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PLoS Computational Biology

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https://www.readbyqxmd.com/read/28107358/modeling-an-excitable-biosynthetic-tissue-with-inherent-variability-for-paired-computational-experimental-studies
#1
Tanmay A Gokhale, Jong M Kim, Robert D Kirkton, Nenad Bursac, Craig S Henriquez
To understand how excitable tissues give rise to arrhythmias, it is crucially necessary to understand the electrical dynamics of cells in the context of their environment. Multicellular monolayer cultures have proven useful for investigating arrhythmias and other conduction anomalies, and because of their relatively simple structure, these constructs lend themselves to paired computational studies that often help elucidate mechanisms of the observed behavior. However, tissue cultures of cardiomyocyte monolayers currently require the use of neonatal cells with ionic properties that change rapidly during development and have thus been poorly characterized and modeled to date...
January 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28103241/contextual-refinement-of-regulatory-targets-reveals-effects-on-breast-cancer-prognosis-of-the-regulome
#2
Erik Andrews, Yue Wang, Tian Xia, Wenqing Cheng, Chao Cheng
Gene expression regulators, such as transcription factors (TFs) and microRNAs (miRNAs), have varying regulatory targets based on the tissue and physiological state (context) within which they are expressed. While the emergence of regulator-characterizing experiments has inferred the target genes of many regulators across many contexts, methods for transferring regulator target genes across contexts are lacking. Further, regulator target gene lists frequently are not curated or have permissive inclusion criteria, impairing their use...
January 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28103239/identifying-t-cell-receptors-from-high-throughput-sequencing-dealing-with-promiscuity-in-tcr%C3%AE-and-tcr%C3%AE-pairing
#3
Edward S Lee, Paul G Thomas, Jeff E Mold, Andrew J Yates
Characterisation of the T cell receptors (TCR) involved in immune responses is important for the design of vaccines and immunotherapies for cancer and autoimmune disease. The specificity of the interaction between the TCR heterodimer and its peptide-MHC ligand derives largely from the juxtaposed hypervariable CDR3 regions on the TCRα and TCRβ chains, and obtaining the paired sequences of these regions is a standard for functionally defining the TCR. A brute force approach to identifying the TCRs in a population of T cells is to use high-throughput single-cell sequencing, but currently this process remains costly and risks missing small clones...
January 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28099436/a-new-approach-to-model-pitch-perception-using-sparse-coding
#4
Oded Barzelay, Miriam Furst, Omri Barak
Our acoustical environment abounds with repetitive sounds, some of which are related to pitch perception. It is still unknown how the auditory system, in processing these sounds, relates a physical stimulus and its percept. Since, in mammals, all auditory stimuli are conveyed into the nervous system through the auditory nerve (AN) fibers, a model should explain the perception of pitch as a function of this particular input. However, pitch perception is invariant to certain features of the physical stimulus...
January 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28095421/approximate-inference-for-time-varying-interactions-and-macroscopic-dynamics-of-neural-populations
#5
Christian Donner, Klaus Obermayer, Hideaki Shimazaki
The models in statistical physics such as an Ising model offer a convenient way to characterize stationary activity of neural populations. Such stationary activity of neurons may be expected for recordings from in vitro slices or anesthetized animals. However, modeling activity of cortical circuitries of awake animals has been more challenging because both spike-rates and interactions can change according to sensory stimulation, behavior, or an internal state of the brain. Previous approaches modeling the dynamics of neural interactions suffer from computational cost; therefore, its application was limited to only a dozen neurons...
January 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28095406/a-two-locus-model-of-the-evolution-of-insecticide-resistance-to-inform-and-optimise-public-health-insecticide-deployment-strategies
#6
Bethany Levick, Andy South, Ian M Hastings
We develop a flexible, two-locus model for the spread of insecticide resistance applicable to mosquito species that transmit human diseases such as malaria. The model allows differential exposure of males and females, allows them to encounter high or low concentrations of insecticide, and allows selection pressures and dominance values to differ depending on the concentration of insecticide encountered. We demonstrate its application by investigating the relative merits of sequential use of insecticides versus their deployment as a mixture to minimise the spread of resistance...
January 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28095404/entropy-transfer-between-residue-pairs-and-allostery-in-proteins-quantifying-allosteric-communication-in-ubiquitin
#7
Aysima Hacisuleyman, Burak Erman
It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others...
January 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28085884/a-looping-based-model-for-quenching-repression
#8
Yaroslav Pollak, Sarah Goldberg, Roee Amit
We model the regulatory role of proteins bound to looped DNA using a simulation in which dsDNA is represented as a self-avoiding chain, and proteins as spherical protrusions. We simulate long self-avoiding chains using a sequential importance sampling Monte-Carlo algorithm, and compute the probabilities for chain looping with and without a protrusion. We find that a protrusion near one of the chain's termini reduces the probability of looping, even for chains much longer than the protrusion-chain-terminus distance...
January 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28085876/inference-of-transmission-network-structure-from-hiv-phylogenetic-trees
#9
Federica Giardina, Ethan Obie Romero-Severson, Jan Albert, Tom Britton, Thomas Leitner
Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks...
January 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28085875/is-the-conformational-ensemble-of-alzheimer-s-a%C3%AE-10-40-peptide-force-field-dependent
#10
Christopher M Siwy, Christopher Lockhart, Dmitri K Klimov
By applying REMD simulations we have performed comparative analysis of the conformational ensembles of amino-truncated Aβ10-40 peptide produced with five force fields, which combine four protein parameterizations (CHARMM36, CHARMM22*, CHARMM22/cmap, and OPLS-AA) and two water models (standard and modified TIP3P). Aβ10-40 conformations were analyzed by computing secondary structure, backbone fluctuations, tertiary interactions, and radius of gyration. We have also calculated Aβ10-40 3JHNHα-coupling and RDC constants and compared them with their experimental counterparts obtained for the full-length Aβ1-40 peptide...
January 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28076353/a-topological-criterion-for-filtering-information-in-complex-brain-networks
#11
Fabrizio De Vico Fallani, Vito Latora, Mario Chavez
In many biological systems, the network of interactions between the elements can only be inferred from experimental measurements. In neuroscience, non-invasive imaging tools are extensively used to derive either structural or functional brain networks in-vivo. As a result of the inference process, we obtain a matrix of values corresponding to a fully connected and weighted network. To turn this into a useful sparse network, thresholding is typically adopted to cancel a percentage of the weakest connections...
January 11, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28068428/a-network-model-of-local-field-potential-activity-in-essential-tremor-and-the-impact-of-deep-brain-stimulation
#12
Nada Yousif, Michael Mace, Nicola Pavese, Roman Borisyuk, Dipankar Nandi, Peter Bain
Essential tremor (ET), a movement disorder characterised by an uncontrollable shaking of the affected body part, is often professed to be the most common movement disorder, affecting up to one percent of adults over 40 years of age. The precise cause of ET is unknown, however pathological oscillations of a network of a number of brain regions are implicated in leading to the disorder. Deep brain stimulation (DBS) is a clinical therapy used to alleviate the symptoms of a number of movement disorders. DBS involves the surgical implantation of electrodes into specific nuclei in the brain...
January 9, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28068331/modelling-systemic-iron-regulation-during-dietary-iron-overload-and-acute-inflammation-role-of-hepcidin-independent-mechanisms
#13
Mihaela Enculescu, Christoph Metzendorf, Richard Sparla, Maximilian Hahnel, Johannes Bode, Martina U Muckenthaler, Stefan Legewie
Systemic iron levels must be maintained in physiological concentrations to prevent diseases associated with iron deficiency or iron overload. A key role in this process plays ferroportin, the only known mammalian transmembrane iron exporter, which releases iron from duodenal enterocytes, hepatocytes, or iron-recycling macrophages into the blood stream. Ferroportin expression is tighly controlled by transcriptional and post-transcriptional mechanisms in response to hypoxia, iron deficiency, heme iron and inflammatory cues by cell-autonomous and systemic mechanisms...
January 9, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28060821/customized-regulation-of-diverse-stress-response-genes-by-the-multiple-antibiotic-resistance-activator-mara
#14
Nicholas A Rossi, Mary J Dunlop
Stress response networks frequently have a single upstream regulator that controls many downstream genes. However, the downstream targets are often diverse, therefore it remains unclear how their expression is specialized when under the command of a common regulator. To address this, we focused on a stress response network where the multiple antibiotic resistance activator MarA from Escherichia coli regulates diverse targets ranging from small RNAs to efflux pumps. Using single-cell experiments and computational modeling, we showed that each downstream gene studied has distinct activation, noise, and information transmission properties...
January 6, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28060813/using-chemical-reaction-kinetics-to-predict-optimal-antibiotic-treatment-strategies
#15
Pia Abel Zur Wiesch, Fabrizio Clarelli, Ted Cohen
Identifying optimal dosing of antibiotics has proven challenging-some antibiotics are most effective when they are administered periodically at high doses, while others work best when minimizing concentration fluctuations. Mechanistic explanations for why antibiotics differ in their optimal dosing are lacking, limiting our ability to predict optimal therapy and leading to long and costly experiments. We use mathematical models that describe both bacterial growth and intracellular antibiotic-target binding to investigate the effects of fluctuating antibiotic concentrations on individual bacterial cells and bacterial populations...
January 6, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28056033/fiji-macro-3d-art-veselect-3d-automated-reconstruction-tool-for-vesicle-structures-of-electron-tomograms
#16
Kristin Verena Kaltdorf, Katja Schulze, Frederik Helmprobst, Philip Kollmannsberger, Thomas Dandekar, Christian Stigloher
Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models...
January 5, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/27997542/systematic-approximations-to-susceptible-infectious-susceptible-dynamics-on-networks
#17
Matt J Keeling, Thomas House, Alison J Cooper, Lorenzo Pellis
Network-based infectious disease models have been highly effective in elucidating the role of contact structure in the spread of infection. As such, pair- and neighbourhood-based approximation models have played a key role in linking findings from network simulations to standard (random-mixing) results. Recently, for SIR-type infections (that produce one epidemic in a closed population) on locally tree-like networks, these approximations have been shown to be exact. However, network models are ideally suited for Sexually Transmitted Infections (STIs) due to the greater level of detail available for sexual contact networks, and these diseases often possess SIS-type dynamics...
December 20, 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27984591/the-multilayer-connectome-of-caenorhabditis-elegans
#18
Barry Bentley, Robyn Branicky, Christopher L Barnes, Yee Lian Chew, Eviatar Yemini, Edward T Bullmore, Petra E Vértes, William R Schafer
Connect omics has focused primarily on the mapping of synaptic links in the brain; yet it is well established that extra synaptic volume transmission, especially via monoamines and neuropeptides, is also critical to brain function and occurs primarily outside the synaptic connectome. We have mapped the putative monoamine connections, as well as a subset of neuropeptide connections, in C. elegans based on new and published gene expression data. The monoamine and neuropeptide networks exhibit distinct topological properties, with the monoamine network displaying a highly dissertated star-like structure with a rich-club of interconnected broadcasting hubs, and the neuropeptide network showing a more recurrent, highly clustered topology...
December 16, 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/28107344/psychotic-experiences-and-overhasty-inferences-are-related-to-maladaptive-learning
#19
Heiner Stuke, Hannes Stuke, Veith Andreas Weilnhammer, Katharina Schmack
Theoretical accounts suggest that an alteration in the brain's learning mechanisms might lead to overhasty inferences, resulting in psychotic symptoms. Here, we sought to elucidate the suggested link between maladaptive learning and psychosis. Ninety-eight healthy individuals with varying degrees of delusional ideation and hallucinatory experiences performed a probabilistic reasoning task that allowed us to quantify overhasty inferences. Replicating previous results, we found a relationship between psychotic experiences and overhasty inferences during probabilistic reasoning...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28107341/complex-dynamics-of-virus-spread-from-low-infection-multiplicities-implications-for-the-spread-of-oncolytic-viruses
#20
Ignacio A Rodriguez-Brenes, Andrew Hofacre, Hung Fan, Dominik Wodarz
While virus growth dynamics have been well-characterized in several infections, data are typically collected once the virus population becomes easily detectable. Earlier dynamics, however, remain less understood. We recently reported unusual early dynamics in an experimental system using adenovirus infection of human embryonic kidney (293) cells. Under identical experimental conditions, inoculation at low infection multiplicities resulted in either robust spread, or in limited spread that eventually stalled, with both outcomes occurring with approximately equal frequencies...
January 2017: PLoS Computational Biology
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