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Sökning: hsv:(NATURVETENSKAP) hsv:(Biologi) hsv:(Biokemi och molekylärbiologi) > Högskolan Dalarna

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1.
  • Hintze, Arend, Professor, et al. (författare)
  • Evolution of complex modular biological networks
  • 2008
  • Ingår i: PloS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 4:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their modularity of function, with modules defined as sets of genes that are strongly interconnected but whose function is separable from those of other modules. Here, we investigate the in silico evolution of modularity and robustness in complex artificial metabolic networks that encode an increasing amount of information about their environment while acquiring ubiquitous features of biological, social, and engineering networks, such as scale-free edge distribution, small-world property, and fault-tolerance. These networks evolve in environments that differ in their predictability, and allow us to study modularity from topological, information-theoretic, and gene-epistatic points of view using new tools that do not depend on any preconceived notion of modularity. We find that for our evolved complex networks as well as for the yeast protein-protein interaction network, synthetic lethal gene pairs consist mostly of redundant genes that lie close to each other and therefore within modules, while knockdown suppressor gene pairs are farther apart and often straddle modules, suggesting that knockdown rescue is mediated by alternative pathways or modules. The combination of network modularity tools together with genetic interaction data constitutes a powerful approach to study and dissect the role of modularity in the evolution and function of biological networks. © 2008 Hintze and Adami.
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2.
  • Adami, C., et al. (författare)
  • Information content of colored motifs in complex networks
  • 2011
  • Ingår i: Artificial Life. - : MIT Press - Journals. - 1064-5462 .- 1530-9185. ; 17:4, s. 375-390
  • Tidskriftsartikel (refereegranskat)abstract
    • We study complex networks in which the nodes are tagged with different colors depending on their function (colored graphs), using information theory applied to the distribution of motifs in such networks. We find that colored motifs can be viewed as the building blocks of the networks (much more than the uncolored structural motifs can be) and that the relative frequency with which these motifs appear in the network can be used to define its information content. This information is defined in such a way that a network with random coloration (but keeping the relative number of nodes with different colors the same) has zero color information content. Thus, colored motif information captures the exceptionality of coloring in the motifs that is maintained via selection. We study the motif information content of the C. elegans brain as well as the evolution of colored motif information in networks that reflect the interaction between instructions in genomes of digital life organisms. While we find that colored motif information appears to capture essential functionality in the C. elegans brain (where the color assignment of nodes is straightforward), it is not obvious whether the colored motif information content always increases during evolution, as would be expected from a measure that captures network complexity. For a single choice of color assignment of instructions in the digital life form Avida, we find rather that colored motif information content increases or decreases during evolution, depending on how the genomes are organized, and therefore could be an interesting tool to dissect genomic rearrangements. © 2011 Massachusetts Institute of Technology.
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3.
  • Labar, T., et al. (författare)
  • Evolvability tradeoffs in emergent digital replicators
  • 2016
  • Ingår i: Artificial Life. - : MIT Press Journals. - 1064-5462 .- 1530-9185. ; 22:4, s. 483-498
  • Tidskriftsartikel (refereegranskat)abstract
    • The role of historical contingency in the origin of life is one of the great unknowns in modern science. Only one example of life exists - one that proceeded from a single self-replicating organism (or a set of replicating hypercycles) to the vast complexity we see today in Earth's biosphere. We know that emergent life has the potential to evolve great increases in complexity, but it is unknown if evolvability is automatic given any self-replicating organism. At the same time, it is difficult to test such questions in biochemical systems. Laboratory studies with RNA replicators have had some success with exploring the capacities of simple self-replicators, but these experiments are still limited in both capabilities and scope. Here, we use the digital evolution system Avida to explore the interplay between emergent replicators (rare randomly assembled self-replicators) and evolvability. We find that we can classify fixed-length emergent replicators in Avida into two classes based on functional analysis. One class is more evolvable in the sense of optimizing the replicators' replication abilities. However, the other class is more evolvable in the sense of acquiring evolutionary innovations. We tie this tradeoff in evolvability to the structure of the respective classes' replication machinery, and speculate on the relevance of these results to biochemical replicators. © 2016 Massachusetts Institute of Technology.
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4.
  • Ohlsson, Anna B., et al. (författare)
  • UV-B Exposure of Indoor-Grown Picea abies Seedlings Causes an Epigenetic Effect and Selective Emission of Terpenes
  • 2013
  • Ingår i: Zeitschrift für Naturforschung C - A Journal of Biosciences. - Tübingen : Verlag der Zeitschrift für Naturforschung. - 0939-5075 .- 1865-7125. ; 68:3-4, s. 139-147
  • Tidskriftsartikel (refereegranskat)abstract
    • Terpenoids are involved in various defensive functions in plants, especially conifers. Epigenetic mechanisms, for example DNA methylation, can influence plant defence systems. The purpose of the present study was to investigate the influence of UV-B exposure on the release of terpenoids from spruce seedlings and on needle DNA methylation. Ten-week-old seedlings grown indoors were exposed to UV-B radiation during 4 h, and the volatile compounds emitted from the seedlings were analysed. Analysis of the volatiles 1, 3, and 22 d after this UV-B exposure showed that bornyl acetate, borneol, myrcene, and limonene contents increased during the first 3 days, while at day 22 the level of emission had returned to the control level. UV-B exposure decreased the level of DNA methylation in needles of young seedlings, reflected in methylation changes in CCGG sequences. Exposure of young seedlings to UV-B radiation might be a way to potentiate the general defensive capacity, improving their ability to survive in outdoor conditions. UV-B-induced defence is discussed in the light of epigenetic mechanisms.
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5.
  • Patra, B., et al. (författare)
  • A genome wide dosage suppressor network reveals genomic robustness
  • 2017
  • Ingår i: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 45:1, s. 255-270
  • Tidskriftsartikel (refereegranskat)abstract
    • Genomic robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of genomic robustness in budding yeast by genome wide dosage suppressor analysis of 53 conditional lethal mutations in cell division cycle and RNA synthesis related genes, revealing 660 suppressor interactions of which 642 are novel. This collection has several distinctive features, including high cooccurrence of mutant-suppressor pairs within protein modules, highly correlated functions between the pairs and higher diversity of functions among the co-suppressors than previously observed. Dosage suppression of essential genes encoding RNA polymerase subunits and chromosome cohesion complex suggests a surprising degree of functional plasticity of macromolecular complexes, and the existence of numerous degenerate pathways for circumventing the effects of potentially lethal mutations. These results imply that organisms and cancer are likely able to exploit the genomic robustness properties, due the persistence of cryptic gene and pathway functions, to generate variation and adapt to selective pressures. © 2016 The Author(s).
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6.
  • Westin, Jerker, et al. (författare)
  • A new computer method for assessing drawing impairment in Parkinson's disease
  • 2010
  • Ingår i: Journal of Neuroscience Methods. - Amsterdam : Elsevier. - 0165-0270 .- 1872-678X. ; 190:1, s. 143-148
  • Tidskriftsartikel (refereegranskat)abstract
    • A test battery, consisting of self-assessments and motor tests (tapping and spiral drawing tasks) was used on 9482 test occasions by 62 patients with advanced Parkinson's disease (PD) in a telemedicine setting. On each test occasion, three Archimedes spirals were traced. A new computer method, using wavelet transforms and principal component analysis processed the spiral drawings to generate a spiral score. In a web interface, two PD specialists rated drawing impairment in spiral drawings from three random test occasions per patient, using a modification of the Bain & Findley 10-category scale. A standardised manual rating was defined as the mean of the two raters’ assessments. Bland-Altman analysis was used to evaluate agreement between the spiral score and the standardised manual rating. Another selection of spiral drawings was used to estimate the Spearman rank correlations between the raters (r = 0.87), and between the mean rating and the spiral score (r = 0.89). The 95% confidence interval for the method's prediction errors was ±1.5 scale units, which was similar to the differences between the human raters. In conclusion, the method could assess PD-related drawing impairments well comparable to trained raters.
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