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PLoS Computational Biology

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https://www.readbyqxmd.com/read/28723903/automatic-analysis-and-3d-modelling-of-hi-c-data-using-tadbit-reveals-structural-features-of-the-fly-chromatin-colors
#1
François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume Filion, Marc A Marti-Renom
The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights in the spatial organization of genomes. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions...
July 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28719607/stress-induced-mutagenesis-stress-diversity-facilitates-the-persistence-of-mutator-genes
#2
Marta Lukačišinová, Sebastian Novak, Tiago Paixão
Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment...
July 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28719601/clic-a-tool-for-expanding-biological-pathways-based-on-co-expression-across-thousands-of-datasets
#3
Yang Li, Alexis A Jourdain, Sarah E Calvo, Jun S Liu, Vamsi K Mootha
In recent years, there has been a huge rise in the number of publicly available transcriptional profiling datasets. These massive compendia comprise billions of measurements and provide a special opportunity to predict the function of unstudied genes based on co-expression to well-studied pathways. Such analyses can be very challenging, however, since biological pathways are modular and may exhibit co-expression only in specific contexts. To overcome these challenges we introduce CLIC, CLustering by Inferred Co-expression...
July 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28715501/diversity-and-distribution-of-nuclease-bacteriocins-in-bacterial-genomes-revealed-using-hidden-markov-models
#4
Connor Sharp, James Bray, Nicholas G Housden, Martin C J Maiden, Colin Kleanthous
Bacteria exploit an arsenal of antimicrobial peptides and proteins to compete with each other. Three main competition systems have been described: type six secretion systems (T6SS); contact dependent inhibition (CDI); and bacteriocins. Unlike T6SS and CDI systems, bacteriocins do not require contact between bacteria but are diffusible toxins released into the environment. Identified almost a century ago, our understanding of bacteriocin distribution and prevalence in bacterial populations remains poor. In the case of protein bacteriocins, this is because of high levels of sequence diversity and difficulties in distinguishing their killing domains from those of other competition systems...
July 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28715483/atomistic-fingerprint-of-hyaluronan-cd44-binding
#5
Joni Vuorio, Ilpo Vattulainen, Hector Martinez-Seara
Hyaluronan is a polyanionic, megadalton-scale polysaccharide, which initiates cell signaling by interacting with several receptor proteins including CD44 involved in cell-cell interactions and cell adhesion. Previous studies of the CD44 hyaluronan binding domain have identified multiple widespread residues to be responsible for its recognition capacity. In contrast, the X-ray structural characterization of CD44 has revealed a single binding mode associated with interactions that involve just a fraction of these residues...
July 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28715420/blood-vessel-tortuosity-selects-against-evolution-of-aggressive-tumor-cells-in-confined-tissue-environments-a-modeling-approach
#6
András Szabó, Roeland M H Merks
Cancer is a disease of cellular regulation, often initiated by genetic mutation within cells, and leading to a heterogeneous cell population within tissues. In the competition for nutrients and growth space within the tumors the phenotype of each cell determines its success. Selection in this process is imposed by both the microenvironment (neighboring cells, extracellular matrix, and diffusing substances), and the whole of the organism through for example the blood supply. In this view, the development of tumor cells is in close interaction with their increasingly changing environment: the more cells can change, the more their environment will change...
July 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28715411/a-curated-genome-scale-metabolic-model-of-bordetella-pertussis-metabolism
#7
Nick Fyson, Jerry King, Thomas Belcher, Andrew Preston, Caroline Colijn
The Gram-negative bacterium Bordetella pertussis is the causative agent of whooping cough, a serious respiratory infection causing hundreds of thousands of deaths annually worldwide. There are effective vaccines, but their production requires growing large quantities of B. pertussis. Unfortunately, B. pertussis has relatively slow growth in culture, with low biomass yields and variable growth characteristics. B. pertussis also requires a relatively expensive growth medium. We present a new, curated flux balance analysis-based model of B...
July 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28708827/deciphering-the-regulation-of-p2x4-receptor-channel-gating-by-ivermectin-using-markov-models
#8
Laurent Mackay, Hana Zemkova, Stanko S Stojilkovic, Arthur Sherman, Anmar Khadra
The P2X4 receptor (P2X4R) is a member of a family of purinergic channels activated by extracellular ATP through three orthosteric binding sites and allosterically regulated by ivermectin (IVM), a broad-spectrum antiparasitic agent. Treatment with IVM increases the efficacy of ATP to activate P2X4R, slows both receptor desensitization during sustained ATP application and receptor deactivation after ATP washout, and makes the receptor pore permeable to NMDG+, a large organic cation. Previously, we developed a Markov model based on the presence of one IVM binding site, which described some effects of IVM on rat P2X4R...
July 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28704399/cooperative-stochastic-binding-and-unbinding-explain-synaptic-size-dynamics-and-statistics
#9
Aseel Shomar, Lukas Geyrhofer, Noam E Ziv, Naama Brenner
Synapses are dynamic molecular assemblies whose sizes fluctuate significantly over time-scales of hours and days. In the current study, we examined the possibility that the spontaneous microscopic dynamics exhibited by synaptic molecules can explain the macroscopic size fluctuations of individual synapses and the statistical properties of synaptic populations. We present a mesoscopic model, which ties the two levels. Its basic premise is that synaptic size fluctuations reflect cooperative assimilation and removal of molecules at a patch of postsynaptic membrane...
July 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28704374/spatial-organization-of-the-budding-yeast-genome-in-the-cell-nucleus-and-identification-of-specific-chromatin-interactions-from-multi-chromosome-constrained-chromatin-model
#10
Gamze Gürsoy, Yun Xu, Jie Liang
Nuclear landmarks and biochemical factors play important roles in the organization of the yeast genome. The interaction pattern of budding yeast as measured from genome-wide 3C studies are largely recapitulated by model polymer genomes subject to landmark constraints. However, the origin of inter-chromosomal interactions, specific roles of individual landmarks, and the roles of biochemical factors in yeast genome organization remain unclear. Here we describe a multi-chromosome constrained self-avoiding chromatin model (mC-SAC) to gain understanding of the budding yeast genome organization...
July 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28704373/possible-roles-of-mechanical-cell-elimination-intrinsic-to-growing-tissue-from-the-perspective-of-tissue-growth-efficiency-and-homeostasis
#11
Sang-Woo Lee, Yoshihiro Morishita
Cell competition is a phenomenon originally described as the competition between cell populations with different genetic backgrounds; losing cells with lower fitness are eliminated. With the progress in identification of related molecules, some reports described the relevance of cell mechanics during elimination. Furthermore, recent live imaging studies have shown that even in tissues composed of genetically identical cells, a non-negligible number of cells are eliminated during growth. Thus, mechanical cell elimination (MCE) as a consequence of mechanical cellular interactions is an unavoidable event in growing tissues and a commonly observed phenomenon...
July 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28692700/noise-multisensory-integration-and-previous-response-in-perceptual-disambiguation
#12
Cesare V Parise, Marc O Ernst
Sensory information about the state of the world is generally ambiguous. Understanding how the nervous system resolves such ambiguities to infer the actual state of the world is a central quest for sensory neuroscience. However, the computational principles of perceptual disambiguation are still poorly understood: What drives perceptual decision-making between multiple equally valid solutions? Here we investigate how humans gather and combine sensory information-within and across modalities-to disambiguate motion perception in an ambiguous audiovisual display, where two moving stimuli could appear as either streaming through, or bouncing off each other...
July 10, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28692643/inverse-stochastic-resonance-in-networks-of-spiking-neurons
#13
Muhammet Uzuntarla, Ernest Barreto, Joaquin J Torres
Inverse Stochastic Resonance (ISR) is a phenomenon in which the average spiking rate of a neuron exhibits a minimum with respect to noise. ISR has been studied in individual neurons, but here, we investigate ISR in scale-free networks, where the average spiking rate is calculated over the neuronal population. We use Hodgkin-Huxley model neurons with channel noise (i.e., stochastic gating variable dynamics), and the network connectivity is implemented via electrical or chemical connections (i.e., gap junctions or excitatory/inhibitory synapses)...
July 10, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28692642/hybrid-modeling-and-prediction-of-dynamical-systems
#14
Franz Hamilton, Alun L Lloyd, Kevin B Flores
Scientific analysis often relies on the ability to make accurate predictions of a system's dynamics. Mechanistic models, parameterized by a number of unknown parameters, are often used for this purpose. Accurate estimation of the model state and parameters prior to prediction is necessary, but may be complicated by issues such as noisy data and uncertainty in parameters and initial conditions. At the other end of the spectrum exist nonparametric methods, which rely solely on data to build their predictions...
July 10, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28686599/flux-balance-analysis-predicts-warburg-like-effects-of-mouse-hepatocyte-deficient-in-mir-122a
#15
Hua-Qing Wu, Mei-Ling Cheng, Jin-Mei Lai, Hsuan-Hui Wu, Meng-Chun Chen, Wen-Huan Liu, Wu-Hsiung Wu, Peter Mu-Hsin Chang, Chi-Ying F Huang, Ann-Ping Tsou, Ming-Shi Shiao, Feng-Sheng Wang
The liver is a vital organ involving in various major metabolic functions in human body. MicroRNA-122 (miR-122) plays an important role in the regulation of liver metabolism, but its intrinsic physiological functions require further clarification. This study integrated the genome-scale metabolic model of hepatocytes and mouse experimental data with germline deletion of Mir122a (Mir122a-/-) to infer Warburg-like effects. Elevated expression of MiR-122a target genes in Mir122a-/-mice, especially those encoding for metabolic enzymes, was applied to analyze the flux distributions of the genome-scale metabolic model in normal and deficient states...
July 7, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28671999/speciation-trajectories-in-recombining-bacterial-species
#16
Pekka Marttinen, William P Hanage
It is generally agreed that bacterial diversity can be classified into genetically and ecologically cohesive units, but what produces such variation is a topic of intensive research. Recombination may maintain coherent species of frequently recombining bacteria, but the emergence of distinct clusters within a recombining species, and the impact of habitat structure in this process are not well described, limiting our understanding of how new species are created. Here we present a model of bacterial evolution in overlapping habitat space...
July 3, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28732007/a-data-driven-modeling-approach-to-identify-disease-specific-multi-organ-networks-driving-physiological-dysregulation
#17
Warren D Anderson, Danielle DeCicco, James S Schwaber, Rajanikanth Vadigepalli
Multiple physiological systems interact throughout the development of a complex disease. Knowledge of the dynamics and connectivity of interactions across physiological systems could facilitate the prevention or mitigation of organ damage underlying complex diseases, many of which are currently refractory to available therapeutics (e.g., hypertension). We studied the regulatory interactions operating within and across organs throughout disease development by integrating in vivo analysis of gene expression dynamics with a reverse engineering approach to infer data-driven dynamic network models of multi-organ gene regulatory influences...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28727821/advances-in-using-internet-searches-to-track-dengue
#18
Shihao Yang, Samuel C Kou, Fred Lu, John S Brownstein, Nicholas Brooke, Mauricio Santillana
Dengue is a mosquito-borne disease that threatens over half of the world's population. Despite being endemic to more than 100 countries, government-led efforts and tools for timely identification and tracking of new infections are still lacking in many affected areas. Multiple methodologies that leverage the use of Internet-based data sources have been proposed as a way to complement dengue surveillance efforts. Among these, dengue-related Google search trends have been shown to correlate with dengue activity...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28727789/lumpgem-systematic-generation-of-subnetworks-and-elementally-balanced-lumped-reactions-for-the-biosynthesis-of-target-metabolites
#19
Meric Ataman, Vassily Hatzimanikatis
In the post-genomic era, Genome-scale metabolic networks (GEMs) have emerged as invaluable tools to understand metabolic capabilities of organisms. Different parts of these metabolic networks are defined as subsystems/pathways, which are sets of functional roles to implement a specific biological process or structural complex, such as glycolysis and TCA cycle. Subsystem/pathway definition is also employed to delineate the biosynthetic routes that produce biomass building blocks. In databases, such as MetaCyc and SEED, these representations are composed of linear routes from precursors to target biomass building blocks...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28727743/effect-of-depth-information-on-multiple-object-tracking-in-three-dimensions-a-probabilistic-perspective
#20
James R H Cooke, Arjan C Ter Horst, Robert J van Beers, W Pieter Medendorp
Many daily situations require us to track multiple objects and people. This ability has traditionally been investigated in observers tracking objects in a plane. This simplification of reality does not address how observers track objects when targets move in three dimensions. Here, we study how observers track multiple objects in 2D and 3D while manipulating the average speed of the objects and the average distance between them. We show that performance declines as speed increases and distance decreases and that overall tracking accuracy is always higher in 3D than in 2D...
July 2017: PLoS Computational Biology
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