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  • 201.
    De La Torre, Amanda R
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Lin, Yao-Cheng
    Van de Peer, Yves
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families2015In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 7, no 4, 1002-1015 p.Article in journal (Refereed)
    Abstract [en]

    The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (> 50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.

  • 202. Decker, Jared E.
    et al.
    McKay, Stephanie D.
    Rolf, Megan M.
    Kim, JaeWoo
    Molina Alcala, Antonio
    Sonstegard, Tad S.
    Hanotte, Olivier
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Seabury, Christopher M.
    Praharani, Lisa
    Babar, Masroor Ellahi
    de Almeida Regitano, Luciana Correia
    Yildiz, Mehmet Ali
    Heaton, Michael P.
    Liu, Wan-Sheng
    Lei, Chu-Zhao
    Reecy, James M.
    Saif-Ur-Rehman, Muhammad
    Schnabel, Robert D.
    Taylor, Jeremy F.
    Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle2014In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 10, no 3, e1004254- p.Article in journal (Refereed)
    Abstract [en]

    The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.

  • 203.
    Delgado Vega, Angélica María
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medical Genetics.
    Dissecting the Genetic Basis of Systemic Lupus Erythematosus: The Pursuit of Functional Variants2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Systemic lupus erythematosus (SLE) is a chronic and systemic autoimmune disease that primarily affects women during the childbearing years. SLE is characterized by the production of autoantibodies against nucleic acids and their interacting proteins. The exact molecular mechanisms leading to the breakdown of self-tolerance remain to a large extent unknown, but it is well established that they are influenced by both non-genetic (i.e. environmental and hormonal) and genetic factors. SLE is a complex, polygenic disease. Several susceptibility variants have been identified in SLE. However, the functional role in disease pathogenesis for the majority of them remains largely unknown.

    This thesis includes case-control association studies where the role of the genes TNFSF4 (Paper I), STAT4 (Paper II), CD226 (Paper III), and BLK (Papers IV and V) in the susceptibility of developing SLE was investigated. The primary focus was on the identification of the functional variants underlying the association. For each of these genes, fine mapping was performed using single nucleotide polymorphisms (SNPs), the linkage disequilibrium (LD) was characterized, and the association was narrowed down to specific haplotypes by means of several different statistical genetic strategies. Candidate variants were prioritized for further functional analysis on the basis of their potential effect on the gene function, their association, and/or biological plausibility. In Paper I, the association of TNFSF4 with SLE was validated and attributed to a risk haplotype tagged by SNPs rs1234317-T and rs12039904-T. Paper II provides evidence supporting the presence of at least two independent genetic effects within the STAT4 gene represented by rs3821236-A and rs7574865-A, which correlated with increased levels of gene expression. In Paper III, a functional allele in CD226 (rs727088-C) was identified, which was responsible for decreased levels in both mRNA and protein expression. In Paper IV, two independent genetic effects in the BLK gene were demonstrated. The first one comprised multiple regulatory variants in high LD that were enriched for NFκB and IRF4 binding sites and correlated with low BLK mRNA levels. The second was a low-frequency missense substitution (Ala71Thr) that decreased the BLK protein half-life. In Paper V, a genetic epistatic interaction between BANK1 rs10516487 (GG) and BLK rs2736340 (TT+TC) was demonstrated. Additional molecular analyses established that these molecules interact physically.  

    These studies have contributed to the dissection of the genetic architecture of SLE. They highlight the allelic heterogeneity of the disease and provide functional links to the associated variants, which has significantly aided in the understanding of SLE disease pathogenesis.

  • 204.
    Demczuk, Walter H.B.
    et al.
    National Microbiology Laboratory, Winnipeg, Canada.
    Sidhu, S.
    National Microbiology Laboratory, Winnipeg, Canada.
    Unemo, Magnus
    WHO Collaborating Centre for Gonorrhoea and Other STIs, Örebro University Hospital, Örebro, Sweden; School of Medical Sciences, Örebro University, Örebro, Sweden.
    Whiley, David M.
    The University of Queensland, Centre for Clinical Research, Brisbane, Australia.
    Allen, Vanessa G. Public Health Ontario, Toronto, Canada
    Public Health Ontario Laboratories, Toronto , Canada.
    Dillon, Jeremiah R.
    Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada.
    Cole, Michelle J.
    Public Health England, London, United Kingdom.
    Seah, Christine
    Public Health Ontario Laboratories, Toronto, Canada.
    Trembizki, Ella
    The University of Queensland, Centre for Clinical Research, Brisbane, Australia.
    Trees, David L.
    Centers for Disease Control and Prevention, Atlanta GA, United States.
    Kersh, Ellen N. Centers for Disease Control and Prevention, Division of Sexually Transmitted Disease Prevention, Atlanta, United States
    Centers for Disease Control and Prevention, Atlanta GA, United States.
    Abrams, A. Jeanine
    Centers for Disease Control and Prevention, Atlanta GA, United States.
    de Vries, Henry J.C.
    STI Outpatient Clinic, Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands; Department of Dermatology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands; Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
    van Dam, Alje P.
    Public Health Laboratory, Public Health Service Amsterdam, Amsterdam, the NetheDepartment of Medical Microbiology, OLVG General Hospital, Amsterdam, the Netherlandsrlands; .
    Medina, I.
    Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg MB, Canada.
    Bharat, Amrita
    Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg MB, Canada.
    Mulvey, Michael Richard
    Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg MB, Canada.
    Van Domselaar, Gary
    Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg MB, Canada.
    Martin, Irene E.
    Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg MB, Canada.
    Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance: a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains2017In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 55, no 5, 1454-1468 p.Article in journal (Refereed)
    Abstract [en]

    A curated Web-based user-friendly sequence typing tool based on antimicrobial resistance determinants in Neisseria gonorrhoeae was developed and is publicly accessible (https://ngstar.canada.ca). The N. gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) molecular typing scheme uses the DNA sequences of 7 genes (penA, mtrR, porB, ponA, gyrA, parC, and 23S rRNA) associated with resistance to β-lactam antimicrobials, macrolides, or fluoroquinolones. NG-STAR uses the entire penA sequence, combining the historical nomenclature for penA types I to XXXVIII with novel nucleotide sequence designations; the full mtrR sequence and a portion of its promoter region; portions of ponA, porB, gyrA, and parC; and 23S rRNA sequences. NG-STAR grouped 768 isolates into 139 sequence types (STs) (n = 660) consisting of 29 clonal complexes (CCs) having a maximum of a single-locus variation, and 76 NG-STAR STs (n = 109) were identified as unrelated singletons. NG-STAR had a high Simpson's diversity index value of 96.5% (95% confidence interval [CI] = 0.959 to 0.969). The most common STs were NG-STAR ST-90 (n = 100; 13.0%), ST-42 and ST-91 (n = 45; 5.9%), ST-64 (n = 44; 5.72%), and ST-139 (n = 42; 5.5%). Decreased susceptibility to azithromycin was associated with NG-STAR ST-58, ST-61, ST-64, ST-79, ST-91, and ST-139 (n = 156; 92.3%); decreased susceptibility to cephalosporins was associated with NG-STAR ST-90, ST-91, and ST-97 (n = 162; 94.2%); and ciprofloxacin resistance was associated with NG-STAR ST-26, ST-90, ST-91, ST-97, ST-150, and ST-158 (n = 196; 98.0%). All isolates of NG-STAR ST-42, ST-43, ST-63, ST-81, and ST-160 (n = 106) were susceptible to all four antimicrobials. The standardization of nomenclature associated with antimicrobial resistance determinants through an internationally available database will facilitate the monitoring of the global dissemination of antimicrobial-resistant N. gonorrhoeae strains.

  • 205.
    den Tex, Robert-Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Patterns and Processes of Evolution in Sundaland2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biodiversity in the tropics is disproportionately high compared to other habitats, and also under disproportionate threat from human impact. It is necessary to understand how this diversity evolved and how it is partitioned across space in order to preserve it. In this thesis I construct phylogenies of tropical forest dependent vertebrates from Southeast Asia and the islands of the Sunda shelf, a region referred to as Sundaland. I focus on the tree squirrels (genus Sundasciurus) and Asian barbets (Aves: Family Megalaimidae), two taxa with similar ecological characteristics. I use these phylogenies to test hypotheses that have been put forward to explain high levels of tropical diversity including the Pleistocene pump and museum hypotheses. I also use phylogenies to elucidate phylogeographic patterns within the region. I find no evidence for an increase in speciation in the Pleistocene, but I do find within species structure that dates to this period. Common phylogeographic patterns were identified between many forest dependent vertebrates that suggest that populations on the island of Sumatra are generally more closely related to Malay Peninsula populations than to populations on Borneo.

    From a methodological viewpoint we propose careful usage of universal primers in ancient DNA studies because of our finding of increased risk of amplifying pseudogenes of the mtDNA.

  • 206. Dessimoz, Christophe
    et al.
    Gabaldón, Toni
    Roos, David S
    Sonnhammer, Erik L L
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Herrero, Javier
    Toward community standards in the quest for orthologs.2012In: Bioinformatics (Oxford, England), ISSN 1367-4811, Vol. 28, no 6, 900-4 p.Article in journal (Refereed)
    Abstract [en]

    The identification of orthologs-genes pairs descended from a common ancestor through speciation, rather than duplication-has emerged as an essential component of many bioinformatics applications, ranging from the annotation of new genomes to experimental target prioritization. Yet, the development and application of orthology inference methods is hampered by the lack of consensus on source proteomes, file formats and benchmarks. The second 'Quest for Orthologs' meeting brought together stakeholders from various communities to address these challenges. We report on achievements and outcomes of this meeting, focusing on topics of particular relevance to the research community at large. The Quest for Orthologs consortium is an open community that welcomes contributions from all researchers interested in orthology research and applications.

  • 207. Didinger, Chelsea
    et al.
    Eimes, John
    Lillie, Mette
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Waldman, Bruce
    Multiple major histocompatibility complex class I genes in Asian anurans: Ontogeny and phylogeny2017In: Developmental and Comparative Immunology, ISSN 0145-305X, E-ISSN 1879-0089, Vol. 70, 69-79 p.Article in journal (Refereed)
    Abstract [en]

    Amphibians, as the first terrestrial vertebrates, offer a window into early major histocompatibility complex (MHC) evolution. We characterized the MHC class I of two Korean amphibians, the Asiatic toad (Bufo gargarizans) and the Japanese tree frog (Hyla japonica). We found at least four transcribed MHC class I (MHC I) loci, the highest number confirmed in any anuran to date. Furthermore, we identified MHC I transcripts in terrestrial adults, and possibly in aquatic larvae, of both species. We conducted a phylogenetic analysis based on MHC I sequence data and found that B. gargarizans and H. japonica cluster together in the superfamily Nobleobatrachia. We further identified three supertypes shared by the two species. Our results reveal substantial variation in the number of MHC I loci in anurans and suggest that certain supertypes have particular physiochemical properties that may confer pathogen resistance.

  • 208.
    Dinca, Vlad
    et al.
    Univ Guelph, Biodivers Inst Ontario, Guelph, ON N1G 2W1, Canada..
    Backstrom, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dapporto, Leonardo
    Oxford Brookes Univ, Dept Biol & Med Sci, Oxford OX3 0BP, England..
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Garcia-Barros, Enrique
    Univ Autonoma Madrid, Dept Biol, Madrid 28049, Spain..
    Hebert, Paul D. N.
    Univ Guelph, Biodivers Inst Ontario, Guelph, ON N1G 2W1, Canada..
    Hernandez-Roldan, Juan
    Univ Autonoma Madrid, Dept Biol, Madrid 28049, Spain..
    Hornett, Emily
    Univ Cambridge, Dept Zool, Cambridge CB2 3EJ, England..
    Lukhtanov, Vladimir
    Russian Acad Sci, Inst Zool, Dept Karyosystemat, St Petersburg 199034, Russia..
    Marec, Frantisek
    Univ South Bohemia, Fac Sci, Ceske Budejovice 37005, Czech Republic..
    DNA barcodes highlight unique research models in European butterflies2015In: Genome, ISSN 0831-2796, E-ISSN 1480-3321, Vol. 58, no 5, 212-212 p.Article in journal (Other academic)
  • 209.
    Dinca, Vlad
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wiklund, Christer
    Stockholm University, Faculty of Science, Department of Zoology.
    Lukhtanov, V. A.
    Kodandaramaiah, U.
    Norén, Karin
    Stockholm University, Faculty of Science, Department of Zoology.
    Dapporto, L.
    Wahlberg, N.
    Vila, R.
    Friberg, Mange
    Stockholm University, Faculty of Science, Department of Zoology.
    Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex2013In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 26, no 10, 2095-2106 p.Article in journal (Refereed)
    Abstract [en]

    Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter- and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence.

  • 210.
    Dirks-Mulder, Anita
    et al.
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    Butot, Roland
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands..
    van Schaik, Peter
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    Wijnands, Jan Willem P. M.
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    van den Berg, Roel
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    Krol, Louie
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    Doebar, Sadhana
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    van Kooperen, Kelly
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Univ Oslo, Nat Hist Museum, POB 1172 Blindern, N-0318 Oslo, Norway..
    Kramer, Elena M.
    Harvard Univ, Dept Organism & Evolutionary Biol, 16 Div Ave, Cambridge, MA 02138 USA..
    Smets, Erik F.
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Katholieke Univ Leuven, Ecol Evolut & Biodivers Conservat cluster, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium..
    Vos, Rutger A.
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Univ Amsterdam, Inst Biodivers & Ecosyst Dynam, Sci Pk 904, NL-1098 XH Amsterdam, Netherlands..
    Vrijdaghs, Alexander
    Katholieke Univ Leuven, Ecol Evolut & Biodivers Conservat cluster, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium..
    Gravendeel, Barbara
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands.;Leiden Univ, Inst Biol, Sylviusweg 72, NL-2333 BF Leiden, Netherlands..
    Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system2017In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, 89Article in journal (Refereed)
    Abstract [en]

    Background: Thousands of flowering plant species attract pollinators without offering rewards, but the evolution of this deceit is poorly understood. Rewardless flowers of the orchid Erycina pusilla have an enlarged median sepal and incised median petal ('lip') to attract oil-collecting bees. These bees also forage on similar looking but rewarding Malpighiaceae flowers that have five unequally sized petals and gland-carrying sepals. The lip of E. pusilla has a 'callus' that, together with winged 'stelidia', mimics these glands. Different hypotheses exist about the evolutionary origin of the median sepal, callus and stelidia of orchid flowers. Results: The evolutionary origin of these organs was investigated using a combination of morphological, molecular and phylogenetic techniques to a developmental series of floral buds of E. pusilla. The vascular bundle of the median sepal indicates it is a first whorl organ but its convex epidermal cells reflect convergence of petaloid features. Expression of AGL6 EpMADS4 and APETALA3 EpMADS14 is low in the median sepal, possibly correlating with its petaloid appearance. A vascular bundle indicating second whorl derivation leads to the lip. AGL6 EpMADS5 and APETALA3 EpMADS13 are most highly expressed in lip and callus, consistent with current models for lip identity. Six vascular bundles, indicating a stamen-derived origin, lead to the callus, stelidia and stamen. AGAMOUS is not expressed in the callus, consistent with its sterilization. Out of three copies of AGAMOUS and four copies of SEPALLATA, EpMADS22 and EpMADS6 are most highly expressed in the stamen. Another copy of AGAMOUS, EpMADS20, and the single copy of SEEDSTICK, EpMADS23, are most highly expressed in the stelidia, suggesting EpMADS22 may be required for fertile stamens. Conclusions: The median sepal, callus and stelidia of E. pusilla appear to be derived from a sepal, a stamen that gained petal identity, and stamens, respectively. Duplications, diversifying selection and changes in spatial expression of different MADS-box genes shaped these organs, enabling the rewardless flowers of E. pusilla to mimic an unrelated rewarding flower for pollinator attraction. These genetic changes are not incorporated in current models and urge for a rethinking of the evolution of deceptive flowers.

  • 211. Dixon, Christopher J
    et al.
    Schoenswetter, Peter
    Suda, Jan
    Wiedermann, Magdalena M
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Schneeweiss, Gerald M
    Reciprocal Pleistocene origin and postglacial range formation of an allopolyploid and its sympatric ancestors (Androsace adfinis group, Primulaceae)2009In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 50, no 1, 74-83 p.Article in journal (Refereed)
    Abstract [en]

    The biogeographic history of polyploids and their lower-ploid ancestors is an important feature to achieve a better understanding of polyploid evolution. This is exemplified here using the ecologically congruent members of the Androsace adfinis group (Primulaceae) endemic to the southwestern European Alps. Employing relative genome size, AFLP fingerprint and chloroplast sequence haplotype data, we show that Androsace brigantiaca is a recent (probably no more than 0.2 million years) allopolyploid derivative of the geographically close A adfinis and A puberula, which formed reciprocally in a comparatively restricted area in the southern Southwestern Alps. Bayesian admixture analysis-also of artificial additive AFLP profiles-shows that the nuclear genome of A. brigantiaca is significantly biased towards the puberula-genome irrespective of maternal parentage. Nevertheless, there is no evidence for genetic interaction (hybridization, introgression) of A brigantiaca with either of its ancestors, including the widely sympatric A. puberula. Sympatry might be facilitated by ecological displacement on a local scale or might be a transitory phase on the way to competitive replacement via, for instance, polyploid superiority.

  • 212.
    Dnyansagar, Rohit
    University of Skövde, School of Life Sciences.
    Investigation of phylogenetic relationships using microRNA sequences and secondary structures2010Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    MicroRNAs are important biomolecules for regulating biological processes. Moreover, the secondary structure of microRNA is important for its activity and has been used previously as a mean for finding unknown microRNAs. A phylogenetic study of the microRNA secondary structure reveals more information than its primary sequence, because the primary sequence can undergo mutations that give rise to different phylogenetic relationships, whereas the secondary structure is more robust against mutations and therefore sometimes  more informative.

    Here we constructed a phylogenetic tree entirely based on microRNA secondary structures using tools PHYLIP (Felsenstein, 1995) and RNAforester (Matthias Höchsmann, 2003, Hochsmann et al., 2004), and compared the overall topology and clusters with the phylogenetic tree constructed using microRNA sequence. The purpose behind this comparison was to investigate the sequence and structure similarity in phylogenetic context and also to investigate if functionally similar microRNA genes are closer in their structure-derived phylogenetic tree.

    Our phylogenetic comparison shows that the sequence similarity has hardly any effect on the structure similarity in the phylogenetic tree. MicroRNAs that have similar function are closer in the phylogenetic tree based on secondary structure than its respective sequence phylogeny. Hence, this approach can be very useful in predicting the functions of the new microRNAs whose function is yet to be known, since the function of the miRNAs heavily relies on its secondary structure.

     

  • 213. Dobbins, Sara E.
    et al.
    Broderick, Peter
    Melin, Beatrice
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Oncology.
    Feychting, Maria
    Johansen, Christoffer
    Andersson, Ulrika
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Oncology.
    Brännström, Thomas
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Schramm, Johannes
    Olver, Bianca
    Lloyd, Amy
    Ma, Yussanne P.
    Hosking, Fay J.
    Lönn, Stefan
    Ahlbom, Anders
    Henriksson, Roger
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Oncology.
    Schoemaker, Minouk J.
    Hepworth, Sarah J.
    Hoffmann, Per
    Muehleisen, Thomas W.
    Noethen, Markus M.
    Moebus, Susanne
    Eisele, Lewin
    Kosteljanetz, Michael
    Muir, Kenneth
    Swerdlow, Anthony
    Simon, Matthias
    Houlston, Richard S.
    Common variation at 10p12.31 near MLLT10 influences meningioma risk2011In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 43, no 9, 825-827 p.Article in journal (Refereed)
    Abstract [en]

    To identify susceptibility loci for meningioma, we conducted a genome-wide association study of 859 affected individuals (cases) and 704 controls with validation in two independent sample sets totaling 774 cases and 1,764 controls. We identified a new susceptibility locus for meningioma at 10p12.31 (MLLT10, rs11012732, odds ratio = 1.46, P(combined) = 1.88 x 10(-14)). This finding advances our understanding of the genetic basis of meningioma development.

  • 214.
    Domingo-Prim, Judit
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    The exosome and the maintenance of genome integrity2016Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The RNA exosome acts on different RNA substrates and plays important roles in RNA metabolism. The fact that short non-coding RNAs are involved in the DNA damage response led us to investigate whether the exosome plays a role in DNA repair. We have shown that the exosome catalytic subunit RRP6/EXOSC10 is recruited to DNA double-strand breaks (DSBs) in Drosophila S2 cells and human HeLa cells exposed to either ionizing radiation or I-PpoI endonuclease cleavage. DIS3, the other catalytic subunit of the nuclear exosome, is also recruited to DSBs, whereas the exosome core subunit EXOSC7 is not. Depletion of different exosome subunits does not interfere with the phosphorylation of the histone variants H2Av (Drosophila) or H2AX (humans), but depletion of RRP6/EXOSC10 impairs the recruitment of the homologous recombination factor RAD51 to the damaged sites, without affecting RAD51 levels. The recruitment of RAD51 to DSBs in S2 cells is also inhibited by overexpression of RRP6-Y361A–V5, a catalytically inactive RRP6 mutant. Furthermore, cells depleted of RRP6 or EXOSC10 are more sensitive to radiation, which is consistent with RRP6/EXOSC10 playing a role in DNA repair. RRP6/EXOSC10 can be co-immunoprecipitated with RAD51, which links RRP6/EXOSC10 to the homologous recombination pathway in animal cells. Taken together, our results suggest that a 3’-5’ ribonucleolytic activity is required for efficient DNA repair. 

  • 215.
    Dondorp, Wybo
    et al.
    Maastricht Univ, Res Sch CAPHRI, Dept Hlth Eth & Soc, NL-6200 MD Maastricht, Netherlands.;Maastricht Univ, Res Sch GROW, Dept Hlth Eth & Soc, NL-6200 MD Maastricht, Netherlands..
    de Wert, Guido
    Maastricht Univ, Res Sch CAPHRI, Dept Hlth Eth & Soc, NL-6200 MD Maastricht, Netherlands.;Maastricht Univ, Res Sch GROW, Dept Hlth Eth & Soc, NL-6200 MD Maastricht, Netherlands..
    Bombard, Yvonne
    Univ Toronto, Fac Med, Li Ka Shing Knowledge Inst, St Michaels Hosp, Toronto, ON, Canada.;Univ Toronto, Fac Med, Inst Hlth Policy Management & Evaluat, Toronto, ON, Canada..
    Bianchi, Diana W.
    Tufts Univ, Sch Med, Dept Pediat Obstet & Gynecol, Boston, MA 02111 USA..
    Bergmann, Carsten
    Ctr Human Genet Biosci, Ingelheim, Germany.;Univ Freiburg, Med Ctr, Dept Med, D-79106 Freiburg, Germany..
    Borry, Pascal
    Leuven Univ, Ctr Biomed Eth & Law, Dept Publ Hlth & Primary Care, Louvain, Belgium..
    Chitty, Lyn S.
    Great Ormond St Hosp & UCLH NHS Fdn Trusts, UCL Inst Child Hlth, Clin & Mol Genet Unit, London, England..
    Fellmann, Florence
    Univ Lausanne Hosp, Serv Med Genet, Lausanne, Switzerland..
    Forzano, Francesca
    Osped Galliera, Med Genet Unit, Genoa, Italy..
    Hall, Alison
    PHG Fdn, Cambridge, England..
    Henneman, Lidewij
    Vrije Univ Amsterdam Med Ctr, Sect Community Genet, Dept Clin Genet, Amsterdam, Netherlands.;Vrije Univ Amsterdam Med Ctr, EMGO Inst Hlth & Care Res, Amsterdam, Netherlands..
    Howard, Heidi C.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences, Centre for Research Ethics and Bioethics.
    Lucassen, Anneke
    Univ Southampton, Dept Clin Eth & Law CELS, Southampton, Hants, England.;Wessex Clin Genet Serv, Southampton, Hants, England..
    Ormond, Kelly
    Stanford Univ, Sch Med, Dept Genet, Stanford, CA USA.;Stanford Univ, Sch Med, Stanford Ctr Biomed Eth, Stanford, CA USA..
    Peterlin, Borut
    Univ Ljubljana, Med Ctr, Clin Inst Med Genet, Ljubljana 61000, Slovenia..
    Radojkovic, Dragica
    Univ Belgrade, IMGGE, Lab Mol Biol, Belgrade, Serbia..
    Rogowski, Wolf
    Helmholtz Zentrum, Deutsch Forschungszentrum Gesundheit & Umwelt, Munich, Germany..
    Soller, Maria
    Lund Univ, Div Clin Genet, Lund, Sweden.;Univ Lund Hosp, Reg Labs Reg Skane, S-22185 Lund, Sweden..
    Tibben, Aad
    Leiden Univ, Med Ctr, Dept Clin Genet, Leiden, Netherlands..
    Tranebjaerg, Lisbeth
    Bispebjerg Hosp, Rigshosp, Dept Audiol, Copenhagen, Denmark.;Univ Copenhagen, Kennedy Ctr, Dept Clin Genet, Copenhagen, Denmark.;Univ Copenhagen, ICMM, Inst Cellular & Mol Med, Copenhagen, Denmark..
    van El, Carla G.
    Vrije Univ Amsterdam Med Ctr, Sect Community Genet, Dept Clin Genet, Amsterdam, Netherlands.;Vrije Univ Amsterdam Med Ctr, EMGO Inst Hlth & Care Res, Amsterdam, Netherlands..
    Cornel, Martina C.
    Vrije Univ Amsterdam Med Ctr, Sect Community Genet, Dept Clin Genet, Amsterdam, Netherlands.;Vrije Univ Amsterdam Med Ctr, EMGO Inst Hlth & Care Res, Amsterdam, Netherlands..
    Non-invasive prenatal testing for aneuploidy and beyond: challenges of responsible innovation in prenatal screening2015In: European Journal of Human Genetics, ISSN 1018-4813, E-ISSN 1476-5438, Vol. 23, no 11, 1438-1450 p.Article in journal (Refereed)
    Abstract [en]

    This paper contains a joint ESHG/ASHG position document with recommendations regarding responsible innovation in prenatal screening with non-invasive prenatal testing (NIPT). By virtue of its greater accuracy and safety with respect to prenatal screening for common autosomal aneuploidies, NIPT has the potential of helping the practice better achieve its aim of facilitating autonomous reproductive choices, provided that balanced pretest information and non-directive counseling are available as part of the screening offer. Depending on the health-care setting, different scenarios for NIPT-based screening for common autosomal aneuploidies are possible. The trade-offs involved in these scenarios should be assessed in light of the aim of screening, the balance of benefits and burdens for pregnant women and their partners and considerations of cost-effectiveness and justice. With improving screening technologies and decreasing costs of sequencing and analysis, it will become possible in the near future to significantly expand the scope of prenatal screening beyond common autosomal aneuploidies. Commercial providers have already begun expanding their tests to include sex-chromosomal abnormalities and microdeletions. However, multiple false positives may undermine the main achievement of NIPT in the context of prenatal screening: the significant reduction of the invasive testing rate. This document argues for a cautious expansion of the scope of prenatal screening to serious congenital and childhood disorders, only following sound validation studies and a comprehensive evaluation of all relevant aspects. A further core message of this document is that in countries where prenatal screening is offered as a public health programme, governments and public health authorities should adopt an active role to ensure the responsible innovation of prenatal screening on the basis of ethical principles. Crucial elements are the quality of the screening process as a whole (including non-laboratory aspects such as information and counseling), education of professionals, systematic evaluation of all aspects of prenatal screening, development of better evaluation tools in the light of the aim of the practice, accountability to all stakeholders including children born from screened pregnancies and persons living with the conditions targeted in prenatal screening and promotion of equity of access.

  • 216.
    D'Onofrio, Brian M.
    et al.
    Department of Psychological and Brain Sciences, Indiana University, Bloomington, USA.
    Class, Quetzal A.
    Department of Psychological and Brain Sciences, Indiana University, Bloomington, USA.
    Rickert, Martin E.
    Department of Psychological and Brain Sciences, Indiana University, Bloomington, USA.
    Sujan, Ayesha C.
    Department of Psychological and Brain Sciences, Indiana University, Bloomington, USA.
    Larsson, Henrik
    Karolinska Institutet, Stockholm, Sweden.
    Kuja-Halkola, Ralf
    Karolinska Institutet, Stockholm, Sweden.
    Sjölander, Arvid
    Karolinska Institutet, Stockholm, Sweden.
    Almqvist, Catarina
    Karolinska Institutet, Stockholm, Sweden.
    Lichtenstein, Paul
    Karolinska Institutet, Stockholm, Sweden.
    Oberg, A. Sara
    Karolinska Institutet, Stockholm, Sweden; Harvard T.H. Chan School of Public Health, Boston, USA.
    Translational Epidemiologic Approaches to Understanding the Consequences of Early-Life Exposures2016In: Behavior Genetics, ISSN 0001-8244, E-ISSN 1573-3297, Vol. 46, no 3, 315-328 p.Article, review/survey (Refereed)
    Abstract [en]

    Prominent developmental theories posit a causal link between early-life exposures and later functioning. Yet, observed associations with early exposures may not reflect causal effects because of genetic and environmental confounding. The current manuscript describes how a systematic series of epidemiologic analyses that combine several genetically-informative designs and statistical approaches can help distinguish between competing theories. In particular, the manuscript details how combining the use of measured covariates with sibling-comparisons, cousin-comparisons, and additional designs can help elucidate the sources of covariation between early-life exposures and later outcomes, including the roles of (a) factors that are not shared in families, including a potential causal effect of the exposure; (b) carryover effects from the exposure of one child to the next; and (c) familial confounding. We also describe key assumptions and how they can be critically evaluated. Furthermore, we outline how subsequent analyses, including effect decomposition with respect to measured, plausible mediators, and quantitative genetic models can help further specify the underlying processes that account for the associations between early-life exposures and offspring outcomes.

  • 217.
    Dowling, Damian K
    et al.
    Animal Ecology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Friberg, Urban
    Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå , Sweden.
    Hailer, Frank
    Animal Ecology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Arnqvist, Göran
    Animal Ecology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Intergenomic epistasis for fitness: within-population interactions between cytoplasmic and nuclear genes in Drosophila melanogaster.2007In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 175, no 1, 235-44 p.Article in journal (Refereed)
    Abstract [en]

    The symbiotic relationship between the mitochondrial and nuclear genomes coordinates metabolic energy production and is fundamental to life among eukaryotes. Consequently, there is potential for strong selection to shape interactions between these two genomes. Substantial research attention has focused on the possibility that within-population sequence polymorphism in mitochondrial DNA (mtDNA) is maintained by mitonuclear fitness interactions. Early theory predicted that selection will often eliminate mitochondrial polymorphisms. However, recent models demonstrate that intergenomic interactions can promote the maintenance of polymorphism, especially if the nuclear genes involved are linked to the X chromosome. Most empirical studies to date that have assessed cytonuclear fitness interactions have studied variation across populations and it is still unclear how general and strong such interactions are within populations. We experimentally tested for cytonuclear interactions within a laboratory population of Drosophila melanogaster using 25 randomly sampled cytoplasmic genomes, expressed in three different haploid nuclear genetic backgrounds, while eliminating confounding effects of intracellular bacteria (e.g., Wolbachia). We found sizable cytonuclear fitness interactions within this population and present limited evidence suggesting that these effects were sex specific. Moreover, the relative fitness of cytonuclear genotypes was environment specific. Sequencing of mtDNA (2752 bp) revealed polymorphism within the population, suggesting that the observed cytoplasmic genetic effects may be mitochondrial in origin.

  • 218.
    Dowling, Damian K.
    et al.
    Centre for Evolutionary Biology, School of Animal Biology (M092), The University of Western Australia, Crawley, WA, Australia / Animal Ecology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Friberg, Urban
    Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA.
    Lindell, Johan
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Evolutionary implications of non-neutral mitochondrial genetic variation2008In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 23, no 10, 546-554 p.Article, review/survey (Refereed)
    Abstract [en]

    Sequence variation in mitochondrial DNA (mtDNA) was traditionally considered to be selectively neutral. However, an accumulating body of evidence indicates that this assumption is invalid. Furthermore, recent advances indicate that mtDNA polymorphism can be maintained within populations via selection on the joint mitochondrial-nuclear genotype. Here, we review the latest findings that show mitochondrial and cytoplasmic genetic variation for life-history traits and fitness. We highlight the key importance of the mitochondrial-nuclear interaction as a unit of selection and discuss the consequences of mitochondrially encoded fitness effects on several key evolutionary processes. Our goal is to draw attention to the profound, yet neglected, influence of the mitochondrial genome on the fields of ecology and evolution.

  • 219.
    Dragan, Smiljic
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Studies of small bicoid knock-down and overexpression at early and late stage of development in Drosophila melanogaster.2016Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
  • 220. Drotz, Marcus K
    et al.
    Brodin, Tomas
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Nilsson, Anders N
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Changing Names with Changed Address: Integrated Taxonomy and Species Delimitation in the Holarctic Colymbetes paykulli Group (Coleoptera: Dytiscidae)2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 11, e0143577Article in journal (Refereed)
    Abstract [en]

    Species delimitation of geographically isolated forms is a long-standing problem in less studied insect groups. Often taxonomic decisions are based directly on morphologic variation, and lack a discussion regarding sample size and the efficiency of migration barriers or dispersal/migration capacity of the studied species. These problems are here exemplified in a water beetle complex from the Bering Sea region that separates North America from Eurasia. Only a few sampled specimens occur from this particular area and they are mostly found in museum and private collections. Here we utilize the theory of integrated taxonomy to discuss the speciation of the Holarctic Colymbetes paykulli water beetle complex, which historically has included up to five species of which today only two are recognized. Three delimitation methods are used; landmark based morphometry of body shape, variation in reticulation patterns of the pronotum exo-skeleton and sequence variation of the partial mitochondrial gene Cyt b. Our conclusion is that the Palearctic and Nearctic populations of C. paykulli are given the status of separate species, based on the fact that all methods showed significant separation between populations. As a consequence the name of the Palearctic species is C. paykulli Erichson and the Nearctic species should be known as C. longulus LeConte. There is no clear support for delineation between Palearctic and Nearctic populations of C. dahuricus based on mtDNA. However, significant difference in size and reticulation patterns from the two regions is shown. The combined conclusion is that the C. dahuricus complex needs a more thorough investigation to fully disentangle its taxonomic status. Therefore it is here still regarded as a Holarctic species. This study highlights the importance to study several diagnosable characters that has the potential to discriminate evolutionary lineage during speciation.

  • 221. Du, Qingzhang
    et al.
    Tian, Jiaxing
    Yang, Xiaohui
    Pan, Wei
    Xu, Baohua
    Li, Bailian
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zhang, Deqiang
    Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa2015In: DNA research, ISSN 1340-2838, E-ISSN 1756-1663, Vol. 22, no 1, 53-67 p.Article in journal (Refereed)
    Abstract [en]

    Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P < 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R-2). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q <= 0.10), representing 38 SNPs from nine genes, and its average effect (R-2 = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene-gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding.

  • 222.
    Duan, Chen
    et al.
    Medical College of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
    Guo, Xiong
    Medical College of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
    Zhang, Xiao-Dong
    First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
    Yu, Han-Jie
    Northwest University, Xi'an, Shaanxi, China.
    Yan, Hua
    Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
    Gao, Ying
    Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
    Ma, Wei-Juan
    Medical College of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
    Gao, Zong-Qiang
    Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
    Xu, Peng
    Xi'an Red Cross Hospital, Xi'an, Shaanxi, China.
    Lammi, Mikko
    University of Kuopio, Kuopio, Finland.
    Comparative analysis of gene expression profiles between primary knee osteoarthritis and an osteoarthritis endemic to Northwestern China, Kashin-Beck disease.2010In: Arthritis and Rheumatism, ISSN 0004-3591, E-ISSN 1529-0131, Vol. 62, no 3, 771-780 p., 20131229Article in journal (Refereed)
    Abstract [en]

    OBJECTIVE: To investigate the differences in gene expression profiles of adult articular cartilage from patients with Kashin-Beck disease (KBD) versus those with primary knee osteoarthritis (OA).

    METHODS: The messenger RNA expression profiles of articular cartilage from patients with KBD, diagnosed according to the clinical criteria for KBD in China, were compared with those of cartilage from patients with OA, diagnosed according to the Western Ontario and McMaster Universities OA Index. Total RNA was isolated separately from 4 pairs of the KBD and OA cartilage samples, and the expression profiles were evaluated by Agilent 4x44k Whole Human Genome density oligonucleotide microarray analysis. The microarray data for selected transcripts were confirmed by quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) amplification.

    RESULTS: For 1.2 x 10(4) transcripts, corresponding to 58.4% of the expressed transcripts, 2-fold changes in differential expression were revealed. Expression levels higher in KBD than in OA samples were observed in a mean + or - SD 6,439 + or - 1,041 (14.6 + or - 2.4%) of the transcripts, and expression levels were lower in KBD than in OA samples in 6,147 + or - 1,222 (14.2 + or - 2.8%) of the transcripts. After application of the selection criteria, 1.85% of the differentially expressed genes (P < 0.001 between groups) were detected. These included 233 genes, of which 195 (0.4%) were expressed at higher levels and 38 (0.08%) were expressed at lower levels in KBD than in OA cartilage. Comparisons of the quantitative RT-PCR data supported the validity of our microarray data.

    CONCLUSION: Differences between KBD and OA cartilage exhibited a similar pattern among all 4 of the pairs examined, indicating the presence of disease mechanisms, mainly chondrocyte matrix metabolism, cartilage degeneration, and apoptosis induction pathways, which contribute to cartilage destruction in KBD.

  • 223. Dudgeon, Crissy
    et al.
    Shreeram, Sathyavageeswaran
    Tanoue, Kan
    Mazur, Sharlyn J
    Sayadi, Ahmed
    Institute of Molecular and Cell Biology; Proteos; Singapore.
    Robinson, Robert C
    Appella, Ettore
    Bulavin, Dmitry V
    Genetic variants and mutations of PPM1D control the response to DNA damage2013In: Cell Cycle, ISSN 1538-4101, E-ISSN 1551-4005, Vol. 12, no 16Article in journal (Refereed)
    Abstract [en]

    The Wip1 phosphatase is an oncogene that is overexpressed in a variety of primary human cancers. We were interested in identifying genetic variants that could change Wip1 activity. We identified 3 missense SNPs of the human Wip1 phosphatase, L120F, P322Q, and I496V confer a dominant-negative phenotype. On the other hand, in primary human cancers, PPM1D mutations commonly result in a gain-of-function phenotype, leading us to identify a hot-spot truncating mutation at position 525. Surprisingly, we also found a significant number of loss-of-function mutations of PPM1D in primary human cancers, both in the phosphatase domain and in the C terminus. Thus, PPM1D has evolved to generate genetic variants with lower activity, potentially providing a better fitness for the organism through suppression of multiple diseases. In cancer, however, the situation is more complex, and the presence of both activating and inhibiting mutations requires further investigation to understand their contribution to tumorigenesis.

  • 224. Eisfeldt, Jesper
    et al.
    Nazaryan-Petersen, Lusine
    Lundin, Johanna Lundin
    Pettersson, Maria
    Nilsson, Daniel
    Wincent, Josephine
    Lieden, Agne
    Vezzi, Francesco
    Wirta, Valteri
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Käller, Max
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Duelund, Tina
    Houssari, Rayan
    Pignata, Laura
    Bak, Mads
    Tommerup, Niels
    Lundberg, Elisabeth Syk
    Tumer, Zeynep
    Lindstrand, Anna
    Whole genome characterization of array defined clustered CNVs reveals two distinct complex rearrangement subclasses generated through either non homologous repair or template switching2017In: Molecular Cytogenetics, ISSN 1755-8166, E-ISSN 1755-8166, Vol. 10Article in journal (Other academic)
  • 225. Ek, Weronica
    et al.
    Sahlqvist, Anna-Stina
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Autoimmunity.
    Crooks, Lucy
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Sgonc, Roswitha
    Dietrich, Hermann
    Wick, Georg
    Ekwall, Olov
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Autoimmunity.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Carlborg, Örjan
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Kämpe, Olle
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Autoimmunity.
    Kerje, Susanne
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Mapping QTL affecting a systemic sclerosis-like disorder in a cross between UCD-200 and red jungle fowl chickens2012In: Developmental and Comparative Immunology, ISSN 0145-305X, E-ISSN 1879-0089, Vol. 38, no 2, 352-359 p.Article in journal (Refereed)
    Abstract [en]

    Systemic sclerosis (SSc) or scleroderma is a rare, autoimmune, multi-factorial disease characterized by early microvascular alterations, inflammation, and fibrosis. Chickens from the UCD-200 line develop a hereditary SSc-like disease, showing all the hallmarks of the human disorder, which makes this line a promising model to study genetic factors underlying the disease. A backcross was generated between UCD-200 chickens and its wild ancestor - the red jungle fowl and a genome-scan was performed to identify loci affecting early (21days of age) and late (175days of age) ischemic lesions of the comb. A significant difference in frequency of disease was observed between sexes in the BC population, where the homogametic males were more affected than females, and there was evidence for a protective W chromosome effect. Three suggestive disease predisposing loci were mapped to chromosomes 2, 12 and 14. Three orthologues of genes implicated in human SSc are located in the QTL region on chromosome 2, TGFRB1, EXOC2-IRF4 and COL1A2, as well as CCR8, which is more generally related to immune function. IGFBP3 is also located within the QTL on chromosome 2 and earlier studies have showed increased IGFBP3 serum levels in SSc patients. To our knowledge, this study is the first to reveal a potential genetic association between IGFBP3 and SSc. Another gene with an immunological function, SOCS1, is located in the QTL region on chromosome 14. These results illustrate the usefulness of the UCD-200 chicken as a model of human SSc and motivate further in-depth functional studies of the implicated candidate genes.

  • 226.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Slate, Jon
    Horsburgh, Gavin J
    Birkhead, Tom
    Burke, Terry
    Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies2012In: Comparative and functional genomics, ISSN 1531-6912, E-ISSN 1532-6268, Vol. 2012, 281693- p.Article in journal (Refereed)
    Abstract [en]

    Next-generation sequencing of transcriptomes (RNA-Seq) is being used increasingly in studies of nonmodel organisms. Here, we evaluate the effectiveness of normalising cDNA libraries prior to sequencing in a small-scale study of the zebra finch. We find that assemblies produced from normalised libraries had a larger number of contigs but used fewer reads compared to unnormalised libraries. Considerably more genes were also detected using the contigs produced from normalised cDNA, and microsatellite discovery was up to 73% more efficient in these. There was a positive correlation between the detected expression level of genes in normalised and unnormalised cDNA, and there was no difference in the number of genes identified as being differentially expressed between blood and spleen for the normalised and unnormalised libraries. We conclude that normalised cDNA libraries are preferable for many applications of RNA-Seq and that these can also be used in quantitative gene expression studies.

  • 227.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Sæther, Stein Are
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Grahn, Mats
    Fiske, Peder
    Kålås, John Atle
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Major histocompatibility complex variation and mate choice in a lekking bird, the great snipe (Gallinago media)2004In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 13, no 12, 3821-3828 p.Article in journal (Refereed)
    Abstract [en]

    Genes of the major histocompatibility complex (MHC) play a major part in the activation of the vertebrate immune system. In addition, they also appear to function as cues for mate choice. In mammals especially, several kinds of MHC-dependent mate choice have been hypothesized and observed. These include choice of mates that share no or few alleles with the choosing individual, choice of mates with alleles that differ as much as possible from the choosing individual, choice of heterozygous mates, choice of certain genotypes and choice of rare alleles. We investigated these different aspects of mate choice in relation to MHC in a lekking bird species, the great snipe (Gallinago media). We found no evidence for MHC disassortative mating, no preference for males with many MHC alleles and no preference for rare alleles. However, we did find that some allelic lineages were more often found in males with mating success than in males without mating success. Females do not seem to use themselves as references for the MHC-dependent mate choice, rather they seem to prefer males with certain allele types. We speculate that these alleles may be linked to resistance to common parasites.

  • 228.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wennekes, Paul
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Horsburgh, Gavin J.
    Burke, Terry
    Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics2014In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 14, no 3, 636-646 p.Article in journal (Refereed)
    Abstract [en]

    The house sparrow (Passer domesticus) is an important model species in ecology and evolution. However, until recently, genomic resources for molecular ecological projects have been lacking in this species. Here, we present transcriptome sequencing data (RNA-Seq) from three different house sparrow tissues (spleen, blood and bursa). These tissues were specifically chosen to obtain a diverse representation of expressed genes and to maximize the yield of immune-related gene functions. After de novo assembly, 15250 contigs were identified, representing sequence data from a total of 8756 known avian genes (as inferred from the closely related zebra finch). The transcriptome assembly contain sequence data from nine manually annotated MHC genes, including an almost complete MHC class I coding sequence. There were 407, 303 and 68 genes overexpressed in spleen, blood and bursa, respectively. Gene ontology terms related to ribosomal function were associated with overexpression in spleen and oxygen transport functions with overexpression in blood. In addition to the transcript sequences, we provide 327 gene-linked microsatellites (SSRs) with sufficient flanking sequences for primer design, and 3177 single-nucleotide polymorphisms (SNPs) within genes, that can be used in follow-up molecular ecology studies of this ecological well-studied species.

  • 229.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Epigenetic control of centromere behavior2007In: Annual review of genetics / [ed] Allan Campbell, Wyatt W Anderson, Elizabeth W Jones, Palo Atlo: Annual Reviews , 2007, 63-81 p.Chapter in book (Refereed)
    Abstract [en]

    The centromere is the DNA region that ensures genetic stability and is therefore of vital importance. Paradoxically, centromere proteins and centromeric structural domains are conserved despite that fact that centromere DNA sequences are highly variable and are not conserved. Remarkably, heritable states at the centromere can be propagated independent of the underlying centromeric DNA sequences. This review describes the epigenetic mechanisms governing centromere behavior, i.e., the mechanisms that control centromere assembly and propagation. A centromeric histone variant, CenH3, and histone modifications play key roles at centromeric chromatin. Histone modifications and RNA interference are important in assembly of pericentric heterochromatin structures. The molecular machinery that is directly involved in epigenetic control of centromeres is shared with regulation of gene expression. Nucleosome remodeling factors, histone chaperones, histone-modifying enzymes, transcription factors, and even RNA polymerase II itself control epigenetic states at centromeres.

  • 230.
    Ekwall, Karl
    Södertörn University, School of Life Sciences.
    Genome-wide analysis of HDAC function2005In: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 21, no 11, 608-615 p.Article in journal (Refereed)
    Abstract [en]

    This article focuses on new developments in the genome-wide analysis of histone deacetylase (HDAC) function in yeast. HDACs are highly conserved in many organisms; therefore, their basic functions can be investigated using experimentally tractable model organisms, such as the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. New microarray techniques have enabled the systematic study of HDACs by identifying their direct and indirect gene targets in addition to their physiological functions and enzymatic specificity. These new approaches have already provided new surprising insights into the basic function of HDACs.

  • 231.
    Elisabeth, Ahlgren
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, The Institute of Technology.
    Marker generation for Fine Mapping a QTL in the chicken2014Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    The purpose of this study was to design and test five SNP markers in an inbred chicken cross between Red Junglefowl and domestic White Leghorn of the 8th generation. The markers lie in a region affecting the tonic immobility behaviour which differs significantly between the two species. The markers could be identified by usage of PCR and pyrosequencing. The data obtained were further used in a small scale quantitative trait locus (QTL) analysis. QTL analysis is a statistical method to link phenotypic traits to genotypic data. Four out of five markers could be genotypes and thereby, made it possible to proceed with the QTL analysis. The results showed that there is no QTL associated with the markers identified. The two flanking markers were closest to a significant difference between genotypes and it is therefore a possibility that a QTL lies close further down or up the searched region. From the line map it is indicated that there is little recombination in the marker region.

  • 232.
    Ellegaard, Kirsten M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Tamarit, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Javelind, Emelie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Olofsson, Tobias C.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Vasquez, Alejandra
    Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut2015In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 16, 284Article in journal (Refereed)
    Abstract [en]

    Background: In the honeybee Apis mellifera, the bacterial gut community is consistently colonized by eight distinct phylotypes of bacteria. Managed bee colonies are of considerable economic interest and it is therefore important to elucidate the diversity and role of this microbiota in the honeybee. In this study, we have sequenced the genomes of eleven strains of lactobacilli and bifidobacteria isolated from the honey crop of the honeybee Apis mellifera. Results: Single gene phylogenies confirmed that the isolated strains represent the diversity of lactobacilli and bifidobacteria in the gut, as previously identified by 16S rRNA gene sequencing. Core genome phylogenies of the lactobacilli and bifidobacteria further indicated extensive divergence between strains classified as the same phylotype. Phylotype-specific protein families included unique surface proteins. Within phylotypes, we found a remarkably high level of gene content diversity. Carbohydrate metabolism and transport functions contributed up to 45% of the accessory genes, with some genomes having a higher content of genes encoding phosphotransferase systems for the uptake of carbohydrates than any previously sequenced genome. These genes were often located in highly variable genomic segments that also contained genes for enzymes involved in the degradation and modification of sugar residues. Strain-specific gene clusters for the biosynthesis of exopolysaccharides were identified in two phylotypes. The dynamics of these segments contrasted with low recombination frequencies and conserved gene order structures for the core genes. Hits for CRISPR spacers were almost exclusively found within phylotypes, suggesting that the phylotypes are associated with distinct phage populations. Conclusions: The honeybee gut microbiota has been described as consisting of a modest number of phylotypes; however, the genomes sequenced in the current study demonstrated a very high level of gene content diversity within all three described phylotypes of lactobacilli and bifidobacteria, particularly in terms of metabolic functions and surface structures, where many features were strain-specific. Together, these results indicate niche differentiation within phylotypes, suggesting that the honeybee gut microbiota is more complex than previously thought.

  • 233.
    Ellegaard, Kirsten Maren
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Klasson, Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Näslund, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bourtzis, Kostas
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Comparative Genomics of Wolbachia and the Bacterial Species Concept2013In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 9, no 4, e1003381- p.Article in journal (Refereed)
    Abstract [en]

    The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double infections in Drosophila simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa belong to supergroup A and wNo to supergroup B. A comparative genomics study including additional strains supported the supergroup classification scheme and revealed 24 and 33 group-specific genes, putatively involved in host-adaptation processes. Recombination frequencies were high for strains of the same supergroup despite different host-preference patterns, leading to genomic cohesion. The inferred recombination fragments for strains of different supergroups were of short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo were not more similar to each other and did not share more genes than other A- and B-group strains that infect different hosts. We conclude that Wolbachia strains of supergroup A and B represent genetically distinct clades, and that strains of different supergroups can co-exist in the same arthropod host without converging into the same species. This suggests that the supergroups are irreversibly separated and that barriers other than host-specialization are able to maintain distinct clades in recombining endosymbiont populations. Acquiring a good knowledge of the barriers to genetic exchange in Wolbachia will advance our understanding of how endosymbiont communities are constructed from vertically and horizontally transmitted genes.

  • 234.
    Ellegren, H.
    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.
    DNA löser brott med djur.2004In: Kriminalteknik, no 3, 10-11 p.Article in journal (Other (popular scientific, debate etc.))
  • 235.
    Ellegren, H.
    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.
    Genetisk forskning visar på den framgångsrike hingsten.2004In: Miljöforskning: (FORMAS), Vol. 2, no 22-24Article in journal (Other (popular scientific, debate etc.))
  • 236.
    Ellegren, H.
    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.
    Microsatellites: simple sequences with complex evolution.2004In: Nature Reviews Genetics, no 5, 435-445 p.Article in journal (Refereed)
  • 237.
    Ellegren, H.
    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.
    Vad är en människa?2004In: Forsking och framsteg, no 4, 16- p.Article in journal (Other (popular scientific, debate etc.))
  • 238.
    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.
    Evolution: Natural selection in the evolution of humans and chimps.2005In: Curren Biology, no 22, R919-922 p.Article in journal (Refereed)
  • 239.
    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.
    The avian genome uncovered.2005In: Trends in Ecology and Evolution, no 20, 180-186 p.Article in journal (Refereed)
  • 240.
    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.
    The dog has its day.2005In: Nature, no 438, 745-746 p.Article in journal (Refereed)
  • 241.
    Ellegren, Hans
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Galtier, Nicolas
    Univ Montpellier 2, French Natl Ctr Sci Res CNRS, Inst Evolutionary Sci, Pl E Bataillon, F-34095 Montpellier, France..
    Determinants of genetic diversity2016In: Nature reviews genetics, ISSN 1471-0056, E-ISSN 1471-0064, Vol. 17, no 7, 422-433 p.Article, review/survey (Refereed)
    Abstract [en]

    Genetic polymorphism varies among species and within genomes, and has important implications for the evolution and conservation of species. The determinants of this variation have been poorly understood, but population genomic data from a wide range of organisms now make it possible to delineate the underlying evolutionary processes, notably how variation in the effective population size (Ne) governs genetic diversity. Comparative population genomics is on its way to providing a solution to 'Lewontin's paradox' - the discrepancy between the many orders of magnitude of variation in population size and the much narrower distribution of diversity levels. It seems that linked selection plays an important part both in the overall genetic diversity of a species and in the variation in diversity within the genome. Genetic diversity also seems to be predictable from the life history of a species.

  • 242.
    Ellencrona, Ellen
    et al.
    Södertörn University, School of Life Sciences.
    Melik, Wessam
    Södertörn University, School of Life Sciences.
    Johansson, Magnus
    Södertörn University, School of Life Sciences.
    Novel PDZ dependent cell associations of the NS5 proteins of Tick-borne encephalitis virus and West-Nile virusManuscript (preprint) (Other academic)
  • 243.
    Ellencrona, Karin
    Södertörn University, School of Life Sciences.
    Functional characterization of interactions between the flavivirus NS5 protein and PDZ proteins of the mammalian host2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Flaviviruses are found all over the world and affect and infect millions of people every year. Flavivirus infection can lead to severe clinical outcomes resulting in neuronal damages e.g. Tick-borne encephalitis virus (TBEV), or severe hemorrhagic fevers e.g. Dengue virus (DENV). In order to effectively treat infected patients and to prevent these diseases we must understand how these viruses work and how they interfere with the mammalian host. This thesis is focusing on interactions between the virus protein NS5 and human host cell proteins. The interactions presented here might be key factors for out-come of viral disease. NS5 is the largest of the non-structural proteins and is essential for the replication and the capping as it contains both RNA dependent RNA polymerase and Methyltransferase domains. We found that TBEV NS5 interacts with human PDZ domain protein Scribble, a polarization protein important e.g. in regulating membrane trafficking. We determined that the interaction depend on a novel internal motif in TBEVNS5. This interaction could be correlated to NS5s ability to interfere with the immune system as absence of Scribble prevented NS5 from blocking phosphorylation of STAT upon Interferon induction. The role of NS5 in human PDZ domain targeting was addressed further by using a PDZ array system. Both TBEVNS5 and DENVNS5 bind additional PDZ domains using the internal motif. The tight junction protein ZO-1 binds both DENVNS5 and TBEVNS5. DENVNS5 is mainly present in the nucleus and co-localize with ZO-1 in un-polarized cells. In polarized cells TBEVNS5 and ZO-1 co-localize at the plasmamembrane. Putative C-terminal PDZ binding motifs of TBEVNS5 and WNVNS5 were characterized using the PDZ array system. This detected four novel binding partners of TBEVNS5 but numerous of potential WNVNS5 binding partners. We found that TBEVNS5 co-localizes with ZO-2 in the cellular membrane. Further, we found that TBEVNS5 induce the AP-1 by a 2 fold over the control.

  • 244.
    Ellencrona, Karin
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Functional characterization of interactions between the flavivirus NS5 protein and PDZ proteins of the mammalian host2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Flaviviruses are found all over the world and affect and infect millions of people every year. Flavivirus infection can lead to severe clinical outcomes resulting in neuronal damages e.g. Tick-borne encephalitis virus (TBEV), or severe hemorrhagic fevers e.g. Dengue virus (DENV). In order to effectively treat infected patients and to prevent these diseases we must understand how these viruses work and how they interfere with the mammalian host. This thesis is focusing on interactions between the virus protein NS5 and human host cell proteins. The interactions presented here might be key factors for out-come of viral disease. NS5 is the largest of the non-structural proteins and is essential for the replication and the capping as it contains both RNA dependent RNA polymerase and Methyltransferase domains. We found that TBEV NS5 interacts with human PDZ domain protein Scribble, a polarization protein important e.g. in regulating membrane trafficking. We determined that the interaction depend on a novel internal motif in TBEVNS5. This interaction could be correlated to NS5s ability to interfere with the immune system as absence of Scribble prevented NS5 from blocking phosphorylation of STAT upon Interferon induction. The role of NS5 in human PDZ domain targeting was addressed further by using a PDZ array system. Both TBEVNS5 and DENVNS5 bind additional PDZ domains using the internal motif. The tight junction protein ZO-1 binds both DENVNS5 and TBEVNS5. DENVNS5 is mainly present in the nucleus and co-localize with ZO-1 in un-polarized cells. In polarized cells TBEVNS5 and ZO-1 co-localize at the plasmamembrane. Putative C-terminal PDZ binding motifs of TBEVNS5 and WNVNS5 were characterized using the PDZ array system. This detected four novel binding partners of TBEVNS5 but numerous of potential WNVNS5 binding partners. We found that TBEVNS5 co-localizes with ZO-2 in the cellular membrane. Further, we found that TBEVNS5 induce the AP-1 by a 2 fold over the control.

  • 245.
    Elmberg, Johan
    et al.
    Kristianstad University, School of Education and Environment, Avdelningen för Naturvetenskap. Kristianstad University, Research environment Man & Biosphere Health (MABH).
    Söderquist, Pär
    Kristianstad University, Research environment Man & Biosphere Health (MABH). Kristianstad University, School of Education and Environment, Avdelningen för Naturvetenskap.
    Gunnarsson, Gunnar
    Kristianstad University, School of Education and Environment, Avdelningen för Naturvetenskap. Kristianstad University, Research environment Man & Biosphere Health (MABH).
    Thulin, Carl-Gustaf
    SLU, Umeå.
    Champagnon, Jocelyn
    Frankrike.
    Guillemain, Matthieu
    Frankrike.
    Kreisinger, Jakub
    Tjeckien.
    Prins, H. H. T.
    Nederländerna.
    Crooijmans, R. P. M. A.
    Nederländerna.
    Kraus, R. H. S.
    Tyskland.
    Farmed European mallards are genetically different and cause introgression in the wild population following releases2016Conference paper (Refereed)
    Abstract [en]

    The practice of restocking already viable populations to increase harvest potential has since long been common in forestry, fisheries and wildlife management. The potential risks of restocking native species have long been overshadowed by the related issue of invasive alien species. However, during the last decade releases of native species with potentially non-native genome have received more attention. A suitable model to study genetic effects of large-scale releases of native species is the Mallard Anas platyrhynchos, being the most widespread duck in the world, largely migratory, and an important quarry species. More than 3 million unfledged hatchlings are released each year around Europe to increase local harvest. The aims of this study were to determine if wild and released farmed Mallards differ genetically, if there are signs of previous or ongoing introgression between wild and farmed birds, and if the genetic structure of the wild Mallard population has changed since large-scale releases started in Europe in the 1970s. Using 360 Single Nucleotide Polymorphisms (SNPs) we found that the genetic structure differed among historical wild, present-day wild, and farmed Mallards in Europe. We also found signs of introgression in the wild Mallard population, that is, individuals with a genetic background of farmed stock are part of the present free-living population. Although only a small proportion of the released Mallards appears to survive to merge with the free-living breeding population, their numbers are still so large that the genetic impact may have significance for the wild population in terms of individual survival and longterm fitness.

  • 246. El-Sayed, Najib M.
    et al.
    Myler, Peter J
    Bartholomeu, Daniella C
    Nilsson, Daniel
    Aggarwal, Gautam
    Tran, Anh-Nhi
    Ghedin, Elodie
    Worthey, Elizabeth A
    Delcher, Arthur L
    Blandin, Gaêlle
    Westenberger, Scott J
    Caler, Elisabet
    Cerqueira, Gustavo C
    Branche, Carole
    Haas, Brian
    Anupama, Atashi
    Arner, Erik
    Aslund, Lena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Attipoe, Philip
    Bontempi, Esteban
    Bringaud, Frederic
    Burton, Peter
    Cadag, Eithon
    Campbell, David A
    Carrington, Mark
    Crabtree, Jonathan
    Darban, Hamid
    da Silveira, Jose Franco
    de Jong, Pieter
    Edwards, Kimberly
    Englund, Paul T
    Fazelina, Gholam
    Feldblyum, Tamara
    Ferella, Marcela
    Frasch, Alberto Carlos
    Gull, Keith
    Horn, David
    Hou, Lihua
    Huang, Yiting
    Kindlund, Ellen
    Klingbeil, Michele
    Kluge, Sindy
    Koo, Hean
    Lacerda, Daniela
    Levin, Mariano J
    Lorenzi, Hernan
    Louie, Tin
    Machado, Carlos Renato
    McCulloch, Richard
    McKenna, Alan
    Mizuno, Yumi
    Mottram, Jeremy C
    Nelson, Siri
    Ochaya, Stephen
    Osoegawa, Kazutoyo
    Pai, Grace
    Parsons, Marilyn
    Pentony, Martin
    Pettersson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Pop, Mihai
    Ramirez, Jose Luis
    Rinta, Joel
    Robertson, Laura
    Salzberg, Steven L
    Sanchez, Daniel O
    Seyler, Amber
    Sharma, Reuben
    Shetty, Jyoti
    Simpson, Anjana J
    Sisk, Ellen
    Tammi, Martti T
    Tarleton, Rick
    Teixeira, Santuza
    Van Aken, Susan
    Vogt, Christy
    Ward, Pauline N
    Wickstead, Bill
    Wortman, Jennifer
    White, Owen
    Fraser, Claire M
    Stuart, Kenneth D
    Andersson, Björn
    The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease.2005In: Science, ISSN 1095-9203, Vol. 309, no 5733, 409-15 p.Article in journal (Refereed)
    Abstract [en]

    Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.

  • 247.
    Emilsson, Lina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Nilsson, Tatjana
    Cedazo-Minguez, Angel
    Benedikz, Eirikur
    Jazin, Elena
    RGS4: A novel mediator of APP processingManuscript (Other academic)
  • 248.
    Emilsson, Lina
    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.
    Balciuniene, Jorune
    Castensson, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Cairns, Nigel
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Increased monoamine oxidase messenger RNA expression levels in frontal cortex of Alzheimer's disease patients2002In: Neuroscience Letters, ISSN 0304-3940, E-ISSN 1872-7972, Vol. 326, no 1, 56-60. p.Article in journal (Refereed)
    Abstract [en]

    Alzheimer's disease (AD) is a neurodegenerative disorder and the most common cause of dementia in the industrialised world. The two monoamine oxidase (MAO) enzymes, monoamine oxidase A (MAOA) and monoamine oxidase B (MAOB), are important in the metabolism of monoamine neurotransmitters. AD and ageing have been shown to increase enzyme activity for both MAOA and MAOB. An increase (rather than decrease) of enzyme activity is a rare event in a disease that results in a decrease in the number of cells in the brain. The mechanism, transcriptional or post-transcriptional, responsible for the increase in protein activity, is not known. In this study, we investigate for the first time the messenger RNA (mRNA) expression levels of both MAOA and MAOB in 246 cortical brain samples obtained at autopsy from 62 AD patients and 61 normal controls. We found a significant increase in mRNA levels for both MAOA (P=0.001) and MAOB (P=0.002) in disease brain tissue. This indicates that both MAO enzymes might be important in the progression of AD.

  • 249.
    Emilsson, Lina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Animal Development and Genetics.
    Alzheimer’s disease: mRNA expression profiles of multiple patients show alterations of genes involved with calcium signalling2006In: Neurobiology of Disease, ISSN 0969-9961, E-ISSN 1095-953X, Vol. 21, no 3, 618-625 p.Article in journal (Refereed)
    Abstract [en]

    We combined global and high-resolution strategies to find genes with altered mRNA expression levels in one of the largest collection of brain autopsies from Alzheimer's patients and controls ever studied. Our global analysis involved microarray hybridizations of large pools of samples obtained from 114 individuals, using two independent sets of microarrays. Ten genes selected from the microarray experiments were quantified on each individual separately using real-time RT-PCR. This high-resolution analysis accounted for systematic differences in age, postmortem interval, brain pH, and reference gene expression, and it estimated the effect of disease on mRNA levels, on top of the effect of all other variables. Differential expression was confirmed for eight out of ten genes. Among them, Type B inositol 1,4,5-trisphosphate 3-kinase (ITPKB), and regulator of G protein signaling 4 (RGS4) showed highly altered expression levels in patients (P values < 0.0001). Our results point towards increased inositol triphospate (IP3)-mediated calcium signaling in Alzheimer's disease.

  • 250.
    Emma, Lind
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Södertörns högskola.
    Ohlin, Helena
    Mälardalens högskola.
    Grahn, Mats
    Södertörns högskola.
    Fine scale genetic structure in Thresspine sticklback (Gasterosteus aculeatus) along Sweden's coastManuscript (preprint) (Other academic)
    Abstract [en]

    There are three basic types of population structures in marine environments; populations that are distinct, with a continuous change and without any differentiation. In each type the population units are characterized by groups of individuals with panmixia within groups and site fidelity to a limited geographic area. Earlier studies of the population genetic structure on sticklebacks in the Baltic Sea have shown none or only little structure. We have sampled 8 sites (253 individuals) along Sweden’s coast to estimate the genetic structure, using five microsatellites and 173 Amplified Fragment Length Polymorphism (AFLP) markers and detected a fine scale genetic structure (AFLP FST= 25%, microsatellites FST = 2.7%). With AFLPs the observed variation followed isolation by distance model (but not with microsatellites). Even sites separated by only 2 km of water are significantly separated. Both Bayesian clustering analysis and Capscale separated populations and identified populations from Gulf of Bothnia (4 psu) and from the west coast (20 psu) as genetically distinctly different from Baltic populations (about 7-8 psu).  In conclusion, gene flow is limited between sampled sites, and since no geographic barriers can be distinguished the population structure is likely caused by the sticklebacks’ behavior. Hence, we have probably sampled either stationary populations of marine sticklebacks, or homing sticklebacks. In this study AFLP and microsatellites did not give congruent results; with AFLPs we got high separation, and genetic variation followed isolation by distance model and supported the continuous change type of population structure.

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