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  • 1001.
    Wallin, Anita
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Fysiologisk botanik.
    Iwarsson, Mattias
    Botanical Garden.
    Artonårig provodling av mikroförökad masurbjörk2004In: Lustgården, Vol. 84, p. 35-40Article in journal (Other scientific)
    Abstract [en]

    Propagation and cultivation of masur figure birch. Figure wood has fascinated foresters and craftsmen for centuries. The curly birch, Betula pendula var. carelica, is the most common curly-grained wood, displaying a characteristic pattern of curly fibers. Three different types of curly birch, one with protuberances, one with neck masur and one slow-growing clone, were selected and micropropagated 1985 and planted at Pustnäs at Fyrisån, Uppsala, 1987. Micropropagated individuals of the same clone are very similar in tree morphology, growth and masur characteristics.

    Furthermore a birch from Valls Hage, featuring extreme tumours were micropropageted and plants were replanted in the arboretum.

  • 1002.
    Wallin, Anita
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. fysiologisk botanik.
    Iwarsson, Mattias
    Botanical Garden.
    Mikroförökning av björkar2004In: Lustgården, ISSN 0349-0033, Vol. 84, p. 41-54Article in journal (Other (popular scientific, debate etc.))
    Abstract [en]

    To preserv biodiversity, individual birches of special interest have been propagated in-vitro. All selected clones have characteristics that should have been lost if sexually propagated. Many of the propagated birches were selected and cultivated in Botanical gardens 50 years ago and must be renewed if they shall be saved for future.

    A technical description of the micropropagation process is given, and the development of in-vitro shoots is visually documented

    The history and taxonomy of birches from the time of Carl Linnaeus to present day are reviewed.

  • 1003.
    Wallin, Anita
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Physiological Botany. Fysiologisk botanik.
    Nylinder, Mats
    Inst. f .skogens produkter och marknader, SLU.
    Träd- och virkesegenskaper hos två kloner av mikroförökad masurbjörk2005Report (Other scientific)
    Abstract [en]

    The curly birch (Betula pendula var. carelica) has a wood that deviates from the non-curly form of birch. The curly birch has wavy lines or grains in the wood.

    The masur formation is genetically controlled by sexual crossing or can eventually be formed by new formations of curly birches. Each individual has a unique pattern of curly-grained wood. In order to preserv the same pattern in many trees vegetative propagation has to be utilized. Rooting of birch cuttings is more or less impossible. Micropropagation is a more efficient method than grafting or inoculation.

    Cloning of curly birch would be a possibility to produce trees with a predetermined stucture of the wood and in large quantities. In the light of these facts one need a model to characterize the wood and to make sure that the individuals from the same clone give a similar wood.

    In 1985 three different curly birches and one non-curly birch were micropropagated in an examination work supervised by Anita Wallin. Of each clone about 15 micropropagated plants were planted and fenced.

    The aim of this study was to classify the curly-grained wood and to compare the wood from 5 trees in two different micropropagated curly birches.

    Wood characteristics. The difference is great between the wood structure of the cross-section of fully developed masur rose in the two clones. The disturbances of the wood are more extensive in M3 and the angle somewhat more acute in M3 than in M1.

    The utility of the clones in industríal trade. There is a great difference in prerequisite for industrial processing of the wood. Clone M1 yields relatively straight and long logs with homogenous wood structure, compared to M3. Clone M1 would be usable in veneer turnings and veneer cuttings as the veneer surface would be uniform all over.

    Micropropagation foir efficient curly-grained wood producation. Cloning of curly birch by micropropagation is proven to be a reliable method to obtain many individuals with the same stem form and equivalent masur quality.

  • 1004. Wang, Yan
    et al.
    Henriksson, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Söderman, Eva
    Nordin Henriksson, Kerstin
    Sundberg, Eva
    Engström, Peter
    The Arabidopsis homeobox gene, ATHB16, regulates leaf development and the sensitivity to photoperiod in Arabidopsis2003In: Developmental Biology, Vol. 264, p. 228-239Article in journal (Refereed)
  • 1005. Wayne, R.K
    et al.
    Geffen, E.
    Vilà, C.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Conservation Genetics of Canids2004In: Canids: Foxes, Wolves, Jackals and Dogs.: Status Survey and Conservation Aciton Plan, IUCN/SSC Canid Specialist Group, Gland, Switzerland. Cambridge, UK. , 2004Chapter in book (Other scientific)
  • 1006. Wayne, R.K.
    et al.
    Geffen, E.
    Vilà, C.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Population and conservation genetics of canids.2004In: Biology and Conservation of Wild Canids., Oxford University Press , 2004Chapter in book (Other scientific)
  • 1007. Wayne, RK
    et al.
    Leonard, JA
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Evol Biol.
    Vila, C
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Evol Biol.
    Genetic analysis of dog domestication2006In: Documenting Domestication: New genetic and archaeological paradigms, University of California Press, Berkeley , 2006Chapter in book (Other scientific)
  • 1008. Webster, Matthew T.
    et al.
    Axelsson, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Ellegren, Hans
    Strong regional biases in nucleotide substitution in the chicken genome2006In: Mol. Biol. Evol., ISSN 0737-4038, Vol. 23, no 6, p. 1203-1216Article in journal (Refereed)
  • 1009.
    Webster, Matthew T
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Axelsson, Erik
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Ellegren, Hans
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Strong regional biases in nucleotide substitution in the chicken genome.2006In: Mol Biol Evol, ISSN 0737-4038, Vol. 23, no 6, p. 1203-16Article in journal (Refereed)
    Abstract [en]

    Department of Evolution, Genomics and Systematics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. websterm@tcd.ie

    Interspersed repeats have emerged as a valuable tool for studying neutral patterns of molecular evolution. Here we analyze variation in the rate and pattern of nucleotide substitution across all autosomes in the chicken genome by comparing the present-day CR1 repeat sequences with their ancestral copies and reconstructing nucleotide substitutions with a maximum likelihood model. The results shed light on the origin and evolution of large-scale heterogeneity in GC content found in the genomes of birds and mammals--the isochore structure. In contrast to mammals, where GC content is becoming homogenized, heterogeneity in GC content is being reinforced in the chicken genome. This is also supported by patterns of substitution inferred from alignments of introns in chicken, turkey, and quail. Analysis of individual substitution frequencies is consistent with the biased gene conversion (BGC) model of isochore evolution, and it is likely that patterns of evolution in the chicken genome closely resemble those in the ancestral amniote genome, when it is inferred that isochores originated. Microchromosomes and distal regions of macrochromosomes are found to have elevated substitution rates and a more GC-biased pattern of nucleotide substitution. This can largely be accounted for by a strong correlation between GC content and the rate and pattern of substitution. The results suggest that an interaction between increased mutability at CpG motifs and fixation biases due to BGC could explain increased levels of divergence in GC-rich regions.

  • 1010.
    Webster, Matthew T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Hagberg, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Is there evidence for convergent evolution around human microsatellites?2007In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 24, no 5, p. 1097-1100Article in journal (Refereed)
    Abstract [en]

    A study by Vowles and Amos (2004) identified atypical patterns of base composition around human microsatellites and argued that microsatellites generate mutational biases in their flanking regions. Here, we perform simulations of molecular evolution using a simple model that suggest similar patterns can be produced without any such biases in genome evolution.

  • 1011.
    Webster, Matthew T
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Smith, Nick G C
    Hultin-Rosenberg, Lina
    Arndt, Peter F
    Ellegren, Hans
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Male-driven biased gene conversion governs the evolution of base composition in human alu repeats.2005In: Mol Biol Evol, ISSN 0737-4038, Vol. 22, no 6, p. 1468-74Article in journal (Refereed)
    Abstract [en]

    Regional biases in substitution pattern are likely to be responsible for the large-scale variation in base composition observed in vertebrate genomes. However, the evolutionary forces responsible for these biases are still not clearly defined. In order to study the processes of mutation and fixation across the entire human genome, we analyzed patterns of substitution in Alu repeats since their insertion. We also studied patterns of human polymorphism within the repeats. There is a highly significant effect of recombination rate on the pattern of substitution, whereas no such effect is seen on the pattern of polymorphism. These results suggest that regional biases in substitution are caused by biased gene conversion, a process that increases the probability of fixation of mutations that increase GC content. Furthermore, the strongest correlate of substitution patterns is found to be male recombination rates rather than female or sex-averaged recombination rates. This indicates that in addition to sexual dimorphism in recombination rates, the sexes also differ in the relative rates of crossover and gene conversion.

  • 1012.
    Webster, Matthew T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Smith, Nick G.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Lercher, M.J.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Gene expression, synteny, and local similarity in human noncoding mutation rates2004In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 21, no 10, p. 1820-1830Article in journal (Refereed)
    Abstract [en]

    The human genome is organized with regard to many features such as isochores, Giemsa bands, clusters of genes with similar expression patterns, and contiguous regions with shared evolutionary histories (synteny blocks). In addition to these genomic features, it is clear that mutation rates also vary across the human genome. To address how mutation rates and genomic features are related, we analyzed substitution rates at three classes of putatively neutral noncoding sites (nongenic, intronic, and ancestral repeats) in approximately 14 Mb of human-chimpanzee alignments covering human chromosome 7. Patterns of mutation rate variation inferred from substitution rate variation differ among the three site classes. In particular, we find that intronic mutation rates are strongly affected by the breadth of expression of the genes in which they reside, with broadly expressed genes exhibiting low mutation rates, probably as a consequence of the transcription-coupled repair process acting in the germ line. All site classes show significant local similarities in mutation rate at the megabase scale, and regional similarities in nongenic mutation rate covary with blocks of synteny between the human and mouse genomes, indicating that the evolutionary history of a genomic region is an important determinant of mutation rate.

  • 1013.
    Webster, Matthew Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Smith, Nick G.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Fixation biases affecting human SNPs?2004In: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 20, no 3, p. 122-126Article in journal (Refereed)
    Abstract [en]

    Under neutrality all classes of mutation have an equal probability of becoming fixed in a population. In this article, we describe our analysis of the frequency distributions of >5000 human SNPs and provide evident of biases in the process of fixation of certain classes of point mutation that are most likely to be attributable to biased gene conversion. The results indicate an increased fixation probability of mutations that result in the incorporation of a GC base pair. Furthermore, in transcribed regions this process exhibits strand asymmetry, and is biased towards preserving a G base on the coding strand. Biased gene conversion has the potential to explain both existence of isochores and the compositional asymmetry in mammalian transcribed regions.

  • 1014.
    Wedén, Christina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Black Truffles of Sweden: Systematics, Population Studies, Ecology and Cultivation of Tuber aestivum syn. T. uncinatum2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Tuber aestivum is an ectomycorrhizal ascomycete with underground fruit bodies. It is an economically important species, but has been regarded as endangered in Sweden. My inventory has increased the number of reported localities from 3 to 31.

    It has long been debated whether T. aestivum and T. uncinatum are conspecific or not, so a clarification would help conservation biology and cultivation. My study included 117 fruit bodies of both taxa from 8 countries. The phylogenetic (ITS) and microscopic analyses showed that the two taxa were synonyms and that the spore reticulum height, used to separate the taxa, is not diagnostic. T. aestivum was clearly different from T. mesentericum, which I reported new to Sweden.

    The Gotland T. aestivum population was genetically distinct (RAPD) from other European specimens. The genetic variation suggested sexual reproduction. The habitat of 18 T. aestivum sites on Gotland were analysed and compared with data from France. No striking functional differences in soil chemistry were found, so a possible T. aestivum ecotype on Gotland would rather be an adaptation to the colder and drier climate. Selecting local T. aestivum inoculum for truffle orchards in Northern Europe could be important for successful truffle production.

    In 1999, 10 experimental truffle orchards with a total of 240 oak and hazel seedlings were established on Gotland, and as a result of this project 3000 commercial oak seedlings were planted in 2000-2001. In 2004, T. aestivum mycorrhiza was still present in all of the 22 orchards studied on Gotland, some in soils different from natural habitats. In addition, the project has also generated a truffle cultivation association, a truffle company, truffle dog breeding and export of T. aestivum to France.

    List of papers
    1. Species recognition in the truffle genus Tuber: the synonyms Tuber aestivum and Tuber uncinatum
    Open this publication in new window or tab >>Species recognition in the truffle genus Tuber: the synonyms Tuber aestivum and Tuber uncinatum
    2005 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 7, no 10, p. 1535-1546Article in journal (Refereed) Published
    Abstract [en]

    The two morphologically similar truffles Tuber aestivum and T. uncinatum have caused confusion because T. uncinatum is regarded by different authors, as either a distinct species, variety, subspecies, or synonym of T. aestivum. A clarification of the relationship between the two truffles would help both conservation biology and cultivation. We aimed both to test the reliability of the only quantitative morphological character used to distinguish the two taxa, i.e. the height of the spore reticulum, and to compare sequences of the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region. Our study included 117 fruit bodies of T. aestivum and T. uncinatum, originating from eight European countries. The results showed that the spore reticulum height is not diagnostic. The phylogenetic analysis of ITS sequences from 81 fruit bodies and an additional 32 sequences from GenBank showed that T. aestivum and T. uncinatum were intermingled in one highly supported (100% bootstrap) monophyletic clade, separate from its sister species Tuber mesentericum. We conclude that T. aestivum and T. uncinatum are synonyms and the species should be named T. aestivum, as the oldest name has priority. For traders, T. aestivum syn. T. uncinatum should be used until conformity has been reached.

    National Category
    Biological Systematics
    Identifiers
    urn:nbn:se:uu:diva-92400 (URN)10.1111/j.1462-2920.2005.00837.x (DOI)16156727 (PubMedID)
    Available from: 2004-11-05 Created: 2004-11-05 Last updated: 2018-03-29Bibliographically approved
    2.
    The record could not be found. The reason may be that the record is no longer available or you may have typed in a wrong id in the address field.
    3. Tuber aestivum syn. T. uncinatum biotopes and their history on Gotland, Sweden
    Open this publication in new window or tab >>Tuber aestivum syn. T. uncinatum biotopes and their history on Gotland, Sweden
    2004 (English)In: Mycological Research, ISSN 0953-7562, Vol. 108, no 3, p. 304-310Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92402 (URN)
    Available from: 2004-11-05 Created: 2004-11-05 Last updated: 2009-04-02Bibliographically approved
    4. Cultivation of the Burgundy truffle, Tuber aestivum syn. T. uncinatum in Sweden
    Open this publication in new window or tab >>Cultivation of the Burgundy truffle, Tuber aestivum syn. T. uncinatum in Sweden
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92403 (URN)
    Available from: 2004-11-05 Created: 2004-11-05 Last updated: 2010-01-14Bibliographically approved
  • 1015.
    Wedén, Christina
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Systematisk botanik.
    Bourgognetryffel: -en äkta, svart, svensk delikatess2005In: Biodiverse, ISSN 1401-5064, Vol. 10, no 3, p. 10-11Article in journal (Other (popular scientific, debate etc.))
    Abstract [en]

    Forskningsprojektet om den rödlistade svampen sommartryffel (Tuber aestivum, även kallad bourgognetryffel) var finansierat av myndigheterna på Gotland i samarbete med Högskolan på Gotland. Arbetet resulterade i en doktorsavhandling som Christina Wedén försvarade vid Uppsala universitet i november 2004.

  • 1016.
    Wedén, Christina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Research on Choiromyces venosus — a new delicacy?2007In: Opera Mycologica, ISSN 1654-5079, Vol. 1, p. 42-49Article in journal (Other academic)
  • 1017.
    Wedén, Christina
    et al.
    systematisk biologi. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Danell, Eric
    Uppsala University, Music and Museums, Museum of Evolution. botansiska sektionen. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Stjärnhovstryffel - Släktet Choiromyces i Sverige och Europa2007In: Systematikdagarna 2007: Lund 28-29 november, 2007Conference paper (Other academic)
    Abstract [sv]

    Forskning om tryffeln på Gotland och odling av Tuber aestivum startades 1997. Ett grundläggande arbete var att genetiskt och morfologiskt visa att T. aestivum och det i Frankrike använda namnet T. uncinatum är synonyma, trots tidigare hävdade morfologiska och genetiska skillnader. Intresse finns idag att odla tryffel även på det svenska fastlandet. Tryffelodling innebär plantering av ympade trädplantor av ex. ek och hassel. På det svenska fastlandet växer Choiromyces venosus (stjärnhovstryffel), en intressant kandidat för utveckling av tryffelodling. Till skillnad från T. aestivum som växer på Gotland och Öland, har stjärnhovstryffeln ätits av lokalbefolkningen i mer än hundra år i Sverige, men mycket lite är känt om dess ekologi och biologi. Den är även en uppskattad delikatess i ex. Tyskland och Ungern, medan den i Frankrike och Italien anses giftig. I det pågående forskningsprojektet ämnar vi undersöka systematik, ekologi, vitamininnehåll, kemi och möjlighet till odling av stjärhovstryffeln. Släktet Choiromyces är dåligt utrett i Europa. Choiromyces venosus och C. meandriformis används som synonymer, ibland också C. gangliiformis. Nyinsamlat- och herbariematerial från Sverige och Europa kommer att studeras morfologiskt, genetiskt (DNA) och kemiskt för att utreda systematik och möjliga fylogenetiska kopplingar till dess påstådda giftighet i södra Europa.

  • 1018.
    Wedén, Christina
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk Botanik.
    Chevalier, Gérard
    Danell, Eric
    Uppsala University, Museums etc., Museum of Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Botanik.
    Characterisation of Tuber aestivum syn. T. uncinatum biotopes and their history on Gotland2004In: Mycological Research, ISSN 0953-7562, Vol. 108, no 3, p. 304-310Article in journal (Refereed)
    Abstract [en]

    This study aimed at testing the hypothesis that the genetically distinct Tuber aestivum population on the island of Gotland, Sweden, is adapted to habitats different from French T. aestivum populations. The soil structure, soil chemistry, bedrock, climate, vegetation and host tree continuity of 18 T. aestivum sites on Gotland were analysed and compared with data from France. We conclude that T. aestivum can grow in soils with a broad soil structure range and that no striking differences in soil chemistry were found. No T. aestivum indicator plants other than the host trees were found, but the host tree continuity on the T. aestivum sites on Gotland was more than 300 yr. If the T. aestivum population on Gotland constitutes an ecotype it is rather an adaptation to the colder and drier climate on Gotland. Selecting local T. aestivum inoculum for truffle orchards in northern Europe could be important for successfull truffle production.

  • 1019.
    Wedén, Christina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Chevalier, Gérard
    Danell, Eric
    Tuber aestivum syn. T. uncinatum biotopes and their history on Gotland, Sweden2004In: Mycological Research, ISSN 0953-7562, Vol. 108, no 3, p. 304-310Article in journal (Refereed)
  • 1020.
    Wedén, Christina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Danell, Eric
    Uppsala University, Museums etc., Museum of Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    The first cultivated truffle in Scandinavia produced on Gotland2007In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 101, no 5, p. 289-291Article in journal (Other academic)
    Abstract [en]

    On the 29th of November 2005 the Swedish-trained truffle dog Biscuit found the first cultivated truffle in Scandinavia on the island of Gotland, Sweden. The truffle orchard at Mulde, Fröjel parish, is one of ten orchards established on Gotland in 1999 by the Swedish truffle research project in cooperation between Gotland University and Uppsala University. Each orchard harbours 12 oak seedlings (Quercus robur) and 12 hazel seedlings (Corylus avellana) inoculated with the Burgundy truffle Tuber aestivum syn. T. uncinatum by the French truffle nurseries Agri-truffe and Robin pépinères. The truffle was found a few centimetres below the earth surface, 20 centimetres from the trunk of an oak tree. It had mature spores and weighed 15 g. The finding of the first cultivated truffle six years after planting the orchard is comparable with French results and promising for the future establishment of new oak and hazel biotopes for truffle cultivation in Scandinavia.

  • 1021.
    Wedén, Christina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Danell, Eric
    Uppsala University, Music and Museums, Museum of Evolution. botaniska sektionen. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Jägerstad, Margaretha
    Systematics, ecology, pharmacognosy, vitamin content and cultivation of Choiromyces in Sweden2007In: The fifth international workshop of edible mycorrhizal mushrooms, 2007Conference paper (Other academic)
    Abstract [en]

    In spite of a world market for mushrooms estimated at 5 million tonnes, and in spite of fungi being six times richer in species than plants, and in spite of the demand for functional foods, research on edible and medicinal mushrooms has been neglected in Sweden. Our Tuber aestivum (syn. T. uncinatum) truffle project on the Swedish island of Gotland has been scientifically and economically a success. Since landowners familiar with Choiromyces truffles in Sweden have urged for research, we intend to illuminate the following questions: Are there one or several species in Europe? What are the preferred mycorrhizal hosts, soils and climate? Can mycelium be cultivated in large scale? Is it possible to synthesise mycorrhiza and to establish truffle orchards? Does the Swedish Choiromyces contain any toxic or anti-inflammatory substances? Could Choiromyces be an important source of vitamins?

    From 2006 we have confirmed three new localities for Choiromyces venosus in Sweden, using a trained truffle dog to find the mature fruit bodies. By using the dog, completely hypogeous, mature fruit bodies were found in contrast to the former observations that mature fruit bodies always protrude up through the soil surface. We have pure cultures of C. venosus growing on modified Fries media, confirmed by PCR.

    This project combines basic and applied research with the aim to create a new cash crop and new products of benefit to rural economy and Swedish industry. The project also addresses important questions about the taxonomy and biology of a mushroom genus. A successful project may generate new plantations on the Swedish main land of benefit to rural economy and biodiversity, new export products similar to the Gotland project mentioned above and more research devoted at edible and medicinal mushrooms.

  • 1022.
    Wedén, Christina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Danell, Eric
    Uppsala University, Music and Museums, Museum of Evolution.
    Camacho, Francisco J.
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    The population of the hypogeous fungus Tuber aestivum syn T. uncinatum on the island of Gotland2004In: Mycorrhiza, ISSN 0940-6360, E-ISSN 1432-1890, Vol. 14, no 1, p. 19-23Article in journal (Refereed)
    Abstract [en]

    The aim of our study was to examine the genetic variation within Tuber aestivum on the Baltic island of Gotland, Sweden. Variation in such a limited geographical area should help illuminate the dispersal abilities of T. aestivum. Knowledge of the genetic variation in this northern outpost could also be useful in the selection of inoculum for the establishment of truffle orchards. Genetic structure and homogeneity of the population were studied using principal component and parsimony analyses of randomly amplified polymorphic DNA data. Our inventories showed that T. aestivum is abundantly distributed in suitable habitats on Gotland. The genetic variation observed suggests sexual reproduction and slow dispersal on the island. It is possible that the present population was established from one introduction, which may be due to ability to survive in this habitat rather than to rare colonising events. The T. aestivum population on Gotland may be an ecotype adapted to the climate and soil conditions on the island.

  • 1023.
    Wedén, Christina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Danell, Eric
    Uppsala University, Music and Museums, Museum of Evolution.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Species recognition in the truffle genus Tuber: the synonyms Tuber aestivum and Tuber uncinatum2005In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 7, no 10, p. 1535-1546Article in journal (Refereed)
    Abstract [en]

    The two morphologically similar truffles Tuber aestivum and T. uncinatum have caused confusion because T. uncinatum is regarded by different authors, as either a distinct species, variety, subspecies, or synonym of T. aestivum. A clarification of the relationship between the two truffles would help both conservation biology and cultivation. We aimed both to test the reliability of the only quantitative morphological character used to distinguish the two taxa, i.e. the height of the spore reticulum, and to compare sequences of the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region. Our study included 117 fruit bodies of T. aestivum and T. uncinatum, originating from eight European countries. The results showed that the spore reticulum height is not diagnostic. The phylogenetic analysis of ITS sequences from 81 fruit bodies and an additional 32 sequences from GenBank showed that T. aestivum and T. uncinatum were intermingled in one highly supported (100% bootstrap) monophyletic clade, separate from its sister species Tuber mesentericum. We conclude that T. aestivum and T. uncinatum are synonyms and the species should be named T. aestivum, as the oldest name has priority. For traders, T. aestivum syn. T. uncinatum should be used until conformity has been reached.

  • 1024.
    Wedén, Christina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Pettersson, Lina
    Danell, Eric
    Cultivation of the Burgundy truffle, Tuber aestivum syn. T. uncinatum in SwedenManuscript (Other (popular science, discussion, etc.))
  • 1025.
    Widenfalk, Olof
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Gyllenstrand, Niclas
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Sylvén, Edvard
    Solbreck, Christer
    Identity and phylogenetic status of two sibling gall midge species (Diptera: Cecidomyiidae: Contarinia) on the perennial herb Vincetoxicum hirundinaria2002In: Systematic Entomology, Vol. 27, p. 1-10Article in journal (Refereed)
  • 1026. Wik, Lotta
    et al.
    Karlsson, Magnus
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    The evolutionary trajectory of the mating-type (mat) genes in Neurospora relates to reproductive behavior of taxa2008In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 8, no 1, p. 109-Article in journal (Refereed)
    Abstract [en]

    Background: Comparative sequencing studies among a wide range of taxonomic groups, including fungi, have led to the discovery that reproductive genes evolve more rapidly than other genes. However, for fungal reproductive genes the question has remained whether the rapid evolution is a result of stochastic or deterministic processes. The mating-type (mat) genes constitute the master regulators of sexual reproduction in filamentous ascomycetes and here we present a study of the molecular evolution of the four mat-genes (mat a-1, mat A-1, mat A-2 and mat A-3) of 20 Neurospora taxa. Results: We estimated nonsynonymous and synonymous substitution rates of genes to infer their evolutionary rate, and confirmed that the mat-genes evolve rapidly. Furthermore, the evolutionary trajectories are related to the reproductive modes of the taxa; likelihood methods revealed that positive selection acting on specific codons drives the diversity in heterothallic taxa, while among homothallic taxa the rapid evolution is due to a lack of selective constraint. The latter finding is supported by presence of stop codons and frame shift mutations disrupting the open reading frames of mat a-1, mat A-2 and mat A-3 in homothallic taxa. Lower selective constraints of matgenes was found among homothallic than heterothallic taxa, and comparisons with nonreproductive genes argue that this disparity is not a nonspecific, genome-wide phenomenon. Conclusion: Our data show that the mat-genes evolve rapidly in Neurospora. The rapid divergence is due to either adaptive evolution or lack of selective constraints, depending on the reproductive mode of the taxa. This is the first instance of positive selection acting on reproductive genes in the fungal kingdom, and illustrates how the evolutionary trajectory of reproductive genes can change after a switch in reproductive behaviour of an organism.

  • 1027.
    Wikström, Niklas
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Pryer, Kathleen M
    Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails2005In: Molecular Phylogenetics and Evolution, Vol. 36, no 484-493Article in journal (Refereed)
  • 1028.
    Wikström, Niklas
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk Botanik.
    Savolainen, Vincent
    Chase, Mark W.
    Angiosperm divergence times: congruence and incongruence between fossils and sequence divergence estimates2003In: Telling the Evolutionary Time: Molecular Clocks and the Fossil Record, Taylor & Francis , 2003, p. 142-165Chapter in book (Refereed)
    Abstract [en]

    The documentation of derived angiosperm lineages from increasingly older geological deposits, and growing evidence of considerable diversity in ower, seed, and pollen morphology in the mid-Cretaceous both imply that the timing of early angiosperm cladogenesis may be older then our current fossil-based estimates indicate. An alternative to fossils for calibrating the phylogenetic tree comes from divergence in DNA sequence data. Here, we report on an analysis using non-parametric rate smoothing and a three gene dataset covering c. 75 per cent of all angiosperm families recognized in recent classi cations. The results provide an initial hypothesis of angiosperm diversi cation times; by using an internal calibration point, an independent evaluation of angiosperm and eudicot origins is accomplished. Results are compared with fossil-based estimates of both magnolids and eudicot divergence times, and possible directions of future analyses are discussed.

  • 1029. Willems, Wim R.
    et al.
    Sandberg, Maria I.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Jondélius, Ulf
    First report on Rhabdocoela (Rhabditophora) from deep parts of Skagerrak, with the description of four new species2007In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 1616, p. 1-21Article in journal (Refereed)
    Abstract [en]

    In this contribution we report on 13 species of Rhabdocoela, found during a marine inventory of Skagerrak by the Swedish Taxonomy Initiative. Four new species are described, two of which are Kalyptorhynchia (Gnathorhychidae and Polycystididae) and two belong to Dalytyphloplanoida (Solenopharyngidae). Uncinorhynchus vorago sp. nov., (Gnathorhynchidae) has a triangular stylet consisting of a double-folded plate, which proximally forms a tube, but without a distal, needle-shaped tip. Austrorhynchus artoisi sp. nov. ( Polycystididae), has two prostate stylets. Prostate stylet type II consists of a distal tube and a short proximal funnel, which has a stirrup-shaped ornament, whereas the stylet type III shows an unpronounced foot and style connected to each other by a narrow clasp and a comb-bearing plate. The foot and plate are connected to a thread-like flagellum. Lenopharynx bathos sp. nov. (Solenopharyngidae) resembles Lenopharynx tubatus Schockaert & Martens, 1985, but differs in the detailed structure of the stylet and by the lack of colouration and eyes. Proceropharynx profundum sp. nov. has a unique combination of small spines and hard ridges on the cirrus. Additional data are given for the remaining nine species, three of which are new for the Swedish fauna. Espegrendia norvegica Westblad, 1954 ( Solenopharyngidae) is redescribed. For the sake of completeness, two more species are mentioned. One is identified as a new species of Acrumena Brunet, but lack of material prevents its formal description. The second one is probably a representative of the taxon Ceratopera Den Hartog, but cannot be identified with certainty because of the poor quality of the preserved material. This contribution is one of very few reports on Rhabdocoela collected from a depth exceeding 100 m and some preliminary biogeographical remarks are therefore given.

  • 1030.
    Willems, Wim R.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Wallberg, Andreas
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Zoology. Systematic Zoology.
    Jondelius, Ulf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Zoology. Systematic Zoology.
    Littlewood, David T. J.
    Backeljau, Thierry
    Schockaert, Ernest R.
    Artois, Tom J.
    Filling a gap in the phylogeny of flatworms: Relationships within the Rhabdocoela (Platyhelminthes), inferred from 18S ribosomal DNA sequences2006In: Zoologica Scripta, Vol. 35, p. 1-17Article in journal (Refereed)
  • 1031. Williams, Cameron B.
    et al.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Calicium sequoiae, a new lichen species from north-western California, USA2008In: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 40, no Part 3, p. 185-194Article in journal (Refereed)
    Abstract [en]

    We describe Calicium sequoiae as a new species of lichenized Ascomycota from northwestern California, USA. The species is distinguished morphologically from other known members of Calicium by its stalks that react I+ blue, mature ascospores that are ornamented with spiral ridges, and apothecia that produce prominent white pruina. It is also the only Calicium known to produce thamnolic acid as a major secondary substance. Sequences from the ITS-region showed C. sequoiae to be unique among calicioid Physciaceae, and phylogenetic analysis positioned it close to C. adspersum, C. chlorosporum, C. lenticulare, Cyphelium notarisii, and C. tigillare. Thus far, Calicium sequoiae has been collected only from old-growth redwood (Sequoia sempervirens) forests, where it occurred on thick, fibrous bark of large redwood trees. A key to the 12 species of Calicium known from the Pacific Northwest is provided.

  • 1032. Wiweger, M
    et al.
    Farbos, I
    Ingouff, M
    Lagercrantz, U
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Von Arnold, S
    Expression of Chia4-Pa chitinase genes during somatic and zygotic embryo development in Norway spruce (Picea abies): similarities and differences between gymnosperm and angiosperm class IV chitinases.2003In: J Exp Bot, ISSN 0022-0957, Vol. 54, no 393, p. 2691-9Article in journal (Refereed)
  • 1033.
    Wolf, Jochen B. W.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Kuenstner, Axel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Nam, Kiwoong
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Nonlinear Dynamics of Nonsynonymous (d(N)) and Synonymous (d(S)) Substitution Rates Affects Inference of Selection2009In: Genome Biology and Evolution, ISSN 1759-6653, Vol. 1, p. 308-319Article in journal (Refereed)
    Abstract [en]

    Selection modulates gene sequence evolution in different ways by constraining potential changes of amino acid sequences (purifying selection) or by favoring new and adaptive genetic variants (positive selection). The number of nonsynonymous differences in a pair of protein-coding sequences can be used to quantify the mode and strength of selection. To control for regional variation in substitution rates, the proportionate number of nonsynonymous differences (d(N)) is divided by the proportionate number of synonymous differences (d(S)). The resulting ratio (d(N)/d(S)) is a widely used indicator for functional divergence to identify particular genes that underwent positive selection. With the ever-growing amount of genome data, summary statistics like mean d(N)/d(S) allow gathering information on the mode of evolution for entire species. Both applications hinge on the assumption that d(S) and mean d(S) (similar to branch length) are neutral and adequately control for variation in substitution rates across genes and across organisms, respectively. We here explore the validity of this assumption using empirical data based on whole-genome protein sequence alignments between human and 15 other vertebrate species and several simulation approaches. We find that d(N)/d(S) does not appropriately reflect the action of selection as it is strongly influenced by its denominator (d(S)). Particularly for closely related taxa, such as human and chimpanzee, d(N)/d(S) can be misleading and is not an unadulterated indicator of selection. Instead, we suggest that inconsistencies in the behavior of d(N)/d(S) are to be expected and highlight the idea that this behavior may be inherent to taking the ratio of two randomly distributed variables that are nonlinearly correlated. New null hypotheses will be needed to adequately handle these nonlinear dynamics.

  • 1034. Wong, Gane Ka-Shu
    et al.
    Liu, Bin
    Wang, Jun
    Zhang, Yong
    Yang, Xu
    Zhang, Zengjin
    Meng, Qingshun
    Zhou, Jun
    Li, Dawei
    Zhang, Jingjing
    Ni, Peixiang
    Li, Songgang
    Ran, Longhua
    Li, Heng
    Zhang, Jianguo
    Li, Ruiqiang
    Li, Shengting
    Zheng, Hongkun
    Lin, Wei
    Li, Guangyuan
    Wang, Xiaoling
    Zhao, Wenming
    Li, Jun
    Ye, Chen
    Dai, Mingtao
    Ruan, Jue
    Zhou, Yan
    Li, Yuanzhe
    He, Ximiao
    Zhang, Yunze
    Wang, Jing
    Huang, Xiangang
    Tong, Wei
    Chen, Jie
    Ye, Jia
    Chen, Chen
    Wei, Ning
    Li, Guoqing
    Dong, Le
    Lan, Fengdi
    Sun, Yongqiao
    Zhang, Zhenpeng
    Yang, Zheng
    Yu, Yingpu
    Huang, Yanqing
    He, Dandan
    Xi, Yan
    Wei, Dong
    Qi, Qiuhui
    Li, Wenjie
    Shi, Jianping
    Wang, Miaoheng
    Xie, Fei
    Wang, Jianjun
    Zhang, Xiaowei
    Wang, Pei
    Zhao, Yiqiang
    Li, Ning
    Yang, Ning
    Dong, Wei
    Hu, Songnian
    Zeng, Changqing
    Zheng, Weimou
    Hao, Bailin
    Hillier, Ladeana W
    Yang, Shiaw-Pyng
    Warren, Wesley C
    Wilson, Richard K
    Brandström, Mikael
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Ellegren, Hans
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Crooijmans, Richard P M A
    van der Poel, Jan J
    Bovenhuis, Henk
    Groenen, Martien A M
    Ovcharenko, Ivan
    Gordon, Laurie
    Stubbs, Lisa
    Lucas, Susan
    Glavina, Tijana
    Aerts, Andrea
    Kaiser, Pete
    Rothwell, Lisa
    Young, John R
    Rogers, Sally
    Walker, Brian A
    van Hateren, Andy
    Kaufman, Jim
    Bumstead, Nat
    Lamont, Susan J
    Zhou, Huaijun
    Hocking, Paul M
    Morrice, David
    de Koning, Dirk-Jan
    Law, Andy
    Bartley, Neil
    Burt, David W
    Hunt, Henry
    Cheng, Hans H
    Gunnarsson, Ulrika
    Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Wahlberg, Per
    Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Andersson, Leif
    Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Kindlund, Ellen
    Tammi, Martti T
    Andersson, Björn
    Webber, Caleb
    Ponting, Chris P
    Overton, Ian M
    Boardman, Paul E
    Tang, Haizhou
    Hubbard, Simon J
    Wilson, Stuart A
    Yu, Jun
    Wang, Jian
    Yang, Huanming
    A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.2004In: Nature, ISSN 1476-4687, Vol. 432, no 7018, p. 717-22Article in journal (Refereed)
  • 1035.
    Wänstrand, Ingrid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Pigment and Thiamine Dynamics in Marine Phytoplankton and Copepods2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Based on a field study and several mesocosm experiments, I evaluated the use of pigments as chemotaxonomical biomarkers for phytoplankton community composition in the Baltic Sea and I examined effects of inorganic nutrients on the dynamics of carotenoids and thiamine (vitamin B1) at the phytoplankton–copepod level in marine pelagic food webs.

    My results show that HPLC pigment analysis combined with CHEMTAX data processing was an accurate alternative to microscopic analysis of Baltic Sea phytoplankton.

    Experimental supply of N, P and Si affected copepod growth and biochemical status via changes in biomass and composition of their phytoplankton diet. Net population growth rates were generally higher when phytoflagellates dominated (low Si:N ratio) and lower when diatoms dominated (high Si:N ratio).

    Copepod body concentrations of astaxanthin decreased with fertilization. Correlations with reduced under-water irradiance were consistent with the photo-protective function of this antioxidant. Thiamine concentrations in phytoplankton also decreased with fertilization. In copepods, low Si:N ratios resulted in higher thiamine concentrations than high Si:N ratios. Thiamine concentration and degree of phosphorylation were useful as indicators of thiamine shortage both in phytoplankton and copepods. The concentrations of thiamine and astaxanthin in the copepod communities were positively correlated.

    As copepods constitute a major link between pelagic primary producers and higher trophic levels, fertilization effects may be responsible for astaxanthin and thiamine deficiencies in salmon suffering from the M74 syndrome, which appeared concurrently with large-scale eutrophication in the Baltic Sea. As both thiamine and astaxanthin are deficient in M74-affected salmon, there is a need for physiological and molecular investigations of possible interactions between the two compounds in living cells.

    List of papers
    1. Seasonal phytoplankton pigment dynamics in the northern Baltic Sea: assessment by ships-of-opportunity
    Open this publication in new window or tab >>Seasonal phytoplankton pigment dynamics in the northern Baltic Sea: assessment by ships-of-opportunity
    (English)Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-92153 (URN)
    Available from: 2004-10-01 Created: 2004-10-01 Last updated: 2009-03-31Bibliographically approved
    2. Phytoplankton community dynamics in nutrient-enriched mesocosms in the Baltic Sea: a chemotaxonomical approach
    Open this publication in new window or tab >>Phytoplankton community dynamics in nutrient-enriched mesocosms in the Baltic Sea: a chemotaxonomical approach
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92154 (URN)
    Available from: 2004-10-01 Created: 2004-10-01 Last updated: 2010-01-14Bibliographically approved
    3. Growth and C:N:P ratios in copepods grazing on N- or Si-limited phytoplankton blooms
    Open this publication in new window or tab >>Growth and C:N:P ratios in copepods grazing on N- or Si-limited phytoplankton blooms
    2004 (English)In: Hydrobiologia, Vol. 514, p. 57-72Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92155 (URN)
    Available from: 2004-10-01 Created: 2004-10-01 Last updated: 2009-03-31Bibliographically approved
    4. Astaxanthin production in marine pelagic copepods grazing on two different phytoplankton diets
    Open this publication in new window or tab >>Astaxanthin production in marine pelagic copepods grazing on two different phytoplankton diets
    2005 (English)In: Journal of Sea Research, ISSN 1385-1101, E-ISSN 1873-1414, Vol. 53, no 3, p. 147-160Article in journal (Refereed) Published
    Abstract [en]

    The red carotenoid astaxanthin is a powerful natural antioxidant of great importance in aquatic food webs where it is abundant in eggs and body tissues of fish and crustaceans. Little is known about the impact of the phytoplankton diet on astaxanthin production in copepods, its major pelagic producers. We followed the transfer of carotenoids from phytoplankton to copepods in a mesocosm experiment on the northern Atlantic coast (Norway) and recorded the astaxanthin production in copepods. Wild copepods grazed on nutrient-manipulated phytoplankton blooms, which differed in community composition and nutrient status (nitrogen or silicate limitation). The copepod pigments consisted mainly of free astaxanthin and mono- and diesters of astaxanthin. We found no significant difference in astaxanthin production per copepod individual or per unit C depending on the phytoplankton community. However, in the mesocosms astaxanthin per unit C decreased compared with natural levels, probably through a lower demand for photoprotection by the copepods in the dense phytoplankton blooms. The total astaxanthin production per litre was higher in the silicate-limited mesocosms through increased copepod density. Pigment ratio comparisons suggested that the copepod diet here consisted more of diatoms than in the nitrogen-limited mesocosms. Silicate-saturated diatoms were less grazed, possibly because they could invest more in defence mechanisms against their predators. Our study suggests that the production of astaxanthin in aquatic systems can be affected by changes in nutrient dynamics mediated by phytoplankton community composition and copepod population growth. This bottom-up force may have implications for antioxidant protection at higher trophic levels in the food web.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-92156 (URN)10.1016/j.seares.2004.07.003 (DOI)
    Available from: 2004-10-01 Created: 2004-10-01 Last updated: 2017-12-14Bibliographically approved
    5. Inorganic nutrients regulate astaxanthin production in copepods via phytoplankton community dynamics
    Open this publication in new window or tab >>Inorganic nutrients regulate astaxanthin production in copepods via phytoplankton community dynamics
    Show others...
    (English)Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-92157 (URN)
    Available from: 2004-10-01 Created: 2004-10-01 Last updated: 2009-03-31Bibliographically approved
    6. Thiamine (vitamin B1) dynamics in phytoplankton and copepods is regulated by inorganic nutrient supply
    Open this publication in new window or tab >>Thiamine (vitamin B1) dynamics in phytoplankton and copepods is regulated by inorganic nutrient supply
    Show others...
    (English)Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-92158 (URN)
    Available from: 2004-10-01 Created: 2004-10-01 Last updated: 2009-03-31Bibliographically approved
  • 1036.
    Wänstrand, Ingrid
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Barros, Marcelo Paes de
    Pinto, Ernani
    Pedersén, Marianne
    Snoeijs, Pauli
    Inorganic nutrients regulate astaxanthin production in copepods via phytoplankton community dynamicsArticle in journal (Refereed)
  • 1037.
    Wänstrand, Ingrid
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Snoeijs, Pauli
    Phytoplankton community dynamics in nutrient-enriched mesocosms in the Baltic Sea: a chemotaxonomical approachManuscript (Other (popular science, discussion, etc.))
  • 1038.
    Wänstrand, Ingrid
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Snoeijs, Pauli
    Seasonal phytoplankton pigment dynamics in the northern Baltic Sea: assessment by ships-of-opportunityArticle in journal (Refereed)
  • 1039. Yu, Bao-Zhu
    et al.
    Apitz-Castro, Rafael J.
    Jain, Mahendra K.
    Berg, Otto G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Role of 57-72 loop in the allosteric action of bile salts on pancreatic IB phospholipase A(2): Regulation of fat and cholesterol homeostasis2007In: Biochimica et Biophysica Acta - Biomembranes, ISSN 0005-2736, E-ISSN 1879-2642, Vol. 1768, no 10, p. 2478-2490Article in journal (Refereed)
    Abstract [en]

    Mono- and biphasic kinetic effects of bile salts on the pancreatic IB phospholipase A2 (PLA2) catalyzed interfacial hydrolysis are characterized. This novel phenomenon is modeled as allosteric action of bile salts with PLA2 at the interface. The results and controls also show that these kinetic effects are not due to surface dilution or solubilization or disruption of the bilayer interface where in the mixed-micelles substrate replenishment becomes the rate-limiting step. The PLA2-catalyzed rate of hydrolysis of zwitterionic dimyristoylphosphatidylcholine (DMPC) vesicles depends on the concentration and structure of the bile salt. The sigmoidal rate increase with cholate saturates at 0.06 mole fraction and changes little at the higher mole fractions. Also, with the rate-lowering bile salts (B), such as taurochenodeoxycholate (TCDOC), the initial sigmoidal rate increase at lower mole fraction is followed by nearly complete reversal to the rate at the pre-activation level at higher mole fractions. The rate-lowering effect of TCDOC is not observed with the (62–66)-loop deleted ΔPLA2, or with the Naja venom PLA2 that is evolutionarily devoid of the loop. The rate increase is modeled with the assumption that the binding of PLA2 to DMPC interface is cooperatively promoted by bile salt followed by allosteric kcat-activation of the bound enzyme by the anionic interface. The rate-lowering effect of bile salts is attributed to the formation of a specific catalytically inert EB complex in the interface, which is noticeably different than the 1:1 EB complex in the aqueous phase. The cholate-activated rate of hydrolysis is lowered by hypolidemic ezetimibe and guggul extract which are not interfacial competitive inhibitors of PLA2. We propose that the biphasic modulation of the pancreatic PLA2 activity by bile salts regulates gastrointestinal fat metabolism and cholesterol homeostasis.

  • 1040. Yu, Bao-Zhu
    et al.
    Bai, Shi
    Berg, Otto G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Jain, Mahendra K.
    Allosteric Effect of Amphiphile Binding to Phospholipase A22009In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 48, no 14, p. 3219-3229Article in journal (Refereed)
    Abstract [en]

    In the preceding paper, we showed that the formation of the second premicellar complex of pig pancreatic IB phospholipase A2 (PLA2) can be considered a proxy for interface-activated substrate binding. Here we show that this conclusion is supported by results from premicellar;E-i(#) (i = 1, 2, or 3) complexes with a wide range of mutants of PLA2. Results also show a structural bass-for the correlated functional changes during the formation of E-2(#), and this is interpreted as an allosteric T (inactive) to R (active) transition. For example, the dissociation constant K-2(#) for decylsulfate bound to E-2(#) is lower at lower pH, at higher calcium concentrations, or with an inhibitor bound to the active site. Also, the lower limits of the K-2(#) values are comparable under these conditions. The pH-dependent increase in K-2(#) with a pK(a) of 6.5 is attributed to E71 which participates in the binding of the second calcium which in turn influences the enzyme binding to phosphatidylcholine interface. Most mutants exhibited kinetic and spectroscopic behavior that is comparable to that of native PLA2 and Delta PLA2 with a deleted 62-66 loop. However, the Delta Y52L substitution mutant cannot undergo the calcium-, pH-, or interface-dependent changes. We suggest that the Y52L substitution impairs the R to T transition and also hinders the approach of the Michaelis complex to the transition state. This allosteric change may be mediated by the structural motifs that connect the D48-D99 catalytic diad, the substrate-binding slot, and the residues of the i-face. Our interpretation is that the 57-72 loop and the H48DNCY52 segment of PLA2 are involved in transmitting the effect of the cooperative amphiphile binding to the i-face as a structural change in the active site.

  • 1041. Yu, Bao-Zhu
    et al.
    Kaimal, Rajani
    Bai, Shi
    El Sayed, Khalid A.
    Tatulian, Suren A.
    Apitz, Rafael J.
    Jain, Mahendra K.
    Deng, Ruitang
    Berg, Otto G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Effect of Guggulsterone and Cembranoids of Commiphora mukul on Pancreatic Phospholipase A(2): Role in Hypocholesterolemia2009In: Journal of natural products (Print), ISSN 0163-3864, E-ISSN 1520-6025, Vol. 72, no 1, p. 24-28Article in journal (Refereed)
    Abstract [en]

    Guggulsterone (7) and cembranoids (8-12) from Commiphora mukul stem bark resin guggul were shown to be specific modulators of two independent sites that are also modulated by bile salts (1-6) to control cholesterol absorption and catabolism. Guggulsterone (7) antagonized the chenodeoxycholic acid (3)-activated nuclear farnesoid X receptor (FXR), which regulates cholesterol metabolism in the liver. The cembranoids did not show a noticeable effect on FXR, but lowered the cholate (I)-activated rate of human pancreatic 113 phospholipase A2 (hPLA2), which controls gastrointestinal absorption of fat and cholesterol. Analysis of the data using a kinetic model has suggested an allosteric mechanism for the rate increase of hPLA2 by cholate and also for the rate-lowering effect by certain bile salts or cembranoids on the cholate-activated hPLA2 hydrolysis of phosphatidylcholine vesicles. The allosteric inhibition of PLA2 by certain bile salts and cembranoids showed some structural specificity. Biophysical studies also showed specific interaction of the bile salts with the interface-bound cholate-activated PLA2. Since cholesterol homeostasis in mammals is regulated by FXR in the liver for metabolism and by PLA2 in the intestine for absorption, modulation of PLA2 and FXR by bile acids and selected guggul components suggests novel possibilities for hypolipidemic and hypocholesterolemic therapies.

  • 1042. Yu, Bao-Zhu
    et al.
    Polenova, Tatyana
    Jain, Mahendra Kumar
    Berg, Otto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Premicellar complexes of sphingomyelinase mediate enzyme exchange for the stationary phase turnover2005In: Biochimica et Biophysica Acta - Biomembranes, ISSN 0005-2736, E-ISSN 1879-2642, Vol. 1712, no 2, p. 137-151Article in journal (Refereed)
    Abstract [en]

    During the steady state reaction progress in the scooting mode with highly processive turnover, Bacillus cereus sphingomyelinase (SMase) remains tightly bound to sphingomyelin (SM) vesicles (Yu et al., Biochim. Biophys. Acta 1583, 121–131, 2002). In this paper, we analyze the kinetics of SMase-catalyzed hydrolysis of SM dispersed in diheptanoylphosphatidyl-choline (DC7PC) micelles. Results show that the resulting decrease in the turnover processivity induces the stationary phase in the reaction progress. The exchange of the bound enzyme (E*) between the vesicle during such reaction progress is mediated via the premicellar complexes (Ei#) of SMase with DC7PC. Biophysical studies indicate that in Ei# monodisperse DC7PC is bound to the interface binding surface (i-face) of SMase that is also involved in its binding to micelles or vesicles. In the presence of magnesium, required for the catalytic turnover, three different complexes of SMase with monodisperse DC7PC (Ei# with i = 1, 2, 3) are sequentially formed with Hill coefficients of 3, 4 and 8, respectively. As a result, during the stationary phase reaction progress, the initial rate is linear for an extended period and all the substrate in the reaction mixture is hydrolyzed at the end of the reaction progress. At low mole fraction (X) of total added SM, exchange is rapid and the processive turnover is limited by the steps of the interfacial turnover cycle without becoming microscopically limited by local substrate depletion or enzyme exchange. At high X, less DC7PC will be monodisperse, Ei# does not form and the turnover becomes limited by slow enzyme exchange. Transferred NOESY enhancement results show that monomeric DC7PC in solution is in a rapid exchange with that bound to Ei# at a rate comparable to that in micelles. Significance of the exchange and equilibrium properties of the Ei# complexes for the interpretation of the stationary phase reaction progress is discussed.

  • 1043.
    Åberg, Karolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Finding Genes for Schizophrenia2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Schizophrenia is one of our most common psychiatric diseases. It severely affects all aspects of psychological functions and results in loss of contact with reality. No cure exists and the treatments available today produce only partial relief for disease symptoms. The aim of this work is to better understand the etiology of schizophrenia by identification of candidate genes and gene pathways involved in the development of the disease.

    In a preliminarily study, the effects of medication and genetic factors were investigated in a candidate gene, serotonin 2C receptor. This study distinguished pharmacological effects, caused by neuroleptics, and/or genetic effects, caused by unique polymorphisms, from other effects responsible for mRNA expression changes on candidate genes.

    The core of the thesis describes a new candidate gene for schizophrenia, the quaking homolog, KH domain RNA binding (mouse) or QKI, located on chromosome 6q26-q27. The identification of QKI is supported by previous linkage studies, current association studies and mRNA expression studies using three different sample sets. The investigated samples included a 12-generation pedigree with 16 distantly related schizophrenic cases and their parents, 176 unrelated nuclear families with at least one affected child in each family and human brain autopsies from 55 schizophrenic cases and from 55 controls. Indirect evidence showing involvement of QKI in myelin regulation of central nervous system is presented. Myelin plays an important role in development of normal brains and disruption of QKI might lead to schizophrenia symptoms.

    In a forth sample set, including extended pedigrees originated from a geographically isolated area above the Arctic Circle, in northeast Sweden, two additional schizophrenia susceptibility loci were identified, 2q13 and 5q21. Both these regions have previously been highlighted as potential schizophrenia loci in several other investigations, including a large Finnish study. This suggests common schizophrenia susceptibility loci for Nordic populations.

    A pilot investigation including a genome wide haplotype analysis is presented. This statistical strategy could be further developed and applied to the artic Swedish families, including analysis of 900 microsatellites and 10,000 SNPs.

    These findings will facilitate the understanding of the schizophrenia etiology and may lead to development of more efficient treatments for patients that suffer from schizophrenia.

    List of papers
    1. Serotonin Receptor 2C (HTR2C) and Schizophrenia: Examination of Possible Medication and Genetic Influences on Expression Levels
    Open this publication in new window or tab >>Serotonin Receptor 2C (HTR2C) and Schizophrenia: Examination of Possible Medication and Genetic Influences on Expression Levels
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    2005 (English)In: American Journal of Medical Genetics, ISSN 0148-7299, E-ISSN 1096-8628, Vol. 134B, p. 84-89Article in journal (Refereed) Published
    Abstract [en]

    The serotonin receptor 2C (HTR2C) gene is of interest in schizophrenia due to its involvement in regulation of dopamine activity in the prefrontal cortex. We have previously reported a decreased expression of HTR2C mRNA levels in the prefrontal cortex of schizophrenia patients. The variability in mRNA expression levels is evaluated here more closely in relation to promoter haplotypes and neuroleptic treatment received by the patients. The decrease in HTR2C mRNA was present in neuroleptic treated individuals and in patients untreated at death, indicating that the lower expression is not a short-term medication effect. Three promoter polymorphisms were used to construct haplotypes. No SNP displayed genotypic or haplotypic association with the disease. Gene expression of HTR2C was not affected by haplotype and the expression decrease in schizophrenia patients was similar in all haplotype combinations (diplotypes). We conclude that the decrease in HTR2C expression in schizophrenia may be related to the disease mechanism rather than to drug treatment. The disease related changes in HTR2C expression are not related to the promoter variants typed in our sample, but could be due to other regulatory variants or trans-acting factors.

    Keywords
    mRNA expression, neuroleptic drugs, psychiatric disease, serotonin receptor 2C, promoter polymorphisms
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-93323 (URN)10.1002/ajmg.b.30151 (DOI)15717293 (PubMedID)
    Available from: 2005-09-01 Created: 2005-09-01 Last updated: 2017-12-14Bibliographically approved
    2. Reconstruction of Ancestral Haplotypes in a 12-Generation Schizophrenia Pedigree
    Open this publication in new window or tab >>Reconstruction of Ancestral Haplotypes in a 12-Generation Schizophrenia Pedigree
    Show others...
    2004 (English)In: Psychiatric Genetics, ISSN 0955-8829, E-ISSN 1473-5873, Vol. 14, no 1, p. 1-8Article in journal (Refereed) Published
    Abstract [en]

    We searched for candidate chromosomal regions inherited identical by descent in 19 patients suffering from schizophrenia or schizoaffective disorder that are related 12 generations back, to an ancestral couple born in the middle of the seventeenth century. To accomplish this goal, we constructed complete chromosomal haplotypes for each patient using genotype data from 450 markers. In total, 12 haplotype regions (with sizes ranging from 0.6 to 10.9 cM) constituted by three markers each were identical in three or more of the affected individuals. The largest genomic segment was located on 6q25, a region previously shown to be significantly more frequent in patients than controls, and proposed to contain a schizophrenia susceptibility locus. For the remaining 11 candidate haplotypes, we estimated haplotype frequencies from all the 43 affected members collected from the same family and 46 unrelated control individuals. This analysis indicated that at least four of the 11 candidate haplotypes are ancestral, since the frequencies were significantly higher in patients than in controls. Five additional haplotypes showed higher estimated frequencies in the patients but the differences were not significant. Interestingly, five of these 11 genomic regions are located in, or close to, candidate regions previously suggested to contain susceptibility genes for schizophrenia. The regions are 5q21-23, 8p21-22, 10p13-15, 13q12-13 and 22q12-13. Several of these haplotypes are probably ancestral linkage disequilibrium blocks inherited from the original couple. There exists, however, the possibility that one or more of these regions harbour schizophrenia susceptibility loci that may have epistatic interactions among them.

    Keywords
    psychiatric genetics, schizophrenia, ancestral haplotypes, susceptibility loci
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-93324 (URN)10.1097/01.ypg.0000084941.07075.f9 (DOI)15091309 (PubMedID)
    Available from: 2005-09-01 Created: 2005-09-01 Last updated: 2017-12-14Bibliographically approved
    3. Human QKI, a New Candidate Gene for Schizophrenia Involved in Myelination
    Open this publication in new window or tab >>Human QKI, a New Candidate Gene for Schizophrenia Involved in Myelination
    Show others...
    2005 (English)In: American journal of medical genetics. Part B, Neuropsychiatric genetics, ISSN 1552-4841, Vol. 141B, no 1, p. 84-90Article in journal (Refereed) Published
    Abstract [en]

    We have previously shown that chromosome 6q25-6q27 includes a susceptibility locus for schizophrenia in a large pedigree from northern Sweden. In this study, we fine-mapped a 10.7 Mb region, included in this locus, using 42 microsatellites or SNP markers. We found a 0.5 Mb haplotype, likely to be inherited identical by decent, within the large family that is shared among the majority of the patients (69%). A gamete competition test of this haplotype in 176 unrelated nuclear families from the same geographical area as the large family showed association to schizophrenia (empirical P-value 0.041). The only gene located in the region, the quaking homolog, KH domain RNA binding (mouse) (QKI), was investigated in human brain autopsies from 55 cases and 55 controls using a high-resolution mRNA expression analysis. Relative mRNA expression levels of two QKI splice variants were clearly downregulated in schizophrenic patients (P-value 0.0004 and 0.03, respectively). The function of QKI has not been studied in humans, but the mouse homolog is involved in neural development and myelination. In conclusion, we present evidence from three unrelated sample-sets that propose the involvement of the QKI gene in schizophrenia. The two family based studies suggest that there may be functional variants of the QKI gene that increase the susceptibility of schizophrenia in northern Sweden, whereas the case-control study suggest that splicing of the gene may be disturbed in schizophrenic patients from other geographical origins. Taken together, we propose QKI as a possible target for functional studies related to the role of myelination in schizophrenia.

    Keywords
    mRNA-expression, haplotype investigation, fine-mapping, large pedigree
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-93325 (URN)10.1002/ajmg.b.30243 (DOI)16342280 (PubMedID)
    Available from: 2005-09-01 Created: 2005-09-01 Last updated: 2010-02-02Bibliographically approved
    4. Human QKI, a potential regulator of mRNA expression of human oligodendrocyte-related genes involved in schizophrenia
    Open this publication in new window or tab >>Human QKI, a potential regulator of mRNA expression of human oligodendrocyte-related genes involved in schizophrenia
    2006 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 103, no 19, p. 7482-7487Article in journal (Refereed) Published
    Abstract [en]

    The quaking viable mouse mutation (qkv) is a deletion including the 5′ regulatory region of the quaking gene (Qki), which causes body tremor and severe dysmyelination in mouse. The function of the human quaking gene, called quaking homolog KH domain RNA-binding (mouse) (QKI), is not well known. We have previously shown that QKI is a new candidate gene for schizophrenia. Here we show that human QKI mRNA levels can account for a high proportion (47%) of normal interindividual mRNA expression variation (and covariation) of six oligodendrocyte-related genes (PLP1, MAG, MBP, TF, SOX10, and CDKN1B) in 55 human brain autopsy samples from individuals without psychiatric diagnoses. In addition, the tightly coexpressed myelin-related genes (PLP1, MAG, and TF) have decreased mRNA levels in 55 schizophrenic patients, as compared with 55 control individuals, and most of this difference (68–96%) can be explained by variation in the relative mRNA levels of QKI-7kb, the same QKI splice variant previously shown to be down-regulated in patients with schizophrenia. Taken together, our results suggest that QKI levels may regulate oligodendrocyte differentiation and maturation in human brain, in a similar way as in mouse. Moreover, we hypothesize that previously observed decreased activity of myelin-related genes in schizophrenia might be caused by disturbed QKI splicing.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-93326 (URN)10.1073/pnas.0601213103 (DOI)
    Available from: 2005-09-01 Created: 2005-09-01 Last updated: 2017-12-14Bibliographically approved
    5. Genome Wide Investigation of an Isolated Schizophrenia Population Using a Dense Map of Microsatellites and SNPs in Combination
    Open this publication in new window or tab >>Genome Wide Investigation of an Isolated Schizophrenia Population Using a Dense Map of Microsatellites and SNPs in Combination
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-93327 (URN)
    Available from: 2005-09-01 Created: 2005-09-01 Last updated: 2010-02-02Bibliographically approved
  • 1044.
    Åberg, Karolina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Axelsson, Elin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Department of Animal Development and Genetics.
    Jiang, Lin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Department of Animal Development and Genetics.
    Wetterberg, Lennart
    Pettersson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Lindholm, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Department of Animal Development and Genetics.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Department of Animal Development and Genetics.
    Support for schizophrenia susceptibility locus on chromosome 2q detected in a Swedish isolate using a dense map of microsatellites and SNPs2008In: American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, ISSN 1552-485X, Vol. 147B, no 7, p. 1238-44Article in journal (Refereed)
    Abstract [en]

    Extended pedigrees are not only very useful to identify disease genes for rare Mendelian conditions, but they may also help unravel the genetics of complex diseases such as schizophrenia. In this study we performed genome-wide multipoint non-parametric linkage (NPL) score calculations using 825 microsatellites and 5,366 single nucleotide polymorphisms (SNPs), respectively, and searched for haplotypes shared by affected individuals, in three multiplex families including 29 genotyped affected individuals which in total contains 49 relative pairs useful for linkage studies. The most consistent results for microsatellites and SNPs were observed on 2q12.3-q14.1 (NPL scores 2.0, empirical P-value 0.009). However, the overall highest NPL score was observed on chromosome 2q33.3 using SNPs (NPL score 2.2, empirical P-value 0.007). Other chromosomal regions were detected on 5q15-q22.1, with microsatellites (NPL scores 1.7, empirical P-value 0.021) and with SNPs (NPL scores 2.0, empirical P-value 0.010) and on 5q23.1 (NPL score 1.9, empirical P-value 0.012) and 8q24.1-q24.2 (NPL score 2.1, empirical P-value 0.009) when using SNPs. The analysis of extended pedigrees allowed the search for haplotypes inherited identical by decent (IBD) by affected individuals. In all regions with NPL score >1.9 we found haplotypes inherited IBD by multiple cases. However, no common haplotypes were found for affected individuals in all families. In conclusion our NPL results support earlier findings suggesting that 2q and possibly 5q and 8q contain susceptibility loci for schizophrenia. Haplotype sharing in families helped to delimit the detected regions that potentially are susceptibility loci for schizophrenia.

  • 1045.
    Åberg, Karolina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Lindholm, Eva
    Saetre, Peter
    Wetterberg, Lennart
    Pettersson, Ulf
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Genome Wide Investigation of an Isolated Schizophrenia Population Using a Dense Map of Microsatellites and SNPs in CombinationManuscript (Other (popular science, discussion, etc.))
  • 1046.
    Åberg, Karolina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Department of Animal Development and Genetics.
    Jareborg, Niclas
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Department of Animal Development and Genetics.
    Human QKI, a potential regulator of mRNA expression of human oligodendrocyte-related genes involved in schizophrenia2006In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 103, no 19, p. 7482-7487Article in journal (Refereed)
    Abstract [en]

    The quaking viable mouse mutation (qkv) is a deletion including the 5′ regulatory region of the quaking gene (Qki), which causes body tremor and severe dysmyelination in mouse. The function of the human quaking gene, called quaking homolog KH domain RNA-binding (mouse) (QKI), is not well known. We have previously shown that QKI is a new candidate gene for schizophrenia. Here we show that human QKI mRNA levels can account for a high proportion (47%) of normal interindividual mRNA expression variation (and covariation) of six oligodendrocyte-related genes (PLP1, MAG, MBP, TF, SOX10, and CDKN1B) in 55 human brain autopsy samples from individuals without psychiatric diagnoses. In addition, the tightly coexpressed myelin-related genes (PLP1, MAG, and TF) have decreased mRNA levels in 55 schizophrenic patients, as compared with 55 control individuals, and most of this difference (68–96%) can be explained by variation in the relative mRNA levels of QKI-7kb, the same QKI splice variant previously shown to be down-regulated in patients with schizophrenia. Taken together, our results suggest that QKI levels may regulate oligodendrocyte differentiation and maturation in human brain, in a similar way as in mouse. Moreover, we hypothesize that previously observed decreased activity of myelin-related genes in schizophrenia might be caused by disturbed QKI splicing.

  • 1047.
    Åberg, Karolina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Lindholm, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ekholm, Birgit
    Pettersson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Adolfsson, Rolf
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Human QKI, a New Candidate Gene for Schizophrenia Involved in Myelination2005In: American journal of medical genetics. Part B, Neuropsychiatric genetics, ISSN 1552-4841, Vol. 141B, no 1, p. 84-90Article in journal (Refereed)
    Abstract [en]

    We have previously shown that chromosome 6q25-6q27 includes a susceptibility locus for schizophrenia in a large pedigree from northern Sweden. In this study, we fine-mapped a 10.7 Mb region, included in this locus, using 42 microsatellites or SNP markers. We found a 0.5 Mb haplotype, likely to be inherited identical by decent, within the large family that is shared among the majority of the patients (69%). A gamete competition test of this haplotype in 176 unrelated nuclear families from the same geographical area as the large family showed association to schizophrenia (empirical P-value 0.041). The only gene located in the region, the quaking homolog, KH domain RNA binding (mouse) (QKI), was investigated in human brain autopsies from 55 cases and 55 controls using a high-resolution mRNA expression analysis. Relative mRNA expression levels of two QKI splice variants were clearly downregulated in schizophrenic patients (P-value 0.0004 and 0.03, respectively). The function of QKI has not been studied in humans, but the mouse homolog is involved in neural development and myelination. In conclusion, we present evidence from three unrelated sample-sets that propose the involvement of the QKI gene in schizophrenia. The two family based studies suggest that there may be functional variants of the QKI gene that increase the susceptibility of schizophrenia in northern Sweden, whereas the case-control study suggest that splicing of the gene may be disturbed in schizophrenic patients from other geographical origins. Taken together, we propose QKI as a possible target for functional studies related to the role of myelination in schizophrenia.

18192021 1001 - 1047 of 1047
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