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  • 1.
    Esteban-Martin, Santiago
    et al.
    Joint BSC-CRG-IRB Research Programme in Computational Biology, Barcelona Supercomputing Center - BSC, Barcelona, Spain.
    Fenwick, Robert Bryn
    Joint BSC-CRG-IRB Research Programme in Computational Biology, Institute for Research in Biomedicine – IRB Barcelona, Barcelona, Spain.
    Ådén, Jörgen
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Cossins, Benjamin
    Joint BSC-CRG-IRB Research Programme in Computational Biology, Barcelona Supercomputing Center - BSC, Barcelona, Spain.
    Bertoncini, Carlos W.
    Joint BSC-CRG-IRB Research Programme in Computational Biology, Institute for Research in Biomedicine – IRB Barcelona, Barcelona, Spain.
    Guallar, Victor
    Joint BSC-CRG-IRB Research Programme in Computational Biology, Barcelona Supercomputing Center - BSC, Barcelona, Spain.
    Wolf-Watz, Magnus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Salvatella, Xavier
    Joint BSC-CRG-IRB Research Programme in Computational Biology, Institute for Research in Biomedicine – IRB Barcelona, Barcelona, Spain.
    Correlated Inter-Domain Motions in Adenylate Kinase2014Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 10, nr 7, s. e1003721-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Correlated inter-domain motions in proteins can mediate fundamental biochemical processes such as signal transduction and allostery. Here we characterize at structural level the inter-domain coupling in a multidomain enzyme, Adenylate Kinase (AK), using computational methods that exploit the shape information encoded in residual dipolar couplings (RDCs) measured under steric alignment by nuclear magnetic resonance (NMR). We find experimental evidence for a multi-state equilibrium distribution along the opening/closing pathway of Adenylate Kinase, previously proposed from computational work, in which inter-domain interactions disfavour states where only the AMP binding domain is closed. In summary, we provide a robust experimental technique for study of allosteric regulation in AK and other enzymes.

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  • 2.
    Holme, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik. Department of Energy Science, Sungkyunkwan University, Suwon, Korea ; Department of Sociology, Stockholm University, Stockholm, Sweden.
    Epidemiologically optimal static networks from temporal network data2013Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 9, nr 7, s. e1003142-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    One of network epidemiology's central assumptions is that the contact structure over which infectious diseases propagate can be represented as a static network. However, contacts are highly dynamic, changing at many time scales. In this paper, we investigate conceptually simple methods to construct static graphs for network epidemiology from temporal contact data. We evaluate these methods on empirical and synthetic model data. For almost all our cases, the network representation that captures most relevant information is a so-called exponential-threshold network. In these, each contact contributes with a weight decreasing exponentially with time, and there is an edge between a pair of vertices if the weight between them exceeds a threshold. Networks of aggregated contacts over an optimally chosen time window perform almost as good as the exponential-threshold networks. On the other hand, networks of accumulated contacts over the entire sampling time, and networks of concurrent partnerships, perform worse. We discuss these observations in the context of the temporal and topological structure of the data sets.

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  • 3. Joshi, Jaideep
    et al.
    Brännström, Åke
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik. Evolution and Ecology Program, International Institute for Applied Systems Analysis, Laxenburg, Austria.
    Dieckmann, Ulf
    Emergence of social inequality in the spatial harvesting of renewable public goods2020Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 16, nr 1, artikel-id e1007483Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Spatially extended ecological public goods, such as forests, grasslands, and fish stocks, are at risk of being overexploited by selfish consumers-a phenomenon widely recognized as the 'tragedy of the commons.' The interplay of spatial and ecological dimensions introduces new features absent in non-spatial ecological contexts, such as consumer mobility, local information availability, and strategy evolution through social learning in neighborhoods. It is unclear how these features interact to influence the harvesting and dispersal strategies of consumers. To answer these questions, we develop and analyze an individual-based, spatially structured, eco-evolutionary model with explicit resource dynamics. We report the following findings. (1) When harvesting efficiency is low, consumers evolve a sedentary consumption strategy, through which the resource is harvested sustainably, but with harvesting rates far below their maximum sustainable value. (2) As harvesting efficiency increases, consumers adopt a mobile 'consume-and-disperse' strategy, which is sustainable, equitable, and gives maximum sustainable yield. (3) A further increase in harvesting efficiency leads to large-scale overexploitation. (4) If costs of dispersal are significant, increased harvesting efficiency also leads to social inequality between frugal sedentary consumers and overexploitative mobile consumers. Whereas overexploitation can occur without social inequality, social inequality always leads to overexploitation. Thus, we identify four conditions that-while being characteristic of technological progress in modern societies-risk social inequality and overexploitation: high harvesting efficiency, moderately low costs of dispersal, high consumer density, and the tendency of consumers to adopt new strategies rapidly. We also show how access to global information-another feature widespread in modern societies-helps mitigate these risks.

    Author summary: Throughout history, humans have shaped ecological landscapes, which in turn have influenced human behavior. This mutual dependence is epitomized when human consumers harvest a spatially extended renewable resource. Simple models predict that, when multiple consumers harvest a shared resource, each is tempted to harvest faster than his/her peers, putting the resource at risk of overexploitation. It is unclear, however, how the interplay among resource productivity, consumer mobility, and social learning in spatial ecological public goods games influences evolved consumer behavior. Here, using an individual-based, spatially structured, eco-evolutionary model of consumers and a resource, we find that increasing resource productivity initially promotes efficient resource use by enabling mobile consumption strategies, but eventually leads to inequality and overexploitation, as overexploitative mobile consumers coexist with frugal sedentary consumers. When consumers are impatient (i.e., eager to imitate successful strategies) or myopic (i.e., unaware of conditions outside of their neighborhoods), inequality and overexploitation tend to aggravate.

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  • 4.
    Libby, Eric
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik. Santa Fe Institute, Santa Fe, New Mexico, United States of America.
    Hebert-Dufresne, Laurent
    Hosseini, Sayed-Rzgar
    Wagner, Andreas
    Syntrophy emerges spontaneously in complex metabolic systems2019Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 15, nr 7, artikel-id e1007169Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Syntrophy allows a microbial community as a whole to survive in an environment, even though individual microbes cannot. The metabolic interdependence typical of syntrophy is thought to arise from the accumulation of degenerative mutations during the sustained co-evolution of initially self-sufficient organisms. An alternative and underexplored possibility is that syntrophy can emerge spontaneously in communities of organisms that did not co-evolve. Here, we study this de novo origin of syntrophy using experimentally validated computational techniques to predict an organism's viability from its metabolic reactions. We show that pairs of metabolisms that are randomly sampled from a large space of possible metabolism and viable on specific primary carbon sources often become viable on new carbon sources by exchanging metabolites. The same biochemical reactions that are required for viability on primary carbon sources also confer viability on novel carbon sources. Our observations highlight a new and important avenue for the emergence of metabolic adaptations and novel ecological interactions.

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  • 5.
    Rocha, Luis E C
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Liljeros, Fredrik
    Stockholm University.
    Holme, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Simulated epidemics in an empirical spatiotemporal network of 50,185 sexual contacts2011Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 7, nr 3, s. e1001109-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Sexual contact patterns, both in their temporal and network structure, can influence the spread of sexually transmitted infections (STI). Most previous literature has focused on effects of network topology; few studies have addressed the role of temporal structure. We simulate disease spread using SI and SIR models on an empirical temporal network of sexual contacts in high-end prostitution. We compare these results with several other approaches, including randomization of the data, classic mean-field approaches, and static network simulations. We observe that epidemic dynamics in this contact structure have well-defined, rather high epidemic thresholds. Temporal effects create a broad distribution of outbreak sizes, even if the per-contact transmission probability is taken to its hypothetical maximum of 100%. In general, we conclude that the temporal correlations of our network accelerate outbreaks, especially in the early phase of the epidemics, while the network topology (apart from the contact-rate distribution) slows them down. We find that the temporal correlations of sexual contacts can significantly change simulated outbreaks in a large empirical sexual network. Thus, temporal structures are needed alongside network topology to fully understand the spread of STIs. On a side note, our simulations further suggest that the specific type of commercial sex we investigate is not a reservoir of major importance for HIV.

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  • 6.
    Schiffthaler, Bastian
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Kostadima, Myrto
    Delhomme, Nicolas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Rustici, Gabriella
    Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability2016Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 12, nr 6, artikel-id e1004937Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The advancement of high-throughput sequencing (HTS) technologies and the rapid development of numerous analysis algorithms and pipelines in this field has resulted in an unprecedentedly high demand for training scientists in HTS data analysis. Embarking on developing new training materials is challenging for many reasons. Trainers often do not have prior experience in preparing or delivering such materials and struggle to keep them up to date. A repository of curated HTS training materials would support trainers in materials preparation, reduce the duplication of effort by increasing the usage of existing materials, and allow for the sharing of teaching experience among the HTS trainers' community. To achieve this, we have developed a strategy for materials' curation and dissemination. Standards for describing training materials have been proposed and applied to the curation of existing materials. A Git repository has been set up for sharing annotated materials that can now be reused, modified, or incorporated into new courses. This repository uses Git; hence, it is decentralized and self-managed by the community and can be forked/built-upon by all users. The repository is accessible at http://bioinformatics.upsc.se/htmr.

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  • 7. Yazdi, Samira
    et al.
    Stein, Matthias
    Elinder, Fredrik
    Andersson, Magnus
    KTH, Science for Life Laboratory, SciLifeLab.
    Lindahl, Erik
    KTH, Science for Life Laboratory, SciLifeLab.
    The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel2016Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 12, nr 1, artikel-id e1004704Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Voltage-gated potassium (K-V) channels are membrane proteins that respond to changes in membrane potential by enabling K+ ion flux across the membrane. Polyunsaturated fatty acids (PUFAs) induce channel opening by modulating the voltage-sensitivity, which can provide effective treatment against refractory epilepsy by means of a ketogenic diet. While PUFAs have been reported to influence the gating mechanism by electrostatic interactions to the voltage-sensor domain (VSD), the exact PUFA-protein interactions are still elusive. In this study, we report on the interactions between the Shaker K-V channel in open and closed states and a PUFA-enriched lipid bilayer using microsecond molecular dynamics simulations. We determined a putative PUFA binding site in the open state of the channel located at the protein-lipid interface in the vicinity of the extracellular halves of the S3 and S4 helices of the VSD. In particular, the lipophilic PUFA tail covered a wide range of non-specific hydrophobic interactions in the hydrophobic central core of the protein-lipid interface, while the carboxylic head group displayed more specific interactions to polar/charged residues at the extracellular regions of the S3 and S4 helices, encompassing the S3-S4 linker. Moreover, by studying the interactions between saturated fatty acids (SFA) and the Shaker K-V channel, our study confirmed an increased conformational flexibility in the polyunsaturated carbon tails compared to saturated carbon chains, which may explain the specificity of PUFA action on channel proteins.

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