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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/30419249/predicting-the-ligand-binding-properties-of-borrelia-burgdorferi-s-s-bmp-proteins-in-light-of-the-conserved-features-of-related-borrelia-proteins
#1
Mia Åstrand, Julia Cuellar, Jukka Hytönen, Tiina A Salminen
Bacteria of the genus Borrelia cause vector-borne infections like the most important hard tick-borne disease in the northern hemisphere, Lyme borreliosis (LB), and soft tick or louse transmitted relapsing fevers (RF), prevalent in temperate and tropical areas. Borrelia burgdorferi sensu lato (s.l.) includes several genospecies and causes LB in humans. In infected patients, Borrelia burgdorferi sensu stricto (s.s.) expresses the BmpA, BmpB, BmpC and BmpD proteins. The role of these proteins in the pathogenesis of LB remains incompletely characterized, but they are, however, closely related to Treponema pallidum PnrA (Purine nucleoside receptor A), a substrate-binding lipoprotein of the ATP-binding cassette (ABC) transporter family preferentially binding purine nucleosides...
November 9, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30412699/an-ordination-approach-to-explore-similarities-among-communities
#2
Sandrine Pavoine
Analysis of similarities among communities can help to decipher the biogeographical, evolutionary, and ecological factors that drive local diversity. Recent indices of similarity among communities incorporate not only information on species presence and abundance but also information on how similar species are in their traits and how closely related they are in terms of taxonomy or phylogeny. Towards this aim, trait-based, taxonomic or phylogenetic similarities among species have been defined and bounded between 0 (species are maximally distinct) and 1 (species are similar)...
November 6, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30412698/the-regulatory-role-of-shikimate-in-plant-phenylalanine-metabolism
#3
Z P Adams, J Ehlting, R Edwards
In higher plants, the amino acid phenylalanine is a substrate of both primary and secondary metabolic pathways. The primary pathway that consumes phenylalanine, protein biosynthesis, is essential for the viability of all cells. Meanwhile, the secondary pathways are not necessary for the survival of individual cells, but benefit of the plant as a whole. Here we focus on the monolignol pathway, a secondary metabolic pathway in the cytosol that rapidly consumes phenylalanine to produce the precursors of lignin during wood formation...
November 6, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30395807/mathematical-modeling-of-the-cgas-pathway-reveals-robustness-of-dna-sensing-to-trex1-feedback
#4
Robert W Gregg, Saumendra N Sarkar, Jason E Shoemaker
Cyclic GMP-AMP synthase (cGAS) has recently been identified as the primary protein that detects cytosolic double stranded DNA to invoke a type I interferon response. The cGAS pathway is vital in the recognition of DNA encoded viruses as well as self-DNA leaked from the nucleus of damaged cells. Currently, the dynamics regulating the cGAS pathway are poorly understood; limiting our knowledge of how DNA-induced immune responses are regulated. Using systems biology approaches, we formulated a mathematical model to describe the dynamics of this pathway and examine the resulting system-level emergent properties...
November 2, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30391649/insights-into-the-interaction-of-key-biofilm-proteins-in-pseudomonas-aeruginosa-pao1-with-tio-2-nanoparticle-an-in-silico-analysis
#5
Rani Anupama, Sajitha Lulu, Rout Madhusmita, Sundararajan Vino, Amitava Mukherjee, Subramanian Babu
Pseudomonas aeruginosa is a pathogenic biofilm forming bacteria which exist in wide range of environments such as water, soil and human body. In an earlier study, we used a system biology approach based analysis of biofilm forming genes of P. aeruginosa and their possible role in TiO2 nanoparticle binding. The major protein of P. aeruginosa targeted by TiO2 was found to be KatA, a major catalase required for H2 O2 resistance and acute virulence and the direct interacting protein partners of KatA were found to be DnaK, Hfq, RpoA and RpoS...
November 2, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30391647/the-effect-of-sexual-selection-on-phenotypic-diversification-among-human-populations-a-simulation-study
#6
Saori Nojo, Yasuo Ihara
Despite the generally low level of inter-population genetic differentiation in humans as compared with great apes, it has long been acknowledged that there is a considerable amount of geographic variations in human phenotypes, for example, skin pigmentation, cranial morphology, and soft-tissue facial morphology, to name but a few. Indeed, recent studies have suggested that the extent of inter-population diversity in some human phenotypes is greater than expected from random drift alone. Such an excess of phenotypic diversity is often attributed to adaptation to local environment...
November 2, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30391648/eqtl-analysis-from-co-localization-of-2739-gwas-loci-detects-associated-genes-across-14-human-cancers
#7
Weidong Li, Qingniao Zhou, Yong Gao, Yonghua Jiang, Yuanjie Huang, Zengnan Mo, Yiming Zou, Yanling Hu
Genetic variants can predict other "linked" diseases because alterations in one or more genes in vivo may affect relevant phenotype properties. Our study systematically explored the pan-cancer common gene and cancer type-specific genes based on GWAS loci and TCGA data of multiple cancers. It was found that there were 17 SNPs were significantly associated with the expression of 18 genes. Associations between the 18 cis-regulatory genes and the pathologic stage of each cancer showed that MYL2 and PTGFR in HNSC, 4 genes(F8, SATB2, G6PD and UGT1A6) in KIRP, 3 genes(CHMP4C, MAP3K1 and MECP2) in LUAD were all strongly associated with cancer stage levels...
November 1, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30389532/heterogeneous-viral-strategies-promote-coexistence-in-virus-microbe-systems
#8
Hayriye Gulbudak, Joshua S Weitz
Viral infections of microbial cells often culminate in lysis and the release of new virus particles. However, viruses of microbes can also initiate chronic infections, in which new viruses particles are released via budding and without cell lysis. In chronic infections, viral genomes may also be passed on from mother to daughter cells during division. The consequences of chronic infections for the population dynamics of viruses and microbes remains under-explored. In this paper we present a model of chronic infections as well as a model of interactions between lytic and chronic viruses competing for the same microbial population...
October 30, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30385313/endogenous-mirna-sponges-mediate-the-generation-of-oscillatory-dynamics-for-a-non-coding-rna-network
#9
Andrew Dhawan, Adrian L Harris, Francesca M Buffa, Jacob G Scott
Oscillations are crucial to the normal function of living organisms, across a wide variety of biological processes. In eukaryotes, oscillatory dynamics are thought to arise from interactions at the protein and RNA levels; however, the role of non-coding RNA in regulating these dynamics remains understudied. In this work, we show how non-coding RNA acting as microRNA (miRNA) sponges in a conserved miRNA - transcription factor feedback motif, can give rise to oscillatory behaviour, and how to test for this experimentally...
October 30, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30385311/hybrid-approach-to-modeling-spatial-dynamics-of-systems-with-generalist-predators
#10
Elizabeth F Fussell, Andrew L Krause, Robert A Van Gorder
We consider hybrid spatial modeling approaches for ecological systems with a generalist predator utilizing a prey and either a second prey or an allochthonous resource. While spatial dispersion of populations is often modeled via stepping-stone (discrete spatial patches) or continuum (one connected spatial domain) formulations, we shall be interested in hybrid approaches which we use to reduce the dimension of certain components of the spatial domain, obtaining either a continuum model of varying spatial dimensions, or a mixed stepping-stone-continuum model...
October 30, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30385310/global-dynamics-of-parasitism-competition-systems-with-one-host-and-multiple-parasites
#11
Yuanshi Wang, Hong Wu
This paper studies a new parasitism-competition model with one host and multiple parasites, where a plant is the host and nectar robbers are the parasites that compete for nectar of the plant but do not kill and eat the host itself. Based on the plant-nectar-robber interaction, a parasitism model is derived, which is different from previous parasitism models. Then the two-species model is extended to an n-dimensional system characterizing one plant and multiple robbers. Using dynamical system theory, qualitative behavior of the two-species model is exhibited by excluding existence of periodic solution, and global dynamics of the n-species system in the positive octant are completely shown...
October 30, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30385312/the-biokinetic-spectrum-for-temperature-and-optimal-darwinian-fitness
#12
Ross Corkrey, Cameron Macdonald, Tom McMeekin
Darwinian fitness is maximised at a temperature below Topt , but what this temperature is remains unclear. By linking our previous work on the Biokinetic Spectrum for Temperature with a model for temperature-dependent biological growth rate we obtain a plausible value for such a temperature. We find this approach reveals considerable commonalities in how life responds to temperature with implications that follow in evolution, physiology and ecology. We describe a data set consisting of 17,021 observations of temperature-dependent population growth rates from 2,411 bacterial, archaeal and eukaryal strains...
October 29, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30381147/identifying-key-factors-of-the-transmission-dynamics-of-drug-resistant-malaria
#13
Tamsin E Lee, Melissa A Penny
Development of resistance to malaria treatments remains a great threat to continued malaria burden reduction and elimination. Quantifying the impact of key factors which increase the emergence and spread of drug resistance can guide intervention strategies. Whilst modelling provides a framework to understand these factors, we show that a simple of model with a sensitive-resistant dichotomy leads to incorrectly focusing on reducing the treatment rate as a means to prevent resistance. Instead we present a model that considers the development of resistance within hosts as a scale, and we then quantify the number of resistant infections that would arise from a single sensitive infection...
October 28, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30420333/microvscular-networks-with-uniform-flow
#14
Shyr-Shea Chang, Marcus Roper
Within animals, oxygen exchange occurs within vascular transport networks containing potentially billions of microvessels that are distributed throughout the body. By comparison, large blood vessels are theorized to minimize transport costs, leading to tree-like networks that satisfy Murray's law. We know very little about the principles underlying the organization of healthy micro-vascular networks. Indeed capillary networks must also perfuse tissues with oxygen, and efficient perfusion may be incompatible with minimization of transport costs...
October 27, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30409756/in-silico-analysis-of-plasmodium-falciparum-cdpk5-protein-through-molecular-modeling-docking-and-dynamics
#15
Subhashree Rout, Rajani Kanta Mahapatra
Calcium-Dependent Protein Kinase 5 (CDPK5) protein is one of the family members of a calcium-dependent protein kinase that is found in plants and some species of protozoa which includes Plasmodium falciparum (Pf), the pathogen responsible for malaria. CDPKs regulate many biological processes in Apicomplexans such as Plasmodium, Toxoplasma or Cryptosporidium. The study addresses the similarity in sequences and evolutionary relationship of CDPK5 across Apicomplexans. Further, the three-dimensional structural conformation of PfCDPK5 is generated through homology modeling...
October 27, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30393109/using-mathematical-modeling-to-infer-the-valence-state-of-arsenicals-in-tissues-a-pbpk-model-for-dimethylarsinic-acid-dma-v-and-dimethylarsinous-acid-dma-iii-in-mice
#16
Lydia M Bilinsky, David J Thomas, Jeffrey W Fisher
Chronic exposure to inorganic arsenic (iAs), a contaminant of water and food supplies, is associated with many adverse health effects. A notable feature of iAs metabolism is sequential methylation reactions which produce mono- and di-methylated arsenicals that can contain arsenic in either the trivalent (III) or pentavalent (V) valence states. Because methylated arsenicals containing trivalent arsenic are more potent toxicants than their pentavalent counterparts, the ability to distinguish between the +3 and +5 valence states is a crucial property for physiologically based pharmacokinetic (PBPK) models of arsenicals to possess if they are to be of use in risk assessment...
October 26, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30393108/wave-pinning-in-competition-diffusion-models-in-variable-environments
#17
M C Köhnke, H Malchow
Numerical results on conditions for the emergence of propagation failure of diffusive fronts in two-species competition models for populations with either logistic growth or strong Allee effect are presented. Particularly, the stability against environmental perturbations is investigated. Two different density dependencies of the noise intensities are considered. They mimic a differential functional response of the competitors to the variable environment. Assuming classical linearly density-dependent noise intensities, stochastic wave pinning can occur...
October 25, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30365946/an-energetic-reformulation-of-kinetic-rate-laws-enables-scalable-parameter-estimation-for-biochemical-networks
#18
John C Mason, Markus W Covert
The technology for building functionally complete or 'whole-cell' biological simulations is rapidly developing. However, the predictive capabilities of these simulations are hindered by the availability of parameter values, which are often difficult or even impossible to obtain experimentally and must therefore be estimated. Using E. coli's glycolytic network as a model system, we describe and apply a new method which can estimate the values of all the system's 102 parameters - fit to observations from studies of proteomics, metabolomics, enzyme kinetics and chemical energetics - and find that the resulting metabolic models are not only well-fit, but also dynamically stable...
October 24, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30365947/fu-sulfpred-identification-of-protein-s-sulfenylation-sites-by-fusing-forests-via-chou-s-general-pseaac
#19
Lidong Wang, Ruijun Zhang, Yashuang Mu
Protein S-sulfenylation is an essential post-translational modification (PTM) that provides critical information to understand molecular mechanisms of cell signaling transduction, stress response and regulation of cellular functions. Recent advancements in computational methods have contributed towards the detection of protein S-sulfenylation sites. However, the performance of identifying protein S-sulfenylation sites can be influenced by a class imbalance of training datasets while the application of various computational methods...
October 23, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30365945/prediction-and-functional-analysis-of-prokaryote-lysine-acetylation-site-by-incorporating-six-types-of-features-into-chou-s-general-pseaac
#20
Guodong Chen, Man Cao, Jialin Yu, Xinyun Guo, Shaoping Shi
Lysine acetylation is one of the most important types of protein post-translational modifications (PTM) that are widely involved in cellular regulatory processes. To fully understand the regulatory mechanism of acetylation, identification of acetylation sites is first and most important. However, experimental identification of protein acetylation sites is often time consuming and expensive. Thus, it is popular that predicts PTM sites by computational methods in recent years. Here, we developed a novel method, ProAcePred 2...
October 23, 2018: Journal of Theoretical Biology
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