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  • 1
    Online Resource
    Online Resource
    Sunlight exposure exerts immunomodulatory effects to reduce multiple sclerosis severity
    Proceedings of the National Academy of Sciences ; 2021
    In:  Proceedings of the National Academy of Sciences Vol. 118, No. 1 ( 2021-01-05)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 118, No. 1 ( 2021-01-05)
    Abstract: Multiple sclerosis (MS) disease risk is associated with reduced sun-exposure. This study assessed the relationship between measures of sun exposure (vitamin D [vitD], latitude) and MS severity in the setting of two multicenter cohort studies ( n NationMS = 946, n BIONAT = 990). Additionally, effect-modification by medication and photosensitivity-associated MC1R variants was assessed. High serum vitD was associated with a reduced MS severity score (MSSS), reduced risk for relapses, and lower disability accumulation over time. Low latitude was associated with higher vitD, lower MSSS, fewer gadolinium-enhancing lesions, and lower disability accumulation. The association of latitude with disability was lacking in IFN-β–treated patients. In carriers of MC1R :rs1805008(T), who reported increased sensitivity toward sunlight, lower latitude was associated with higher MRI activity, whereas for noncarriers there was less MRI activity at lower latitudes. In a further exploratory approach, the effect of ultraviolet (UV)-phototherapy on the transcriptome of immune cells of MS patients was assessed using samples from an earlier study. Phototherapy induced a vitD and type I IFN signature that was most apparent in monocytes but that could also be detected in B and T cells. In summary, our study suggests beneficial effects of sun exposure on established MS, as demonstrated by a correlative network between the three factors: Latitude, vitD, and disease severity. However, sun exposure might be detrimental for photosensitive patients. Furthermore, a direct induction of type I IFNs through sun exposure could be another mechanism of UV-mediated immune-modulation in MS.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2018457118
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2021
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
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  • 2
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    Baseline susceptibility and insecticide resistance monitoring in European populations of M eligethes aeneus and C eutorhynchus assimilis collected in winter oilseed rape
    Wiley ; 2014
    In:  Entomologia Experimentalis et Applicata Vol. 150, No. 3 ( 2014-03), p. 279-288
    Details
    In: Entomologia Experimentalis et Applicata, Wiley, Vol. 150, No. 3 ( 2014-03), p. 279-288
    Abstract: P ollen beetle, M eligethes aeneus ( F abricius) ( C oleoptera: N itidulidae), and cabbage seed weevil, C eutorhynchus assimilis ( P aykull) ( C oleoptera: C urculionidae), are important pests in the production of E uropean winter oilseed rape, B rassica napus L . ( B rassicaceae), which is grown on several million hectares in E urope. Insecticide treatments are common to control both pests once they exceed economic damage thresholds; however, not many chemical classes are available for their control in European oilseed rape. Particularly pollen beetles recently developed high levels of pyrethroid resistance impairing field control at recommended rates in many countries, whereas no resistance is yet reported to another important insecticide, thiacloprid. The major objective of this study was to investigate the spatio‐temporal susceptibility status of pollen beetle against the recently introduced insecticide thiacloprid. From 2009 to 2012 more than 630 populations of pollen beetle collected in 13 countries were monitored for resistance to thiacloprid by using an adult vial test. No shifting to lower susceptibility of pollen beetle to thiacloprid has been observed between 2009 and 2012. Furthermore, we were able to show that pollen beetle larvae are extremely susceptible to thiacloprid, whereas within strains larvae are significantly more resistant than adults to pyrethroids such as lambda‐cyhalothrin. Dose‐response data for thiacloprid against cabbage seed weevil populations collected in 2011 in G ermany, S weden, and U kraine showed a 10‐fold higher intrinsic sensitivity compared to pollen beetle, and showed only a low variation in response. In addition, we also tested 17 cabbage seed weevil populations collected in five countries against lambda‐cyhalothrin with low variation in response (three‐fold), suggesting full baseline susceptibility and no resistance to pyrethroids. The implications of the data presented for resistance management in coleopteran pests in winter oilseed rape are discussed.
    Type of Medium: Online Resource
    ISSN: 0013-8703 , 1570-7458
    URL: Issue
    URL: Article
    DOI: 10.1111/eea.2014.150.issue-3
    DOI: 10.1111/eea.12162
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 2015286-3
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  • 3
    Online Resource
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    Toward the complete interactome
    Springer Science and Business Media LLC ; 2006
    In:  Nature Biotechnology Vol. 24, No. 6 ( 2006-06-01), p. 614-615
    Details
    In: Nature Biotechnology, Springer Science and Business Media LLC, Vol. 24, No. 6 ( 2006-06-01), p. 614-615
    Type of Medium: Online Resource
    ISSN: 1087-0156 , 1546-1696
    URL: Article
    DOI: 10.1038/nbt0606-614
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2006
    detail.hit.zdb_id: 1494943-X
    detail.hit.zdb_id: 1311932-1
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  • 4
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    Protein structure alignment considering phenotypic plasticity
    Oxford University Press (OUP) ; 2008
    In:  Bioinformatics Vol. 24, No. 16 ( 2008-08-15), p. i98-i104
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 24, No. 16 ( 2008-08-15), p. i98-i104
    Abstract: Motivation: Protein structure comparison exhibits differences and similarities of proteins and protein families and may help to elucidate protein sequence and structure evolution. Despite many methods to score protein structure similarity with and without flexibility and to align proteins accurately based on their structures, a meaningful evolutionary distance measure and alignment method which models the cost of mutations, insertions and deletions occurring in protein sequences on the structure level is still missing. Results: Here, we introduce a new measure for protein structure similarity and propose a novel method called phenotypic plasticity method (PPM) which explicitly tries to model the evolutionary distance of two proteins on the structure level by measuring the cost of ‘morphing’ one structure into the other one. PPM aligns protein structures taking variations naturally observed in groups of structures (‘phenotypic plasticity’) into account while preserving the overall topological arrangement of the structures. The performance of PPM in detecting similarities between protein structures is evaluated against well-known structure classification methods on two benchmark sets. The larger set consists of more than 3.6 million structure pairs from the SCOP database which are also consistently classified in CATH. In the current parameterization, PPM already performs comparable or better than other methods such as TM-Align and Vorolign on those two sets according to various evaluation criteria showing that the method is able to reliably classify known protein structures, to detect their similarities and to compute accurate alignments despite phenotypic plasticity. Availability: Executables are available upon request. Datasets and supplementary data (datasets and superpositions) can be accessed on http://www.bio.ifi.lmu.de/PPM Contact:  ralf.zimmer@bio.ifi.lmu.de
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/btn271
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2008
    detail.hit.zdb_id: 1468345-3
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  • 5
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    Rigorous assessment of gene set enrichment tests
    Oxford University Press (OUP) ; 2012
    In:  Bioinformatics Vol. 28, No. 11 ( 2012-06-01), p. 1480-1486
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 28, No. 11 ( 2012-06-01), p. 1480-1486
    Abstract: Motivation: Several statistical tests are available to detect the enrichment of differential expression in gene sets. Such tests were originally proposed for analyzing gene sets associated with biological processes. The objective evaluation of tests on real measurements has not been possible as it is difficult to decide a priori, which processes will be affected in given experiments. Results: We present a first large study to rigorously assess and compare the performance of gene set enrichment tests on real expression measurements. Gene sets are defined based on the targets of given regulators such as transcription factors (TFs) and microRNAs (miRNAs). In contrast to processes, TFs and miRNAs are amenable to direct perturbations, e.g. regulator over-expression or deletion. We assess the ability of 14 different statistical tests to predict the perturbations from expression measurements in Escherichia coli, Saccharomyces cerevisiae and human. We also analyze how performance depends on the quality and comprehensiveness of the regulator targets via a permutation approach. We find that ANOVA and Wilcoxons test consistently perform better than for instance Kolmogorov–Smirnov and hypergeometric tests. For scenarios where the optimal test is not known, we suggest to combine all evaluated tests into an unweighted consensus, which also performs well in our assessment. Our results provide a guide for the selection of existing tests as well as a basis for the development and assessment of novel tests. Contact:  robert.kueffner@bio.ifi.lmu.de Supplementary information:  Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/bts164
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2012
    detail.hit.zdb_id: 1468345-3
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  • 6
    Online Resource
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    A Turing test for artificial expression data
    Oxford University Press (OUP) ; 2013
    In:  Bioinformatics Vol. 29, No. 20 ( 2013-10-15), p. 2603-2609
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 29, No. 20 ( 2013-10-15), p. 2603-2609
    Abstract: Motivation: The lack of reliable, comprehensive gold standards complicates the development of many bioinformatics tools, particularly for the analysis of expression data and biological networks. Simulation approaches can provide provisional gold standards, such as regulatory networks, for the assessment of network inference methods. However, this just defers the problem, as it is difficult to assess how closely simulators emulate the properties of real data. Results: In analogy to Turing’s test discriminating humans and computers based on responses to questions, we systematically compare real and artificial systems based on their gene expression output. Different expression data analysis techniques such as clustering are applied to both types of datasets. We define and extract distributions of properties from the results, for instance, distributions of cluster quality measures or transcription factor activity patterns. Distributions of properties are represented as histograms to enable the comparison of artificial and real datasets. We examine three frequently used simulators that generate expression data from parameterized regulatory networks. We identify features distinguishing real from artificial datasets that suggest how simulators could be adapted to better emulate real datasets and, thus, become more suitable for the evaluation of data analysis tools. Availability: See http://www2.bio.ifi.lmu.de/∼kueffner/attfad/ and the supplement for precomputed analyses; other compendia can be analyzed via the CRAN package attfad. The full datasets can be obtained from http://www2.bio.ifi.lmu.de/∼kueffner/attfad/data.tar.gz. Contact:  robert.kueffner@bio.ifi.lmu.de Supplementary information:  Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/btt438
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2013
    detail.hit.zdb_id: 1468345-3
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  • 7
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    Molecular innovations underlying resistance to nicotine and neonicotinoids in the aphid Myzus persicae
    Wiley ; 2021
    In:  Pest Management Science Vol. 77, No. 12 ( 2021-12), p. 5311-5320
    Details
    In: Pest Management Science, Wiley, Vol. 77, No. 12 ( 2021-12), p. 5311-5320
    Abstract: The green peach aphid, Myzus persicae , is a globally distributed highly damaging crop pest. This species has demonstrated an exceptional ability to evolve resistance to both synthetic insecticides used for control, and natural insecticides produced by certain plants as a chemical defense against insect attack. Here we review work characterizing the evolution of resistance in M. persicae to the natural insecticide nicotine and the structurally related class of synthetic neonicotinoid insecticides. We outline how research on this topic has provided insights into long‐standing questions of both evolutionary and applied importance. These include questions pertaining to the origins of novel traits, the number and nature of mutational events or ‘adaptive steps’ underlying the evolution of new phenotypes, and whether host plant adaptations can be co‐opted to confer resistance to synthetic insecticides. Finally, research on the molecular mechanisms underlying insecticide resistance in M. persicae has generated several outstanding questions on the genetic architecture of resistance to both natural and synthetic xenobiotics, and we conclude by identifying key knowledge gaps for future research. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
    Type of Medium: Online Resource
    ISSN: 1526-498X , 1526-4998
    URL: Issue
    URL: Article
    DOI: 10.1002/ps.v77.12
    DOI: 10.1002/ps.6558
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2003455-6
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  • 8
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    Differential Contribution of the Olfactory CNG Channel Subunits to the Activation Process
    Elsevier BV ; 2011
    In:  Biophysical Journal Vol. 100, No. 3 ( 2011-02), p. 103a-
    Details
    In: Biophysical Journal, Elsevier BV, Vol. 100, No. 3 ( 2011-02), p. 103a-
    Type of Medium: Online Resource
    ISSN: 0006-3495
    URL: Article
    DOI: 10.1016/j.bpj.2010.12.769
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2011
    detail.hit.zdb_id: 1477214-0
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  • 9
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    Functional Role of the Modulatory Subunits in the Olfactory CNG Channels
    Elsevier BV ; 2012
    In:  Biophysical Journal Vol. 102, No. 3 ( 2012-01), p. 130a-131a
    Details
    In: Biophysical Journal, Elsevier BV, Vol. 102, No. 3 ( 2012-01), p. 130a-131a
    Type of Medium: Online Resource
    ISSN: 0006-3495
    URL: Article
    DOI: 10.1016/j.bpj.2011.11.725
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2012
    detail.hit.zdb_id: 1477214-0
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  • 10
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    Inferring topology from clustering coefficients in protein-protein interaction networks
    Springer Science and Business Media LLC ; 2006
    In:  BMC Bioinformatics Vol. 7, No. 1 ( 2006-12)
    Details
    In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2006-12)
    Type of Medium: Online Resource
    ISSN: 1471-2105
    URL: Article
    DOI: 10.1186/1471-2105-7-519
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2006
    detail.hit.zdb_id: 2041484-5
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