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Sökning: WFRF:(Moran Jennifer)

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1.
  • Richards, Stephen, et al. (författare)
  • Genome sequence of the pea aphid Acyrthosiphon pisum
  • 2010
  • Ingår i: PLoS Biology. - Public Library of Science. - 1544-9173. ; 8:2, s. 1-24
  • Tidskriftsartikel (refereegranskat)abstract
    • Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
2.
  • Goes, Fernando S, et al. (författare)
  • Exome Sequencing of Familial Bipolar Disorder.
  • 2016
  • Ingår i: JAMA psychiatry. - 2168-6238. ; 73:6, s. 590-7
  • Tidskriftsartikel (refereegranskat)abstract
    • Complex disorders, such as bipolar disorder (BD), likely result from the influence of both common and rare susceptibility alleles. While common variation has been widely studied, rare variant discovery has only recently become feasible with next-generation sequencing.
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3.
  • Alexander, Peter, et al. (författare)
  • Drivers for global agricultural land use change: The nexus of diet, population, yield and bioenergy
  • 2015
  • Ingår i: Global Environmental Change. - Global Environmental Change, Elsevier. - 0959-3780. ; 35, s. 138-147
  • Tidskriftsartikel (refereegranskat)abstract
    • The nexus of population growth and changing diets has increased the demands placed on agriculture to supply food for human consumption, animal feed and fuel. Rising incomes lead to dietary changes, from staple crops, towards commodities with greater land requirements, e.g. meat and dairy products. Despite yield improvements partially offsetting increases in demand, agricultural land has still been expanding, causing potential harm to ecosystems, e.g. through deforestation. We use country-level panel data (1961-2011) to allocate the land areas used to produce food for human consumption, waste and biofuels, and to attribute the food production area changes to diet, population and yields drivers. The results show that the production of animal products dominates agricultural land use and land use change over the 50-year period, accounting for 65% of land use change. The rate of extensification of animal production was found to have reduced more recently, principally due to the smaller effect of population growth. The area used for bioenergy was shown to be relatively small, but formed a substantial contribution (36%) to net agricultural expansion in the most recent period. Nevertheless, in comparison to dietary shifts in animal products, bioenergy accounted for less than a tenth of the increase in demand for agricultural land. Population expansion has been the largest driver for agricultural land use change, but dietary changes are a significant and growing driver. China was a notable exception, where dietary transitions dominate food consumption changes, due to rapidly rising incomes. This suggests that future dietary changes will become the principal driver for land use change, pointing to the potential need for demand-side measures to regulate agricultural expansion. (C) 2015 Elsevier Ltd. All rights reserved.
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4.
  • Charney, Alexander W, et al. (författare)
  • Contribution of Rare Copy Number Variants to Bipolar Disorder Risk Is Limited to Schizoaffective Cases.
  • 2018
  • Ingår i: Biological psychiatry. - 1873-2402.
  • Tidskriftsartikel (refereegranskat)abstract
    • Genetic risk for bipolar disorder (BD) is conferred through many common alleles, while a role for rare copy number variants (CNVs) is less clear. Subtypes of BD including schizoaffective disorder bipolar type (SAB), bipolar I disorder (BD I), and bipolar II disorder (BD II) differ according to the prominence and timing of psychosis, mania, and depression. The genetic factors contributing to the combination of symptoms among these subtypes are poorly understood.Rare large CNVs were analyzed in 6353 BD cases (3833 BD I [2676 with psychosis, 850 without psychosis, and 307 with unknown psychosis history], 1436 BD II, 579 SAB, and 505 BD not otherwise specified) and 8656 controls. CNV burden and a polygenic risk score (PRS) for schizophrenia were used to evaluate the relative contributions of rare and common variants to risk of BD, BD subtypes, and psychosis.CNV burden did not differ between BD and controls when treated as a single diagnostic entity. However, burden in SAB was increased relative to controls (p = .001), BD I (p = .0003), and BD II (p = .0007). Burden and schizophrenia PRSs were increased in SAB compared with BD I with psychosis (CNV p = .0007, PRS p = .004), and BD I without psychosis (CNV p = .0004, PRS p = 3.9 × 10-5). Within BD I, psychosis was associated with increased schizophrenia PRSs (p = .005) but not CNV burden.CNV burden in BD is limited to SAB. Rare and common genetic variants may contribute differently to risk for psychosis and perhaps other classes of psychiatric symptoms.
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5.
  • Ching, Yung-Hao, et al. (författare)
  • High resolution mapping and positional cloning of ENU-induced mutations in the Rw region of mouse chromosome 5
  • 2010
  • Ingår i: BMC Genetics. - 1471-2156 .- 1471-2156. ; 11, s. 106
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Forward genetic screens in mice provide an unbiased means to identify genes and other functional genetic elements in the genome. Previously, a large scale ENU mutagenesis screen was conducted to query the functional content of a similar to 50 Mb region of the mouse genome on proximal Chr 5. The majority of phenotypic mutants recovered were embryonic lethals. Results: We report the high resolution genetic mapping, complementation analyses, and positional cloning of mutations in the target region. The collection of identified alleles include several with known or presumed functions for which no mutant models have been reported (Tbc1d14, Nol14, Tyms, Cad, Fbxl5, Haus3), and mutations in genes we or others previously reported (Tapt1, Rest, Ugdh, Paxip1, Hmx1, Otoe, Nsun7). We also confirmed the causative nature of a homeotic mutation with a targeted allele, mapped a lethal mutation to a large gene desert, and localized a spermiogenesis mutation to a region in which no annotated genes have coding mutations. The mutation in Tbc1d14 provides the first implication of a critical developmental role for RAB-GAP-mediated protein transport in early embryogenesis. Conclusion: This collection of alleles contributes to the goal of assigning biological functions to all known genes, as well as identifying novel functional elements that would be missed by reverse genetic approaches.
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6.
  • de Jong, Simone, et al. (författare)
  • Applying polygenic risk scoring for psychiatric disorders to a large family with bipolar disorder and major depressive disorder
  • 2018
  • Ingår i: Communications Biology. - Nature Publishing Group. - 2399-3642. ; 1
  • Tidskriftsartikel (refereegranskat)abstract
    • Psychiatric disorders are thought to have a complex genetic pathology consisting of interplay of common and rare variation. Traditionally, pedigrees are used to shed light on the latter only, while here we discuss the application of polygenic risk scores to also highlight patterns of common genetic risk. We analyze polygenic risk scores for psychiatric disorders in a large pedigree (n ~ 260) in which 30% of family members suffer from major depressive disorder or bipolar disorder. Studying patterns of assortative mating and anticipation, it appears increased polygenic risk is contributed by affected individuals who married into the family, resulting in an increasing genetic risk over generations. This may explain the observation of anticipation in mood disorders, whereby onset is earlier and the severity increases over the generations of a family. Joint analyses of rare and common variation may be a powerful way to understand the familial genetics of psychiatric disorders.
7.
  • Genovese, Giulio, et al. (författare)
  • Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence
  • 2014
  • Ingår i: New England Journal of Medicine. - 0028-4793 .- 1533-4406. ; 371:26, s. 2477-2487
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Cancers arise from multiple acquired mutations, which presumably occur over many years. Early stages in cancer development might be present years before cancers become clinically apparent. Methods We analyzed data from whole-exome sequencing of DNA in peripheral-blood cells from 12,380 persons, unselected for cancer or hematologic phenotypes. We identified somatic mutations on the basis of unusual allelic fractions. We used data from Swedish national patient registers to follow health outcomes for 2 to 7 years after DNA sampling. Results Clonal hematopoiesis with somatic mutations was observed in 10% of persons older than 65 years of age but in only 1% of those younger than 50 years of age. Detectable clonal expansions most frequently involved somatic mutations in three genes (DNMT3A, ASXL1, and TET2) that have previously been implicated in hematologic cancers. Clonal hematopoiesis was a strong risk factor for subsequent hematologic cancer (hazard ratio, 12.9; 95% confidence interval, 5.8 to 28.7). Approximately 42% of hematologic cancers in this cohort arose in persons who had clonality at the time of DNA sampling, more than 6 months before a first diagnosis of cancer. Analysis of bone marrow-biopsy specimens obtained from two patients at the time of diagnosis of acute myeloid leukemia revealed that their cancers arose from the earlier clones. Conclusions Clonal hematopoiesis with somatic mutations is readily detected by means of DNA sequencing, is increasingly common as people age, and is associated with increased risks of hematologic cancer and death. A subset of the genes that are mutated in patients with myeloid cancers is frequently mutated in apparently healthy persons; these mutations may represent characteristic early events in the development of hematologic cancers.
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8.
  • Genovese, Giulio, et al. (författare)
  • Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence.
  • 2014
  • Ingår i: The New England journal of medicine. - 1533-4406. ; 371:26, s. 2477-87
  • Tidskriftsartikel (refereegranskat)abstract
    • Cancers arise from multiple acquired mutations, which presumably occur over many years. Early stages in cancer development might be present years before cancers become clinically apparent.
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9.
  • Harrison, Paula A., et al. (författare)
  • Synthesizing plausible futures for biodiversity and ecosystem services in Europe and Central Asia using scenario archetypes
  • 2019
  • Ingår i: Ecology & society. - 1708-3087. ; 24:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Scenarios are a useful tool to explore possible futures of social-ecological systems. The number of scenarios has increased dramatically over recent decades, with a large diversity in temporal and spatial scales, purposes, themes, development methods, and content. Scenario archetypes generically describe future developments and can be useful in meaningfully classifying scenarios, structuring and summarizing the overwhelming amount of information, and enabling scientific outputs to more effectively interface with decision-making frameworks. The Intergovernmental Platform for Biodiversity and Ecosystem Services (IPBES) faced this challenge and used scenario archetypes in its assessment of future interactions between nature and society. We describe the use of scenario archetypes in the IPBES Regional Assessment of Europe and Central Asia. Six scenario archetypes for the region are described in terms of their driver assumptions and impacts on nature (including biodiversity) and its contributions to people (including ecosystem services): business-as-usual, economic optimism, regional competition, regional sustainability, global sustainable development, and inequality. The analysis shows that trade-offs between nature's contributions to people are projected under different scenario archetypes. However, the means of resolving these trade-offs depend on differing political and societal value judgements within each scenario archetype. Scenarios that include proactive decision making on environmental issues, environmental management approaches that support multifunctionality, and mainstreaming environmental issues across sectors, are generally more successful in mitigating tradeoffs than isolated environmental policies. Furthermore, those scenario archetypes that focus on achieving a balanced supply of nature's contributions to people and that incorporate a diversity of values are estimated to achieve more policy goals and targets, such as the UN Sustainable Development Goals and the Convention on Biological Diversity Aichi targets. The scenario archetypes approach is shown to be helpful in supporting science-policy dialogue for proactive decision making that anticipates change, mitigates undesirable trade-offs, and fosters societal transformation in pursuit of sustainable development.
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10.
  • Huckins, Laura M., et al. (författare)
  • Gene expression imputation across multiple brain regions provides insights into schizophrenia risk
  • 2019
  • Ingår i: Nature genetics. - 1546-1718. ; 51:4, s. 659-
  • Tidskriftsartikel (refereegranskat)abstract
    • Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression.
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