Stig W Omholt

Publications (45)177.91 Total impact

• Article: Arterial stiffening provides sufficient explanation for primary hypertension

  Klas H. Pettersen, Scott M. Bugenhagen, Javaid Nauman, Daniel A. Beard, Stig W. Omholt
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  ABSTRACT: Hypertension is one of the most common age-related chronic diseases and by predisposing individuals for heart failure, stroke and kidney disease, it is a major source of morbidity and mortality. Its etiology remains enigmatic despite intense research efforts over many decades. By use of empirically well-constrained computer models describing the coupled function of the baroreceptor reflex and mechanics of the circulatory system, we demonstrate quantitatively that arterial stiffening seems sufficient to explain age-related emergence of hypertension. Specifically, the empirically observed chronic changes in pulse pressure with age, and the impaired capacity of hypertensive individuals to regulate short-term changes in blood pressure, arise as emergent properties of the integrated system. Results are consistent with available experimental data from chemical and surgical manipulation of the cardio-vascular system. In contrast to widely held opinions, the results suggest that primary hypertension can be attributed to a mechanogenic etiology without challenging current conceptions of renal and sympathetic nervous system function. The results support the view that a major target for treating chronic hypertension in the elderly is the reestablishment of a proper baroreflex response.
  05/2013;
• Article: Effect of Regulatory Architecture on Broad versus Narrow Sense Heritability.

  Yunpeng Wang, Jon Olav Vik, Stig W Omholt, Arne B Gjuvsland
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  ABSTRACT: Additive genetic variance (VA ) and total genetic variance (VG ) are core concepts in biomedical, evolutionary and production-biology genetics. What determines the large variation in reported VA /VG ratios from line-cross experiments is not well understood. Here we report how the VA /VG ratio, and thus the ratio between narrow and broad sense heritability (h(2) /H(2) ), varies as a function of the regulatory architecture underlying genotype-to-phenotype (GP) maps. We studied five dynamic models (of the cAMP pathway, the glycolysis, the circadian rhythms, the cell cycle, and heart cell dynamics). We assumed genetic variation to be reflected in model parameters and extracted phenotypes summarizing the system dynamics. Even when imposing purely linear genotype to parameter maps and no environmental variation, we observed quite low VA /VG ratios. In particular, systems with positive feedback and cyclic dynamics gave more non-monotone genotype-phenotype maps and much lower VA /VG ratios than those without. The results show that some regulatory architectures consistently maintain a transparent genotype-to-phenotype relationship, whereas other architectures generate more subtle patterns. Our approach can be used to elucidate these relationships across a whole range of biological systems in a systematic fashion.
  PLoS Computational Biology 05/2013; 9(5):e1003053. · 5.22 Impact Factor
• Article: Electrodiffusive model for astrocytic and neuronal ion concentration dynamics

  Geir Halnes, Ivar Østby, Klas H. Pettersen, Stig W. Omholt, Gaute T. Einevoll
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  ABSTRACT: Electrical neural signalling typically takes place at the time-scale of milliseconds, and is typically modeled using the cable equation. This is a good approximation for processes when ionic concentrations vary little during the time course of a simulation. During periods of intense neural signalling, however, the local extracellular K+ concentration may increase by several millimolars. Clearance of excess K+ likely depends partly on diffusion in the extracellular space, partly on local uptake by- and intracellular transport within astrocytes. This process takes place at the time scale of seconds, and can not be modeled accurately without accounting for the spatiotemporal variations in ion concentrations. The work presented here consists of two main parts: First, we developed a general electrodiffusive formalism for modeling ion concentration dynamics in a one-dimensional geometry, including both an intra- and extracellular domain. The formalism was based on the Nernst-Planck equations. It ensures (i) consistency between the membrane potential and ion concentrations, (ii) global particle/charge conservation, and (iii) accounts for diffusion and concentration dependent variations in resistivities. Second, we applied the formalism to model how astrocytes exchange ions with the ECS, and identified the key astrocytic mechanisms involved in K+ removal from high concentration regions. We found that a local increase in extracellular K\textsuperscript{+} evoked a local depolarization of the astrocyte membrane, which at the same time (i) increased the local astrocytic uptake of K\textsuperscript{+}, (ii) suppressed extracellular transport of K+, (iii) increased transport of K+ within astrocytes, and (iv) facilitated astrocytic relase of K+ in extracellular low concentration regions. In summary, these mechanisms seem optimal for shielding the extracellular space from excess K+.
  04/2013;
• Source

  Available from: Jonas Warringer

  Article: Ancient Evolutionary Trade-Offs between Yeast Ploidy States.

  Enikö Zörgö, Karolina Chwialkowska, Arne B Gjuvsland, Elena Garré, Per Sunnerhagen, Gianni Liti, Anders Blomberg, Stig W Omholt, Jonas Warringer
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  ABSTRACT: The number of chromosome sets contained within the nucleus of eukaryotic organisms is a fundamental yet evolutionarily poorly characterized genetic variable of life. Here, we mapped the impact of ploidy on the mitotic fitness of baker's yeast and its never domesticated relative Saccharomyces paradoxus across wide swaths of their natural genotypic and phenotypic space. Surprisingly, environment-specific influences of ploidy on reproduction were found to be the rule rather than the exception. These ploidy-environment interactions were well conserved across the 2 billion generations separating the two species, suggesting that they are the products of strong selection. Previous hypotheses of generalizable advantages of haploidy or diploidy in ecological contexts imposing nutrient restriction, toxin exposure, and elevated mutational loads were rejected in favor of more fine-grained models of the interplay between ecology and ploidy. On a molecular level, cell size and mating type locus composition had equal, but limited, explanatory power, each explaining 12.5%-17% of ploidy-environment interactions. The mechanism of the cell size-based superior reproductive efficiency of haploids during Li(+) exposure was traced to the Li(+) exporter ENA. Removal of the Ena transporters, forcing dependence on the Nha1 extrusion system, completely altered the effects of ploidy on Li(+) tolerance and evoked a strong diploid superiority, demonstrating how genetic variation at a single locus can completely reverse the relative merits of haploidy and diploidy. Taken together, our findings unmasked a dynamic interplay between ploidy and ecology that was of unpredicted evolutionary importance and had multiple molecular roots.
  PLoS Genetics 03/2013; 9(3):e1003388. · 8.69 Impact Factor
• Article: Bridging the genotype-phenotype gap: what does it take?

  Arne B Gjuvsland, Jon Olav Vik, Daniel A Beard, Peter J Hunter, Stig W Omholt
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  ABSTRACT: The genotype-phenotype map (GP map) concept applies to any time point in the ontogeny of a living system. It is the outcome of very complex dynamics that include environmental effects, and bridging the genotype-phenotype gap is synonymous with understanding these dynamics. The context for this understanding is physiology, and the disciplinary goals of physiology do indeed demand the physiological community to seek this understanding. We claim that this task is beyond reach without use of mathematical models that bind together genetic and phenotypic data in a causally cohesive way. We provide illustrations of such causally cohesive genotype-phenotype models where the phenotypes span from gene expression profiles to development of whole organs. Bridging the genotype-phenotype gap also demands that large-scale biological ("omics") data and associated bioinformatics resources be more effectively integrated with computational physiology than what is currently the case. A third major element is the need for developing a phenomics technology way beyond current state of the art, and we advocate the establishment of a Human Phenome Program solidly grounded on biophysically based mathematical descriptions of human physiology.
  The Journal of Physiology 02/2013; · 4.72 Impact Factor
• Source

  Available from: Per Sunnerhagen

  Article: Ancient Evolutionary Trade-Offs between Yeast Ploidy States

  Enikö Zö Rgö, Karolina Chwialkowska, Arne B Gjuvsland, Elena Garré, Per Sunnerhagen, Gianni Liti, Anders Blomberg, Stig W Omholt, Jonas Warringer
  [show abstract] [hide abstract]
  ABSTRACT: The number of chromosome sets contained within the nucleus of eukaryotic organisms is a fundamental yet evolutionarily poorly characterized genetic variable of life. Here, we mapped the impact of ploidy on the mitotic fitness of baker's yeast and its never domesticated relative Saccharomyces paradoxus across wide swaths of their natural genotypic and phenotypic space. Surprisingly, environment-specific influences of ploidy on reproduction were found to be the rule rather than the exception. These ploidy–environment interactions were well conserved across the 2 billion generations separating the two species, suggesting that they are the products of strong selection. Previous hypotheses of generalizable advantages of haploidy or diploidy in ecological contexts imposing nutrient restriction, toxin exposure, and elevated mutational loads were rejected in favor of more fine-grained models of the interplay between ecology and ploidy. On a molecular level, cell size and mating type locus composition had equal, but limited, explanatory power, each explaining 12.5%–17% of ploidy– environment interactions. The mechanism of the cell size–based superior reproductive efficiency of haploids during Li + exposure was traced to the Li + exporter ENA. Removal of the Ena transporters, forcing dependence on the Nha1 extrusion system, completely altered the effects of ploidy on Li + tolerance and evoked a strong diploid superiority, demonstrating how genetic variation at a single locus can completely reverse the relative merits of haploidy and diploidy. Taken together, our findings unmasked a dynamic interplay between ploidy and ecology that was of unpredicted evolutionary importance and had multiple molecular roots.
  PLoS Genetics 01/2013; 9:e1003388. · 8.69 Impact Factor
• Article: Interpreting genetic effects through models of cardiac electromechanics.

  Steven Alexander Niederer, Sander Land, Stig W Omholt, Nicolas P Smith
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  ABSTRACT: Multi-scale models of cardiac electro-mechanics are being increasingly focused on understanding how genetic variation and environment underpin multiple disease states. In this paper we review the current state of the art in both the development of specific models and the physiological insights they have produced. This growing research body includes the development of models for capturing the effects of changes in function in both single and multiple proteins in both specific expression systems and in vivo contexts. Finally, the potential for using this approach for ultimately predicting phenotypes from genetic sequence information is discussed.
  AJP Heart and Circulatory Physiology 10/2012; · 3.71 Impact Factor
• Article: Multi-way metamodelling facilitates insight into the complex input-output maps of nonlinear dynamic models.

  Kristin Tøndel, Ulf G Indahl, Arne B Gjuvsland, Stig W Omholt, Harald Martens
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  ABSTRACT: BACKGROUND: Statistical approaches to describing the behaviour, including the complex relationships between input parameters and model outputs, of nonlinear dynamic models (referred to as metamodelling) are gaining more and more acceptance as a means for sensitivity analysis and to reduce computational demand. Understanding such input-output maps is necessary for efficient model construction and validation. Multi-way metamodelling provides the opportunity to retain the block-wise structure of the temporal data typically generated by dynamic models throughout the analysis. Furthermore, a cluster-based approach to regional metamodelling allows description of highly nonlinear input-output relationships, revealing additional patterns of covariation. RESULTS: By presenting the N-way Hierarchical Cluster-based Partial Least Squares Regression (N-way HC-PLSR) method, we here combine multi-way analysis with regional cluster-based metamodelling, together making a powerful methodology for extensive exploration of the input-output maps of complex dynamic models. We illustrate the potential of the N-way HC-PLSR by applying it both to predict model outputs as functions of the input parameters, and in the inverse direction (predicting input parameters from the model outputs), to analyse the behaviour of a dynamic model of the mammalian circadian clock. Our results display a more complete cartography of how variation in input parameters is reflected in the temporal behaviour of multiple model outputs than has been previously reported. CONCLUSIONS: Our results indicated that the N-way HC-PLSR metamodelling provides a gain in insight into which parameters that are related to a specific model output behaviour, as well as variations in the model sensitivity to certain input parameters across the model output space. Moreover, the N-way approach allows a more transparent and detailed exploration of the temporal dimension of complex dynamic models, compared to alternative 2-way methods.
  BMC Systems Biology 07/2012; 6(1):88. · 3.15 Impact Factor
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  Available from: PubMed Central

  Article: Parameters in dynamic models of complex traits are containers of missing heritability.

  Yunpeng Wang, Arne B Gjuvsland, Jon Olav Vik, Nicolas P Smith, Peter J Hunter, Stig W Omholt
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  ABSTRACT: Polymorphisms identified in genome-wide association studies of human traits rarely explain more than a small proportion of the heritable variation, and improving this situation within the current paradigm appears daunting. Given a well-validated dynamic model of a complex physiological trait, a substantial part of the underlying genetic variation must manifest as variation in model parameters. These parameters are themselves phenotypic traits. By linking whole-cell phenotypic variation to genetic variation in a computational model of a single heart cell, incorporating genotype-to-parameter maps, we show that genome-wide association studies on parameters reveal much more genetic variation than when using higher-level cellular phenotypes. The results suggest that letting such studies be guided by computational physiology may facilitate a causal understanding of the genotype-to-phenotype map of complex traits, with strong implications for the development of phenomics technology.
  PLoS Computational Biology 04/2012; 8(4):e1002459. · 5.22 Impact Factor
• Article: Aquaporin-4 regulates extracellular space volume dynamics during high-frequency synaptic stimulation: a gene deletion study in mouse hippocampus.

  Nadia Nabil Haj-Yasein, Vidar Jensen, Ivar Østby, Stig W Omholt, Juha Voipio, Kai Kaila, Ole P Ottersen, Øivind Hvalby, Erlend A Nagelhus
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  ABSTRACT: Little is known about the physiological roles of aquaporin-4 (AQP4) in the central nervous system. AQP4 water channels are concentrated in endfeet membranes of astrocytes but also localize to the fine astrocytic processes that abut central synapses. Based on its pattern of expression, we predicted that AQP4 could be involved in controlling water fluxes and changes in extracellular space (ECS) volume that are associated with activation of excitatory pathways. Here, we show that deletion of Aqp4 accentuated the shrinkage of the ECS that occurred in the mouse hippocampal CA1 region during activation of Schaffer collateral/commissural fibers. This effect was found in the stratum radiatum (where perisynaptic astrocytic processes abound) but not in the pyramidal cell layer (where astrocytic processes constitute but a minor volume fraction). For both genotypes the ECS shrinkage was most pronounced in the pyramidal cell layer. Our data attribute a physiological role to AQP4 and indicate that this water channel regulates extracellular volume dynamics in the mammalian brain.
  Glia 03/2012; 60(6):867-74. · 4.82 Impact Factor
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  Available from: PubMed Central

  Article: Towards a quantitative understanding of the MITF-PIAS3-STAT3 connection.

  Josef Thingnes, Timothy J Lavelle, Arne B Gjuvsland, Stig W Omholt, Eivind Hovig
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  ABSTRACT: Expression of the two transcription factors microphthalmia-associated transcription factor (MITF) and signal transducer and activator of transcription 3 (STAT3) are tightly connected to cell proliferation and survival, and are important for melanocyte development. The co-regulation of MITF and STAT3 via their binding to a common inhibitor Protein Inhibitor of Activated STAT3 (PIAS3) is intriguing. A better quantitative understanding of this regulation is likely to be important for elucidation of the melanocyte biology. We present a mathematical model describing the MITF-PIAS3-STAT3 signalling network. A default parameter set was developed, partly informed by the literature and partly by constraining the model to mimic reported behavioural features of the system. In addition, a set of experiment-specific parameters was derived for each of 28 experiments reported in the literature. The model seems capable of accounting for most of these experiments in terms of observed temporal development of protein amounts and phosphorylation states. Further, the results also suggest that this system possesses some regulatory features yet to be elucidated. We find that the experimentally observed crosstalk between MITF and STAT3 via PIAS3 in melanocytes is faithfully reproduced in our model, offering mechanistic explanations for this behaviour, as well as providing a scaffold for further studies of MITF signalling in melanoma.
  BMC Systems Biology 02/2012; 6:11. · 3.15 Impact Factor
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  Available from: Jonas Warringer

  Article: Life history shapes trait heredity by accumulation of loss-of-function alleles in yeast.

  Enikö Zörgö, Arne Gjuvsland, Francisco A Cubillos, Edward J Louis, Gianni Liti, Anders Blomberg, Stig W Omholt, Jonas Warringer
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  ABSTRACT: A fundamental question in biology is whether variation in organisms primarily emerges as a function of adaptation or as a function of neutral genetic drift. Trait variation in the model organism baker's yeast follows population bottlenecks rather than environmental boundaries suggesting that it primarily results from genetic drift. Based on the yeast life history, we hypothesized that population-specific loss-of-function mutations emerging in genes recently released from selection is the predominant cause of trait variation within the species. As retention of one functional copy of a gene in diploid yeasts is typically sufficient to maintain completely unperturbed performance, we also conjectured that a crossing of natural yeasts from populations with different loss-of-function mutations would provide a further efficient test bed for this hypothesis. Charting the first species-wide map of trait inheritance in a eukaryotic organism, we found trait heredity to be strongly biased toward diploid hybrid performance exactly mimicking the performance of the best of the parents, as expected given a complete dominance of functional over nonfunctional alleles. Best parent heterosis, partial dominance, and negative nonadditivity were all rare phenomena. Nonadditive inheritance was observed primarily in crosses involving at least one very poor performing parent, most frequently of the West African population, and when molecularly dissected, loss-of-function alleles were identified as the underlying cause. These findings provide support for that population-specific loss-of-function mutations do have a strong impact on genotype-phenotype maps and underscores the role of neutral genetic drift as a driver for trait variation within species.
  Molecular Biology and Evolution 01/2012; 29(7):1781-9. · 5.55 Impact Factor
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  Available from: PubMed Central

  Article: Understanding the melanocyte distribution in human epidermis: an agent-based computational model approach.

  Josef Thingnes, Timothy J Lavelle, Eivind Hovig, Stig W Omholt
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  ABSTRACT: The strikingly even color of human skin is maintained by the uniform distribution of melanocytes among keratinocytes in the basal layer of the human epidermis. In this work, we investigated three possible hypotheses on the mechanism by which the melanocytes and keratinocytes organize themselves to generate this pattern. We let the melanocyte migration be aided by (1) negative chemotaxis due to a substance produced by the melanocytes themselves, or (2) positive chemotaxis due to a substance produced by keratinocytes lacking direct physical contact with a melanocyte, or (3) positive chemotaxis due to a substance produced by keratinocytes in a distance-to-melanocytes dependent manner. The three hypotheses were implemented in an agent-based computational model of cellular interactions in the basal layer of the human epidermis. We found that they generate mutually exclusive predictions that can be tested by existing experimental protocols. This model forms a basis for further understanding of the communication between melanocytes and other skin cells in skin homeostasis.
  PLoS ONE 01/2012; 7(7):e40377. · 4.09 Impact Factor
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  Available from: William S Davidson

  Article: A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns.

  Sigbjørn Lien, Lars Gidskehaug, Thomas Moen, Ben J Hayes, Paul R Berg, William S Davidson, Stig W Omholt, Matthew P Kent
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  ABSTRACT: The Atlantic salmon genome is in the process of returning to a diploid state after undergoing a whole genome duplication (WGD) event between 25 and100 million years ago. Existing data on the proportion of paralogous sequence variants (PSVs), multisite variants (MSVs) and other types of complex sequence variation suggest that the rediplodization phase is far from over. The aims of this study were to construct a high density linkage map for Atlantic salmon, to characterize the extent of rediploidization and to improve our understanding of genetic differences between sexes in this species. A linkage map for Atlantic salmon comprising 29 chromosomes and 5650 single nucleotide polymorphisms (SNPs) was constructed using genotyping data from 3297 fish belonging to 143 families. Of these, 2696 SNPs were generated from ESTs or other gene associated sequences. Homeologous chromosomal regions were identified through the mapping of duplicated SNPs and through the investigation of syntenic relationships between Atlantic salmon and the reference genome sequence of the threespine stickleback (Gasterosteus aculeatus). The sex-specific linkage maps spanned a total of 2402.3 cM in females and 1746.2 cM in males, highlighting a difference in sex specific recombination rate (1.38:1) which is much lower than previously reported in Atlantic salmon. The sexes, however, displayed striking differences in the distribution of recombination sites within linkage groups, with males showing recombination strongly localized to telomeres. The map presented here represents a valuable resource for addressing important questions of interest to evolution (the process of re-diploidization), aquaculture and salmonid life history biology and not least as a resource to aid the assembly of the forthcoming Atlantic salmon reference genome sequence.
  BMC Genomics 12/2011; 12:615. · 4.07 Impact Factor
• Article: Is the brain water channel aquaporin-4 a pathogenetic factor in idiopathic intracranial hypertension? Results from a combined clinical and genetic study in a Norwegian cohort.

  Emilia Kerty, Kjell Heuser, Ulf G Indahl, Paul R Berg, Sigve Nakken, Sigbjørn Lien, Stig W Omholt, Ole P Ottersen, Erlend A Nagelhus
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  ABSTRACT: Purpose:  Idiopathic intracranial hypertension (IIH) is a condition of increased intracranial pressure of unknown aetiology. Patients with IIH usually suffer from headache and visual disturbances. High intracranial pressure despite normal ventricle size and negative MRI indicate perturbed water flux across cellular membranes, which is provided by the brain water channel aquaporin-4 (AQP4). IIH could be associated with malfunctioning intracerebral water homeostasis and cerebrospinal fluid (CSF) reabsorption based on functional or regulatory alterations of AQP4. Methods:  Clinical data, blood and CSF samples were collected from 28 patients with IIH. Clinical characteristics were assessed, and a genetic association study was performed by sequencing the AQP4 gene on chromosome 18. Genetic data were compared with 52 healthy controls and matched by age, sex and ethnicity. Chi-square test and linear discriminant analysis (LDA) were used in the search of a genotype-phenotype association. Results:  While the majority of patients responded to medical treatment, four required shunt application. All, except one, had a good visual outcome. The 24 AQP4 gene SNPs showed no association with IIH. Full cross-validation of the LDA modelling resulted in only 55.1% correct classification of the cases and controls, with a corresponding estimated p-value 0.37. Conclusions:  Our genetic case-control study did not indicate an association between AQP4 gene variants and IIH. However, the theory of an etiopathogenic link between IIH and AQP4 is tempting, and discussed in this article. Association studies with large sample size are difficult to perform owing is the rarity of the condition.
  Acta ophthalmologica 09/2011; · 2.44 Impact Factor
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  Available from: Trine B Rounge

  Article: The genome sequence of Atlantic cod reveals a unique immune system.

  Bastiaan Star, Alexander J Nederbragt, Sissel Jentoft, Unni Grimholt, Martin Malmstrøm, Tone F Gregers, Trine B Rounge, Jonas Paulsen, Monica H Solbakken, Animesh Sharma, [......], Richard Reinhardt, Lei Du, Steinar D Johansen, Steve Searle, Sigbjørn Lien, Frank Nilsen, Inge Jonassen, Stig W Omholt, Nils Chr Stenseth, Kjetill S Jakobsen
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  ABSTRACT: Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.
  Nature 08/2011; 477(7363):207-10. · 36.28 Impact Factor
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  Available from: Gaute T Einevoll

  Article: Dependence of spontaneous neuronal firing and depolarisation block on astroglial membrane transport mechanisms.

  Leiv Øyehaug, Ivar Østby, Catherine M Lloyd, Stig W Omholt, Gaute T Einevoll
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  ABSTRACT: Exposed to a sufficiently high extracellular potassium concentration ([K( + )]₀), the neuron can fire spontaneous discharges or even become inactivated due to membrane depolarisation ('depolarisation block'). Since these phenomena likely are related to the maintenance and propagation of seizure discharges, it is of considerable importance to understand the conditions under which excess [K( + )]₀ causes them. To address the putative effect of glial buffering on neuronal activity under elevated [K( + )](o) conditions, we combined a recently developed dynamical model of glial membrane ion and water transport with a Hodgkin-Huxley type neuron model. In this interconnected glia-neuron model we investigated the effects of natural heterogeneity or pathological changes in glial membrane transporter density by considering a large set of models with different, yet empirically plausible, sets of model parameters. We observed both the high [K( + )]₀-induced duration of spontaneous neuronal firing and the prevalence of depolarisation block to increase when reducing the magnitudes of the glial transport mechanisms. Further, in some parameter regions an oscillatory bursting spiking pattern due to the dynamical coupling of neurons and glia was observed. Bifurcation analyses of the neuron model and of a simplified version of the neuron-glia model revealed further insights about the underlying mechanism behind these phenomena. The above insights emphasise the importance of combining neuron models with detailed astroglial models when addressing phenomena suspected to be influenced by the astroglia-neuron interaction. To facilitate the use of our neuron-glia model, a CellML version of it is made publicly available.
  Journal of Computational Neuroscience 06/2011; 32(1):147-65. · 2.51 Impact Factor
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  Available from: PubMed Central

  Article: Hierarchical cluster-based partial least squares regression (HC-PLSR) is an efficient tool for metamodelling of nonlinear dynamic models.

  Kristin Tøndel, Ulf G Indahl, Arne B Gjuvsland, Jon Olav Vik, Peter Hunter, Stig W Omholt, Harald Martens
  [show abstract] [hide abstract]
  ABSTRACT: Deterministic dynamic models of complex biological systems contain a large number of parameters and state variables, related through nonlinear differential equations with various types of feedback. A metamodel of such a dynamic model is a statistical approximation model that maps variation in parameters and initial conditions (inputs) to variation in features of the trajectories of the state variables (outputs) throughout the entire biologically relevant input space. A sufficiently accurate mapping can be exploited both instrumentally and epistemically. Multivariate regression methodology is a commonly used approach for emulating dynamic models. However, when the input-output relations are highly nonlinear or non-monotone, a standard linear regression approach is prone to give suboptimal results. We therefore hypothesised that a more accurate mapping can be obtained by locally linear or locally polynomial regression. We present here a new method for local regression modelling, Hierarchical Cluster-based PLS regression (HC-PLSR), where fuzzy C-means clustering is used to separate the data set into parts according to the structure of the response surface. We compare the metamodelling performance of HC-PLSR with polynomial partial least squares regression (PLSR) and ordinary least squares (OLS) regression on various systems: six different gene regulatory network models with various types of feedback, a deterministic mathematical model of the mammalian circadian clock and a model of the mouse ventricular myocyte function. Our results indicate that multivariate regression is well suited for emulating dynamic models in systems biology. The hierarchical approach turned out to be superior to both polynomial PLSR and OLS regression in all three test cases. The advantage, in terms of explained variance and prediction accuracy, was largest in systems with highly nonlinear functional relationships and in systems with positive feedback loops. HC-PLSR is a promising approach for metamodelling in systems biology, especially for highly nonlinear or non-monotone parameter to phenotype maps. The algorithm can be flexibly adjusted to suit the complexity of the dynamic model behaviour, inviting automation in the metamodelling of complex systems.
  BMC Systems Biology 06/2011; 5:90. · 3.15 Impact Factor
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  Available from: Dag Inge Våge

  Article: Characterisation of a novel paralog of scavenger receptor class B member I (SCARB1) in Atlantic salmon (Salmo salar).

  Hilde Sundvold, Hanna Helgeland, Matthew Baranski, Stig W Omholt, Dag Inge Våge
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  ABSTRACT: Red flesh colour is a unique trait found in some salmonid genera. Carotenoid pigments are not synthesized de novo in the fish, but are provided by dietary uptake. A better understanding of the molecular mechanisms underlying the cellular uptake and deposition of carotenoids could potentially be used to improve the low muscle deposition rate that is typically found in farmed Atlantic salmon. In addition, from an evolutionary point of view, the establishment and maintenance of this trait is still poorly understood. It has been demonstrated in several species that scavenger receptor class B, member 1 (SCARB1) is involved in intestinal absorption of carotenoids, which makes this gene a possible source of genetic variation in salmonid flesh pigmentation. In this study, a novel paralog of SCARB1 (SCARB1-2) was detected through screening for genetic variation in Atlantic salmon SCARB1. Full length SCARB1-2 encodes a protein with 89% identity to Atlantic salmon SCARB1, except for the C-terminal cytoplasmic tail that shows only 12% identity. The most prominent site of SCARB1 mRNA expression was in the mid gut, while a five-fold lower level was detected in Atlantic salmon skeletal muscle and liver. The SCARB1-2 mRNA was equally expressed in liver, muscle and mid gut, and at a lower level than SCARB1 mRNA. A total of seven different SCARB1-2 alleles comprising repetitive enhancer of zeste motifs (EZH2) were identified in the founding parents of a resource Atlantic salmon population. We mapped the SCARB1-2 paralog to a region on Atlantic salmon chromosome 1, containing a putative QTL for flesh colour. Addition of the SCARB1-2 marker increased the significance of this QTL, however the large confidence interval surrounding the QTL precludes confirmation of SCARB1-2 as a causative gene underlying variation in this trait. We have characterised a novel paralog of SCARB1 (SCARB1-2), have mapped it to Atlantic salmon chromosome 1 and have described its expression in various tissues. Mapping with SCARB1-2 alleles added further evidence for a QTL affecting flesh colour on this chromosome, however further studies are needed to confirm a functional role for this gene in flesh colour pigmentation.
  BMC Genetics 01/2011; 12:52. · 2.47 Impact Factor
• Article: Genotype-Phenotype Map Characteristics of an In silico Heart Cell.

  Jon Olav Vik, Arne B Gjuvsland, Liren Li, Kristin Tøndel, Steven Niederer, Nicolas P Smith, Peter J Hunter, Stig W Omholt
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  ABSTRACT: Understanding the causal chain from genotypic to phenotypic variation is a tremendous challenge with huge implications for personalized medicine. Here we argue that linking computational physiology to genetic concepts, methodology, and data provides a new framework for this endeavor. We exemplify this causally cohesive genotype-phenotype (cGP) modeling approach using a detailed mathematical model of a heart cell. In silico genetic variation is mapped to parametric variation, which propagates through the physiological model to generate multivariate phenotypes for the action potential and calcium transient under regular pacing, and ion currents under voltage clamping. The resulting genotype-to-phenotype map is characterized using standard quantitative genetic methods and novel applications of high-dimensional data analysis. These analyses reveal many well-known genetic phenomena like intralocus dominance, interlocus epistasis, and varying degrees of phenotypic correlation. In particular, we observe penetrance features such as the masking/release of genetic variation, so that without any change in the regulatory anatomy of the model, traits may appear monogenic, oligogenic, or polygenic depending on which genotypic variation is actually present in the data. The results suggest that a cGP modeling approach may pave the way for a computational physiological genomics capable of generating biological insight about the genotype-phenotype relation in ways that statistical-genetic approaches cannot.
  Frontiers in physiology. 01/2011; 2:106.