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  • 301. Ahlner, Sten
    Svensk Botanisk Tidskrift: Volym 61: Häfte 3, 19671967Collection (editor) (Other academic)
    Abstract [sv]

    INNEHÅLLSFÖRTECKNING. L. RODENBORG: Flora och vegetation i och vid Albrunna lund på södra Öland. III. Betesgång och vegetationsutveckling, m. m. M. RYBERG: Några synpunkter på lundgräsens ekologi i östra Svealand. N. HAKELIER: Three New Swedish Species of Geoglossum. B. M. P. LARSSON: Melica ciliata funnen vid Vänern i Västergötland. RECENSIONER: A. HOLST: Henrik Lundegårdh; Plant Physiology. A. HOLST: Hans Molisch; Botanische Versuche und Beobachtungen ohne Apparate. Vierte umgearbeitete und ergänzte Auflage von Richard Biebl. A. HOLST: Stig Fred & Hans-Jörgen Karlsson; Studieplan i biologi. Årskurs 7. Anders Kylin; Växternas livsföreteelser. K. AFZELIUS: E. J. H. Corner; The Natural History of Palms. B. M. P. LARSSON: Advances in Ecological Research. Vol. 1-2. Edited by J. B. Cragg. B. PETERSON: G. W. Lawson; Plant Life in West Africa. S. AHLNER: John G. Dony; Flora of Hertfordshire.

  • 302. Ahlner, Sten
    Svensk Botanisk Tidskrift: Volym 61: Häfte 4, 19671967Collection (editor) (Other academic)
    Abstract [sv]

    INNEHÅLLSFÖRTECKNING. L. HOLM: Taxonomic Notes on Ascomycetes. V. On Sphaeria parmeliarum Phill. & Plowr. and the Genus Cucurbidothis Petr. L. FRIES: The Sporophyte of Nemalion multifidum (Weber et Mohr) J. Ag. Å. LUNDQVIST: Orchideen Ölands. M. OHLANDER: Kärlväxtfloran i Gällinge och Förlanda socknar i norra Halland. RECENSIONER: D. LIHNELL: The Journal of General Virology. J. SÖDERSTRÖM: J. R. Lewis; The Ecology of Rocky Shores. J. SÖDERSTRÖM: M. B. E. Godward (Ed.); The Chromosomes of the Algae. S. AHLNER: Tyge W. Böcher, Kjeld Holmen o. Knud Jakobsen; Grønlands Flora. 2. reviderede udgave. DIVERSE: Notiser. Svensk Botanisk Tidskrift: Titelblad, innehållsförteckning och artförteckning till Bd 61.

  • 303. Ahlner, Sten
    Svensk Botanisk Tidskrift: Volym 62: Häfte 1, 19681968Collection (editor) (Other academic)
    Abstract [sv]

    INNEHÅLLSFÖRTECKNING. S. SUNESON: Vegetation och flora i Skaftö socken i mellersta Bohuslän. G. A. WESTFELDT: Floran i Vedens härad (inkl. Borås stad). R. MOBERG: Luftföroreningars inverkan på epifytiska lavar i Köpmanholmen. L. E. KERS: A New Species of Cleome (Capparidaceae) from N.W. Australia. H. J. BRODIE: Tetrapolarity and Comparison in Culture of Some Tropical Species. L. HOLM: Taxonomic Notes on Ascomycetes. VI. On the Genus Gibberidea Fuck. and Some Alleged Relatives. U. ELIASSON: Studies in Galápagos Plants. V. Some New Botanical Records from the Archipelago. G. LUNDEBERG: The Formation of Mycorrhizae in Different Provenances of Pine (Pinus silvestris L.). SMÄRRE UPPSATSER OCH MEDDELANDEN: B. M. P. LARSSON: Bidrag till Västergötlands mossflora. 2. Grimmia funalis funnen vid Vänern. L. RODENBORG: Dracocephalum ruyschiana L. återfunnen på Öland. T. SUNDIN: Floristiska anteckningar från Nynäshamn och trakterna däromkring. T. SUNDIN: Ytterligare fynd av Ricciocarpus natans (L.) Corda i Vänern. B. TOFTGÅRD: Floran i Brandstorp socken. F. BJÖRKBÄCK: Juncus arcticus ssp. balticus (Willd.) Hyl. funnen vid Ånnsjön i västra Jämtland. R. H. PETERSEN: Announcement of Symposium on Fungi. RECENSIONER: B. M. P. LARSSON: Karl Hasselrot; Västergötlands flora. B. M. P. LARSSON: Ernst Gerhard Mahn; Vegetationsaufbau und Standortsverhaltnisse der kontinental beeinflussten Xerothermrasengesellschaften Mitteldeutschlands. B. M. P. LARSSON: Josef Brun-Hool; Ackerunkraut-Gesellschaften der Nordwestschweiz. B. M. P. LARSSON: Jean-Louis Richard; Extraits de la carte phytosociologique des forêts du canton de Neuchâtel. B. M. P. LARSSON: M. E. D. Poore and V. C. Robertson; An Approach to the Rapid Description and Mapping of Biological Habitats. B. M. P. LARSSON: Eugene P. Odum; Samspelet i naturen. B. M. P. LARSSON: Paul B. Sears; Det levande landskapet. T. GUSTAFSSON: Alfred Kühn; Vorlesungen über Entwicklungsphysiologie. M. RYBERG: Stella Ross-Craig; Drawings of British Plants, XVI-XXIII. B. PETERSON: G. Kunkel; Helechos cultivados. A. L. STORK: Index to European Taxonomic Literature for 1965. Compiled by R. K. Brummit. A. L. STORK: Strasburger, Noll, Schenk und Schimper; Lehrbuch der Botanik für Hochschulen. 29. Auflage. A. L. STORK: J. Hutchinson; Key to the Families of Flowering Plants of the World. J. ERIKSSON: Josiah L. Lowe; Polyporaceae of North America. The Genus Poria.

  • 304. Ahlner, Sten
    Svensk Botanisk Tidskrift: Volym 62: Häfte 2, 19681968Collection (editor) (Other academic)
    Abstract [sv]

    INNEHÅLLSFÖRTECKNING. K. HJORTSTAM: Kärlväxtfloran i Alingsås samt Bälinge, Hols och Horla socknar. S. NILSSON: Pollen Morphology in the Genus Macrocarpaea (Gentianaceae) and Its Taxonomical Significance. U. ELIASSON: Studies in Galápagos Plants. VI. On the Identity of Calandrinia galapagosa St. John. H. PERSSON: Bryophytes from the Aleutian Islands, Collected Mainly by Hansford T. Shacklette. M. SIMAK und F. SIMANČÍK: Die Veränderungen der Zucker in Kiefernsamen mit verschiedenem Embryoentwicklungsgrad. SMÄRRE UPPSATSER OCH MEDDELANDEN: G. DEGELIUS: Några växtgeografiskt intressanta lavfynd. G. DEGELIUS: En förekomst av Hypericum humifusum L. vid Göteborg. I. ASPLUND: Embryological Studies in the Genera Sparganium and Typha. A Preliminary Report. Y. JOHANSSON: Bidrag till Hallands flora. K. HJORTSTAM: Ett par för Skepplanda socken i västra Västergötland nya fanerogamer. RECENSIONER: N. LUNDQVIST: J. van Brummelen; A World Monograph of the Genera Ascobolus and Saccobolus (Ascomycetes, Pezizales). C.-F. LUNDEVALL: H. Palmstierna; Plundring, svält, förgiftning. S. AHLNER: Ivar Elvers; Vår flora i färg. SAMMANKOMSTER ÅR 1967. SVENSKA BOTANISKA FÖRENINGEN: Föreningens 60-årsjubileum. Revisionssammanträdet 1967. Årsmötet 1967. L. E. KERS: Föreningens vårutflykt till Trosa-trakten 1967. Nya medlemmar. DIVERSE: Notiser. Undersökningsfartyget Sunbeam. Vädjan. XI International Botanical Congress.

  • 305. Ahlner, Sten
    Svensk Botanisk Tidskrift: Volym 62: Häfte 3, 19681968Collection (editor) (Other academic)
    Abstract [sv]

    INNEHÅLLSFÖRTECKNING. E. HENRIKSSON and L. C. Pearson; Carotenoids Extracted from Mycobionts of Collema tenax, Baeomyces roseus, and Some Other Lichens. G. DAS: The Influence of Calcium on Development, Phosphate, Assimilation and ATP Level in Synchronized Cultures of Scenedesmus. G. DAS: Growth and Appearance of Scenedesmus as Influenced by Deficient Inorganic Nutrition. L. HOLM: Études urédinologiques. 8. Gymnosporangium Gaeumannii - une espèce primitive? N. L. BOR: Lindbergia Bor: a New Genus of Grasses from Cyprus. M. BIZOT: Mousses récoltées par Mr. Gillis Een dans les Iles Maurice et de la Réunion. SMÄRRE UPPSATSER OCH MEDDELANDEN: E. NYHOLM: Nordisk bryologisk förening. Meeting in 1967. P. A. ERIKSSON: Några Sphagna från Västerdalarna och angränsande delar av Värmland. I. SEGELBERG: Vicia giacominiana sp. nov. A. BOHLIN: Ny lokal för ascomyceten Hypocreopsis lichenoides (Tode ex Fr.) Seaver. K. BOHLIN: Tre geasterfynd på Öland. R. SANTESSON: A New Name of an Alectoria. RECENSIONER: E. ALMQUIST: J. Lid; Norsk og svensk flora. B. SPARE: Alan Eyre; The Botanic Gardens of Jamaica. B. SPARRE: H. C. D. de Wit; Alverdens Planter. Fröplanter, Bind 2. K. B. Boedijn; Alverdens Planter. Sporeplanter. B. SPARRE: Fred A. Barkley; Outline Classification of Organisms.

  • 306. Ahlner, Sten
    Svensk Botanisk Tidskrift: Volym 62: Häfte 4, 19681968Collection (editor) (Other academic)
    Abstract [sv]

    INNEHÅLLSFÖRTECKNING. A. G. CRUNDWELL and E. NYHOLM: New Records of Scandinavian Bryophytes. L. RYVARDEN: The Genus Datronia in Fennoscandia. SMÄRRE UPPSATSER OCH MEDDELANDEN: H.-G. WALLENTINUS: Utbredningen av Eleocharis acicularis och E. parvula på strandängslokaler vid den svenska norrlandskusten. I. OTTOSSON: Usnea longissima Ach. found in north-western Spain. S. BERGH: Fynd av Sonchus palustris L. i Bohuslän. L. THOFELT: Ny lokal för Neottia nidus-avis på Frösön i Jämtland. RECENSIONER: E. HULTÉN: Flora of the Queen Charlotte Islands. Part 1. Systematics of the Vascular Plants. By James A. Calder and Roy L. Taylor. Do., Part 2. Cytological Aspects of the Vascular Plants. By Roy L. Taylor and Gerard A. Mulligan. E. HULTÉN: The Evolution of Canada’s Flora. Edited by Roy L. Calder and R. A. Ludwig. E. HULTÉN: William A. Weber; Rocky Mountain Flora. E. HULTÉN: Stanwyn G. Shetler; The Komarov Botanical Institute. 250 Years of Russian Research. H. VIRGIN: Ulrich Rüge; Angewandte Pflanzenphysiologie als Grundlage für den Gartenbau. M. RYBERG: Rüdiger Knapp; Experimentelle Soziologie und gegenseitige Beeinflussung der Pflanzen. 2. Aufl. H. TRALAU: H. Döring, W. Krutzsch, D. H. Mai und E. Schulz; Erläuterungen zu den sporenstratigraphischen Tabellen vom Zechstein bis zum Oligozän. H. TRALAU: W. Krutzsch; Atlas der mittel- und jungtertiären dispersen Sporen- und Pollen- sowie der Mikroplanktonformen des nördlichen Mitteleuropas. H. TRALAU: G. Andreánszky; On the Upper Oligocene Flora of Hungary. S. AHLNER: Natur i Lappland. Under redaktion av Kai Curry-Lindahl. S. AHLNER: Hugo Sjörs; Nordisk växtgeografi. Andra upplagan. S. AHLNER: Ernst Nilsson; Sommartorpets trädgård. S. AHLNER: F. H. Perring (assisted by P. D. Sell); Critical Supplement to the Atlas of the British Flora. S. AHLNER: A. R. Clapham, T. G. Tutin and E. F. Warburg, Excursion Flora of the British Isles. Second edition. S. AHLNER: David McClintock; Companion to Flowers. IN MEMORIAM (nekrolog): M.-B. FLORIN: Astrid Cleve von Euler 22/1 1875 – 8/4 1968. DIVERSE: Notiser. Svenska botanister i Latinamerika (Benkt Sparre). Rättelse (Kurt Hjortstam). Föreningens medlemsförteckning för år 1968 stencilerad. Särtryck av Svante Sunesons Skaftö-flora till salu. Svensk Botanisk Tidskrift: Titelblad, innehållsförteckning och artförteckning till Bd 62.

  • 307. Ahlner, Sten
    Svensk Botanisk Tidskrift: Volym 63: Häfte 1, 19691969Collection (editor) (Other academic)
    Abstract [sv]

    INNEHÅLLSFÖRTECKNING. L. E. KERS: Studies in Cleome. II. Cleome angustifolia Forssk. s. lat. and Cleome semitetrandra Sond. C. FORSBERG and B. FORSBERG: Some Limnological Features of Lake Långsjön, Björklinge. S. K. KAMRA: Studies on the Effect of Different Distances between Water Level and Seed Bed on Jacobsen Apparatus on the Germination of Picea abies (L.) Karst. Seed. E. GENBERG: Kärlväxtfloran på Vikbolandet och i dess skärgård. En inventering och en sammanfattning. A. HENSSEN: Eine Studie über die Gattung Arctomia. L. FRIES: The Sporophyte of Nemalion multifidum (Weber et Mohr) J. Ag. Found on the Swedish West Coast. M.-B. FLORIN: Late-glacial and Pre-boreal Vegetation in Central Sweden. I. Records of Pollen Species. T. W. BÖCHER: Experimental and Cytological Studies on Plant Species. XII. Sibbaldia procumbens and S. macrophylla. SMÄRRE UPPSATSER OCH MEDDELANDEN: G. LOHAMMAR: Presentation av några växtfynd. G. LOHAMMAR: Betvivlat Elatine-fynd. RECENSIONER: H. PERSSON: Rudolf M. Schuster; The Hepaticae and Anthocerotae of North America, East of the Hundreth Meridian. I. A. L. STORK: Index to European Taxonomic Literature for 1966. Compiled by R. K. Brummit and I. K. Ferguson. Index to Plant Chromosome numbers for 1966. Edited by R. Ornduff. A. L. STORK: An Annotated Glossary of Botanical Nomenclature. By R. McVaugh, R. Ross & F. A. Stafleu. A. L. STORK: A. G. Tansley; Britain’s Green Mantle. Past, Present and Future. 2:a omarb. uppl. A. L. STORK: Tor Nitzelius & Helge Vedel; Skogens träd och buskar i färg. B. SPARRE: Carlos Muñoz Pizarro; Sinopsis de la flora chilena. Claves para la identificación de familias y géneros. 2. utök. uppl. Carlos Muñoz Pizarro; Flores silvestres de Chile.

  • 308. Ahlner, Sten
    Svensk Botanisk Tidskrift: Volym 63: Häfte 2, 19691969Collection (editor) (Other academic)
    Abstract [sv]

    INNEHÅLLSFÖRTECKNING. J. ERIKSSON and K. HJORTSTAM: Four New Taxa of Hyphodontia (Basidiomycetes). I. HEDBERG: Cytotaxonomic Studies on Anthoxanthum odoratum L. s. lat. III. Investigations of Swiss and Austrian Population Samples. H. BERGLUND: On the Cultivation of Multicellular Marine Green Algae in Axenic Culture. S. K. KAMRA: Further Studies on the Effect of Different Distances between Water Level and Seed Bed on Jacobsen Apparatus on the Germination of Pinus silvestris and Picea abies Seed. M. OHLANDER: Kärlväxtfloran i Frillesås och Idala socknar i norra Halland. K. A. LYE: The Distribution and Ecology of Sphaerophorus melanocarpus. RECENSIONER: J. A. NANNFELDT: Eric Hultén; Flora of Alaska and Neighboring Territories. A. Manual of the Vascular Plants. E. HULTÉN: C. G. G. J. van Steenis; Pacific Plant Areas I. C. G. G. J. van Steenis & M. M. J. van Balgooy; Pacific Plant Areas II. D. LIHNELL: R. K. S. Wood; Physiological Plant Pathology. D. LIHNELL: The Ecology of Soil Bacteria. Edited by T. R. G. Gray and D. Parkinson. A. L. STORK: Peter R. Bell & Christopher L. F. Woodcock; The Diversity of Green Plants. SAMMANKOMSTER ÅR 1968. SVENSKA BOTANISKA FÖRENINGEN: Revisionssammanträdet 1968. Årsmötet 1968. O. PERSSON: Föreningens exkursion till Rydbo och Bogesundslandet 1968. Nya medlemmar.

  • 309. Ahlner, Sten
    Svensk Botanisk Tidskrift: Volym 63: Häfte 3, 19691969Collection (editor) (Other academic)
    Abstract [sv]

    INNEHÅLLSFÖRTECKNING. H.-E. WANNTORP: Microloma hereroense Wanntorp (Asclepiadaceae), a New Species from South West Africa. R. MOBERG: Physcia kairamoi in Scandinavia. J. A. VON ARX and T. NILSSON: Xylogone sphaerospora, a New Ascomycete from Stored Pulpwood Chips.L. HOLM: Études urédinologiques. 9. Sur l’urédo des Gymnosporangium. S. K. KAMRA: Studies to Find the Effect of Temporary Removal of Bell Jars from Seed Beds on Jacobsen Apparatus on the Germination of Pinus silvestris and Picea abies Seed. SMÄRRE UPPSATSER OCH MEDDELANDEN: L. KARLSSON: Some New Localities of Rare Plants in Lule Lappmark in Northern Sweden. N. L. BOR: A Correction. G. ERIKSSON: Anteckningar om jordstjärnor på Gotland. G. DEGELIUS: Soteskärs lavar. Till kännedomen om lavfloran i Bohusläns yttersta skärgård. G. SERNANDER-DU RIETZ: Förekomster av Physcia magnussonii Frey i Skandinavien och på sydvästra Grönland. RECENSIONER: K. THOMASSON: T. Hortobágyi; Phytoplankton Organisms from Three Reservoirs on the Jamuna River, India. K. THOMASSON: Francis Drouet; Revision of the Classification of the Oscillatoriaceae. J. LUNDQVIST: N. Kuhn; Natürliche Waldgesellschaften und Waldstandorte der Umgebung von Zürich. J. LUNDQVIST: K.-F. Schreiber; Les conditions thermiques du Canton de Vaud et leur graduation. G. ERDTMAN: K. Fægri and L. van der Pijl; The Principles of Pollination Ecology. G. ERDTMAN: J. Hutchinson; The Genera of Flowering Plants. Dicotyledones. Vol. II. I. NORDIN: Leif Ryvarden; Flora over kjuker. A. L. STORK: Modern Methods in Plant Taxonomy. Edited by V. H. Heywood. C. Jeffrey; An Introduction to Plant Taxonomy. E. VON KRUSENSTJERNA: Ádám Boros; Bryogeographie und Bryoflora Ungarns. E. VON KRUSENSTJERNA: Kåre Arnstein Lye; Moseflora. H. PERSSON: E. V. Watson; British Mosses and Liverworts. 2. uppl.

  • 310. Ahlner, Sten
    Svensk Botanisk Tidskrift: Volym 63: Häfte 4, 19691969Collection (editor) (Other academic)
    Abstract [sv]

    INNEHÅLLSFÖRTECKNING. R. A. MAAS GEESTERANUS and J.A. NANNFELDT: The Genus Sarcodon in Sweden in the Light of Recent Investigations. M. BIZOT: Mousses des Iles du Cap Vert. A. v. HOFSTEN: The Ultrastructure of Mycorrhiza I. Ectotrophic and Ectendotrophic Mycorrhiza of Pinus silvestris. L. TIBELL: The Genus Cyphelium in Northern Europe. J. PRAGLOWSKI: Pollen Types in Species of Haloragis. K. HJORTSTAM: Studies in the Swedish Species of the Genus Tomentella (Thelephoraceae). I. SMÄRRE UPPSATSER OCH MEDDELANDEN: G. DEGELIUS: Nytt fynd av Sonchus palustris L. på Västkusten. E. JULIN: Rubus arcticus funnen i Södermanland. RECENSIONER: J. A. NANNFELDT: Armen Takhtajan; Flowering Plants. Origin and Dispersal. M. RYBERG: Les multiples fonctions d’un jardin botanique. M. RYBERG: Winnifred Pennington; The History of British Vegetation. B. WALLES: F. A. L. Clowes and B. E. Juniper; Plant Cells. B. WALLES: C. Bresch; Klassische und molekulare Genetik. B. WALLES: W. Neilson-Jones; Plant Chimaeras. Second edition. B. WALLES: Ernst Nilsson; Ärftlighetslärans urkunder. Mendelismens födelse och pånyttfödelse. B. WALLES: Arne Hagberg and Erik Åkerberg; Mutations and Polyploidy in Plant Breeding. A. L. STORK: Frans A. Stafleu; Taxonomie Literature. A Selective Guide to Botanical Publications with Dates, Commentaries and Types. H.-G. WALLENTINUS: A. Öye; Handbok i mikroskopi. Mikroskopet, mikrofotografering, preparatframställning. S. AHLNER: Kai Curry-Lindahl; Sarek, Stora Sjöfallet, Padjelanta - Three National Parks in Swedish Lapland. S. AHLNER: Kai Curry-Lindahl; Fjäll och savann. Natur och naturvård världen runt. S. AHLNER: Bertil Gullander; Linné i Lappland. En antologi. S. AHLNER: Poul Holm Joensen och Claus Bering; Hösten, en årstidsbok. C.-F. LUNDEWALL: Greta Berggren; Atlas of Seeds and Small Fruits of Northwest-European Plant Species with Morphological Descriptions. Part 2. Cyperaceae. DIVERSE: Notiser. Svensk Botanisk Tidskrift: Titelblad, innehållsförteckning och artförteckning till Bd 63.

  • 311.
    Ahlner, Sten
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Philosophy, Mathematics and Science Section.
    Utbredningstyper bland nordiska barrträdslavar1948Doctoral thesis, monograph (Other academic)
  • 312.
    Ahlrot, Ulrica
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Welfare in zoo kept felids: A study of resource usage2016Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Due to a large number of felid species being endangered they are subjects of conservation projects both in situ and ex situ. Keeping felids in zoos are problematic with stereotypic behaviours such as pacing and reproduction difficulties often occurring. The aim of this study was to review research and zoo husbandry knowledge about which resources are most important for the welfare of zoo kept felids, and in addition perform behavioural observations in seven felid species in four Swedish zoos to try to find an order of priority of resources. Observations were performed during opening hours in 36 sessions per species and zoo. The results showed that studies of felid resource usage are missing. Zoo husbandry practice is probably based mainly on traditions and anecdotal knowledge. The observations showed that except for minor differences felids behave similarly regardless of species but the use of resources varies. Small felid species seems to be hiding rather than pacing as a way of coping. Elevated resources and areas as well as numerous hiding places are important to felids but many factors might affect the choice of resting places. Therefore it is important to provide the felids with multiple choices. It is also important to evaluate both species and individuals when designing enclosures and providing resources. More multi-institutional studies with large number of individuals of all zoo kept felid species are needed to gather knowledge about felids needs and preferences of resources.

  • 313. Ahlstrand, Tuuli
    et al.
    Torittu, Annamari
    Elovaara, Heli
    Välimaa, Hannamari
    Pöllänen, Marja T.
    Kasvandik, Sergo
    Högbom, Martin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Ihalin, Riikka
    Interactions between the Aggregatibacter actinomycetemcomitans secretin HofQ and host cytokines indicate a link between natural competence and interleukin-8 uptake2018In: Virulence, ISSN 2150-5594, E-ISSN 2150-5608, Vol. 9, no 1, p. 1205-1223Article in journal (Refereed)
    Abstract [en]

    Naturally competent bacteria acquire DNA from their surroundings to survive in nutrient-poor environments and incorporate DNA into their genomes as new genes for improved survival. The secretin HofQ from the oral pathogen Aggregatibacter actinomycetemcomitans has been associated with DNA uptake. Cytokine sequestering is a potential virulence mechanism in various bacteria and may modulate both host defense and bacterial physiology. The objective of this study was to elucidate a possible connection between natural competence and cytokine uptake in A. actinomycetemcomitans. The extramembranous domain of HofQ (emHofQ) was shown to interact with various cytokines, of which IL-8 exhibited the strongest interaction. The dissociation constant between emHofQ and IL-8 was 43nM in static settings and 2.4M in dynamic settings. The moderate binding affinity is consistent with the hypothesis that emHofQ recognizes cytokines before transporting them into the cells. The interaction site was identified via crosslinking and mutational analysis. By structural comparison, relateda type I KH domain with a similar interaction site was detected in the Neisseria meningitidis secretin PilQ, which has been shown to participate in IL-8 uptake. Deletion of hofQ from the A. actinomycetemcomitans genome decreased the overall biofilm formation of this organism, abolished the response to cytokines, i.e., decreased eDNA levels in the presence of cytokines, and increased the susceptibility of the biofilm to tested -lactams. Moreover, we showed that recombinant IL-8 interacted with DNA. These results can be used in further studies on the specific role of cytokine uptake in bacterial virulence without interfering with natural-competence-related DNA uptake.

  • 314. Ahlstrand, Tuuli
    et al.
    Tuominen, Heidi
    Beklen, Arzu
    Torittu, Annamari
    Oscarsson, Jan
    Umeå University, Faculty of Medicine, Department of Odontology.
    Sormunen, Raija
    Pöllänen, Marja T.
    Permi, Perttu
    Ihalin, Riikka
    A novel intrinsically disordered outer membrane lipoprotein of Aggregatibacter actinomycetemcomitans binds various cytokines and plays a role in biofilm response to interleukin-1β and interleukin-82017In: Virulence, ISSN 2150-5594, E-ISSN 2150-5608, Vol. 8, no 2, p. 115-134Article in journal (Refereed)
    Abstract [en]

    Intrinsically disordered proteins (IDPs) do not have a well-defined and stable 3-dimensional fold. Some IDPs can function as either transient or permanent binders of other proteins and may interact with an array of ligands by adopting different conformations. A novel outer membrane lipoprotein, bacterial interleukin receptor I (BilRI) of the opportunistic oral pathogen Aggregatibacter actinomycetemcomitans binds a key gatekeeper proinflammatory cytokine interleukin (IL)-1β. Because the amino acid sequence of the novel lipoprotein resembles that of fibrinogen binder A of Haemophilus ducreyi, BilRI could have the potential to bind other proteins, such as host matrix proteins. However, from the tested host matrix proteins, BilRI interacted with neither collagen nor fibrinogen. Instead, the recombinant non-lipidated BilRI, which was intrinsically disordered, bound various pro/anti-inflammatory cytokines, such as IL-8, tumor necrosis factor (TNF)-α, interferon (IFN)-γ and IL-10. Moreover, BilRI played a role in the in vitro sensing of IL-1β and IL-8 because low concentrations of cytokines did not decrease the amount of extracellular DNA in the matrix of bilRI− mutant biofilm as they did in the matrix of wild-type biofilm when the biofilms were exposed to recombinant cytokines for 22 hours. BilRI played a role in the internalization of IL-1β in the gingival model system but did not affect either IL-8 or IL-6 uptake. However, bilRI deletion did not entirely prevent IL-1β internalization, and the binding of cytokines to BilRI was relatively weak. Thus, BilRI might sequester cytokines on the surface of A. actinomycetemcomitans to facilitate the internalization process in low local cytokine concentrations.

  • 315.
    Ahlstrom, Christina A.
    et al.
    US Geol Survey, Alaska Sci Ctr, Anchorage, AK 99508 USA.
    Bonnedahl, Jonas
    Linkoping Univ, Dept Clin & Expt Med, SE-58183 Linkoping, Sweden;Kalmar Cty Hosp, Dept Infect Dis, SE-39185 Kalmar, Sweden.
    Woksepp, Hanna
    Kalmar Cty Hosp, Dept Clin Microbiol, SE-39185 Kalmar, Sweden.
    Hernandez, Jorge
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Ramey, Andrew M.
    US Geol Survey, Alaska Sci Ctr, Anchorage, AK 99508 USA.
    Acquisition and dissemination of cephalosporin-resistant E.coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 7361Article in journal (Refereed)
    Abstract [en]

    Antimicrobial resistance (AMR) in bacterial pathogens threatens global health, though the spread of AMR bacteria and AMR genes between humans, animals, and the environment is still largely unknown. Here, we investigated the role of wild birds in the epidemiology of AMR Escherichia coli. Using next-generation sequencing, we characterized cephalosporin-resistant E. coli cultured from sympatric gulls and bald eagles inhabiting a landfill habitat in Alaska to identify genetic determinants conferring AMR, explore potential transmission pathways of AMR bacteria and genes at this site, and investigate how their genetic diversity compares to isolates reported in other taxa. We found genetically diverse E. coli isolates with sequence types previously associated with human infections and resistance genes of clinical importance, including blaCTX-M and blaCMY. Identical resistance profiles were observed in genetically unrelated E. coli isolates from both gulls and bald eagles. Conversely, isolates with indistinguishable core-genomes were found to have different resistance profiles. Our findings support complex epidemiological interactions including bacterial strain sharing between gulls and bald eagles and horizontal gene transfer among E. coli harboured by birds. Results suggest that landfills may serve as a source for AMR acquisition and/or maintenance, including bacterial sequence types and AMR genes relevant to human health.

  • 316.
    Ahlström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Testing the specificity of the pBAD arabinose reporter2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The project highlights Salmonella enterica subspecies enterica serovar Typhimurium (S. Tm)'s ability to metabolize simple sugars released from dead commensal bacteria, by using the pBAD (araBAD promoter) system as a reporter of L-arabinose availability. Using bioinformatics and homology of conserved L-arabinose transporter genes shared in Escherichia coli K12 (E. coli) and S. Tm, we aimed to create a S. Tm mutant strain unable to obtain L-arabinose from it environment. During the projects course of time it was discovered that L-arabinose transporters are not a shared gene trait between E. coli and S. Tm, and that putative L-arabinose transporter orthologues may exists in the S. Tm genome.

  • 317.
    Ahlsén, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry.
    Structure-activity and resistance studies of HIV-1 protease inhibitors2000Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The present investigation was undertaken in order to identify inhibitors of HIV-1 protease that would be efficient in vivo and against HIV-1 protease carrying mutations known to confer resistance to inhibitors in clinical use. A second interest was to understand details of inhibitory mechanisms and to gain understanding of the molecular details of resistance.

    Linear inhibitors of transition-state type showed to have a resistance pattern similar to protease inhibitors in clinical use, whereas cyclic inhibitors of sulfonamide were somewhat different in their inhibitory profiles. It was found that mutation L90M in some situations could lessen the decrease in overall efficiency suffered by the enzyme when aquiring other mutations. Also presented are results from the characterization of double mutation I84V/L90M, formerly not investigated. Testing of triple and quadruple mutant confirmed the additive features of some mutations. In an attempt to find new leads for inhibitor development, extracts from bee propolis, a natural product, was investigated, and it was found that one extract inhibited wild-type enzyme with an I50-value of 0.2 μg/mL. Even more interesting is the result that propolis extract also inhibited all the investigated mutant enzymes.

  • 318.
    Ahlsén, Hanna
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    The Effects of Abiotic Stress on Alternative Splicing in Non-specific Lipid Transfer Proteins in Marchantia polymorpha2018Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    Due to global warming, our planet will experience more extreme weather conditions. Plants can protect themselves against these abiotic stress conditions with their stress response, which includes alternative splicing of certain genes. Alternative splicing is a post-transcriptional process where a single gene gives rise to different mRNAs, which in turn produces different proteins. In plants, this is usually done by intron retention. One type of protein that may be involved in this stress response are the non-specific lipid transfer proteins (LTPs). Indeed, evidence of intron retention has been found in the LTP genes in the liverwort Marchantia polymorpha, called MpLTPd. To investigate whether this alternative splicing is caused by abiotic stress or not, I subjected the moss to two different types of stress trials, drought and cold, and compared the general expression of the intron in MpLTPd2 and MpLTPd3 from the stressed samples to samples from a moss grown under normal conditions. I found that the expression of the intron did change in the stressed moss, but none of the differences were significant. This suggests that alterative splicing in MpLTPd2 and MpLTPd3 is not caused by cold and drought and that the intron-containing protein plays no role in the protection of M. polymorpha against abiotic stress.

  • 319. Ahltorp, Magnus
    et al.
    Skeppstedt, Maria
    Kitajima, Shiho
    Henriksson, Aron
    Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
    Rzepka, Rafal
    Araki, Kenji
    Expansion of medical vocabularies using distributional semantics on Japanese patient blogs2016In: Journal of Biomedical Semantics, ISSN 2041-1480, E-ISSN 2041-1480, Vol. 7, article id 58Article in journal (Refereed)
    Abstract [en]

    Background: Research on medical vocabulary expansion from large corpora has primarily been conducted using text written in English or similar languages, due to a limited availability of large biomedical corpora in most languages. Medical vocabularies are, however, essential also for text mining from corpora written in other languages than English and belonging to a variety of medical genres. The aim of this study was therefore to evaluate medical vocabulary expansion using a corpus very different from those previously used, in terms of grammar and orthographics, as well as in terms of text genre. This was carried out by applying a method based on distributional semantics to the task of extracting medical vocabulary terms from a large corpus of Japanese patient blogs. Methods: Distributional properties of terms were modelled with random indexing, followed by agglomerative hierarchical clustering of 3x100 seed terms from existing vocabularies, belonging to three semantic categories: Medical Finding, Pharmaceutical Drug and Body Part. By automatically extracting unknown terms close to the centroids of the created clusters, candidates for new terms to include in the vocabulary were suggested. The method was evaluated for its ability to retrieve the remaining n terms in existing medical vocabularies. Results: Removing case particles and using a context window size of 1 + 1 was a successful strategy for Medical Finding and Pharmaceutical Drug, while retaining case particles and using a window size of 8 + 8 was better for Body Part. For a 10n long candidate list, the use of different cluster sizes affected the result for Pharmaceutical Drug, while the effect was only marginal for the other two categories. For a list of top n candidates for Body Part, however, clusters with a size of up to two terms were slightly more useful than larger clusters. For Pharmaceutical Drug, the best settings resulted in a recall of 25 % for a candidate list of top n terms and a recall of 68 % for top 10n. For a candidate list of top 10n candidates, the second best results were obtained for Medical Finding: a recall of 58 %, compared to 46 % for Body Part. Only taking the top n candidates into account, however, resulted in a recall of 23 % for Body Part, compared to 16 % for Medical Finding. Conclusions: Different settings for corpus pre-processing, window sizes and cluster sizes were suitable for different semantic categories and for different lengths of candidate lists, showing the need to adapt parameters, not only to the language and text genre used, but also to the semantic category for which the vocabulary is to be expanded. The results show, however, that the investigated choices for pre-processing and parameter settings were successful, and that a Japanese blog corpus, which in many ways differs from those used in previous studies, can be a useful resource for medical vocabulary expansion.

  • 320.
    Ahlén, Ingemar
    et al.
    SLU.
    Angelstam, Per
    SLU.
    Bensch, Staffan
    Lunds universitet.
    Elmberg, Johan
    Kristianstad University, School of Education and Environment, Avdelningen för Naturvetenskap.
    Enemar, Anders
    Göteborgs universitet.
    Fagerström,, Torbjörn
    SLU.
    Green, Martin
    Lunds universitet.
    Gustafsson, Lars
    Uppsala universitet.
    Gustafsson, Lena
    SLU.
    Mikael, Hake
    SLU.
    Dennis, Hasselquist,
    Lunds universitet.
    Hedenström, Anders
    Lunds universitet.
    H-Lindgren, Christina
    Umeå universitet.
    Lindberg, Peter
    Göteborgs universitet.
    Lindström, Åke
    Lunds universitet.
    Michanek, Gabriel
    Luleå tekniska universitet.
    Nilsson, Leif
    Lunds universitet.
    Nilsson, Sven G
    Lunds universitet.
    Pärt, Tomas
    SLU.
    Sundberg, Jan
    Uppsala universitet.
    Svensson, Sören
    Lunds universitet.
    Tjernberg, Martin
    SLU.
    Ulfstrand, Staffan
    Uppsala universitet.
    Brusewitz, Gunnar
    Stockholms universitet.
    Edman, Stefan
    Chalmers tekniska högskola.
    Jonsson, Lars
    Uppsala universitet.
    Landell, Nils-Erik
    Wahlstedt, Jens
    Emanuelsson, Urban
    Centrum för biologisk mångfald.
    Ingelög, Torleif
    Artdatabanken.
    Karlsson, Mikael
    Svenska naturskyddsföreningen.
    Kristoferson, Lars
    WWF.
    Lindell, Lars
    Sveriges Ornitologiska Förening.
    Nya järnvägen hotar unikt naturområde2002In: Aftonbladet, ISSN 1103-9000Article in journal (Other (popular science, discussion, etc.))
  • 321.
    Ahmad, Abrar
    Örebro University, School of Science and Technology.
    Kras and Braf mutation analysis in colon cancer by pyrosequencing2012Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • 322.
    Ahmad, Fareed
    et al.
    Hannover Medical Sch, Germany.
    Shankar, Esaki M.
    University of Malaya, Malaysia; University of Malaya, Malaysia; School Basic Appl Science, India.
    Yong, Yean K.
    University of Malaya, Malaysia.
    Tan, Hong Y.
    University of Malaya, Malaysia.
    Ahrenstorf, Gerrit
    Hannover Medical Sch, Germany.
    Jacobs, Roland
    Hannover Medical Sch, Germany.
    Larsson, Marie
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Schmidt, Reinhold E.
    Hannover Medical Sch, Germany.
    Kamarulzaman, Adeeba
    University of Malaya, Malaysia; University of Malaya, Malaysia.
    Ansari, Abdul W.
    University of Malaya, Malaysia; University of Malaya, Malaysia.
    Negative Checkpoint Regulatory Molecule 2B4 (CD244) Upregulation Is Associated with Invariant Natural Killer T Cell Alterations and Human Immunodeficiency Virus Disease Progression2017In: Frontiers in Immunology, ISSN 1664-3224, E-ISSN 1664-3224, Vol. 8, article id 338Article in journal (Refereed)
    Abstract [en]

    The CD1d-restricted invariant natural killer T (iNKT) cells are implicated in innate immune responses against human immunodeficiency virus (HIV). However, the determinants of cellular dysfunction across the iNKT cells subsets are seldom defined in HIV disease. Herein, we provide evidence for the involvement of the negative checkpoint regulator (NCR) 2B4 in iNKT cell alteration in a well-defined cohort of HIV-seropositive anti-retroviral therapy (ART) naive, ART-treated, and elite controllers (ECs). We report on exaggerated 2B4 expression on iNKT cells of HIV-infected treatment-naive individuals. In sharp contrast to CD4-iNKT cells, 2B4 expression was significantly higher on CD4+ iNKT cell subset. Notably, an increased level of 2B4 on iNKT cells was strongly correlated with parameters associated with HIV disease progression. Further, iNKT cells from ARTnaive individuals were defective in their ability to produce intracellular IFN-gamma Together, our results suggest that the levels of 2B4 expression and the downstream co-inhibitory signaling events may contribute to impaired iNKT cell responses.

  • 323.
    Ahmad, Irfan
    et al.
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
    Rouf, Syed Fazle
    Sun, Lei
    Cimdins, Annika
    Shafeeq, Sulman
    Le Guyon, Soazig
    Schottkowski, Marco
    Rhen, Mikael
    Romling, Ute
    BcsZ inhibits biofilm phenotypes and promotes virulence by blocking cellulose production in Salmonella enterica serovar Typhimurium2016In: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 15, article id 177Article in journal (Refereed)
    Abstract [en]

    Background: Cellulose, a 1,4 beta-glucan polysaccharide, is produced by a variety of organisms including bacteria. Although the production of cellulose has a high biological, ecological and economical impact, regulatory mechanisms of cellulose biosynthesis are mostly unknown. Family eight cellulases are regularly associated with cellulose biosynthesis operons in bacteria; however, their function is poorly characterized. In this study, we analysed the role of the cellulase BcsZ encoded by the bcsABZC cellulose biosynthesis operon of Salmonella enterica serovar Typhimurium (S. Typhimurium) in biofilm related behavior. We also investigated the involvement of BcsZ in pathogenesis of S. Typhimurium including a murine typhoid fever infection model. Result: In S. Typhimurium, cellulase BcsZ with a putative periplasmic location negatively regulates cellulose biosynthesis. Moreover, as assessed with a non-polar mutant, BcsZ affects cellulose-associated phenotypes such as the rdar biofilm morphotype, cell clumping, biofilm formation, pellicle formation and flagella-dependent motility. Strikingly, although upregulation of cellulose biosynthesis was not observed on agar plate medium at 37 degrees C, BcsZ is required for efficient pathogen-host interaction. Key virulence phenotypes of S. Typhimurium such as invasion of epithelial cells and proliferation in macrophages were positively regulated by BcsZ. Further on, a bcsZ mutant was outcompeted by the wild type in organ colonization in the murine typhoid fever infection model. Selected phenotypes were relieved upon deletion of the cellulose synthase BcsA and/or the central biofilm activator CsgD. Conclusion: Although the protein scaffold has an additional physiological role, our findings indicate that the catalytic activity of BcsZ effectively downregulates CsgD activated cellulose biosynthesis. Repression of cellulose production by BcsZ subsequently enables Salmonella to efficiently colonize the host.

  • 324. Ahmad, S.
    et al.
    Zhao, W.
    Renström, F.
    Rasheed, A.
    Zaidi, M.
    Samuel, M.
    Shah, N.
    Mallick, N. H.
    Shungin, Dmitry
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Medicine. Umeå University, Faculty of Medicine, Department of Odontology.
    Zaman, K. S.
    Ishaq, M.
    Rasheed, S. Z.
    Memon, F-ur-R
    Hanif, B.
    Lakhani, M. S.
    Ahmed, F.
    Kazmi, S. U.
    Deloukas, P.
    Frossard, P.
    Franks, P. W.
    Saleheen, D.
    A novel interaction between theFLJ33534locus and smokingin obesity: a genome-wide study of 14 131 Pakistani adults2016In: International Journal of Obesity, ISSN 0307-0565, E-ISSN 1476-5497, Vol. 40, no 1, p. 186-190Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Obesity is a complex disease caused by the interplay of genetic and lifestyle factors, but identification of gene-lifestyle interactions in obesity has remained challenging. Few large-scale studies have reported use of genome-wide approaches to investigate gene-lifestyle interactions in obesity. METHODS: In the Pakistan Risk of Myocardial Infraction Study, a cross-sectional study based in Pakistan, we calculated body mass index (BMI) variance estimates (square of the residual of inverse-normal transformed BMI z-score) in 14 131 participants and conducted genome-wide heterogeneity of variance analyses (GWHVA) for this outcome. All analyses were adjusted for age, age(2), sex and genetic ancestry. RESULTS: The GWHVA analyses identified an intronic variant, rs140133294, in the FLJ33544 gene in association with BMI variance (P-value = 3.1 x 10(-8)). In explicit tests of gene x lifestyle interaction, smoking was found to significantly modify the effect of rs140133294 on BMI (Pinteraction = 0.0005), whereby the minor allele (T) was associated with lower BMI in current smokers, while positively associated with BMI in never smokers. Analyses of ENCODE data at the FLJ33534 locus revealed features indicative of open chromatin and high confidence DNA-binding motifs for several transcription factors, providing suggestive biological support for a mechanism of interaction. CONCLUSIONS: In summary, we have identified a novel interaction between smoking and variation at the FLJ33534 locus in relation to BMI in people from Pakistan.

  • 325.
    Ahmad, Shabbir
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Hysteretic Behavior, Regioselectivity, and Role of Salt Bridging Residues at the Domain Interface of Potato Epoxide Hydrolase StEH1, Site-Directed Mutagenesis and Kinetic Study2009Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • 326. Ahmad, Shabbir
    et al.
    Thulasingam, Madhuranayaki
    Palombo, Isolde
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Daley, Daniel O.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Johnson, Kenneth A.
    Morgenstern, Ralf
    Haeggström, Jesper Z.
    Rinaldo-Matthis, Agnes
    Trimeric microsomal glutathione transferase 2 displays one third of the sites reactivity2015In: Biochimica et Biophysica Acta - Proteins and Proteomics, ISSN 1570-9639, E-ISSN 1878-1454, Vol. 1854, no 10, p. 1365-1371Article in journal (Refereed)
    Abstract [en]

    Human microsomal glutathione transferase 2 (MGST2) is a trimeric integral membrane protein that belongs to the membrane-associated proteins in eicosanoid and glutathione metabolism (MAPEG) family. The mammalian MAPEG family consists of six members where four have been structurally determined. MGST2 activates glutathione to form a thiolate that is crucial for GSH peroxidase activity and GSH conjugation reactions with electrophilic substrates, such as 1-chloro-2,4-dinitrobenzene (CDNB). Several studies have shown that MGST2 is able to catalyze a GSH conjugation reaction with the epoxide LTA(4) forming the pro-inflammatory LTC4. Unlike its closest homologue leukotriene C-4 synthase (LTC4S), MGST2 appears to activate its substrate GSH using only one of the three potential active sites [Ahmad S, et al. (2013) Biochemistry. 52, 1755-1764]. In order to demonstrate and detail the mechanism of one-third of the sites reactivity of MGST2, we have determined the enzyme oligomeric state, by Blue native PAGE and Differential Scanning Calorimetry, as well as the stoichiometty of substrate and substrate analog inhibitor binding to MGST2, using equilibrium dialysis and Isothermal Titration Calorimetry, respectively. Global simulations were used to fit kinetic data to determine the catalytic mechanism of MGST2 with GSH and CDNB (1-chloro-2,4-dinitrobenzene) as substrates. The best fit was observed with 1/3 of the sites catalysis as compared with a simulation where all three sites were active. In contrast to LTC4S, MGST2 displays a 1/3 the sites reactivity, a mechanism shared with the more distant family member MGST1 and recently suggested also for microsomal prostaglandin E synthase-1.

  • 327. Ahmadi-Afzadi, Masoud
    et al.
    Orsel, Mathilde
    Pelletier, Sandra
    Bruneau, Maryline
    Proux-Wéra, Estelle
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). Swedish University of Agricultural Sciences, Sweden.
    Nybom, Hilde
    Renou, Jean-Pierre
    Genome-wide expression analysis suggests a role for jasmonates in the resistance to blue mold in apple2018In: Plant growth regulation (Print), ISSN 0167-6903, E-ISSN 1573-5087, Vol. 85, no 3, p. 375-387Article in journal (Refereed)
    Abstract [en]

    Blue mold, caused by the necrotrophic fungal pathogen Penicillium expansum, causes serious postharvest losses in apple, and threatens human health through production of the potent mycotoxin patulin. Recent studies indicate a quantitative control of resistance against this disease in apple cultivars. A whole genome apple microarray covering 60k transcripts was used to identify gene(s) that appear to be differentially regulated between resistant and susceptible cultivars in P. expansum-infected fruits. A number of potential candidates was encountered among defense- and oxidative stress-related genes, cell wall modification and lignification genes, and genes related to localization and transport. Induction of one cell wall-related gene and three genes involved in the 'down-stream' flavonoid biosynthesis pathway, demonstrates the fundamental role of the cell wall as an important barrier, and suggests that fruit flavonoids are involved in the resistance to blue mold. Moreover, exogenous application of the plant hormone methyl jasmonate (MeJA) reduced the symptoms resulting from inoculating apples with P. expansum. This is the first report linking MeJA and activation of cell wall and flavonoid pathway genes to resistance against blue mold in a study comparing different cultivars of domesticated apple. Our results provide an initial categorization of genes that are potentially involved in the resistance mechanism, and should be useful for developing tools for gene marker-assisted breeding of apple cultivars with an improved resistance to blue mold.

  • 328. Ahmadian, Afshin
    et al.
    Pettersson, Erik
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology.
    Method for amplification2005Patent (Other (popular science, discussion, etc.))
    Abstract [en]

    The invention refers to a method for multiplex amplification of at least one specific nucleic acid locus, comprising the steps of: providing at least one oligonucleotide probe pair that is designed so that the first and second probe of the pair anneal to a specific nucleic acid locus on a target molecule, in which pair the first probe has an extendable 3'-end, and a second probe has a 5'-end that is directly or indirectly labelled with a phosphate group; providing a target molecule comprising at least one specific nucleic acid locus; allowing the probe pair to anneal to the target molecule; allowing the 3'-end of the first probe to extend by influence of polymerase by adding a set of three different dNTPs; ligating the 3'-end of the extended first probe to the 5'-end of the second probe. Hereby, a method is provided which allows a high specificity for simultaneous amplification of several loci. Further, the invention involves a kit for use in the method of the invention.

  • 329.
    Ahmadova, Nigar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Mamedov, Fikret
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Formation of tyrosine radicals in photosystem II under far-red illumination2018In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 136, no 1, p. 93-106Article in journal (Refereed)
    Abstract [en]

    Photosystem II (PS II) contains two redox-active tyrosine residues on the donor side at symmetrical positions to the primary donor, P680. TyrZ, part of the water-oxidizing complex, is a preferential fast electron donor while TyrD is a slow auxiliary donor to P680 +. We used PS II membranes from spinach which were depleted of the water oxidation complex (Mn-depleted PS II) to study electron donation from both tyrosines by time-resolved EPR spectroscopy under visible and far-red continuous light and laser flash illumination. Our results show that under both illumination regimes, oxidation of TyrD occurs via equilibrium with TyrZ at pH 4.7 and 6.3. At pH 8.5 direct TyrD oxidation by P680 + occurs in the majority of the PS II centers. Under continuous far-red light illumination these reactions were less effective but still possible. Different photochemical steps were considered to explain the far-red light-induced electron donation from tyrosines and localization of the primary electron hole (P680 +) on the ChlD1 in Mn-depleted PS II after the far-red light-induced charge separation at room temperature is suggested.

  • 330. Ahmed, Aisha S
    et al.
    Li, Jian
    Erlandsson-Harris, Helena
    Stark, André
    Bakalkin, Georgy
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Mahmood, Ahmed
    Suppression of pain and joint destruction by inhibition of the proteasome system in experimental osteoarthritis2012In: Pain, ISSN 0304-3959, E-ISSN 1872-6623, Vol. 153, no 1, p. 18-26Article in journal (Refereed)
    Abstract [en]

    Osteoarthritis is a degenerative joint disease with pain and loss of joint function as major pathological features. Recent studies show that proteasome inhibitors reduce pain in various pathological conditions. We evaluated the effects of MG132, a reversible proteasome inhibitor on pain and joint destruction in a rat model of osteoarthritis. Osteoarthritis was induced by intraarticular injection of monosodium iodoacetate into the rat knee. Knee joint stiffness was scored and nociception was evaluated by mechanical pressure applied to the respective hind paw. Knee joint destruction was assessed by radiological and histological analyses. Expression of matrix metalloproteinase-3 (MMP-3) was analyzed by quantitative reverse transcription polymerase chain reaction in the knee articular cartilage. Expression of substance P (SP) and calcitonin gene-related peptide (CGRP) was studied in the dorsal root ganglia (L4–L6) by quantitative reverse transcription polymerase chain reaction and in the knee joints by immunohistochemistry. Our results indicate that daily treatment of osteoarthritic rats with MG132 significantly increases their mobility while the swelling, pain thresholds, and pathological features of the affected joints were reduced. Furthermore, the upregulated expression of MMP-3, SP, and CGRP in the arthritic rats was normalized by MG132 administration. We conclude that the proteasome inhibitor MG132 reduces pain and joint destruction, probably by involving the peripheral nervous system, and that changes in SP and CGRP expression correlate with alterations in behavioural responses. Our findings suggest that nontoxic proteasome inhibitors may represent a novel pharmacotherapy for osteoarthritis.

  • 331.
    Ahmed, Engy
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holmström, Sara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Soil Microorganisms and Mineral Weathering: Mechanics of Biotite Dissolution2012Conference paper (Other academic)
    Abstract [en]

    Soil microorganisms play an important role in the environment by contributing to leach and release of essential elements from soil minerals that are required not only for their own nutrition but also for plants growth. This study aims to compare between the mechanisms of different fungal and bacterial species isolated from podzol soil in biotite dissolution. Microplate devices with 6 wells were used for the biological weathering experiments. All of the sterilized microplate wells were filled with 4g/l of biotite followed by 12 ml of an iron free diluted mineral liquid medium. In these conditions, biotite particles are the only source of the essential elements for the microorganisms. To characterize the mechanisms of biotite dissolution, we monitored siderophores production, microbial biomass, pH, exchangeable cations concentration and SEM analysis for mineral surface. There was a significant difference between the behavior of the fungal and bacterial species in dissolution of biotite. This difference may be due to the variation of these microorganisms in their mechanics of interaction with mineral surface. It was observed also that these microorganisms directly and indirectly induce biotite dissolution. Defining soil as a system driven by biological mechanisms rather than chemical processes has major implications for our understanding of how the system functions and how it will respond to changing conditions.

  • 332.
    Ahmed, Engy
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holmström, Sara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    THE MICROBE-MINERAL INTERACTIONS IN THE ACIDIC PODZOL SOIL2013In: Mineralogical magazine, ISSN 0026-461X, E-ISSN 1471-8022, Vol. 77, no 5, p. 564-Article in journal (Other (popular science, discussion, etc.))
    Abstract [en]

    Iron is a key component of the chemical architecture of the biosphere. Due to the low bioavailability of iron in the environment, microorganisms have developed specific uptake strategies, like siderophores, which are operationally defined as low-molecular-mass biogenic Fe(III)-binding compounds, that can increase iron’s bioavailability by promoting the dissolution of iron-bearing minerals. In the present study, we aimed to investigate the composition of hydroxamate siderophores in the soil horizons of the acidic podzol, and study how they are affected by the presence of specific mineral types and microbial communities.

     Three different minerals (apatite, biotite and oligioclase) were inserted in the soil horizons (O (organic), E (eluvial), B (upper illuvial), and C (mineral)). After two years, soil samples were collected from both the bulk soil (next to the minerals) and from the soil attached to the mineral surfaces. The concentration of ten different fungal tri-hydroxamates and five bacterial ones were determined by high-performance liquid chromatography coupled to electrospray ionization mass spectrometry (HPLC-ESI-MS). In addition, total microbial composition and diversity were studied.

    Our field experiment succeeded in describing the relationship between the presence of siderophores, soil horizon and mineral type, in addition to understanding the interaction between mineral type and soil microbial composition. A wide range of fungal and bacterial hydroxamates were detected throughout the soil profile. On the other hand, the presence of the minerals completely altered the diversity of siderophores. In addition, each mineral had a unique interaction with hydroxamates in the different soil horizons. There were also a good relationship between the microbial diversity and the siderophore distribution. 

  • 333.
    Ahmed, Engy
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holmström, Sara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    The Roles and Applications of Siderophores in Natural Environments2013Conference paper (Other academic)
    Abstract [en]

    Siderophores are organic compounds with low molecular mass that are produced by microorganisms growing under conditions of low iron. The primary function of these compounds is to chelate ferric iron from different terrestrial and aquatic habitats and thereby make it available for microbial cells.

    Siderophores have received much attention in recent years because of their potential roles and applications in various areas of environmental research. For instance, the production of siderophores can provide a quick identification of microbes to the species level that called “siderotyping”. On the other hand, siderophores could also function as biocontrol, biosensor, and bioremediation agents, in addition to their important role in mineral weathering and enhancing plant growth. In the present study, we aimed to investigate the composition of trihydroxamate siderophores in soil samples from different horizons (O (organic), E (eluvial), B (upper illuvial), and C (parent material)) of a podzol soil in Sweden, and study how they are affected by the presence of specific mineral types (apatite, biotite and oligioclase) that were inserted in the soil for two years in a field experiment.

    Our field experiment succeeded in describing the relationship between the presence of siderophores, soil horizons and mineral types. A wide range of fungal and bacterial hydroxamates were detected throughout the soil profile. On the other hand, the presence of the minerals completely altered the diversity of siderophores. In addition, each mineral had a unique interaction with hydroxamates in the different soil horizons. Our next step is to gain greater insight into the siderotyping to illustrate the relationship between the siderophore types that was found throughout the soil profile and on the different mineral surfaces and the microbial diversity by using metagenomic applications.

  • 334.
    Ahmed, Engy
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holmström, Sara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Brüchert, Volker
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Holm, Nils G.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    The Role of Microorganisms in the diversity and distribution of siderophores in Podzolic Forest Soil2013In: Mineralogical magazine, ISSN 0026-461X, E-ISSN 1471-8022, Vol. 77, no 2, p. 161--208(48)Article in journal (Other academic)
    Abstract [en]

    Iron is a key component of the chemical architecture of the biosphere. Due to the low bioavailability of iron in the environment, microorganisms have developed specific uptake strategies. The most important one is the production of siderophores, which are operationally defined as low-molecular-mass biogenic Fe (III)-binding compounds which may greatly increase bioavailability of Fe [1]. One of the primary biogeochemical functions of siderophores is therefore to increase Fe bioavailability by promoting the dissolution of iron-bearing minerals [2]. This study aims to understand the role of microorganisms in the chemical diversity and distribution of siderophores in podzol soil and how this diversity can contribute to the bioavailability of Fe in forest soil.Soil samples were collected from an experimental site in the area of Bispgården in central Sweden (63°07′N, 16°70′E) from the O (organic), E (eluvial), B1 (upper illuvial), and C (mineral) horizons. Concentration and chemical composition of dissolved and adsorbed siderophores in the soil samples were determined using colorimetric assays and high-performance liquid chromatography.The highest siderophore concentrations were found in the O layer and thereafter decreased by depth. Concentrations of dissolved hydroxamate, catecholate and carboxylate siderophores were up to 84, 17 and 0.2 nmol/ g soil, respectively. In contrast, concentrations of adsorbed hydroxamates, catecholates and carboxylates were only up to 1.8, 3 and 0.2 nmol/ g soil, respectively.Siderophore-producing microorganisms were isolated from the same soil samples. Viable fungi, bacteria and actinomycete counts ranged from 7 to 300, from 300 to 1800, and from 0 to 5 cfu/gm, respectively. The highest counts were found in the O and E layers. Only the E layer contained the three types of siderophore-producing microorganisms investigated in this study. Siderophores were extracted from culture filtrates of the isolated microorganisms when grown under iron-limited conditions. These extracts varied considerably in siderophore composition. Fungal isolates produced up to 183 μM of hydroxamates, especially those isolated from the O layer, whereas bacteria and actinomycete isolated from the O and E layers of the soil produced high amounts of carboxylate, catecholate and hydroxamate siderophores. Actinomycete produced up to 93 μM of hydroxamates and 47 μM of catecholates, while bacteria produced up to 34 μM of carboxylates and up to 14 μM of catecholates.The depth variability in concentration and chemical composition and the good correlation between abundance of siderophore-producing microorganisms and siderophore soil concentrations strongly suggest that these siderophore-producing microorganisms play an important role in the mobilization of iron in the podzol soil that may be important in iron availability to plants in forest environment.

    [1] Clay et al. (1981) Biochemistry 20, 2432-2436. [2] Duckworth et al. (2009) ChemGeol 260, 149-158.

  • 335.
    Ahmed Osman, Omneya
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Beier, Sara
    Leibniz Inst Balt Sea Res, Warnemunde, Germany..
    Grabherr, Manfred
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Interactions of Freshwater Cyanobacteria with Bacterial Antagonists2017In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 83, no 7, article id UNSP e02634Article in journal (Refereed)
    Abstract [en]

    Cyanobacterial and algal mass development, or blooms, have severe effects on freshwater and marine systems around the world. Many of these phototrophs produce a variety of potent toxins, contribute to oxygen depletion, and affect water quality in several ways. Coexisting antagonists, such as cyanolytic bacteria, hold the potential to suppress, or even terminate, such blooms, yet the nature of this interaction is not well studied. We isolated 31 cyanolytic bacteria affiliated with the genera Pseudomonas, Stenotrophomonas, Acinetobacter, and Delftia from three eutrophic freshwater lakes in Sweden and selected four phylogenetically diverse bacterial strains with strong-to-moderate lytic activity. To characterize their functional responses to the presence of cyanobacteria, we performed RNA sequencing (RNA-Seq) experiments on coculture incubations, with an initial predator-prey ratio of 1: 1. Genes involved in central cellular pathways, stress-related heat or cold shock proteins, and antitoxin genes were highly expressed in both heterotrophs and cyanobacteria. Heterotrophs in coculture expressed genes involved in cell motility, signal transduction, and putative lytic activity. L, D-Transpeptidase was the only significantly upregulated lytic gene in Stenotrophomonas rhizophila EK20. Heterotrophs also shifted their central metabolism from the tricarboxylic acid cycle to the glyoxylate shunt. Concurrently, cyanobacteria clearly show contrasting antagonistic interactions with the four tested heterotrophic strains, which is also reflected in the physical attachment to their cells. In conclusion, antagonistic interactions with cyanobacteria were initiated within 24 h, and expression profiles suggest varied responses for the different cyanobacteria and studied cyanolytes. IMPORTANCE Here, we present how gene expression profiles can be used to reveal interactions between bloom-forming freshwater cyanobacteria and antagonistic heterotrophic bacteria. Species-specific responses in both heterotrophs and cyanobacteria were identified. The study contributes to a better understanding of the interspecies cellular interactions underpinning the persistence and collapse of cyanobacterial blooms.

  • 336. Ahmed, Saheeb
    et al.
    Wittenmayer, Nina
    Kremer, Thomas
    Hoeber, Jan
    Kiran Akula, Asha
    Urlaub, Henning
    Islinger, Markus
    Kirsch, Joachim
    Dean, Camin
    Dresbach, Thomas
    Mover is a homomeric phospho-protein present on synaptic vesicles2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 5, p. e63474-Article in journal (Refereed)
    Abstract [en]

    With remarkably few exceptions, the molecules mediating synaptic vesicle exocytosis at active zones are structurally and functionally conserved between vertebrates and invertebrates. Mover was found in a yeast-2-hybrid assay using the vertebrate-specific active zone scaffolding protein bassoon as a bait. Peptides of Mover have been reported in proteomics screens for self-interacting proteins, phosphorylated proteins, and synaptic vesicle proteins, respectively. Here, we tested the predictions arising from these screens. Using flotation assays, carbonate stripping of peripheral membrane proteins, mass spectrometry, immunogold labelling of purified synaptic vesicles, and immuno-organelle isolation, we found that Mover is indeed a peripheral synaptic vesicle membrane protein. In addition, by generating an antibody against phosphorylated Mover and Western blot analysis of fractionated rat brain, we found that Mover is a bona fide phospho-protein. The localization of Mover to synaptic vesicles is phosphorylation dependent; treatment with a phosphatase caused Mover to dissociate from synaptic vesicles. A yeast-2-hybrid screen, co-immunoprecipitation and cell-based optical assays of homomerization revealed that Mover undergoes homophilic interaction, and regions within both the N- and C- terminus of the protein are required for this interaction. Deleting a region required for homomeric interaction abolished presynaptic targeting of recombinant Mover in cultured neurons. Together, these data prove that Mover is associated with synaptic vesicles, and implicate phosphorylation and multimerization in targeting of Mover to synaptic vesicles and presynaptic sites.

  • 337. Ahmed, S.E.
    et al.
    Lees, A.C.
    Moura, N.G.
    Gardner, Toby A.
    Stockholm University, Stockholm Environment Institute.
    Road networks predict human influence on Amazonian bird communities2014In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, no 1795Article in journal (Refereed)
    Abstract [en]

    Road building can lead to significant deleterious impacts on biodiversity, varying from direct road-kill mortality and direct habitat loss associated with road construction, to more subtle indirect impacts from edge effects and fragmentation. However, little work has been done to evaluate the specific effects of road networks and biodiversity loss beyond the more generalized effects of habitat loss. Here, we compared forest bird species richness and composition in the municipalities of Santarém and Belterra in Pará state, eastern Brazilian Amazon, with a road network metric called ‘roadless volume (RV)’ at the scale of small hydrological catchments (averaging 3721 ha). We found a significant positive relationship between RV and both forest bird richness and the average number of unique species (species represented by a single record) recorded at each site. Forest bird community composition was also significantly affected by RV. Moreover, there was no significant correlation between RV and forest cover, suggesting that road networks may impact biodiversity independently of changes in forest cover. However, variance partitioning analysis indicated that RV has partially independent and therefore additive effects, suggesting that RV and forest cover are best used in a complementary manner to investigate changes in biodiversity. Road impacts on avian species richness and composition independent of habitat loss may result from road-dependent habitat disturbance and fragmentation effects that are not captured by total percentage habitat cover, such as selective logging, fire, hunting, traffic disturbance, edge effects and road-induced fragmentation

  • 338. Ahn, Ji Hoon
    et al.
    Schmid, Markus
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Editorial overview: Growth and development: Change is in the air: how plants modulate development in response to the environment2017In: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 35, p. IV-VIArticle in journal (Refereed)
  • 339. Ahn, Young O.
    et al.
    Lee, Hyun Ju
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Kaluka, Daniel
    Yeh, Syun-Ru
    Rousseau, Denis L.
    Ädelroth, Pia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Gennis, Robert B.
    The two transmembrane helices of CcoP are sufficient for assembly of the cbb(3)-type heme-copper oxygen reductase from Vibrio cholerae2015In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1847, no 10, p. 1231-1239Article in journal (Refereed)
    Abstract [en]

    The C-family (cbb(3)) of heme-copper oxygen reductases are proton-pumping enzymes terminating the aerobic respiratory chains of many bacteria, including a number of human pathogens. The most common form of these enzymes contains one copy each of 4 subunits encoded by the ccoNOQP operon. In the cbb3 from Rhodobacter capsulatus, the enzyme is assembled in a stepwise manner, with an essential role played by an assembly protein CcoH. Importantly, it has been proposed that a transient interaction between the transmembrane domains of CcoP and CcoH is essential for assembly. Here, we test this proposal by showing that a genetically engineered form of cbb(3) from Vibrio cholerae (CcoNOQP(X)) that lacks the hydrophilic domain of CcoP, where the two heme c moieties are present, is fully assembled and stable. Single-turnover kinetics of the reaction between the fully reduced CcoNOQP(X) and O-2 are essentially the same as the wild type enzyme in oxidizing the 4 remaining redox-active sites. The enzyme retains approximately 10% of the steady state oxidase activity using the artificial electron donor TMPD, but has no activity using the physiological electron donor cytochrome c(4), since the docking site for this cytochrome is presumably located on the absent domain of CcoP. Residue E49 in the hydrophobic domain of CcoP is the entrance of the K-C-channel for proton input, and the E49A mutation in the truncated enzyme further reduces the steady state activity to less than 3%. Hence, the same proton channel is used by both the wild type and truncated enzymes.

  • 340. Ahn, Young O.
    et al.
    Mahinthichaichan, Paween
    Lee, Hyun Ju
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Ouyang, Hanlin
    Kaluka, Daniel
    Yeh, Syun-Ru
    Arjona, Davinia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Rousseau, Denis L.
    Tajkhorshid, Emad
    Ädelroth, Pia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Gennis, Robert B.
    Conformational coupling between the active site and residues within the K-C-channel of the Vibrio cholerae cbb(3)-type (C-family) oxygen reductase2014In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 42, p. E4419-E4428Article in journal (Refereed)
    Abstract [en]

    The respiratory chains of nearly all aerobic organisms are terminated by proton-pumping heme-copper oxygen reductases (HCOs). Previous studies have established that C-family HCOs contain a single channel for uptake from the bacterial cytoplasm of all chemical and pumped protons, and that the entrance of the K-C-channel is a conserved glutamate in subunit III. However, the majority of the K-C-channel is within subunit I, and the pathway from this conserved glutamate to subunit I is not evident. In the present study, molecular dynamics simulations were used to characterize a chain of water molecules leading from the cytoplasmic solution, passing the conserved glutamate in subunit III and extending into subunit I. Formation of the water chain, which controls the delivery of protons to the K-C-channel, was found to depend on the conformation of Y241(Vc), located in subunit I at the interface with subunit III. Mutations of Y241(Vc) (to A/F/H/S) in the Vibrio cholerae cbb(3) eliminate catalytic activity, but also cause perturbations that propagate over a 28-angstrom distance to the active site heme b(3). The data suggest a linkage between residues lining the KC-channel and the active site of the enzyme, possibly mediated by transmembrane helix alpha 7, which contains both Y241(Vc) and the active site crosslinked Y255(Vc), as well as two Cu-B histidine ligands. Other mutations of residues within or near helix alpha 7 also perturb the active site, indicating that this helix is involved in modulation of the active site of the enzyme.

  • 341.
    Ahnesjo, Ingrid
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology.
    Kvarnemo, C
    Merilaita, S
    Using potential reproductive rates to predict mating competition among individuals qualified to mate2001In: BEHAVIORAL ECOLOGY, ISSN 1045-2249, Vol. 12, no 4, p. 397-401Article in journal (Refereed)
    Abstract [en]

    The potential reproductive rate (PRR), which is the offspring production per unit time each sex would achieve if unconstrained by mate availability, often differs between the sexes. An increasing sexual difference in PRR predicts an intensified mating com

  • 342.
    Ahnesjö, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Behavioural temperature preference in a brooding male pipefish Syngnathus typhle2008In: Journal of Fish Biology, ISSN 0022-1112, E-ISSN 1095-8649, Vol. 73, no 4, p. 1039-1045Article in journal (Refereed)
    Abstract [en]

    In the broad-nosed pipefish Syngnathus typhle, brooding males positioned themselves significantly more often towards the warmer part (18 degrees C) of an aquarium. whereas females were indifferent in this respect. This behavioural temperature preference may increase male brooding rate and indirectly influence patterns of mating competition. (c) 2008 The Author Journal compilation (c) 2008 The Fisheries Society of the British Isles.

  • 343.
    Ahnesjö, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Seahorses and Their Relatives2010In: Journal of Fish Biology, ISSN 0022-1112, E-ISSN 1095-8649, Vol. 77, no 1, p. 308-309Article, book review (Other academic)
  • 344.
    Ahnoff, Martin
    et al.
    Univ Gothenburg, Dept Chem Mol Biol, SE-41296 Gothenburg, Sweden.;Denator AB, Gothenburg, Sweden..
    Cazares, Lisa H.
    US Army Med Res Inst Infect Dis, Mol & Translat Sci, Frederick, MD 21702 USA.;US Army Med Res & Mat Command, DoD Biotechnol High Performance Comp Software App, Telemed & Adv Technol Res Ctr, Ft Detrick, MD 21702 USA..
    Sköld, Karl
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cancer Pharmacology and Computational Medicine. Denator AB, Gothenburg, Sweden.;Uppsala Univ, Dept Med Sci Canc Pharmacol & Computat Med, Uppsala, Sweden..
    Thermal inactivation of enzymes and pathogens in biosamples for MS analysis2015In: Bioanalysis, ISSN 1757-6180, E-ISSN 1757-6199, Vol. 7, no 15, p. 1885-1899Article, review/survey (Refereed)
    Abstract [en]

    Protein denaturation is the common basis for enzyme inactivation and inactivation of pathogens, necessary for preservation and safe handling of biosamples for downstream analysis. While heat-stabilization technology has been used in proteomic and peptidomic research since its introduction in 2009, the advantages of using the technique for simultaneous pathogen inactivation have only recently been addressed. The time required for enzyme inactivation by heat (approximate to 1 min) is short compared with chemical treatments, and inactivation is irreversible in contrast to freezing. Heat stabilization thus facilitates mass spectrometric studies of biomolecules with a fast conversion rate, and expands the chemical space of potential biomarkers to include more short-lived entities, such as phosphorylated proteins, in tissue samples as well as whole-blood (dried blood sample) samples.

  • 345. Ahnström, G.
    et al.
    Nygren, Jonas
    Södertörn University, Avdelning Naturvetenskap. Karlinska Instiutet.
    Eriksson, S.
    The effect of dimethyl sulphoxide on the induction and repair of double-strand breaks in human cells after irradiation with γ-rays and accelerated ions: Rapid or slow repair may depend on accessibility of breaks in chromatin of different compactness2000In: International Journal of Radiation Biology, ISSN 0955-3002, E-ISSN 1362-3095, Vol. 76, no 4, p. 533-538Article in journal (Refereed)
    Abstract [en]

    Purpose: The repair of double-strand breaks (dsb) in mammalian cells is characterized by a rapid phase with a half-life of less than half an hour and a slower phase that lasts for many hours. The proportion of slow repair increase with LET and it has been suggested that the slow repair component consists of more complex damage and is more deleterious to the cells. To see if removal of OH radicals could remove part of the damage in complex dsb and make them easier to repair, human cells were irradiated in the presence of dimethyl sulphoxide (DMSO). Methods: Induction and repair of dsb were studied by neutral elution in human VH10 cells exposed to γ-rays, helium ions (mean LET 40 keV/μm) and 80 and 125 keV/μm monoenergetic nitrogen ions in the presence and absence of 2 M DMSO. Results: Incubation of cells exposed to γ-rays, 40 keV/μm helium and 80 keV/μm N ions demonstrated that scavenging of OH radicals by DMSO removed most of the rapid repair component. The response to DMSO was less marked after 125 keV/μm nitrogen ions, where about half of the repair was resistant to DMSO. Conclusions: It is unlikely that the complexity of dsb is responsible for the slow repair because the removal of OH radicals did not make the breaks easier to repair. Instead, it is suggested that rapid and slow repair can be explained on the basis of how different parts of the chromatin are accessible to repair enzymes.

  • 346. Aho, Teija
    et al.
    Liljestrand Rönn, Johanna
    Uppsala universitet.
    Piironen, Jorma
    Björklund, Mats
    Impacts of effective population size on genetic diversity and relatedness in hatchery reared Brown trout (Salmo trutta L.)2006In: Aquaculture, ISSN 0044-8486, E-ISSN 1873-5622, Vol. 253, no 1-4, p. 244-248Article in journal (Refereed)
    Abstract [en]

    Many populations of brown trout are managed by hatchery breeding and supportive release. Using a limited number of individuals as founders creates a bottleneck, which can lead to loss of genetic diversity in a population. In this study 17 populations of hatchery-reared brown trout were examined genetically using microsatellite markers. Genetic variation measured as gene diversity and allelic richness were analysed and the effects of effective population size of founders and time since founding on these parameters were explored. Allelic richness and gene diversity decreased with increasing time since founding of the stock, and there was a negative relationship between current effective population size and time since founding. Allelic richness was positively correlated with effective population size at founding. The results indicate that considerations concerning effective population size in hatcheries must be taken seriously to promote high levels of genetic variation among individuals and minimise loss of genetic diversity.

  • 347. Aho, Vilma
    et al.
    Ollila, Hanna M.
    Rantanen, Ville
    Kronholm, Erkki
    Surakka, Ida
    van Leeuwen, Wessel M. A.
    Stockholm University, Faculty of Social Sciences, Stress Research Institute. University of Helsinki, Finland; Finnish Institute of Occupational Health, Finland.
    Lehto, Maili
    Matikainen, Sampsa
    Ripatti, Samuli
    Härmä, Mikko
    Sallinen, Mikael
    Salomaa, Veikko
    Jauhiainen, Matti
    Alenius, Harri
    Paunio, Tiina
    Porkka-Heiskanen, Tarja
    Partial Sleep Restriction Activates Immune Response-Related Gene Expression Pathways: Experimental and Epidemiological Studies in Humans2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 10, article id e77184Article in journal (Refereed)
    Abstract [en]

    Epidemiological studies have shown that short or insufficient sleep is associated with increased risk for metabolic diseases and mortality. To elucidate mechanisms behind this connection, we aimed to identify genes and pathways affected by experimentally induced, partial sleep restriction and to verify their connection to insufficient sleep at population level. The experimental design simulated sleep restriction during a working week: sleep of healthy men (N = 9) was restricted to 4 h/night for five nights. The control subjects (N = 4) spent 8 h/night in bed. Leukocyte RNA expression was analyzed at baseline, after sleep restriction, and after recovery using whole genome microarrays complemented with pathway and transcription factor analysis. Expression levels of the ten most up-regulated and ten most down-regulated transcripts were correlated with subjective assessment of insufficient sleep in a population cohort (N = 472). Experimental sleep restriction altered the expression of 117 genes. Eight of the 25 most up-regulated transcripts were related to immune function. Accordingly, fifteen of the 25 most up-regulated Gene Ontology pathways were also related to immune function, including those for B cell activation, interleukin 8 production, and NF-kappa B signaling (P<0.005). Of the ten most up-regulated genes, expression of STX16 correlated negatively with self-reported insufficient sleep in a population sample, while three other genes showed tendency for positive correlation. Of the ten most down-regulated genes, TBX21 and LGR6 correlated negatively and TGFBR3 positively with insufficient sleep. Partial sleep restriction affects the regulation of signaling pathways related to the immune system. Some of these changes appear to be long-lasting and may at least partly explain how prolonged sleep restriction can contribute to inflammation-associated pathological states, such as cardiometabolic diseases.

  • 348. Ahola, Virpi
    et al.
    Lehtonen, Rainer
    Somervuo, Panu
    Salmela, Leena
    Koskinen, Patrik
    Rastas, Pasi
    Valimaki, Niko
    Paulin, Lars
    Kvist, Jouni
    Wahlberg, Niklas
    Tanskanen, Jaakko
    Hornett, Emily A.
    Ferguson, Laura C.
    Luo, Shiqi
    Cao, Zijuan
    de Jong, Maaike A.
    Duplouy, Anne
    Smolander, Olli-Pekka
    Vogel, Heiko
    McCoy, Rajiv C.
    Qian, Kui
    Chong, Wong Swee
    Zhang, Qin
    Ahmad, Freed
    Haukka, Jani K.
    Joshi, Aruj
    Salojarvi, Jarkko
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Grosse-Wilde, Ewald
    Hughes, Daniel
    Katainen, Riku
    Pitkanen, Esa
    Ylinen, Johannes
    Waterhouse, Robert M.
    Turunen, Mikko
    Vaharautio, Anna
    Ojanen, Sami P.
    Schulman, Alan H.
    Taipale, Minna
    Lawson, Daniel
    Ukkonen, Esko
    Makinen, Veli
    Goldsmith, Marian R.
    Holm, Liisa
    Auvinen, Petri
    Frilander, Mikko J.
    Hanski, Ilkka
    The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 4737-Article in journal (Refereed)
    Abstract [en]

    Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n = 31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n = 31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.

  • 349.
    Ahrenstedt, Lage
    KTH, School of Biotechnology (BIO).
    Surface modification of cellulose materials: from wood pulps to artificial blood vessels2007Licentiate thesis, comprehensive summary (Other scientific)
    Abstract [en]

    This thesis describes the improvement of two radically different cellulose materials, paper and artificial blood vessels, constructed from two diverse cellulose sources, wood pulp and Acetobacter xylinum. The improvement of both materials was possible due to the natural affinity of the hemicellulose xyloglucan for cellulose.

    Chemical and mechanical pulps were treated with xyloglucan in the wet-end prior to hand sheet formation or by spray application of dry hand sheets, loading a comparable amount of xyloglucan. The tensile strength increases for the wet-end treatment and spray application were 28% and 71% respectively for bleached soft wood, compared to untreated sheets (20.7 Nm/g). The corresponding strength increases for hand sheets made of thermo-mechanical pulp were 6% and 13% respectively compared to untreated sheets (42.4 Nm/g). The tendency for chemical pulp to be superior to mechanical pulp with respect to strength increase was valid even for tear strength and Scott-Bond. These results suggest, in agreement with other studies, that adhesion of xyloglucan to wood fibres is dependent on their degree of surface lignification.

    Also, a method was developed to increase the blood compatibility of artificial blood vessels constructed of bacterial cellulose. Xyloglucan was covalently linked to the endothelial cell adhesion motif (Arg-Gly-Asp). To obtain this, new solid-phase coupling chemistry was developed. Xyloglucan oligosaccharides (XGO) were transformed into XGO-succinamic acid via the corresponding XGO--NH2 derivative prior to coupling with the N-terminus of the solid-phase synthesised Gly-Arg-Gly-Asp-Ser peptide. The resin-bound glyco-peptide was then cleaved and enzymatically re-incorporated into high molecular weight xyloglucan. The glyco-peptide was further adsorbed onto bacterial cellulose scaffolds, increasing the adhesion and proliferation of endothelial cells and therefore blood compatibility.

  • 350. Ahrentorp, Fredrik
    et al.
    Blomgren, Jakob
    Jonasson, Christian
    Sarwe, Anna
    Sepehri, Sobhan
    Eriksson, Emil
    Kalaboukhov, Alexei
    Jesorka, Aldo
    Winkler, Dag
    Schneiderman, Justin F.
    Nilsson, Mats
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Albert, Jan
    Gómez de la Torre, Teresa Zardán
    Strømme, Maria
    Johansson, Christer
    Sensitive magnetic biodetection using magnetic multi-core nanoparticles and RCA coils2017In: Journal of Magnetism and Magnetic Materials, ISSN 0304-8853, E-ISSN 1873-4766, Vol. 427, p. 14-18Article in journal (Refereed)
    Abstract [en]

    We use functionalized iron oxide magnetic multi-core particles of 100 nm in size (hydrodynamic particle diameter) and AC susceptometry (ACS) methods to measure the binding reactions between the magnetic nanoparticles (MNPs) and bio-analyte products produced from DNA segments using the rolling circle amplification (RCA) method. We use sensitive induction detection techniques in order to measure the ACS response. The DNA is amplified via RCA to generate RCA coils with a specific size that is dependent on the amplification time. After about 75 min of amplification we obtain an average RCA coil diameter of about 1 mu m. We determine a theoretical limit of detection (LOD) in the range of 11 attomole (corresponding to an analyte concentration of 55 fM for a sample volume of 200 mu L) from the ACS dynamic response after the MNPs have bound to the RCA coils and the measured ACS readout noise. We also discuss further possible improvements of the LOD.

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