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  • 251.
    Bremer, B., K, Bremer, N. Heidari, P. Erixon, R. G. Olmstead, A. A. Anderberg, M. Källersjö, & E. Borkhardarian
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic level2002In: Molecular Phylogenetics and Evolution, Vol. 24, p. 273-300.Article in journal (Refereed)
  • 252.
    Bremer, B
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Manen, JF
    Phylogeny and classification of the subfamily Rubioideae (Rubiaceae)2000In: PLANT SYSTEMATICS AND EVOLUTION, ISSN 0378-2697, Vol. 225, no 1-4, p. 43-72Article in journal (Refereed)
    Abstract [en]

    We performed phylogenetic analyses of the subfamily Rubioideae (Rubiaceae) based on three different pieces of chloroplast DNA, the protein coding rbcL gene, the spacer sequence between atpB and rbcL (atpB-rbcL), and the recently published (Andersson and R

  • 253.
    Bremer, K
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Early Cretaceous lineages of monocot flowering plants2000In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, ISSN 0027-8424, Vol. 97, no 9, p. 4707-4711Article in journal (Refereed)
    Abstract [en]

    The phylogeny of flowering plants is now rapidly being disclosed by analysis of DNA sequence data, and currently, many Cretaceous fossils of flowering plants are being described. Combining molecular phylogenies with reference fossils of known minimum age

  • 254.
    Bremer, K.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Gondwanan evolution of the grass alliance of families (Poales)2002In: Evolution, Vol. 56, no 7, p. 1374-1387Article in journal (Refereed)
  • 255.
    Brindefalk, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Loss of Mitochondrial tRNA Genes Correlates with Loss of Genes for Aminoacyl-tRNA SynthetasesManuscript (Other academic)
    Abstract [en]

    Most mitochondrial genomes encode their own tRNAs, whereas the mitochondrial aminoacyl-tRNA synthetases (aaRS) are encoded by the nuclear genome. It has been suggested that the loss of mitochondrial tRNA genes from the mitocchondrial genome correlates with the sequence similarity between bacterial and eukaryotic aaRSs, in that aaRSs that are similar across the two domains can easily shift between charging mitochondrial and cytosolic tRNAs (Schneider 2001). However, recent work has shown that mitochondrial and cytosolic aaRSs have complex evolutionary histories and are not always of bacterial and eukaryotic origin, respectively (Brindefalk et al. 2007). We repeated the analysis performed by Schneider using all available mitochondrial genomes as of December 2006 and found that the loss of mitochondrial tRNA genes correlates with replacements of the genes for the corresponding aaRS. Our observations provide new insights into the co-evolution of mitochondrial tRNAs and their charging enzymes.

  • 256.
    Brindefalk, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Ettema, Thijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Viklund, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Tholleson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Lost and Found at Sea: a Phylomentagenomic Exploration of Mitochondrial Affiliations with Oceanic Bacteria.Manuscript (Other academic)
    Abstract [en]

     

    Background

    According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from a free-living bacterium related to present-day alpha-proteobacteria. Recent studies have identified two lineages as the closest mitochondrial relatives among bacteria with sequenced genomes; the Rickettsiales, a lineage comprising obligate intracellular pathogens, and Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the upper surface waters of the global oceans.

     

    Principal Findings

    Here, we present a phylogenetic study incorporating metagenomic data of mitochondrial genes for aerobic respiration that includes sequence data from the Global Ocean Sampling (GOS) Expedition, thereby increasing the sampling of alpha-proteobacterial sequences available for analysis greatly. Phylogenetic analysis of these expanded datasets including oceanic sequences that had been pruned down in numbers but still maintained the full genetic diversity present failed to show an increased support for a specific mitochondrial affiliation to any alpha-proteobacterial group, although concatenated datasets of different genes gave good support for conflicting mitochondrial placement. We utilized a jack-knifing method to randomly sample sequences from the GOS dataset and examined how the inclusion of such sequences influenced the support for mitochondrial affiliation in trees inferred from proteins in aerobic respiration. No evidence of an increased support for a specific mitochondrial placement in the alpha-proteobacterial tree in the jack-knifing analysis was obtained. A systematic search for sequences affiliated with mitochondria in the GOS dataset suggests the existence of previously unidentified clades of deeply diverging alpha-proteobacteria, with an unclear affiliation.

     

    Conclusions/Significance

    Our findings have several important implications. First, they support an early divergence of the mitochondrial ancestor from the alpha-proteobacterial lineage, possibly pre-dating the radiation of alpha-proteobacterial species with sequenced genomes. Second, they reject the hypothesis that the system for aerobic respiration in mitochondria is affiliated with the SAR11 clade. Third, they indicate horizontal transfer of genes for respiratory chain proteins in bacteria adapted to the upper surface waters of the oceans. Fourth, they show the presence of oceanic sequences for respiratory chain proteins that diverge as deeply as mitochondria in the alpha-proteobacterial phylogeny, possibly indicating a previously unidentified alpha-proteobacterial group at a basal position of the alpha-proteobacterial tree, underscoring the importance of expanding studies on mitochondrial origins beyond those of cultivated and intracellular bacteria. Finally, our study outlines a new methodology, phylometagenomics, which provides guidance on how to incorporate metagenome data into a phylogenetic framework for inferences of early evolutionary events.

     

  • 257.
    Britton, Tom
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Mathematics and Computer Science, Department of Mathematics.
    Oxelman, Bengt.
    Vinnersten, Annika
    Bremer, Kåre
    Phylogenetic dating by mean branch lengths with confidence limits2002In: Molecular Phylogenetics and Evolution, Vol. 24, no 1, p. 58-65Article in journal (Refereed)
  • 258.
    Broberg, Anders
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Malmgren, Louise
    Jansson, Mats
    Relations between resuspension and the content of 137Cs in freshwater fish in some Swedish lakes1995In: Journal of Ecosystem Health, Vol. 4, p. 285-294Article in journal (Refereed)
  • 259.
    Brohede, Jesper
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Rates and Patterns of Mutation in Microsatellite DNA2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Sequence comparisons of orthologous microsatellite loci in cattle and sheep revealed that the substitution rate in microsatellite flanking sequences does not differ from the rate in presumably neutrally evolving intron sequences. This suggests that microsatellites are generally located in regions that are not subjected to selection. Interestingly, a propensity for substitutions to occur in the border region between flanking and repeat sequence was found.

    Pedigree analysis of large numbers of barn swallows revealed extremely high mutation frequencies for the tetranucleotide HrU6 and pentanucleotide HrU10 repeat loci. A detailed analysis showed that both the rate and the pattern of mutation differed significantly between the two loci.

    Further analysis of HrU6 and HrU10 mutations, as well as mutation data for another hypermutable locus (HrU9) in barn swallows, revealed that mutations were more likely to arise in some families than others. This was partly, but probably not only, due to an effect of allele length on mutation rate. The mutation rate was found to vary between colonies of breeding birds, but, overall, not between two different populations.

    Single molecule genotyping of DNA prepared from human sperm cells was used to detect mutations at the tetranucleotide repeat D21S1245. A tenfold difference in mutation rate between alleles was found. Three phylogenetically distinct allele lineages could be defined, which differed significantly in mutation rate. Unexpectedly, the mutation rate was not found to increase with male age.

    Microsatellites are commonly applied in a wide range of genetic contexts including linkage mapping, forensic science and population genetics. Obtaining a detailed picture of the evolution of these tandem repeats is important in order to fully understand how to interpret microsatellite data. In addition, studies of the mechanisms underlying microsatellite mutation will provide insights in the processes that shape the eukaryotic genome.

    This thesis demonstrates that microsatellite evolution is a highly heterogeneous process that is dependent on more factors than was previously thought. As the rate and pattern may vary between loci, caution must therefore be taken when building models to handle microsatellite data.

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  • 260.
    Brunberg, Anna-Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Contribution of bacteria in the mucilage of Microcystis spp. (Cyanobacteria) to benthic and pelagic bacterial production in a hypereutrophic lake1999In: FEMS MICROBIOLOGY ECOLOGY, ISSN 0168-6496, Vol. 29, no 1, p. 13-22Article in journal (Refereed)
    Abstract [en]

    The mucilage of cyanobacteria represents a unique habitat for both water column and sediment bacteria. In Lake Vallentunasjon, Sweden, the pelagic Microcystis-associated bacteria constituted 19-40% of the total bacterial abundance, and their contribution

  • 261.
    Brunberg, Anna-Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Blomqvist, Peter
    Quantification of anthropogenic threats to lakes in a lowland county of central Sweden2001In: Ambio, ISSN 0044-7447, Vol. 30, no 3, p. 127-134Article in journal (Refereed)
    Abstract [en]

    An evaluation of the negative effects caused by anthropogenic influence on lake ecosystems was performed, using data from 143 catchments in

  • 262.
    Brunberg, Anna-Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. limnologi.
    Blomqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology. limnologi.
    Recruitment of Microcystis (Cyanophyceae) from lake sediments: the importance of littoral inocula2003In: J. Phycol., Vol. 39, p. 58-63.Article in journal (Refereed)
  • 263.
    Brunberg, Anna-Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Blomqvist, Peter
    Rydin, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Contrasting ontogeny among ephemeral hardwater lakes as revealed by sediment P-fractionation2002In: Archiv fur Hydrobiologie, Vol. 153, no 3, p. 491-502Article in journal (Refereed)
  • 264.
    Brunberg, Anna-Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Limnology.
    Nilsson, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Limnology.
    Blomqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Limnology.
    Characteristics of oligotrophic hardwater lakes in a postglacial land-rise area in mid-Sweden2002In: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 47, no 8, p. 1451-1462Article in journal (Refereed)
    Abstract [en]

    1. We describe some remarkable ephemeral, oligotrophic hardwater lakes formed becauseof land rise in the coastal areas of the Baltic Sea, that are unique in Sweden and probablyalso worldwide. Two younger, coastal lakes were studied by regular sampling for 1 yearand compared with an older (i.e. greater altitude) lake, that passed through theoligotrophic hardwater stage some 3–4000 years ago.

    2. Despite some differences in composition of the catchment, the two younger lakes weresimilar with regard to water chemistry and plankton community composition. Theconcentration of phosphorus was low while nitrogen was high, resulting in very high N/Pquotients (101 and 131). Although water colour was moderate, the concentration of organiccarbon was extremely high (average values of ‡ 20 lg TOC L–1), consisting mainly ofdissolved compounds (DOC).

    3. While the plankton was poorly developed, sediments in both lakes were covered by alayer of photosynthesising micro-organisms. This substantial 'microbial mat', which hasnot been described in detail before, was up to 15 cm thick and dominated by cyanobacteriaand purple sulphur bacteria. The concentration of sediment phosphorus was extremelylow (352 lg g–1 dw) in one of the lakes and dominated by organic-bound (residual)phosphorus.

    4. Deep sediments in the older lake, representing its oligotrophic hardwater period,differed in phosphorus composition from the currently oligotrophic hardwater lakes byhaving a strong dominance of HCl-extractable (Ca-bound) phosphorus. This indicates thatphosphorus, initially organic-bound within the microbial mat, is subsequently bound tocalcium. We hypothesise that this is promoted by the environmental conditions created bythe benthic photosynthetic activity, in combination with the prevailing hardwaterconditions.

    5. The rich and flourishing microbial community on the sediments may also explain thehigh concentration of DOC in the lake.

  • 265.
    Brunet, J
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    von, Oheimb G
    Migration of vascular plants to secondary woodlands in southern Sweden.1998In: Journal of Ecology, Vol. 86, p. 429-438Report (Other scientific)
  • 266.
    Burton, T
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Parasitism of bumble bees by Microsporidia (Protista).1998In: Senior Research Thesis, Whitman College, USA, , p. 1-19Report (Other scientific)
  • 267.
    Burén, T
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Fytometrisk undersökning av näringsämnesbegränsningen i sediment från öländska alvarsjöar.1999In: Rapport Inst Naturvetenskap, Högskolan i KalmarReport (Other scientific)
  • 268.
    Busse, S. and Snoeijs, P.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Ecology and Evolution, Plant Ecology. PLANT ECOLGY.
    Gradient responses of diatom communities in the Bothnian Sea (northern Baltic Sea), with emphasis on responses to water movement2003In: Phycologia, Vol. 42, p. 451-464Article in journal (Refereed)
  • 269.
    Busse, S.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Snoeijs, P.
    Diatom communities in the Gulf of Bothnia: their biodiversity, gradient responses and application in paleo-ecology.2002In: BFU Res. Bull, Vol. 4-5, p. 45-Article in journal (Refereed)
  • 270.
    Busse, S.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Snoeijs, P.
    Gradient responses of diatom communities in the Bothnian Bay, northern Baltic Sea.2002In: Nova Hedwigia, Vol. 74, p. 501-525Article in journal (Refereed)
  • 271.
    Busse, S.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Snoeijs, P.
    Navicula sjoersii sp. nov., N. bossvikensis sp. nov. and N. perminuta Grunow from the Baltic Sea.2002In: Diatom Res., Vol. 17, p. 271-282Article in journal (Refereed)
  • 272.
    Busse, Svenja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Plant Ecology.
    Benthic diatoms in the Gulf of Bothnia: Community analysis and diversity2002Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Benthic diatoms are valuable tools for biological monitoring and paleo-ecological reconstruction of past environmental conditions. This thesis aims at describing size-related properties of benthic diatoms and suggests that data assessment for community analysis can be improved by considering the importance of scale. It investigates which environmental factors structure epilithic diatom communities on the coast of the Gulf of Bothnia and identifies environmental factors correlated with phytobenthic biomass. It also contributes to the floristic knowledge of the Baltic Sea.

    Diatom species show large variation in size. The responses of large species (≥1000 μm3) in diatom communities to environmental factors are underestimated if solely measured as relative abundance, as is the common practice. However, relative abundance gives the best gradient resolution, as compared to surface area and biovolume, if species are counted separately in two biovolume classes. Small and large species in the same community may respond differently to the same environmental factors.

    To assess the principal environmental factors structuring diatom communities in the Gulf of Bothnia, 270 quantitative samples were collected from submerged stones. Sampling was carried out in spring in four areas of the Bothnian Bay, characterized by a stable north-south salinity gradient (0.4-3.3 psu), and in three areas of the Bothnian Sea which has a rather uniform salinity of ca. 5 psu. Canonical correspondence analysis (CCA) identified salinity and exposure to wave action as the principal factors structuring the diatom communities of the Bothnian Bay, whereas exposure to wave action was the principal factor in the Bothnian Sea. Measurements of relative ignition loss suggested that the cover of macroalgae, and thereby the higher abundance of epiphytic diatoms in the epilithic samples, was positively correlated with salinity in the Bothnian Bay and with water movement in the Bothnian Sea.

    Two new brackish water species are described, Navicula sjoersii S. Busse & Snoeijs and N. bossvikensis S. Busse & Snoeijs. The new species are compared with N. perminuta Grunow, a common brackish-water species.

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  • 273.
    Cafferty Steve, Oxelman Bengt, Eggens Frida
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Proposal to reject the name Silene polyphylla L. 1753 (Caryophyllaceae)2001In: Taxon, Vol. 50, p. 923-925Article in journal (Refereed)
  • 274.
    Cajal, Y
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. MOLECULAR EVOLUTION.
    Berg, OG
    Jain, MK
    On the origin of lag phase in monolayer enzymology2000In: Langmuir, Vol. 16, p. 252-257Article in journal (Refereed)
  • 275.
    Canbäck, B.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. MOLECULAR EVOLUTION.
    Andersson, S.G.E.
    Kurland, C.G.
    The global phylogeny of glycotic enzymes.2002In: Proc. Natl. Acad. Sci., Vol. USA 99, p. 6097-6102Article in journal (Refereed)
  • 276.
    Canbäck, Björn
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    In silico Studies of Early Eukaryotic Evolution2002Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A question of great interest in evolutionary biology is how and why the eukaryotic cell evolved. Several hypotheses have been proposed, ranging from an early emergence of a primitive eukaryotic cell, to various fusion models like the hydrogen hypothesis. Within this context, relevant bacterial gene families and genomes are examined in this thesis.

    The mitochondrion, the energy producing organelle in the eukaryotic cell, is generally believed to be of α-proteobacterial descent. To learn more about mitochondrial evolution, and therefore eukaryotic evolution, the genomes of the α-proteobacteria Bartonella henselae and Bartonella quintana were sequenced. Software was developed and used in the annotation of these genomes.

    Several gene products of nuclear-encoded genes are exported to the mitochondrion. Many of these genes are thought to originate from the emerging organelle. An analysis of the more than 400 genes encoding proteins targeted to the yeast mitochondrion indicates that one set of genes originated from the bacterial symbiont, while the eukaryotic host contributed another. Thus, the mitochondrial proteome has a dual origin.

    The hydrogen hypothesis postulates that the glycolytic genes belong to the group of genes that were transferred from symbiont to host. These genes are thoroughly analysed from a phylogenetic perspective. Contrary to the predictions of the hydrogen hypothesis, the results provide no support for a close relationship between nuclear genes encoding glycolytic enzymes and their α-proteobacterial homologs.

    In general, it is thought that intensive gene transfers may limit our ability to reconstruct gene and species evolution, especially among microbes. A phylogenetic analysis of a large cohort of genes from the AT-rich genome of the γ-proteobacterium Buchnera aphidicola (Sg) resulted in a high fraction of atypical tree topologies, previously interpreted as horizontal gene transfers. By applying methods that accommodate for asymmetric nucleotide substitutions, it is shown that many well-supported gene topologies are drastically altered, so that they now agree with the rRNA topology. The conclusion is that atypical topologies may not necessarily be evidence for horizontal gene transfers.

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  • 277.
    Carlsbecker, Annelie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Physiological Botany.
    MADS-Box Gene Phylogeny and the Evolution of Plant Form: Characterisation of a Family of Regulators of Reproductive Development from the Conifer Norway Spruce, Picea abies2002Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The evolutionary relationships between the angiosperm floral organs and the reproductive organs of other seed plants is not known. Flower organ development requires transcription factors encoded by the MADS-box genes. Since the evolution of novel morphology likely involve changes in developmental regulators, I have analysed MADS-box genes from the conifer Norway spruce, Picea abies, a representative of the gymnosperm group of seed plants.

    The results show that the MADS-box gene family has evolved via gene duplications and subsequent diversifications in correlation in time with the evolution of morphological novelties along the seed-plant lineage.

    Angiosperm MADS-box genes that determine petal and stamen development have homologues in the conifers, that are specifically active in pollen cones. It is, therefore, likely that the common ancestor of these genes controlled the development of the pollen-bearing organs in the early seed plants, and later were recruited for petal development in the angiosperms.

    Norway spruce set cones at an age of 15-20 years. One of the spruce MADS-box genes analysed may have a function in the control of the transition to reproductive phase, supported by expression data and the effect of the gene on development of transgenic Arabidopsis plants.

    Two of the spruce genes identified are not closely related to any known angiosperm gene. These may have roles in gymnosperm-specific developmental processes, possibly in the patterning of the conifer cones, as suggested by their expression patterns.

    The molecular regulation of cone- and flower development in fundamental aspects is highly conserved between conifers and angiosperms, however, differences detected may be informative regarding the origin of morphological complexity.

    List of papers
    1. MADS-box genes active in developing pollen cones of Norway spruce (Picea abies) are homologous to the B-class floral homeotic genes in angiosperms
    Open this publication in new window or tab >>MADS-box genes active in developing pollen cones of Norway spruce (Picea abies) are homologous to the B-class floral homeotic genes in angiosperms
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    1999 (English)In: Developmental Genetics, ISSN 0192-253X, E-ISSN 1520-6408, Vol. 25, no 3, p. 253-266Article in journal (Refereed) Published
    Abstract [en]

    The reproductive organs of conifers, the pollen cones and seed cones, differ in morphology from the angiosperm flower in several fundamental respects. In this report we present evidence to suggest that the two plant groups, in spite of these morphological differences and the long evolutionary distance between them, share important features in regulating the development of the reproductive organs. We present the cloning of three genes, DAL11, DAL12, and DAL13, from Norway spruce, all of which are related to the angiosperm B-class of homeotic genes. The B-class genes determine the identities of petals and stamens. They are members of a family of MADS-box genes, which also includes C-class genes that act to determine the identity of carpels and, in concert with B genes specify stamens in the angiosperm flower. Phylogenetic analyses and the presence of B-class specific C-terminal motifs in the DAL protein sequences imply homology to the B-class genes. Specific expression of all three genes in developing pollen cones suggests that the genes are involved in one aspect of B function, the regulation of development of the pollen-bearing organs. The different temporal and spatial expression patterns of the three DAL genes in the developing pollen cones indicate that the genes have attained at least in part distinct functions. The DAL11, DAL12, and 13 expression patterns in the pollen cone partly overlap with that of the previously identified DAL2 gene, which is structurally and functionally related to the angiosperm C-class genes. This result supports the hypothesis that an interaction between B- and C-type genes is required for male organ development in conifers like in the angiosperms. Taken together, our data suggests that central components in the regulatory mechanisms for reproductive organ development are conserved between conifers and angiosperms and, thus, among all seed plants.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-89833 (URN)10.1002/(SICI)1520-6408(1999)25:3<253::AID-DVG8>3.0.CO;2-P (DOI)10528266 (PubMedID)
    Note

    De två första författarna delar förstaförfattarskapet.

    Available from: 2002-04-29 Created: 2002-04-29 Last updated: 2017-12-14Bibliographically approved
    2. The DAL10 gene from Norway spruce Picea abies belongs to a potentially gymnosperm-specific subgroup of MADS-box genes and is specifically active in seed- and pollen cones
    Open this publication in new window or tab >>The DAL10 gene from Norway spruce Picea abies belongs to a potentially gymnosperm-specific subgroup of MADS-box genes and is specifically active in seed- and pollen cones
    Show others...
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-89834 (URN)
    Available from: 2002-04-29 Created: 2002-04-29 Last updated: 2016-04-25Bibliographically approved
    3. The MADS-box gene DAL1 is a potential mediator of the juvenile to adult transition in the conifer Norway spruce, Picea abies
    Open this publication in new window or tab >>The MADS-box gene DAL1 is a potential mediator of the juvenile to adult transition in the conifer Norway spruce, Picea abies
    Show others...
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-89835 (URN)
    Available from: 2002-04-29 Created: 2002-04-29 Last updated: 2016-04-25Bibliographically approved
    4. Evolutionary diversification of the MADS-box gene family; an analysis of nine novel genes from the conifer Norway spruce
    Open this publication in new window or tab >>Evolutionary diversification of the MADS-box gene family; an analysis of nine novel genes from the conifer Norway spruce
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-89836 (URN)
    Available from: 2002-04-29 Created: 2002-04-29 Last updated: 2016-04-25Bibliographically approved
    Download full text (pdf)
    FULLTEXT01
  • 278.
    Carlsbecker, Annelie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Physiological Botany.
    Izquierdo, Liz
    Sundström, Jens
    Engström, Peter
    Evolutionary diversification of the MADS-box gene family; an analysis of nine novel genes from the conifer Norway spruceManuscript (Other academic)
  • 279.
    Carlsbecker, Annelie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Physiological Botany.
    Sundström, Jens
    Tandre, Karolina
    Englund, Marie
    Kvarnheden, Anders
    Johanson, Urban
    Engström, Peter
    The DAL10 gene from Norway spruce Picea abies belongs to a potentially gymnosperm-specific subgroup of MADS-box genes and is specifically active in seed- and pollen conesManuscript (Other academic)
  • 280.
    Carlsbecker, Annelie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany.
    Sundström, Jens
    Tandre, Karolina
    Englund, Marie
    Kvarnheden, Anders
    Johansson, Urban
    Engström, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany.
    The DAL10 gene from Norway spruce (Picea abies) belongs to a potentially gymnosperm-specific subclass of MADS-box genes and is specifically active in seed cones and pollen cones.2003In: Evolution & Development, Vol. 5, no 6, p. 551-561Article in journal (Refereed)
  • 281.
    Carlsbecker, Annelie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Physiological Botany.
    Tandre, Karolina
    Johanson, Urban
    Englund, Marie
    Engström, Peter
    The MADS-box gene DAL1 is a potential mediator of the juvenile to adult transition in the conifer Norway spruce, Picea abiesManuscript (Other academic)
  • 282.
    Carlsson, C.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Pärt, P.
    EROD induction in rainbow trout (Oncorhynchus mykiss) gill epithelium cultured on permeable supports: Assymetrical distribution of substrate metabolites.2001In: Aquatic Toxicology, Vol. 54, p. 29-38Article in journal (Refereed)
  • 283.
    Carlsson, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Environmental Toxicology.
    Neurotoxic Effects of Dichlorophenyl Methylsulphones Related to Olfactory Mucosal Lesions2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis deals with the highly potent olfactory mucosa toxicant 2,6-dichlorophenyl methylsulphone (2,6-diClPh-MeSO2) and its non-toxic 2,5-chlorinated isomer (2,5-diClPh-MeSO2). In mice, both substances bind firmly in the olfactory mucosa and the olfactory bulb, which are important components of the sensory system. The 2,6-isomer induces olfactory mucosal necrosis with permanent loss of olfactory neuroepithelium and olfactory nerves. A major objective was to clarify the cause of this isomer-specific toxicity, and to identify which physicochemical characteristics determine the olfactory toxicity. The neurobehavioural toxicity of these substances was also examined.

    The results revealed a rapid CYP-catalysed covalent binding of 2,6-diClPh-MeSO2 in the rat olfactory mucosa, whereas the 2,5-dichlorinated isomer was not covalently bound.

    Acute and chronic olfactory mucosal pathology were investigated and compared in rats and mice. Twenty-four hours after dosing to rats, 2,6-diClPh-MeSO2 induced Bowman’s glands necrosis and sloughing of the olfactory epithelium similar to that previously reported in mice. At 3 weeks, however, there were dramatic differences in histological lesions. In mice, large parts of olfactory epithelium were replaced by respiratory-like epithelium. Large, bilateral, fibrous, cartilage and bone containing polyps occluding the lumen were confirmed. In rats, only minor patches of olfactory epithelium were replaced by a metaplastic atypical respiratory-like epithelium. 2,5-diClPh-MeSO2 was non-toxic in rats as well as in mice.

    In mice, 2,6-diClPh-MeSO2 induced a dose-dependent and long-lasting ( ≥12 weeks) hyperactivity as well as long-lasting maze learning deficits. At 2 weeks hyperactivity and maze learning deficits were observed also in rats. Unexpectedly, 2,5-diClPh-MeSO2 induced hyperactivity that lasted for two weeks. No effect on maze learning was observed with this isomer. No major differences between male and female rats or mice were found.

    In conclusion, the results show that a CYP-catalysed formation and covalent binding of a reactive 2,6-diClPh-MeSO2-metabolite in the Bowman’s glands precede the high olfactory mucosal toxicity in rodents. As determined by QSAR-modelling, a 2,6-dichlorinated benzene derivative with a large, polar, and strong electron withdrawing substituent in the primary position has the potential of being an olfactory mucosal toxicant. The observed 2,6-diClPh-MeSO2-induced increase in motor activity, and maze learning deficits, were not correlated to the olfactory mucosal lesions. I propose that 2,6-diClPh-MeSO2 causes a direct effect in the brain leading to neurobehaviuoral deficits.

    List of papers
    1. Isomer-specific Bioactivation and Toxicity of Dichlorophenyl Methylsulphone in Rat Olfactory Mucosa
    Open this publication in new window or tab >>Isomer-specific Bioactivation and Toxicity of Dichlorophenyl Methylsulphone in Rat Olfactory Mucosa
    2003 (English)In: Toxicologic pathology (Print), ISSN 0192-6233, E-ISSN 1533-1601, Vol. 31, no 4, p. 364-372Article in journal (Refereed) Published
    Abstract [en]

    This study aimed to explain the isomer- and site-specific toxic effects of dichlorophenyl methylsulphone in the olfactory mucosa of rats. A single ip dose of the 2,6-chlorinated isomer (16 or 65 mg/kg) induced necrosis preferentially in the Bowman's glands and neuroepithelium in the dorsomedial part of the olfactory region. Only minor damage occurred at this site in rats dosed with the 2,5-chlorinated isomer (65 mg/kg). A strong concentration- and time-dependent covalent binding of the C-14-labeled 2,6-isomer to rat olfactory microsomes was demonstrated. In contrast, no significant covalent binding of the C-14-labeled 2,5-isomer was observed. The cytochrome P450 (CYP) inhibitors metyrapone, tranylcypromine and acetonitrile inhibited covalent binding of the 2,6-isomer to olfactory microsomes. Glutathione (GSH) appeared to play a protective role as a scavenger of a reactive intermediate whereas methyl-GSH did not alter covalent binding to olfactory microsomes. As determined by microautoradiography, binding of the 2,6-chlorinated isomer in the olfactory mucosa was confined to the Bowman's glands. Both isomers showed a low binding to liver microsomes and caused no liver injury. We suggest that a CYP2A-catalyzed activation of the 2,6-chlorinated dichlorophenyl methylsulphone to a reactive intermediate and adduct formation in the Bowman's glands will initiate a site-specific toxicity of this isomer in the olfactory mucosa.

    Keywords
    Bowman's gland, olfactory epithelium, 2, 6-dichlorophenyl methylsulphone, covalent binding, CYP2A, olfactory mucosa, rat, nasal toxicity
    National Category
    Pharmacology and Toxicology
    Identifiers
    urn:nbn:se:uu:diva-93786 (URN)10.1080/01926230390201075 (DOI)12851101 (PubMedID)
    Available from: 2005-11-25 Created: 2005-11-25 Last updated: 2018-01-13Bibliographically approved
    2. Behavioural changes related to olfactory mucosal metaplasia and bulbar Glial Fibrillary Acidic Protein (GFAP) induction in methylsulphonyl-dichlorobenzene-treated mice
    Open this publication in new window or tab >>Behavioural changes related to olfactory mucosal metaplasia and bulbar Glial Fibrillary Acidic Protein (GFAP) induction in methylsulphonyl-dichlorobenzene-treated mice
    2002 In: Archives of Toxicology, ISSN 0340-5761, Vol. 76, no 8, p. 474-483Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-90538 (URN)
    Available from: 2003-05-12 Created: 2003-05-12Bibliographically approved
    3. 2,6-Dichlorophenyl methylsulphone induced behavioural impairments in rats and mice in relation to olfactory mucosal metaplasia
    Open this publication in new window or tab >>2,6-Dichlorophenyl methylsulphone induced behavioural impairments in rats and mice in relation to olfactory mucosal metaplasia
    2003 (English)In: Pharmacology and Toxicology, ISSN 0901-9928, E-ISSN 1600-0773, Vol. 93, no 4, p. 156-168Article in journal (Refereed) Published
    Abstract [en]

    2,6-Dichlorophenyl methylsulphone (2,6-diClPh-MeSO2) induces persistent olfactory mucosal metaplasia and a strong glial fibrillary acidic protein increase in the olfactory bulb of mice. Furthermore, 2,6-diClPh-MeSO2 gives rise to a long-lasting hyperactivity along with an impaired radial arm maze performance. To study cause-effect relationships, olfactory mucosal histopathology, glial fibrillary acidic protein induction and neurobehavioural deficits were re-examined in mice and rats of both sexes given a single intraperitoneal dose of 2,6-diClPh-MeSO2 (16 and 65 mg/kg). There was a clear difference in the character of the olfactory mucosal lesions in the two species. In mice, an extensive metaplasia characterised by severe fibrosis, cartilage and bone formation accompanied with large polyps filling the nasal lumen was confirmed. In rats, a dose-dependent weak metaplasia with patchy loss of olfactory epithelium was observed three weeks after dosing, preferentially at the dorsal meatus, nasal septum, and the tips of the middle ethmoturbinates. Large areas of intact olfactory epithelium remained in all animals, particularly in the low dose rats. In both species, 2,6-diClPh-MeSO2 gave rise to significantly increased motor-activities, impaired performance in the radial arm maze, and glial fibrillary acidic protein-induction. Only rats showed hyperactivity at the low dose. Performance in the Morris water maze was unaffected in rats of both sexes indicating that a general impairment in spatial learning could not be supported. We propose that the observed hyperactivity and radial arm maze acquisition deficits originated from a direct effect of 2,6-diClPh-MeSO2 in the brain rather than being a consequence of the olfactory mucosal lesion.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-90539 (URN)10.1034/j.1600-0773.2003.930402.x (DOI)14629739 (PubMedID)
    Available from: 2003-05-12 Created: 2003-05-12 Last updated: 2017-12-14Bibliographically approved
    4. Olfactory mucosal toxicity screening and multivariate QSAR modelling for chlorinated benzene derivatives
    Open this publication in new window or tab >>Olfactory mucosal toxicity screening and multivariate QSAR modelling for chlorinated benzene derivatives
    Show others...
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-90540 (URN)
    Available from: 2003-05-12 Created: 2003-05-12 Last updated: 2010-01-13Bibliographically approved
    Download full text (pdf)
    FULLTEXT01
  • 284.
    Carlsson, Carina
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Department of Environmental Toxicology.
    Bahrami, Fariba
    Fredriksson, Anders
    Brandt, Ingvar
    Behavioural changes related to olfactory mucosal metaplasia and bulbar Glial Fibrillary Acidic Protein (GFAP) induction in methylsulphonyl-dichlorobenzene-treated mice2002In: Archives of Toxicology, ISSN 0340-5761, Vol. 76, no 8, p. 474-483Article in journal (Refereed)
  • 285.
    Carlsson, Carina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Environmental Toxicology.
    Fredriksson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Environmental Toxicology.
    Brandt, Ingvar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Environmental Toxicology.
    2,6-Dichlorophenyl methylsulphone induced behavioural impairments in rats and mice in relation to olfactory mucosal metaplasia2003In: Pharmacology and Toxicology, ISSN 0901-9928, E-ISSN 1600-0773, Vol. 93, no 4, p. 156-168Article in journal (Refereed)
    Abstract [en]

    2,6-Dichlorophenyl methylsulphone (2,6-diClPh-MeSO2) induces persistent olfactory mucosal metaplasia and a strong glial fibrillary acidic protein increase in the olfactory bulb of mice. Furthermore, 2,6-diClPh-MeSO2 gives rise to a long-lasting hyperactivity along with an impaired radial arm maze performance. To study cause-effect relationships, olfactory mucosal histopathology, glial fibrillary acidic protein induction and neurobehavioural deficits were re-examined in mice and rats of both sexes given a single intraperitoneal dose of 2,6-diClPh-MeSO2 (16 and 65 mg/kg). There was a clear difference in the character of the olfactory mucosal lesions in the two species. In mice, an extensive metaplasia characterised by severe fibrosis, cartilage and bone formation accompanied with large polyps filling the nasal lumen was confirmed. In rats, a dose-dependent weak metaplasia with patchy loss of olfactory epithelium was observed three weeks after dosing, preferentially at the dorsal meatus, nasal septum, and the tips of the middle ethmoturbinates. Large areas of intact olfactory epithelium remained in all animals, particularly in the low dose rats. In both species, 2,6-diClPh-MeSO2 gave rise to significantly increased motor-activities, impaired performance in the radial arm maze, and glial fibrillary acidic protein-induction. Only rats showed hyperactivity at the low dose. Performance in the Morris water maze was unaffected in rats of both sexes indicating that a general impairment in spatial learning could not be supported. We propose that the observed hyperactivity and radial arm maze acquisition deficits originated from a direct effect of 2,6-diClPh-MeSO2 in the brain rather than being a consequence of the olfactory mucosal lesion.

  • 286.
    Carlsson, Carina
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Department of Environmental Toxicology.
    Harju, Mikael
    Bahrami, Fariba
    Cantillana, Tatiana
    Tysklind, Mats
    Brandt, Ingvar
    Olfactory mucosal toxicity screening and multivariate QSAR modelling for chlorinated benzene derivativesManuscript (Other academic)
  • 287.
    Carlsson, M
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Höggren, M
    Jaarola, M
    Tegelstrom, H
    Postglacial colonization history of Scaninavian adders (Vipera berus).1995In: Memoranda Soc. Fauna Flora Fennica, Vol. 71, p. 89-92Article in journal (Refereed)
  • 288.
    Carlsson, M.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. CONSERVATION BIOLOGY AND GENETICS.
    Höggren, M.
    Tegelström, H.
    Characterization of polymorphic microsatellite markers in the adder, Vipera berus2003In: Molecular Ecology Notes, Vol. 3, no 1, p. 73-75Article in journal (Refereed)
  • 289.
    Carlsson, M.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Tegelström, H
    Phylogeography of adders (Vipera berus) from Fennoscandia2002Chapter in book (Refereed)
  • 290.
    Carlsson, Martin
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Asymmetrical nuclear genetic variation across a contact zone between two populations of adders (Vipera berus) in Northern EuropeManuscript (Other academic)
  • 291.
    Carlsson, Martin
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Phylogeography of the Adder, Vipera berus2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The phylogeography of a wide ranging temperate species, the adder, Vipera berus, was investigated using several genetic tools, with special emphasis on the post-glacial colonisation pattern of Fennoscandia. The area was colonised from two directions by adder populations representing different glacial refugia. The two populations meet in three places and the main contact zone is situated in Northern Finland. The two other contact zones are the result of dispersal across the Baltic Sea to the Umeå archepelago and South-Western Finland. Asymmetrically distributed nuclear genetic variation compared to mitochondrial DNA in the northern contact zone suggests a skewed gene flow from the east to the west across the zone. This pattern might reflect differences in dispersal among sexes and lineages, or may be accounted for by a selective advantage for nuclear variation of eastern origin among Fennoscandian adders.

    The phylogeographic pattern for adders across the entire species range was addressed by sequencing part of the mitochondrial genome and scoring microsatellite markers. The adder can be divided into three major genetic groups. One group is confined to the Balkan peninsula harbouring the distribution range of V. b. bosniensis. A second, well differentiated group is restricted to the Southern Alps. These two areas have probably served as refugia for adders during a number of ice ages for the adders. The third group is distributed across the remainder of the species’ range, from extreme Western Europe to Pacific Russia and can be further divided into one ancestral group inhabiting the Carpathians refugial area, and three more recent groups inhabiting areas west, north and east of the Alps. The adder provides an example of a species where the Mediterranean areas are housing endemic populations, rather than the sources for post-glacial continental colonisation. Continent-wide colonisation has instead occurred from up to three cryptic northern refugia.

    List of papers
    1. The phylogeography of adders (Vipera berus) from Fennoscandia
    Open this publication in new window or tab >>The phylogeography of adders (Vipera berus) from Fennoscandia
    2002 In: Biology of the Vipers, 2002, p. 1-9Chapter in book (Other academic) Published
    Identifiers
    urn:nbn:se:uu:diva-90575 (URN)
    Available from: 2003-05-12 Created: 2003-05-12Bibliographically approved
    2. The genetic structure of adders (Vipera berus) in Fennoscandia assayed using microsatellite and RAPD markers
    Open this publication in new window or tab >>The genetic structure of adders (Vipera berus) in Fennoscandia assayed using microsatellite and RAPD markers
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-90576 (URN)
    Available from: 2003-05-12 Created: 2003-05-12 Last updated: 2010-01-13Bibliographically approved
    3. Asymmetrical nuclear genetic variation across a contact zone between two populations of adders (Vipera berus) in Northern Europe
    Open this publication in new window or tab >>Asymmetrical nuclear genetic variation across a contact zone between two populations of adders (Vipera berus) in Northern Europe
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-90577 (URN)
    Available from: 2003-05-12 Created: 2003-05-12 Last updated: 2010-01-13Bibliographically approved
    4. Phylogeography and Pleistocene refugia of the Adder (Vipera berus) as inferred from mitochondrial DNA sequence data
    Open this publication in new window or tab >>Phylogeography and Pleistocene refugia of the Adder (Vipera berus) as inferred from mitochondrial DNA sequence data
    Show others...
    2006 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 15, no 11, p. 3425-3437Article in journal (Refereed) Published
    Abstract [en]

    In order to contribute to the debate about southern glacial refugia used by temperate species and more northern refugia used by boreal or cold-temperate species, we examined the phylogeography of a widespread snake species (Vipera berus) inhabiting Europe up to the Arctic Circle. The analysis of the mitochondrial DNA (mtDNA) sequence variation in 1043 bp of the cytochrome b gene and in 918 bp of the noncoding control region was performed with phylogenetic approaches. Our results suggest that both the duplicated control region and cytochrome b evolve at a similar rate in this species. Phylogenetic analysis showed that V. berus is divided into three major mitochondrial lineages, probably resulting from an Italian, a Balkan and a Northern (from France to Russia) refugial area in Eastern Europe, near the Carpathian Mountains. In addition, the Northern clade presents an important substructure, suggesting two sequential colonization events in Europe. First, the continent was colonized from the three main refugial areas mentioned above during the Lower-Mid Pleistocene. Second, recolonization of most of Europe most likely originated from several refugia located outside of the Mediterranean peninsulas (Carpathian region, east of the Carpathians, France and possibly Hungary) during the Mid-Late Pleistocene, while populations within the Italian and Balkan Peninsulas fluctuated only slightly in distribution range, with larger lowland populations during glacial times and with refugial mountain populations during interglacials, as in the present time. The phylogeographical structure revealed in our study suggests complex recolonization dynamics of the European continent by V. berus, characterized by latitudinal as well as altitudinal range shifts, driven by both climatic changes and competition with related species.

    Keywords
    colonization history, mitochondrial DNA, molecular phylogeography, snake, Vipera berus
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-90578 (URN)10.1111/j.1365-294X.2006.03031.x (DOI)000240440800024 ()16968280 (PubMedID)
    Available from: 2003-05-12 Created: 2003-05-12 Last updated: 2017-12-14Bibliographically approved
    5. Population structure in European adders (Vipera berus) north of the Alps
    Open this publication in new window or tab >>Population structure in European adders (Vipera berus) north of the Alps
    Show others...
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-90579 (URN)
    Available from: 2003-05-12 Created: 2003-05-12 Last updated: 2010-01-13Bibliographically approved
    Download full text (pdf)
    FULLTEXT01
  • 292.
    Carlsson, Martin
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Söderberg, Linda
    Tegelström, Håkan
    The genetic structure of adders (Vipera berus) in Fennoscandia assayed using microsatellite and RAPD markersManuscript (Other academic)
  • 293.
    Carlsson, Martin
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Tegelström, Håkan
    The phylogeography of adders (Vipera berus) from Fennoscandia2002In: Biology of the Vipers, 2002, p. 1-9Chapter in book (Other academic)
  • 294.
    Carlsson, Martin
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Vila, Marta
    Ursenbacher, Sylvain
    Ananjeva, Natalia
    Tegelström, Håkan
    Population structure in European adders (Vipera berus) north of the AlpsManuscript (Other academic)
  • 295.
    Carmichael, AN
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology.
    Fridolfsson, AK
    Halverson, J
    Ellegren, H
    Male-biased mutation rates revealed from Z and W chromosome-linked ATP synthase alpha-subunit (ATP5A1) sequences in birds2000In: JOURNAL OF MOLECULAR EVOLUTION, ISSN 0022-2844, Vol. 50, no 5, p. 443-447Article in journal (Refereed)
    Abstract [en]

    Whether the mutation rate differs between sexes has been a matter of discussion for years. Molecular analyses of mammals have indicated that males mutate more often than females, as manifested by the faster rate of neutral sequence evolution on the Y chro

  • 296.
    Cassel, Anna
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Department of Conservation Biology and Genetics.
    Conservation biology and genetic structure of fringe populations of the scarce heath butterfly in Sweden2002Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    During the past century, about 82% of meadows and pastures have been lost in Sweden, with negative consequences for their flora and fauna. An example is the scarce heath butterfly, which is one of the red-listed species threatened by such habitat loss through afforestation. The main aim of this thesis was to study how the scarce heath may be affected by the ongoing loss of habitat and fragmentation. Another aim was to study how the globally peripheral and isolated position of the Swedish populations contributed to the genetic variability and differentiation of the species in Northern Europe. Mark-release-recapture techniques, habitat surveys, breeding experiments and molecular genetic analyses were used to address these questions.

    Genetic variability was lower in the Swedish populations than populations in more central parts of its distribution. At a local scale, the occurrence and local abundance of the scarce heath were correlated with patch size and isolation, and the abundance of certain plant species. Populations within a six km2 area showed significant genetic differentiation, and small and isolated populations expressed signs of inbreeding depression. Mark-release-recapture studies indicated that mobility between patches was restricted, and the species seemed to disperse primarily in a stepping-stone like fashion. However, the genetic differentiation did not follow an isolation-by-distance pattern. This discrepancy may be due to the relatively recent changes of the landscape. If the ongoing loss of habitat is not stopped and reversed, there is risk of a chain reaction of local extinctions, which may entail collapse of the whole metapopulation.

  • 297.
    Cassel Anna, Tammaru Toomas
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. CONSERVATION BIOLOGY AND GENETICS.
    Allozyme variability in central, peripheral and isolated populations of the scarce heath (Coenonympha hero: Lepidoptera, Nymphalidae); implications for conservation2003In: Conservation GeneticsArticle in journal (Refereed)
    Abstract [en]

    Genetic drift tends to lower genetic variability in peripheral and isolated populations. These populations also tend to diverge from more central populations if the degree of isolation is high enough. These processes could have opposite effects on the val

  • 298.
    Cassel, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology.
    Windig, Jack
    Nylin, Sören
    Wiklund, Christer
    Effects of population size and food stress on fitness-related characters in the scarce heath, a rare butterfly in Western Europe2001In: Conservation Biology, ISSN 0888-8892, E-ISSN 1523-1739, Vol. 15, no 6, p. 1667-1673Article in journal (Refereed)
    Abstract [en]

    Abstract: Knowledge about the effects of inbreeding in natural populations is scarce, especially in invertebrates. We analyzed to what extent fitness-related traits in the scarce heath ( Coenonympha hero), a butterfly, are affected by population size and isolation and whether differences in food quality influence these effects. We categorized nine populations as either large or small and isolated. Full-sib groups of offspring from 27 females were followed under seminatural conditions. Because of increased zygote mortality, egg hatchability was significantly lower in the small and isolated populations than in the large ones. Population category had no effect on larval weight under optimal conditions, but weight was significantly lower in the small-isolated category with low food quality. The effects of inbreeding can thus be hidden when conditions are benign but can appear under stress. Survival also differed significantly between population categories, and larval developmental time tended to be longer in the small-isolated category, irrespective of food conditions. We suggest that the differences in fitness between offspring from large and small isolated populations are at least partly due to inbreeding. This adds a further threat to a species that is already suffering from decreasing population sizes and increasing isolation among populations.

  • 299.
    Castensson, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    High-resolution Studies of mRNA Expression in Brain: A Search for Genes Differently Expressed in Schizophrenia2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Gene expression differences between patients and controls can be used to find susceptibility genes and drug targets for a disease. High-resolution strategies are required because the differences between the investigated groups may be small and numerous factors may affect the mRNA quantity. This thesis is based on the use of real-time RT-PCR combined with a new statistical approach, developed to detect small differences between patients and controls and differences due to patient subgroups.

    Comparisons between human brain biopsy and autopsy samples showed that post-mortem tissue can be used to make conclusions on the relative mRNA levels in the living brain.

    Power analysis based on human brain mRNA expression from 14 genes adjusted with two reference genes, revealed that a sample size of 50 patients and 50 controls was required to detect a 2-fold difference with a power and a confidence of 95%. A similar study in rats revealed that approximately the same sample size was required for rat brain mRNA expression studies.

    The mRNA levels of several genes were studied in 55 schizophrenia and 55 control prefrontal brain autopsies, using a novel and more powerful statistical analysis. The serotonin receptor 2C gene (HTR2C) showed a significant 1.5-fold decrease in the patients as compared to controls, and the monoamine oxidase B gene (MAOB) a 1.2-fold increase.

    The mechanism behind the decrease of HTR2C mRNA levels was investigated by studying the correlation of drug treatment and HTR2C promoter polymorphisms to the HTR2C expression levels. The observed decrease was present in untreated patients, suggesting that the HTR2C mRNA decrease is correlated with the disease and not the treatment. There was no association between promoter polymorphisms and HTR2C expression levels. Thus, the molecular mechanism for the decreased expression remains unclear. Nevertheless, the results support a role for monoaminergic synapses in schizophrenia.

    List of papers
    1. High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies
    Open this publication in new window or tab >>High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies
    2000 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 10, no 8, p. 1219-29Article in journal (Refereed) Published
    Abstract [en]

    Quantification of mRNA levels in human cortical brain biopsies and autopsies was performed using a fluorogenic 5' nuclease assay. The reproducibility of the assay using replica plates was 97%-99%. Relative quantities of mRNA from 16 different genes were evaluated using a statistical approach based on ANCOVA analysis. Comparison of the relative mRNA levels between two groups of samples with different time postmortem revealed unchanged relative expression levels for most genes. Only CYP26A1 mRNA levels showed a significant decrease with prolonged time postmortem (p = 0.00004). Also, there was a general decrease in measured mRNA levels for all genes in autopsies compared to biopsies; however, on comparing mRNA levels after adjusting with reference genes, no significant differences were found between mRNA levels in autopsies and biopsies. This observation indicates that studies of postmortem material can be performed to reveal the relative in vivo mRNA levels of genes. Power calculations were done to determine the number of individuals necessary to detect differences in mRNA levels of 1.5-fold to tenfold using the strategy described here. This analysis showed that samples from at least 50 individuals per group, patients and controls, are required for high-resolution ( approximately twofold changes) differential expression screenings in the human brain. Experiments done on ten individuals per group will result in a resolution of approximately fivefold changes in expression levels. In general, the sensitivity and resolution of any differential expression study will depend on the sample size used and the between-individual variability of the genes analyzed.

    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-90900 (URN)10.1101/gr.10.8.1219 (DOI)10958640 (PubMedID)
    Available from: 2003-10-14 Created: 2003-10-14 Last updated: 2017-12-14Bibliographically approved
    2. Analysis of gene expression in the rat hippocampus using Real Time PCR reveals high inter-individual variation in mRNA expression levels
    Open this publication in new window or tab >>Analysis of gene expression in the rat hippocampus using Real Time PCR reveals high inter-individual variation in mRNA expression levels
    Show others...
    2002 (English)In: Journal of Neuroscience Research, ISSN 0360-4012, E-ISSN 1097-4547, Vol. 67, no 2, p. 225-34Article in journal (Refereed) Published
    Abstract [en]

    In mammals, gene transcription is a step subjected to tight regulation mechanisms. In fact, changes in mRNA levels in the central nervous system (CNS) can account for numerous phenotypic differences in brain function. We performed a high-resolution analysis of mRNA expression levels for 37 genes selected from a normal rat hippocampus cDNA library. mRNA amounts were quantified using a Real Time PCR SYBR Green assay. We found that, in general, individuals from an inbred rat population (n = 20) have shown 2-3 times differences in the basal level of expression of the genes analyzed. Up to several fold differences among individuals were observed for certain genes. These inter-individual differences were obtained after correction for the different amounts of mRNA in each sample. Power calculations were performed to determine the number of individuals required to detect reliable differences in expression levels between a control and an experimental group. These data indicated that, depending on the variability of the candidate gene selected, it was necessary to analyze from five to 135 individuals in each group to detect differences of 50% in the levels of mRNA expression between two groups investigated. The comparison of mRNA abundance from different genes revealed a wide range of expression levels for the 37 genes, showing a 26,000-fold difference between the highest and lowest expressed gene.

    National Category
    Genetics Physiology
    Identifiers
    urn:nbn:se:uu:diva-90901 (URN)10.1002/jnr.10105 (DOI)
    Available from: 2003-10-14 Created: 2003-10-14 Last updated: 2018-01-13Bibliographically approved
    3. Decrease of serotonin receptor 2C in schizophrenia brains identified by high-resolution mRNA expression analysis
    Open this publication in new window or tab >>Decrease of serotonin receptor 2C in schizophrenia brains identified by high-resolution mRNA expression analysis
    2003 (English)In: Biological Psychiatry, ISSN 0006-3223, E-ISSN 1873-2402, Vol. 54, no 11, p. 1212-1221Article in journal (Refereed) Published
    Abstract [en]

    BACKGROUND: RNA expression profiling can provide hints for the selection of candidate susceptibility genes, for formulation of hypotheses about the development of a disease, and/or for selection of candidate gene targets for novel drug development. We measured messenger RNA expression levels of 16 candidate genes in brain samples from 55 schizophrenia patients and 55 controls. This is the largest sample so far used to identify genes differentially expressed in schizophrenia brains. METHODS: We used a sensitive real-time polymerase chain reaction methodology and a novel statistical approach, including the development of a linear model of analysis of covariance type. RESULTS: We found two genes differentially expressed: monoamine oxidase B was significantly increased in schizophrenia brain (p =.001), whereas one of the serotonin receptor genes, serotonin receptor 2C, was significantly decreased (p =.001). Other genes, previously proposed to be differentially expressed in schizophrenia brain, were invariant in our analysis. CONCLUSIONS:The differential expression of serotonin receptor 2C is particularly relevant for the development of new atypical antipsychotic drugs. The strategy presented here is useful to evaluate hypothesizes for the development of the disease proposed by other investigators.

    National Category
    Physiology Genetics
    Identifiers
    urn:nbn:se:uu:diva-90902 (URN)10.1016/S0006-3223(03)00526-2 (DOI)
    Available from: 2003-10-14 Created: 2003-10-14 Last updated: 2018-01-13Bibliographically approved
    4. Statistical methodology in case-control 5'-nuclease assays: statistical design, modelling and inference for identification of differentially expressed genes
    Open this publication in new window or tab >>Statistical methodology in case-control 5'-nuclease assays: statistical design, modelling and inference for identification of differentially expressed genes
    (English)Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-90903 (URN)
    Available from: 2003-10-14 Created: 2003-10-14 Last updated: 2010-02-11Bibliographically approved
    5. Serotonin receptor 2C (HTR2C) and schizophrenia: effect of medication and genetic variants on expression levels
    Open this publication in new window or tab >>Serotonin receptor 2C (HTR2C) and schizophrenia: effect of medication and genetic variants on expression levels
    Show others...
    (English)Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-90904 (URN)
    Available from: 2003-10-14 Created: 2003-10-14 Last updated: 2010-02-11Bibliographically approved
    Download full text (pdf)
    FULLTEXT01
  • 300.
    Castensson, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Emilsson, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Preece, Paul
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies2000In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 10, no 8, p. 1219-29Article in journal (Refereed)
    Abstract [en]

    Quantification of mRNA levels in human cortical brain biopsies and autopsies was performed using a fluorogenic 5' nuclease assay. The reproducibility of the assay using replica plates was 97%-99%. Relative quantities of mRNA from 16 different genes were evaluated using a statistical approach based on ANCOVA analysis. Comparison of the relative mRNA levels between two groups of samples with different time postmortem revealed unchanged relative expression levels for most genes. Only CYP26A1 mRNA levels showed a significant decrease with prolonged time postmortem (p = 0.00004). Also, there was a general decrease in measured mRNA levels for all genes in autopsies compared to biopsies; however, on comparing mRNA levels after adjusting with reference genes, no significant differences were found between mRNA levels in autopsies and biopsies. This observation indicates that studies of postmortem material can be performed to reveal the relative in vivo mRNA levels of genes. Power calculations were done to determine the number of individuals necessary to detect differences in mRNA levels of 1.5-fold to tenfold using the strategy described here. This analysis showed that samples from at least 50 individuals per group, patients and controls, are required for high-resolution ( approximately twofold changes) differential expression screenings in the human brain. Experiments done on ten individuals per group will result in a resolution of approximately fivefold changes in expression levels. In general, the sensitivity and resolution of any differential expression study will depend on the sample size used and the between-individual variability of the genes analyzed.

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