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PLoS Computational Biology

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https://www.readbyqxmd.com/read/28934196/spatiotemporal-network-coding-of-physiological-mossy-fiber-inputs-by-the-cerebellar-granular-layer
#1
Shyam Kumar Sudhakar, Sungho Hong, Ivan Raikov, Rodrigo Publio, Claus Lang, Thomas Close, Daqing Guo, Mario Negrello, Erik De Schutter
The granular layer, which mainly consists of granule and Golgi cells, is the first stage of the cerebellar cortex and processes spatiotemporal information transmitted by mossy fiber inputs with a wide variety of firing patterns. To study its dynamics at multiple time scales in response to inputs approximating real spatiotemporal patterns, we constructed a large-scale 3D network model of the granular layer. Patterned mossy fiber activity induces rhythmic Golgi cell activity that is synchronized by shared parallel fiber input and by gap junctions...
September 21, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28931004/the-logic-of-the-floral-transition-reverse-engineering-the-switch-controlling-the-identity-of-lateral-organs
#2
Jean-Louis Dinh, Etienne Farcot, Charlie Hodgman
Much laboratory work has been carried out to determine the gene regulatory network (GRN) that results in plant cells becoming flowers instead of leaves. However, this also involves the spatial distribution of different cell types, and poses the question of whether alternative networks could produce the same set of observed results. This issue has been addressed here through a survey of the published intercellular distribution of expressed regulatory genes and techniques both developed and applied to Boolean network models...
September 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28926564/probabilistic-models-for-neural-populations-that-naturally-capture-global-coupling-and-criticality
#3
Jan Humplik, Gašper Tkačik
Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical...
September 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28922399/probing-eukaryotic-cell-mechanics-via-mesoscopic-simulations
#4
Kirill Lykov, Yasaman Nematbakhsh, Menglin Shang, Chwee Teck Lim, Igor V Pivkin
Cell mechanics has proven to be important in many biological processes. Although there is a number of experimental techniques which allow us to study mechanical properties of cell, there is still a lack of understanding of the role each sub-cellular components plays during cell deformations. We present a new mesoscopic particle-based eukaryotic cell model which explicitly describes cell membrane, nucleus and cytoskeleton. We employ Dissipative Particle Dynamics (DPD) method that provides us with the unified framework for modeling of a cell and its interactions in the flow...
September 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28922394/sequence-features-of-viral-and-human-internal-ribosome-entry-sites-predictive-of-their-activity
#5
Alexey A Gritsenko, Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Dick de Ridder, Eran Segal
Translation of mRNAs through Internal Ribosome Entry Sites (IRESs) has emerged as a prominent mechanism of cellular and viral initiation. It supports cap-independent translation of select cellular genes under normal conditions, and in conditions when cap-dependent translation is inhibited. IRES structure and sequence are believed to be involved in this process. However due to the small number of IRESs known, there have been no systematic investigations of the determinants of IRES activity. With the recent discovery of thousands of novel IRESs in human and viruses, the next challenge is to decipher the sequence determinants of IRES activity...
September 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28922377/c-reactive-protein-upregulates-the-whole-blood-expression-of-cd59-an-integrative-analysis
#6
Kaido Lepik, Tarmo Annilo, Viktorija Kukuškina, Kai Kisand, Zoltán Kutalik, Pärt Peterson, Hedi Peterson
Elevated C-reactive protein (CRP) concentrations in the blood are associated with acute and chronic infections and inflammation. Nevertheless, the functional role of increased CRP in multiple bacterial and viral infections as well as in chronic inflammatory diseases remains unclear. Here, we studied the relationship between CRP and gene expression levels in the blood in 491 individuals from the Estonian Biobank cohort, to elucidate the role of CRP in these inflammatory mechanisms. As a result, we identified a set of 1,614 genes associated with changes in CRP levels with a high proportion of interferon-stimulated genes...
September 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28922358/quantifying-the-effects-of-antiangiogenic-and-chemotherapy-drug-combinations-on-drug-delivery-and-treatment-efficacy
#7
Sirin Yonucu, Defne Yιlmaz, Colin Phipps, Mehmet Burcin Unlu, Mohammad Kohandel
Tumor-induced angiogenesis leads to the development of leaky tumor vessels devoid of structural and morphological integrity. Due to angiogenesis, elevated interstitial fluid pressure (IFP) and low blood perfusion emerge as common properties of the tumor microenvironment that act as barriers for drug delivery. In order to overcome these barriers, normalization of vasculature is considered to be a viable option. However, insight is needed into the phenomenon of normalization and in which conditions it can realize its promise...
September 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28922356/mathematical-modeling-and-quantitative-analysis-of-hiv-1-gag-trafficking-and-polymerization
#8
Yuewu Liu, Xiufen Zou
Gag, as the major structural protein of HIV-1, is necessary for the assembly of the HIV-1 sphere shell. An in-depth understanding of its trafficking and polymerization is important for gaining further insights into the mechanisms of HIV-1 replication and the design of antiviral drugs. We developed a mathematical model to simulate two biophysical processes, specifically Gag monomer and dimer transport in the cytoplasm and the polymerization of monomers to form a hexamer underneath the plasma membrane. Using experimental data, an optimization approach was utilized to identify the model parameters, and the identifiability and sensitivity of these parameters were then analyzed...
September 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28922354/reconstructing-promoter-activity-from-lux-bioluminescent-reporters
#9
Mudassar Iqbal, Neil Doherty, Anna M L Page, Saara N A Qazi, Ishan Ajmera, Peter A Lund, Theodore Kypraios, David J Scott, Philip J Hill, Dov J Stekel
The bacterial Lux system is used as a gene expression reporter. It is fast, sensitive and non-destructive, enabling high frequency measurements. Originally developed for bacterial cells, it has also been adapted for eukaryotic cells, and can be used for whole cell biosensors, or in real time with live animals without the need for euthanasia. However, correct interpretation of bioluminescent data is limited: the bioluminescence is different from gene expression because of nonlinear molecular and enzyme dynamics of the Lux system...
September 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28922353/synthesizing-developmental-trajectories
#10
Paul Villoutreix, Joakim Andén, Bomyi Lim, Hang Lu, Ioannis G Kevrekidis, Amit Singer, Stanislav Y Shvartsman
Dynamical processes in biology are studied using an ever-increasing number of techniques, each of which brings out unique features of the system. One of the current challenges is to develop systematic approaches for fusing heterogeneous datasets into an integrated view of multivariable dynamics. We demonstrate that heterogeneous data fusion can be successfully implemented within a semi-supervised learning framework that exploits the intrinsic geometry of high-dimensional datasets. We illustrate our approach using a dataset from studies of pattern formation in Drosophila...
September 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28910283/stochastic-principles-governing-alternative-splicing-of-rna
#11
Jianfei Hu, Eli Boritz, William Wylie, Daniel C Douek
The dominance of the major transcript isoform relative to other isoforms from the same gene generated by alternative splicing (AS) is essential to the maintenance of normal cellular physiology. However, the underlying principles that determine such dominance remain unknown. Here, we analyzed the physical AS process and found that it can be modeled by a stochastic minimization process, which causes the scaled expression levels of all transcript isoforms to follow the same Weibull extreme value distribution. Surprisingly, we also found a simple equation to describe the median frequency of transcript isoforms of different dominance...
September 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28902867/analysis-of-the-relationship-between-coexpression-domains-and-chromatin-3d-organization
#12
María E Soler-Oliva, Jose A Guerrero-Martínez, Valentina Bachetti, Jose C Reyes
Gene order is not random in eukaryotic chromosomes, and co-regulated genes tend to be clustered. The mechanisms that determine co-regulation of large regions of the genome and its connection with chromatin three-dimensional (3D) organization are still unclear however. Here we have adapted a recently described method for identifying chromatin topologically associating domains (TADs) to identify coexpression domains (which we term "CODs"). Using human normal breast and breast cancer RNA-seq data, we have identified approximately 500 CODs...
September 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28898249/projecting-social-contact-matrices-in-152-countries-using-contact-surveys-and-demographic-data
#13
Kiesha Prem, Alex R Cook, Mark Jit
Heterogeneities in contact networks have a major effect in determining whether a pathogen can become epidemic or persist at endemic levels. Epidemic models that determine which interventions can successfully prevent an outbreak need to account for social structure and mixing patterns. Contact patterns vary across age and locations (e.g. home, work, and school), and including them as predictors in transmission dynamic models of pathogens that spread socially will improve the models' realism. Data from population-based contact diaries in eight European countries from the POLYMOD study were projected to 144 other countries using a Bayesian hierarchical model that estimated the proclivity of age-and-location-specific contact patterns for the countries, using Markov chain Monte Carlo simulation...
September 12, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28886026/population-fba-predicts-metabolic-phenotypes-in-yeast
#14
Piyush Labhsetwar, Marcelo C R Melo, John A Cole, Zaida Luthey-Schulten
Using protein counts sampled from single cell proteomics distributions to constrain fluxes through a genome-scale model of metabolism, Population flux balance analysis (Population FBA) successfully described metabolic heterogeneity in a population of independent Escherichia coli cells growing in a defined medium. We extend the methodology to account for correlations in protein expression arising from the co-regulation of genes and apply it to study the growth of independent Saccharomyces cerevisiae cells in two different growth media...
September 8, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28934208/ten-simple-rules-for-developing-a-mentor-mentee-expectations-document
#15
EDITORIAL
Kristyn S Masters, Pamela K Kreeger
No abstract text is available yet for this article.
September 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28934204/how-can-computation-advance-microbiome-research
#16
EDITORIAL
Ruth Nussinov, Jason A Papin
No abstract text is available yet for this article.
September 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28934200/ten-simple-rules-for-successfully-completing-a-graduate-degree-in-latin-america
#17
EDITORIAL
Ernesto Ruelas Inzunza, Gabriela I Salazar-Rivera, Magdiel Láinez, María Guadalupe Ruiz-Gómez, Carlo A Domínguez-Eusebio, Griselda Cristóbal-Sánchez, Issaac A Teodosio Faustino, Edel Pérez-López, Meagan L Campbell, Marcus Vinicius Merfa, Ivonne Tatiana Latorre Beltrán, Fernanda Armas, Claudio Mota-Vargas
No abstract text is available yet for this article.
September 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28931005/correction-dose-response-relationships-for-environmentally-mediated-infectious-disease-transmission-models
#18
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pcbi.1005481.].
September 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28926574/correction-lumpgem-systematic-generation-of-subnetworks-and-elementally-balanced-lumped-reactions-for-the-biosynthesis-of-target-metabolites
#19
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pcbi.1005513.].
September 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28915236/modeling-antibiotic-treatment-in-hospitals-a-systematic-approach-shows-benefits-of-combination-therapy-over-cycling-mixing-and-mono-drug-therapies
#20
Burcu Tepekule, Hildegard Uecker, Isabel Derungs, Antoine Frenoy, Sebastian Bonhoeffer
Multiple treatment strategies are available for empiric antibiotic therapy in hospitals, but neither clinical studies nor theoretical investigations have yielded a clear picture when which strategy is optimal and why. Extending earlier work of others and us, we present a mathematical model capturing treatment strategies using two drugs, i.e the multi-drug therapies referred to as cycling, mixing, and combination therapy, as well as monotherapy with either drug. We randomly sample a large parameter space to determine the conditions determining success or failure of these strategies...
September 2017: PLoS Computational Biology
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