| 11. |
- Grundberg, Elin, et al.
(författare)
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Mapping cis- and trans-regulatory effects across multiple tissues in twins.
- 2012
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 44:10
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Tidskriftsartikel (refereegranskat)abstract
- Sequence-based variation in gene expression is a key driver of disease risk. Common variants regulating expression in cis have been mapped in many expression quantitative trait locus (eQTL) studies, typically in single tissues from unrelated individuals. Here, we present a comprehensive analysis of gene expression across multiple tissues conducted in a large set of mono- and dizygotic twins that allows systematic dissection of genetic (cis and trans) and non-genetic effects on gene expression. Using identity-by-descent estimates, we show that at least 40% of the total heritable cis effect on expression cannot be accounted for by common cis variants, a finding that reveals the contribution of low-frequency and rare regulatory variants with respect to both transcriptional regulation and complex trait susceptibility. We show that a substantial proportion of gene expression heritability is trans to the structural gene, and we identify several replicating trans variants that act predominantly in a tissue-restricted manner and may regulate the transcription of many genes.
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| 12. |
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| 13. |
- Hough, Josh, et al.
(författare)
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Evolutionarily Stable Sex Ratios And Mutation Load
- 2013
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 67:7, s. 1915-1925
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Tidskriftsartikel (refereegranskat)abstract
- Frequency-dependent selection should drive dioecious populations toward a 1:1 sex ratio, but biased sex ratios are widespread, especially among plants with sex chromosomes. Here, we develop population genetic models to investigate the relationships between evolutionarily stable sex ratios, haploid selection, and deleterious mutation load. We confirm that when haploid selection acts only on the relative fitness of X- and Y-bearing pollen and the sex ratio is controlled by the maternal genotype, seed sex ratios evolve toward 1:1. When we also consider haploid selection acting on deleterious mutations, however, we find that biased sex ratios can be stably maintained, reflecting a balance between the advantages of purging deleterious mutations via haploid selection, and the disadvantages of haploid selection on the sex ratio. Our results provide a plausible evolutionary explanation for biased sex ratios in dioecious plants, given the extensive gene expression that occurs across plant genomes at the haploid stage.
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| 14. |
- Keildson, Sarah, et al.
(författare)
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Expression of phosphofructokinase in skeletal muscle is influenced by genetic variation and associated with insulin sensitivity.
- 2014
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Ingår i: Diabetes. - : American Diabetes Association. - 0012-1797 .- 1939-327X. ; 63:3
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Tidskriftsartikel (refereegranskat)abstract
- Using an integrative approach in which genetic variation, gene expression, and clinical phenotypes are assessed in relevant tissues may help functionally characterize the contribution of genetics to disease susceptibility. We sought to identify genetic variation influencing skeletal muscle gene expression (expression quantitative trait loci [eQTLs]) as well as expression associated with measures of insulin sensitivity. We investigated associations of 3,799,401 genetic variants in expression of >7,000 genes from three cohorts (n = 104). We identified 287 genes with cis-acting eQTLs (false discovery rate [FDR] <5%; P < 1.96 × 10(-5)) and 49 expression-insulin sensitivity phenotype associations (i.e., fasting insulin, homeostasis model assessment-insulin resistance, and BMI) (FDR <5%; P = 1.34 × 10(-4)). One of these associations, fasting insulin/phosphofructokinase (PFKM), overlaps with an eQTL. Furthermore, the expression of PFKM, a rate-limiting enzyme in glycolysis, was nominally associated with glucose uptake in skeletal muscle (P = 0.026; n = 42) and overexpressed (Bonferroni-corrected P = 0.03) in skeletal muscle of patients with T2D (n = 102) compared with normoglycemic controls (n = 87). The PFKM eQTL (rs4547172; P = 7.69 × 10(-6)) was nominally associated with glucose uptake, glucose oxidation rate, intramuscular triglyceride content, and metabolic flexibility (P = 0.016-0.048; n = 178). We explored eQTL results using published data from genome-wide association studies (DIAGRAM and MAGIC), and a proxy for the PFKM eQTL (rs11168327; r(2) = 0.75) was nominally associated with T2D (DIAGRAM P = 2.7 × 10(-3)). Taken together, our analysis highlights PFKM as a potential regulator of skeletal muscle insulin sensitivity.
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| 15. |
- Keogan, Katharine, et al.
(författare)
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Global phenological insensitivity to shifting ocean temperatures among seabirds
- 2018
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Ingår i: Nature Climate Change. - : Springer Science and Business Media LLC. - 1758-678X .- 1758-6798. ; 8:4, s. 313-318
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Tidskriftsartikel (refereegranskat)abstract
- Reproductive timing in many taxa plays a key role in determining breeding productivity(1), and is often sensitive to climatic conditions(2). Current climate change may alter the timing of breeding at different rates across trophic levels, potentially resulting in temporal mismatch between the resource requirements of predators and their prey(3). This is of particular concern for higher-trophic-level organisms, whose longer generation times confer a lower rate of evolutionary rescue than primary producers or consumers(4). However, the disconnection between studies of ecological change in marine systems makes it difficult to detect general changes in the timing of reproduction(5). Here, we use a comprehensive meta-analysis of 209 phenological time series from 145 breeding populations to show that, on average, seabird populations worldwide have not adjusted their breeding seasons over time (-0.020 days yr(-1)) or in response to sea surface temperature (SST) (-0.272 days degrees C-1) between 1952 and 2015. However, marked between-year variation in timing observed in resident species and some Pelecaniformes and Suliformes (cormorants, gannets and boobies) may imply that timing, in some cases, is affected by unmeasured environmental conditions. This limited temperature-mediated plasticity of reproductive timing in seabirds potentially makes these top predators highly vulnerable to future mismatch with lower-trophic-level resources(2).
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| 16. |
- Leclere, David, et al.
(författare)
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Bending the curve of terrestrial biodiversity needs an integrated strategy
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 585:7826, s. 551-556
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Tidskriftsartikel (refereegranskat)abstract
- Increased efforts are required to prevent further losses to terrestrial biodiversity and the ecosystem services that it provides(1,2). Ambitious targets have been proposed, such as reversing the declining trends in biodiversity(3); however, just feeding the growing human population will make this a challenge(4). Here we use an ensemble of land-use and biodiversity models to assess whether-and how-humanity can reverse the declines in terrestrial biodiversity caused by habitat conversion, which is a major threat to biodiversity(5). We show that immediate efforts, consistent with the broader sustainability agenda but of unprecedented ambition and coordination, could enable the provision of food for the growing human population while reversing the global terrestrial biodiversity trends caused by habitat conversion. If we decide to increase the extent of land under conservation management, restore degraded land and generalize landscape-level conservation planning, biodiversity trends from habitat conversion could become positive by the mid-twenty-first century on average across models (confidence interval, 2042-2061), but this was not the case for all models. Food prices could increase and, on average across models, almost half (confidence interval, 34-50%) of the future biodiversity losses could not be avoided. However, additionally tackling the drivers of land-use change could avoid conflict with affordable food provision and reduces the environmental effects of the food-provision system. Through further sustainable intensification and trade, reduced food waste and more plant-based human diets, more than two thirds of future biodiversity losses are avoided and the biodiversity trends from habitat conversion are reversed by 2050 for almost all of the models. Although limiting further loss will remain challenging in several biodiversity-rich regions, and other threats-such as climate change-must be addressed to truly reverse the declines in biodiversity, our results show that ambitious conservation efforts and food system transformation are central to an effective post-2020 biodiversity strategy. To promote the recovery of the currently declining global trends in terrestrial biodiversity, increases in both the extent of land under conservation management and the sustainability of the global food system from farm to fork are required.
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| 17. |
- Leebens-Mack, James H., et al.
(författare)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Tidskriftsartikel (refereegranskat)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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| 18. |
- Mills, Katherine, et al.
(författare)
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A randomised controlled trial of integrated psychological therapy for traumatic stress and substance use among adolescents: Trial protocol
- 2020
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Ingår i: BMJ Open. - : BMJ. - 2044-6055. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Post-traumatic stress disorder (PTSD) and substance use disorder frequently co-occur and tend to have their onset during adolescence. Although research has highlighted the importance of treating these disorders in an integrated fashion, there is a dearth of empirically validated integrated treatment options for adolescents with this comorbidity. This paper describes the study protocol for a randomised controlled trial (RCT) examining the efficacy of an integrated trauma-focused cognitive–behavioural treatment for traumatic stress and substance use among adolescents (Concurrent Treatment of PTSD and Substance Use Using Prolonged Exposure - Adolescent (COPE-A)), relative to a supportive counselling control condition (Person-Centred Therapy (PCT)). Methods and analysis: A two-arm, parallel, single-blind RCT with blinded follow-up at 4 and 12 months poststudy entry will be conducted in Sydney, Australia. Participants (n~100 adolescents aged 12–18 years) and their caregivers (caregiver participation is optional) will be allocated to undergo either COPE-A or PCT (allocation ratio 1:1) using minimisation. Both therapies will be delivered individually by project psychologists over a maximum of 16 sessions of 60–90 min duration and will include provision of up to four 30 min optional caregiver sessions. The primary outcome will be between-group differences in change in the severity of PTSD symptoms from baseline to 4-month follow-up, as measured by the Clinician-Administered PTSD Scale for Children and Adolescents for DSM-5. Ethics and dissemination: Ethical approval has been obtained from the human research ethics committees of the Sydney Children’s Hospital Network (HREC/17/SCHN/306) and the University of Sydney (HREC 2018/863). Findings will be published in peer-reviewed journals and presented at scientific conferences. Trial registration number: ACTRN12618000785202; Pre-reults.
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| 19. |
- Mills, Katherine, et al.
(författare)
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Comorbidity: Trauma, substance use and mental health
- 2022
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Ingår i: Drug and Alcohol Review. - : Wiley. - 0959-5236 .- 1465-3362. ; 41, s. 15-15
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Konferensbidrag (refereegranskat)abstract
- Substance use and mental health disorders commonly co-occur and they are frequently underpinned by history of psychological trauma. This symposium presents new data on the clinical presentation and documentation of trauma exposure, trauma-related disorders, and their treatment among adults entering substance use treatment, the implementation of integrated trauma-focused therapy in substance use treatment, and presenting issues among adolescents seeking integrated treatment for substance use and traumatic stress.
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| 20. |
- Mills, Katherine, et al.
(författare)
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Treating trauma and substance use in adolescents
- 2018. - S3
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Ingår i: Drug Alcohol and Review : The official journal of the Australasian Professional Society on Alcohol and other Drugs - The official journal of the Australasian Professional Society on Alcohol and other Drugs. - : Wiley. ; 37, s. 14-14
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Konferensbidrag (refereegranskat)abstract
- Up to 80% of adolescents have experienced trauma and one‐in‐seven suffer from post‐traumatic stress disorder (PTSD), a chronic, debilitating psychiatric disorder. For 50% of these adolescents, the course of their illness is further complicated by a co‐occurring substance use disorder, which often develops from repeated self‐medication of PTSD symptoms. Once established, both disorders serve to maintain and exacerbate the other leading to extensive social, educational, physical and psychological impairments and a chronic course of illness. It is imperative to intervene early in the trajectory in order to prevent the severe and long lasting burden associated with this common comorbidity. In this presentation we provide an overview of the evidence regarding treatment options available for co‐occurring PTSD and substance use, and promising new early interventions for adolescents. A review of the peer‐reviewed literature regarding treatment of PTSD and substance use was undertaken, and best practice approaches for the treatment of adolescents identified. There is growing evidence for the integrated treatment of PTSD and substance use disorders among adults, but the research pertaining to adolescents is in its infancy. Our current trial examining the efficacy of COPE‐A will provide much needed evidence as to how these conditions may best be treated in adolescence before they become chronic disabling conditions.
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