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  • 1.
    Andersson, Niki
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Biology and biodiversity of tardigrades in the world and in Sweden: Current status and future visions2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Tardigrades are small water-dwelling invertebrates that can live almost anywhere in the world. Even though they are well-known our knowledge about them is still scarce. The aim of this study was therefore to explore our current knowledge about tardigrades by: (1) explore their global phylogeny and biogeography based on bioinformatics (2) screen for tardigrades in select locations of northern Sweden and compare with other Swedish locations, and (3) identify at least one tardigrade from northern Sweden and explore the published biomarkers for further identification. The bulk of this thesis was based on evaluation of the Silva database for analyzing SSU (small subunit) and LSU (large subunit) tardigrade sequences and create phylogenetic trees. Some initial lab work was performed using samples of moss and lichen from Piteå, Vindeln and Öland. Results show that only few countries have been explored with regard to tardigrades, and in Sweden more research have been performed in the south compared to the north. The phylogenetic trees give a rough overview of tardigrade relatedness but many of the sequences need to be improved and more sequence work from additional environments is needed. In the lab tardigrades were only found from the Piteå samples, and one of those was identified as Macrobiotus hufelandi, for which a new biomarker was created. Overall, tardigrade research need to continue and expand to other regions in order to understand how these organisms differ between different environments, and more work is needed to ensure higher quality of sequences added to databases.

  • 2.
    Benlloch, Reyes
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Kim, Min Chul
    Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea.
    Sayou, Camille
    Thevenon, Emmanuel
    CEA, iRTSV, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France.
    Parcy, Francois
    CEA, iRTSV, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France.
    Nilsson, Ove
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Integrating long-day flowering signals: a LEAFY binding site is essential for proper photoperiodic activation of APETALA12011In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 67, no 6, p. 1094-1102Article in journal (Refereed)
    Abstract [en]

    The transition to flowering in Arabidopsis is characterized by the sharp and localized upregulation of APETALA1 (AP1) transcription in the newly formed floral primordia. Both the flower meristem-identity gene LEAFY (LFY) and the photoperiod pathway involving the FLOWERING LOCUS T (FT) and FD genes contribute to this upregulation. These pathways have been proposed to act independently but their respective contributions and mode of interaction have remained elusive. To address these questions, we studied the AP1 regulatory region. Combining in vitro and in vivo approaches, we identified which of the three putative LFY binding sites present in the AP1 promoter is essential for its activation by LFY. Interestingly, we found that this site is also important for the correct photoperiodic-dependent upregulation of AP1. In contrast, a previously proposed putative FD-binding site appears dispensable and unable to bind FD and we found no evidence for FD binding to other sites in the AP1 promoter, suggesting that the FT/FD-dependent activation of AP1 might be indirect. Altogether, our data give new insight into the interaction between the FT and LFY pathways in the upregulation of AP1 transcription under long-day conditions.

  • 3.
    Berglund, Åsa
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Responses to reduced industrial metal emissions: An ecotoxicological study on Pied Flycatcher (Ficedula hypoleuca, Aves)2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Metals have been used by humans for thousands of years, and this has resulted in increased concentrations in the biosphere. The environment around point-sources, such as mines and smelters, are of particular concern, as metals may accumulate to high concentrations, and potentially reach levels toxic to the local flora and fauna. This thesis focuses on the effects on pied flycatcher populations of two such point-sources, a lead mine and enrichment plant, and a sulfide ore smelter. Mining activities at the lead mine ceased in 2001 and pied flycatcher populations were assessed before and after the closure. At the sulfide ore smelter, pied flycatchers were studied during the 1980s. Since then, the metal emissions to air from the smelter (e.g. arsenic, cadmium, copper, mercury, lead and zinc) have been greatly reduced (by 93 – 99%).

    Pied flycatchers from these two contaminated environments differed in their responses to reduced atmospheric deposition. At the mine site, nestling responses reflected the reduced atmospheric deposition and less lead accumulated in their tissues. However, lead levels were still high enough to cause negative effects on blood status (δ-aminolevulinic acid dehydratase [ALAD], hemoglobin [Hb], hematocrit [ht], and mean cell hemoglobin concentration) and reproduction (reduced clutch size, increased mortality and reduced breeding success), as was observed when the mine was in operation. Along the pollution gradient away from the smelter, nestling concentrations reflected the metal load in the soil pool, accumulating over time, rather than the atmospheric deposition. This resulted in only a minor response to decreased metal deposition (slightly reduced liver lead concentrations at 3.5 – 90 km from the smelter). This suggests that in environments with highly polluted soils, decreased inputs of atmospheric metal deposition have only minor impacts, and recovery from contamination should not be expected within decades.

    The high metal concentrations in the vicinity of the smelter contributed to poorer blood status (ALAD, Hb and ht), induced oxidative damage and defenses, and decreased reproduction (increased mortality and reduced breeding success). There were only minor improvements in blood and reproductive variables at 3.5 km from the smelter.

  • 4.
    Berglund, Åsa M. M.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Rainio, Miia J.
    Kanerva, Mirella
    Nikinmaa, Mikko
    Eeva, Tapio
    Antioxidant status in relation to age, condition, reproductive performance and pollution in three passerine species2014In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 45, no 3, p. 235-246Article in journal (Refereed)
    Abstract [en]

    Oxidative stress has been suggested as a mediator in life-history trade-off. By spending more resources on for example reproduction an organism might sacrifice its antioxidant defence. So far, most conclusions on trade-offs between life-history traits and oxidative stress have been drawn from laboratory studies using a few model species and there is a need for studies conducted in natural settings. We investigated associations between markers for antioxidant status (antioxidant enzyme activities and antioxidant levels), body condition, age and reproduction in three species of wild-living passerines. The impact from an anthropogenic stressor (metal pollution) was also assessed. The three bird species showed interspecific variation in their SOD and CAT activities, indicating different pathways to eliminate radicals. The age of females affected both antioxidant status and the breeding performance, indicating the importance of age as a factor in life-history studies. Old birds had lower levels of antioxidants/antioxidant enzyme activities and they produced larger broods/more successful broods, though the latter might be confounded by surviving females having increased fitness. Metal exposure had a negative impact on breeding, and improved breeding outcome was also associated with increased antioxidant defence, but metal exposure was not directly related to the oxidative status of birds, emphasizing that additional stressors might independently affect the same traits. Our results highlight that caution has to be taken when generalizing and extrapolating results to even closely related species. The results support the idea that there is a cost of reproduction, in terms of increased resources spent on antioxidant defence, though this should be confirmed with experimental studies.

  • 5.
    Buckland, Philip I.
    Umeå University, Faculty of Arts, Department of historical, philosophical and religious studies, Environmental Archaeology Lab. Umeå University, Faculty of Arts, Humlab.
    SEAD - The Strategic Environmental Archaeology Database Inter-linking Multiproxy Environmental Data with Archaeological Investigations and Ecology2013In: Archaeology in the Digital Era: Papers from the 40th Annual Conference of Computer Applications and Quantitative Methods in Archaeology (CAA), Southampton, 26-29 March 2012 / [ed] Graeme Earl, Tim Sly, Angeliki Chrysanthi, Patricia Murrieta-Flores, Constantinos Papadopoulos, Iza Romanowska & David Wheatley, Amsterdam University Press, 2013, Vol. 1, p. 320-331Conference paper (Refereed)
    Abstract [en]

    The volume of data on past environmental and climate changes, as well as human interactions with these, has long since passed the level where it is manageable outside of large scale database systems. The Strategic Environmental Archaeology Database project aims to not only store and disseminate such data, but also provide tools for querying and analysing them, whilst maintaining a close connection with the archaeological and ecological data that are essential for their comprehensive interpretation. Large scale, geographically and chronologically unrestricted databases provide us with essentially unlimited scope for putting individual sites into a broader context and applying locally collated data to the investigation of earth system level changes. By providing integrated access to data from a variety of proxies, including plant macrofossils, pollen, insects and geochemistry, along with dating evidence, more complex questions can be answered where any single proxy would not be able to provide comprehensive answers.

  • 6.
    Buckland, Philip I.
    et al.
    Umeå University, Faculty of Arts, Department of historical, philosophical and religious studies, Environmental Archaeology Lab.
    Eriksson, Erik J.
    Umeå University, Faculty of Arts, Department of historical, philosophical and religious studies, Environmental Archaeology Lab.
    Palm, Fredrik
    Umeå University, Faculty of Arts, Humlab.
    SEAD - The Strategic Environmental Archaeology Database: Progress Report Spring 20142014Report (Other academic)
    Abstract [en]

    This report provides an overview of the progress and results of the VR:KFI infrastructure projects 2007-7494 and (825-)2010-5976. It should be considered as a status report in an on-going long-term research infrastructure development project.

  • 7.
    Buckland, Philip I.
    et al.
    Umeå University, Faculty of Arts, Department of historical, philosophical and religious studies, Environmental Archaeology Lab.
    Linderholm, Johan
    Umeå University, Faculty of Arts, Department of historical, philosophical and religious studies, Environmental Archaeology Lab.
    Östman, Sofi
    Umeå University, Faculty of Arts, Department of historical, philosophical and religious studies, Environmental Archaeology Lab.
    Samuel, Ericson
    Umeå University, Faculty of Arts, Department of historical, philosophical and religious studies, Environmental Archaeology Lab.
    Wallin, Jan-Erik
    Pollenlaboratoriet i Umeå AB.
    Engelmark, Roger
    Environmental archaeological analysis from the archaeological excavations at Ørland kampflybase, Vik 70/1, Ørland, Sør-Trøndelag, Norway. 2015-20162017Report (Other academic)
    Abstract [en]

    A total of 322 bulk samples, 267 bulk subsamples and 1632 survey samples from the excavation of Iron Age settlements at Ørland, Vik, Sør-Trondelag, were analysed at the Environmental Archaeology Laboratory (MAL) at Umeå University. The overall aim of these analyses was to look for evidence which could help identify possible prehistoric activity areas, understand building functions and divisions, and shed light on land management around the farmsteads.

  • 8.
    Dongre, M.
    et al.
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Nyunt Wai, S.
    The Protease of Vibrio cholerae (PrtV)2013In: Handbook of Proteolytic Enzymes, Elsevier, 2013, Vol. 1, p. 1219-1225Chapter in book (Refereed)
  • 9.
    Dorafshan Esfahani, Eshagh
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University.
    Methyltransferase Ash1, histone methylation and their impact on Polycomb repression2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Antagonistic interactions between Polycomb Group (PcG) and Trithorax Group (TrxG) proteins orchestrate the expression of key developmental genes. Distinct maternally loaded repressors establish the silenced state of these genes in cells where they should not be expressed and later PcG proteins sense whether a target gene is inactive and maintain the repression throughout multiple cell divisions. PcG proteins are targeted to genes by DNA elements called Polycomb Response Elements (PREs). The proteins form two major classes of complexes, namely Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2). Mechanistic details of Polycomb repression are not fully understood, however, tri-methylation of Lysine 27 of histone H3 (H3K27me3) is essential for this process. Using Drosophila cell lines deficient for either PRC1 or PRC2, I investigated the role of H3K27 methylation and the interdependence of PRC1 complexes for their recruitment to PREs. My results indicate that recruitment of PcG complexes to PREs proceed via multiple pathways and that H3K27 methylation is not needed for their targeting. However, the methylation is required to stabilize interactions of PRE-anchored PcG complexes with surrounding chromatin.

    TrxG proteins prevent erroneous repression of Polycomb target genes where these genes need to be expressed. Ash1 is a TrxG protein which binds Polycomb target genes when they are transcriptionally active. It contains a SET domain which methylates Lysine 36 of histone H3 (H3K36). In vitro, histone H3 methylated at K36 is a poor substrate for H3K27 methylation by PRC2. This prompted a model where Ash1 counteracts Polycomb repression through H3K36 methylation. However, this model was never tested in vivo and does not consider several experimental observations. First, in the ash1 mutant flies the bulk H3K36me2/H3K36me3 levels remain unchanged. Second, in Drosophila, there are two other H3K36-specific histone methyltransferases, NSD and Set2, which should be capable to inhibit PRC2. Third, Ash1 contains multiple evolutionary conserved domains whose roles have not been investigated. Therefore, I asked whether H3K36 methylation is critical for Ash1 to counteract Polycomb repression in vivo and whether NSD and Set2 proteins contribute to this process. I used flies lacking endogenous histone genes and complemented them with transgenic histone genes where Lysine 36 is replaced by Arginine. In these animals, I assayed erroneous repression of HOX genes as a readout for erroneous Polycomb repression. I used the same readout in the NSD or Set2 mutant flies. I also asked if other conserved domains of Ash1 are essential for its function. In addition to SET and domain, Ash1 contains three AT hook motifs as well as BAH and PHD domains. I genetically complemented ash1 loss of function animals with transgenic Ash1 variants, in each, one domain of Ash1 is deleted. I found that Ash1 is the only H3K36-specific histone methyltransferase which counteracts Polycomb repression in Drosophila. My findings suggest that the model, where Ash1 counteracts PcG repression by inhibiting PRC2 via methylation of H3K36, has to be revised. I also showed that, in vivo, Ash1 acts as a multimer and requires SET, BAH and PHD domains to counteract Polycomb repression.

    This work led to two main conclusions. First, trimethylation of H3K27 is not essential for targeting PcG proteins to PREs but acts afterwards to stabilize their interaction with the chromatin of the neighboring genes. Second, while SET domain is essential for Ash1 to oppose Polycomb repression, methylation of H3K36 does not play a central role in the process.

    The full text will be freely available from 2019-12-18 00:01
  • 10.
    Eilertsen, H. C.
    et al.
    Universitetet i Tromsø.
    Huseby, Siv
    Universitetet i Tromsø.
    Degerlund, M.
    Universitetet i Tromsø.
    Eriksen, G. K.
    Universitetet i Tromsø.
    Ingebrigtsen, R. A.
    Universitetet i Tromsø.
    Hansen, E.
    Universitetet i Tromsø.
    The effect of freeze/thaw cycles on reproducibility of metabolic profiling of marine microalgal extracts using direct infusion high-resolution mass spectrometry (HR-MS)2014In: Molecules, Vol. 19, no 10, p. 16373-80Article in journal (Refereed)
    Abstract [en]

    During normal sample preparation, storage in freezers and subsequent freeze/thaw cycles are commonly introduced. The effect of freeze/thaw cycles on the metabolic profiling of microalgal extracts using HR-MS was investigated. Methanolic extracts of monocultures of Arctic marine diatoms were analyzed immediately after extraction, after seven days of storage at -78 degrees C (one freeze/thaw cycle), and after additional seven days at -20 degrees C (two freeze/thaw cycles). Repeated direct infusion high-resolution mass spectrometry analysis of microalgae extracts of the same sample showed that reproducibility was ca. 90% when a fresh (unfrozen) sample was analyzed. The overall reproducibility decreased further by ca. 10% after the first freeze/thaw-cycle, and after one more freeze/thaw cycle the reproducibility decreased further by ca. 7%. The decrease in reproducibility after freeze-thaw cycles could be attributed to sample degradation and not to instrument variability.

  • 11. Elvarsson, B. P.
    et al.
    Taylor, L.
    Trenkel, V. M.
    Kupca, Vojtech
    Umeå University, Faculty of Science and Technology, High Performance Computing Center North (HPC2N).
    Stefansson, G.
    A bootstrap method for estimating bias and variance in statistical fisheries modelling frameworks using highly disparate datasets2014In: African Journal of Marine Science, ISSN 1814-232X, E-ISSN 1814-2338, Vol. 36, no 1, p. 99-110Article in journal (Refereed)
    Abstract [en]

    Statistical models of marine ecosystems use a variety of data sources to estimate parameters using composite or weighted likelihood functions with associated weighting issues and questions on how to obtain variance estimates. Regardless of the method used to obtain point estimates, a method is required for variance estimation. A bootstrap technique is introduced for the evaluation of uncertainty in such models, taking into account inherent spatial and temporal correlations in the datasets, which are commonly transferred as assumptions from a likelihood estimation procedure into Hessian-based variance estimation procedures. The technique is demonstrated on a real dataset and the effects of the number of bootstrap samples on estimation bias and variance estimates are studied. Although the modelling framework and bootstrap method can be applied to multispecies and multiarea models, for clarity the case study described is of a single-species and single-area model.

  • 12.
    Ferro, Lorenza
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wastewater treatment and biomass generation by Nordic microalgae: growth in subarctic climate and microbial interactions2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Nordic native microalgal strains were isolated, genetically classified and tested for their ability to grow in municipal wastewater. Eight of the isolated strains could efficiently remove nitrogen and phosphate in less than two weeks. Two of these strains, Coelastrella sp. and Chlorella vulgaris, were found to have high biomass concentration and total lipid content; also two Desmodesmus sp. strains showed desirable traits for biofuel-feedstock, due to their fast growth rates and high oil content.

    The adaptation to subarctic climate was comparatively evaluated in three Nordic strains (C. vulgaris, Scenedesmus sp. and Desmodesmus sp.) and a collection strain (S. obliquus). Their growth performance, biomass composition and nutrients removal was investigated at standard (25°C) or low temperature (5°C), under continuous light at short photoperiod (3 h light, 25°C) or moderate winter conditions (6 h light, 15°C). Only the Nordic strains could grow and produce biomass at low temperature, and efficiently removed nitrogen and phosphate during both cold- and dark-stress. Phenotypic plasticity was observed in Scenedesmus and Desmodesmus under different growth conditions, adaptation to low temperature increased their carbohydrate content. Short photoperiod strongly reduced growth rates, biomass and storage compounds in all strains and induced flocculation in C. vulgaris, which, however, performed best under moderate winter conditions.

    The symbiotic relationships between the Nordic microalga C. vulgaris and the naturally co-occurring bacterium Rhizobium sp. were investigated batchwise under photoautotrophic, heterotrophic and mixotrophic conditions, comparing the co-culture to the axenic cultures. The photoautotrophic algal growth in BG11 medium mainly supported Rhizobium activity in the co-culture, with no significant effects on C. vulgaris. In synthetic wastewater, a synergistic interaction only occurred under mixotrophic conditions, supported by CO2/O2 exchange and a lower pH in the culture, resulting in higher biomass and fatty acids content and more efficient wastewater treatment in the co-culture. Under heterotrophic conditions, the lower biomass production in the co-culture suggested a competition for nutrients, although nutrients removal remained efficient.

    A pilot-scale high rate algal pond (HRAP) located in Northern Sweden was inoculated with the collection strain Scenedesmus dimorphus UTEX 417 and operated from spring to autumn. Using metabarcoding of 18S and 16S rRNA genes, the microbial diversity of eukaryotic and prokaryotic communities was revealed. S. dimorphus was initially stable in the culture, but other microalgal species later colonized the system, mainly due to parasitic infections and predation by zooplankton in summer. The main competitor algal species were Desmodesmus, Pseudocharaciopsis, Chlorella, Characium and Oocystis. Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundant bacterial phyla in the HRAP. The structure of the microbial communities followed a seasonal variation and partially correlated to environmental factors such as light, temperature and nutrients concentrations.

    Overall, these results contribute with new knowledge on the establishment and optimization of microalgal-based wastewater treatment systems coupled with biomass generation in Nordic areas. The use of native microalgal species is proposed as a potential strategy to overcome the limitations posed to algal cultivation in subarctic regions.

  • 13. Förlin, Lars
    et al.
    Asker, Noomi
    Töpel, Mats
    Österlund, Tobias
    Kristiansson, Erik
    Parkkonen, Jari
    Haglund, Peter
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Faxneld, Suzanne
    Sturve, Joachim
    mRNA Expression and Biomarker Responses in Perch at a Biomonitoring Site in the Baltic Sea - Possible Influence of Natural Brominated Chemicals2019In: Frontiers in Marine Science, E-ISSN 2296-7745, Vol. 6, article id 316Article in journal (Refereed)
    Abstract [en]

    Perch (Perca fluviatilis) has been used in biological effect monitoring in a program for integrated coastal fish monitoring at the reference site Kvadofjarden along the Swedish east coast, which is a site characterized by no or minor local anthropogenic influences. Using a set of physiological and biochemical endpoints (i.e., biomarkers), clear time trends for "early warning" signs of impaired health were noted in the perch from this site, possibly as a result of increased baseline pollution. The data sets also showed relatively large variations among years. To identify additional temporal variation in biological parameters, global mRNA expression studies using RNA sequencing was performed. Perch collected in 2010 and 2014 were selected, as they showed variations in several biomarkers, such as the activity of the detoxification enzyme CYP1A (EROD), the plasma levels of vitellogenin, markers for oxidative stress, white blood cells count and gonad sizes. The RNA sequencing study identified approximately 4800 genes with a significantly difference in mRNA expression levels. A gene ontology enrichment analysis showed that these differentially expressed genes were involved in biological processes such as complement activation, iron ion homeostasis and cholesterol biosynthetic process. In addition, differences in immune system parameters and responses to the exposure of toxic substances have now been verified in two different biological levels (mRNA and protein) in perch collected in 2010 and 2014. Markedly higher mRNA expression of the membrane transporter (MATE) and the detoxification enzyme COMT, together with higher concentrations of bioactive naturally produced brominated compounds, such as brominated indoles and carbazoles, seem to indicate that the perch collected in 2014 had been exposed to macro- and microalga blooming to a higher degree than did perch from 2010. These results and the differential mRNA expression between the 2 years in genes related to immune and oxidative stress parameters suggest that attention must be given to algae blooming when elucidating the well-being of the perch at Kvadofjarden and other Baltic coastal sites.

  • 14.
    Gallegos, Åsa
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Design and evaluation of a computer aided calibration program för visual estimation of vegetation cover2005Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
  • 15.
    Guinea Diaz, Manuel
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hernandez-Verdeja, Tamara
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Kremnev, Dmitry
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Crawford, Tim
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Dubreuil, Carole
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Strand, Åsa
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Redox regulation of PEP activity during seedling establishment in Arabidopsis thaliana2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 50Article in journal (Refereed)
    Abstract [en]

    Activation of the plastid-encoded RNA polymerase is tightly controlled and involves a network of phosphorylation and, as yet unidentified, thiol-mediated events. Here, we characterize PLASTID REDOX INSENSITIVE2, a redox-regulated protein required for full PEP-driven transcription. PRIN2 dimers can be reduced into the active monomeric form by thioredoxins through reduction of a disulfide bond. Exposure to light increases the ratio between the monomeric and dimeric forms of PRIN2. Complementation of prin2-2 with different PRIN2 protein variants demonstrates that the monomer is required for light-activated PEP-dependent transcription and that expression of the nuclear-encoded photosynthesis genes is linked to the activity of PEP. Activation of PEP during chloroplast development likely is the source of a retrograde signal that promotes nuclear LHCB expression. Thus, regulation of PRIN2 is the thiol-mediated mechanism required for full PEP activity, with PRIN2 monomerization via reduction by TRXs providing a mechanistic link between photosynthetic electron transport and activation of photosynthetic gene expression.

  • 16.
    Hall, David
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ma, Xiao-Fei
    Program in Evolutionary Functional Genomics, Evolutionary Biology Center, Uppsala University.
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Adaptive evolution of the Populus tremula photoperiod pathway2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 7, p. 1463-1474Article in journal (Refereed)
    Abstract [en]

    Environmental cues entrain the circadian clock, a core component of the photoperiod pathway in plants, to daily and seasonal changes. The circadian clock mediates input signals from light and temperature receptors to downstream target genes through feedback loops. Several studies have shown that a correct timing of the circadian system is a fitness advantage and genes in photoperiod network have been implied to evolve in response to the diversifying selection in heterogeneous environment. In an attempt to quantify the extent of the historical patterns of selection on genes in the photoperiod pathway in the widely distributed tree species European aspen (Populus tremula) we obtained sequences for twenty-five of the genes in the network and these genes were compared to patterns of nucleotide diversity in 77 randomly chosen genes from across the genome of P. tremula. We found a significant reduction in synonymous diversity in photoperiod genes while non-synonymous diversity was in line with data from control genes. A substantial fraction of the genes show signs of selection, with eight genes showing signs of rapid protein evolution. In contrast to our expectations, genes closely associated with the core circadian clock show rapid protein evolution despite their central position in the pathway. Furthermore, selection on non-synonymous mutations is negatively correlated with synonymous diversity across all genes, indicating the action of recurrent selective sweeps.

  • 17. Heikkila, Katriina
    et al.
    Nyberg, Solja T.
    Fransson, Eleonor I.
    Alfredsson, Lars
    De Bacquer, Dirk
    Bjorner, Jakob B.
    Bonenfant, Sebastien
    Borritz, Marianne
    Burr, Hermann
    Clays, Els
    Casini, Annalisa
    Dragano, Nico
    Erbel, Raimund
    Geuskens, Goedele A.
    Goldberg, Marcel
    Hooftman, Wendela E.
    Houtman, Irene L.
    Joensuu, Matti
    Joeckel, Karl-Heinz
    Kittel, France
    Knutsson, Anders
    Koskenvuo, Markku
    Koskinen, Aki
    Kouvonen, Anne
    Leineweber, Constanze
    Lunau, Thorsten
    Madsen, Ida E. H.
    Hanson, Linda L. Magnusson
    Marmot, Michael G.
    Nielsen, Martin L.
    Nordin, Maria
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Occupational and Environmental Medicine. Umeå University, Faculty of Social Sciences, Department of Psychology.
    Pentti, Jaana
    Salo, Paula
    Rugulies, Reiner
    Steptoe, Andrew
    Siegrist, Johannes
    Suominen, Sakari
    Vahtera, Jussi
    Virtanen, Marianna
    Vaananen, Ari
    Westerholm, Peter
    Westerlund, Hugo
    Zins, Marie
    Theorell, Tores
    Hamer, Mark
    Ferrie, Jane E.
    Singh-Manoux, Archana
    Batty, G. David
    Kivimaeki, Mika
    Job Strain and Tobacco Smoking: An Individual-Participant Data Meta-Analysis of 166 130 Adults in 15 European Studies2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 7, p. e35463-Article in journal (Refereed)
    Abstract [en]

    Background: Tobacco smoking is a major contributor to the public health burden and healthcare costs worldwide, but the determinants of smoking behaviours are poorly understood. We conducted a large individual-participant meta-analysis to examine the extent to which work-related stress, operationalised as job strain, is associated with tobacco smoking in working adults. Methodology and Principal Findings: We analysed cross-sectional data from 15 European studies comprising 166 130 participants. Longitudinal data from six studies were used. Job strain and smoking were self-reported. Smoking was harmonised into three categories never, ex- and current. We modelled the cross-sectional associations using logistic regression and the results pooled in random effects meta-analyses. Mixed effects logistic regression was used to examine longitudinal associations. Of the 166 130 participants, 17% reported job strain, 42% were never smokers, 33% ex-smokers and 25% current smokers. In the analyses of the cross-sectional data, current smokers had higher odds of job strain than never-smokers (age, sex and socioeconomic position-adjusted odds ratio: 1.11, 95% confidence interval: 1.03, 1.18). Current smokers with job strain smoked, on average, three cigarettes per week more than current smokers without job strain. In the analyses of longitudinal data (1 to 9 years of follow-up), there was no clear evidence for longitudinal associations between job strain and taking up or quitting smoking. Conclusions: Our findings show that smokers are slightly more likely than non-smokers to report work-related stress. In addition, smokers who reported work stress smoked, on average, slightly more cigarettes than stress-free smokers.

  • 18.
    Hägglund, Anna-Carin
    et al.
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Dahl, Lina
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Carlsson, Leif
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Lhx2 is required for patterning and expansion of a distinct progenitor cell population committed to eye development2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 8, p. e23387-Article in journal (Refereed)
    Abstract [en]

    Progenitor cells committed to eye development become specified in the prospective forebrain and develop subsequently into the optic vesicle and the optic cup. The optic vesicle induces formation of the lens placode in surface ectoderm from which the lens develops. Numerous transcription factors are involved in this process, including the eye-field transcription factors. However, many of these transcription factors also regulate the patterning of the anterior neural plate and their specific role in eye development is difficult to discern since eye-committed progenitor cells are poorly defined. By using a specific part of the Lhx2 promoter to regulate Cre recombinase expression in transgenic mice we have been able to define a distinct progenitor cell population in the forebrain solely committed to eye development. Conditional inactivation of Lhx2 in these progenitor cells causes an arrest in eye development at the stage when the optic vesicle induces lens placode formation in the surface ectoderm. The eye-committed progenitor cell population is present in the Lhx2(-/-) embryonic forebrain suggesting that commitment to eye development is Lhx2-independent. However, re-expression of Lhx2 in Lhx2(-/-) progenitor cells only promotes development of retinal pigment epithelium cells, indicating that Lhx2 promotes the acquisition of the oligopotent fate of these progenitor cells. This approach also allowed us to identify genes that distinguish Lhx2 function in eye development from that in the forebrain. Thus, we have defined a distinct progenitor cell population in the forebrain committed to eye development and identified genes linked to Lhx2’s function in the expansion and patterning of these progenitor cells.

  • 19.
    Ingvarsson, Pär K
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Street, Nathaniel R
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Association genetics of complex traits in plants2011In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 189, no 4, p. 909-922Article in journal (Refereed)
    Abstract [en]

    Association mapping is rapidly becoming the main method for dissecting the genetic architecture of complex traits in plants. Currently most association mapping studies in plants are preformed using sets of genes selected to be putative candidates for the trait of interest, but rapid developments in genomics will allow for genome-wide mapping in virtually any plant species in the near future. As the costs for genotyping are decreasing, the focus has shifted towards phenotyping. In plants, clonal replication and/or inbred lines allows for replicated phenotyping under many different environmental conditions. Reduced sequencing costs will increase the number of studies that use RNA sequencing data to perform expression quantitative trait locus (eQTL) mapping, which will increase our knowledge of how gene expression variation contributes to phenotypic variation. Current population sizes used in association mapping studies are modest in size and need to be greatly increased if mutations explaining less than a few per cent of the phenotypic variation are to be detected. Association mapping has started to yield insights into the genetic architecture of complex traits in plants, and future studies with greater genome coverage will help to elucidate how plants have managed to adapt to a wide variety of environmental conditions.

  • 20. Johansson, Karin S. L.
    et al.
    Luhrig, Katharina
    Klaminder, Jonatan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Rengefors, Karin
    Development of a quantitative PCR method to explore the historical occurrence of a nuisance microalga under expansion2016In: Harmful Algae, ISSN 1568-9883, E-ISSN 1878-1470, Vol. 56, p. 67-76Article in journal (Refereed)
    Abstract [en]

    A number of marine and freshwater harmful algal bloom (HAB) species have colonized new areas and expanded their habitat range in recent years. Nevertheless it is notoriously difficult to establish when colonization first occurred, what the dispersal routes are, and to separate recent invasion from increases in existent but small populations. The freshwater raphidophyte Gonyostomum semen is a nuisance species that has expanded its habitat range and increased in abundance in northern Europe during the past decades. To evaluate to what extent sediments can be used for determining historic occurrence of G. semen, a quantitative real-time PCR method for detecting cysts of this algae was developed. This paper presents a qPCR protocol with a set of primers that are specific to Gonyostomum and with PCR conditions optimized for sediment samples from humic lakes, which are the common habitat of G. semen. With this sensitive method as few as 1.6 cysts per PCR reaction could be reliably quantified, corresponding to 320 cysts per g wet weight sediment Cysts were present in sediments with ages ranging from years to decades and their persistence allows detection of historic populations up to at least 50 years old. With this qPCR assay it will be possible to trace the presence of G. semen in environments prior to the onset of algae-specific monitoring programs as well as for quantification in water column samples.

  • 21.
    Klaminder, Jonatan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Hellström, Gustav
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Fahlman, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Jonsson, Micael
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lagesson, Annelie
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bergman, Eva
    Brodin, Tomas
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Drug-Induced Behavioral Changes: Using Laboratory Observations to Predict Field Observations2016In: Frontiers in Environmental Science, E-ISSN 2296-665X, Vol. 4, article id 81Article in journal (Refereed)
    Abstract [en]

    Behavioral assays constitute important research tools when assessing how fish respond to environmental change. However, it is unclear how behavioral modifications recorded in laboratory assays are expressed in natural ecosystems, a limitation that makes it difficult to evaluate the predictive power of laboratory-based measurements. In this study, we hypothesized that exposure to a benzodiazepine (i.e., oxazepam) increases boldness and activity in laboratory assays as well as in field assays – that is, laboratory results can be used to predict field results. Moreover, we expected the modified behavior to affect other important ecological measures such as habitat selection and home range. To test our hypothesis, we exposed European perch (Perca fluviatilis) to oxazepam and measured subsequent changes in behavioral trials both in laboratory assays and in a lake ecosystem populated with a predatory fish species, pike (Esox lucius). In the lake, the positions of both perch and pike were tracked every three minutes for a month using acoustic telemetry. In the laboratory assay, the oxazepam-exposed perch were bolder and more active than the non-exposed perch. In the lake assay, the oxazepam-exposed perch were also more bold and active, had a larger home range, and used pelagic habitats more than the non-exposed perch. We conclude that ecotoxicological behavioral assays are useful for predicting the effects of exposure in natural systems. However, although individual responses to exposure were similar in both the laboratory and field trials, effects were more obvious in the field study, mainly due to reduced variability in the behavior measures from the lake. Hence, short-term behavioral assays may fail to detect all the effects expressed in natural environments. Nevertheless, our study clearly demonstrates that behavior modifications observed in laboratory settings can be used to predict how fish perform in aquatic ecosystems. 

  • 22.
    Kremnev, Dmitry
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Get in tune: chloroplast and nucleus harmony2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Photosynthetic eukaryots emerged as a result of several billion years of evolution between proeukaryotic cell and ancestral cyanobacteria that formed modern chloroplasts. The symbiotic relationship led to significant rearrangements in the genomes of the plastid and the nucleus: as many as 90 % of all the plastid genes were transferred to the nucleus. The gene transfer has been accompanied by the development of sophisticated regulatory signaling networks originating in the organelle (retrograde) and in the nucleus (anterograde) that coordinate development of the plastid and ensure adequate cell responses to stress signals. In this thesis I have demonstrated that transcriptional activity of PEP in the chloroplast is essential for proper embryo and seedling development in Arabidopsis thaliana. The function of PEP is dependent on the nuclear encoded PEPassociated factor PRIN2 that is able to sense the redox status of the plastid during seedling development and different stress. In response to the plastid status PRIN2 modulates the transcription activity of the PEP enzyme complex. We further established that PRIN2, as an essential component for full PEP activity, is also required to emit the Plastid Gene Expression (PGE) retrograde signal to regulate the Photosynthesis-Associated Nuclear Genes (PhANG) in the nucleus during early seedling growth via GUN1. On the other hand, regulation of PhANG expression during the High Light (HL) conditions requires functional PRIN2 and PEP activity but is GUN1-independent. Another retrograde signal produced by the developing chloroplast is associated with the tetrapyrrole biosynthesis pathway. We have established that accumulation of the chlorophyll intermediate MgProtoIX-ME in the crd mutant triggers repression of the PhANG expression, and this negative signal is mediated by a cytoplasmic protein complex containing the PAPP5 phosphatase. The nuclear targets that receive the tetrapyrrole mediated signal are GLK1 and GLK2 transcription factors that control the PhANG expression and the expression of the enzymes involved in the biosynthesis of chlorophyll.

  • 23.
    Kremnev, Dmitry
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Strand, Åsa
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Plastid encoded RNA polymerase activity and expression of photosynthesis genes required for embryo and seed development in Arabidopsis2014In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462XArticle in journal (Refereed)
    Abstract [en]

    Chloroplast biogenesis and function is essential for proper plant embryo and seed development but the molecular mechanisms underlying the role of plastids during embryogenesis are poorly understood. Expression of plastid encoded genes is dependent on two different transcription machineries; a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. However, the division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear. We show here that PLASTID REDOX INSENSITIVE 2 (PRIN2) and CHLOROPLAST STEM-LOOP BINDING PROTEIN 41 kDa (CSP41b), two proteins identified in plastid nucleoid preparations, are essential for proper plant embryo development. Using Co-IP assays and native PAGE we have shown a direct physical interaction between PRIN2 and CSP41b. Moreover, PRIN2 and CSP41b form a distinct protein complex in vitro that binds DNA. The prin2.2 and csp41b-2 single mutants displayed pale phenotypes, abnormal chloroplasts with reduced transcript levels of photosynthesis genes and defects in embryo development. The respective csp41b-2prin2.2 homo/heterozygote double mutants produced abnormal white colored ovules and shrunken seeds. Thus, the csp41b-2prin2.2 double mutant is embryo lethal. In silico analysis of available array data showed that a large number of genes traditionally classified as PEP dependent genes are transcribed during early embryo development from the pre-globular stage to the mature-green-stage. Taken together, our results suggest that PEP activity and consequently the switch from NEP to PEP activity, is essential during embryo development and that the PRIN2-CSP41b DNA binding protein complex possibly is important for full PEP activity during this process.

  • 24.
    Lundgren, Andreas
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Relation between herbivore abundance, herbivore diversity and vegetation diversity2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 25.
    Nordling, Johanna
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Modigare mörtar: En beteendestudie av oxazepams påverkan på vild mört2018Independent thesis Basic level (degree of Bachelor), 180 HE creditsStudent thesis
  • 26. Olenina, I
    et al.
    Hajdu, S
    Edler, L
    Andersson, A
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wasmund, N
    Busch, S
    Göbel, J
    Gromisz, S
    Huseby, Siv
    Huttunen, M
    Jaanus, A
    Kokkonen, P
    Ledaine, I
    Niemkiewicz, E
    Biovolumes and size-classes of phytoplankton in the Baltic Sea2006In: HELCOM, Balt. Sea Environ. Proc, Vol. 106, p. 1-144Article in journal (Refereed)
  • 27. Pohl, Johannes
    et al.
    Björlenius, Berndt
    Brodin, Tomas
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Carlsson, Gunnar
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Larsson, D. G. Joakim
    Norrgren, Leif
    Örn, Stefan
    Effects of ozonated sewage effluent on reproduction and behavioral endpoints in zebrafish (Danio rerio)2018In: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 200, p. 93-101Article in journal (Refereed)
    Abstract [en]

    Pharmaceutical residues and other micro-contaminants may enter aquatic environments through effluent from sewage treatment plants (STPs) and could cause adverse effects in wild fish. One strategy to alleviate this situation is to improve wastewater treatment by ozonation. To test the effectiveness of full-scale wastewater effluent ozonation at a Swedish municipal STP, the added removal efficiency was measured for 105 pharmaceuticals. In addition, gene expression, reproductive and behavioral endpoints were analyzed in zebrafish (Danio rerio) exposed on-site over 21 days to ozonated or non-ozonated effluents as well as to tap water. Ozone treatment (7 g O-3/m(3)) removed pharmaceuticals by an average efficiency of 77% in addition to the conventional treatment, leaving 11 screened pharmaceuticals above detection limits. Differences in biological responses of the exposure treatments were recorded in gene expression, reproduction and behavior. Hepatic vitellogenin gene expression was higher in male zebrafish exposed to the ozonated effluent compared to the non-ozonated effluent and tap water treatments. The reproductive success was higher in fish exposed to ozonated effluent compared to non-ozonated effluent and to tap water. The behavioral measurements showed that fish exposed to the ozonated STP effluent were less active in swimming the first minute after placed in a novel vessel. Ozonation is a capable method for removing pharmaceuticals in effluents. However, its implementation should be thoroughly evaluated for any potential biological impact. Future research is needed for uncovering the factors which produced the in vivo responses in fish.

  • 28.
    Schuman, Irina
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    The Molecular Diversity and Biogeography of Tardigrades2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Tardigrades can handle extreme conditions such as heat, cold and drought, thanks to a process called cryptobiosis which can be found in a limited amount of taxa on Earth. More knowledge about such animals may help us to understand the potential and limitations of life both on Earth and possibly in space. Such knowledge may also help develop novel, useful applications for the society, such as better storage of sensitive medicine. However, our knowledge about tardigrades is limited. We know little about their distribution and diversity, especially in Sweden, and above all in northern Sweden. The aim of this study was threefold; i) to explore the biogeography of the tardigrades based on molecular data; ii) to screen for tardigrades in Umeå by examining moss samples from different locations; and iii) to explore some of the associates of tardigrades in moss (such as bacteria and micro- and meiofauna).

    The biogeography was explored by collecting all published ribosomal gene sequences (the small subunit 18S rRNA) from the Silva gene database. These sequences were used for plotting the locations from which these gene sequences had been retrieved on a world map and the correlation between gene sequence, country and biotope was examined. The tardigrade groups most sequenced are Macrobiotus, Ramazottius and Echiniscus, and the milieu most studied seems to be different types of soil. Other investigated isolation sources are drinking water, cryconite and church walls. However, much remains to be further explored. For example, the world map showed that the only molecular data on Swedish tardigrades have been retrieved from Öland.

    In the lab, tardigrades were found in some of the moss samples, together with other micro- and meiofauna. Three groups of bacteria (Betaproteobacteria, Gammaproteobacteria and Firmicutes) could be identified in one of the investigated mosses. These results suggest that tardigrades live in a diverse environment with different types of organisms both on the microbial as well as on the micro-meio-fauna level.

  • 29.
    Svensson, Johan
    et al.
    Department of Environmental Toxicology, Uppsala University, Norbyvägen 18A, SE-75 236 Uppsala, Sweden.
    Fick, Jerker
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Brandt, Ingvar
    Department of Environmental Toxicology, Uppsala University, Norbyvägen 18A, SE-75 236 Uppsala, Sweden.
    Brunström, Björn
    Department of Environmental Toxicology, Uppsala University, Norbyvägen 18A, SE-75 236 Uppsala, Sweden.
    The synthetic progestin levonorgestrel is a potent androgen in the three-spined stickleback (Gasterosteus aculeatus)2013In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 47, no 4, p. 2043-2051Article in journal (Refereed)
    Abstract [en]

    The use of progestins has resulted in contamination of aquatic environments and some progestins have in experimental studies been shown to impair reproduction in fish and amphibians at low ng L(-1) concentrations. The mechanisms underlying their reproductive toxicity are largely unknown. Some progestins, such as levonorgestrel (LNG), exert androgenic effects in mammals by activating the androgen receptor (AR). Male three-spined stickleback (Gasterosteus aculeatus) kidneys produce spiggin, a glue-like glycoprotein used in nest building, and its production is directly governed by androgens. Spiggin is normally absent in females but its production in female kidneys can be induced by AR agonists. Spiggin serves as the best known biomarker for androgens in fish. We exposed adult female sticklebacks to LNG at 5.5, 40 and 358 ng L(-1) for 21 days. Androgenic effects were found at LNG concentrations ≥40 ng L(-1) including induction of spiggin transcription, kidney hypertrophy and suppressed liver vitellogenin transcription. These are the first in vivo quantitative data showing that LNG is a potent androgen in fish, supporting the contention that androgenic effects of certain progestins contribute to their reproductive toxicity.

  • 30.
    Taheri, Nayyer
    et al.
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Fahlgren, Anna
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Fällman, Maria
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Yersinia pseudotuberculosis Blocks Neutrophil Degranulation2016In: Infection and Immunity, ISSN 0019-9567, E-ISSN 1098-5522, Vol. 84, no 12, p. 3369-3378Article in journal (Refereed)
    Abstract [en]

    Neutrophils are essential components of immunity and are rapidly recruited to infected or injured tissue. Upon their activation, neutrophils release granules to the cell's exterior, through a process called degranulation. These granules contain proteins with antimicrobial properties that help combat infection. The enteropathogenic bacterium Yersinia pseudotuberculosis successfully persists as an extracellular bacterium during infection by virtue of its translocation of virulence effectors (Yersinia outer proteins [Yops]) that act in the cytosol of host immune cells to subvert phagocytosis and proinflammatory responses. Here, we investigated the effect of Y. pseudotuberculosis on neutrophil degranulation upon cell contact. We found that virulent Y. pseudotuberculosis was able to prevent secondary granule release. The blocking effect was general, as the release of primary and tertiary granules was also reduced. Degranulation of secondary granules was also blocked in primed neutrophils, suggesting that this mechanism could be an important element of immune evasion. Further, wild-type bacteria conferred a transient block on neutrophils that prevented their degranulation upon contact with plasmid-cured, avirulent Y. pseudotuberculosis and Escherichia coli Detailed analyses showed that the block was strictly dependent on the cooperative actions of the two antiphagocytic effectors, YopE and YopH, suggesting that the neutrophil target structures constituting signaling molecules needed to initiate both phagocytosis and general degranulation. Thus, via these virulence effectors, Yersinia can impair several mechanisms of the neutrophil's antimicrobial arsenal, which underscores the power of its virulence effector machinery.

  • 31.
    Thoresson, Joakim
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Effects of a fish farm on downstream macroinvertebrates2018Independent thesis Basic level (degree of Bachelor), 180 HE creditsStudent thesis
    Abstract [en]

    The number of fish farms is increasing worldwide tomeet the global demand for fish used as a food source for humans. The WorldBank predicts that by 2030, 62 percent of all consumed fish globally will beproduced in fish farms. Due to this increasing demand for fish, fish farming isa growing business and the numbers of fish farms are increasing. Today, thereare fish farms situated in more than one hundred municipalities in rural partsof Sweden. Fish farms may besituated in hydropower plant reservoirs, which have been foundto be suitable locations for cage fish farming. However, environmental concernshave been raised regarding excess dissolved nutrients from fish farms thatmight enrich downstream ecosystems. The source of this enrichment is primarilyfish feces and uneaten fish feed, which contain both nitrogen and phosphorus. The overall objective of this study is to evaluate the effects of a largefish farm located in north-central Sweden on the downstream river ecosystem. Todo this, I compared benthic macroinvertebrate diversity, functional feedinggroup representation, community composition, and indices of biotic integritybetween a site downstream of a fish farm and a nearby (control) reach withoutan upstream fish farm. No significant difference between these sites wasobserved for any metric accept for the species richness, but due to the lowreplication results should be interpreted with caution. Further studies areneeded to assess the possible impact of fish farms on the water quality andecological health of rivers.

  • 32.
    Thornell, Lars-Eric
    et al.
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Carlsson, Lena
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Eriksson, Per-Olof
    Umeå University, Faculty of Medicine, Department of Odontology, Clinical Oral Physiology.
    Liu, Jing-Xia
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Österlund, Catharina
    Stål, Per
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Pedrosa-Domellöf, Fatima
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Fibre typing of intrafusal fibres2015In: Journal of Anatomy, ISSN 0021-8782, E-ISSN 1469-7580, Vol. 227, no 2, p. 136-156Article, review/survey (Refereed)
    Abstract [en]

    The first descriptions of muscle spindles with intrafusal fibres containing striated myofibrils and nervous elements were given approximately 150years ago. It took, however, another 100years to establish the presence of two types of intrafusal muscle fibres: nuclear bag and nuclear chain fibres. The present paper highlights primarily the contribution of Robert Banks in fibre typing of intrafusal fibres: the confirmation of the principle of two types of nuclear bag fibres in mammalian spindles and the variation in occurrence of a dense M-band along the fibres. Furthermore, this paper summarizes how studies from the Umea University group (Laboratory of Muscle Biology in the Department of Integrative Medical Biology) on fibre typing and the structure and composition of M-bands have contributed to the current understanding of muscle spindle complexity in adult humans as well as to muscle spindle development and effects of ageing. The variable molecular composition of the intrafusal sarcomeres with respect to myosin heavy chains and M-band proteins gives new perspectives on the role of the intrafusal myofibrils as stretch-activated sensors influencing tension/stiffness and signalling to nuclei.

  • 33.
    Vickers, Kim
    et al.
    Department of Archaeology, University of Sheffield, UK.
    Buckland, Philip I
    Umeå University, Faculty of Arts, Department of historical, philosophical and religious studies, Environmental Archaeology Lab.
    Predicting island beetle faunas by their climate ranges: the tabula rasa/refugia theory in the North Atlantic2015In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 42, no 11, p. 2031-2048Article in journal (Refereed)
    Abstract [en]

    Aim: This paper addresses two opposing theories put forward for the origins of the beetle fauna of the North Atlantic islands. The first is that the biota of the isolated oceanic islands of the Faroes, Iceland and Greenland immigrated across a Palaeogene–Neogene land bridge from Europe, and survived Pleistocene glaciations in ameliorated refugia. The second argues for a tabula rasa in which the biota of the islands was exterminated during glaciations and is Holocene in origin. The crux of these theories lies in the ability of the flora and fauna to survive in a range of environmental extremes. This paper sets out to assess the viability of the refugia hypothesis using the climatic tolerances of one aspect of the biota: the beetle fauna. Location: The paper focuses on Iceland, the Faroe Islands and Greenland. Methods: The known temperature requirements of the recorded beetle faunas of the North Atlantic islands were compared with published proxy climate reconstructions for successive climate periods since the severing of a North Atlantic land bridge. We used the MCR (mutual climatic range) method available in the open access BugsCEP database software. Results: We show that most of the MCR faunas of the North Atlantic islands could not have survived in situ since the Palaeogene–Neogene, and are likely to have been exterminated by the Pleistocene glaciations. Main conclusions: The discrepancy between the climatic tolerances of the North Atlantic beetle fauna and the estimated climatic regimes since the severing of a land bridge strongly support the tabula rasa theory and suggests that the North Atlantic coleopteran fauna is Holocene in origin.

  • 34. Werding, Bernd
    et al.
    Christensen, Bent
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Hiller, Alexandra
    Three way symbiosis between a goby, a shrimp, and a crab2016In: Marine Biodiversity, ISSN 1867-1616, E-ISSN 1867-1624, Vol. 46, no 4, p. 897-900Article in journal (Refereed)
    Abstract [en]

    A unique case of triple symbiosis between a goby, a pistol shrimp, and a porcellanid crab sharing the same burrow close to reef patches in Lembeh Strait, Indonesia, is described from direct observations for the first time. The burrow, typically occupied by shrimps and gobies, is shared with the porcellanid Enosteoides lobatus. In the goby-shrimp association, the fish inhabits the burrow, which is constructed and kept clean by the shrimp, and the fish warns the shrimp of potential dangers approaching their refuge. The porcellanid lives in the burrow and also benefits from living in a habitat where it could not survive without the two sentinel species. Because the limiting resource for the suspension-feeding porcellanid is protected space, this liaison is an adaptation by E. lobatus to a symbiotic life in a habitat that protects it from predation, and is optimal for filter feeding.

  • 35.
    Wieloch, Thomas
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Intramolecular isotope analysis reveals plant ecophysiological signals covering multiple timescales2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Our societies' wellbeing relies on stable and healthy environments. However, our current lifestyles, growth-oriented economic policies and the population explosion are leading to potentially catastrophic degradation of ecosystems and progressive disruption of food chains. Hopefully, more clarity about what the future holds in store will trigger stronger efforts to find, and adopt, problem-focused coping strategies and encourage environmentally friendly lifestyles.

    Forecasting environmental change/destruction is complicated (inter alia) by lack of complete understanding of plant-environment interactions, particularly those involved in slow processes such as plant acclimatisation and adaptation. This stems from deficiencies in tools to analyse such slow processes. The present work aims at developing tools that can provide retrospective ecophysiological information covering timescales from days to millennia.

    Natural archives, such as tree-rings, preserve plant metabolites over long timescales. Analyses of intramolecular isotope abundances in plant metabolites have the potential to provide retrospective information about metabolic processes and underlying environmental controls. Thus, my colleagues and I (hereafter we) analysed intramolecular isotope patterns in tree rings to develop analytical tools that can convey information about clearly-defined plant metabolic processes over multiple timescales. Such tools might help (inter alia) to constrain plants' capacities to sequester excess amounts of anthropogenic CO2; the so-called CO2 fertilisation effect. This, in turn, might shed light on plants' sink strength for the greenhouse gas CO2, and future plant performance and growth under climate change.

    In the first of three studies, reported in appended papers, we analysed intramolecular 13C/12C ratios in tree-ring glucose. In six angiosperm and six gymnosperm species we found pronounced intramolecular 13C/12C differences, exceeding 10‰. These differences are transmitted into major global C pools, such as soil organic matter. Taking intramolecular 13C/12C differences into account might improve isotopic characterisation of soil metabolic processes and soil CO2 effluxes. In addition, we analysed intramolecular 13C/12C ratios in a Pinus nigra tree-ring archive spanning the period 1961 to 1995. These data revealed new ecophysiological 13C/12C signals, which can facilitate climate reconstructions and assessments of plant-environment interactions at higher resolution; thus providing higher quality information. We proposed that 13C/12C signals at glucose C-1 to C-2 derive from carbon injection into the Calvin-Benson cycle via the oxidative pentose phosphate pathway. We concluded that intramolecular 13C/12C measurements provide valuable new information about long-term metabolic dynamics for application in biogeochemistry, plant physiology, plant breeding, and paleoclimatology.

    In the second study, we developed a comprehensive theory on the metabolic and ecophysiological origins of 13C/12C signals at tree-ring glucose C-5 and C-6. According to this theory and theoretical implications of the first study on signals at C-1 to C-3, analysis of such intramolecular signals can provide information about several metabolic processes. At C-3, a well-known signal reflecting CO2 uptake is preserved. The glucose-6-phosphate shunt around the Calvin-Benson cycle affects 13C/12C compositions at C-1 and C-2, while the 13C/12C signals at C-5 and C-6 reflect carbon fluxes into downstream metabolism. This theoretical framework enables further experimental studies to be conducted in a hypothesis-driven manner. In conclusion, the intramolecular approach provides information about carbon allocation in plant leaves. Thus, it gives access to long-term information on key ecophysiological processes, which could not be acquired by previous approaches.

    The abundance of the hydrogen isotope deuterium, δD, is important for linking the water cycle with plant ecophysiology. The main factors affecting δD in plant organic matter are commonly assumed to be the δD in source water and leaf-level evaporative enrichment. Current δD models incorporate biochemical D fractionations as constants. In the third study we showed that biochemical D fractionations respond strongly to low ambient CO2 levels and low light intensity. Thus, models of δD values in plant organic matter should incorporate biochemical fractionations as variables. In addition, we found pronounced leaf-level δD differences between α-cellulose and wax n-alkanes. We explained this by metabolite-specific contributions of distinct hydrogen sources during biosynthesis.

    Overall, this work advances our understanding of isotope distributions and isotope fractionations in plants. It reveals the immense potential of intramolecular isotope analyses for retrospective assessment of plant metabolism and associated environmental controls.

  • 36.
    Wieloch, Thomas
    et al.
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Sharkey, Thomas David
    Werner, Roland Anton
    Schleucher, Jürgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Intramolecular 13C/12C signals reflect carbon allocation in plant leavesManuscript (preprint) (Other academic)
  • 37.
    Wiklund, Krister
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Zhang, Hanqing
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Stangner, Tim
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Singh, Bhupender
    Bullitt, Esther
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    A drag force interpolation model for capsule-shaped cells in fluid flows near a surface2018In: Microbiology, ISSN 1350-0872, E-ISSN 1465-2080, Vol. 164, no 4, p. 483-494Article in journal (Refereed)
    Abstract [en]

    We report an interpolation model to calculate the hydrodynamic force on tethered capsule-shaped cells in micro-fluidic flows near a surface. Our model is based on numerical solutions of the full Navier–Stokes equations for capsule-shaped objects considering their geometry, aspect ratio and orientation with respect to fluid flow. The model reproduced the results from computational fluid dynamic simulations, with an average error of <0.15 % for objects with an aspect ratio up to 5, and the model exactly reproduced the Goldman approximation of spherical objects close to a surface. We estimated the hydrodynamic force imposed on tethered Escherichia coli cells using the interpolation model and approximate models found in the literature, for example, one that assumes that E. coli is ellipsoid shaped. We fitted the 2D-projected area of a capsule and ellipsoid to segmented E. coli cells. We found that even though an ellipsoidal shape is a reasonable approximation of the cell shape, the capsule gives 4.4 % better agreement, a small difference that corresponds to 15 % difference in hydrodynamic force. In addition, we showed that the new interpolation model provides a significantly better agreement compared to estimates from commonly used models and that it can be used as a fast and accurate substitute for complex and computationally heavy fluid dynamic simulations. This is useful when performing bacterial adhesion experiments in parallel-plate flow channels. We include a MATLAB script that can track cells in a video time-series and estimate the hydrodynamic force using our interpolation formula.

  • 38.
    Åkerlund, Elisabet
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Which is the costlier sex?: Sexual dimorphism and resource allocation in a dioecious herb, Silene dioica2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Life-history theory proposes that different activities, such as growth, maintenance and reproduction compete for limited resources and therefore, life-history traits are bound together by physiological trade-offs. In dioecious species, females are assumed to invest a higher amount of resources in reproduction in comparison with males and this higher investment in reproduction is then assumed to have numerous consequences for the expression of other life-history traits. Some recent papers have, however, suggested that although common, this investment pattern may not be the case in all dioecious plant species. One notable exception is Silene latifolia. Therefore, I examined whether the male sex could be investing more in reproduction than females in a closely related Silene species, Silene dioica. This study was carried out on three islands in the Skeppsvik Archipelago, Umeå, where I examined possible differences between the sexes in different life history traits. On each island, 20 patches were laid out in two different successional zones. In each patch, flowering date was recorded and stem diameter, length and width of cauline leaves, flower diameter, and number of open flowers on male and female plants was measured. At the end of the study, flowering stems were collected and thereafter dried so they could be weighed to estimate biomass allocated to male and female vegetative and reproductive structures. The hypothesis that males of S. dioica should have a higher reproductive cost seemed to be confirmed since males started flowering earlier, produced more and larger flowers, produced smaller and fewer leaves and thinner stems. The males also allocated a greater proportion of their total biomass to reproductive parts and as a consequence, had a higher sink to source ratio. This study has shown that there are exceptions to the "rule" of females having a higher cost of reproduction and when doing research on dioecious species, it is important not to assume that only one and the same sex has the higher investment in reproduction in all species. This higher cost may have consequences for survival and reproductive fitness and can select for differences in other ecological traits, such as phenology, growth, chemical composition and morphology, which could in turn affect the competitive ability and the susceptibility to herbivores and pathogens.

  • 39.
    Åström, Maria
    Umeå University, Faculty of Social Sciences, Department of Educational Measurement.
    Nationellt ämnesprov för år 9: läget inför provet våren 20102009In: Biologen, ISSN 0345-1127, Vol. 74, no 3, p. 16-17Article in journal (Other (popular science, discussion, etc.))
1 - 39 of 39
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