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Sökning: WFRF:(George Julia) > Uppsala universitet

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1.
  • Sodergren, Erica, et al. (författare)
  • The genome of the sea urchin Strongylocentrotus purpuratus.
  • 2006
  • Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
  • Tidskriftsartikel (refereegranskat)abstract
    • We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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2.
  • An, Junghwa, et al. (författare)
  • Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009
  • 2010
  • Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 404-408
  • Tidskriftsartikel (refereegranskat)abstract
    • This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.
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3.
  • Barrenäs, Fredrik, et al. (författare)
  • Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy
  • 2021
  • Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 17:7
  • Tidskriftsartikel (refereegranskat)abstract
    • Simian immunodeficiency virus (SIV) challenge of rhesus macaques (RMs) vaccinated with strain 68-1 Rhesus Cytomegalovirus (RhCMV) vectors expressing SIV proteins (RhCMV/SIV) results in a binary outcome: stringent control and subsequent clearance of highly pathogenic SIV in similar to 55% of vaccinated RMs with no protection in the remaining 45%. Although previous work indicates that unconventionally restricted, SIV-specific, effector-memory (EM)-biased CD8(+) T cell responses are necessary for efficacy, the magnitude of these responses does not predict efficacy, and the basis of protection vs. non-protection in 68-1 RhCMV/SIV vector-vaccinated RMs has not been elucidated. Here, we report that 68-1 RhCMV/SIV vector administration strikingly alters the whole blood transcriptome of vaccinated RMs, with the sustained induction of specific immune-related pathways, including immune cell, toll-like receptor (TLR), inflammasome/cell death, and interleukin-15 (IL-15) signaling, significantly correlating with subsequent vaccine efficacy. Treatment of a separate RM cohort with IL-15 confirmed the central involvement of this cytokine in the protection signature, linking the major innate and adaptive immune gene expression networks that correlate with RhCMV/SIV vaccine efficacy. This change-from-baseline IL-15 response signature was also demonstrated to significantly correlate with vaccine efficacy in an independent validation cohort of vaccinated and challenged RMs. The differential IL-15 gene set response to vaccination strongly correlated with the pre-vaccination activity of this pathway, with reduced baseline expression of IL-15 response genes significantly correlating with higher vaccine-induced induction of IL-15 signaling and subsequent vaccine protection, suggesting that a robust de novo vaccine-induced IL-15 signaling response is needed to program vaccine efficacy. Thus, the RhCMV/SIV vaccine imparts a coordinated and persistent induction of innate and adaptive immune pathways featuring IL-15, a known regulator of CD8(+) T cell function, that support the ability of vaccine-elicited unconventionally restricted CD8(+) T cells to mediate protection against SIV challenge.
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4.
  • Carland, Corinne, et al. (författare)
  • Proteomic analysis of 92 circulating proteins and their effects in cardiometabolic diseases
  • 2023
  • Ingår i: Clinical Proteomics. - : BMC. - 1542-6416 .- 1559-0275. ; 20:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Human plasma contains a wide variety of circulating proteins. These proteins can be important clinical biomarkers in disease and also possible drug targets. Large scale genomics studies of circulating proteins can identify genetic variants that lead to relative protein abundance.Methods: We conducted a meta-analysis on genome-wide association studies of autosomal chromosomes in 22,997 individuals of primarily European ancestry across 12 cohorts to identify protein quantitative trait loci (pQTL) for 92 cardiometabolic associated plasma proteins.Results: We identified 503 (337 cis and 166 trans) conditionally independent pQTLs, including several novel variants not reported in the literature. We conducted a sex-stratified analysis and found that 118 (23.5%) of pQTLs demonstrated heterogeneity between sexes. The direction of effect was preserved but there were differences in effect size and significance. Additionally, we annotate trans-pQTLs with nearest genes and report plausible biological relationships. Using Mendelian randomization, we identified causal associations for 18 proteins across 19 phenotypes, of which 10 have additional genetic colocalization evidence. We highlight proteins associated with a constellation of cardiometabolic traits including angiopoietin-related protein 7 (ANGPTL7) and Semaphorin 3F (SEMA3F).Conclusion: Through large-scale analysis of protein quantitative trait loci, we provide a comprehensive overview of common variants associated with plasma proteins. We highlight possible biological relationships which may serve as a basis for further investigation into possible causal roles in cardiometabolic diseases.
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5.
  • Malm, Andreas, et al. (författare)
  • White Skin, Black Fuel : On the Danger of Fossil Fascism
  • 2021
  • Bok (övrigt vetenskapligt/konstnärligt)abstract
    • What does the rise of the far right mean for the battle against climate change?In the first study of the far right’s role in the climate crisis, White Skin, Black Fuel presents an eye-opening sweep of a novel political constellation, revealing its deep historical roots. Fossil-fuelled technologies were born steeped in racism. No one loved them more passionately than the classical fascists. Now right-wing forces have risen to the surface, some professing to have the solution—closing borders to save the nation as the climate breaks down.Epic and riveting, White Skin, Black Fuel traces a future of political fronts that can only heat up.
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6.
  • Millett, Jonathan, et al. (författare)
  • Geographic variation in Sundew (Drosera) leaf colour : plant-plant interactions counteract expected effects of abiotic factors
  • 2018
  • Ingår i: Journal of Biogeography. - : WILEY. - 0305-0270 .- 1365-2699. ; 45:3, s. 582-592
  • Tidskriftsartikel (refereegranskat)abstract
    • Aim: To identify geographic patterns in leaf colour of roundleaved sundew (Drosera rotundifolia) growing on ombrotrophic (rain fed) bogs across Europe and establish the controls over these patterns. Location: North-west Europe. Taxon: Angiosperms, Drosera rotundifolia. Methods: We measured leaf colour of D. rotundifolia plants growing on 24 ombrotrophic bogs across north-west Europe covering 26.4 degrees of longitude and 21.1 degrees of latitude. We measured the height and cover of co-occurring vascular plant vegetation and the amount of incident light intercepted by the vegetation canopy. We determined the role of abiotic variables in controlling the patterns found. In a separate experimental study, we manipulated plant-plant interactions with D. rotundifolia by removing aboveground vascular plant vegetation and monitoring leaf colour over a single summer. Results: Drosera rotundifolia leaf colour varied between bogs. Leaves were redder in northern latitudes and eastern longitudes, and in sites/plots with lower canopy influence, lower nutrient deposition, and a more continental climate. Canopy influence was greater on sites in southern latitudes, eastern longitudes, and with higher nutrient deposition, longer growing seasons and a more maritime climate. Nutrient deposition was higher at more southerly latitudes, eastern sites had a more continental climate, and southern and western sites had warmer and longer growing seasons. In the insitu experiment, leaves became more red when canopy light transmission was increased by removing vegetation, but not when shade net was subsequently added to reduce light transmission. Main Conclusion: Geographic variation in Drosera rotundifolia leaf colour is strongly affected by its light environment, mediated by plant-plant interactions, but leaf colour is also affected by other abiotic factors. The relative importance of biotic and abiotic factors in determining geographic patterns in traits, and also species responses to environmental change, might depend on the growth form and competitive ability of a species.
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7.
  • Moore, Derek G., et al. (författare)
  • Infants perceive human point-light displays as solid forms
  • 2007
  • Ingår i: Cognition. - : Elsevier BV. - 0010-0277 .- 1873-7838. ; 104, s. 377-396
  • Tidskriftsartikel (refereegranskat)abstract
    • While five-month-old infants show orientation-specific sensitivity to changes in the motion and occlusion patterns of human point-light displays, it is not known whether infants are capable of binding a human representation to these displays. Furthermore, it has been suggested that infants do not encode the same physical properties for humans and material objects. To explore these issues we tested whether infants would selectively apply the principle of solidity to upright human displays. In the first experiment infants aged six and nine months were repeatedly shown a human point-light display walking across a computer screen up to 10 times or until habituated. Next, they were repeatedly shown the walking display passing behind an in-depth representation of a table, and finally they were shown the human display appearing to pass through the table top in violation of the solidity of the hidden human form. Both six- and nine-month-old infants showed significantly greater recovery of attention to this final phase. This suggests that infants are able to bind a solid vertical form to human motion. In two further control experiments we presented displays that contained similar patterns of motion but were not perceived by adults as human. Six- and nine-month-old infants did not show recovery of attention when a scrambled display or an inverted human display passed through the table. Thus, the binding of a solid human form to a display in only seems to occur for upright human motion. The paper considers the implications of these findings in relation to theories of infants’ developing conceptions of objects, humans and animals. ?? 2006 Elsevier B.V. All rights reserved.
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8.
  • Ruggeri, Kai, et al. (författare)
  • The globalizability of temporal discounting
  • 2022
  • Ingår i: Nature Human Behaviour. - : Springer Nature. - 2397-3374. ; 6:10, s. 1386-1397
  • Tidskriftsartikel (refereegranskat)abstract
    • Economic inequality is associated with preferences for smaller, immediate gains over larger, delayed ones. Such temporal discounting may feed into rising global inequality, yet it is unclear whether it is a function of choice preferences or norms, or rather the absence of sufficient resources for immediate needs. It is also not clear whether these reflect true differences in choice patterns between income groups. We tested temporal discounting and five intertemporal choice anomalies using local currencies and value standards in 61 countries (N = 13,629). Across a diverse sample, we found consistent, robust rates of choice anomalies. Lower-income groups were not significantly different, but economic inequality and broader financial circumstances were clearly correlated with population choice patterns. Ruggeri et al. find in a study of 61 countries that temporal discounting patterns are globally generalizable. Worse financial environments, greater inequality and high inflation are associated with extreme or inconsistent long-term decisions.
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9.
  • Stahl, Bernd Carsten, et al. (författare)
  • From Responsible Research and Innovation to responsibility by design
  • 2021
  • Ingår i: Journal of Responsible Innovation. - : Taylor & Francis. - 2329-9460 .- 2329-9037. ; 8:2, s. 175-198
  • Tidskriftsartikel (refereegranskat)abstract
    • Drawing on more than eight years working to implement Responsible Research and Innovation (RRI) in the Human Brain Project, a large EU-funded research project that brings together neuroscience, computing, social sciences, and the humanities, and one of the largest investments in RRI in one project, this article offers insights on RRI and explores its possible future. We focus on the question of how RRI can have long-lasting impact and persist beyond the time horizon of funded projects. For this purpose, we suggest the concept of ‘responsibility by design’ which is intended to encapsulate the idea of embedding RRI in research and innovation in a way that makes it part of the fabric of the resulting outcomes, in our case, a distributed European Research Infrastructure.
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10.
  • Stevens, Kristen N, et al. (författare)
  • 19p13.1 is a triple negative-specific breast cancer susceptibility locus
  • 2012
  • Ingår i: Cancer Research. - 0008-5472 .- 1538-7445. ; 72, s. 1795-
  • Tidskriftsartikel (refereegranskat)abstract
    • The 19p13.1 breast cancer susceptibility locus is a modifier of breast cancer risk in BRCA1 mutation carriers and is also associated with risk of ovarian cancer. Here we investigated 19p13.1 variation and risk of breast cancer subtypes, defined by estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor-2 (HER2) status, using 48,869 breast cancer cases and 49,787 controls from the Breast Cancer Association Consortium (BCAC). Variants from 19p13.1 were not associated with breast cancer overall or with ER-positive breast cancer but were significantly associated with ER-negative breast cancer risk [rs8170 Odds Ratio (OR)=1.10, 95% Confidence Interval (CI) 1.05 - 1.15, p=3.49 x 10-5] and triple negative (TN) (ER, PR and HER2 negative) breast cancer [rs8170 OR=1.22, 95% CI 1.13 - 1.31, p=2.22 x 10-7]. However, rs8170 was no longer associated with ER-negative breast cancer risk when TN cases were excluded [OR=0.98, 95% CI 0.89 - 1.07, p=0.62]. In addition, a combined analysis of TN cases from BCAC and the Triple Negative Breast Cancer Consortium (TNBCC) (n=3,566) identified a genome-wide significant association between rs8170 and TN breast cancer risk [OR=1.25, 95% CI 1.18 - 1.33, p=3.31 x 10-13]. Thus, 19p13.1 is the first triple negative-specific breast cancer risk locus and the first locus specific to a histological subtype defined by ER, PR, and HER2 to be identified. These findings provide convincing evidence that genetic susceptibility to breast cancer varies by tumor subtype and that triple negative tumors and other subtypes likely arise through distinct etiologic pathways.
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