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PLoS Computational Biology

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https://www.readbyqxmd.com/read/28339468/pbmda-a-novel-and-effective-path-based-computational-model-for-mirna-disease-association-prediction
#1
Zhu-Hong You, Zhi-An Huang, Zexuan Zhu, Gui-Ying Yan, Zheng-Wei Li, Zhenkun Wen, Xing Chen
In the recent few years, an increasing number of studies have shown that microRNAs (miRNAs) play critical roles in many fundamental and important biological processes. As one of pathogenetic factors, the molecular mechanisms underlying human complex diseases still have not been completely understood from the perspective of miRNA. Predicting potential miRNA-disease associations makes important contributions to understanding the pathogenesis of diseases, developing new drugs, and formulating individualized diagnosis and treatment for diverse human complex diseases...
March 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28333928/network-perturbation-by-recurrent-regulatory-variants-in-cancer
#2
Kiwon Jang, Kwoneel Kim, Ara Cho, Insuk Lee, Jung Kyoon Choi
Cancer driving genes have been identified as recurrently affected by variants that alter protein-coding sequences. However, a majority of cancer variants arise in noncoding regions, and some of them are thought to play a critical role through transcriptional perturbation. Here we identified putative transcriptional driver genes based on combinatorial variant recurrence in cis-regulatory regions. The identified genes showed high connectivity in the cancer type-specific transcription regulatory network, with high outdegree and many downstream genes, highlighting their causative role during tumorigenesis...
March 23, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28329017/navigating-in-foldonia-using-accelerated-molecular-dynamics-to-explore-stability-unfolding-and-self-healing-of-the-%C3%AE-solenoid-structure-formed-by-a-silk-like-polypeptide
#3
Binwu Zhao, Martien A Cohen Stuart, Carol K Hall
The β roll molecules with sequence (GAGAGAGQ)10 stack via hydrogen bonding to form fibrils which have been themselves been used to make viral capsids of DNA strands, supramolecular nanotapes and pH-responsive gels. Accelerated molecular dynamics (aMD) simulations are used to investigate the unfolding of a stack of two β roll molecules, (GAGAGAGQ)10, to shed light on the folding mechanism by which silk-inspired polypeptides form fibrils and to identify the dominant forces that keep the silk-inspired polypeptide in a β roll configuration...
March 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28328943/structurally-detailed-coarse-grained-model-for-sec-facilitated-co-translational-protein-translocation-and-membrane-integration
#4
Michiel J M Niesen, Connie Y Wang, Reid C Van Lehn, Thomas F Miller
We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations...
March 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28319199/a-computational-analysis-of-in-vivo-vegfr-activation-by-multiple-co-expressed-ligands
#5
Lindsay E Clegg, Feilim Mac Gabhann
The splice isoforms of vascular endothelial growth A (VEGF) each have different affinities for the extracellular matrix (ECM) and the coreceptor NRP1, which leads to distinct vascular phenotypes in model systems expressing only a single VEGF isoform. ECM-immobilized VEGF can bind to and activate VEGF receptor 2 (VEGFR2) directly, with a different pattern of site-specific phosphorylation than diffusible VEGF. To date, the way in which ECM binding alters the distribution of isoforms of VEGF and of the related placental growth factor (PlGF) in the body and resulting angiogenic signaling is not well-understood...
March 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28319153/a-general-model-for-metabolic-scaling-in-self-similar-asymmetric-networks
#6
Alexander Byers Brummer, Van M Savage, Brian J Enquist
How a particular attribute of an organism changes or scales with its body size is known as an allometry. Biological allometries, such as metabolic scaling, have been hypothesized to result from selection to maximize how vascular networks fill space yet minimize internal transport distances and resistances. The West, Brown, Enquist (WBE) model argues that these two principles (space-filling and energy minimization) are (i) general principles underlying the evolution of the diversity of biological networks across plants and animals and (ii) can be used to predict how the resulting geometry of biological networks then governs their allometric scaling...
March 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28306714/reconstruction-and-signal-propagation-analysis-of-the-syk-signaling-network-in-breast-cancer-cells
#7
Aurélien Naldi, Romain M Larive, Urszula Czerwinska, Serge Urbach, Philippe Montcourrier, Christian Roy, Jérôme Solassol, Gilles Freiss, Peter J Coopman, Ovidiu Radulescu
The ability to build in-depth cell signaling networks from vast experimental data is a key objective of computational biology. The spleen tyrosine kinase (Syk) protein, a well-characterized key player in immune cell signaling, was surprisingly first shown by our group to exhibit an onco-suppressive function in mammary epithelial cells and corroborated by many other studies, but the molecular mechanisms of this function remain largely unsolved. Based on existing proteomic data, we report here the generation of an interaction-based network of signaling pathways controlled by Syk in breast cancer cells...
March 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28301477/fragility-of-foot-process-morphology-in-kidney-podocytes-arises-from-chaotic-spatial-propagation-of-cytoskeletal-instability
#8
Cibele V Falkenberg, Evren U Azeloglu, Mark Stothers, Thomas J Deerinck, Yibang Chen, John C He, Mark H Ellisman, James C Hone, Ravi Iyengar, Leslie M Loew
Kidney podocytes' function depends on finger-like projections (foot processes) that interdigitate with those from neighboring cells to form the glomerular filtration barrier. The integrity of the barrier depends on spatial control of dynamics of actin cytoskeleton in the foot processes. We determined how imbalances in regulation of actin cytoskeletal dynamics could result in pathological morphology. We obtained 3-D electron microscopy images of podocytes and used quantitative features to build dynamical models to investigate how regulation of actin dynamics within foot processes controls local morphology...
March 16, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28296888/a-thermodynamically-consistent-model-of-the-post-translational-kai-circadian-clock
#9
Joris Paijmans, David K Lubensky, Pieter Rein Ten Wolde
The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a homohexamer, with each monomer consisting of two domains, CI and CII. Both domains can bind and hydrolyze ATP, but only the CII domain can be phosphorylated, at two residues, in a well-defined sequence. While this system has been studied extensively, how the clock is driven thermodynamically has remained elusive. Inspired by recent experimental observations and building on ideas from previous mathematical models, we present a new, thermodynamically consistent, statistical-mechanical model of the clock...
March 15, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28291787/fast-online-deconvolution-of-calcium-imaging-data
#10
Johannes Friedrich, Pengcheng Zhou, Liam Paninski
Fluorescent calcium indicators are a popular means for observing the spiking activity of large neuronal populations, but extracting the activity of each neuron from raw fluorescence calcium imaging data is a nontrivial problem. We present a fast online active set method to solve this sparse non-negative deconvolution problem. Importantly, the algorithm progresses through each time series sequentially from beginning to end, thus enabling real-time online estimation of neural activity during the imaging session...
March 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28288158/stimulus-specific-adaptation-in-a-recurrent-network-model-of-primary-auditory-cortex
#11
Tohar S Yarden, Israel Nelken
Stimulus-specific adaptation (SSA) occurs when neurons decrease their responses to frequently-presented (standard) stimuli but not, or not as much, to other, rare (deviant) stimuli. SSA is present in all mammalian species in which it has been tested as well as in birds. SSA confers short-term memory to neuronal responses, and may lie upstream of the generation of mismatch negativity (MMN), an important human event-related potential. Previously published models of SSA mostly rely on synaptic depression of the feedforward, thalamocortical input...
March 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28288157/modelling-t-cell-proliferation-dynamics-heterogeneity-depending-on-cell-differentiation-age-and-genetic-background
#12
Julien Vibert, Véronique Thomas-Vaslin
Cell proliferation is the common characteristic of all biological systems. The immune system insures the maintenance of body integrity on the basis of a continuous production of diversified T lymphocytes in the thymus. This involves processes of proliferation, differentiation, selection, death and migration of lymphocytes to peripheral tissues, where proliferation also occurs upon antigen recognition. Quantification of cell proliferation dynamics requires specific experimental methods and mathematical modelling...
March 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28288156/parameter-estimation-for-multistage-clonal-expansion-models-from-cancer-incidence-data-a-practical-identifiability-analysis
#13
Andrew F Brouwer, Rafael Meza, Marisa C Eisenberg
Many cancers are understood to be the product of multiple somatic mutations or other rate-limiting events. Multistage clonal expansion (MSCE) models are a class of continuous-time Markov chain models that capture the multi-hit initiation-promotion-malignant-conversion hypothesis of carcinogenesis. These models have been used broadly to investigate the epidemiology of many cancers, assess the impact of carcinogen exposures on cancer risk, and evaluate the potential impact of cancer prevention and control strategies on cancer rates...
March 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28288155/dynamics-robustness-of-cascading-systems
#14
Jonathan T Young, Tetsuhiro S Hatakeyama, Kunihiko Kaneko
A most important property of biochemical systems is robustness. Static robustness, e.g., homeostasis, is the insensitivity of a state against perturbations, whereas dynamics robustness, e.g., homeorhesis, is the insensitivity of a dynamic process. In contrast to the extensively studied static robustness, dynamics robustness, i.e., how a system creates an invariant temporal profile against perturbations, is little explored despite transient dynamics being crucial for cellular fates and are reported to be robust experimentally...
March 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28288152/patient-specific-modeling-of-individual-sickle-cell-behavior-under-transient-hypoxia
#15
Xuejin Li, E Du, Ming Dao, Subra Suresh, George Em Karniadakis
Sickle cell disease (SCD) is a highly complex genetic blood disorder in which red blood cells (RBC) exhibit heterogeneous morphology changes and decreased deformability. We employ a kinetic model for cell morphological sickling that invokes parameters derived from patient-specific data. This model is used to investigate the dynamics of individual sickle cells in a capillary-like microenvironment in order to address various mechanisms associated with SCD. We show that all RBCs, both hypoxia-unaffected and hypoxia-affected ones, regularly pass through microgates under oxygenated state...
March 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28333921/bioenergetics-based-modeling-of-plasmodium-falciparum-metabolism-reveals-its-essential-genes-nutritional-requirements-and-thermodynamic-bottlenecks
#16
Anush Chiappino-Pepe, Stepan Tymoshenko, Meriç Ataman, Dominique Soldati-Favre, Vassily Hatzimanikatis
Novel antimalarial therapies are urgently needed for the fight against drug-resistant parasites. The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex. Computational methods can handle this complexity and allow integrative analyses of cell metabolism. In this study, we present a genome-scale metabolic model (iPfa) of the deadliest malaria parasite, Plasmodium falciparum, and its thermodynamics-based flux analysis (TFA). Using previous absolute concentration data of the intraerythrocytic parasite, we applied TFA to iPfa and predicted up to 63 essential genes and 26 essential pairs of genes...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28333920/ten-simple-rules-for-forming-a-scientific-professional-society
#17
EDITORIAL
Bruno A Gaëta, Javier De Las Rivas, Paul Horton, Pieter Meysman, Nicola Mulder, Paolo Romano, Lonnie Welch
No abstract text is available yet for this article.
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28319135/plos-computational-biology-2016-reviewer-and-editorial-board-thank-you
#18
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28306731/correction-a-molecular-clock-infers-heterogeneous-tissue-age-among-patients-with-barrett-s-esophagus
#19
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pcbi.1004919.].
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28301476/classification-and-adaptive-behavior-prediction-of-children-with-autism-spectrum-disorder-based-upon-multivariate-data-analysis-of-markers-of-oxidative-stress-and-dna-methylation
#20
Daniel P Howsmon, Uwe Kruger, Stepan Melnyk, S Jill James, Juergen Hahn
The number of diagnosed cases of Autism Spectrum Disorders (ASD) has increased dramatically over the last four decades; however, there is still considerable debate regarding the underlying pathophysiology of ASD. This lack of biological knowledge restricts diagnoses to be made based on behavioral observations and psychometric tools. However, physiological measurements should support these behavioral diagnoses in the future in order to enable earlier and more accurate diagnoses. Stepping towards this goal of incorporating biochemical data into ASD diagnosis, this paper analyzes measurements of metabolite concentrations of the folate-dependent one-carbon metabolism and transulfuration pathways taken from blood samples of 83 participants with ASD and 76 age-matched neurotypical peers...
March 2017: PLoS Computational Biology
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