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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/28927812/bi-pssm-position-specific-scoring-matrix-based-intelligent-computational-model-for-identification-of-mycobacterial-membrane-proteins
#1
Muslim Khan, Maqsood Hayat, Sher Afzal Khan, Saeed Ahmad, Nadeem Iqbal
Mycobacterium is a pathogenic bacterium, which is a causative agent of tuberculosis (TB) and leprosy. These diseases are very crucial and become the cause of death of millions of people every year in the world. So, the characterize structure of membrane proteins of the protozoan play a vital role in the field of drug discovery because, without any knowledge about this Mycobacterium's membrane protein and their types, the scientists are unable to treat this pathogenic protozoan. So, an accurate and competitive computational model is needed to characterize this uncharacterized structure of mycobacterium...
September 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28923372/in-vitro-tubulogenesis-of-madin-darby-canine-kidney-mdck-spheroids-occurs-depending-on-constituent-cell-number-and-scaffold-gel-concentration
#2
Tsuyoshi Hirashima, Miho Hoshuyama, Taiji Adachi
In vitro tubulogenesis has been employed as an experimental model system to study tissue morphogenesis of internal organs. It has been previously shown that Madin-Darby canine kidney (MDCK) cells form tubes in the presence of hepatocyte growth factor in 3D cultures. Although these cells are expected to form tube structures in some microenvironments independent of chemical stimulation, little is known about the cellular mechanisms in organizing such an anisotropic multicellular structure. Here, we report 3D culture conditions that induce MDCK tubulogenesis without growth factor stimulation...
September 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28919399/a-numerical-model-suggests-the-interplay-between-nuclear-plasticity-and-stiffness-during-a-perfusion-assay
#3
Solenne Deveraux, Rachele Allena, Denis Aubry
Cell deformability is a necessary condition for a cell to be able to migrate, an ability that is vital both for healthy and diseased organisms. The nucleus being the largest and stiffest organelle, it often is a barrier to cell migration. It is thus essential to characterize its mechanical behaviour. First, we numerically investigate the visco-elasto-plastic properties of the isolated nucleus during a compression test. This simulation highlights the impact of the mechanical behaviour of the nuclear lamina and the nucleoplasm on the overall plasticity...
September 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28919398/controlling-bovine-paratuberculosis-at-a-regional-scale-towards-a-decision-modelling-tool
#4
Gaël Beaunée, Elisabeta Vergu, Alain Joly, Pauline Ezanno
Johne's disease (paratuberculosis), a worldwide enzootic disease of cattle caused by Mycobacterium avium subsp. paratuberculosis (Map), mainly introduced into farms by purchasing infected animals, has a large economic impact for dairy producers. Since diagnostic tests used in routine are poorly sensitive, observing Map spread in the field is hardly possible, whereas there is a need for evaluating control strategies. Our objective was to provide a modelling framework to compare the efficacy of regional control strategies combining internal biosecurity measures and testing of traded animals, against Map spread in a metapopulation of dairy cattle herds...
September 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28919397/inferring-within-host-bottleneck-size-a-bayesian-approach
#5
R Dybowski, O Restif, D J Price, P Mastroeni
Recent technical developments in microbiology have led to new discoveries on the within-host dynamics of bacterial infections in laboratory animals. In particular, they have highlighted the importance of stochastic bottlenecks at the onset of invasive disease. A number of approaches exist for bottleneck-size estimation with respect to within-host bacterial infections; however, some are more appropriate than others under certain circumstances. A Bayesian comparison of several approaches is made in terms of the availability of isogenic multitype bacteria (e...
September 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28918332/control-of-absence-epilepsy-seizures-in-specific-relay-nuclei-of-thalamus
#6
Bing Hu, Xiaoqiang Zou, Yu Guo, Zhejia Yang, Feng Shi, Wangyuan Dong
In this paper, we used a classic basal ganglia-corticothalamic model(BGCT) to study the onset and control mechanism of absence epilepsy in specific relay nuclei (SRN) of thalamus. It was found that the seizure state may appear in SRN by turning the coupling strength -vsr and signal transmission delay τ on the route "Thalamic reticular nuclei (TRN) of thalamus ⟶ SRN". With increasing of -vsr, the seizure state appeared two times, and its onset mechanism has not been discussed in previous studies. The seizure activity can be well controlled by adjusting the activation level of the substantia nigra pars reticulata (SNr) in basal ganglia, which is a main output tissue to the corticothalamic system through two direct inhibitory pathways "SNr ⟶ SRN" and "SNr ⟶ TRN" in our model...
September 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28918333/the-relationship-between-coherence-and-the-phase-locking-value
#7
LETTER
Kyle Q Lepage, Sujith Vijayan
No abstract text is available yet for this article.
September 13, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28916452/symbolic-dynamics-of-animal-interaction
#8
Maurizio Porfiri, Manuel Ruiz Marín
Since its introduction nearly two decades ago, transfer entropy has contributed to an improved understanding of cause-and-effect relationships in coupled dynamical systems from raw time series. In the context of animal behavior, transfer entropy might help explain the determinants of leadership in social groups and elucidate escape response to predator attacks. Despite its promise, the potential of transfer entropy in animal behavior is yet to be fully tested, and a number of technical challenges in information theory and statistics remain open...
September 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28916451/switches-in-a-genetic-regulatory-system-under-multiplicative-non-gaussian-noise
#9
Xi Chen, Yan-Mei Kang, Yu-Xuan Fu
The non-Gaussian noise is multiplicatively introduced to model the universal fluctuation in the gene regulation of the bacteriophage λ. To investigate the key effect of non-Gaussian noise on the genetic on/off switch dynamics from the viewpoint of quantitative analysis, we employ the high-order perturbation expansion to deduce the stationary probability density of repressor concentration and the mean first passage time from low concentration to high concentration and vice versa. The occupation probability of different concentration states can be estimated from the height and shape of the peaks of the stationary probability density, which could be used to determine the overall expression level...
September 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28899756/stability-based-sorting-the-forgotten-process-behind-not-only-biological-evolution
#10
Jan Toman, Jaroslav Flegr
Natural selection is considered to be the main process that drives biological evolution. It requires selected entities to originate dependent upon one another by the means of reproduction or copying, and for the progeny to inherit the qualities of their ancestors. However, natural selection is a manifestation of a more general persistence principle, whose temporal consequences we propose to name "stability-based sorting" (SBS). Sorting based on static stability, i.e., SBS in its strict sense and usual conception, favours characters that increase the persistence of their holders and act on all material and immaterial entities...
September 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28870620/fixation-probability-of-a-nonmutator-in-a-large-population-of-asexual-mutators
#11
Kavita Jain, Ananthu James
In an adapted population of mutators in which most mutations are deleterious, a nonmutator that lowers the mutation rate is under indirect selection and can sweep to fixation. Using a multitype branching process, we calculate the fixation probability of a rare nonmutator in a large population of asexual mutators. We show that when beneficial mutations are absent, the fixation probability is a nonmonotonic function of the mutation rate of the mutator: it first increases sublinearly and then decreases exponentially...
September 7, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28888947/a-tale-of-three-rnas-in-mitochondria-trna-trna-derived-fragments-and-mitomirs
#12
LETTER
Thejaswini Venkatesh, Shaharabhanu A Hussain, Padmanaban S Suresh
No abstract text is available yet for this article.
September 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28888946/autocatalytic-confusion-clarified
#13
Wim Hordijk
There is frequent confusion about the terms autocatalytic reaction, autocatalytic cycle, and autocatalytic set. As the use of the same adjective implies, these three systems do indeed share common properties, in particular their potential for exponential growth. However, the ways in which they achieve this potential are different, giving rise to different internal network structures and dynamics. Therefore, care should be taken which term is used in which context. Here, we explain and discuss the similarities and differences between the three systems in detail, in an effort to avoid any further confusion...
September 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28888945/mathematical-model-for-the-spread-of-drug-resistance-in-plasmodium-falciparum-parasite-considering-transmission-conditions
#14
REVIEW
Mario Cañón, Hernando Diaz, Andrés Olarte
Antimalarial drugs have been used as one of the main strategies for controlling this disease. However, the spread of drug resistance in the Plasmodium falciparum parasite has generated major challenges for the control of malaria. For this reason, it is necessary to develop an efficient policy considering the parasite behavior in relation to drug treatment and epidemiological parameters. To achieve this goal, we propose a mathematical model that describes the dynamics of parasite population considering the transmission effects between mosquitoes and humans...
September 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28870619/a-causal-bayesian-network-model-of-disease-progression-mechanisms-in-chronic-myeloid-leukemia
#15
Daniel Koch, Robert S Eisinger, Alexander Gebharter
Chronic myeloid leukemia (CML) is a cancer of the hematopoietic system initiated by a single genetic mutation which results in the oncogenic fusion protein Bcr-Abl. Untreated, patients pass through different phases of the disease beginning with the rather asymptomatic chronic phase and ultimately culminating into blast crisis, an acute leukemia resembling phase with a very high mortality. Although many processes underlying the chronic phase are well understood, the exact mechanisms of disease progression to blast crisis are not yet revealed...
September 1, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28870618/revisiting-the-theoretical-basis-of-the-endosymbiotic-origin-of-plastids-in-the-original-context-of-lynn-margulis-on-the-origin-of-mitosing-eukaryotic-cells
#16
Naoki Sato
Fifty years ago, Lynn Margulis proposed a comprehensive hypothesis on the origin of eukaryotic cells with an emphasis on the origin of mitosis. This hypothesis postulated that the eukaryotic cell is a composite of different parts as a result of the symbiosis of various different bacteria. In this hypothesis, she integrated previously proposed ideas that mitochondria and chloroplasts were descendants of endosymbionts that originated from aerobic bacteria and blue-green algae (now cyanobacteria), respectively...
September 1, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28870617/spatial-vs-non-spatial-eco-evolutionary-dynamics-in-a-tumor-growth-model
#17
Li You, Joel S Brown, Frank Thuijsman, Jessica J Cunningham, Robert A Gatenby, Jingsong Zhang, Kateřina Staňková
Metastatic prostate cancer is initially treated with androgen deprivation therapy (ADT). However, resistance typically develops in about 1 year - a clinical condition termed metastatic castrate-resistant prostate cancer (mCRPC). We develop and investigate a spatial game (agent based continuous space) of mCRPC that considers three distinct cancer cell types: 1) those dependent on exogenous testosterone (T(+)), 2) those with increased CYP17A expression that produce testosterone and provide it to the environment as a public good (T(P)), and 3) those independent of testosterone (T(-))...
September 1, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28867224/optional-interactions-and-suspicious-behaviour-facilitates-trustful-cooperation-in-prisoners-dilemma
#18
Tadeas Priklopil, Krishnendu Chatterjee, Martin Nowak
In evolutionary game theory interactions between individuals are often assumed obligatory. However, in many real-life situations, individuals can decide to opt out of an interaction depending on the information they have about the opponent. We consider a simple evolutionary game theoretic model to study such a scenario, where at each encounter between two individuals the type of the opponent (cooperator/defector) is known with some probability, and where each individual either accepts or opts out of the interaction...
September 1, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28867223/protein-protein-interaction-site-predictions-with-minimum-covariance-determinant-and-mahalanobis-distance
#19
Zhijun Qiu, Bo Zhou, Jiangfeng Yuan
Protein-protein interaction site (PPIS) prediction must deal with the diversity of interaction sites that limits their prediction accuracy. Use of proteins with unknown or unidentified interactions can also lead to missing interfaces. Such data errors are often brought into the training dataset. In response to these two problems, we used the minimum covariance determinant (MCD) method to refine the training data to build a predictor with better performance, utilizing its ability of removing outliers. In order to predict test data in practice, a method based on Mahalanobis distance was devised to select proper test data as input for the predictor...
September 1, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28867222/inter-airway-structural-heterogeneity-interacts-with-dynamic-heterogeneity-to-determine-lung-function-and-flow-patterns-in-both-asthmatic-and-control-simulated-lungs
#20
G M Donovan
Asthma is a disease involving both airway remodelling (e.g. thickening of the airway wall) and acute, reversible airway narrowing driven by airway smooth muscle contraction. Both of these processes are known to be heterogeneous, and in this study we consider a new theoretical model which considers the interactions of both mechanisms: structural heterogeneity (variation in airway remodelling) and dynamic heterogeneity (emergent variation in airway narrowing and flow). By integrating both types of inter-airway heterogeneity in a full human lung geometry, we are able to draw several insights regarding the mechanisms underlying observed ventilation heterogeneity...
August 31, 2017: Journal of Theoretical Biology
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