13,876 results match your criteria Journal of theoretical biology[Journal]


Prediction of Antioxidant proteins by incorporating statistical moments based features into Chou's PseAAC.

J Theor Biol 2019 Apr 18. Epub 2019 Apr 18.

Department of Computer Science, School of Systems and Technology, University of Management and Technology, Lahore, Pakistan.

Antioxidant proteins are considered crucial in the areas of research on life sciences and pharmacology. They prevent damage to cells and DNA which are caused by free radicals. The role of antioxidants in the ageing process makes them more significant in their accurate identification. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.019DOI Listing

A theory for investment across defences triggered at different stages of a predator-prey encounter.

J Theor Biol 2019 Apr 17. Epub 2019 Apr 17.

Department of Mathematics, City University of London, London EC1V 0HB, United Kingdom.

We introduce a general theoretical description of a combination of defences acting sequentially at different stages in the predatory sequence in order to make predictions about how animal prey should best allocate investment across different defensive stages. We predict that defensive investment will often be concentrated at stages early in the interaction between a predator individual and the prey (especially if investment is concentrated in only one defence, then it will be in the first defence). Key to making this prediction is the assumption that there is a cost to a prey when it has a defence tested by an enemy, for example because this incurs costs of deployment or tested costs as a defence is exposed to the enemies; and the assumption that the investment functions are the same among defences. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.016DOI Listing

Modeling the Effect of Tat Inhibitors on HIV Latency.

J Theor Biol 2019 Apr 17. Epub 2019 Apr 17.

Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Unidad Monterrey, Via del Conocimiento 201, Parque PIIT, Apodaca CP 66600 NL, México. Electronic address:

Even in the presence of a successful combination therapy stalling the progress of AIDS, developing a cure for this disease is still an open question. One of the major steps towards a cure would be to be able to eradicate latent HIV reservoirs present in patients. During the last decade, multiple findings point to the dominant role of the viral protein Tat in the establishment of latency. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00225193193015
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http://dx.doi.org/10.1016/j.jtbi.2019.04.018DOI Listing
April 2019
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Restoration of cytosolic calcium inhibits Mycobacterium tuberculosis intracellular growth: theoretical evidence and experimental observation.

J Theor Biol 2019 Apr 16. Epub 2019 Apr 16.

Drug Discovery Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121001, India. Electronic address:

Mycobacterium tuberculosis (Mtb) is a highly successful intracellular pathogen because of its ability to modulate host's anti-microbial pathways. Phagocytosis acts as the first line of defence against microbial infection. However, Mtb inhibits Phosphatidylinositol 3-phosphate (PI3P) oscillations which is required for phagolysosomal fusion. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.017DOI Listing

Assessor teaching and the development of the capacity to innovate and to imitate.

J Theor Biol 2019 Apr 16. Epub 2019 Apr 16.

Departamento de Producción Agraria, ETSIAAB-UPM, Spain. Electronic address:

Human beings have generated a system of cumulative cultural learning with great adaptive value. The evolution of this system required an increase in the capacity to innovate and to imitate in hominin lineage. However that development is costly and, moreover, imitation may restrain the adaptive advantage of a greater investment on innovation. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.004DOI Listing

The formation of the Thickveins (Tkv) gradient in Drosophila wing discs: A theoretical study.

Authors:
Zhan Chen

J Theor Biol 2019 Apr 15. Epub 2019 Apr 15.

Department of Mathematical Sciences, Georgia Southern University, Statesboro, GA, United States.

The development of wing imaginal disc (wing disc) is commonly adopted for the studies of patterning and growth which are two fundamental problems in developmental biology. Decapentaplegic (Dpp) signaling regulates several aspects of wing development, such as the anterior (A)-posterior (P) patterning, cellular growth rate, and cell adhesion. The distribution and activity of Dpp signaling are controlled in part by the expression level of its major type I receptor, Thickveins (Tkv). Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.015DOI Listing
April 2019
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The left-hand side of the Fundamental Theorem of Natural Selection: A reply.

J Theor Biol 2019 Apr 13;472:77-83. Epub 2019 Apr 13.

Department of Biology, The University of Pennsylvania, Philadelphia, PA 19104, USA.

In a recent paper, Grafen (2018) discussed the left-hand side in the equation stating Fisher's (1930, 1958) "Fundamental Theorem of Natural Selection" (FTNS). Fisher's original statement of the FTNS is, in effect, "The rate of increase in fitness of any organism is equal to its genetic variance in fitness at that time" with the rate of increase in fitness understood as the one "due to all changes in gene ratios" (Fisher, 1930, p. 35). Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.014DOI Listing
April 2019
4 Reads

Use of age-stage structural models to seek optimal Wolbachia-infected male mosquito releases for mosquito-borne disease control.

J Theor Biol 2019 Apr 13. Epub 2019 Apr 13.

College of Mathematics and Information Sciences, Guangzhou University, Guangzhou, 510006, PRC; Center for Applied Mathematics, Guangzhou University, Guangzhou, 510006 China. Electronic address:

Due to the lack of vaccines and effective clinical cures, current methods to control mosquito-borne viral diseases such as dengue and Zika are primarily targeting to eradicate the major mosquito vectors. However, traditional means, including larval source reduction and applications of insecticides etc, are not sufficient to keep vector population density below the epidemic risk threshold. An innovative and operational strategy is to release Wolbachia-infected male mosquitoes into wild areas to sterilize wild female mosquitoes by cytoplasmic incompatibility. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.010DOI Listing
April 2019
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Boolean network analysis through the joint use of linear algebra and algebraic geometry.

J Theor Biol 2019 Apr 15;472:46-53. Epub 2019 Apr 15.

Dipartimento di Ingegneria Civile e Ingegneria Informatica, Università di Roma Tor Vergata, Roma 00133, Italy. Electronic address:

Among the various phenomena that can be modeled by Boolean networks, i.e., discrete-time dynamical systems with binary state variables, gene regulatory interactions are especially well known. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.012DOI Listing
April 2019
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Evolution of cumulative culture for niche construction.

J Theor Biol 2019 Apr 12;472:67-76. Epub 2019 Apr 12.

SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan.

A mathematical model of the joint evolution of learning and niche construction in a spatially subdivided population is described, in which culture is used to practice niche construction and can evolve by accumulating small improvements over generations. Individuals allocate their lifetimes to social learning, individual learning, niche construction to improve the environment, and exploitation of resources according to their genetically determined strategies. The coordinated optimal strategy (COS) is defined as the allocation strategy which maximizes the equilibrium fecundity of the population, as opposed to the convergence stable strategy (CSS), which is the strategy favored by natural selection. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.013DOI Listing
April 2019
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A vivid cytokines interaction model on psoriasis with the effect of impulse biologic (TNF-α inhibitor) therapy.

J Theor Biol 2019 Apr 10. Epub 2019 Apr 10.

Centre for Mathematical Biology and Ecology, Department of Mathematics, Jadavpur University, Kolkata 700032, India.

Psoriasis is a chronic skin condition that produces plaques of condensed, scaling skin due to excessively rapid proliferation of keratinocytes. Many cytokines influence the proliferation. This article deals with a five dimensional deterministic model, which has been derived using quasi-steady-state approximation for describing the dynamics of psoriasis in various cytokines environment. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.007DOI Listing
April 2019
1 Read

Adaptive damage retention mechanism enables healthier yeast population.

J Theor Biol 2019 Apr 10. Epub 2019 Apr 10.

Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden. Electronic address:

During cytokinesis in budding yeast (Saccharomyces cerevisiae) damaged proteins are distributed asymmetrically between the daughter and the mother cell. Retention of damaged proteins is a crucial mechanism ensuring a healthy daughter cell with full replicative potential and an ageing mother cell. However, the protein quality control (PQC) system is tuned for optimal reproduction success which suggests optimal health and size of the population, rather than long-term survival of the mother cell. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.005DOI Listing

The problem of detrending when analysing potential indicators of disease elimination.

J Theor Biol 2019 Apr 10. Epub 2019 Apr 10.

Mathematics Institute, University of Warwick, Coventry, UK; School of Life Sciences, University of Warwick, Coventry, UK. Electronic address:

As we strive towards the elimination of many burdensome diseases, the question of when intervention efforts may cease is increasingly important. It can be very difficult to know when prevalences are low enough that the disease will die out without further intervention, particularly for diseases that lack accurate tests. The consequences of stopping an intervention prematurely can put back elimination efforts by decades. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.011DOI Listing
April 2019
4 Reads

Molecular dynamics simulations study of influence of Tyr422Ala mutation on transcriptional enhancer activation domain 4 (TEAD4) and transcription co-activators complexes.

J Theor Biol 2019 Apr 10;472:27-35. Epub 2019 Apr 10.

Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China. Electronic address:

Transcriptional enhancer activation domain (TEAD) proteins are the downstream transcriptional factor of the Hippo pathway. The transcription co-activators Yes-associated protein (YAP) and its paralog transcription co-activators with PDZ-binding motif (TAZ), binding to TEAD to promote transcription of genes in cell proliferation and anti-apoptosis, are key effectors of the Hippo pathway. TEAD4, one member of TEAD proteins, is specifically required in embryo implantation. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.009DOI Listing
April 2019
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The effects of cerebral curvature on cortical spreading depression.

J Theor Biol 2019 Apr 9;472:11-26. Epub 2019 Apr 9.

Department of Mechanical Engineering, University of Canterbury, New Zealand.

Neuronal activity evokes a localised increase in cerebral blood flow through neurovascular coupling (NVC), a communication system between a group of cells known as a neurovascular unit (NVU). Dysfunctional NVC can lead to pathologies such as cortical spreading depression (CSD), characterised by a slowly propagating wave of neuronal depolarisation and high extracellular potassium (K) levels. CSD is associated with several neurological disorders such as migraine, stroke, and traumatic brain injury. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.006DOI Listing
April 2019
4 Reads

Non-equilibrium thermodynamics of biological signal transduction predicts conservation of entropy production rate.

J Theor Biol 2019 Apr 10;472:84-87. Epub 2019 Apr 10.

Department of Discovery Medicine, Pathology Division, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8315, Japan. Electronic address:

Studies have reported that bio-cellular signal transduction can be investigated based on thermodynamics. This short article aims to consider signal transduction carried out by signaling molecules from the perspective of non-equilibrium thermodynamics. Under conditions in which total entropy production rate was minimized, the entropy production rate per signaling molecule was conserved independently of the steps during signal transduction. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.008DOI Listing

Testing the rogue taxa hypothesis for clustering instability.

J Theor Biol 2019 Apr 4;472:36-45. Epub 2019 Apr 4.

Department of Molecular and Cellular Biology, University of Guelph, Canada. Electronic address:

There have been longstanding concerns about the stability of hierarchical clustering. A suggested explanation for this instability is the presence of "rogue taxa", i.e. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.002DOI Listing
April 2019
4 Reads

Estimate of the annual risk of tuberculosis infection in a general population of Japan.

J Theor Biol 2019 Apr 4;472:1-3. Epub 2019 Apr 4.

Graduate School of Medicine, Hokkaido University, Kita 15 Jo Nishi 7 Chome, Kitaku, Sapporo 060-8638, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2019.04.003DOI Listing
April 2019
6 Reads

Reconciliation of a gene network and species tree.

J Theor Biol 2019 Apr 3;472:54-66. Epub 2019 Apr 3.

School of BioSciences, The University of Melbourne, Melbourne, Australia.

The phylogenetic trees of genes and the species which they belong to are similar, but distinct due to various evolutionary processes which affect genes but do not create new species. Reconciliations map the gene tree into the species tree, explaining the discrepancies by events including gene duplications and losses. However, when duplicate genes undergo recombination (a phenomenon known as paralog exchange, or non-allelic homologous recombination), the phylogeny of the genes becomes a network, not a tree. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.04.001DOI Listing
April 2019
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The evolutionary game of interspecific mutualism in the multi-species model.

Authors:
Shota Shibasaki

J Theor Biol 2019 Mar 29;471:51-58. Epub 2019 Mar 29.

Department of General Systems Studies, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 1538902, Japan; Department of Fundamental Microbiology, University of Lausanne, Quartier UNIL-Sorge, CH-1015 Lausanne, Switzerland. Electronic address:

Mutualistic interspecific interactions, including Müllerian mimicry and division of labor, are common in nature. In contrast to antagonistic interactions, where faster evolution is favored, mutualism can favor slower evolution under certain conditions. This is called the Red King effect. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.026DOI Listing
March 2019
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Theoretical minimal RNA rings recapitulate the order of the genetic code's codon-amino acid assignments.

J Theor Biol 2019 Mar 29;471:108-116. Epub 2019 Mar 29.

The National Natural History Collections, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel.

Background: Theoretical minimal RNA rings form stem-loop hairpins coding for each of the 20 amino acids and a stop, presumably mimicking life's first minimal coding and self-replicating RNAs. They resemble consensual tRNAs. Mean amino acid positions in proteins follow the genetic code's consensual amino acid inclusion order, a 5'-late-to-3'-early amino acid gradient. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.024DOI Listing
March 2019
2 Reads

A nonlinear mathematical model of cell-mediated immune response for tumor phenotypic heterogeneity.

J Theor Biol 2019 Mar 29;471:42-50. Epub 2019 Mar 29.

Centro de Matemática, Computação e Cognição, UFABC, Santo André, 09210-170, SP, Brazil. Electronic address:

Human cancers display intra-tumor heterogeneity in many phenotypic features, such as expression of cell surface receptors, growth, and angiogenic, proliferative, and immunogenic factors, which represent obstacles to a successful immune response. In this paper, we propose a nonlinear mathematical model of cancer immunosurveillance that takes into account some of these features based on cell-mediated immune responses. The model describes phenomena that are seen in vivo, such as tumor dormancy, robustness, immunoselection over tumor heterogeneity (also called "cancer immunoediting") and strong sensitivity to initial conditions in the composition of tumor microenvironment. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.025DOI Listing
March 2019
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Canalicular fluid flow induced by loading waveforms: A comparative analysis.

J Theor Biol 2019 Mar 29;471:59-73. Epub 2019 Mar 29.

Manipal University Jaipur, Jaipur 303007, Rajasthan, India.

Dynamic loading on the bone is beneficial in prevention and cure of bone loss as it encourages osteogenesis (i.e., new bone formation). Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.023DOI Listing
March 2019
1 Read
2.116 Impact Factor

Configuration of DNA polyhedra of truncated tetrahedron, cuboctahedron, truncated octahedron.

Authors:
Tao Deng

J Theor Biol 2019 Mar 27;472:4-10. Epub 2019 Mar 27.

Key Laboratory of China's Ethnic Languages and Information Technology of Ministry of Education, Northwest Minzu University, Lanzhou 730000, PR China; Key Laboratory of Streaming Data Computing Technologies and Application, Northwest Minzu University, Lanzhou 730030, PR China; School of Mathematics and Computer Science, Northwest Minzu University, Lanzhou 730030, PR China. Electronic address:

The synthesis of DNA polyhedra has attracted more interest because of its wide application prospect, but its formation mechanism from mathematical viewpoint remains poorly understood. This paper presents the assembly process and mechanism of DNA truncated tetrahedron, cuboctahedron and truncated octahedron by the means of mathematics and computer program. Firstly, based on the assumption that the total number of all the crossings within each face of a DNA polyhedron must be an even number, potential types for three DNA polyhedra above are calculated by computer programs; Secondly, the projections of the truncated tetrahedron, the cuboctahedron and the truncated octahedron are plotted based on data fetched by the program; Thirdly, the component number, the odd-crossing edge number and even-crossing edge number for the corresponding polyhedral links are computed by analysis of their projections. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.020DOI Listing
March 2019
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The preliminary efficacy evaluation of the CTLA-4-Ig treatment against Lupus nephritis through in-silico analyses.

J Theor Biol 2019 Mar 27;471:74-81. Epub 2019 Mar 27.

Gordon Life Science Institute, Boston, MA 02478, USA. Electronic address:

The humanized cytotoxic T lymphocyte-associated antigen 4 immunoglobulin (CTLA-4-Ig) has been used to treat Lupus nephritis (LN) based on CTLA-4s negative regulation of T-cell activation through competent to binding with CD80/CD86, the inherent genetic factors influencing the CTLA-4-Ig treatment efficacy are widely unknown. Here, 62 nonsynonymous single nucleotide variants (nsSNVs) of CTLA-4 gene, 184 of CD80 and 201 of CD86 were identified and validated within both EMBL-EBI and dbSNP databases. Next, the nsSNVs rs1466152724 in CTLA-4, rs1196816748, rs765515058, rs1157880125, rs1022857991, and rs142547094 in CD80 and rs1203132714 in CD86 were consistently suggested to be deleterious by SIFT, PolyPhen-2, PROVEAN and meta LR. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.017DOI Listing
March 2019
2 Reads

Sexual transmission and the probability of an end of the Ebola virus disease epidemic.

J Theor Biol 2019 Mar 27;471:1-12. Epub 2019 Mar 27.

Graduate School of Medicine, Hokkaido University, Sapporo 060-8638, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan. Electronic address:

The criteria of zero Ebola cases defined by the World Health Organization did not explicitly account for the sexual transmission and led to multiple recrudescent events in West Africa from 2015 to 2016, partly indeed caused by sexual transmission from survivors. We devised a statistical model to compute the probability of the end of an Ebola virus disease epidemic, accounting for sexual transmission and under-ascertainment of cases. Analyzing the empirical data in Guinea, Liberia and Sierra Leone, the performance of the proposed model was compared with the existing criteria comprising a fixed waiting time of 42 days since the last case testing negative or burial. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.022DOI Listing
March 2019
1 Read
2.116 Impact Factor

Cultural skill and language: How structuration affects cultural evolution.

Authors:
Wataru Nakahashi

J Theor Biol 2019 Mar 26;471:13-21. Epub 2019 Mar 26.

Faculty of Social Sciences, Waseda University, Nishi-Waseda 1-6-1, Shinjuku, Tokyo 169-8050, Japan. Electronic address:

The existence of complex structures involved in cultural skills is one of the unique characteristics in humans. Since human language is also complexly structured, we can presume that the ability to merge and divide units (structuration ability) contributes to their existence. To investigate the emergence of structuration ability archeologically, we must confirm its effect on cultural evolution. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.019DOI Listing

The active selfish herd.

J Theor Biol 2019 Mar 27;471:82-90. Epub 2019 Mar 27.

The University of Western Australia, Department of Mathematics and Statistics, Crawley, 6009, Australia; Mineral Resources, CSIRO, Kensington, 6151, Australia.

The selfish herd hypothesis provides an explanation for group aggregation via the selfish avoidance of predators. Conceptually, and as was first proposed, this movement should aim to minimise the danger domain of each individual. Whilst many reasonable proxies have been proposed, none have directly sought to reduce the danger domain. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.021DOI Listing

Rational Design, Conformational Analysis and Membrane-penetrating Dynamics Study of Bac2A-derived Antimicrobial Peptides against Gram-positive Clinical Strains Isolated from Pyemia.

J Theor Biol 2019 Mar 24. Epub 2019 Mar 24.

Department of Anesthesiology, Shanghai United Family Pudong Hospital, Shanghai 201206, China. Electronic address:

The Bac2A (RLARIVVIRVAR) is a linearized counterpart of cationic cyclic peptide Bactenecin -- one of the smallest naturally occurring antimicrobial peptides (AMPs), which, however, generally exhibits a low or moderate antibacterial potency against gram-positive bacteria. Here, it is found that the Bac2A and its linear derivates cannot spontaneously fold into a well-defined helical conformation in solution, thus impairing the peptide amphipathicity and antibacterial activity. Hydrocarbon stapling is rationally designed to constrain the helical conformation of these linear peptides. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.018DOI Listing
March 2019
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Accelerating invasions and the asymptotics of fat-tailed dispersal.

J Theor Biol 2019 Mar 23;471:22-41. Epub 2019 Mar 23.

Department of Applied Mathematics, University of Washington, Box 353925, Seattle, WA 98195-3925, United States.

Integrodifference equations (IDEs) are used in ecology to model the growth and spatial spread of populations. With IDEs, dispersal is specified with a probability density function, called the dispersal kernel, and the shape of the kernel influences how rapidly invasions progress. In this paper, we apply tail additivity, a property of regularly varying probability densities, to model invasions with fat-tailed (power-law decay) dispersal in one dimension. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.016DOI Listing

A 3-variable PDE model for predicting fungal growth derived from microscopic mechanisms.

J Theor Biol 2019 Jun 21;470:90-100. Epub 2019 Mar 21.

LGPM, CentraleSupélec, SFR Condorcet FR CNRS 3417, Centre Européen de Biotechnologie et de Bioéconomie (CEBB), Université Paris-Saclay, 3 Rue des Rouges Terres, 51110, Pomacle, France; LGPM, CentraleSupélec, Université Paris-Saclay, 8-10 Rue Joliot-Curie, 91190, Gif-sur-Yvette, France. Electronic address:

In this work, we present a new PDE model of the growth of Postia placenta, a species of brown rot fungus. The formulation was derived mainly from the biological mechanisms embedded in our discrete model, validated against experimental data. In order to mimic the growth mechanisms, we propose a new reaction-diffusion formulation, based on three variables: the concentration of tips, the branch density and the total hyphal density. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.015DOI Listing
June 2019
7 Reads

Game dynamic model of optimal budget allocation under individual vaccination choice.

J Theor Biol 2019 Jun 20;470:108-118. Epub 2019 Mar 20.

Disease Modelling Lab, Department of Mathematics, School of Natural Sciences, Shiv Nadar University, India. Electronic address:

Communicable diseases are leading cause of child mortality in developing and under-developed countries. Public health ministries in states and country allocate a considerable amount of budget every year for vaccination campaigns to control infections. Even third-party agencies such as Gates Foundation, UNDP, GAVI, World Bank, WHO also allocate huge funds to under-developed and developing countries for vaccination programs and disease eliminations. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.014DOI Listing
June 2019
7 Reads

Influence of the components of propagule pressure, Allee effects, and stochasticity on the time to establish introduced populations.

J Theor Biol 2019 Mar 20;471:91-107. Epub 2019 Mar 20.

Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France; Université Côte d'Azur, INRA, CNRS, ISA, France.

Forecasting whether individuals of an introduced population will succeed to establish is a challenge in invasion and conservation biology. The present work aims to decouple the impact of the components of propagule pressure on the time for population establishment in the presence of Allee effects and stochasticity in propagule sizes. The mean first passage time (MFPT) for a population to reach a viable size is used as a measure of the establishment success for the introduction processes involving periodic introductions. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.012DOI Listing

Glia-mediated modulation of extracellular potassium concentration determines the sexually dimorphic output frequency of a model brainstem oscillator.

J Theor Biol 2019 Mar 19;471:117-124. Epub 2019 Mar 19.

Laboratory of Neurobiology, Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.

Sexual dimorphism in behavior is widespread among animals, but the cellular mechanisms underlying neural control of this phenomenon are largely unknown. One behavior that has provided some important clues about how such sex differences might develop is the electric organ discharge of Apteronotus leptorhynchus. In this weakly electric fish, the mean discharge frequencies of males and females are 880 Hz and 740 Hz, respectively, with little overlap of the two frequency bands. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.013DOI Listing

dForml(KNN)-PseAAC: Detecting formylation sites from protein sequences using K-nearest neighbor algorithm via Chou's 5-step rule and pseudo components.

J Theor Biol 2019 Jun 14;470:43-49. Epub 2019 Mar 14.

Information Science and Technology, Northeast Normal University, Changchun 130117, China. Electronic address:

Formylation is a type of post-translational modification that can occur on lysine sites, which plays an irreplaceable role in organism. To better understand the mechanism, it is necessary to identify formylation sites in proteins accurately. Computational method is popular because of its more convenience and higher speed than traditional experimental methods. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.011DOI Listing

T-Cell mediated adaptive immunity and antibody-dependent enhancement in secondary dengue infection.

J Theor Biol 2019 Jun 13;470:50-63. Epub 2019 Mar 13.

Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan; PRESTO, Japan Science and Technology Agency, Saitama, 332-0012, Japan. Electronic address:

Dengue infection results in a significant number of deaths, mostly in the tropical and subtropical regions across the world. Yet, despite the seriousness of this disease, vaccine, and antiviral drugs that could be employed in dengue treatment remain elusive. The desire to establish the factors determining the disease severity and the growing need for efficient drugs has prompted extensive research interest in within-host viral dynamics. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.010DOI Listing
June 2019
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Shannon's information, Bernal's biopoiesis and Bernoulli distribution as pillars for building a definition of life.

J Theor Biol 2019 Jun 13;470:101-107. Epub 2019 Mar 13.

Faculty of Chemistry, University of Warsaw, Warsaw, Poland. Electronic address:

The quest for defining life has lasted since the beginning of modern science. During the last century, we have reached a lot of milestones toward the understanding of life and its molecular basis. Also, as living creatures, we have imprinted awareness about what is life and what is not. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.009DOI Listing
June 2019
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Why is glycine cleavage system segmentally expressed in radial glia?

Authors:
Kohji Sato

J Theor Biol 2019 Jun 8;470:17-19. Epub 2019 Mar 8.

Department of Organ & Tissue Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashiku, Hamamatsu, Shizuoka 431-3192, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2019.03.007DOI Listing
June 2019
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The onset mechanism of Parkinson's beta oscillations: A theoretical analysis.

J Theor Biol 2019 Jun 8;470:1-16. Epub 2019 Mar 8.

Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China; Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai 201210, China. Electronic address:

In this paper, we build a basal ganglia-cortex-thalamus model to study the oscillatory mechanisms and boundary conditions of the beta frequency band (13-30 Hz) that appears in the subthalamic nucleus. First, a theoretical oscillatory boundary formula is obtained in a simplified model by using the Laplace transform and linearization process of the system at fixed points. Second, we simulate the oscillatory boundary conditions through numerical calculations, which fit with our theoretical results very well, at least in the changing trend. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.008DOI Listing
June 2019
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Neurons and astrocytes interaction in neuronal network: A game-theoretic approach.

J Theor Biol 2019 Jun 9;470:76-89. Epub 2019 Mar 9.

Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran. Electronic address:

A neuron is the fundamental unit of the nervous system and the brain, crucial for transducing information in form of trains of electrical pulses known as action potentials. The connection between neurons is through synapses, enabling communication between neurons. This communication link is one of the key elements in processing of information from a neuron to another neuron. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.02.024DOI Listing
June 2019
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Reaction-diffusion model for STIM-ORAI interaction: The role of ROS and mutations.

J Theor Biol 2019 Jun 7;470:64-75. Epub 2019 Mar 7.

Center for Biophysics & Department of Theoretical Physics, Saarland University, Saarbrücken 66041, Germany. Electronic address:

Release of Ca from endoplasmatic retriculum (ER) Ca stores causes stromal interaction molecules (STIM) in the ER membrane and ORAI proteins in the plasma membrane (PM) to interact and form the Ca release activated Ca (CRAC) channels, which represent a major Ca entry route in non-excitable cells and thus control various cell functions. It is experimentally possible to mutate ORAI1 proteins and therefore modify, especially block, the Ca influx into the cell. On the basis of the model of Hoover and Lewis (2011), we formulate a reaction-diffusion model to quantify the STIM1-ORAI1 interaction during CRAC channel formation and analyze different ORAI1 channel stoichiometries and different ratios of STIM1 and ORAI1 in comparison with experimental data. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00225193193007
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http://dx.doi.org/10.1016/j.jtbi.2019.02.010DOI Listing
June 2019
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Optimal control of acute myeloid leukaemia.

J Theor Biol 2019 Jun 8;470:30-42. Epub 2019 Mar 8.

School of Mathematical Sciences, Queensland University of Technology (QUT), Australia. Electronic address:

Acute myeloid leukaemia (AML) is a blood cancer affecting haematopoietic stem cells. AML is routinely treated with chemotherapy, and so it is of great interest to develop optimal chemotherapy treatment strategies. In this work, we incorporate an immune response into a stem cell model of AML, since we find that previous models lacking an immune response are inappropriate for deriving optimal control strategies. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.006DOI Listing
June 2019
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Evaluating vaccination strategies for tuberculosis in endemic and non-endemic settings.

J Theor Biol 2019 May 6;469:1-11. Epub 2019 Mar 6.

University of Michigan, Department of Microbiology and Immunology, USA. Electronic address:

According to the World Health Organization, tuberculosis (TB) is the leading cause of death from infectious disease worldwide (WHO, 2017). While there is no effective vaccine against adult pulmonary TB, more than a dozen vaccine candidates are in the clinical trial pipeline. These include both pre-exposure vaccines to prevent initial infections and post-exposure vaccines to prevent reactivation of latent disease. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00225193193008
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http://dx.doi.org/10.1016/j.jtbi.2019.02.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6447051PMC
May 2019
7 Reads

Increased infection severity in downstream cities in infectious disease transmission and tourists surveillance analysis.

J Theor Biol 2019 Jun 6;470:20-29. Epub 2019 Mar 6.

Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China. Electronic address:

Infectious disease severely threatens human life. Human mobility and travel patterns influence the spread of infection between cities and countries. We find that the infection severity in downstream cities during outbreaks is related to transmission rate, recovery rate, travel rate, travel duration and the average number of person-to-person contacts per day. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.004DOI Listing
June 2019
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Energy-information coupling during integrative cognitive processes.

Authors:
Strelnikov Kuzma

J Theor Biol 2019 May 5;469:180-186. Epub 2019 Mar 5.

UMR 5549, Faculté de Médecine Purpan, Centre National de la Recherche Scientifique, Toulouse, France; Centre de Recherche Cerveau et Cognition, Université de Toulouse, Université Paul Sabatier, Toulouse, France; Service d'Oto-Rhino-Laryngologie et Oto-Neurologie, Hopital Purpan Toulouse, France. Electronic address:

The physical conception of energy is a natural and general approach to describe functional interactions in the brain at different levels starting from studies of molecular interactions up to the integrative studies of cognitive neuroimaging. In this article, we describe the representation of the brain as a fluctuating energy field, which adaptively reflects the environment. Within this neuroenergetic conception, we indicate a physically solid approach to the problem of the link between brain function and information processing - transmission and integration of information between neuroglial populations is coupled with the corresponding energy increase used for information encoding. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.005DOI Listing
May 2019
3 Reads

Corrigendum to "Peristaltic transport of multilayered power-law fluids with distinct viscosities: A mathematical model for intestinal flows" [Journal of Theoretical Biology 278 (2011) 11-19].

J Theor Biol 2019 Jun 23;470:119. Epub 2019 Mar 23.

Department of Applied Mathematics, Institute of Technology, Banaras Hindu University, Varanasi 221005, India.

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http://dx.doi.org/10.1016/j.jtbi.2019.02.023DOI Listing

Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson's disease: A molecular dynamics simulation approach.

J Theor Biol 2019 May 4;469:163-171. Epub 2019 Mar 4.

Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar. Electronic address:

The G2019S substitution in the Leucine-rich repeat kinase 2 (LRRK2) is significantly associated with Parkinson's disease (PD). This substitution was identified in both familial and sporadic forms of PD with a higher frequency. Few computational studies have reported the impact of G2019S substitution on inhibitors of the kinase domain of LRRK2. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.003DOI Listing

Mathematical modeling of tumor-immune cell interactions.

J Theor Biol 2019 May 2;469:47-60. Epub 2019 Mar 2.

Department of Bioengineering, University of Louisville, KY, USA; James Graham Brown Cancer Center, University of Louisville, KY, USA; Department of Pharmacology & Toxicology, University of Louisville, KY, USA. Electronic address:

The anti-tumor activity of the immune system is increasingly recognized as critical for the mounting of a prolonged and effective response to cancer growth and invasion, and for preventing recurrence following resection or treatment. As the knowledge of tumor-immune cell interactions has advanced, experimental investigation has been complemented by mathematical modeling with the goal to quantify and predict these interactions. This succinct review offers an overview of recent tumor-immune continuum modeling approaches, highlighting spatial models. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.03.002DOI Listing
May 2019
4 Reads

Calculating stochastic inactivation of individual cells in a bacterial population using variability in individual cell inactivation time and initial cell number.

J Theor Biol 2019 May 2;469:172-179. Epub 2019 Mar 2.

Graduate School of Agricultural Science, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan. Electronic address:

The traditional log-linear inactivation kinetics model considers microbial inactivation as a process that follows first-order kinetics. A basic concept of log reduction is decimal reduction time (D-value), which means time/dose required to kill 90% of the relevant microorganisms. D-value based on the first-order survival kinetics model is insufficient for reliable estimations of bacterial survivors following inactivation treatment. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.042DOI Listing
May 2019
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Cost of auditory sharpness: Model-Based estimate of energy use by auditory brainstem "octopus" neurons.

J Theor Biol 2019 May 2;469:137-147. Epub 2019 Mar 2.

Department of Biophysics, Biological faculty, Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow 119234, Russia; Department of Molecular Neurobiology, Institute of Bioorganic Chemistry RAS, Miklukho-Maklay 16/10, Moscow 117997, Russia. Electronic address:

Octopus cells (OCs) of the mammalian auditory brainstem precisely encode timing of fast transient sounds and tone onsets. Sharp temporal fidelity of OCs relies on low resting membrane resistance, which suggests high energy expenditure on maintaining ion gradients across plasma membrane. We provide a model-based estimate of energy consumption in resting and spiking OCs. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.043DOI Listing
May 2019
3 Reads