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| 2. |
- Ekelund Ugge, Gustaf Magnus Oskar, 1990-
(författare)
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Transcriptional biomarkers of toxicity – powerful tools or random noise? : An applied perspective from studies on bivalves
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Aquatic organisms are constantly at risk of being exposed to potentially harmful chemical compounds of natural or anthropogenic origin. Biological life can for instance respond to chemical stressors by changes in gene expression, and thus, certain gene transcripts can potentially function as biomarkers, i.e. early warnings, of toxicity and chemical stress. A major challenge for biomarker application is the extrapolation of transcriptional data to potential effects at the organism level or above. Importantly, successful biomarker use also requires basal understanding of how to distinguish actual responses from background noise. The aim of this thesis is, based on response magnitude and variation, to evaluate the biomarker potential in a set of putative transcriptional biomarkers of general toxicity and chemical stress.Specifically, I addressed a selection of six transcripts involved in cytoprotection and oxidative stress: catalase (cat), glutathione-S-transferase (gst), heat shock proteins 70 and 90 (hsp70, hsp90), metallothionein (mt) and superoxide dismutase (sod). Moreover, I used metal exposures to serve as a proxy for general chemical stress, and due to their ecological relevance and nature as sedentary filter-feeders, I used bivalves as study organisms.In a series of experiments, I tested transcriptional responses in the freshwater duck mussel, Anodonta anatina, exposed to copper or an industrial wastewater effluent, to address response robustness and sensitivity, and potential controlled (e.g. exposure concentration) and random (e.g. gravidness) sources of variation. In addition, I performed a systematic review and meta-analysis on transcriptional responses in metal exposed bivalves to (1) evaluate what responses to expect from arbitrary metal exposures, (2) assess the influence from metal concentration (expressed as toxic unit), exposure time and analyzed tissue, and (3) address potential impacts from publication bias in the scientific literature.Response magnitudes were generally small in relationship to the observed variation, both for A. anatina and bivalves in general. The expected response to an arbitrary metal exposure would generally be close to zero, based on both experimental observations and on the estimated impact from publication bias. Although many of the transcripts demonstrated concentration-response relationships, large background noise might in practice obscure the small responses even at relatively high exposures. As demonstrated in A. anatina under copper exposure, this can be the case already for single species under high resolution exposures to single pollutants. As demonstrated by the meta-regression, this problem can only be expected to increase further upon extrapolation between different species and exposure scenarios, due to increasing heterogeneity and random variation. Similar patterns can also be expected for time-dependent response variation, although the meta-regression revealed a general trend of slightly increasing response magnitude with increasing exposure times.In A. anatina, gravidness was identified as a source of random variability that can potentially affect the baseline of most assessed biomarkers, particularly when quantified in gills. Response magnitudes and variability in this species were generally similar for selected transcripts as for two biochemical biomarkers included for comparison (AChE, GST), suggesting that the transcripts might not capture early warnings more efficiently than other molecular endpoints that are more toxicologically relevant. Overall, high concentrations and long exposure durations presumably increase the likelihood of a detectable transcriptional response, but not to an extent that justifies universal application as biomarkers of general toxicity and chemical stress. Consequently, without a strictly defined and validated application, this approach on its own appears unlikely to be successful for future environmental risk assessment and monitoring. Ultimately, efficient use of transcriptional biomarkers might require additional implementation of complementary approaches offered by current molecular techniques.
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| 3. |
- Ellis, Vincenzo A., et al.
(författare)
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Explaining prevalence, diversity and host specificity in a community of avian haemosporidian parasites
- 2020
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Ingår i: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 129:9, s. 1314-1329
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Tidskriftsartikel (refereegranskat)abstract
- Many hypotheses attempt to explain parasite–host associations, but rarely are they examined together in a single community. For hosts, key traits are the proportion of infected individuals (prevalence) and the diversity of parasites infecting them. A key parasite trait is host specificity, ranging from specialists infecting one or a few closely related species to generalists infecting many species. We tested 10 hypotheses to explain host-parasite associations; five ‘host-centric’ (e.g. prevalence is related to host abundance) and five ‘parasite-centric’ (e.g. parasite abundance is related to host specificity). We analyzed a community of 67 locally transmitted avian haemosporidian parasite lineages (genera Plasmodium, Haemoproteus or Leucocytozoon), sampled from 2726 birds (64 species) in southern Sweden. Among host-centric hypotheses, Haemoproteus and Leucocytozoon prevalence and Haemoproteus diversity were related to host habitat preferences, whereas there were no relationships with host abundance or body mass. Haemoproteus and Leucocytozoon prevalences were more similar among closely related than among distantly related host species. Haemoproteus prevalence and diversity were lower in host species with few close relatives (‘evolutionarily distinct’ hosts). Among parasite-centric hypotheses, most lineages, even relative generalists, infected closely related host species more often than expected by chance. However, the host species of Haemoproteus and Leucocytozoon lineages overlapped less among lineages than expected by chance. Specialists did not reach higher prevalences than generalists on single host species. However, the abundance of Haemoproteus lineages was related to host specificity with generalists more common than specialists; this was driven by three closely related generalists. Host specificity of parasites was unrelated to the abundance or evolutionarily distinctiveness of their hosts. Parasite communities are likely structured by many factors and cannot be explained by hypotheses focusing solely on hosts or parasites. However, we found consistent effects of host phylogenetic relationships, plausibly a result of evolutionarily conserved host immune systems limiting parasite distributions.
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| 4. |
- Eltschkner, Sandra, et al.
(författare)
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The structure of songbird MHC class I reveals antigen binding that is flexible at the N-terminus and static at the C-terminus
- 2023
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Ingår i: Frontiers in Immunology. - 1664-3224. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Long-distance migratory animals such as birds and bats have evolved to withstand selection imposed by pathogens across the globe, and pathogen richness is known to be particularly high in tropical regions. Immune genes, so-called Major Histocompatibility Complex (MHC) genes, are highly duplicated in songbirds compared to other vertebrates, and this high MHC diversity has been hypothesised to result in a unique adaptive immunity. To understand the rationale behind the evolution of the high MHC genetic diversity in songbirds, we determined the structural properties of an MHC class I protein, Acar3, from a long-distance migratory songbird, the great reed warbler Acrocephalus arundinaceus (in short: Acar). The structure of Acar3 was studied in complex with pathogen-derived antigens and shows an overall antigen presentation similar to human MHC class I. However, the peptides bound to Acar3 display an unusual conformation: Whereas the N-terminal ends of the peptides display enhanced flexibility, the conformation of their C-terminal halves is rather static. This uncommon peptide-binding mode in Acar3 is facilitated by a central Arg residue within the peptide-binding groove that fixes the backbone of the peptide at its central position, and potentially permits successful interactions between MHC class I and innate immune receptors. Our study highlights the importance of investigating the immune system of wild animals, such as birds and bats, to uncover unique immune mechanisms which may neither exist in humans nor in model organisms.
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| 5. |
- Ferraguti, Martina, et al.
(författare)
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Environmental, geographical and time-related impacts on avian malaria infections in native and introduced populations of house sparrows (Passer domesticus), a globally invasive species
- 2023
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Ingår i: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 32:5, s. 809-823
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Tidskriftsartikel (refereegranskat)abstract
- Aim: The increasing spread of vector-borne diseases has resulted in severe health concerns for humans, domestic animals and wildlife, with changes in land use and the introduction of invasive species being among the main possible causes for this increase. We explored several ecological drivers potentially affecting the local prevalence and richness of avian malaria parasite lineages in native and introduced house sparrows (Passer domesticus) populations. Location: Global. Time period: 2002–2019. Major taxa studied: Avian Plasmodium parasites in house sparrows. Methods: We analysed data from 2,220 samples from 69 localities across all continents, except Antarctica. The influence of environment (urbanization index and human density), geography (altitude, latitude, hemisphere) and time (bird breeding season and years since introduction) were analysed using generalized additive mixed models (GAMMs) and random forests. Results: Overall, 670 sparrows (30.2%) were infected with 22 Plasmodium lineages. In native populations, parasite prevalence was positively related to urbanization index, with the highest prevalence values in areas with intermediate urbanization levels. Likewise, in introduced populations, prevalence was positively associated with urbanization index; however, higher infection occurred in areas with either extreme high or low levels of urbanization. In introduced populations, the number of parasite lineages increased with altitude and with the years elapsed since the establishment of sparrows in a new locality. Here, after a decline in the number of parasite lineages in the first 30 years, an increase from 40 years onwards was detected. Main conclusions: Urbanization was related to parasite prevalence in both native and introduced bird populations. In invaded areas, altitude and time since bird introduction were related to the number of Plasmodium lineages found to be infecting sparrows.
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| 6. |
- Garcia-Longoria, Luz, et al.
(författare)
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Reciprocal positive effects on parasitemia between coinfecting haemosporidian parasites in house sparrows
- 2022
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Ingår i: BMC Ecology and Evolution. - : Springer Science and Business Media LLC. - 2730-7182. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Hosts are often simultaneously infected with several parasite species. These co-infections can lead to within-host interactions of parasites, including mutualism and competition, which may affect both virulence and transmission. Birds are frequently co-infected with different haemosporidian parasites, but very little is known about if and how these parasites interact in natural host populations and what consequences there are for the infected hosts. We therefore set out to study Plasmodium and Haemoproteus parasites in house sparrows Passer domesticus with naturally acquired infections using a protocol where the parasitemia (infection intensity) is quantified by qPCR separately for the two parasites. We analysed infection status (presence/absence of the parasite) and parasitemia of parasites in the blood of both adult and juvenile house sparrows repeatedly over the season. Results: Haemoproteus passeris and Plasmodium relictum were the two dominating parasite species, found in 99% of the analyzed Sanger sequences. All birds were infected with both Plasmodium and Haemoproteus parasites during the study period. Seasonality explained infection status for both parasites in the adults: H. passeris was completely absent in the winter while P. relictum was present all year round. Among adults infected with H. passeris there was a positive effect of P. relictum parasitemia on H. passeris parasitemia and likewise among adults infected with P. relictum there was a positive effect of H. passeris parasitemia on P. relictum parasitemia. No such associations on parasitemia were seen in juvenile house sparrows. Conclusions: The reciprocal positive relationships in parasitemia between P. relictum and H. passeris in adult house sparrows suggests either mutualistic interactions between these frequently occurring parasites or that there is variation in immune responses among house sparrow individuals, hence some individuals suppress the parasitemia of both parasites whereas other individuals suppress neither. Our detailed screening of haemosporidian parasites over the season shows that co-infections are very frequent in both juvenile and adult house sparrows, and since co-infections often have stronger negative effects on host fitness than the single infection, it is imperative to use screening systems with the ability to detect multiple parasites in ecological studies of host-parasite interactions.
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| 7. |
- Herbert, Mikaela
(författare)
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Vindlande vägar i bostadsojämlikhetens Sverige : berättelser om marknadspraktiker, flyktingplaceringspolitik och bostadsprekaritet
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Den här doktorsavhandlingen berättar om marknadspraktiker, flyktingplaceringspolitik och bostadsprekaritet i bostadsojämlikhetens Sverige. Huvudpersonerna i berättelserna är människor som sökte asyl och beviljades uppehållstillstånd i Sverige åren runt den så kallade flyktingkrisen 2015 och i fokus är deras boendevägar – deras vindlande vägar – under de första åren i landet. De flesta av forskningsdeltagarna är inkomstfattiga, vilket gör att de har erfarit betydande svårigheter att hitta någonstans att bo – erfarenheter som de delar med ett ökande antal inkomstfattiga hushåll i en tid präglad av bostadsbrist och tilltagande bostadsojämlikhet. Men genom att kategoriseras som asylsökande eller nyanlända omfattas forskningsdeltagarna därtill av särlagstiftning, som genom selektiva åtgärder som både villkorar, underlättar och kringskär deras bostadsmarknadspositioner men också skiljer ut dem från andra hushåll inom ramen för en förment generell bostadspolitisk modell. I syfte att nyansera och fördjupa förståelsen av bostadsojämlikhetens konsekvenser i en svensk kontext studeras i avhandlingen denna partikulära position.Utifrån en etnografisk ansats och med utgångspunkt i intervjuer, samtal, deltagande observationer och policyanalys utforskas hur forskningsdeltagarnas boendevägar formas och hur det går att förstå dessa i relation till å ena sidan de praktiker som forskningsdeltagarna utvecklar på svenska bostadsmarknader och å andra sidan den politiska styrningen av boende och bosättning för kategorierna asylsökande och nyanlända.Avhandlingen visar att boendevägarna kan beskrivas som kaotiska; med återkommande flyttar, in och ut ur olika, ofta trångbodda hushållsformationer och påfallande ofta med osäkra kontraktsförhållanden. Dock framgår att de formas genom beslut som fattas efter noga överväganden, utifrån skiftande behov och med hänsyn till relationer över tid och rum. Vidare framgår att olika marknadspraktiker har betydelse för deras möjligheter att få tillgång till bostad. Framför allt hyr de bostad inom ramen för en marknad för olovlig bostadsuthyrning, där bostäderna förmedlas genom arabiskspråkiga sociala nätverk. I avhandlingen förstås denna marknad i termer av assemblage och visar på hur den samskapas i konstellationer och i interaktioner mellan bland annat bostadssökande, kontraktsinnehavare och informella mäklare; kommunikationsverktyg; hyreskontrakt; lagar och regler samt tilldelningssystem såsom bostadsköer.Utifrån en kritisk ansats analyseras förarbetena till två flyktingplaceringspolitiska lagändringar: ”Bosättningslagen” samt inskränkningen av ”EBO-lagen”. Avhandlingen visar hur kategorierna asylsökande och nyanländas bosättningsmönster problematiseras och hur en ökad styrning av desamma syftar till att inte bara lösa problem direkt kopplade till målgruppernas boende utan också samhällsproblem som segregation, socioekonomiskt ”utsatta områden” och kommunernas kapacitet att erbjuda välfärdstjänster. Analysen visar vidare att skulden för dessa problem förläggs hos individerna (på gruppnivå, som kategori), samtidigt som fokus förflyttas bort från strukturella problem kopplade till byggande och fördelning av bostäder, liksom från kommunernas bostadsförsörjningsansvar för alla dess invånare.En av avhandlingens bärande idéer är att “flyktingkrisen”, genom att sätta press på det svenska bostadspolitiska systemet, fick dess oförmåga att tillgodose inkomstfattiga hushålls behov av bostad att skarpt framträda. Denna oförmåga försätter dessa hushåll i bostadsprekära situationer där de, med utgångspunkt i forskningsdeltagarnas berättelser, i stor utsträckning får förlita sig på informella eller olovliga marknadspraktiker.
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| 8. |
- Löfgren, Helena
(författare)
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Det legitima ägandet : Politiska konstruktioner av allmännyttans privatisering i Stockholms stad 1990–2015
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- During the last decades of the 20th century, a major change in welfare and housing policy was initiated in Sweden. This meant that a significant proportion of public rental housing was privatised through political decisions. This thesis is specifically concerned with how the privatization of public rental housing has been legitimized in the political debate, which is of particular importance given the symbolic value that public rental housing has had for the Swedish welfare policy. The privatisation of public housing has been particularly evident in Stockholm, which has therefore been the main focus of the thesis. The study has an in-depth empirical focus on the budget debate in the Stockholm City Council between the years 1990 and 2015. The material analysed in the thesis consists of the City Council's annual budget debate during the period 1990-2015, as well as other parts of the City Council debate. Additional material consists of campaign material, material from the public housing companies and bills and Swedish Government Official Reports (SOU) . The overall aim of the thesis is to contribute to knowledge about how the privatisation of public rental housing has been legitimised and to critically examine what this means for the way in which responsible politicians have portrayed housing and specifically its ownership. This is done by answering the following research questions: How has the privatization of public rental housing been legitimized in the city of Stockholm between 1990 and 2015? And: How have the applied legitimation strategies influenced the discursive framework of the new housing policy? Using Critical Discourse Theory, the empirical material is analysed with reference to a model of legitimation based on Theo van Leeuwen (2008). Based on van Leeuwen's model of legitimation analysis, the analysis of the policy debate reveals a predominance of moral and rational strategies to legitimize policy decisions. The usage has however varied according to the type of privatisation and when in time the legitimations took place. One of the conclusions of the thesis is how changes have been legitimised with reference to social aspects such as integration and improved conditions for inhabitants of disadvantaged areas, groups that have not primarily benefited from the privatisation practices that have taken place. The gap that emerges between those who have benefited from the policy and those who have not shows that this is a policy that has needed to be justified and thus required a legitimizing discourse. The thesis contributes to research focusing on how privatisations are shaped and understood through discursive orders and constructions.
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| 9. |
- Mellinger, Samantha, et al.
(författare)
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Improved haplotype resolution of highly duplicated MHC genes in a long-read genome assembly using MiSeq amplicons
- 2023
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Ingår i: PeerJ. - : PeerJ Inc. - 2167-8359. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Long-read sequencing offers a great improvement in the assembly of complex genomic regions, such as the major histocompatibility complex (MHC) region, which can contain both tandemly duplicated MHC genes (paralogs) and high repeat content. The MHC genes have expanded in passerine birds, resulting in numerous MHC paralogs, with relatively high sequence similarity, making the assembly of the MHC region challenging even with long-read sequencing. In addition, MHC genes show rather high sequence divergence between alleles, making diploid-aware assemblers incorrectly classify haplotypes from the same locus as sequences originating from different genomic regions. Consequently, the number of MHC paralogs can easily be over-or underestimated in long-read assemblies. We therefore set out to verify the MHC diversity in an original and a haplotype-purged long-read assembly of one great reed warbler Acrocephalus arundinaceus individual (the focal individual) by using Illumina MiSeq amplicon sequencing. Single exons, representing MHC class I (MHC-I) and class IIB (MHC-IIB) alleles, were sequenced in the focal individual and mapped to the annotated MHC alleles in the original long-read genome assembly. Eighty-four percent of the annotated MHC-I alleles in the original long-read genome assembly were detected using 55% of the amplicon alleles and likewise, 78% of the annotated MHC-IIB alleles were detected using 61% of the amplicon alleles, indicating an incomplete annotation of MHC genes. In the haploid genome assembly, each MHC-IIB gene should be represented by one allele. The parental origin of the MHC-IIB amplicon alleles in the focal individual was determined by sequencing MHC-IIB in its parents. Two of five larger scaffolds, containing 6-19 MHC-IIB paralogs, had a maternal and paternal origin, respectively, as well as a high nucleotide similarity, which suggests that these scaffolds had been incorrectly assigned as belonging to different loci in the genome rather than as alternate haplotypes of the same locus. Therefore, the number of MHC-IIB paralogs was overestimated in the haploid genome assembly. Based on our findings we propose amplicon sequencing as a suitable complement to long-read sequencing for independent validation of the number of paralogs in general and for haplotype inference in multigene families in particular.
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| 10. |
- Neto, Júlio Manuel, et al.
(författare)
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Seasonal dynamics of haemosporidian (Apicomplexa, Haemosporida) parasites in house sparrows Passer domesticus at four European sites : comparison between lineages and the importance of screening methods
- 2020
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Ingår i: International Journal for Parasitology. - : Elsevier BV. - 0020-7519. ; 50:6-7, s. 523-532
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Tidskriftsartikel (refereegranskat)abstract
- Infectious diseases often vary seasonally in a predictable manner, and seasonality may be responsible for geographical differences in prevalence. In temperate regions, vector-borne parasites such as malaria are expected to evolve lower virulence and a time-varying strategy to invest more in transmission when vectors are available. A previous model of seasonal variation of avian malaria described a double peak in prevalence of Plasmodium parasites in multiple hosts resulting from spring relapses and transmission to susceptible individuals in summer. However, this model was rejected by a study describing different patterns of seasonal variation of two Plasmodium spp. at the same site, with the double peak only apparent when these species were combined. Here, we assessed the seasonal variation in prevalence of haemosporidian parasites (Plasmodium, Haemoproteus and Leucocytozoon) in house sparrows (Passer domesticus) sampled across 1 year at four temperate European sites spanning a latitudinal range of 17°. We showed that parasite prevalence and diversity decreased with increasing latitude, but the parasite communities differed between sites, with only one Plasmodium lineage (P_SGS1) occurring at all sites. Moreover, the nested PCR method commonly used to detect and identify haemosporidian parasites strongly underestimated co-infections of Haemoproteus and Plasmodium, significantly biasing the pattern of seasonal variation, so additional molecular methods were used. Finally, we showed that: (i) seasonal variation in prevalence of haemosporidian parasites varied between study sites and parasite lineages/species/genera, describing further cases where the double peak model is not met; (ii) the seasonal dynamics of single lineages (P_SGS1) varied between sites; and (iii) unexpectedly, seasonality was greatest at the southernmost site, a pattern that was mostly driven by lineage H_PADOM05. Limitations of the genotyping methods and consequences of pooling (parasite lineages, sites and years) in studies of haemosporidian parasites are discussed and recommendations proposed, since these actions may obscure the patterns of prevalence and limit ecological inferences.
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