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  • 1
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    BiGG Models: A platform for integrating, standardizing and sharing genome-scale models (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models ( http://bigg.ucsd.edu ), a completely redesigned Bi ochemical, G enetic and G enomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    JSBML 1.0: providing a smorgasbord of options to encode systems biology models (2015)
    Oxford University Press
    Details
    Publication Date: 2015-10-08
    Description: : JSBML, the official pure Java programming library for the Systems Biology Markup Language (SBML) format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users. Availability and implementation : Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML . More information about JSBML can be found in the user guide at http://sbml.org/Software/JSBML/docs/ . Contact: jsbml-development@googlegroups.com or andraeger@eng.ucsd.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    Microsatellite DNA analysis of Pacific hake Merluccius productus population structure in the Salish Sea (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-01
    Description: This study presents the first microsatellite DNA study of population structure of Pacific hake, Merluccius productus (also known as Pacific whiting) within the Salish Sea, which has been identified as a distinct population segment under the US Endangered Species Act and is currently listed as a federal Species of Concern. In contrast, a separate coastal stock component of Pacific hake represents the most abundant commercial groundfish species on the US West Coast. We surveyed variation at 10 microsatellite DNA loci in a total of 655 individuals from three Salish Sea locations (Port Susan (PTS) and Dabob Bay in Washington and south-central Strait of Georgia (SOG) in British Columbia), three coastal locations (two off southern California and one in the Gulf of Alaska), and the Northern Gulf of California (GOC), México. No significant differences were detected among temporal samples from both PTS and SOG locations. Multilocus measures of population subdivision between coastal and Salish Sea populations (all pairwise F ST ≥ 0.03) and between PTS and SOG populations ( F ST ≥ 0.01) suggest a moderate degree of demographic isolation among these spawning populations. No significant genetic differences were found among the three coastal Pacific hake samples; however, Pacific hake from the GOC were significantly differentiated from both coastal ( F ST 〉 0.05) and Salish Sea ( F ST ≥ 0.03) Pacific hake. Correlations between genetic and geographic distance showed that Pacific hake display a very strong isolation by distance signal, both over the whole study area (~4500 km; r 2 = 0.94) and within the Salish Sea (~280 km; r 2 = 0.72). This study suggests that PTS and SOG populations are to some extent demographically isolated from each other.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 4
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    Evolution of Escherichia coli to 42 {degrees}C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations (2014)
    Oxford University Press
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    Publication Date: 2014-09-19
    Description: Adaptive laboratory evolution (ALE) has emerged as a valuable method by which to investigate microbial adaptation to a desired environment. Here, we performed ALE to 42 °C of ten parallel populations of Escherichia coli K-12 MG1655 grown in glucose minimal media. Tightly controlled experimental conditions allowed selection based on exponential-phase growth rate, yielding strains that uniformly converged toward a similar phenotype along distinct genetic paths. Adapted strains possessed as few as 6 and as many as 55 mutations, and of the 144 genes that mutated in total, 14 arose independently across two or more strains. This mutational recurrence pointed to the key genetic targets underlying the evolved fitness increase. Genome engineering was used to introduce the novel ALE-acquired alleles in random combinations into the ancestral strain, and competition between these engineered strains reaffirmed the impact of the key mutations on the growth rate at 42 °C. Interestingly, most of the identified key gene targets differed significantly from those found in similar temperature adaptation studies, highlighting the sensitivity of genetic evolution to experimental conditions and ancestral genotype. Additionally, transcriptomic analysis of the ancestral and evolved strains revealed a general trend for restoration of the global expression state back toward preheat stressed levels. This restorative effect was previously documented following evolution to metabolic perturbations, and thus may represent a general feature of ALE experiments. The widespread evolved expression shifts were enabled by a comparatively scant number of regulatory mutations, providing a net fitness benefit but causing suboptimal expression levels for certain genes, such as those governing flagellar formation, which then became targets for additional ameliorating mutations. Overall, the results of this study provide insight into the adaptation process and yield lessons important for the future implementation of ALE as a tool for scientific research and engineering.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Rare mutations associating with serum creatinine and chronic kidney disease (2014)
    Oxford University Press
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    Publication Date: 2014-11-27
    Description: Chronic kidney disease (CKD) is a complex disorder with a strong genetic component. A number of common sequence variants have been found to associate with serum creatinine (SCr), estimated glomerular filtration rate (eGFR) and/or CKD. We imputed 24 million single-nucleotide polymorphisms and insertions/deletions identified by whole-genome sequencing of 2230 Icelanders into 81 656 chip-typed individuals and 112 630 relatives of genotyped individuals over the age of 18 with SCr measurements. The large set of sequenced individuals allowed accurate imputation of variants to a minor allele frequency (MAF) of 0.1%. We tested the imputed variants for association with SCr. In addition to replicating established loci, we discovered missense and loss-of-function variants associating with SCr in three solute carriers ( SLC6A19 , SLC25A45  and SLC47A1 ) and two E3 ubiquitin ligases ( RNF186 and RNF128 ). All the variants are within coding sequences and all but one are rare (MAF 〈2%) with SCr effects between 0.085 and 0.129 standard deviations. These rare variants have a larger effect on SCr than previously reported common variants, explaining 0.5% of the variability of SCr in Icelanders in addition to the 1% already accounted for. We tested the five variants associating with SCr for association with CKD in an Icelandic sample of 15 594 cases and 291 428 controls. Three of the variants also associated with CKD. These variants may either affect kidney function or creatinine synthesis and excretion. Of note were four mutations in SLC6A19 that associate with reduced SCr, three of which have been shown to cause Hartnup disease.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli (2015)
    Oxford University Press
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    Publication Date: 2015-04-02
    Description: DNA-binding motifs that are recognized by transcription factors (TFs) have been well studied; however, challenges remain in determining the in vivo architecture of TF-DNA complexes on a genome-scale. Here, we determined the in vivo architecture of Escherichia coli arginine repressor (ArgR)-DNA complexes using high-throughput sequencing of exonuclease-treated chromatin-immunoprecipitated DNA (ChIP-exo). The ChIP-exo has a unique peak-pair pattern indicating 5' and 3' ends of ArgR-binding region. We identified 62 ArgR-binding loci, which were classified into three groups, comprising single, double and triple peak-pairs. Each peak-pair has a unique 93 base pair (bp)-long (±2 bp) ArgR-binding sequence containing two ARG boxes (39 bp) and residual sequences. Moreover, the three ArgR-binding modes defined by the position of the two ARG boxes indicate that DNA bends centered between the pair of ARG boxes facilitate the non-specific contacts between ArgR subunits and the residual sequences. Additionally, our approach may also reveal other fundamental structural features of TF-DNA interactions that have implications for studying genome-scale transcriptional regulatory networks.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    InSAR observations and models of crustal deformation due to a glacial surge in Iceland (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-04
    Description: Surges are common at all the major ice caps in Iceland. Ice masses of gigatons may shift from the upper part of the outlet glacier towards the terminus in a few months, advancing the glacier front by up to several kilometres. The advancing ice front may be up to 100 m thick, increasing the load on crustal rocks correspondingly. We use the observed change in crustal loading during a surge of the western part of the Vatnajökull ice cap, Iceland, during 1993–1995 and the corresponding elastic crustal deformation, surveyed with interferometric synthetic aperture radar, to investigate the material properties of the solid Earth in this region. Crustal subsidence due to the surge reaches ~75 mm at the edge of the Síðujökull outlet glacier. This signal is mixed with a broad uplift signal of ~12 mm yr –1 , relative to our reference area, caused by the ongoing retreat of Vatnajökull in response to climate change. We disentangle the two signals by linear inversion. Finite element modelling is used to investigate the elastic Earth response of the surge, as well as to confirm that no significant viscoelastic deformation occurred as a consequence of the surge. The modelling leads to estimates of the Young's modulus and Poisson's ratio of the underlying Earth. Comparison between the observed and modelled deformation fields is made using a Bayesian approach that yields the estimate of a probability distribution for each of the free parameters. Residuals indicate a good agreement between models and observations. One-layer elastic models result in a Young's modulus of 43.2–49.7 GPa (95 per cent confidence) and Poisson's ratio of 0–0.27, after removal of outliers. Our preferred model, with two elastic layers, provides a better fit to the whole surge signal. This model consists of a 1-km-thick upper layer with an average Young's modulus of 12.9–15.3 GPa and Poisson's ratio of 0.17, overlying a layer with an average Young's modulus of 67.3–81.9 GPa and Poisson's ratio of 0.25.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 8
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    GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data (2013)
    Oxford University Press
    Details
    Publication Date: 2013-10-30
    Description: Motivation: Genome-scale metabolic models have been used extensively to investigate alterations in cellular metabolism. The accuracy of these models to represent cellular metabolism in specific conditions has been improved by constraining the model with omics data sources. However, few practical methods for integrating metabolomics data with other omics data sources into genome-scale models of metabolism have been developed. Results: GIM 3 E (Gene Inactivation Moderated by Metabolism, Metabolomics and Expression) is an algorithm that enables the development of condition-specific models based on an objective function, transcriptomics and cellular metabolomics data. GIM 3 E establishes metabolite use requirements with metabolomics data, uses model-paired transcriptomics data to find experimentally supported solutions and provides calculations of the turnover (production/consumption) flux of metabolites. GIM 3 E was used to investigate the effects of integrating additional omics datasets to create increasingly constrained solution spaces of Salmonella Typhimurium metabolism during growth in both rich and virulence media. This integration proved to be informative and resulted in a requirement of additional active reactions (12 in each case) or metabolites (26 or 29, respectively). The addition of constraints from transcriptomics also impacted the allowed solution space, and the cellular metabolites with turnover fluxes that were necessarily altered by the change in conditions increased from 118 to 271 of 1397. Availability: GIM 3 E has been implemented in Python and requires a COBRApy 0.2.x. The algorithm and sample data described here are freely available at: http://opencobra.sourceforge.net/ Contacts: brianjamesschmidt@gmail.com or hyduke@usu.edu Supplementary information: Supplementary information is available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 9
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    Can permanent closures of nearshore areas reduce the proportions of undersized fish in the Icelandic longline fishery? (2015)
    Oxford University Press
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    Publication Date: 2015-03-07
    Description: In recent years, about one-third of the cod ( Gadus morhua ) and haddock ( Melanogrammus aeglefinus ) catches in Icelandic waters have been obtained with longline. Although longlining has been regarded as a conservation-oriented fishing method, a serious drawback of this fishing gear is the high catches of undersized fish. Our purpose was to locate areas where catches of undersized fish are high and consider if it may be feasible to close them permanently for longlining. Extensive length measurements used in the analysis were made by official inspectors on-board longliners during 2005–2013 in the main fishing area around Iceland. We found that the percentage of undersized cod (〈55 cm total length) and haddock (〈45 cm) in those samples decreased in relation to both depth and distance from shore. Our results suggest that permanent closures of large nearshore areas for longlining is a feasible option to reduce catch of undersized cod and haddock.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 10
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    The effect of signal leakage and glacial isostatic rebound on GRACE-derived ice mass changes in Iceland (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-11
    Description: Monthly gravity field models from the GRACE satellite mission are widely used to determine ice mass changes of large ice sheets as well as smaller glaciers and ice caps. Here, we investigate in detail the ice mass changes of the Icelandic ice caps as derived from GRACE data. The small size of the Icelandic ice caps, their location close to other rapidly changing ice covered areas and the low viscosity of the mantle below Iceland make this especially challenging. The mass balance of the ice caps is well constrained by field mass balance measurements, making this area ideal for such investigations. We find that the ice mass changes of the Icelandic ice caps derived from GRACE gravity field models are influenced by both the large gravity change signal resulting from ice mass loss in southeast Greenland and the mass redistribution within the Earth mantle due to glacial isostatic adjustment since the Little Ice Age (∼1890 AD). To minimize the signal that leaks towards Iceland from Greenland, we employ an independent mass change estimate of the Greenland Ice Sheet derived from satellite laser altimetry. We also estimate the effect of post Little Ice Age glacial isostatic adjustment, from knowledge of the ice history and GPS network constrained crustal deformation data. We find that both the leakage from Greenland and the post Little Ice Age glacial isostatic adjustment are important to take into account, in order to correctly determine Iceland ice mass changes from GRACE, and when applying these an average mass balance of the Icelandic ice caps of −11.4 ± 2.2 Gt yr−1 for the period 2003–2010 is found. This number corresponds well with available mass balance measurements.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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