Change search
Refine search result
1234567 151 - 200 of 34646
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 151. Agalou, Adamantia
    et al.
    Purwantomo, Sigit
    Övernäs, Elin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Johannesson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Zhu, Xiaoyi
    Estiati, Amy
    de Kam, Rolf J.
    Engström, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Slamet-Loedin, Inez H.
    Zhu, Zhen
    Wang, Mei
    Xiong, Lizhong
    Meijer, Annemarie H.
    Ouwerkerk, Pieter B. F.
    A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members2008In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 66, no 1-2, p. 87-103Article in journal (Refereed)
    Abstract [en]

    The homeodomain leucine zipper (HD-Zip) genes encode transcription factors that have diverse functions in plant development and have often been implicated in stress adaptation. The HD-Zip genes are the most abundant group of homeobox (HB) genes in plants and do not occur in other eukaryotes. This paper describes the complete annotation of the HD-Zip families I, II and III from rice and compares these gene families with Arabidopsis in a phylogeny reconstruction. Orthologous pairs of rice and Arabidopsis HD-Zip genes were predicted based on neighbour joining and maximum parsimony (MP) trees with support of conserved intron-exon organization. Additionally, a number of HD-Zip genes appeared to be unique to rice. Searching of EST and cDNA databases and expression analysis using RT-PCR showed that 30 out of 31 predicted rice HD-Zip genes are expressed. Most HD-Zip genes were broadly expressed in mature plants and seedlings, but others showed more organ specific patterns. Like in Arabidopsis and other dicots, a subset of the rice HD-Zip I and II genes was found to be regulated by drought stress. We identified both drought-induced and drought-repressed HD-Zip genes and demonstrate that these genes are differentially regulated in drought-sensitive versus drought-tolerant rice cultivars. The drought-repressed HD-Zip family I gene, Oshox4, was selected for promoter-GUS analysis, showing that drought-responsiveness of Oshox4 is controlled by the promoter and that Oshox4 expression is predominantly vascular-specific. Loss-of-function analysis of Oshox4 revealed no specific phenotype, but overexpression analysis suggested a role for Oshox4 in elongation and maturation processes.

  • 152.
    Agarwal, Prasoon
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Hematology and Immunology.
    Regulation of Gene Expression in Multiple Myeloma Cells and Normal Fibroblasts: Integrative Bioinformatic and Experimental Approaches2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The work presented in this thesis applies integrative genomic and experimental approaches to investigate mechanisms involved in regulation of gene expression in the context of disease and normal cell biology.

    In papers I and II, we have explored the role of epigenetic regulation of gene expression in multiple myeloma (MM). By using a bioinformatic approach we identified the Polycomb repressive complex 2 (PRC2) to be a common denominator for the underexpressed gene signature in MM. By using inhibitors of the PRC2 we showed an activation of the genes silenced by H3K27me3 and a reduction in the tumor load and increased overall survival in the in vivo 5TMM model. Using ChIP-sequencing we defined the distribution of H3K27me3 and H3K4me3 marks in MM patients cells. In an integrated bioinformatic approach, the H3K27me3-associated genes significantly correlated to under-expression in patients with less favorable survival. Thus, our data indicates the presence of a common under-expressed gene profile and provides a rationale for implementing new therapies focusing on epigenetic alterations in MM.

    In paper III we address the existence of a small cell population in MM presenting with differential tumorigenic properties in the 5T33MM murine model. We report that the predominant population of CD138+ cells had higher engraftment potential, higher clonogenic growth, whereas the CD138- MM cells presented with less mature phenotype and higher drug resistance. Our findings suggest that while designing treatment regimes for MM, both the cellpopulations must be targeted.

    In paper IV we have studied the general mechanism of differential gene expression regulation by CGGBP1 in response to growth signals in normal human fibroblasts. We found that CGGBP1 binding affects global gene expression by RNA Polymerase II. This is mediated by Alu RNAdependentinhibition of RNA Polymerase II. In presence of growth signals CGGBP1 is retained in the nuclei and exhibits enhanced Alu binding thus inhibiting RNA Polymerase III binding on Alus. Hence we suggest a mechanism by which CGGBP1 orchestrates Alu RNA-mediated regulation of RNA Polymerase II. This thesis provides new insights for using integrative bioinformatic approaches to decipher gene expression regulation mechanisms in MM and in normal cells.

  • 153.
    Agarwal, Prasoon
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Hematology and Immunology.
    Enroth, Stefan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Genomics.
    Teichmann, Martin
    Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux 2, rue , Robert Escarpit, 33607 Pessac, France..
    Jernberg Wiklund, Helena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Hematology and Immunology.
    Smit, Arian
    Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109-5234, USA.
    Westermark, Bengt
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Cancer and Vascular Biology.
    Singh, Umashankar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Cancer and Vascular Biology.
    Growth signals employ CGGBP1 to suppress transcription of Alu-SINEs2016In: Cell Cycle, ISSN 1538-4101, E-ISSN 1551-4005, Vol. 15, no 12, p. 1558-1571Article in journal (Refereed)
    Abstract [en]

    CGGBP1 (CGG triplet repeat-binding protein 1) regulates cell proliferation, stress response,cytokinesis, telomeric integrity and transcription. It could affect these processes by modulatingtarget gene expression under different conditions. Identification of CGGBP1-target genes andtheir regulation could reveal how a transcription regulator affects such diverse cellular processes.Here we describe the mechanisms of differential gene expression regulation by CGGBP1 inquiescent or growing cells. By studying global gene expression patterns and genome-wide DNAbindingpatterns of CGGBP1, we show that a possible mechanism through which it affects theexpression of RNA Pol II-transcribed genes in trans depends on Alu RNA. We also show that itregulates Alu transcription in cis by binding to Alu promoter. Our results also indicate thatpotential phosphorylation of CGGBP1 upon growth stimulation facilitates its nuclear retention,Alu-binding and dislodging of RNA Pol III therefrom. These findings provide insights into howAlu transcription is regulated in response to growth signals.

  • 154.
    Agaton, Charlotta
    et al.
    KTH, Superseded Departments, Biotechnology.
    Uhlén, Mathias
    KTH, Superseded Departments, Biotechnology.
    Hober, Sophia
    KTH, Superseded Departments, Biotechnology.
    Genome-based proteomics2004In: Electrophoresis, ISSN 0173-0835, E-ISSN 1522-2683, Vol. 25, no 9, p. 1280-1288Article in journal (Refereed)
    Abstract [en]

    Protein-protein interactions play crucial roles in various biological pathways and functions. Therefore, the characterization of protein levels and also the network of interactions within an organism would contribute considerably to the understanding of life. The availability of the human genome sequence has created a range of new possibilities for biomedical research. A crucial challenge is to utilize the genetic information for better understanding of protein distribution and function in normal as well as in pathological biological processes. In this review, we have focused on different platforms used for systematic genome-based proteome analyses. These technologies are in many ways complementary and should be seen as various ways to elucidate different functions of the proteome.

  • 155.
    Ageheim, Sofia
    et al.
    Executive, Länsstyrelser, Länsstyrelsen Gävleborg.
    Nordin, Hans
    Executive, Länsstyrelser, Länsstyrelsen Gävleborg.
    Sundin, Sara
    Executive, Länsstyrelser, Länsstyrelsen Gävleborg.
    Inventering av stora rovdjur i Gävleborgs län 2014-20152015Report (Other academic)
    Abstract [sv]

     

    Länsstyrelsen ansvarar för att årliga rovdjursinventeringar genomförs i Gävleborgs län. Syftet är att

    övervaka rovdjursstammarnas storlek, utbredning, genetiska status och hur stammarna utvecklas

    över tiden.

     

    I den här rapporten redovisas resultaten från inventeringar av lodjur, varg, järv och kungsörn, samt

    länsstyrelsens bedömning av förekomsten av björn i Gävleborg under inventeringssäsongen

    2014/2015.

     

    Vid lodjursinventeringen 2014/2015 kvalitetssäkrades 15 familjegrupper, det vill säga 15 honor som

    fött ungar 2014. Lodjursstammen i Gävleborg kan därmed uppskattas till cirka 83 individer vintern

    2014/2015. Fyra av familjegrupperna delades med angränsande län.

     

    Gävleborg berördes av tio vargrevir vintern 2014/2015: Prästskogen/Haverö, Naggen, Kukumäki,

    Sjösveden, Tandsjön, Lingbo, Åmot/Ockelbo, Bondskog, Björnås och Glamsen. I sju av reviren

    bekräftades att föryngring skett våren 2014. Sex av reviren delades med andra län. Det innebär att

    Gävleborg anses ha haft 4,7 familjegrupper vintern 2014/2015, enligt Viltskadecenters fördelning.

    Vargarna i Korsåreviret, som tidigare delades mellan Gävleborg och Dalarna, har denna säsong vistats

    väster om länsgränsen och har inte spårats i Gävleborg. Tandsjö-reviret försvann under

    inventeringssäsongen genom skyddsjakt i februari 2015.

     

    Ingen inventering av björn har genomförts denna säsong. Länsstyrelsen bedömer att björnstammens

    storlek och spridning i länet sannolikt överensstämmer med resultatet från 2012 års spillningsinventering. Björnstammen uppskattades då till cirka 380 individer i Gävleborgs län.

     

    En riktad järvinventering har för första gången på många år genomförts i Gävleborgs län vintern

    2014/2015. Med hjälp av fotostationer har bilder på järv erhållits på flera ställen i hela norra delen av

    Gävleborg och en föryngring 2014 har kvalitetssäkrats.

     

    Vid inventeringen av kungsörn i Gävleborg 2014 konstaterades totalt 25 revir, varav 8 hade lyckade

    häckningar och 3 av dessa var dubbelkullar, det vill säga kullar med två ungar. Storleken på länets

    fasta kungsörnspopulation 2014 uppskattas till 50-65 individer.

     

    Inventeringarna av lo, järv och varg utfördes av länsstyrelsens personal, medan kungsörn

    inventerades av Kungsörnsgruppen Gävleborg på uppdrag av länsstyrelsen. Allmänhetens

    rapportering av rovdjursobservationer har varit till stor hjälp i arbetet med att göra så bra

    inventeringar som möjligt utifrån de resurser som finns.

  • 156.
    Agerstrand, Marlene
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Philosophy and History of Technology, Philosophy.
    Kuester, A.
    Bachmann, J.
    Breitholtz, M.
    Ebert, I.
    Rechenberg, B.
    Ruden, Christina
    KTH, School of Architecture and the Built Environment (ABE), Philosophy and History of Technology, Philosophy.
    Reporting and evaluation criteria as means towards a transparent use of ecotoxicity data for environmental risk assessment of pharmaceuticals2011In: Environmental Pollution, ISSN 0269-7491, E-ISSN 1873-6424, Vol. 159, no 10, p. 2487-2492Article in journal (Refereed)
    Abstract [en]

    Ecotoxicity data with high reliability and relevance are needed to guarantee the scientific quality of environmental risk assessments of pharmaceuticals. The main advantages of a more structured approach to data evaluation include increased transparency and predictability of the risk assessment process, and the possibility to use non-standard data. In this collaboration, between the research project MistraPharma and the German Federal Environment Agency, a new set of reporting and evaluation criteria is presented and discussed. The new criteria are based on the approaches in the literature and the OECD reporting requirements, and have been further developed to include both reliability and relevance of test data. Intended users are risk assessors and researchers performing ecotoxicological experiments, but the criteria can also be used for education purposes and in the peer-review process for scientific papers. This approach intends to bridge the gap between the regulator and the scientist's needs and way of work.

  • 157.
    Agervald, Åsa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    Baebprasert, Wipawee
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    Zhang, Xiaohui
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    Incharoensakdi, Aran
    Lindblad, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    Stensjö, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    The CyAbrB transcription factor CalA regulates the iron superoxide dismutase in Nostoc sp. strain PCC 71202010In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 12, no 10, p. 2826-2837Article in journal (Refereed)
    Abstract [en]

    P>In the present investigation the results of induced over-production of the CyAbrB transcription factor CalA (Cyanobacterial AbrB-like, annotated as Alr0946) in the cyanobacterium Nostoc sp. PCC 7120 were analysed. The CalA overexpression strain showed a bleaching phenotype with lower growth rate and truncated filaments 2 days after induction of overexpression. The phenotype was even more pronounced when illumination was increased from 35 to 125 mu mol m-2 s-1. Using gel-based quantitative proteomics, the induced overexpression of CalA was shown to downregulate the abundance of FeSOD, one of two types of superoxide dismutases in Nostoc sp. PCC 7120. The change in protein abundance was also accompanied by lower transcript as well as activity levels. Purified recombinant CalA from Nostoc sp. PCC 7120 was shown to interact with the promoter region of alr2938, encoding FeSOD, indicating a transcriptional regulation of FeSOD by CalA. The bleaching phenotype is in line with a decreased tolerance against oxidative stress and indicates that CalA is involved in regulation of cellular responses in which FeSOD has an important and specific function in the filamentous cyanobacterium Nostoc sp. PCC 7120.

  • 158.
    Agervald, Åsa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    Zhang, Xiaohui
    Department of Biological Sciences, Purdue University.
    Stensjö, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    Devine, Ellenor
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    Lindblad, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Microbial Chemistry.
    CalA, a cyanobacterial AbrB protein, interacts with the upstream region of hypC and acts as a repressor of its transcription in the cyanobacterium Nostoc sp. strain PCC 71202010In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 76, no 3, p. 880-890Article in journal (Refereed)
    Abstract [en]

    The filamentous, heterocystous, nitrogen-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain, depending on growth condition, up to two hydrogenases directly involved in hydrogen metabolism. HypC is one out of at least seven auxiliary gene products required for synthesis of a functional hydrogenase, specifically involved in the maturation of the large subunit. In this study we present a protein, Alr0946, belonging to the transcription regulator family AbrB, which in protein-DNA assays was found to interact with the upstream region of hypC. Transcriptional investigations showed that alr0946 is co-transcribed with the downstream gene alr0947, which encodes a putative protease from the abortive infection superfamily, Abi. Alr0946 was shown to interact specifically not only with the upstream region of hypC but also with its own upstream region, acting as a repressor on both. The bidirectional hydrogenase activity was significant down-regulated when Alr0946 was over-expressed demonstrating a correlation to the transcription factor, either direct or indirect. In silico studies showed that homologues to both Alr0946 and Alr0947 are highly conserved proteins within cyanobacteria with a very similar physical organisation of the corresponding structural genes. Possible functions of the co-transcribed downstream protein Alr0947 are presented. In addition, we present a 3D model of the CyAbrB domain of Alr0946 and putative DNA-binding mechanisms are discussed.

  • 159.
    Aggemyr, Elsa
    et al.
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Auffret, Alistair G.
    Stockholm University, Faculty of Science, Department of Physical Geography. Swedish University of Agricultural Sciences, Sweden.
    Jädergård, Love
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Cousins, Sara A. O.
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Species richness and composition differ in response to landscape and biogeography2018In: Landscape Ecology, ISSN 0921-2973, E-ISSN 1572-9761, Vol. 33, no 12, p. 2273-2284Article in journal (Refereed)
    Abstract [en]

    Context Understanding how landscape patterns affect species diversity is of great importance in the fields of biogeography, landscape ecology and conservation planning, but despite the rapid advance in biodiversity analysis, investigations of spatial effects on biodiversity are still largely focused on species richness.

    Objectives We wanted to know if and how species richness and species composition are differentially driven by the spatial measures dominating studies in landscape ecology and biogeography. As both measures require the same limited presence/absence information, it is important to choose an appropriate diversity measure, as differing results could have important consequences for interpreting ecological processes.

    Methods We recorded plant occurrences on 112 islands in the Baltic archipelago. Species richness and composition were calculated for each island, and the explanatory power of island area and habitat heterogeneity, distance to mainland and structural connectivity at three different landscape sizes were examined.

    Results A total of 354 different plant species were recorded. The influence of landscape variables differed depending on which diversity measure was used. Island area and structural connectivity determined plant species richness, while species composition revealed a more complex pattern, being influenced by island area, habitat heterogeneity and structural connectivity.

    Conclusions Although both measures require the same basic input data, species composition can reveal more about the ecological processes affecting plant communities in fragmented landscapes than species richness alone. Therefore, we recommend that species community composition should be used as an additional standard measure of diversity for biogeography, landscape ecology and conservation planning.

  • 160. Agianian, Bogos
    et al.
    Lesch, Christine
    Loseva, Olga
    Dushay, Mitchell S.
    Södertörn University, School of Life Sciences. Uppsala University.
    Preliminary characterization of hemolymph coagulation in Anopheles gambiae larvae2007In: Developmental and Comparative Immunology, ISSN 0145-305X, E-ISSN 1879-0089, Vol. 31, no 9, p. 879-888Article in journal (Refereed)
    Abstract [en]

    Hemolymph coagulation is a first response to injury, impeding infection, and ending bleeding. Little is known about its molecular basis in insects, but clotting factors have been identified in the fruit fly Drosophila melanogaster. Here, we have begun to study coagulation in the aquatic larvae of the malaria vector mosquito Anopheles gambiae using methods developed for Drosophila. A delicate clot was seen by light microscopy, and pullout and proteomic analysis identified phenoloxidase and apolipophorin-I as major candidate clotting factors. Electron microscopic analysis confirmed clot formation and revealed it contains fine molecular sheets, most likely a result of lipophorin assembly. Phenoloxidase appears to be more critical in clot formation in Anopheles than in Drosophila. The Anopheles larval clot thus differs in formation, structure, and composition from the clot in Drosophila, confirming the need to study coagulation in different insect species to learn more about its evolution and adaptation to different lifestyles.

  • 161. Agianian, Bogos
    et al.
    Lesch, Christine
    Loseva, Olga
    Dushay, Mitchell S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Comparative Physiology.
    Preliminary characterization of hemolymph coagulation in Anopheles gambiae larvae2007In: Developmental and Comparative Immunology, ISSN 0145-305X, E-ISSN 1879-0089, Vol. 31, no 9, p. 879-888Article in journal (Refereed)
    Abstract [en]

    Hemolymph coagulation is a first response to injury, impeding infection, and ending bleeding. Little is known about its molecular basis in insects, but clotting factors have been identified in the fruit fly Drosophila melanogaster. Here, we have begun to study coagulation in the aquatic larvae of the malaria vector mosquito Anopheles gambiae using methods developed for Drosophila. A delicate clot was seen by light microscopy, and pullout and proteomic analysis identified phenoloxidase and apolipophorin-I as major candidate clotting factors. Electron microscopic analysis confirmed clot formation and revealed it contains fine molecular sheets, most likely a result of lipophorin assembly. Phenoloxidase appears to be more critical in clot formation in Anopheles than in Drosophila. The Anopheles larval clot thus differs in formation, structure, and composition from the clot in Drosophila, confirming the need to study coagulation in different insect species to learn more about its evolution and adaptation to different lifestyles.

  • 162.
    Agić, Heda
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    A new species of small acritarch with porous wall structure from the early Cambrian of Estonia, and implications for the fossil record of eukaryotic picoplankton2015In: Palynology, ISSN 0191-6122, E-ISSN 1558-9188, Vol. 40, no 3, p. 343-356Article in journal (Refereed)
    Abstract [en]

    The Proterozoic-Phanerozoic transition records a general trend of decrease in phytoplankton cell size, in contrast tothe earlier and much larger Ediacaran acritarchs. Particularly minute, unornamented but sculptured organic-walledmicrofossils have been recovered from the lower Cambrian Lükati Formation in northern Estonia. The lack of anysignificant thermal alteration in the formation allowed for excellent preservation of fine microstructures on thesemicrofossils. Among the rich palynomorph assemblage in Lükati, a new species of tiny, spheroidal eukaryoticmicrofossil is recorded: Reticella corrugata gen. et sp. nov. It is characterised by a corrugated and flexible vesicle wallthat is densely perforated by nano-scale pores. Despite its unique morphology, the new species shares diagnosticcharacters with fossil and extant prasinophyte algae. R. corrugata is among the smallest microfossils with typicaleukaryotic morphology (conspicuous wall sculpture) and contributes to the diversity of the size class of smallacritarchs. Size, abundance, inferred prasinophyte affinity and eukaryotic wall sculpture make this new taxon alikely member of the early eukaryotic picoplankton.

  • 163.
    Agić, Heda
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Moczydłowska, Małgorzata
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Canfield, Donald
    University of Southern Denmark .
    Reproductive cyst and operculum formation in the Cambrian-Ordovician galeate-plexus microfossils2016In: GFF, ISSN 1103-5897, E-ISSN 2000-0863, Vol. 138, no 2, p. 278-294Article in journal (Refereed)
    Abstract [en]

    Unicellular organic-walled microfossils from the Cambrian-Ordovician transition in Estonia (ca. 490-480 million years ago) exhibit rare characters reflecting their function as reproductive algal cysts. The studied assemblages record the evolutionary history of phytoplankton in the early Paleozoic Era: novel morphologies appearing through the Cambrian and subsequently diversifying in the Ordovician. Well preserved specimens were extracted following a standard palynological method and studied by light transmitted microscopy. The galeate plexus acritarchs Caldariola, Priscogalea and Stelliferidium have revealed exceptionally preserved morphological elements and a rare structure among both fossil and extant protists – an opening with operculum (lid) in reproductive cysts, in addition to lavish vesicle ornamentation and sculpture. Analogous morphology is observed in the living dasycladalean alga Acetabularia (Chlorophyta), which possesses an intrinsic lid-forming apparatus used during organism’s reproductive stage. Based on the observations on the fossil material and studies on the Acetabularia lid-formation, we propose a model of operculum formation in the galeate plexus microorganisms. Due to strong morphological and ecological similarities between galeate fossils and dasycladalean cysts, and the antiquity of this algal order, galeates may be positioned within green algae, more specifically Dasycladales. Unique morphology of the operculum-bearing microbiota would have required a high degree of intracellular complexity for its development, suggesting that advanced intracellular machinery was present already in the early Paleozoic phytoplankton. Additionally, minute prasinophyte microfossils Reticella corrugata  are reported for the first time in the Upper Cambrian strata. 

  • 164. Agler, Caryline
    et al.
    Nielsen, Dahlia M.
    Urkasemsin, Ganokon
    Singleton, Andrew
    Tonomura, Noriko
    Sigurdsson, Snaevar
    Tang, Ruqi
    Linder, Keith
    Arepalli, Sampath
    Hernandez, Dena
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    van de Leemput, Joyce
    Motsinger-Reif, Alison
    O'Brien, Dennis P.
    Bell, Jerold
    Harris, Tonya
    Steinberg, Steven
    Olby, Natasha J.
    Canine Hereditary Ataxia in Old English Sheepdogs and Gordon Setters Is Associated with a Defect in the Autophagy Gene Encoding RAB242014In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 10, no 2, p. e1003991-Article in journal (Refereed)
    Abstract [en]

    Old English Sheepdogs and Gordon Setters suffer from a juvenile onset, autosomal recessive form of canine hereditary ataxia primarily affecting the Purkinje neuron of the cerebellar cortex. The clinical and histological characteristics are analogous to hereditary ataxias in humans. Linkage and genome-wide association studies on a cohort of related Old English Sheepdogs identified a region on CFA4 strongly associated with the disease phenotype. Targeted sequence capture and next generation sequencing of the region identified an A to C single nucleotide polymorphism (SNP) located at position 113 in exon 1 of an autophagy gene, RAB24, that segregated with the phenotype. Genotyping of six additional breeds of dogs affected with hereditary ataxia identified the same polymorphism in affected Gordon Setters that segregated perfectly with phenotype. The other breeds tested did not have the polymorphism. Genome-wide SNP genotyping of Gordon Setters identified a 1.9 MB region with an identical haplotype to affected Old English Sheepdogs. Histopathology, immunohistochemistry and ultrastructural evaluation of the brains of affected dogs from both breeds identified dramatic Purkinje neuron loss with axonal spheroids, accumulation of autophagosomes, ubiquitin positive inclusions and a diffuse increase in cytoplasmic neuronal ubiquitin staining. These findings recapitulate the changes reported in mice with induced neuron-specific autophagy defects. Taken together, our results suggest that a defect in RAB24, a gene associated with autophagy, is highly associated with and may contribute to canine hereditary ataxia in Old English Sheepdogs and Gordon Setters. This finding suggests that detailed investigation of autophagy pathways should be undertaken in human hereditary ataxia. Author Summary Neurodegenerative diseases are one of the most important causes of decline in an aging population. An important subset of these diseases are known as the hereditary ataxias, familial neurodegenerative diseases that affect the cerebellum causing progressive gait disturbance in both humans and dogs. We identified a mutation in RAB24, a gene associated with autophagy, in Old English Sheepdogs and Gordon Setters with hereditary ataxia. Autophagy is a process by which cell proteins and organelles are removed and recycled and its critical role in maintenance of the continued health of cells is becoming clear. We evaluated the brains of affected dogs and identified accumulations of autophagosomes within the cerebellum, suggesting a defect in the autophagy pathway. Our results suggest that a defect in the autophagy pathway results in neuronal death in a naturally occurring disease in dogs. The autophagy pathway should be investigated in human hereditary ataxia and may represent a therapeutic target in neurodegenerative diseases.

  • 165.
    Agliari, Elena
    et al.
    Dipartimento di Fisica, Universita` degli Studi di Parma, viale G. Usberti 7, 43100 Parma, Italy.
    Barra, Adriano
    Del Ferraro, Gino
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
    Guerra, Francesco
    Tantari, Daniele
    Anergy in self-directed B lymphocytes: A statistical mechanics perspective2013In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 375, p. 21-31Article in journal (Refereed)
    Abstract [en]

    Self-directed lymphocytes may evade clonal deletion at ontogenesis but still remain harmless due to a mechanism called clonal anergy. For B-lymphocytes, two major explanations for anergy developed over the last decades: according to Varela theory, anergy stems from a proper orchestration of the whole B-repertoire, such that self-reactive clones, due to intensive feed-back from other clones, display strong inertia when mounting a response. Conversely, according to the model of cognate response, self-reacting cells are not stimulated by helper lymphocytes and the absence of such signaling yields anergy. Through statistical mechanics we show that helpers do not prompt activation of a sub-group of B-cells: remarkably, the latter are just those broadly interacting in the idiotypic network. Hence Varela theory can finally be reabsorbed into the prevailing framework of the cognate response model. Further, we show how the B-repertoire architecture may emerge, where highly connected clones are self-directed as a natural consequence of ontogenetic learning. 

  • 166. Agnarsdottir, Margret
    et al.
    Sooman, Linda
    Bolander, Asa
    Stromberg, Sara
    Rexhepaj, Elton
    Bergqvist, Michael
    Ponten, Fredrik
    Gallagher, William
    Lennartsson, Johan
    Ekman, Simon
    Uhlen, Mathias
    KTH, School of Biotechnology (BIO), Proteomics. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Hedstrand, Hakan
    SOX10 expression in superficial spreading and nodular malignant melanomas2010In: Melanoma research, ISSN 0960-8931, E-ISSN 1473-5636, Vol. 20, no 6, p. 468-478Article in journal (Refereed)
    Abstract [en]

    SOX10 is a transcription factor expressed in nerve cells and melanocytes. The aim of this study was to investigate the protein expression pattern of SOX10 in malignant melanoma tumors and to analyze whether the results correlated with clinical parameters and the proliferation marker Ki-67. Furthermore, proliferation and migration were analyzed in three different cell lines employing SOX10 small interfering RNA-mediated silencing. Expression patterns were determined in 106 primary tumors and 39 metastases in addition to 16 normal skin samples and six benign nevi employing immunohistochemistry and tissue microarrays. The immunohistochemical staining was evaluated manually and with an automated algorithm. SOX10 was strongly expressed in the benign tissues, but for the malignant tumors superficial spreading melanomas stained stronger than nodular malignant melanomas (P = 0.008). The staining intensity was also inversely correlated with T-stage (Spearman's rho = -0.261, P = 0.008). Overall survival and time to recurrence were significantly correlated with SOX10 intensity, but not in multivariate analysis including T-stage. With the automated algorithm there was an inverse correlation between the SOX10 staining intensity and the proliferation marker, Ki-67 (rho = -0.173, P = 0.02) and a significant difference in the intensity signal between the benign tissues, the primary tumors and the metastases where the metastases stained the weakest (P <= 0.001). SOX10 downregulation resulted in variable effects on proliferation and migration rates in the melanoma cell lines. In conclusion, the SOX10 intensity level differed depending on the tissue studied and SOX10 might have a role in survival. No conclusion regarding the role of SOX10 for in-vitro proliferation and migration could be drawn. Melanoma Res 20:468-478

  • 167.
    Agnas, Axel Jönses Bernard
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Non-Independent Mate Choice in Female Humans (Homo sapiens): Progression to the Field 2016Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    There is much evidence that mate-choice decisions made by humans are affected by social/contextual information. Women seem to rate men portrayed in a relationship as more desirable than the same men when portrayed as single. Laboratory studies have found evidence suggesting that human mate choice, as in other species, is dependent on the mate choice decisions made by same-sex rivals. Even though non-independent mate choice is an established and well-studied area of mate choice, very few field studies have been performed. This project aims to test whether women’s evaluation of potential mates desirability is dependent/non-independent of same-sex rivals giving the potential mates sexual interest. This is the first field study performed in a modern human’s natural habitat aiming to test for non- independent mate choice in humans.

    No desirability enhancement effect was found. The possibilities that earlier studies have found an effect that is only present in laboratory environments or have measured effects other than non-independent mate choice are discussed. I find differences in experimental design to be the most likely reason why the present study failed to detect the effect found in previous studies. This field study, the first of its sort, has generated important knowledge for future experimenters, where the most important conclusion is that major limitations in humans ability to register and remember there surrounding should be taken in consideration when designing any field study investigating human mate choice. 

  • 168.
    Agnolin, Federico L.
    et al.
    Museo Argentino Ciencias Nat Bernardino Rivadavia, Lab Anat Comparada & Evoluc Vertebrados, Buenos Aires, DF, Argentina.; Univ Maimonides, CEBBAD, Dept Ciencias Nat & Antropol, Fundac Hist Nat Felix de Azara, Buenos Aires, DF, Argentina.
    Powell, Jaime E.
    Inst Miguel Lillo, RA-4000 San Miguel De Tucuman, Tucuman, Argentina.; Consejo Nacl Invest Cient & Tecn, RA-1033 Buenos Aires, DF, Argentina.
    Novas, Fernando E.
    Museo Argentino Ciencias Nat Bernardino Rivadavia, Lab Anat Comparada & Evoluc Vertebrados, Buenos Aires, DF, Argentina.; Consejo Nacl Invest Cient & Tecn, RA-1033 Buenos Aires, DF, Argentina.
    Kundrát, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    New alvarezsaurid (Dinosauria, Theropoda) from Latest Cretaceous of North-western Patagonia with associated eggs2012In: Cretaceous research (Print), ISSN 0195-6671, E-ISSN 1095-998X, Vol. 35, p. 33-56Article in journal (Refereed)
    Abstract [en]

    The Alvarezsauridae represents a branch of peculiar basal coelurosaurs with an increasing representationof their Cretaceous radiation distributed worldwide. Here we describe a new member of the group, Bonapartenykus ultimus gen. et sp. nov. from Campanian-Maastrichtian strata of Northern Patagonia, Argentina. Bonapartenykus is represented by a single, incomplete postcranial skeleton. The morphologyof the known skeletal elements suggests close affinities with the previously described taxon from Patagonia, Patagonykus, and both conform to a new clade, here termed Patagonykinae nov. Two incomplete eggs have been discovered in association with the skeletal remains of Bonapartenykus, andseveral clusters of broken eggshells of the same identity were also found in a close proximity. These belong to the new ooparataxon Arriagadoolithus patagoniensis of the new oofamily Arriagadoolithidae, which provides first insights into unique shell microstructure and fungal contamination of eggs laid by alvarezsaurid theropods. The detailed study of the eggs sheds new light on the phylogenetic position of alvarezsaurids within the Theropoda, and the evolution of eggs among Coelurosauria. We suggest thatplesiomorphic alvarezsaurids survived in Patagonia until the latest Cretaceous, whereas these basal forms became extinct elsewhere.

  • 169.
    Agnvall, Beatrix
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Early domestication?: Phenotypic alterations of Red Junglefowl selected for divergent fear of humans2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Domestication is the process through which animals adapt to conditions provided by humans. The domesticated phenotype differs from wild ancestors in a number of traits relating to physiology, morphology and behaviour. One of the most striking differences is the animals’ fear response towards humans, and reduced fear of humans is assumed to have been an early prerequisite for the success of domestication. The early alterations seen in the domesticated phenotype may be traits developed as a correlated selection response due to tameness rather than selected upon one by one.

    This thesis summarizes a project where Red Junglefowl were selected for divergent fear of humans during six generations. In every generation, fear response to human was assessed in a standardized test and, according to fear score, the animals were bred for either high fear of humans (H) or low fear of humans (L). The animals were, above that of the standardized selection test, behaviourally phenotyped in different tests in each generation mainly focusing on fear, exploration and social behaviour. In addition to behaviour, the animals were phenotyped for body weight, egg weight, metabolism, feed intake, plumage condition, blood plasma corticosterone and peripheral serotonin. After culling, vital organs and brains were harvested and weighed.

    In paper I, we demonstrated that the selection trait has a significant genetic heritability and is genetically correlated with other behavioural responses associated with fearfulness and exploration. In paper II, we concluded that animals from the L strain had better plumage condition, higher weight, laid larger eggs and also generated larger offspring. Furthermore, when tested in a social dominance test with a limited resource, they received less and performed more aggression regardless of whether the restricted source was edible or not. In paper III, we revealed that animals from the L strain had higher basal metabolic rate as chicks, gained more weight in relation to feed intake and were bolder in a Novel Object test. Furthermore, the L males had higher plasma levels of peripheral serotonin, but the corticosterone after a restraint stress test did not differ. In paper IV and V, we concluded the project by comparing brain and organ weights as well as behaviour of the parental generation (P0) with the fifth selected generation (S5). The absolute brain weight as well as the weight specific brain weight were larger in the animals selected on H than in the L-animals. The relative weight of telencephalon was significantly higher in H whereas relative weight of cerebellum was significantly lower. Heart, liver, spleen and testes were all relatively heavier in H animals than in L. Interestingly, the behaviours assessed in P0 and S5 seemed to be rather resilient to the selection with only small differences in S5.

    To summarize, the selection on divergent tameness in Red Junglefowl has affected several phenotypic traits associated with the domesticated phenotype. The results of this project indicate that tameness in Red Junglefowl could be an underlying factor driving trait modifications towards the domesticated phenotype.

  • 170.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Ali, A.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Olby, S.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Red Junglefowl (Gallus gallus) selected for low fear of humans are larger, more dominant and produce larger offspring2014In: animal, ISSN 1751-7311, Vol. 8, no 9, p. 1498-1505Article in journal (Refereed)
    Abstract [en]

    Many traits associated with domestication are suggested to have developed as correlated responses to reduced fear of humans. Tameness may have reduced the stress of living in human proximity and improved welfare in captivity. We selected Red Junglefowl (ancestors of all domestic chickens) for four generations on high or low fear towards humans, mimicking an important aspect of the earliest period of domestication, and tested birds from the third and fourth generation in three different social tests. Growth and plumage condition, as well as size of eggs and offspring were also recorded, as indicators of some aspects of welfare. Birds selected for low fear had higher weight, laid larger eggs and generated larger offspring, and had a better plumage condition. In a social dominance test they also performed more aggressive behaviour and received less of the same, regardless of whether the restricted resource was feed or not. Hence, dominance appeared to increase as a consequence of reduced fear of humans. Furthermore, egg size and the weight of the offspring were larger in the less fearful birds, and plumage condition better, which could be interpreted as the less fearful animals being better adapted to the environment in which they were selected.

  • 171.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Bélteky, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Brain size is reduced by selectionfor tameness in Red Junglefowl–correlated effects in vital organs2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 3306Article in journal (Refereed)
    Abstract [en]

    During domestication animals have undergone changes in size of brain and other vital organs. We hypothesize that this could be a correlated effect to increased tameness. Red Junglefowl (ancestors of domestic chickens) were selected for divergent levels of fear of humans for five generations. The parental (P0) and the fifth selected generation (S5) were culled when 48–54 weeks old and the brains were weighed before being divided into telencephalon, cerebellum, mid brain and optic lobes. Each single brain part as well as the liver, spleen, heart and testicles were also weighed. Brains of S5 birds with high fear scores (S5 high) were heavier both in absolute terms and when corrected for body weight. The relative weight of telencephalon (% of brain weight) was significantly higher in S5 high and relative weight of cerebellum was lower. Heart, liver, testes and spleen were all relatively heavier (% of body weight) in S5 high. Hence, selection for tameness has changed the size of the brain and other vital organs in this population and may have driven the domesticated phenotype as a correlated response.

  • 172.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Bélteky, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Katajamaa, Rebecca
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Is evolution of domestication driven by tameness? A selective review with focus on chickens2018In: Applied Animal Behaviour Science, ISSN 0168-1591, E-ISSN 1872-9045, Vol. 205, p. 227-233Article in journal (Refereed)
    Abstract [en]

    Domestication of animals offers unique possibilities to study evolutionary changes caused by similar selection pressures across a range of species. Animals from separate genera tend to develop a suite of phenotypic alterations referred to as "the domesticated phenotype". This involves changes in appearance, including loss of pigmentation, and alterations in body size and proportions. Furthermore, effects on reproduction and behaviour are typical. It is hypothesized that this recurring phenotype may be secondary effects of the increased tameness that is an inevitable first step in the domestication of any species. We first provide a general overview of observations and experiments from different species and then review in more detail a project attempting to recreate the initial domestication of chickens. Starting from an outbred population of Red Junglefowl, ancestors of all modem chickens, divergent lines were selected based on scores in a standardized fear-of-human test applied to all birds at 12 weeks of age. Up to the eighth selected generation, observations have been made on correlated effects of this selection on various phenotypes. The fear score had a significant heritability and was genetically correlated to several other behavioural traits. Furthermore, low-fear birds were larger at hatch, grew faster, laid larger eggs, had a modified metabolism and increased feed efficiency, had modified social behaviour and reduced brain size. Selection affected gene expression and DNA-methylation in the brains, but the genetic and epigenetic effects were not specifically associated with stress pathways. Further research should be focused on unraveling the genetic and epigenetic mechanisms underlying the correlated side-effects of reduced fear of humans.

  • 173.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Effects of Divergent Selection for Fear of Humans on Behaviour in Red Junglefowl2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 11, p. 1-12Article in journal (Refereed)
    Abstract [en]

    Domestication has caused a range of similar phenotypic changes across taxa, relating to physiology, morphology and behaviour. It has been suggested that this recurring domesticated phenotype may be a result of correlated responses to a central trait, namely increased tameness. We selected Red Junglefowl, the ancestors of domesticated chickens, during five generations for reduced fear of humans. This caused a marked and significant response in tameness, and previous studies have found correlated effects on growth, metabolism, reproduction, and some behaviour not directly selected for. Here, we report the results from a series of behavioural tests carried out on the initial parental generation (P0) and the fifth selected generation (S5), focusing on behaviour not functionally related to tameness, in order to study any correlated effects. Birds were tested for fear of humans, social reinstatement tendency, open field behaviour at two different ages, foraging/exploration, response to a simulated aerial predator attack and tonic immobility. In S5, there were no effects of selection on foraging/exploration or tonic immobility, while in the social reinstatement and open field tests there were significant interactions between selection and sex. In the aerial predator test, there were significant main effects of selection, indicating that fear of humans may represent a general wariness towards predators. In conclusion, we found only small correlated effects on behaviours not related to the tameness trait selected for, in spite of them showing high genetic correlations to fear of humans in a previous study on the same population. This suggests that species-specific behaviour is generally resilient to changes during domestication.

  • 174.
    Agnvall, Beatrix
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Katajamaa, Rebecca
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Altimiras, Jordi
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Is domestication driven by reduced fear of humans? Boldness, metabolism and serotonin levels in divergently selected red junglefowl (Gallus gallus)2015In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 11, no 9, article id 20150509Article in journal (Refereed)
    Abstract [en]

    Domesticated animals tend to develop a coherent set of phenotypic traits. Tameness could be a central underlying factor driving this, and we therefore selected red junglefowl, ancestors of all domestic chickens, for high or low fear of humans during six generations. We measured basal metabolic rate (BMR), feed efficiency, boldness in a novel object (NO) test, corticosterone reactivity and basal serotonin levels (related to fearfulness) in birds from the fifth and sixth generation of the high- and low-fear lines, respectively (44-48 individuals). Corticosterone response to physical restraint did not differ between selection lines. However, BMR was higher in low-fear birds, as was feed efficiency. Low-fear males had higher plasma levels of serotonin and both low-fear males and females were bolder in an NO test. The results show that many aspects of the domesticated phenotype may have developed as correlated responses to reduced fear of humans, an essential trait for successful domestication.

  • 175. Agnès E., Sjöstrand
    et al.
    Per, Sjödin
    Carina, Schlebusch
    Thijessen, Naidoo
    Lucie, Gattepaille
    Nina, Hollfelder
    Torsten, Günther
    Mattias, Jakobsson
    Patterns of local adaptation in AfricansManuscript (preprint) (Other academic)
  • 176. Agnès E., Sjöstrand
    et al.
    Per, Sjödin
    Farhad, Shayimkulov
    Tatiana, Hegay
    Michael G. B., Blum
    Evelyne, Heyer
    Mattias, Jakobsson
    Taste and lifestyle: insights from SNP-chip data.Manuscript (preprint) (Other academic)
  • 177. Agostinelli, Marta
    et al.
    Cleary, Michelle
    Martin, Juan A.
    Albrectsen, Benedicte R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Witzell, Johanna
    Pedunculate Oaks (Quercus robur L.) Differing in Vitality as Reservoirs for Fungal Biodiversity2018In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, article id 1758Article in journal (Refereed)
    Abstract [en]

    Ecological significance of trees growing in urban and peri-urban settings is likely to increase in future land-use regimes, calling for better understanding of their role as potential reservoirs or stepping stones for associated biodiversity. We studied the diversity of fungal endophytes in woody tissues of asymptomatic even aged pedunculate oak trees, growing as amenity trees in a peri-urban setting. The trees were classified into three groups according to their phenotypic vitality (high, medium, and low). Endophytes were cultured on potato dextrose media from surface sterilized twigs and DNA sequencing was performed to reveal the taxonomic identity of the morphotypes. In xylem tissues, the frequency and diversity of endophytes was highest in oak trees showing reduced vitality. This difference was not found for bark samples, in which the endophyte infections were more frequent and communities more diverse than in xylem. In general, most taxa were shared across the samples with few morphotypes being recovered in unique samples. Leaf phenolic profiles were found to accurately classify the trees according to their phenotypic vitality. Our results confirm that xylem is more selective substrate for endophytes than bark and that endophyte assemblages in xylem are correlated to the degree of host vitality. Thus, high vitality of trees may be associated with reduced habitat quality to wood-associated endophytes.

  • 178. Agostinho, A.
    et al.
    Kouznetsova, A.
    Hernández-Hernández, A.
    Bernhem, Kristoffer
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Blom, Hans
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Höög, C.
    Sexual dimorphism in the width of the mouse synaptonemal complex2018In: Journal of Cell Science, ISSN 0021-9533, E-ISSN 1477-9137, Vol. 131, no 5, article id jcs212548Article in journal (Refereed)
    Abstract [en]

    Sexual dimorphism has been used to describe morphological differences between the sexes, but can be extended to any biologically related process that varies between males and females. The synaptonemal complex (SC) is a tripartite structure that connects homologous chromosomes in meiosis. Here, aided by superresolution microscopy techniques, we show that the SC is subject to sexual dimorphism, in mouse germ cells. We have identified a significantly narrower SC in oocytes and have established that this difference does not arise from a different organization of the lateral elements nor from a different isoform of transverse filament protein SYCP1. Instead, we provide evidence for the existence of a narrower central element and a different integration site for the C-termini of SYCP1, in females. In addition to these female-specific features, we speculate that post-translation modifications affecting the SYCP1 coiled-coil region could render a more compact conformation, thus contributing to the narrower SC observed in females.

  • 179. Agostinho, Ana
    et al.
    Manneberg, Otto
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    van Schendel, Robin
    Hernandez-Hernandez, Abrahan
    Kouznetsova, Anna
    Blom, Hans
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Höög, Christer
    High density of REC8 constrains sister chromatid axes and prevents illegitimate synaptonemal complex formation2016In: EMBO Reports, ISSN 1469-221X, E-ISSN 1469-3178, Vol. 17, no 6, p. 901-913Article in journal (Refereed)
    Abstract [en]

    During meiosis, cohesin complexes mediate sister chromatid cohesion (SCC), synaptonemal complex (SC) assembly and synapsis. Here, using super-resolution microscopy, we imaged sister chromatid axes in mouse meiocytes that have normal or reduced levels of cohesin complexes, assessing the relationship between localization of cohesin complexes, SCC and SC formation. We show that REC8 foci are separated from each other by a distance smaller than 15% of the total chromosome axis length in wild-type meiocytes. Reduced levels of cohesin complexes result in a local separation of sister chromatid axial elements (LSAEs), as well as illegitimate SC formation at these sites. REC8 but not RAD21 or RAD21L cohesin complexes flank sites of LSAEs, whereas RAD21 and RAD21L appear predominantly along the separated sister-chromatid axes. Based on these observations and a quantitative distribution analysis of REC8 along sister chromatid axes, we propose that the high density of randomly distributed REC8 cohesin complexes promotes SCC and prevents illegitimate SC formation.

  • 180. Agren, Rasmus
    et al.
    Mardinoglu, Adil
    Asplund, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular and Morphological Pathology.
    Kampf, Caroline
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular and Morphological Pathology.
    Uhlen, Mathias
    Nielsen, Jens
    Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling2014In: Molecular Systems Biology, ISSN 1744-4292, E-ISSN 1744-4292, Vol. 10, no 3Article in journal (Refereed)
    Abstract [en]

    Synopsis image Personalized GEMs for six hepatocellular carcinoma patients are reconstructed using proteomics data and a task-driven model reconstruction algorithm. These GEMs are used to predict antimetabolites preventing tumor growth in all patients or in individual patients. The presence of proteins encoded by 15,841 genes in tumors from 27 HCC patients is evaluated by immunohistochemistry. Personalized GEMs for six HCC patients and GEMs for 83 healthy cell types are reconstructed based on HMR 2.0 and the tINIT algorithm for task-driven model reconstruction. 101 antimetabolites are predicted to inhibit tumor growth in all patients. Antimetabolite toxicity is tested using the 83 cell type-specific GEMs. An l-carnitine analog inhibits the proliferation of HepG2 cells. Abstract Genome-scale metabolic models (GEMs) have proven useful as scaffolds for the integration of omics data for understanding the genotype-phenotype relationship in a mechanistic manner. Here, we evaluated the presence/absence of proteins encoded by 15,841 genes in 27 hepatocellular carcinoma (HCC) patients using immunohistochemistry. We used this information to reconstruct personalized GEMs for six HCC patients based on the proteomics data, HMR 2.0, and a task-driven model reconstruction algorithm (tINIT). The personalized GEMs were employed to identify anticancer drugs using the concept of antimetabolites; i.e., drugs that are structural analogs to metabolites. The toxicity of each antimetabolite was predicted by assessing the in silico functionality of 83 healthy cell type-specific GEMs, which were also reconstructed with the tINIT algorithm. We predicted 101 antimetabolites that could be effective in preventing tumor growth in all HCC patients, and 46 antimetabolites which were specific to individual patients. Twenty-two of the 101 predicted antimetabolites have already been used in different cancer treatment strategies, while the remaining antimetabolites represent new potential drugs. Finally, one of the identified targets was validated experimentally, and it was confirmed to attenuate growth of the HepG2 cell line.

  • 181. Aguiar, Francisca C.
    et al.
    Segurado, Pedro
    Martins, Maria Joao
    Bejarano, Maria Dolores
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Nilsson, Christer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Portela, Maria Manuela
    Merritt, David M.
    The abundance and distribution of guilds of riparian woody plants change in response to land use and flow regulation2018In: Journal of Applied Ecology, ISSN 0021-8901, E-ISSN 1365-2664, Vol. 55, no 5, p. 2227-2240Article in journal (Refereed)
    Abstract [en]

    1. Many riparian ecosystems in Mediterranean Europe are affected by land use and flow alteration by dams. We focused on understanding how these stressors and their components affect riparian forests in the region. We asked the following questions: (1) Are there well‐defined, responsive riparian guilds? (2) Do dam‐induced streamflows determine abundance and distribution of riparian guilds? (3) What are the main drivers governing composition and cover of riparian guilds in regulated rivers?

    2. We inventoried the cover of riparian woody species in free‐flowing rivers and downstream of dams. We performed a cluster analysis and ordination to derive riparian guilds, using abundance data from 66 riparian woody species and 26 functional plant traits. We used a reduced set of principal components for the environment, land use and hydrology, and general linear modelling to explore the effect of these factors (separately and combined) on riparian guilds.

    3. We found that: (1) four dominant guilds are responsive to disturbance in southwestern European streams, namely the obligate riparian, water‐stress tolerant, deciduous competitive and Mediterranean evergreen guilds; (2) a set of land use and hydrological variables differentially affect the diverse co‐occurring riparian guilds; (3) frequency and duration of high flow pulses and the low‐flow conditions were major drivers of change in landscapes dominated by intensive agriculture and forestry; (4) storage reservoirs reduced the cover of obligate riparian and Mediterranean evergreen guilds, and increased the abundance of water‐stress tolerant and deciduous competitive guilds, while run‐of‐river dams, having limited water storage, reduced both obligate and deciduous competitive guilds.

    4. Synthesis and applications. Future research in southwestern Europe should address the resilience of riparian guilds and the effects of interacting landscape factors and stressors on guild distribution. Streamflow regulations downstream of reservoirs should focus on specific flow components, namely the magnitude of flows, and frequency and duration of extreme flow events. For successful mitigation of the dam‐induced effects on riparian vegetation, river management plans must incorporate the environmental and land use site‐specific contexts.

  • 182.
    Aguilar, Ximena
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Folding and interaction studies of subunits in protein complexes2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Proteins function as worker molecules in the cell and their natural environment is crowded. How they fold in a cell-like environment and how they recognize their interacting partners in such conditions, are questions that underlie the work of this thesis.

    Two distinct subjects were investigated using a combination of biochemical- and biophysical methods. First, the unfolding/dissociation of a heptameric protein (cpn10) in the presence of the crowding agent Ficoll 70. Ficoll 70 was used to mimic the crowded environment in the cell and it has been used previously to study macromolecular crowding effects, or excluded volume effects, in protein folding studies. Second, the conformational changes upon interaction between the Mediator subunit Med25 and the transcription factor Dreb2a from Arabidopsis thaliana. Mediator is a transcriptional co-regulator complex which is conserved from yeast to humans. The molecular mechanisms of its action are however not entirely understood. It has been proposed that the Mediator complex conveys regulatory signals from promoter-bound transcription factors (activators/repressors) to the RNA polymerase II machinery through conformational rearrangements.

    The results from the folding study showed that cpn10 was stabilized in the presence of Ficoll 70 during thermal- and chemical induced unfolding (GuHCl). The thermal transition midpoint increased by 4°C, and the chemical midpoint by 0.5 M GuHCl as compared to buffer conditions. Also the heptamer-monomer dissociation was affected in the presence of Ficoll 70, the transition midpoint was lower in Ficoll 70 (3.1 μM) compared to in buffer (8.1 μM) thus indicating tighter binding in crowded conditions. The coupled unfolding/dissociation free energy for the heptamer increased by about 36 kJ/mol in Ficoll. Altogether, the results revealed that the stability effect on cpn10 due to macromolecular crowding was larger in the individual monomers (33%) than at the monomer-monomer interfaces (8%).

    The results from the interaction study indicated conformational changes upon interaction between the A. thaliana Med25 ACtivator Interaction Domain (ACID) and Dreb2a. Structural changes were probed to originate from unstructured Dreb2a and not from the Med25-ACID. Human Med25-ACID was also found to interact with the plant-specific Dreb2a, even though the ACIDs from human and A. thaliana share low sequence homology. Moreover, the human Med25-interacting transcription factor VP16 was found to interact with A. thaliana Med25. Finally, NMR, ITC and pull-down experiments showed that the unrelated transcription factors Dreb2a and

    VP16 interact with overlapping regions in the ACIDs of A. thaliana and human Med25.

    The results presented in this thesis contribute to previous reports in two different aspects. Firstly, they lend support to the findings that the intracellular environment affects the biophysical properties of proteins. It will therefore be important to continue comparing results between in vitro and cell-like conditions to measure the magnitude of such effects and to improve the understanding of protein folding and thereby misfolding of proteins in cells. Better knowledge of protein misfolding mechanisms is critical since they are associated to several neurodegenerative diseases such as Alzheimer’s and Parkinson's. Secondly, our results substantiate the notion that transcription factors are able to bind multiple targets and that they gain structure upon binding. They also show that subunits of the conserved Mediator complex, despite low sequence homologies, retain a conserved structure and function when comparing evolutionary diverged species.

  • 183.
    Aguilar, Ximena
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Blomberg, Jeanette
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Brännström, Kristoffer
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Olofsson, Anders
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Schleucher, Jurgen
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Björklund, Stefan
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Interaction Studies of the Human and Arabidopsis thaliana Med25-ACID Proteins with the Herpes Simplex Virus VP16-and Plant-Specific Dreb2a Transcription Factors2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 5, p. e98575-Article in journal (Refereed)
    Abstract [en]

    Mediator is an evolutionary conserved multi-protein complex present in all eukaryotes. It functions as a transcriptional coregulator by conveying signals from activators and repressors to the RNA polymerase II transcription machinery. The Arabidopsis thaliana Med25 (aMed25) ACtivation Interaction Domain (ACID) interacts with the Dreb2a activator which is involved in plant stress response pathways, while Human Med25-ACID (hMed25) interacts with the herpes simplex virus VP16 activator. Despite low sequence similarity, hMed25-ACID also interacts with the plant-specific Dreb2a transcriptional activator protein. We have used GST pull-down-, surface plasmon resonance-, isothermal titration calorimetry and NMR chemical shift experiments to characterize interactions between Dreb2a and VP16, with the hMed25 and aMed25-ACIDs. We found that VP16 interacts with aMed25-ACID with similar affinity as with hMed25-ACID and that the binding surface on aMed25-ACID overlaps with the binding site for Dreb2a. We also show that the Dreb2a interaction region in hMed25-ACID overlaps with the earlier reported VP16 binding site. In addition, we show that hMed25-ACID/Dreb2a and aMed25-ACID/Dreb2a display similar binding affinities but different binding energetics. Our results therefore indicate that interaction between transcriptional regulators and their target proteins in Mediator are less dependent on the primary sequences in the interaction domains but that these domains fold into similar structures upon interaction.

  • 184.
    Aguilar-Calvo, Patricia
    et al.
    University of Calif San Diego, CA 92093 USA; University of Calif San Diego, CA 92093 USA.
    Xiao, Xiangzhu
    Case Western Reserve University, OH 44116 USA.
    Bett, Cyrus
    University of Calif San Diego, CA 92093 USA; University of Calif San Diego, CA 92093 USA; US FDA, MD USA.
    Erana, Hasier
    CIC bioGUNE, Spain.
    Soldau, Katrin
    University of Calif San Diego, CA 92093 USA.
    Castilla, Joaquin
    University of Calif San Diego, CA 92093 USA; CIC bioGUNE, Spain; Ikerbasque, Spain.
    Nilsson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Surewicz, Witold K.
    Case Western Reserve University, OH 44116 USA.
    Sigurdson, Christina J.
    University of Calif San Diego, CA 92093 USA; University of Calif San Diego, CA 92093 USA; University of Calif Davis, CA 95616 USA.
    Post-translational modifications in PrP expand the conformational diversity of prions in vivo2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 43295Article in journal (Refereed)
    Abstract [en]

    Misfolded prion protein aggregates (PrPSc) show remarkable structural diversity and are associated with highly variable disease phenotypes. Similarly, other proteins, including amyloid-beta, tau, alpha-synuclein, and serum amyloid A, misfold into distinct conformers linked to different clinical diseases through poorly understood mechanisms. Here we use mice expressing glycophosphatidylinositol (GPI)anchorless prion protein, PrPC, together with hydrogen-deuterium exchange coupled with mass spectrometry (HXMS) and a battery of biochemical and biophysical tools to investigate how posttranslational modifications impact the aggregated prion protein properties and disease phenotype. Four GPI-anchorless prion strains caused a nearly identical clinical and pathological disease phenotype, yet maintained their structural diversity in the anchorless state. HXMS studies revealed that GPIanchorless PrPSc is characterized by substantially higher protection against hydrogen/deuterium exchange in the C-terminal region near the N-glycan sites, suggesting this region had become more ordered in the anchorless state. For one strain, passage of GPI-anchorless prions into wild type mice led to the emergence of a novel strain with a unique biochemical and phenotypic signature. For the new strain, histidine hydrogen-deuterium mass spectrometry revealed altered packing arrangements of beta-sheets that encompass residues 139 and 186 of PrPSc. These findings show how variation in posttranslational modifications may explain the emergence of new protein conformations in vivo and also provide a basis for understanding how the misfolded protein structure impacts the disease.

  • 185.
    Aguileta, Gabriela
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Bielawski, Joseph P.
    Yang, Ziheng
    Proposed standard nomenclature for the alpha- and beta-globin gene families2006In: Genes & Genetic Systems, ISSN 1341-7568, E-ISSN 1880-5779, Vol. 81, no 5, p. 367-371Article in journal (Refereed)
    Abstract [en]

    The globin family of genes and proteins has been a recurrent object of study for many decades. This interest has generated a vast amount of knowledge. However it has also created an inconsistent and confusing nomenclature, due to the lack of a systematic approach to naming genes and failure to reflect the phylogenetic relationships among genes of the gene family. To alleviate the problems with the existing system, here we propose a standardized nomenclature for the alpha and beta globin family of genes, based on a phylogenetic analysis of vertebrate alpha and beta globins, and following the Guidelines for Human Gene Nomenclature.

  • 186.
    Aguilo, Francesca
    et al.
    Umeå University, Faculty of Medicine, Wallenberg Centre for Molecular Medicine at Umeå University (WCMM). Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology. Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
    Walsh, Martin J.
    The N6-Methyladenosine RNA modification in pluripotency and reprogramming2017In: Current Opinion in Genetics and Development, ISSN 0959-437X, E-ISSN 1879-0380, Vol. 46, p. 77-82Article, review/survey (Refereed)
    Abstract [en]

    Chemical modifications of RNA provide a direct and rapid way to manipulate the existing transcriptome, allowing rapid responses to the changing environment further enriching the regulatory capacity of RNA. N-6-Methyladenosine(m(6)A) has been identified as the most abundant internal modification of messenger RNA in eukaryotes, linking external stimuli to an intricate network of transcriptional, post-transcriptional and translational processes. M(6)A modification affects a broad spectrum of cellular functions, including maintenance of the pluripotency of embryonic stem cells (ESCs) and the reprogramming of somatic cells into induced pluripotent stem cells (iPSCs). In this review, we summarize the most recent findings on m(6)A modification with special focus on the different studies describing how m(6)A is implicated in ESC self-renewal, cell fate specification and iPSC generation.

  • 187.
    Aguilo, Francesca
    et al.
    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
    Zakirova, Zuchra
    Nolan, Katie
    Wagner, Ryan
    Sharma, Rajal
    Hogan, Megan
    Wei, Chengguo
    Sun, Yifei
    Walsh, Martin J.
    Kelley, Kevin
    Zhang, Weijia
    Ozelius, Laurie J.
    Gonzalez-Alegre, Pedro
    Zwaka, Thomas P.
    Ehrlich, Michelle E.
    THAP1: Role in Mouse Embryonic Stem Cell Survival and Differentiation2017In: Stem Cell Reports, ISSN 2213-6711, Vol. 9, no 1, p. 92-107Article in journal (Refereed)
    Abstract [en]

    THAP1 (THAP [Thanatos-associated protein] domain-containing, apoptosis-associated protein 1) is a ubiquitously expressed member of a family of transcription factors with highly conserved DNA-binding and protein-interacting regions. Mutations in THAP1 cause dystonia, DYT6, a neurologic movement disorder. THAP1 downstream targets and the mechanism via which it causes dystonia are largely unknown. Here, we show that wild-type THAP1 regulates embryonic stem cell (ESC) potential, survival, and proliferation. Our findings identify THAP1 as an essential factor underlying mouse ESC survival and to some extent, differentiation, particularly neuroectodermal. Loss of THAP1 or replacement with a disease-causing mutation results in an enhanced rate of cell death, prolongs Nanog, Prdm14, and/or Rex1 expression upon differentiation, and results in failure to upregulate ectodermal genes. ChIP-Seq reveals that these activities are likely due in part to indirect regulation of gene expression.

  • 188. Aguirre, A. A.
    et al.
    Angerbjörn, A.
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Tannerfeldt, Magnus
    Stockholm University, Faculty of Science, Department of Zoology.
    Mörner, T.
    Health evaluation of arctic fox (Alopex lagopus) cubs in Sweden2000In: Journal of Zoo and Wildlife Medicine, Vol. 31, no 1, p. 36-40Article in journal (Refereed)
    Abstract [en]

    Hematologic. serum biochemistry, and serum cortisol reference ranges were established and tonsil/rectal bacterial and fecal parasite examinations were performed on 21 wild arctic fox (Alopex lagopus) cubs during July 1996. Several of the hematologic and serum biochemistry values fell within normal ranges for other wild canids or domestic dogs of the same age class. Serum alanine transaminase and creatine phosphokinase values were significantly higher in the youngest cubs. Proteus vulgaris and Escherichia coli were isolated from both tonsilar and rectal swabs of several cubs in all dens. The most common gastrointestinal parasite ova were Toxascaris leonina (59%), Isospora spp. (52%), Uncinaria stenocephala (33%), and Capillaria spp. (26%). Prevalence of T. leonina differed significantly between dens and between age groups. Hematologic and serum biochemistry values and degree of parasitism may be indicators of health, stress, and nutritional status of arctic foxes.

  • 189. Aguirre, A. Alonso
    et al.
    Principe, B.
    Tannerfeldt, Magnus
    Stockholm University, Faculty of Science, Department of Zoology.
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Mörner, Torsten
    Field anesthesia of wild arctic fox (Alopex lagopus) cubs in the Swedish lapland using medetomidine-ketamine-atipamezole2000In: Journal of Zoo and Wildlife Medicine, Vol. 31, no 2, p. 244-246Article in journal (Refereed)
    Abstract [en]

    A safe and effective anesthetic regime for use in arctic fox (Alopex lagopus) cubs was developed. During July 1996, six free-ranging 6-8-wk-old cubs were captured near their den in Vindelfjallen Nature Reserve, Sweden. Medetomidine and ketamine HCl, followed by atipamezole, were selected for the anesthetic trial because of the well-documented safety and efficacy of this drug combination in a broad range of species. The dosage regimen used was 50 mu g/kg medetomidine combined with 2.5 mg/kg ketamine followed by reversal with 250 mu g/kg atipamezole. induction was rapid, with a mean induction time of 1 min and 32 sec (range: 58-150 sec). The cubs were anesthetized for a mean time of 18 +/- 5 min (range: 13-25 min). Serially recorded heart rate, respiratory rate, temperature, and pulse oximetry were stable throughout the anesthetic period for all cubs. Anesthetic depth was suitable for safe handling and minor clinical procedures, including venipuncture. Following atipamezole, all cubs were standing within 12 +/- 7 min (range: 5-24 min) and fully recovered at 27 +/- 5 min (range: 19-36 min). This information will be useful for future captive breeding and management programs involving the endangered arctic fox.

  • 190.
    Aguirre-Gutierrez, Jesus
    et al.
    Naturalis Biodivers Ctr, Netherlands;Univ Oxford, UK;Univ Amsterdam, Netherlands.
    WallisDeVries, Michiel F.
    De Vlinderstichting, Netherlands;Wageningen Univ, Netherlands.
    Marshall, Leon
    Naturalis Biodivers Ctr, Netherlands;Univ Namur, Belgium.
    van't Zelfde, Maarten
    Naturalis Biodivers Ctr, Netherlands;Leiden Univ, Netherlands.
    Villalobos-Arambula, Alma R.
    Univ Guadalajara, Mexico.
    Boekelo, Bastiaen
    Wageningen Univ & Res, Netherlands.
    Bartholomeus, Harm
    Wageningen Univ & Res, Netherlands.
    Franzén, Markus
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. UFZ, Helmholtz Ctr Environm Res, Germany.
    Biesmeijer, Jacobus C.
    Naturalis Biodivers Ctr, Netherlands;Leiden Univ, Netherlands.
    Butterflies show different functional and species diversity in relationship to vegetation structure and land use2017In: Global Ecology and Biogeography, ISSN 1466-822X, E-ISSN 1466-8238, Vol. 26, no 10, p. 1126-1137Article in journal (Refereed)
    Abstract [en]

    AimBiodiversity is rapidly disappearing at local and global scales also affecting the functional diversity of ecosystems. We aimed to assess whether functional diversity was correlated with species diversity and whether both were affected by similar land use and vegetation structure drivers. Better understanding of these relationships will allow us to improve our predictions regarding the effects of future changes in land use on ecosystem functions and services. LocationThe Netherlands. MethodsWe compiled a dataset of c.3 million observations of 66 out of 106 known Dutch butterfly species collected across 6,075 sampling locations during a period of 7 years, together with very high-resolution maps of land use and countrywide vegetation structure data. Using a mixed-effects modelling framework, we investigated the relationship between functional and species diversity and their main land use and vegetation structure drivers. ResultsWe found that high species diversity does not translate into high functional diversity, as shown by their different spatial distribution patterns in the landscape. Functional and species diversity are mainly driven by different sets of structural and land use parameters (especially average vegetation height, amount of vegetation between 0.5 and 2m, natural grassland, sandy soils vegetation, marsh vegetation and urban areas). We showed that it is a combination of both vegetation structural characteristics and land use variables that defines functional and species diversity. Main conclusionsFunctional diversity and species diversity of butterflies are not consistently correlated and must therefore be treated separately. High functional diversity levels occurred even in areas with low species diversity. Thus, conservation actions may differ depending on whether the focus is on conservation of high functional diversity or high species diversity. A more integrative analysis of biodiversity at both species and trait levels is needed to infer the full effects of environmental change on ecosystem functioning.

  • 191.
    Aguirre-Gutiérrez, Jesús
    et al.
    Naturalis Biodiversity Center, The Netherlands ; University of Amsterdam, The Netherlands.
    Kissling, W. Daniel
    University of Amsterdam, The Netherlands.
    Carvalheiro, Luísa G.
    Universidade de Brasília, Brazil ; University of Lisbon, Portugal.
    WallisDeVries, Michiel F.
    Wageningen University, The Netherlands.
    Franzén, Markus
    Helmholtz-Centre for Environmental Research - UFZ, Germany.
    Biesmeijer, Jacobus C.
    Naturalis Biodiversity Center, The Netherlands ; University of Amsterdam, The Netherlands.
    Functional traits help to explain half-century long shifts in pollinator distributions2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 24451Article in journal (Refereed)
    Abstract [en]

    Changes in climate and land use can have important impacts on biodiversity. Species respond to such environmental modifications by adapting to new conditions or by shifting their geographic distributions towards more suitable areas. The latter might be constrained by species’ functional traits that influence their ability to move, reproduce or establish. Here, we show that functional traits related to dispersal, reproduction, habitat use and diet have influenced how three pollinator groups (bees, butterflies and hoverflies) responded to changes in climate and land-use in the Netherlands since 1950. Across the three pollinator groups, we found pronounced areal range expansions (>53%) and modelled range shifts towards the north (all taxa: 17–22 km), west (bees: 14 km) and east (butterflies: 11 km). The importance of specific functional traits for explaining distributional changes varied among pollinator groups. Larval diet preferences (i.e. carnivorous vs. herbivorous/detritivorous and nitrogen values of host plants, respectively) were important for hoverflies and butterflies, adult body size for hoverflies, and flight period length for all groups. Moreover, interactions among multiple traits were important to explain species’ geographic range shifts, suggesting that taxon-specific multi-trait analyses are needed to predict how global change will affect biodiversity and ecosystem services.

  • 192. Aguirre-Hudson, B.
    et al.
    Kokubun, T.
    Spooner, B.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Taxonomy of Calicium victorianum (F. Wilson) Tibell (Caliciaceae, Lecanorales), a lichenized ascomycete new to Europe2007In: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 39, no 5, p. 401-407Article in journal (Refereed)
    Abstract [en]

    The morphological features and chemical compounds found in the first European collection of Calicium victorianum are compared with type material from Australia of C. piperatum F. Wilson. The phylogenetic relationships of the species are discussed by comparing its nuclear rDNA ITS 1-5.8S-ITS2 with that of other species of Calicium.

  • 193.
    Agurell, Eva
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Comparative studies of alkylating and N-heterocyclic compounds on different genetic endpoints with special emphasis on amplification of minisatellite sequences1992Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Several mutational events are involved in the multistage process of cancer. Genetic instability of tumor DNA is shown in a variety of genetic changes such as point mutations, chromosomal aberrations, aneuploidy, DNA amplification and somatic recombination. Highly repetitive sequences, minisatellite DNA, have been changed in tumors, most probably by DNA amplification.

    To better predict carcinogens all these genetic changes should be considered. The present investigation has focused on the study of genetic changes especially DNA amplification with the use of genetic instability of minisatellites. DNA alterations in human bladder tumors were examined. A new in vitro test system was developed to study DNA amplification.

    In this study DNA fingerprint analysis, with the use of minisatellite DNA, of 22 bladder tumor patients is performed. DNA alterations were determined in approximately 50% of the examined bladder tumor patients. In eight of these ten patients a loss of bands was demonstrated.

    To study DNA amplifications an in vitro test system was developed. A haploid yeast strain was constructed, the TR(MS1)-1, which carries a chromosomal integration of the human minisatellite sequence MSI. The spontaneous frequency of new MSI length alleles was approximately 30%. Both amplifications and deamplifications can be detected in this system without selection. A plasmid pop-out frequency can also be meausured.

    A number of model compounds was used during this study, namely three alkylating agents, a nongenotoxic carcinogen and several nitrogen heterocyclic compounds. To compare genotoxicity and the mechanism of action, these compounds are tested in several in vitro test systems. Ethylene oxide (EO) was demonstrated to be more potent than propylene oxide (PO) in several of the measured endpoints in yeast. EO induced changes in the amplification spectrum of new MSI length alleles in TR(MS1)-1 while PO increased the plasmid pop-out frequency. 2,3,7,8-Tetrachlorodibenzo(p)dioxin (TCDD) was also seen to induce changes in the amplification spectrum of new MSI length alleles, thus demonstrating an effect of TCDD at the DNA level. Among the N-heterocyclic compounds, camptothecin increased the plasmid pop-out frequency in TR(MS1)-1. Two tryptophan photoproducts, "284" and "312", were shown to bind to the A A-receptor. They were demonstrated to be nongenotoxic and antimutagenic in bacteria and slightly genotoxic in yeast. These two compounds are antimutagenic by inhibiting the cytochrome P450IA1. "284" increased cell survival or cell division. These two tryptophan photoproducts, ”284" and "312", are postulated to be biological signal substances by being the endogenous ligand to the Ah -receptor.

  • 194. Agustí, J.
    et al.
    Werdelin, LarsSwedish Museum of Natural History, Department of Paleobiology.
    Influence of climate on faunal evolution in the Quaternary of Europe1995Collection (editor) (Refereed)
  • 195. Agvald-Öhman, C
    et al.
    Wernerman, J
    Nord, C E
    Edlund, Charlotta
    Södertörn University, Avdelning Naturvetenskap.
    Anaerobic bacteria commonly colonize the lower airways of intubated ICU patients2003In: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 9, no 5, p. 397-405Article in journal (Refereed)
    Abstract [en]

    Objectives To investigate respiratory tract colonization by aerobic and anaerobic bacteria in mechanically ventilated patients. Methods Bacterial colonization of the stomach and the respiratory tract was qualitatively and quantitatively analyzed over time in 41 consecutive mechanically ventilated patients in a Swedish intensive care unit (ICU), with special emphasis on elucidation of the role of anaerobic bacteria in the lower respiratory tract. Samples were taken from the oropharynx, gastric juice, subglottic space and trachea within 24 h (median 14 h) of intubation, and then every third day until day 18 and every fifth day until day 33. Results The patients were often heavily colonized with microorganisms not considered to belong to a healthy normal oropharyngeal and gastric flora on admission to the ICU. A majority harbored enterococci, coagulase-negative staphylococci and Candida spp. in at least one site on day 1. Anaerobic bacteria, mainly peptostreptococci and Prevotella spp., were isolated from subglottic and/or tracheal secretions in 59% of the patients. Different routes of tracheal colonization for different groups of microorganisms were found. Primary or concomitant colonization of the oropharynx with staphylococci, enterococci, enterobacteria and Candida was often seen, while Pseudomonas spp., other non-fermenting Gram-negative rods and several anaerobic species often primarily colonized the trachea, indicating exogenous or direct gastrointestinal routes of colonization. Conclusions Mechanically ventilated patients were heavily colonized in their lower airways by potential pathogenic microorganisms, including a high load of anaerobic bacteria. Different routes of colonization were shown for different species.

  • 196. Ahad, Abdul
    et al.
    Keech, Olivier
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Lindén, Pernilla
    Brouwer, Bastiaan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Stenlund, Hans
    Moritz, Thomas
    Jansson, Stefan
    Gardeström, Per
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Comparison between leaves from darkened plants and individually-darkened leaves reveals differential metabolic strategies in response to darknessManuscript (preprint) (Other academic)
  • 197.
    Ahi, Ehsan Pashay
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Richter, Florian
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Lecaudey, Laurene Alicia
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Sefc, Kristina M.
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Gene expression profiling suggests differences in molecular mechanisms of fin elongation between cichlid species2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 9052Article in journal (Refereed)
    Abstract [en]

    Comparative analyses of gene regulation inform about the molecular basis of phenotypic trait evolution. Here, we address a fin shape phenotype that evolved multiple times independently across teleost fish, including several species within the family Cichlidae. In a previous study, we proposed a gene regulatory network (GRN) involved in the formation and regeneration of conspicuous filamentous elongations adorning the unpaired fins of the Neolamprologus brichardi. Here, we tested the members of this network in the blockhead cichlid, Steatocranus casuarius, which displays conspicuously elongated dorsal and moderately elongated anal fins. Our study provided evidence for differences in the anatomy of fin elongation and suggested gene regulatory divergence between the two cichlid species. Only a subset of the 20 genes tested in S. casuarius showed the qPCR expression patterns predicted from the GRN identified in N. brichardi, and several of the gene-by-gene expression correlations differed between the two cichlid species. In comparison to N. brichardi, gene expression patterns in S. casuarius were in better (but not full) agreement with gene regulatory interactions inferred in zebrafish. Within S. casuarius, the dorsoventral asymmetry in ornament expression was accompanied by differences in gene expression patterns, including potential regulatory differentiation, between the anal and dorsal fin.

  • 198.
    Ahi, Ehsan Pashay
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Singh, Pooja
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Duenser, Anna
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Gessl, Wolfgang
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Sturmbauer, Christian
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Divergence in larval jaw gene expression reflects differential trophic adaptation in haplochromine cichlids prior to foraging2019In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 19, article id 150Article in journal (Refereed)
    Abstract [en]

    BackgroundUnderstanding how variation in gene expression contributes to morphological diversity is a major goal in evolutionary biology. Cichlid fishes from the East African Great lakes exhibit striking diversity in trophic adaptations predicated on the functional modularity of their two sets of jaws (oral and pharyngeal). However, the transcriptional basis of this modularity is not so well understood, as no studies thus far have directly compared the expression of genes in the oral and pharyngeal jaws. Nor is it well understood how gene expression may have contributed to the parallel evolution of trophic morphologies across the replicate cichlid adaptive radiations in Lake Tanganyika, Malawi and Victoria.ResultsWe set out to investigate the role of gene expression divergence in cichlid fishes from these three lakes adapted to herbivorous and carnivorous trophic niches. We focused on the development stage prior to the onset of exogenous feeding that is critical for understanding patterns of gene expression after oral and pharyngeal jaw skeletogenesis, anticipating environmental cues. This framework permitted us for the first time to test for signatures of gene expression underlying jaw modularity in convergent eco-morphologies across three independent adaptive radiations. We validated a set of reference genes, with stable expression between the two jaw types and across species, which can be important for future studies of gene expression in cichlid jaws. Next we found evidence of modular and non-modular gene expression between the two jaws, across different trophic niches and lakes. For instance, prdm1a, a skeletogenic gene with modular anterior-posterior expression, displayed higher pharyngeal jaw expression and modular expression pattern only in carnivorous species. Furthermore, we found the expression of genes in cichlids jaws from the youngest Lake Victoria to exhibit low modularity compared to the older lakes.ConclusionOverall, our results provide cross-species transcriptional comparisons of modularly-regulated skeletogenic genes in the two jaw types, implicating expression differences which might contribute to the formation of divergent trophic morphologies at the stage of larval independence prior to foraging.

  • 199.
    Ahi, Ehsan Pashay
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Singh, Pooja
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Lecaudey, Laurene Alicia
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Gessl, Wolfgang
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Sturmbauer, Christian
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Maternal mRNA input of growth and stress-response-related genes in cichlids in relation to egg size and trophic specialization2018In: EvoDevo, ISSN 2041-9139, E-ISSN 2041-9139, Vol. 9, article id 23Article in journal (Refereed)
    Abstract [en]

    Background: Egg size represents an important form of maternal effect determined by a complex interplay of long-term adaptation and short-term plasticity balancing egg size with brood size. Haplochromine cichlids are maternal mouthbrooders showing differential parental investment in different species, manifested in great variation in egg size, brood size and duration of maternal care. Little is known about maternally determined molecular characters of eggs in fishes and their relation to egg size and trophic specialization. Here we investigate maternal mRNA inputs of selected growth- and stress-related genes in eggs of mouthbrooding cichlid fishes adapted to different trophic niches from Lake Tanganyika, Lake Malawi, Lake Victoria and compare them to their riverine allies.

    Results: We first identified two reference genes, atf7ip and mid1ip1, to be suitable for cross-species quantification of mRNA abundance via qRT-PCR in the cichlid eggs. Using these reference genes, we found substantial variation in maternal mRNA input for a set of candidate genes related to growth and stress response across species and lakes. We observed negative correlation of mRNA abundance between two of growth hormone receptor paralogs (ghr1 and ghr2) across all haplochromine cichlid species which also differentiate the species in the two younger lakes, Malawi and Lake Victoria, from those in Lake Tanganyika and ancestral riverine species. Furthermore, we found correlations between egg size and maternal mRNA abundance of two growth-related genes igf2 and ghr2 across the haplochromine cichlids as well as distinct clustering of the species based on their trophic specialization using maternal mRNA abundance of five genes (ghr1, ghr2, igf2, gr and sgk1).

    Conclusions: These findings indicate that variations in egg size in closely related cichlid species can be linked to differences in maternal RNA deposition of key growth-related genes. In addition, the cichlid species with contrasting trophic specialization deposit different levels of maternal mRNAs in their eggs for particular growth-related genes; however, it is unclear whether such differences contribute to differential morphogenesis at later stages of development. Our results provide first insights into this aspect of gene activation, as a basis for future studies targeting their role during ecomorphological specialization and adaptive radiation.

  • 200.
    Ah-King, Malin
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Centre for Gender Research.
    Challenging popular myths of sex, gender and biology2013Collection (editor) (Refereed)
1234567 151 - 200 of 34646
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf