move in response to the forces they experience. We distinguish two types of endothelial cells: vessel elements are contained within the network and tip cells are located at the ends of vessels. Tip cells move in response to mechanical forces caused by interactions with neighbouring vessel elements and the local tissue environment, chemotactic forces and a persistence force which accounts for their tendency to continue moving in the same direction...
November 24, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27889411/modelling-three-dimensional-fungal-growth-in-response-to-environmental-stimuli
#10
G Vidal-Diez de Ulzurrun, J M Baetens, J Van den Bulcke, B De Baets
Most fungi grow by developing complex networks that enable the translocation of nutrients over large distances. Spatially explicit mathematical models are able to capture both the complexity of the fungal network and the biomass evolution, as such providing a powerful alternative to classical modelling paradigms. Unfortunately, most of these models restrict growth to two dimensions or confine it to a lattice, thereby resulting in unrealistic representations of fungal networks. In addition, interactions between fungi and their environment are often neglected...
November 24, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27889410/multiple-states-of-environmental-regulation-in-well-mixed-model-biospheres
#11
Arwen E Nicholson, David M Wilkinson, Hywel T P Williams, Timothy M Lenton
The Gaia hypothesis postulates that life influences Earth's feedback mechanisms to form a self regulating system. This provokes the question: how can global self-regulation evolve? Most models demonstrating environmental regulation involving life have relied on alignment between local selection and global regulation. In these models environment-improving individuals or communities spread to outcompete environment degrading individuals/communities, leading to global regulation, but this depends on local differences in environmental conditions...
November 23, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27887877/a-discrete-stage-structured-model-of-california-newt-population-dynamics-during-a-period-of-drought
#12
Marjorie T Jones, William R Milligan, Lee B Kats, Thomas L Vandergon, Rodney L Honeycutt, Robert N Fisher, Courtney L Davis, Timothy A Lucas
We introduce a mathematical model for studying the population dynamics under drought of the California newt (Taricha torosa), a species of special concern in the state of California. Since 2012, California has experienced a record-setting drought, and multiple studies predict drought conditions currently underway will persist and even increase in severity. Recent declines and local extinctions of California newt populations in Santa Monica Mountain streams motivate our study of the impact of drought on newt population sizes...
November 22, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27884495/a-homogenization-model-of-the-voigt-type-for-skeletal-muscle
#13
L A Spyrou, M Agoras, K Danas
A three-dimensional constitutive model for skeletal muscle incorporating microstructural characteristics is developed and numerically implemented in a general purpose finite element program. The proposed model takes into account explicitly the volume fractions of muscle fibers and connective tissue by using the Voigt homogenization approach to bridge the different length scales of the muscle structure. The model is used to estimate the active and passive homogenized muscle response. Next, the model is validated by experimental data and periodic three-dimensional unit cell calculations comprising various fiber volume fractions and mechanical properties of the constituents...
November 22, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27880875/stable-polymorphism-of-cooperators-and-punishers-in-a-public-goods-game
#14
Gaku Oya, Hisashi Ohtsuki
The role of punishment in the maintenance of cooperation has been emphasized recently. However, the maintenance of punishment is not an obvious consequence because punishment itself is also a public good; it is costly to perform and hence vulnerable to exploitation. For example, cooperative punishers, who help others and punish free riders, are disadvantageous in competition against pure cooperators, who cooperate but do not punish free riders. In addition, pure punishers, who do not help others but punish free riders, have been considered to be selfish in conventional models, because they do not perform cooperation...
November 20, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27880874/specialized-hybrid-learners-resolve-rogers-paradox-about-the-adaptive-value-of-social-learning
#15
Milad Kharratzadeh, Marcel Montrey, Alex Metz, Thomas R Shultz
Culture is considered an evolutionary adaptation that enhances reproductive fitness. A common explanation is that social learning, the learning mechanism underlying cultural transmission, enhances mean fitness by avoiding the costs of individual learning. This explanation was famously contradicted by Rogers (1988), who used a simple mathematical model to show that cheap social learning can invade a population without raising its mean fitness. He concluded that some crucial factor remained unaccounted for, which would reverse this surprising result...
November 20, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27876621/translational-resistivity-conductivity-of-coding-sequences-during-exponential-growth-of-escherichia-coli
#16
Kazuyuki Takai
Codon adaptation index (CAI) has been widely used for prediction of expression of recombinant genes in Escherichia coli and other organisms. However, CAI has no mechanistic basis that rationalizes its application to estimation of translational efficiency. Here, I propose a model based on which we could consider how codon usage is related to the level of expression during exponential growth of bacteria. In this model, translation of a gene is considered as an analog of electric current, and an analog of electric resistance corresponding to each gene is considered...
November 19, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27871852/some-pungent-arguments-against-the-physico-chemical-theories-of-the-origin-of-the-genetic-code-and-corroborating-the-coevolution-theory
#17
Massimo Di Giulio
Whereas it is extremely easy to prove that "if the biosynthetic relationships between amino acids were fundamental in the structuring of the genetic code, then their physico-chemical properties might also be revealed in the genetic code table"; it is, on the contrary, impossible to prove that "if the physico-chemical properties of amino acids were fundamental in the structuring of the genetic code, then the presence of the biosynthetic relationships between amino acids should not be revealed in the genetic code"...
November 19, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27866979/species-tree-estimation-using-neighbor-joining
#18
LETTER
Joseph Rusinko, Matthew McPartlon
Recent theoretical work has demonstrated that Neighbor Joining applied to concatenated DNA sequences is a statistically consistent method of species tree reconstruction. This brief note compares the accuracy of this approach to other popular statistically consistent species tree reconstruction algorithms including ASTRAL-II Neighbor Joining using average gene-tree internode distances (NJst) and SVD-Quartets+PAUP*, as well as concatenation using maximum likelihood (RaxML). We find that the faster Neighbor Joining, applied to concatenated sequences, is among the most effective of these methods for accurate species tree reconstruction...
November 17, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27866978/stability-and-structural-properties-of-gene-regulation-networks-with-coregulation-rules
#19
Jonathan Warrell, Musa Mhlanga
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated expression of modules (and module groups) of functionally related genes across the genome. Coregulation can also arise through the physical association of multi-gene complexes through chromosomal looping, which are then transcribed together. We present a general formalism for modeling coregulation rules in the framework of Random Boolean Networks (RBN), and develop specific models for transcription factor networks with modular structure (including module groups, and multi-input modules (MIM) with autoregulation) and multi-gene complexes (including hierarchical differentiation between multi-gene complex members)...
November 17, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27864097/post-translational-regulation-by-structural-changes-of-4-dihydromethyltrisporate-dehydrogenase-a-key-enzyme-in-sexual-and-parasitic-communication-mediated-by-the-trisporic-acid-pheromone-system-of-the-fungal-fusion-parasite-parasitella-parasitica
#20
Sabrina Ellenberger, Anke Burmester, Stefan Schuster, Johannes Wöstemeyer
Sexual communication between complementary mating partners in the fungal group of zygomycetes is mediated by the trisporoid pheromone system. A key enzyme towards biosynthesis of hormonally active trisporoids is 4-dihydromethyltrisporate dehydrogenase (TSP1), an enzyme occurring in all zygomycetous fungi. Trisporic acid and some of its precursor molecules serve as pheromones for recognizing complementary mating partners and for induction of the differentiation program towards sexual spore formation. In the parasitic zygomycete Parasitella parasitica, a biotrophic fusion parasite infecting many other zygomycetes, these substances have an additional function: They are also responsible for host-parasite recognition and the formation of the characteristic infection structures...
November 15, 2016: Journal of Theoretical Biology
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