| 1. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Bengtsson, Margot, et al.
(författare)
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Gendered subjectivity in Sweden 1959-1993: Psychological discourses of gendered subjectivity in relaton to history, materiality, political appeals and psychological truth-regimes. What about 2007?
- 2007
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Ingår i: Critical Psychology in North America. Special Student Edition (Critical Psychology; 19). - 1471-4167. - 9781905007585 ; 19:19, s. 147-183
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- To demonstrate the psychological importance of social changes in behavioural practice, three interview studies were carried out in Sweden, each in the decade of 1970, 1980 and 1990. All subjects were university students, as were te subjects in a study performed 1959 which served as an "anchor study". The results were analysed using the following three perspectives:(1)Hegemonic social appeals regarding gender and subjectivity, (2)Lived experiences regarding conditions of upbringing as well as personal history, and (3)Local context such as study area, and how this related to the preferred position of parental identification. The women´s movement in the 1970s contested the hegemonic social appeals, which were the cultural social context of the 1959 study, both in relation to the dominant political appeals in society as well as in relation to the dominant psy-complex of the time and place.The psy-complex of the 1970s still positioned young adults according to the same normative psychological truth-regime which was dominant in 1959, i.e. "Become like your parent of the same sex". In the 1970s the women students contested this position call of parental identification and a lot of the women took up the position of identification with their father, while other women refused the parental identification call altogether. In the 1980s study a good deal of the young men took up the position of identification with their mother, while in the 1990s study of both young women and young men there was again a division according to sex, as in 1959; most young women took up the position of identification with their mother and most of the young men took up the position of identification with their father. The students interviewed in the 1990s were born in the 1970s, and their parents were born in the 1940s, both generations being parts of the gender revolution in Swedish society during the period 1960-1990.During most of this period the Swedish government was run by the Social Democratic party, which advocated gender equality. What will the gender effects be of the political changes in September 2006, which brought an alliance of Conservative and Liberal parties to power?
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| 4. |
- Bidleman, Terry, et al.
(författare)
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Chapter 2: Properties, sources, global fate and transport
- 2013
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Ingår i: Canadian Arctic Contaminants Assessment Report III 2013. - Ottawa : Northern Contaminants Program, Aboriginal Affairs and Northern Development Canada. - 9781100546520 ; , s. 19-146
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Bokkapitel (refereegranskat)abstract
- Part II of the second Canadian Arctic Contaminants Assessment Report (CACAR-II) began with a section on “Physicochemical Properties of Persistent Organic Pollutants”, which identified key physicochemical (pchem) properties, provided the rationale for their measurement or prediction and tabulated literature citations for chemicals that are of concern to the NCP (Bidleman et al. 2003). The section also discussed temperature dependence of pchem properties and their applications to describing partitioning in the physical environment.There is, and will continue to be, emphasis on predictive approaches to screening chemicals for persistence, bioaccumulation and toxic (PB&T)properties, as well as long-range atmospheric transport (LRAT) potential (Brown and Wania 2008, Czub et al. 2008, Fenner et al. 2005, Gouin andWania 2007, Howard and Muir 2010, Klasmeier et al. 2006, Matthies et al. 2009, Muir and Howard 2006). This has created the need for determining pchem properties of new and emerging chemicals of concern.Predicting gas exchange cycles of legacy persistent organic pollutants (POPs) and new and emerging chemicals of concern places a high demand on the accuracy of pchem properties, particularly the air/water partition coefficient, KAW. Hexachlorocyclohexanes (HCHs) in Arctic Ocean surface waters are close to air-water equilibrium, with excursions toward net volatilization or deposition that vary with location and season (Hargrave et al. 1993, Jantunen et al. 2008a, Lohmann et al. 2009, Su et al. 2006, Wong et al. 2011) while hexachlorobenzene (HCB) (Lohmann et al. 2009, Su et al. 2006, Wong et al. 2011) and some current use pesticides (CUPs) (Wong et al. 2011) are undergoing net deposition. The predicted Arctic Contamination Potential (ACP) for persistent organic chemicals is strongly influenced by ice cover due to its effect on air-water gas exchange (Meyer and Wania 2007).Many advances have taken place and numerous papers have been published since CACAR-II, which present new measurements and predictions of pchem properties. This section does not attempt to provide a comprehensive review of the field, or to compile pchem properties from the many studies. The approach taken is to highlight the reports which are most relevant to polar science, particularly in areas of improving reliability of pchem properties for POPs, improving experimental techniques and comparing predictive methods. The section ends with a discussion of polyparameter linear free energy relationships (pp-LFERs), which goes beyond partitioning descriptions based on single pchem properties by taking into account specific chemical interactions that can take place in airsurface and water-surface exchange processes. A detailed list of chemical names and nomenclature are provided in the Glossary.
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| 5. |
- Dahn, Hollis A., et al.
(författare)
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Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
- 2022
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Ingår i: GigaScience. - : Oxford University Press. - 2047-217X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types.Results: We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4 degrees C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4 degrees C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield.Conclusion: We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all similar to 70,000 extant vertebrate species.
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| 6. |
- Degiacomi, Giulia, et al.
(författare)
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Micrococcin P1-A bactericidal thiopeptide active against Mycobacterium tuberculosis
- 2016
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Ingår i: Tuberculosis. - : Elsevier BV. - 1472-9792 .- 1873-281X. ; 100, s. 95-101
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Tidskriftsartikel (refereegranskat)abstract
- The lack of proper treatment for serious infectious diseases due to the emergence of multidrug resistance reinforces the need for the discovery of novel antibiotics. This is particularly true for tuberculosis (TB) for which 3.7% of new cases and 20% of previously treated cases are estimated to be caused by multi-drug resistant strains. In addition, in the case of TB, which claimed 1.5 million lives in 2014, the treatment of the least complicated, drug sensitive cases is lengthy and disagreeable. Therefore, new drugs with novel targets are urgently needed to control resistant Mycobacterium tuberculosis strains. In this manuscript we report the characterization of the thiopeptide micrococcin P1 as an anti-tubercular agent. Our biochemical experiments show that this antibiotic inhibits the elongation step of protein synthesis in mycobacteria. We have further identified micrococcin resistant mutations in the ribosomal protein L11 (RplK); the mutations were located in the proline loop at the N-terminus. Reintroduction of the mutations into a clean genetic background, confirmed that they conferred resistance, while introduction of the wild type RplK allele into resistant strains re-established sensitivity. We also identified a mutation in the 23S rRNA gene. These data, in good agreement with previous structural studies suggest that also in M. tuberculosis micrococcin P1 functions by binding to the cleft between the 23S rRNA and the L11 protein loop, thus interfering with the binding of elongation factors Tu and G (EF-Tu and EF-G) and inhibiting protein translocation.
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| 7. |
- Hoshino, Ayuko, et al.
(författare)
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Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers
- 2020
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Ingår i: Cell. - : CELL PRESS. - 0092-8674 .- 1097-4172. ; 182:4, s. 1044-
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Tidskriftsartikel (refereegranskat)abstract
- There is an unmet clinical need for improved tissue and liquid biopsy tools for cancer detection. We investigated the proteomic profile of extracellular vesicles and particles (EVPs) in 426 human samples from tissue explants (TEs), plasma, and other bodily fluids. Among traditional exosome markers, CD9, HSPA8, ALIX, and HSP90AB1 represent pan-EVP markers, while ACTB, MSN, and RAP1B are novel pan-EVP markers. To confirm that EVPs are ideal diagnostic tools, we analyzed proteomes of TE- (n =151) and plasma-derived (n =120) EVPs. Comparison of TE EVPs identified proteins (e.g., VCAN, TNC, and THBS2) that distinguish tumors from normal tissues with 90% sensitivity/94% specificity. Machine-learning classification of plasma-derived EVP cargo, including immunoglobulins, revealed 95% sensitivity/90% specificity in detecting cancer Finally, we defined a panel of tumor-type-specific EVP proteins in TEs and plasma, which can classify tumors of unknown primary origin. Thus, EVP proteins can serve as reliable biomarkers for cancer detection and determining cancer type.
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| 8. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 9. |
- Lindblad-Toh, Kerstin, et al.
(författare)
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Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
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Tidskriftsartikel (refereegranskat)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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| 10. |
- MacKenzie, Alison, et al.
(författare)
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Dissolving the Dichotomies Between Online and Campus-Based Teaching : a Collective Response to The Manifesto for Teaching Online (Bayne et al. 2020)
- 2022
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Ingår i: Postdigital Science and Education. - : Springer. - 2524-4868 .- 2524-485X. ; , s. 271-329
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Tidskriftsartikel (refereegranskat)abstract
- This article is a collective response to the 2020 iteration of The Manifesto for Teaching Online. Originally published in 2011 as 20 simple but provocative statements, the aim was, and continues to be, to critically challenge the normalization of education as techno-corporate enterprise and the failure to properly account for digital methods in teaching in Higher Education. The 2020 Manifesto continues in the same critically provocative fashion, and, as the response collected here demonstrates, its publication could not be timelier. Though the Manifesto was written before the Covid-19 pandemic, many of the responses gathered here inevitably reflect on the experiences of moving to digital, distant, online teaching under unprecedented conditions. As these contributions reveal, the challenges were many and varied, ranging from the positive, breakthrough opportunities that digital learning offered to many students, including the disabled, to the problematic, such as poor digital networks and access, and simple digital poverty. Regardless of the nature of each response, taken together, what they show is that The Manifesto for Teaching Online offers welcome insights into and practical advice on how to teach online, and creatively confront the supremacy of face-to-face teaching.
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