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PLoS Computational Biology

Stefano Giaimo, Jordi Arranz, Arne Traulsen
Population structure can strongly affect evolutionary dynamics. The most general way to describe population structures are graphs. An important observable on evolutionary graphs is the probability that a novel mutation spreads through the entire population. But what drives this spread of a mutation towards fixation? Here, we propose a novel way to understand the forces driving fixation by borrowing techniques from evolutionary demography to quantify the invasion fitness and the effective population size for different graphs...
November 12, 2018: PLoS Computational Biology
Laura Anton-Sanchez, Felix Effenberger, Concha Bielza, Pedro Larrañaga, Hermann Cuntz
Neurons collect their inputs from other neurons by sending out arborized dendritic structures. However, the relationship between the shape of dendrites and the precise organization of synaptic inputs in the neural tissue remains unclear. Inputs could be distributed in tight clusters, entirely randomly or else in a regular grid-like manner. Here, we analyze dendritic branching structures using a regularity index R, based on average nearest neighbor distances between branch and termination points, characterizing their spatial distribution...
November 12, 2018: PLoS Computational Biology
Jason E Pina, Mark Bodner, Bard Ermentrout
Neural oscillations have been recorded and implicated in many different basic brain and cognitive processes. For example, oscillatory neural activity has been suggested to play a role in binding and in the maintenance of information in working memory. With respect to the latter, the majority of work has focused primarily on oscillations in terms of providing a "code" in working memory. However, oscillations may additionally play a fundamental role by enabling or facilitating essential properties and behaviors that neuronal networks must exhibit in order to produce functional working memory and the processes it supports, such as combining items in memory into bound objects or separating bound objects into distinct items...
November 12, 2018: PLoS Computational Biology
James A Henderson, Pulin Gong
Diverse plasticity mechanisms are orchestrated to shape the spatiotemporal dynamics underlying brain functions. However, why these plasticity rules emerge and how their dynamics interact with neural activity to give rise to complex neural circuit dynamics remains largely unknown. Here we show that both Hebbian and homeostatic plasticity rules emerge from a functional perspective of neuronal dynamics whereby each neuron learns to encode its own activity in the population activity, so that the activity of the presynaptic neuron can be decoded from the activity of its postsynaptic neurons...
November 12, 2018: PLoS Computational Biology
Anton Arkhipov, Nathan W Gouwens, Yazan N Billeh, Sergey Gratiy, Ramakrishnan Iyer, Ziqiang Wei, Zihao Xu, Reza Abbasi-Asl, Jim Berg, Michael Buice, Nicholas Cain, Nuno da Costa, Saskia de Vries, Daniel Denman, Severine Durand, David Feng, Tim Jarsky, Jerome Lecoq, Brian Lee, Lu Li, Stefan Mihalas, Gabriel K Ocker, Shawn R Olsen, R Clay Reid, Gilberto Soler-Llavina, Staci A Sorensen, Quanxin Wang, Jack Waters, Massimo Scanziani, Christof Koch
Despite advances in experimental techniques and accumulation of large datasets concerning the composition and properties of the cortex, quantitative modeling of cortical circuits under in-vivo-like conditions remains challenging. Here we report and publicly release a biophysically detailed circuit model of layer 4 in the mouse primary visual cortex, receiving thalamo-cortical visual inputs. The 45,000-neuron model was subjected to a battery of visual stimuli, and results were compared to published work and new in vivo experiments...
November 12, 2018: PLoS Computational Biology
Hongyang Li, Xin-Qiu Yao, Barry J Grant
GTPases regulate a multitude of essential cellular processes ranging from movement and division to differentiation and neuronal activity. These ubiquitous enzymes operate by hydrolyzing GTP to GDP with associated conformational changes that modulate affinity for family-specific binding partners. There are three major GTPase superfamilies: Ras-like GTPases, heterotrimeric G proteins and protein-synthesizing GTPases. Although they contain similar nucleotide-binding sites, the detailed mechanisms by which these structurally and functionally diverse superfamilies operate remain unclear...
November 9, 2018: PLoS Computational Biology
Ruben Zamora, Sebastian Korff, Qi Mi, Derek Barclay, Lukas Schimunek, Riccardo Zucca, Xerxes D Arsiwalla, Richard L Simmons, Paul Verschure, Timothy R Billiar, Yoram Vodovotz
Bacterial lipopolysaccharide (LPS) induces an acute inflammatory response across multiple organs, primarily via Toll-like receptor 4 (TLR4). We sought to define novel aspects of the complex spatiotemporal dynamics of LPS-induced inflammation using computational modeling, with a special focus on the timing of pathological systemic spillover. An analysis of principal drivers of LPS-induced inflammation in the heart, gut, lung, liver, spleen, and kidney to assess organ-specific dynamics, as well as in the plasma (as an assessment of systemic spillover), was carried out using data on 20 protein-level inflammatory mediators measured over 0-48h in both C57BL/6 and TLR4-null mice...
November 6, 2018: PLoS Computational Biology
Francisco J H Heras, Mikko Vähäsöyrinki, Jeremy E Niven
Modulation is essential for adjusting neurons to prevailing conditions and differing demands. Yet understanding how modulators adjust neuronal properties to alter information processing remains unclear, as is the impact of neuromodulation on energy consumption. Here we combine two computational models, one Hodgkin-Huxley type and the other analytic, to investigate the effects of neuromodulation upon Drosophila melanogaster photoreceptors. Voltage-dependent K+ conductances: (i) activate upon depolarisation to reduce membrane resistance and adjust bandwidth to functional requirements; (ii) produce negative feedback to increase bandwidth in an energy efficient way; (iii) produce shunt-peaking thereby increasing the membrane gain bandwidth product; and (iv) inactivate to amplify low frequencies...
November 6, 2018: PLoS Computational Biology
Giovanni B Brandani, Shoji Takada
ATP-dependent chromatin remodelers are molecular machines that control genome organization by repositioning, ejecting, or editing nucleosomes, activities that confer them essential regulatory roles on gene expression and DNA replication. Here, we investigate the molecular mechanism of active nucleosome sliding by means of molecular dynamics simulations of the Snf2 remodeler translocase in complex with a nucleosome. During its inchworm motion driven by ATP consumption, the translocase overwrites the original nucleosome energy landscape via steric and electrostatic interactions to induce sliding of nucleosomal DNA unidirectionally...
November 5, 2018: PLoS Computational Biology
Susann Vorberg, Stefan Seemayer, Johannes Söding
Compensatory mutations between protein residues in physical contact can manifest themselves as statistical couplings between the corresponding columns in a multiple sequence alignment (MSA) of the protein family. Conversely, large coupling coefficients predict residues contacts. Methods for de-novo protein structure prediction based on this approach are becoming increasingly reliable. Their main limitation is the strong systematic and statistical noise in the estimation of coupling coefficients, which has so far limited their application to very large protein families...
November 5, 2018: PLoS Computational Biology
Keisuke Fujii, Takeshi Kawasaki, Yuki Inaba, Yoshinobu Kawahara
Modeling the complex collective behavior is a challenging issue in several material and life sciences. The collective motion has been usually modeled by simple interaction rules and explained by global statistics. However, it remains difficult to bridge the gap between the dynamic properties of the complex interaction and the emerging group-level functions. Here we introduce decomposition methods to directly extract and classify the latent global dynamics of nonlinear dynamical systems in an equation-free manner, even including complex interaction in few data dimensions...
November 5, 2018: PLoS Computational Biology
Stefano Luccioli, David Angulo-Garcia, Rosa Cossart, Arnaud Malvache, Laura Módol, Vitor Hugo Sousa, Paolo Bonifazi, Alessandro Torcini
Spontaneous emergence of synchronized population activity is a characteristic feature of developing brain circuits. Recent experiments in the developing neo-cortex showed the existence of driver cells able to impact the synchronization dynamics when single-handedly stimulated. We have developed a spiking network model capable to reproduce the experimental results, thus identifying two classes of driver cells: functional hubs and low functionally connected (LC) neurons. The functional hubs arranged in a clique orchestrated the synchronization build-up, while the LC drivers were lately or not at all recruited in the synchronization process...
November 2, 2018: PLoS Computational Biology
Yarden Golan, Raphael Alhadeff, Fabian Glaser, Assaf Ganoth, Arieh Warshel, Yehuda G Assaraf
Multiscale modeling provides a very powerful means of studying complex biological systems. An important component of this strategy involves coarse-grained (CG) simplifications of regions of the system, which allow effective exploration of complex systems. Here we studied aspects of CG modeling of the human zinc transporter ZnT2. Zinc is an essential trace element with 10% of the proteins in the human proteome capable of zinc binding. Thus, zinc deficiency or impairment of zinc homeostasis disrupt key cellular functions...
November 2, 2018: PLoS Computational Biology
Daniel S Moore, Conor Brines, Heather Jewhurst, John P Dalton, Irina G Tikhonova
Malaria is a life-threatening disease spread by mosquitoes. Plasmodium falciparum M1 alanyl aminopeptidase (PfM1-AAP) is a promising target for the treatment of malaria. The recently solved crystal structures of PfM1-AAP revealed that the buried active site can be accessed through two channel openings: a short N-terminal channel with the length of 8 Å and a long C-terminal channel with the length of 30 Å. It is unclear, however, how substrates and inhibitors migrate to the active site and a product of cleavage leaves...
October 31, 2018: PLoS Computational Biology
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pcbi.1006182.].
November 2018: PLoS Computational Biology
Weilong Zhao, Xinwei Sher
A number of machine learning-based predictors have been developed for identifying immunogenic T-cell epitopes based on major histocompatibility complex (MHC) class I and II binding affinities. Rationally selecting the most appropriate tool has been complicated by the evolving training data and machine learning methods. Despite the recent advances made in generating high-quality MHC-eluted, naturally processed ligandome, the reliability of new predictors on these epitopes has yet to be evaluated. This study reports the latest benchmarking on an extensive set of MHC-binding predictors by using newly available, untested data of both synthetic and naturally processed epitopes...
November 2018: PLoS Computational Biology
Christiane Ehrt, Tobias Brinkjost, Oliver Koch
The automated comparison of protein-ligand binding sites provides useful insights into yet unexplored site similarities. Various stages of computational and chemical biology research can benefit from this knowledge. The search for putative off-targets and the establishment of polypharmacological effects by comparing binding sites led to promising results for numerous projects. Although many cavity comparison methods are available, a comprehensive analysis to guide the choice of a tool for a specific application is wanting...
November 2018: PLoS Computational Biology
Michael Muthukrishna, Michael Doebeli, Maciej Chudek, Joseph Henrich
In the last few million years, the hominin brain more than tripled in size. Comparisons across evolutionary lineages suggest that this expansion may be part of a broader trend toward larger, more complex brains in many taxa. Efforts to understand the evolutionary forces driving brain expansion have focused on climatic, ecological, and social factors. Here, building on existing research on learning, we analytically and computationally model the predictions of two closely related hypotheses: The Cultural Brain Hypothesis and the Cumulative Cultural Brain Hypothesis...
November 2018: PLoS Computational Biology
Bjoern Peters, Steven E Brenner, Edwin Wang, Donna Slonim, Maricel G Kann
Research in computational biology has given rise to a vast number of methods developed to solve scientific problems. For areas in which many approaches exist, researchers have a hard time deciding which tool to select to address a scientific challenge, as essentially all publications introducing a new method will claim better performance than all others. Not all of these claims can be correct. Equally, for this same reason, developers struggle to demonstrate convincingly that they created a new and superior algorithm or implementation...
November 2018: PLoS Computational Biology
Maurits Dijkstra, Punto Bawono, Sanne Abeln, K Anton Feenstra, Wan Fokkink, Jaap Heringa
Protein or DNA motifs are sequence regions which possess biological importance. These regions are often highly conserved among homologous sequences. The generation of multiple sequence alignments (MSAs) with a correct alignment of the conserved sequence motifs is still difficult to achieve, due to the fact that the contribution of these typically short fragments is overshadowed by the rest of the sequence. Here we extended the PRALINE multiple sequence alignment program with a novel motif-aware MSA algorithm in order to address this shortcoming...
November 2018: PLoS Computational Biology
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