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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/28526527/cellular-scale-model-of-growth-plate-an-in-silico-model-of-chondrocyte-hypertrophy
#1
H A Castro-Abril, J M Guevara, M A Moncayo, S J Shefelbine, L A Barrera, D A Garzón-Alvarado
The growth plate is the responsible for longitudinal bone growth. It is a cartilaginous structure formed by chondrocytes that are continuously undergoing a differentiation process that starts with a highly proliferative state, followed by cellular hypertrophy, and finally tissue ossification. Within the growth plate chondrocytes display a characteristic columnar organization that potentiates longitudinal growth. Both chondrocyte organization and hypertrophy are highly regulated processes influenced by biochemical and mechanical stimuli...
May 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28522360/sex-with-no-regrets-how-sexual-reproduction-uses-a-no-regret-learning-algorithm-for-evolutionary-advantage
#2
Omer Edhan, Ziv Hellman, Dana Sherill-Rofe
The question of 'why sex' has long been a puzzle. The randomness of recombination, which potentially produces low fitness progeny, contradicts notions of fitness landscape hill climbing. We use the concept of evolution as an algorithm for learning unpredictable environments to provide a possible answer. While sex and asex both implement similar machine learning no-regret algorithms in the context of random samples that are small relative to a vast genotype space, the algorithm of sex constitutes a more efficient goal-directed walk through this space...
May 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28522359/a-novel-specialized-single-linkage-clustering-algorithm-for-taxonomically-ordered-data
#3
Markus Schmidt, Arne Kutzner, Klaus Heese
Similarities among ortholog genes for a given set of species S can be expressed by alignment matrices, where each matrix cell results from aligning a gene transcript against the genome of a species within S. Gene clusters can be computed by using single-linkage clustering in time n*m, where n denotes the number of ortholog genes and m denotes the number of inspected assemblies. Our approach can break the O(n*m) complexity of single-linkage clustering by exploiting an order among species that results from an in-order traversal of a given phylogenetic tree...
May 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28522358/self-tolerance-and-autoimmunity-in-a-minimal-model-of-the-idiotypic-network
#4
Stefan Landmann, Nicolas Preuss, Ulrich Behn
We consider self-tolerance and its failure -autoimmunity- in a minimal mathematical model of the idiotypic network. A node in the network represents a clone of B-lymphocytes and its antibodies of the same idiotype which is encoded by a bitstring. The links between nodes represent possible interactions between clones of almost complementary idiotype. A clone survives only if the number of populated neighbored nodes is neither too small nor too large. The dynamics is driven by the influx of lymphocytes with randomly generated idiotype from the bone marrow...
May 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28522357/the-analysis-of-an-effect-of-seed-propagation-on-defense-strategy-against-pathogen-transmission-within-clonal-plant-population-using-lattice-model
#5
Yuma Sakai, Takenori Takada
Many clonal plants have two breeding systems, vegetative and seed propagation. In vegetative propagation, plants reproduce genetically identical offspring that have lower mortality rates. By contrast, the seed propagated offspring has higher mortality rate, however, the seed propagation "acts an important role in maintaining the genetic diversity and reproduce widely. According to the experimental studies, the balance between the breeding systems, vegetative and seed propagation, is determined by several functions, such as resource allocation...
May 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28499582/corrigendum-to-interplay-between-microbial-trait-dynamics-and-population-dynamics-revealed-by-the-combination-of-laboratory-experiment-and-computational-approaches-journal-of-theoretical-biology-419-2017-201-210
#6
https://www.readbyqxmd.com/read/28501637/serial-endosymbiosis-or-singular-event-at-the-origin-of-eukaryotes
#7
Nick Lane
'On the Origin of Mitosing Cells' heralded a new way of seeing cellular evolution, with symbiosis at its heart. Lynn Margulis (then Sagan) marshalled an impressive array of evidence for endosymbiosis, from cell biology to atmospheric chemistry and Earth history. Despite her emphasis on symbiosis, she saw plenty of evidence for gradualism in eukaryotic evolution, with multiple origins of mitosis and sex, repeated acquisitions of plastids, and putative evolutionary intermediates throughout the microbial world...
May 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28501636/determining-whether-observed-eukaryotic-cell-migration-indicates-chemotactic-responsiveness-or-random-chemokinetic-motion
#8
A C Szatmary, R Nossal
Chemotaxis, the motion of cells directed by a gradient of chemoattractant molecules, guides cells in immune response, development, wound healing, and cancer. Unfortunately, this process is difficult to distinguish from chemokinesis, i.e., stimulated random cell motion. Chemotaxis is frequently inferred by determining how many cells cross a boundary in a chemotaxis assay, for example how many cells crawl into a chemoattractant-infused filter, or how many cells enter a defined region in an under-agarose assay or agarose spot assay...
May 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28501635/determining-the-role-of-inflammation-in-the-selection-of-jak2-mutant-cells-in-myeloproliferative-neoplasms
#9
Jie Zhang, Angela G Fleischman, Dominik Wodarz, Natalia L Komarova
Myeloproliferative neoplasm (MPN) is a hematologic malignancy characterized by the clonal outgrowth of hematopoietic cells with a somatically acquired mutation most commonly in JAK2 (JAK2(V617F)). This mutation endows upon myeloid progenitors cytokine independent growth and consequently leads to excessive production of myeloid lineage cells. It has been previously suggested that inflammation may play a role in the clonal evolution of JAK2(V617F) mutants. In particular, it is possible that one or more cellular kinetic parameters of hematopoietic stem cells (HSCs) are affected by inflammation, such as division or death rates of cells, and the probability of HSC differentiation...
May 10, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28483568/mathematical-models-of-retinitis-pigmentosa-the-oxygen-toxicity-hypothesis
#10
Paul A Roberts, Eamonn A Gaffney, Philip J Luthert, Alexander J E Foss, Helen M Byrne
The group of genetically mediated diseases, known collectively as retinitis pigmentosa (RP), cause retinal degeneration and, hence, loss of vision. The most common inherited retinal degeneration, RP is currently untreatable. The retina detects light using cells known as photoreceptors, of which there are two types: rods and cones. In RP, genetic mutations cause patches of photoreceptors to degenerate and typically directly affect either rods or cones, but not both. During disease progression, degenerate patches spread and the unaffected photoreceptor type also begins to degenerate...
May 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28483567/mathematical-model-for-isometric-and-isotonic-muscle-contractions
#11
R De Vita, R Grange, P Nardinocchi, L Teresi
A new mathematical model is presented to describe both the active and passive mechanics of muscles. In order to account for the active response, a two-layer kinematics that introduces both the visible and rest lengths of the muscle is presented within a rational mechanics framework. The formulation is based on an extended version of the principle of virtual power and the dissipation principle. By using an accurate constitutive description of muscle mobility under activation, details of microscopic processes that lead to muscle contraction are glossed over while macroscopic effects of chemical/electrical stimuli on muscle mechanics are retained...
May 5, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28483566/pssm-suc-accurately-predicting-succinylation-using-position-specific-scoring-matrix-into-bigram-for-feature-extraction
#12
Abdollah Dehzangi, Yosvany López, Sunil Pranit Lal, Ghazaleh Taherzadeh, Jacob Michaelson, Abdul Sattar, Tatsuhiko Tsunoda, Alok Sharma
Post-Transcriptional Modification (PTM) is a process which contributes to diversify the proteome. Despite many recently reported PTMs with essential roles in the cellular functioning, lysine succinylation has emerged as a subject of particular interest. The experimental identification of succinylated lysines remains a costly and time-consuming process. As a result, computational predictors have been proposed recently for tackling this important issue. However, the performance of predictors is still very limited...
May 5, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28483565/when-is-allergen-immunotherapy-effective
#13
Akane Hara, Yoh Iwasa
Allergen immunotherapy is used to treat allergic symptoms such as rhinitis and itchy eyes in Japanese patients with cedar pollen allergy (JCPA). Administration of small amounts of pollen over several years may suppress severe allergic symptoms when these patients are later exposed to large amounts of pollen in the environment. Herein, we developed a simple mathematical model to identify conditions in which allergen immunotherapy is effective. We considered the dynamics of type 2 T helper cells (Th2) and regulatory T cells (Treg), both of which differentiate from naive T cells...
May 5, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28483564/the-influence-of-nuclear-compartmentalisation-on-stochastic-dynamics-of-self-repressing-gene-expression
#14
Marc Sturrock, Shiyu Li, Vahid Shahrezaei
Gene expression is an inherently noisy process. This noise is generally thought to be deleterious as precise internal regulation of biochemical reactions is essential for cell growth and survival. Self-repression of gene expression, which is the simplest form of a negative feedback loop, is commonly believed to be employed by cellular systems to decrease the stochastic fluctuations in gene expression. When there is some delay in autoregulation, it is also believed that this system can generate oscillations...
May 5, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28479003/epidemic-characteristics-of-two-classic-sis-models-with-disease-induced-death
#15
Fengqin Zhang, Jianquan Li, Jia Li
The epidemic characteristics of two classic SIS epidemic models, including the epidemic size, peak and turning point, are investigated. The two SIS models are with bilinear and standard incidences, respectively. For the SIS models, the susceptible individuals generally can be divided into two classes. One consists of the individuals who had not been infected by the infection, the other are individuals who have been infected and recovered from the infection. Based on this fact, the classic SIS epidemic models need to be reformulated in order to analyze the turning points of the epidemic for various cumulative cases in detail...
May 4, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28478118/the-evolution-of-site-selection-strategy-during-dispersal
#16
Tuomas Nurmi, Kalle Parvinen, Vesa Selonen
We propose a mathematical model that enables the evolutionary analysis of site-selection process of dispersing individuals that encounter sites of high or low quality. Since each site can be inhabited by at most one individual, all dispersers are not able to obtain a high-quality site. We study the evolutionary dynamics of the low-quality-site acceptance as a function of the time during the dispersal season using adaptive dynamics. We show that environmental changes affect the evolutionary dynamics in two ways: directly and indirectly via density-dependent factors...
May 4, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28476563/computing-the-carbonate-chemistry-of-the-coral-calcifying-medium-and-its-response-to-ocean-acidification
#17
Virginie Raybaud, Sylvie Tambutté, Christine Ferrier-Pagès, Stéphanie Reynaud, Alexander A Venn, Éric Tambutté, Paul Nival, Denis Allemand
Critical to determining vulnerability or resilience of reef corals to Ocean Acidification (OA) is a clearer understanding of the extent to which corals can control carbonate chemistry in their Extracellular Calcifying Medium (ECM) where the CaCO3 skeleton is produced. Here, we employ a mathematical framework to calculate ECM aragonite saturation state (Ωarag.(ECM)) and carbonate system ion concentration using measurements of calcification rate, seawater characteristics (temperature, salinity and pH) and ECM pH (pH(ECM))...
May 3, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28476562/a-novel-alignment-free-method-to-classify-protein-folding-types-by-combining-spectral-graph-clustering-with-chou-s-pseudo-amino-acid-composition
#18
Pooja Tripathi, Paras N Pandey
The present work employs pseudo amino acid composition (PseAAC) for encoding the protein sequences in their numeric form. Later this will be arranged in the similarity matrix, which serves as input for spectral graph clustering method. Spectral methods are used previously also for clustering of protein sequences, but they uses pair wise alignment scores of protein sequences, in similarity matrix. The alignment score depends on the length of sequences, so clustering short and long sequences together may not good idea...
May 3, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28476561/mathematical-descriptions-of-indeterminate-growth
#19
Christopher D Powell, Secundino López, André Dumas, Dominique P Bureau, Sarah E Hook, James France
Two models were derived in an effort to better describe the indeterminate nature of growth exhibited by ectotherms. The models are characterized by their non-sigmoidal shape and are based on three assumptions: quantity of growth machinery works at a rate dependent on feed intake; the relationship between growth rate and intake level follows the law of diminishing returns; and growth is irreversible. The Michaelis-Menten and Mitscherlich equations are used in their formulation. To investigate their potential, the models were fitted to six datasets, representing repeated measures of live body weights of two species: rainbow trout (Oncorhynchus mykiss) and Nile tilapia (Oreochromis niloticus)...
May 3, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28472620/bidirectionality-from-cargo-thermal-fluctuations-in-motor-mediated-transport
#20
Christopher E Miles, James P Keener
Molecular motor proteins serve as an essential component of intracellular transport by generating forces to haul cargoes along cytoskeletal filaments. Two species of motors that are directed oppositely (e.g. kinesin, dynein) can be attached to the same cargo, which is known to produce bidirectional net motion. Although previous work focuses on the motor number as the driving noise source for switching, we propose an alternative mechanism: cargo diffusion. A mean-field mathematical model of mechanical interactions of two populations of molecular motors with cargo thermal fluctuations (diffusion) is presented to study this phenomenon...
May 1, 2017: Journal of Theoretical Biology
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