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  • 51.
    Augstein, Frauke
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany.
    Carlsbecker, Annelie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany.
    Getting to the Roots: A Developmental Genetic View of Root Anatomy and Function From Arabidopsis to Lycophytes2018In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, article id 1410Article, review/survey (Refereed)
    Abstract [en]

    Roots attach plants to the ground and ensure efficient and selective uptake of water and nutrients. These functions are facilitated by the morphological and anatomical structures of the root, formed by the activity of the root apical meristem (RAM) and consecutive patterning and differentiation of specific tissues with distinct functions. Despite the importance of this plant organ, its evolutionary history is not clear, but fossils suggest that roots evolved at least twice, in the lycophyte (clubmosses and their allies) and in the euphyllophyte (ferns and seed plants) lineages. Both lycophyte and euphyllophyte roots grow indeterminately by the action of an apical meristem, which is protected by a root cap. They produce root hairs, and in most species the vascular stele is guarded by a specialized endodermal cell layer. Hence, most of these traits must have evolved independently in these lineages. This raises the question if the development of these apparently analogous tissues is regulated by distinct or homologous genes, independently recruited from a common ancestor of lycophytes and euphyllophytes. Currently, there are few studies of the genetic and molecular regulation of lycophyte and fern roots. Therefore, in this review, we focus on key regulatory networks that operate in root development in the model angiosperm Arabidopsis. We describe current knowledge of the mechanisms governing RAM maintenance as well as patterning and differentiation of tissues, such as the endodermis and the vasculature, and compare with other species. We discuss the importance of comparative analyses of anatomy and morphology of extant and extinct species, along with analyses of gene regulatory networks and, ultimately, gene function in plants holding key phylogenetic positions to test hypotheses of root evolution.

  • 52.
    Ausmees, Kristiina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Sanchez-Quinto, Federico
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    An empirical evaluation of genotype imputation of ancient DNA2019Report (Other academic)
  • 53.
    Aydin, Ebru
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Kloos, Dick-Paul
    Gay, Emmanuel
    Jonker, Willem
    Hu, Lijuan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Bullwinkel, Joern
    Brown, Jeremy P.
    Manukyan, Maria
    Giera, Martin
    Singh, Prim B.
    Fundele, Reinald
    A hypomorphic Cbx3 allele causes prenatal growth restriction and perinatal energy homeostasis defects2015In: Journal of Biosciences, ISSN 0250-5991, E-ISSN 0973-7138, Vol. 40, no 2, p. 325-338Article in journal (Refereed)
    Abstract [en]

    Mammals have three HP1 protein isotypes HP1 beta (CBX1), HPl gamma (CBX3) and HP1 alpha (CBX5) that are encoded by the corresponding genes Cbx1, Cbx3 and Cbx5. Recent work has shown that reduction of CBX3 protein in homozygotes for a hypomorphic allele (Cbx3(hypo)) causes a severe postnatal mortality with around 99% of the homozygotes dying before weaning. It is not known what the causes of the postnatal mortality are. Here we show that Cbx3(hypo/hypo) conceptuses are significantly reduced in size and the placentas exhibit a haplo-insufficiency. Late gestation Cbx3(hypo/hypo) placentas have reduced mRNA transcripts for genes involved in growth regulation, amino acid and glucose transport. Blood vessels within the Cbx3(hypo/hypo) placental labyrinth are narrower than wild-type. Newborn Cbx3(hypo/hypo) pups are hypoglycemic, the livers are depleted of glycogen reserves and there is almost complete loss of stored lipid in brown adipose tissue (BAT). There is a 10-fold reduction in expression of the BAT-specific Ucp1 gene, whose product is responsible for non-shivering themogenesis. We suggest that it is the small size of the ChX3(hypo/hypo) neonates, a likely consequence of placental growth and transport defects, combined with a possible inability to thermoregulate that causes the severe postnatal mortality.

  • 54.
    Backström, Tobias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Comparative Physiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Pettersson, Andreas
    Johansson, Viktoria
    Winberg, Svante
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    CRF and urotensin I effects on aggression and anxiety-like behavior in rainbow trout2011In: Journal of Experimental Biology, ISSN 0022-0949, E-ISSN 1477-9145, Vol. 214, no 6, p. 907-914Article in journal (Refereed)
    Abstract [en]

    Corticotropin-releasing factor (CRF) is central in the stress response but also modulates several behaviors including anxiety-related behaviors and aggression. In this study, juvenile rainbow trout (Oncorhynchus mykiss) were tested for competitive ability, determined during dyadic fights for dominance, after intracerebroventricular (i.c.v.) administration of CRF, urotensin I (UI), the non-specific CRF antagonist alpha-helical RF9-41 (ahCRF) or the CRF receptor subtype 1-specific antagonist antalarmin, when paired with a mass-matched con-specific injected with saline. In addition, isolated fish received the same substances. Plasma cortisol and brain monoamines were monitored in all fish. Most fish receiving CRF showed a conspicuous behavior consisting of flaring the opercula, opening the mouth and violent shaking of the head from side to side. When this occurred, the fish immediately forfeited the fight. Similar behavior was observed in most fish receiving UI but no effect on outcome of dyadic fights was noted. This behavior seems similar to non-ambulatory motor activity seen in rats and could be anxiety related. Furthermore, fish receiving CRF at a dose of 1000. ng became subordinate, whereas all other treatments had no effects on the outcome of dyadic fights. In addition, isolated fish receiving ahCRF had lower brain stem concentrations of 5-hydroxyindoleacetic acid, serotonin, 3,4-dihydroxyphenylacetic acid and dopamine. In conclusion, CRF seems to attenuate competitive ability, and both CRF and UI seem to induce anxiety-like behavior.

  • 55.
    Backström, Tobias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Comparative Physiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Schjolden, Joachim
    Overli, Oyvind
    Thörnqvist, Per-Ove
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Winberg, Svante
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Stress effects on AVT and CRF systems in two strains of rainbow trout (Oncorhynchus mykiss) divergent in stress responsiveness2011In: Hormones and Behavior, ISSN 0018-506X, E-ISSN 1095-6867, Vol. 59, no 1, p. 180-186Article in journal (Refereed)
    Abstract [en]

    The aim for this study was to examine whether the F4 generation of two strains of rainbow trout divergent in their plasma cortisol response to confinement stress (HR: high responder or LR: low responder) would also differ in stress-induced effects on forebrain concentrations of mRNA for corticotropin-releasing factor (CRF). arginine vasotocin (AVT). CRF receptor type 1 (CRF-R1). CRF receptor type 2 (CRF-R2) and AVT receptor (AVT-R). In addition, plasma cortisol concentrations, brainstem levels of monoamines and monoamine metabolites, and behaviour during confinement were monitored. The results confirm that HR and LR trout differ in their cortisol response to confinement and show that fish of these strains also differ in their behavioural response to confinement. The HR trout displayed significantly higher locomotor activity while in confinement than LR trout. Moreover, following 180 min of confinement HR fish showed significantly higher forebrain concentrations of CRF mRNA than LR fish. Also, when subjected to 30 min of confinement HR fish showed significantly lower CRF-R2 mRNA concentrations than LR fish, whereas there were no differences in CRF-R1. AVT or AVT-R mRNA expression between LR and HR fish either at 30 or 180 min of confinement. Differences in the expression of CRF and CRF-R2 mRNA may be related to the divergence in stress coping displayed by these rainbow trout strains.

  • 56.
    Badou, Sylvestre A.
    et al.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Soil Plant Fungi Interact, Lab Ecol Bot & Plant Biol, 03 BOX 125, Parakou, Benin.
    De Kesel, Andre
    Meise Bot Garden, Nieuwelaan 38, B-1860 Meise, Belgium.
    Raspe, Olivier
    Meise Bot Garden, Nieuwelaan 38, B-1860 Meise, Belgium;Federat Wallonie Bruxelles, Rue A Lavallee 1, B-1080 Brussels, Belgium.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Guelly, Atsu K.
    Univ Lome, Fac Sci, Dept Bot & Ecol Vegetale, BP1515, Lome, Togo.
    Yorou, Nourou S.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Soil Plant Fungi Interact, Lab Ecol Bot & Plant Biol, 03 BOX 125, Parakou, Benin.
    Two new African siblings of Pulveroboletus ravenelii (Boletaceae)2018In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 43, p. 115-130Article in journal (Refereed)
    Abstract [en]

    This paper sorts out the taxonomy of species affiliated with Pulveroboletus ravenelii in the Guineo-soudanian and Zambezian woodlands of Africa. Morphological and genetic characters of African Pulveroboletus collections were studied and compared to those of North American and Asian species. A phylogenetic analysis showed that the African specimens form a subclade, sister to the Asian and American taxa. Although clamp connections have previously never been reported from Pulveroboletus, all specimens of the African subclade show very small clamp connections. Two new African species, Pulveroboletus africanus sp. nov. and P. sokponianus sp. nov., are described and illustrated. Comments concerning morphology and identification, as well as distribution and ecology, are given for both species.

  • 57.
    Baeten, Lander
    et al.
    Univ Ghent, Dept Environm, Gontrode, Belgium.
    Bruelheide, Helge
    Martin Luther Univ Halle Wittenberg, Inst Biol, Geobot & Bot Garden, Halle, Germany;German Ctr Integrat Biodivers Res iDiv, Leipzig, Germany.
    van der Plas, Fons
    Univ Leipzig, Dept Systemat Bot & Funct Biodivers, Leipzig, Germany;Senckenberg Gesell Naturforsch, Biodivers & Climate Res Ctr, Frankfurt, Germany.
    Kambach, Stephan
    Martin Luther Univ Halle Wittenberg, Inst Biol, Geobot & Bot Garden, Halle, Germany;German Ctr Integrat Biodivers Res iDiv, Leipzig, Germany.
    Ratcliffe, Sophia
    Univ Leipzig, Dept Systemat Bot & Funct Biodivers, Leipzig, Germany;Natl Biodivers Network Trust, Nottingham, England.
    Jucker, Tommaso
    Univ Cambridge, Dept Plant Sci, Forest Ecol & Conservat, Cambridge, England;CSIRO Land & Water, Floreat, WA, Australia.
    Allan, Eric
    Univ Bern, Inst Plant Sci, Bern, Switzerland.
    Ampoorter, Evy
    Univ Ghent, Dept Environm, Gontrode, Belgium.
    Barbaro, Luc
    Univ Toulouse, INRA INPT, Dynafor, Auzeville, France.
    Bastias, Cristina C.
    CSIC, MNCN, Madrid, Spain.
    Bauhus, Juergen
    Univ Freiburg, Fac Environm & Nat Resources, Chair Silviculture, Freiburg, Germany.
    Benavides, Raquel
    CSIC, MNCN, Madrid, Spain.
    Bonal, Damien
    Univ Lorraine, INRA, UMR Silva, AgroParisTech, Nancy, France.
    Bouriaud, Olivier
    Stefan Cel Mare Univ Suceava, Fac Forestry, Suceava, Romania.
    Bussotti, Filippo
    Univ Firenze, Dept Agrifood & Environm Sci DISPAA, Lab Environm & Appl Bot, Florence, Italy.
    Carnol, Monique
    Univ Liege, InBioS Plant & Microbial Ecol, Liege, Belgium.
    Castagneyrol, Bastien
    INRA, UMR 1202 BIOGECO, Cestas, France;Univ Bordeaux, BIOGECO, UMR 1202, Pessac, France.
    Charbonnier, Yohan
    LPO, Le Bourg, Bourrou, France.
    Checko, Ewa
    Univ Warmia & Mazury, Dept Forestry & Forest Ecol, Olsztyn, Poland.
    Coomes, David A.
    Univ Cambridge, Dept Plant Sci, Forest Ecol & Conservat, Cambridge, England.
    Dahlgren, Jonas
    Swedish Univ Agr Sci, Dept Forest Resource Management, Umea, Sweden.
    Dawud, Seid Muhie
    Wollo Univ, Coll Agr, Dept Forestry, Dessie, Ethiopia.
    De Wandeler, Hans
    Univ Leuven, Dept Earth & Environm Sci, Leuven, Belgium.
    Domisch, Timo
    Nat Resources Inst Finland Luke, Joensuu, Finland.
    Finer, Leena
    Nat Resources Inst Finland Luke, Joensuu, Finland.
    Fischer, Markus
    Univ Bern, Inst Plant Sci, Bern, Switzerland.
    Fotelli, Mariangela
    Greek Agr Org Dimitra, Forest Res Inst Thessaloniki, Thessaloniki, Greece.
    Gessler, Arthur
    Swiss Fed Res Inst WSL, Res Unit Forest Dynam, Birmensdorf, Switzerland.
    Grossiord, Charlotte
    Los Alamos Natl Lab, Earth & Environm Sci Div, Los Alamos, NM USA.
    Guyot, Virginie
    INRA, UMR 1202 BIOGECO, Cestas, France;Univ Bordeaux, BIOGECO, UMR 1202, Pessac, France.
    Hattenschwiler, Stephan
    Univ Montpellier, Univ Paul Valery Montpellier, EPHE, CNRS,Ctr Evolutionary & Funct Ecol, Montpellier, France.
    Jactel, Herve
    INRA, UMR 1202 BIOGECO, Cestas, France;Univ Bordeaux, BIOGECO, UMR 1202, Pessac, France.
    Jaroszewicz, Bogdan
    Univ Warsaw, Bialowieza Geobotan Stn, Fac Biol, Bialowieza, Poland.
    Joly, Francois-Xavier
    Univ Montpellier, Univ Paul Valery Montpellier, EPHE, CNRS,Ctr Evolutionary & Funct Ecol, Montpellier, France.
    Koricheva, Julia
    Royal Holloway Univ London, Sch Biol Sci, Egham, Surrey, England.
    Lehtonen, Aleksi
    Nat Resources Inst Finland Luke, Helsinki, Finland.
    Mueller, Sandra
    Univ Freiburg, Dept Geobot, Fac Biol, Freiburg, Germany.
    Muys, Bart
    Nguyen, Diem
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Pollastrini, Martina
    Univ Firenze, Dept Agrifood & Environm Sci DISPAA, Lab Environm & Appl Bot, Florence, Italy.
    Radoglou, Kalliopi
    Democritus Univ Thrace DUTH, Dept Forestry & Management Environm & Nat, Nea Orestiada, Greece.
    Raulund-Rasmussen, Karsten
    Univ Copenhagen, Dept Geosci & Nat Resource Managemen, Frederiksberg C, Denmark.
    Ruiz-Benito, Paloma
    Univ Alcala De Henares, Dept Ciencias Vida, Grp Ecol & Restaurac Forestal, Madrid, Spain.
    Selvi, Federico
    Univ Firenze, Dept Agrifood & Environm Sci DISPAA, Lab Environm & Appl Bot, Florence, Italy.
    Stenlid, Jan
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden.
    Valladares, Fernando
    CSIC, MNCN, Madrid, Spain.
    Vesterdal, Lars
    Univ Copenhagen, Dept Geosci & Nat Resource Managemen, Frederiksberg C, Denmark.
    Verheyen, Kris
    Univ Ghent, Dept Environm, Gontrode, Belgium.
    Wirth, Christian
    Max Planck Inst Biogeochem, Jena, Germany.
    Zavala, Miguel A.
    Univ Alcala De Henares, Dept Ciencias Vida, Grp Ecol & Restaurac Forestal, Madrid, Spain.
    Scherer-Lorenzen, Michael
    Identifying the tree species compositions that maximize ecosystem functioning in European forests2019In: Journal of Applied Ecology, ISSN 0021-8901, E-ISSN 1365-2664, Vol. 56, no 3, p. 733-744Article in journal (Refereed)
    Abstract [en]

    1. Forest ecosystem functioning generally benefits from higher tree species richness, but variation within richness levels is typically large. This is mostly due to the contrasting performances of communities with different compositions. Evidence-based understanding of composition effects on forest productivity, as well as on multiple other functions will enable forest managers to focus on the selection of species that maximize functioning, rather than on diversity per se.

    2. We used a dataset of 30 ecosystem functions measured in stands with different species richness and composition in six European forest types. First, we quantified whether the compositions that maximize annual above-ground wood production (productivity) generally also fulfil the multiple other ecosystem functions (multifunctionality). Then, we quantified the species identity effects and strength of interspecific interactions to identify the "best" and "worst" species composition for multifunctionality. Finally, we evaluated the real-world frequency of occurrence of best and worst mixtures, using harmonized data from multiple national forest inventories.

    3. The most productive tree species combinations also tended to express relatively high multifunctionality, although we found a relatively wide range of compositions with high- or low-average multifunctionality for the same level of productivity. Monocultures were distributed among the highest as well as the lowest performing compositions. The variation in functioning between compositions was generally driven by differences in the performance of the component species and, to a lesser extent, by particular interspecific interactions. Finally, we found that the most frequent species compositions in inventory data were monospecific stands and that the most common compositions showed below-average multifunctionality and productivity.

    4. Synthesis and applications. Species identity and composition effects are essential to the development of high-performing production systems, for instance in forestry and agriculture. They therefore deserve great attention in the analysis and design of functional biodiversity studies if the aim is to inform ecosystem management. A management focus on tree productivity does not necessarily trade-off against other ecosystem functions; high productivity and multifunctionality can be combined with an informed selection of tree species and species combinations.

  • 58.
    Bagchi, Sonchita
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Fredriksson, Robert
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Wallén-Mackenzie, Åsa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    In Situ Proximity Ligation Assay (PLA)2015In: ELISA: Methods and Protocols / [ed] Hnasko, R, Springer-Verlag New York, 2015, Vol. 1318, p. 149-159Chapter in book (Refereed)
    Abstract [en]

    In situ proximity ligation assay (PLA) is a method to identify physical closeness of proteins, where a signal will only be produced if the two proteins are closer than 40 nm, in tissue section or cell cultures. Modifications of the PLA method can also be used to increase specificity or sensitivity of standard immunohistochemistry protocols.

  • 59.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Ulls Vag 16, S-75651 Uppsala, Sweden.
    Anslan, Sten
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, Tartu, Estonia;Braunschweig Univ Technol, Zool Inst, Mendelssohnstr 4, D-38106 Braunschweig, Germany.
    Hildebrand, Falk
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany.
    Bork, Peer
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany;Max Delbruck Ctr Mol Med, Berlin, Germany;Univ Wurzburg, Bioctr, Dept Bioinformat, Wurzburg, Germany.
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, 14A Ravila, EE-50411 Tartu, Estonia.
    Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment2019In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 11, no 4, p. 487-494Article in journal (Refereed)
    Abstract [en]

    High-throughput studies of microbial communities suggest that Archaea are a widespread component of microbial diversity in various ecosystems. However, proper quantification of archaeal diversity and community ecology remains limited, as sequence coverage of Archaea is usually low owing to the inability of available prokaryotic primers to efficiently amplify archaeal compared to bacterial rRNA genes. To improve identification and quantification of Archaea, we designed and validated the utility of several primer pairs to efficiently amplify archaeal 16S rRNA genes based on up-to-date reference genes. We demonstrate that several of these primer pairs amplify phylogenetically diverse Archaea with high sequencing coverage, outperforming commonly used primers. Based on comparing the resulting long 16S rRNA gene fragments with public databases from all habitats, we found several novel family- to phylum-level archaeal taxa from topsoil and surface water. Our results suggest that archaeal diversity has been largely overlooked due to the limitations of available primers, and that improved primer pairs enable to estimate archaeal diversity more accurately.

  • 60.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hildebrand, Falk
    Forslund, Sofia K
    Anderson, Jennifer L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Soudzilovskaia, Nadejda A
    Bodegom, Peter M
    Bengtsson-Palme, Johan
    Anslan, Sten
    Coelho, Luis Pedro
    Harend, Helery
    Huerta-Cepas, Jaime
    Medema, Marnix H
    Maltz, Mia R
    Mundra, Sunil
    Olsson, Pål Axel
    Pent, Mari
    Põlme, Sergei
    Sunagawa, Shinichi
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tedersoo, Leho
    Bork, Peer
    Structure and function of the global topsoil microbiome.2018In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 560, no 7717, p. 233-237Article in journal (Refereed)
    Abstract [en]

    Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1-4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.

  • 61.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, 40 Lai St, EE-50411 Tartu, Estonia.
    Kohout, Petr
    Anslan, Sten
    Harend, Helery
    Abarenkov, Kessy
    Tedersoo, Leho
    Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, p. 885-896Article in journal (Refereed)
    Abstract [en]

    A central challenge in ecology is to understand the relative importance of processes that shape diversity patterns. Compared with aboveground biota, little is known about spatial patterns and processes in soil organisms. Here we examine the spatial structure of communities of small soil eukaryotes to elucidate the underlying stochastic and deterministic processes in the absence of environmental gradients at a local scale. Specifically, we focus on the fine-scale spatial autocorrelation of prominent taxonomic and functional groups of eukaryotic microbes. We collected 123 soil samples in a nested design at distances ranging from 0.01 to 64 m from three boreal forest sites and used 454 pyrosequencing analysis of Internal Transcribed Spacer for detecting Operational Taxonomic Units of major eukaryotic groups simultaneously. Among the main taxonomic groups, we found significant but weak spatial variability only in the communities of Fungi and Rhizaria. Within Fungi, ectomycorrhizas and pathogens exhibited stronger spatial structure compared with saprotrophs and corresponded to vegetation. For the groups with significant spatial structure, autocorrelation occurred at a very fine scale (<2 m). Both dispersal limitation and environmental selection had a weak effect on communities as reflected in negative or null deviation of communities, which was also supported by multivariate analysis, that is, environment, spatial processes and their shared effects explained on average <10% of variance. Taken together, these results indicate a random distribution of soil eukaryotes with respect to space and environment in the absence of environmental gradients at the local scale, reflecting the dominant role of drift and homogenizing dispersal.

  • 62. Bahram, Mohammad
    et al.
    Kõljalg, Urmas
    Courty, Pierre-Emmanuel
    Diédhiou, Abdala G.
    Kjøller, Rasmus
    Põlme, Sergei
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Veldre, Vilmar
    Tedersoo, Leho
    The distance decay of similarity in communities of ectomycorrhizal fungi in different ecosystems and scales2013In: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 101, no 5, p. 1335-1344Article in journal (Refereed)
    Abstract [en]

    Despite recent advances in understanding community ecology of ectomycorrhizal fungi, little is known about their spatial patterning and the underlying mechanisms driving these patterns across different ecosystems. * This meta-study aimed to elucidate the scale, rate and causes of spatial structure of ectomycorrhizal fungal communities in different ecosystems by analysing 16 and 55 sites at the local and global scales, respectively. We examined the distance decay of similarity relationship in species- and phylogenetic lineage-based communities in relation to sampling and environmental variables. * Tropical ectomycorrhizal fungal communities exhibited stronger distance-decay patterns compared to non-tropical communities. Distance from the equator and sampling area were the main determinants of the extent of distance decay in fungal communities. The rate of distance decay was negatively related to host density at the local scale. At the global scale, lineage-level community similarity decayed faster with latitude than with longitude. * Synthesis. Spatial processes play a stronger role and over a greater scale in structuring local communities of ectomycorrhizal fungi than previously anticipated, particularly in ecosystems with greater vegetation age and closer to the equator. Greater rate of distance decay occurs in ecosystems with lower host density that may stem from increasing dispersal and establishment limitation. The relatively strong latitude effect on distance decay of lineage-level community similarity suggests that climate affects large-scale spatial processes and may cause phylogenetic clustering of ectomycorrhizal fungi at the global scale.

  • 63.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Uppsala, Sweden.
    Vanderpool, Dan
    Univ Montana, Div Biol Sci, 32 Campus Dr, Missoula, MT 59812 USA.
    Pent, Mari
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Hiltunen, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics2018In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 10, no 2, p. 155-166Article in journal (Refereed)
    Abstract [en]

    Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.

  • 64. Bajdek, Piotr
    et al.
    Owocki, Krzysztof
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Putative dicynodont coprolites from the Upper Triassic of Poland2014In: Palaeogeography, Palaeoclimatology, Palaeoecology, ISSN 0031-0182, E-ISSN 1872-616X, Vol. 411, p. 1-17Article in journal (Refereed)
    Abstract [en]

    A significant number (more than 100) of brownto dark and silty, carbonate or pyrite-mineralized, in part organic carbon-rich, spherical or oval-shaped structures have been collected fromthe Upper Triassic (uppermost NorianlowerRhaetian) sediments of the Lipie Śląskie clay-pit at Lisowice near Lubliniec town, Poland. Their geological context, morphology, content, geochemistry and association with skeletal remains suggest they are fecal masses of a sizable herbivorous tetrapod. The only large herbivore known from the site is a giant 5 meter-long dicynodont (Synapsida: Anomodontia), represented by numerous bones and also by large, oval-shaped footprints. The putative dicynodont coprolites were collected from mudstone and siltstone with numerous organic remains that were deposited in anoxic conditions. In addition, REEs and other trace element concentrations suggest that the burial environment and diagenesis of these coprolites were under anoxic conditions. SEM and thin section images of the coprolite matrix show numerous nests with pyrite (probably bacterial in origin) and large amount of mineral particles. The putative dicynodont coprolites contain also amorphous, dark organic matter, poorly preserved palynomorphs, small fragments of plant cuticle. Detailed characteristic of these coprolites reveals possible implications for the ecology and physiology of the source animal species. The δ 13C values of the gymnospermcuticle and dark organic matter measured in three coprolites are −23.4‰, −21.2‰and −20.3‰, all average. The evidence from these coprolites suggests that dicynodonts processed plant soft elements into very small pieces, but wood fragments were found also in a mass accumulation in two coprolites.

  • 65.
    Bajdek, Piotr
    et al.
    Aleja Najswietszej Maryi Panny 20-20A, PL-42200 Czestochowa, Poland..
    Owocki, Krzysztof
    Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland..
    Sennikov, Andrey G.
    Russian Acad Sci, Borissiak Paleontol Inst, Profsoyuznaya 123, Moscow 117997, Russia.;Kazan Fed Univ, Kremlyovskaya 18, Kazan 420008, Russia..
    Golubev, Valeriy K.
    Russian Acad Sci, Borissiak Paleontol Inst, Profsoyuznaya 123, Moscow 117997, Russia.;Kazan Fed Univ, Kremlyovskaya 18, Kazan 420008, Russia..
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Residues from the Upper Permian carnivore coprolites from Vyazniki in Russia - key questions in reconstruction of feeding habits2017In: Palaeogeography, Palaeoclimatology, Palaeoecology, ISSN 0031-0182, E-ISSN 1872-616X, Vol. 482, p. 70-82Article in journal (Refereed)
    Abstract [en]

    Residues of twenty-five coprolite fragments collected from the Upper Permian of Vyazniki (European Russia) were studied in detail. The phosphatic composition, general shape and size, and bone inclusions of these specimens indicate that medium to large-sized carnivores, such as therocephalian therapsids or early archosauriforms, were the most likely coprolite producers. The contents of the examined fossils (i.e. Scale, bone and tooth fragments, mineral grains, and microbial structures) do not differ significantly among the samples, implying fairly comparable feeding habits of their producers. Fragments of large tooth crowns in two of the analyzed samples imply that either (1) the coprolite producer swallowed the cranial elements of its prey or (2) the coprolite producer broke and swallowed its own tooth while feeding (such tooth damage is known in archosaurs that have tooth replacement, e.g. crocodiles and dinosaurs). Indeed, the most complete tooth fragment in these fossils is serrated, most likely belonging to an early archosauriform known from skeletal records from the Late Permian of Vyaznilci. Another coprolite fragment contains the etched tooth of a lungfish, while putative actinopterygian fish remains (scales and small fragments of bones) are abundant in some samples. Mineral particles (mostly quartz grains, feldspars and mica) may have been swallowed accidentally. The preserved microbial colonies (mineralized fossil fungi and bacteria or their pseudomorphs), manifested in the coprolites as Fe-rich mineral structures, seem to have developed on the expelled feces rather than on the items before they were swallowed.

  • 66.
    Bajdek, Piotr
    et al.
    Aleja Najswieztszej Maryi Panny 20-20A, PL-42200 Czestochowa, Poland..
    Qvarnström, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Owocki, Krzysztof
    Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland..
    Sulej, Tomasz
    Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland..
    Sennikov, Andrey G.
    Russian Acad Sci, Borissiak Paleontol Inst, Profsoyuznaya 123, Moscow 117997, Russia.;Kazan Fed Univ, Kremlyovskaya 18, Kazan 420008, Russia..
    Golubev, Valeriy K.
    Russian Acad Sci, Borissiak Paleontol Inst, Profsoyuznaya 123, Moscow 117997, Russia.;Kazan Fed Univ, Kremlyovskaya 18, Kazan 420008, Russia..
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Microbiota and food residues including possible evidence of pre-mammalian hair in Upper Permian coprolites from Russia2016In: Lethaia: an international journal of palaeontology and stratigraphy, ISSN 0024-1164, E-ISSN 1502-3931, Vol. 49, no 4, p. 455-477Article in journal (Refereed)
    Abstract [en]

    Coprolites (fossil faeces) provide direct evidence on the diet of its producer and unique insights on ancient food webs and ecosystems. We describe the contents of seven coprolites, collected from the Late Permian Vyazniki site of the European part of Russia. Two coprolite morphotypes (A, B) contain remains of putative bacteria, cyanobacteria, fungi, protists, invertebrate eggs, arthropod elements, undigested bone and tooth fragments, fish scales and elongated hair-like structures with hollow interiors. Content, size and shape of the coprolites together with the associated body fossil record suggest that the most probable scat-producers were carnivorous tetrapods; the bone-rich morphotype A reveals short food retention time and a fast metabolism and is therefore assigned to therapsid carnivores whereas morphotype B with rarer and degraded bones are assigned to archosauromorphs or other non-therapsid carnivores. The general coprolite matrix contains abundant micron-sized spheres and thin-walled vesicles which are interpreted as oxide and phosphatic pseudomorphs after microbial cells. From analyses of the undigested bones, we infer that they represent remains of actinopterygian fish, a therapsid and unrecognizable parts of amphibians and/or reptiles. Additionally, hair-like structures found in one coprolite specimen occur as diagenetically altered (oxide-replaced) structures and moulds (or partly as pseudomorphs) in a microcrystalline carbonate-fluoride-bearing calcium phosphate. This suggests that the latest Permian therapsids probably were equipped with hair-like integument or hairsuit. If true, this is by far the oldest evidence of this mammalian character in the stem group of mammals.

  • 67. Bakshi, Mayur V
    et al.
    Barjaktarovic, Zarko
    Azimzadeh, Omid
    Kempf, Stefan J.
    Merl, Juliane
    Hauck, Stefanie M.
    Buratovic, Sonja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Eriksson, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Atkinson, Michael J.
    Tapio, Soile
    Total body exposure to low-dose ionizing radiation induces long term alterations to the liver proteome of neonatally exposed mice2015In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 14, no 1, p. 366-373Article in journal (Refereed)
    Abstract [en]

    Tens of thousands of people are being exposed daily toenvironmental low-dose gamma radiation. Epidemiological data indicate thatsuch low radiation doses may negatively affect liver function and result in thedevelopment of liver disease. However, the biological mechanisms behindthese adverse effects are unknown. The aim of this study was to investigateradiation-induced damage in the liver after low radiation doses. Neonatal maleNMRI mice were exposed to total body irradiation on postnatal day 10 usingacute single doses ranging from 0.02 to 1.0 Gy. Early (1 day) and late (7months) changes in the liver proteome were tracked using isotope-codedprotein label technology and quantitative mass spectrometry. Our dataindicate that low and moderate radiation doses induce an immediateinhibition of the glycolysis pathway and pyruvate dehydrogenase availability inthe liver. Furthermore, they lead to significant long-term alterations in lipidmetabolism and increased liver inflammation accompanying inactivation of thetranscription factor peroxisome proliferator-activated receptor alpha. This study contributes to the understanding of the potentialrisk of liver damage in populations environmentally exposed to ionizing radiation.

  • 68. Bakshi, Mayur V.
    et al.
    Barjaktarovic, Zarko
    Azimzadeh, Omid
    Kempf, Stefan J.
    Merl, Juliane
    Hauck, Stefanie M.
    Eriksson, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Buratovic, Sonja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Atkinson, Michael J.
    Tapio, Soile
    Long-term effects of acute low-dose ionizing radiation on the neonatal mouse heart: a proteomic study2013In: Radiation and Environmental Biophysics, ISSN 0301-634X, E-ISSN 1432-2099, Vol. 52, no 4, p. 451-461Article in journal (Refereed)
    Abstract [en]

    Epidemiological studies establish that children and young adults are especially susceptible to radiation-induced cardiovascular disease (CVD). The biological mechanisms behind the elevated CVD risk following exposure at young age remain unknown. The present study aims to elucidate the long-term effects of ionizing radiation by studying the murine cardiac proteome after exposure to low and moderate radiation doses. NMRI mice received single doses of total body Co-60 gamma-irradiation on postnatal day 10 and were sacrificed 7 months later. Changes in cardiac protein expression were quantified using isotope-coded protein label and tandem mass spectrometry. We identified 32, 31, 66, and 34 significantly deregulated proteins after doses of 0.02, 0.1, 0.5, and 1.0 Gy, respectively. The four doses shared 9 deregulated proteins. Bioinformatics analysis showed that most of the deregulated proteins belonged to a limited set of biological categories, including metabolic processes, inflammatory response, and cytoskeletal structure. The transcription factor peroxisome proliferator-activated receptor alpha was predicted as a common upstream regulator of several deregulated proteins. This study indicates that both adaptive and maladaptive responses to the initial radiation damage persist well into adulthood. It will contribute to the understanding of the long-term consequences of radiation-induced injury and developmental alterations in the neonatal heart.

  • 69.
    Baldauf, Sandra L.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fiz-Palacios, Omar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Heidari, Nahid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A Deep Hidden Diversity of Dictyostelia2018In: Protist, ISSN 1434-4610, E-ISSN 1618-0941, Vol. 169, no 1, p. 64-78Article in journal (Refereed)
    Abstract [en]

    Dictyostelia is a monophyletic group of transiently multicellular (sorocarpic) amoebae, whose study is currently limited to laboratory culture. This tends to favour faster growing species with robust sorocarps, while species with smaller more delicate sorocarps constitute most of the group’s taxonomic breadth. The number of known species is also small (∼150) given Dictyostelia’s molecular depth and apparent antiquity (>600 myr). Nonetheless, dictyostelid sequences are rarely recovered in culture independent sampling (ciPCR) surveys. We developed ciPCR primers to specifically target dictyostelid small subunit (SSU or 18S) rDNA and tested them on total DNAs extracted from a wide range of soils from five continents. The resulting clone libraries show mostly dictyostelid sequences (∼90%), and phylogenetic analyses of these sequences indicate novel lineages in all four dictyostelid families and most genera. This is especially true for the species-rich Heterostelium and Dictyosteliaceae but also the less species-rich Raperosteliaceae. However, the most novel deep branches are found in two very species-poor taxa, including the deepest branch yet seen in the highly divergent Cavenderiaceae. These results confirm a deep hidden diversity of Dictyostelia, potentially including novel morphologies and developmental schemes. The primers and protocols presented here should also enable more comprehensive studies of dictyostelid ecology.

  • 70.
    Barcelo, Marta
    et al.
    IFAPA Ctr Malaga, Cortijo Cruz S-N, Malaga 29140, Spain.
    Wallin, Anita
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany.
    Medina, Juan J.
    IFAPA Ctr Torres Tomejfl, Seville 41200, Spain.
    Gil-Ariza, David J.
    IFAPA Ctr Malaga, Cortijo Cruz S-N, Malaga 29140, Spain.
    Lopez-Casado, Gloria
    Univ Malaga, Dept Biol Vegetal, Inst Hortofruticultura Subtrop & Mediterranea La, E-29071 Malaga, Spain.
    Juarez, Jose
    Ctra Moncada Naquera, IVIA, Km 4-5, Valencia 46113, Spain.
    Sanchez-Sevilla, Jose F.
    IFAPA Ctr Malaga, Cortijo Cruz S-N, Malaga 29140, Spain.
    Lopez-Encina, Carlos
    Inst Hortofruticultura Subtrop & Mediterranea La, Malaga 29750, Spain.
    Lopez-Aranda, Jose M.
    IFAPA Ctr Malaga, Cortijo Cruz S-N, Malaga 29140, Spain.
    Mercado, Jose A.
    Univ Malaga, Dept Biol Vegetal, Inst Hortofruticultura Subtrop & Mediterranea La, E-29071 Malaga, Spain.
    Pliego-Alfaro, Fernando
    Univ Malaga, Dept Biol Vegetal, Inst Hortofruticultura Subtrop & Mediterranea La, E-29071 Malaga, Spain.
    Isolation and culture of strawberry protoplasts and field evaluation of regenerated plants2019In: Scientia Horticulturae, ISSN 0304-4238, E-ISSN 1879-1018, Vol. 256, article id 108552Article in journal (Refereed)
    Abstract [en]

    Protoplasts are an useful biotechnological tool for plant improvement In strawberry, very few studies on protoplast technology have been carried out. In this investigation, a procedure for the isolation and culture of strawberry protoplasts, cv. 'Chandler', has been developed. The effect of several factors affecting the successful isolation of protoplasts and formation of microcalli, e.g. explant source, washing procedure, hormonal composition of the culture medium and protoplast density, were evaluated. For shoot regeneration, microcalli derived from isolated protoplasts were transferred to MS medium supplemented with 0.2 mg l(-1) NAA and either 5 mg l(-1) BA or 3 mgl(-1) TDZ, obtaining a similar regeneration rate, 17%, in both media. Twenty-one independent protoclones were transferred to field conditions for agronomic evaluation. Significant alterations in the growth habit, density of foliage, leaf color and leaf morphology were detected in some lines. Fruit yield was significantly reduced in 15 out of the 21 protoclones evaluated due to a reduction in fruit weight and/or the number of fruits. Ploidy level was unaffected in a sample of 6 lines selected at random; however, a study of genetic stability by using 10 EST-SSR markers showed genetic alterations in all the lines analyzed. Despite the high rate of somaclonal variation detected in the protoclones, some of the lines displayed an agronomical behavior similar to control plants, indicating that this protocol could be useful for genetic improvement in this species.

  • 71.
    Bass, David
    et al.
    Ctr Environm Fisheries & Aquaculture Sci Cefas, Barrack Rd, Weymouth, Dorset, England;Nat Hist Museum, Dept Life Sci, Cromwell Rd, London, England.
    Ward, Georgia M.
    Ctr Environm Fisheries & Aquaculture Sci Cefas, Barrack Rd, Weymouth, Dorset, England;Nat Hist Museum, Dept Life Sci, Cromwell Rd, London, England;Univ Exeter, Biosci, Exeter, Devon, England.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ascetosporea2019In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 1, p. R7-R8Article in journal (Other academic)
  • 72.
    Bastiaans, Eric
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Wageningen University.
    Debets, Alfons J. M.
    Aanen, Duur K.
    Experimental evolution reveals that high relatedness protects multicellular cooperation from cheaters2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 11435Article in journal (Refereed)
    Abstract [en]

    In multicellular organisms, there is a potential risk that cheating mutants gain access to the germline. Development from a single-celled zygote resets relatedness among cells to its maximum value each generation, which should accomplish segregation of cheating mutants from non-cheaters and thereby protect multicellular cooperation. Here we provide the crucial direct comparison between high- and low-relatedness conditions to test this hypothesis. We allow two variants of the fungus Neurospora crassa to evolve, one with and one without the ability to form chimeras with other individuals, thus generating two relatedness levels. While multicellular cooperation remains high in the high-relatedness lines, it significantly decreases in all replicate low-relatedness lines, resulting in an average threefold decrease in spore yield. This reduction is caused by cheating mutants with reduced investment in somatic functions, but increased competitive success when fusing with non-cheaters. Our experiments demonstrate that high-genetic relatedness is crucial to sustain multicellular cooperation.

  • 73.
    Bazzi, Mohamad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Kear, Benjamin P.
    Uppsala University, Music and Museums, Museum of Evolution.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Campione, Nicolas E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology. Univ New England, Sch Environm & Rural Sci, Palaeosci Res Ctr, Armidale, NSW 2351, Australia.
    Static Dental Disparity and Morphological Turnover in Sharks across the End-Cretaceous Mass Extinction2018In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 28, no 16, p. 2607-2615Article in journal (Refereed)
    Abstract [en]

    The Cretaceous-Palaeogene (K-Pg) mass extinction profoundly altered vertebrate ecosystems and prompted the radiation of many extant clades [1, 2]. Sharks (Selachimorpha) were one of the few larger-bodied marine predators that survived the K-Pg event and are represented by an almost-continuous dental fossil record. However, the precise dynamics of their transition through this interval remain uncertain [3]. Here, we apply 2D geometric morphometrics to reconstruct global and regional dental morphospace variation among Lamniformes (Mackerel sharks) and Carch-arhiniformes (Ground sharks). These clades are prevalent predators in today's oceans, and were geographically widespread during the late Cretaceous-early Palaeogene. Our results reveal a decoupling of morphological disparity and taxonomic richness. Indeed, shark disparity was nearly static across the K-Pg extinction, in contrast to abrupt declines among other higher-trophic-level marine predators [4, 5]. Nevertheless, specific patterns indicate that an asymmetric extinction occurred among lamniforms possessing lowcrowned/triangular teeth and that a subsequent proliferation of carcharhiniforms with similar tooth morphologies took place during the early Paleocene. This compositional shift in post-Mesozoic shark lineages hints at a profound and persistent K-Pg signature evident in the heterogeneity of modern shark communities. Moreover, such wholesale lineage turnover coincided with the loss of many cephalopod [6] and pelagic amniote [5] groups, as well as the explosive radiation of middle trophic-level teleost fishes [1]. We hypothesize that a combination of prey availability and post-extinction trophic cascades favored extant shark antecedents and laid the foundation for their extensive diversification later in the Cenozoic [7-10].

  • 74.
    Bedarf, J. R.
    et al.
    Univ Bonn, Dept Neurol, Bonn, Germany.;German Ctr Neurodegenerat Dis Res DZNE, Bonn, Germany..
    Hildebrand, F.
    EMBL, Heidelberg, Germany..
    Coelho, L. P.
    EMBL, Heidelberg, Germany..
    Sunagawa, S.
    EMBL, Heidelberg, Germany.;Swiss Fed Inst Technol, Inst Microbiol, Vladimir Prelog 1-5-10, CH-8093 Zurich, Switzerland..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth, 40 Lai St, EE-51005 Tartu, Estonia..
    Goeser, F.
    Univ Bonn, Dept Internal Med 1, Bonn, Germany.;German Ctr Infect Res DZIF, Bonn, Germany..
    Bork, P.
    EMBL, Heidelberg, Germany.;Heidelberg Univ, MMPU, Heidelberg, Germany.;European Mol Biol Lab, Heidelberg, Germany.;Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany.;Univ Wurzburg, Dept Bioinformat, D-97074 Wurzburg, Germany.;Meyerhofstr 1, D-69117 Heidelberg, Germany..
    Wüllner, U.
    Univ Bonn, Dept Neurol, Bonn, Germany.;German Ctr Neurodegenerat Dis Res DZNE, Bonn, Germany.;Sigmund Freud Str 25, D-53127 Bonn, Germany..
    Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson's disease patients2017In: Genome Medicine, ISSN 1756-994X, E-ISSN 1756-994X, Vol. 9, article id 39Article in journal (Refereed)
    Abstract [en]

    Background: Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naive PD patients might also serve as a biomarker.

    Methods: We performed metagenomic shotgun analyses and compared the fecal microbiomes of 31 early stage, L-DOPA-naive PD patients to 28 age-matched controls.

    Results: We found increased Verrucomicrobiaceae (Akkermansia muciniphila) and unclassified Firmicutes, whereas Prevotellaceae (Prevotella copri) and Erysipelotrichaceae (Eubacterium biforme) were markedly lowered in PD samples. The observed differences could reliably separate PD from control with a ROC-AUC of 0.84. Functional analyses of the metagenomes revealed differences in microbiota metabolism in PD involving the beta-glucuronate and tryptophan metabolism. While the abundances of prophages and plasmids did not differ between PD and controls, total virus abundance was decreased in PD participants. Based on our analyses, the intake of either a MAO inhibitor, amantadine, or a dopamine agonist (which in summary relates to 90% of PD patients) had no overall influence on taxa abundance or microbial functions.

    Conclusions: Our data revealed differences of colonic microbiota and of microbiota metabolism between PD patients and controls at an unprecedented detail not achievable through 16S sequencing. The findings point to a yet unappreciated aspect of PD, possibly involving the intestinal barrier function and immune function in PD patients. The influence of the parkinsonian medication should be further investigated in the future in larger cohorts.

  • 75. Behrendt, Lars
    et al.
    Jonsson, Maria E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Goldstone, Jared V.
    Stegeman, John J.
    Induction of cytochrome P450 1 genes and stress response genes in developing zebrafish exposed to ultraviolet radiation2010In: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 98, no 1, p. 74-82Article in journal (Refereed)
  • 76.
    Behrendt, Lars
    et al.
    Woods Hole Oceanographic Institution.
    Jönsson, Maria E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Environmental Toxicology.
    Goldstone, Jared V.
    Woods Hole Oceanographic Institution.
    Stegeman, John J.
    Woods Hole Oceanographic Institution.
    Induction of cytochrome P450 1 genes and stress response genes in developing zebrafish exposed to ultraviolet radiation2010In: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 98, no 1, p. 74-82Article in journal (Refereed)
    Abstract [en]

    Ultraviolet (UV) radiation damages cell molecules, and has been suggested to up-regulate mammalian cytochrome P4501 (CYP1) genes through an aryl hydrocarbon receptor (AHR) mediated mechanism. In this study, embryos and larvae of zebrafish (Danio rerio) were exposed to UV to determine the effects on expression of CYP1 and stress response genes in vivo in these fish. Zebrafish embryos were exposed for varying times to UV on two consecutive days, with exposure beginning at 24 and 48h post-fertilization (hpf). Embryos exposed for 2, 4 or 6h twice over 2 days to UVB (0.62 W/m(2); 8.9-26.7 kJ/m(2)) plus UVA (2.05 W/m(2); 29.5-144.6 kJ/m(2)) had moderately (2.4+/-0.8-fold) but significantly up-regulated levels of CYP1A. UVA alone had no effect on CYP1A expression. Proliferating cellular nuclear antigen (PCNA) and Cu-Zn superoxide dismutase (SOD1) transcript levels were induced (2.1+/-0.2 and 2.3+/-0.5-fold, respectively) in embryos exposed to two 6-h pulses of 0.62 W/m(2) UVB (26.8 kJ/m(2)). CYP1A was induced also in embryos exposed to higher intensity UVB (0.93 W/m(2)) for two 3-h or two 4-h pulses (20.1 or 26.8 kJ/m(2)). CYP1B1, SOD1 and PCNA expression was induced by the two 3-h pulses of the higher intensity UVB, but not after two 4-h pulses of the higher intensity UVB, possibly due to impaired condition of surviving embryos, reflected in a mortality of 34% at that UVB dose. A single 8-h long exposure of zebrafish larvae (8dpf) to UVB at 0.93 W/m(2) (26.8 kJ/m(2)) significantly induced CYP1A and CYP1B1 expression, but other CYP1 genes (CYP1C1, CYP1C2 and CYP1D1) showed no significant increase. The results show that UVB can induce expression of CYP1 genes as well stress response genes in developing zebrafish, and that UVB intensity and duration influence the responses.

  • 77.
    Beijer, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Azoles and Contaminants in Treated Effluents Interact with CYP1 and CYP19 in Fish: 2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Numerous contaminants are present in mixtures in the aquatic environment. Among these are the azoles, a group of chemicals that includes both pharmaceuticals and pesticides. Azole fungicides are designed to inhibit lanosterol 14-demethylase (cytochrome P450 (CYP) 51), while other azoles are intended to inhibit aromatase (CYP19), i.e. the enzyme catalyzing biosynthesis of estrogens. In fish, a variety of CYP enzymes are involved in biotransformation of waterborne contaminants, and in metabolism of endogenous compounds including steroidal hormones. The induction of CYP1A protein and 7-ethoxyresorufin O-deethylase (EROD) activity are common biomarkers for exposure to aryl hydrocarbon receptor (AhR) agonists in fish. We developed an assay to measure inhibition of CYP1A activity (EROD) in three-spined stickleback and rainbow trout gill tissue ex vivo. Several azole fungicides were found to be potent inhibitors of CYP1A activity. A wastewater effluent containing high concentrations of pharmaceuticals was also shown to inhibit CYP1A activity. Further, several azoles inhibited CYP19 activity in rainbow trout brain microsomes in vitro. Azole mixtures reduced both CYP1A and CYP19 activity monotonically and in an additive way. Given the additive action of the azoles, studies to determine adverse effects of azole mixtures on CYP-regulated physiological functions in fish are needed. Induction of EROD and of gene expression of CYP1 in several organs was observed in an in vivo exposure with the same effluent shown to inhibit EROD. This finding could imply that there was a mixture of AhR agonists and CYP1A inhibitors in the effluent. Finally, wastewater treatment technologies were evaluated using biomarker responses in rainbow trout exposed to effluents of different treatments. The results from chemical analysis together with the biomarker results show that ozone and granulated active carbon treatment removed most pharmaceuticals, as well as AhR agonists and other chemicals present in the regular effluent. This part of the thesis demonstrates that biomarkers in fish such as induction of CYP1 gene expression are applicable to evaluate the efficiency of different treatment technologies for wastewater.

    List of papers
    1. CYP1A inhibition in fish gill filaments: a novel assay applied on pharmaceuticals and other chemicals
    Open this publication in new window or tab >>CYP1A inhibition in fish gill filaments: a novel assay applied on pharmaceuticals and other chemicals
    2010 (English)In: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 96, no 2, p. 145-150Article in journal (Refereed) Published
    Abstract [en]

    The gill filament 7-ethoxyresorufin O-deethylase (EROD) assay was originally developed as a biomarker for cytochrome P4501A (CYP1A) induction by Ah-receptor agonists in water. In this study, the assay was adapted to measure inhibition of CYP1A activity in fish gill filaments ex vivo. The experiments were carried out using gill arch filaments from beta-naphthoflavone (betaNF)-exposed three-spined stickleback (Gasterosteus aculeatus). Candidate CYP1A inhibitors were added to the assay buffer. Nine selected pharmaceuticals and five known or suspected CYP1A-modulating chemicals were examined with regard to their ability to reduce EROD activity in gill filaments. Ellipticine, a well characterized CYP1A inhibitor, was the most effective inhibitor of the compounds tested. At a concentration in the assay buffer of 1 microM the antifungal azoles ketoconazole, miconazole and bitertanol, and the plant flavonoid acacetin reduced gill EROD activity by more than 50%, implying IC50 values below 1 microM. These compounds have previously been shown to inhibit EROD activity in liver microsomes from fish and mammals at similar concentrations. The proton pump inhibitor omeprazole reduced the gill EROD activity by 39% at 10 microM. It is concluded that the modified gill filament EROD assay is useful to screen for waterborne pollutants that inhibit catalytic CYP1A activity in fish gills.

    Keywords
    Gill filament assay, CYP inhibition, Pharmaceuticals, Antifungal azoles, Three-spined stickleback, EROD activity
    National Category
    Pharmacology and Toxicology Biological Sciences
    Research subject
    Ecotoxicology
    Identifiers
    urn:nbn:se:uu:diva-120904 (URN)10.1016/j.aquatox.2009.10.018 (DOI)000274978500009 ()19913926 (PubMedID)
    Available from: 2010-03-17 Created: 2010-03-17 Last updated: 2018-01-12Bibliographically approved
    2. Azoles additively inhibit cytochrome P450 1 (EROD) and 19 (aromatase) in rainbow trout (Oncorhynchus mykiss)
    Open this publication in new window or tab >>Azoles additively inhibit cytochrome P450 1 (EROD) and 19 (aromatase) in rainbow trout (Oncorhynchus mykiss)
    Show others...
    2018 (English)In: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 198, p. 73-81Article in journal (Refereed) Published
    Abstract [en]

    Antifungal azoles are widely used in medicine, agriculture, and material protection and several antifungal azoles have been found in environmental samples. Although these compounds were designed to inhibit fungal enzymes such as lanosterol-14-demethylase (cytochrome P450 (CYP) 51), it is well established that the inhibitory actions of azoles are not specific for fungal CYP isozymes.

    We refined a gill filament assay to determine the inhibition of CYP1, measured as reduced 7-ethoxyresorufin-O-deethylase (EROD) activity, in rainbow trout (Oncorhynchus mykiss) gill tissue ex vivo. The advantage of this method is that both induction and inhibition of EROD are performed ex vivo. Among thirteen azoles studied, the five that caused the strongest inhibition of gill EROD activity at a concentration of 5 μM were selected for concentration–response assessment. These compounds (bifonazole, clotrimazole, imazalil, miconazole, and prochloraz) showed IC50 values ranging from 0.1 to 1.5 μM. CYP19 (aromatase) inhibition was measured using microsomes from rainbow trout brains. Concentration-response curves for CYP19 inhibition were determined for letrozole, bifonazole, clotrimazole, imazalil, miconazole and prochloraz, which gave IC50 values ranging from 0.02 to 3.3 μM. It was further found that mixtures of the five most potent azoles reduced both CYP1 and 19 catalytic activity in an additive fashion (IC50 = 0.7 μM and 0.6 μM, in the respective assay). Bifonazole (IC50 = 0.1 μM) is not previously known to inhibit CYP1 activity.

    The additive inhibition of CYP1 and CYP19 catalytic activity is an important finding of the present study. We conclude that this additive action of azoles could mediate adverse impacts on CYP regulated physiological functions in environmentally exposed fish.

    Keywords
    Azole fungicide, EROD activity, cytochrome P450 (CYP), CYP1A, CYP19, aromatase, pharmaceutical, contaminant, chemical, fish, rainbow trout, gill, EROD aktivitet, cytokrom P450 (CYP), CYP1A, CYP19, aromatase, läkemedel, azol, fungicid, kemikalier, förorening, fisk, regnbågslax, gäle
    National Category
    Other Biological Topics
    Research subject
    Biology with specialization in Environmental Toxicology
    Identifiers
    urn:nbn:se:uu:diva-249010 (URN)10.1016/j.aquatox.2018.02.016 (DOI)000430630100008 ()
    Funder
    Mistra - The Swedish Foundation for Strategic Environmental Research
    Available from: 2015-04-15 Created: 2015-04-10 Last updated: 2018-08-07Bibliographically approved
    3. Effluent from drug manufacturing affects cytochrome P450 1 regulation and function in fish
    Open this publication in new window or tab >>Effluent from drug manufacturing affects cytochrome P450 1 regulation and function in fish
    Show others...
    2013 (English)In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 90, no 3, p. 1149-1157Article in journal (Refereed) Published
    Abstract [en]

    We have previously reported very high concentrations of pharmaceuticals in the effluent from a treatment plant receiving wastewater from about 90 bulk drug manufacturers near Hyderabad, India. The main objective of the present study was to examine how high dilutions of this effluent affect mRNA expression of cytochrome P450 (CYP) 1 family genes and ethoxyresorufin O-deethylase (EROD) activity in exposed wildlife, using the three-spined stickleback (Gasterosteus aculeatus) as a model. In gill filaments exposed to diluted effluent ex vivo, EROD activity was strongly inhibited in a concentration-dependent manner. In a subsequent in vivo study, groups of fish were exposed (24. h) to three concentrations of effluent, 0.8%, 1.6% or 3.2%. In this experiment, EROD in gills was induced 27-, 52- or 60-fold, respectively. Accordingly, CYP1A mRNA was markedly up-regulated in gill, liver and brain of fish exposed to all three effluent concentrations. Expression of mRNA for CYP1B1 and CYP1C1 was induced in gills at all concentrations while effects on these genes in liver and brain were weak or absent. The results of a time course study suggested that most CYP1-inducing substances in the effluent were readily metabolised or excreted, because the induced EROD activity and mRNA expression decreased when the fish were transferred to clean water. Considering that CYP1 enzymes play important roles in biotransformation of endogenous and foreign compounds, the observed dual effect of the effluent on CYP1 catalytic activity and mRNA expression suggests that multiple physiological functions could be affected in exposed wildlife.

    Keywords
    CYP1, EROD, Gills, Pharmaceuticals, Three-spined stickleback, Treated wastewater, Drug products, Effluent treatment, Fish, Gene expression, Wastewater treatment, Effluents, cytochrome P450, cytochrome P450 1, cytochrome P450 1A, cytochrome P450 1B1, cytochrome P450 1C1, cytochrome P450 1C2, ethoxyresorufin deethylase, industrial effluent, messenger RNA, tap water, unclassified drug, biotransformation, concentration (composition), drug, ecological modeling, effluent, enzyme activity, manufacturing, metabolism, pollution exposure, teleost, wastewater, water treatment, animal experiment, animal tissue, article, brain, controlled study, enzyme induction, enzyme inhibition, female, Gasterosteus aculeatus, gene, genetic transcription, gill, liver, mortality, nonhuman, spiggin gene, upregulation, vitellogenin gene, waste water treatment plant, Andhra Pradesh, Hyderabad [Andhra Pradesh], India
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-192012 (URN)10.1016/j.chemosphere.2012.09.023 (DOI)000312978700035 ()
    Note

    De två första författarna delar förstaförfattarskapet.

    Available from: 2013-01-24 Created: 2013-01-15 Last updated: 2017-12-06Bibliographically approved
    4. Reduction of pharmaceuticals and other contaminants in sewage treatment effluents by active carbon filtration and ozonation: Evaluation using biomarker responses in fish and chemical analysis
    Open this publication in new window or tab >>Reduction of pharmaceuticals and other contaminants in sewage treatment effluents by active carbon filtration and ozonation: Evaluation using biomarker responses in fish and chemical analysis
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    effluent, STP, wastewater, active carbon, ozonation, rainbow trout
    National Category
    Other Biological Topics
    Research subject
    Biology with specialization in Environmental Toxicology
    Identifiers
    urn:nbn:se:uu:diva-251294 (URN)
    Available from: 2015-04-15 Created: 2015-04-15 Last updated: 2015-07-07
  • 78.
    Beijer, Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Björlenius, Berndt
    Royal Inst Technol KTH, Albanova Univ Ctr, Sch Biotechnol, SE-10691 Stockholm, Sweden..
    Shaik, Siraz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology. IUF Leibniz Res Inst Environm Med, Hennekamp 50, D-40225 Dusseldorf, Germany..
    Lindberg, Richard H.
    Umea Univ, Dept Chem, KBC 6A Linnaeus Vag 6, SE-90187 Umea, Sweden..
    Brunström, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Brandt, Ingvar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Removal of pharmaceuticals and unspecified contaminants in sewage treatment effluents by activated carbon filtration and ozonation: Evaluation using biomarker responses and chemical analysis2017In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 176, p. 342-351Article in journal (Refereed)
    Abstract [en]

    Traces of active pharmaceutical ingredients (APIs) and other chemicals are demonstrated in effluents from sewage treatment plants (STPs) and they may affect quality of surface water and eventually drinking water. Treatment of effluents with granular activated carbon (GAC) or ozone to improve removal of APIs and other contaminants was evaluated at two Swedish STPs, Kappala and Uppsala (88 and 103 APIs analyzed). Biomarker responses in rainbow trout exposed to regular and additionally treated effluents were determined. GAC and ozone treatment removed 87-95% of the total concentrations of APIs detected. In Kappala, GAC removed 20 and ozonation (7 g O-3/m(3)) 21 of 24 APIs detected in regular effluent. In Uppsala, GAC removed 25 and ozonation (5.4 g O-3/m(3)) 15 of 25 APIs detected in effluent. GAC and ozonation also reduced biomarker responses caused by unidentified pollutants in STP effluent water. Elevated ethoxyresorufin-O-deethylase (EROD) activity in gills was observed in fish exposed to effluent in both STPs. Gene expression analysis carried out in Kappala showed increased concentrations of cytochrome P450 (CYP1A5 and CYP1C3) transcripts in gills and of CYP1As in liver of fish exposed to effluent. In fish exposed to GAC- or ozone-treated effluent water, gill EROD activity and expression of CYP1As and CYP1C3 in gills and liver were generally equal to or below levels in fish held in tap water. The joint application of chemical analysis and sensitive biomarkers proved useful for evaluating contaminant removal in STPs with new technologies.

  • 79.
    Beijer, Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Gao, Kai
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Jönsson, Maria E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Larsson, D. G. J.
    Brunström, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Brandt, Ingvar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Effluent from drug manufacturing affects cytochrome P450 1 regulation and function in fish2013In: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 90, no 3, p. 1149-1157Article in journal (Refereed)
    Abstract [en]

    We have previously reported very high concentrations of pharmaceuticals in the effluent from a treatment plant receiving wastewater from about 90 bulk drug manufacturers near Hyderabad, India. The main objective of the present study was to examine how high dilutions of this effluent affect mRNA expression of cytochrome P450 (CYP) 1 family genes and ethoxyresorufin O-deethylase (EROD) activity in exposed wildlife, using the three-spined stickleback (Gasterosteus aculeatus) as a model. In gill filaments exposed to diluted effluent ex vivo, EROD activity was strongly inhibited in a concentration-dependent manner. In a subsequent in vivo study, groups of fish were exposed (24. h) to three concentrations of effluent, 0.8%, 1.6% or 3.2%. In this experiment, EROD in gills was induced 27-, 52- or 60-fold, respectively. Accordingly, CYP1A mRNA was markedly up-regulated in gill, liver and brain of fish exposed to all three effluent concentrations. Expression of mRNA for CYP1B1 and CYP1C1 was induced in gills at all concentrations while effects on these genes in liver and brain were weak or absent. The results of a time course study suggested that most CYP1-inducing substances in the effluent were readily metabolised or excreted, because the induced EROD activity and mRNA expression decreased when the fish were transferred to clean water. Considering that CYP1 enzymes play important roles in biotransformation of endogenous and foreign compounds, the observed dual effect of the effluent on CYP1 catalytic activity and mRNA expression suggests that multiple physiological functions could be affected in exposed wildlife.

  • 80.
    Beijer, Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Jönsson, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Shaik, Siraz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Behrens, Daphné
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Brunström, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Brandt, Ingvar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Azoles additively inhibit cytochrome P450 1 (EROD) and 19 (aromatase) in rainbow trout (Oncorhynchus mykiss)2018In: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 198, p. 73-81Article in journal (Refereed)
    Abstract [en]

    Antifungal azoles are widely used in medicine, agriculture, and material protection and several antifungal azoles have been found in environmental samples. Although these compounds were designed to inhibit fungal enzymes such as lanosterol-14-demethylase (cytochrome P450 (CYP) 51), it is well established that the inhibitory actions of azoles are not specific for fungal CYP isozymes.

    We refined a gill filament assay to determine the inhibition of CYP1, measured as reduced 7-ethoxyresorufin-O-deethylase (EROD) activity, in rainbow trout (Oncorhynchus mykiss) gill tissue ex vivo. The advantage of this method is that both induction and inhibition of EROD are performed ex vivo. Among thirteen azoles studied, the five that caused the strongest inhibition of gill EROD activity at a concentration of 5 μM were selected for concentration–response assessment. These compounds (bifonazole, clotrimazole, imazalil, miconazole, and prochloraz) showed IC50 values ranging from 0.1 to 1.5 μM. CYP19 (aromatase) inhibition was measured using microsomes from rainbow trout brains. Concentration-response curves for CYP19 inhibition were determined for letrozole, bifonazole, clotrimazole, imazalil, miconazole and prochloraz, which gave IC50 values ranging from 0.02 to 3.3 μM. It was further found that mixtures of the five most potent azoles reduced both CYP1 and 19 catalytic activity in an additive fashion (IC50 = 0.7 μM and 0.6 μM, in the respective assay). Bifonazole (IC50 = 0.1 μM) is not previously known to inhibit CYP1 activity.

    The additive inhibition of CYP1 and CYP19 catalytic activity is an important finding of the present study. We conclude that this additive action of azoles could mediate adverse impacts on CYP regulated physiological functions in environmentally exposed fish.

  • 81.
    Beijer, Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Lampa, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm, UCR-Uppsala Clinical Research Center.
    Sundström, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm, UCR-Uppsala Clinical Research Center. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cardiology.
    Nilsson, Peter M.
    SUS Malmo, Dept Clin Sci, Malmo, Sweden..
    Elmstahl, Solve
    Lund Univ, Div Geriatr Med, Dept Hlth Sci, Malmo Univ Hosp, Malmo, Sweden..
    Pedersen, Nancy L.
    Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden..
    Lind, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cardiovascular epidemiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm, UCR-Uppsala Clinical Research Center.
    Interaction between physical activity and television time on blood pressure level: cross-sectional data from 45000 individuals2018In: Journal of Hypertension, ISSN 0263-6352, E-ISSN 1473-5598, Vol. 36, no 5, p. 1041-1050Article in journal (Refereed)
    Abstract [en]

    Objectives:The aim was to investigate if there is an interaction between sitting time and leisure time physical activity on blood pressure and if there are age differences and sex differences in this respect.

    Methods:Linear regression analysis on cross-sectional data was performed in more than 45000 men and women from two Swedish cohort studies, EpiHealth (45-75 years) and LifeGene (18-45 years). Self-reported leisure time physical activity was given in five levels from low (level 1) to vigorous physical activity (level 5) and television time was used as a proxy measure of sitting time.

    Results:High physical activity was associated with lower DBP (P=0.001), but not SBP. Active middle-aged men had lower DBP (-1.1mmHg; 95% CI -1.7 to -0.4) compared with inactive participants. Prolonged television time was associated with higher SBP (P<0.001) and DBP (P=0.011) in both sexes and in most age groups. Watching 3h instead of 1h television per day was associated with higher SBP in middle-aged women (SBP: 1.1mmHg; 95% CI 0.7-1.4) and men (SBP: 1.2mmHg; 95% CI 0.8-1.6). Only in young men, a high physical activity (level 4 instead of level 1) could compensate for a prolonged television time (3h per day) in terms of DBP.

    Conclusion:Prolonged television time was associated with higher SBP and DBP in both sexes and at most ages, whereas an increased physical activity was mainly associated with a lower DBP. Only in young men, a high physical activity could compensate for prolonged television time regarding DBP.

  • 82.
    Beijer, kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Shaik, Siraz
    Berndt, Björlenius
    KTH.
    Lindberg, Richard
    Umeå Universitet.
    Brunström, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Brandt, Ingvar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology.
    Reduction of pharmaceuticals and other contaminants in sewage treatment effluents by active carbon filtration and ozonation: Evaluation using biomarker responses in fish and chemical analysisManuscript (preprint) (Other academic)
  • 83. Bell, Phil R.
    et al.
    Campione, Nicolàs E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Taphonomy of the Danek Bonebed: a monodominant Edmontosaurus (Hadrosauridae) bonebed from the Horseshoe Canyon Formation, Alberta2014In: Canadian journal of earth sciences (Print), ISSN 0008-4077, E-ISSN 1480-3313, Vol. 51, no 11Article in journal (Refereed)
    Abstract [en]

    The Danek Bonebed (Horsethief Member, Horseshoe Canyon Formation, Late Campanian) is dominated by the remains of at least 12 Edmontosaurus regalis. Skeletal remains of a tyrannosaurid and ceratopsid are also known. The predominantly disarticulated remains were interred on a periodically inundated floodplain and, although the cause of death is unknown, a sudden, catastrophic death explains the demographic spread, faunal diversity, rare greenstick fractures, and homogeneous weathering/abrasion categories of the assemblage. The Danek Bonebed shares a similar taphonomic signature to the Liscomb Bonebed (Prince Creek Formation, Alaska), but it is unique among all other described hadrosaurid bonebeds in the unusually high proportion of bite-marked bones (similar to 30%), suggesting scavenging played a major role in the reworking of the assemblage. The highest frequency of bite marks is found on small, often unidentifiable (and commonly ignored) bone fragments, underscoring the role that such fragments can play in taphonomic interpretation. Finally, the recognition of E. regalis from central Alberta is an important datum linking contemporaneous occurrences in southern Alberta with slightly older records of this species from the Wapiti Formation in northwestern Alberta.

  • 84.
    Beltran, D. Campos
    et al.
    Univ Lubeck, Inst Expt & Klin Pharmakol & Toxikol, Lubeck, Germany.
    Konradsson-Geuken, Åsa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology. Karolinska Inst, Dept Neurosci, Stockholm, Sweden.
    Quintero, J. E.
    Univ Kentucky, Ctr Microelectrode Technol CenMeT, Lexington, KY 40506 USA;Quanteon LLC, Nicholasville, KY USA.
    Marshall, L.
    Univ Lubeck, Inst Expt & Klin Pharmakol & Toxikol, Lubeck, Germany.
    Amperometric D-serine detecting self-referenced ceramic-based microelectrode arrays2017In: Naunyn-Schmiedeberg's Archives of Pharmacology, ISSN 0028-1298, E-ISSN 1432-1912, Vol. 390, p. S70-S70Article in journal (Other academic)
  • 85. Bengtsson-Palme, Johan
    et al.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hartmann, Martin
    Branco, Sara
    Wang, Zheng
    Godhe, Anna
    De Wit, Pierre
    Sanchez-Garcia, Marisol
    Ebersberger, Ingo
    de Sousa, Filipe
    Amend, Anthony S.
    Jumpponen, Ari
    Unterseher, Martin
    Kristiansson, Erik
    Abarenkov, Kessy
    Bertrand, Yann J. K.
    Sanli, Kemal
    Eriksson, K. Martin
    Vik, Unni
    Veldre, Vilmar
    Nilsson, R. Henrik
    Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data2013In: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 4, no 10, p. 914-919Article in journal (Refereed)
    Abstract [en]

    The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 - as well as full-length ITS sequences - from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.