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  • 151.
    Papageorgiou, Aristotelis C.
    et al.
    Department of Forestry, Environment and Natural Resources, Democritus University of Thrace, Orestiada, Greece.
    Vidalis, Amaryllis
    Department of Forestry, Environment and Natural Resources, Democritus University of Thrace, Orestiada, Greece.
    Gailing, Oliver
    Institut für Forstgenetik und Forstpflanzenzüchtung, Georg-August-Universität Göttingen, Göttingen, Germany.
    Tsiripidis, Ioannis
    Biology Department, Aristotle University of Thessaloniki, Thessaloniki, Greece .
    Hatziskakis, Seraphim
    Department of Forestry, Environment and Natural Resources, Democritus University of Thrace, Orestiada, Greece.
    Boutsios, Stefanos
    Department of Forestry, Environment and Natural Resources, Democritus University of Thrace, Orestiada, Greece .
    Galatsidas, Spiros
    Department of Forestry, Technical Educational Institute of Kavala, Drama, Greece .
    Finkeldey, Reiner
    Institut für Forstgenetik und Forstpflanzenzüchtung, Georg-August-Universität Göttingen, Göttingen, Germany.
    Genetic variation of beech (Fagus sylvatica L.) in Rodopi (NE Greece)2008In: European Journal of Forest Research, ISSN 1612-4669, E-ISSN 1612-4677, Vol. 127, no 1, p. 81-88Article in journal (Refereed)
    Abstract [en]

    The recent taxonomic classification of beech in Europe considers existence of one species (Fagus sylvatica L.) with two subspecies: F. sylvatica ssp. sylvatica and F. sylvatica ssp. orientalis. Four beech populations growing on the Greek part of the Rodopi Mountains were studied using morphological traits as well as DNA molecular markers (AFLPs and chloroplast DNA SSR). The aim of the study was to describe the variation patterns of beech in the Rodopi Mountains and to test the hypothesis of possible introgression between the beech subspecies' sylvatica and orientalis in this area. Both morphological traits and gene markers revealed a possible influence of F. orientalis on the east side of Rodopi and at the low elevations, while characters resembling F. sylvatica were observed mainly on the western part of the mountains and in higher altitudes. There was a clinal increase of genetic diversity from the west to the east, reaching a level firstly reported for beech populations. These results can be explained either by the existence of a main refugial area for beech during the last glaciation or by the occurrence of a recent hybridization among the subspecies, which were spatially isolated during the last glaciation and came into reproductive contact during their postglacial remigration. These two scenarios are not necessarily mutually exclusive.

  • 152.
    Philip, Philge
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Mining DNA elements involved in targeting of chromatin modifiers2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Background: In all higher organisms, the nuclear DNA is condensed into nucleosomes that consist of DNA wrapped around a core of highly conserved histone proteins. DNA bound to histones and other structural proteins form the chromatin. Generally, only few regions of DNA are accessible and most of the time RNA polymerase and other DNA binding proteins have to overcome this compaction to initiate transcription. Several proteins are involved in making the chromatin more compact or open. Such chromatin-modifying proteins make distinct post-translational modifications of histones – especially in the histone tails – to alter their affinity to DNA. Aim: The main aim of my thesis work is to study the targeting of chromatin modifiers important for correct gene expression in Drosophila melanogaster (fruit flies). Primary DNA sequences, chromatin associated proteins, transcription, and non-coding RNAs are all likely to be involved in targeting mechanisms. This thesis work involves the development of new computational methods for identification of DNA motifs and protein factors involved in the targeting of chromatin modifiers. Targeting and functional analysis of two chromatin modifiers, namely male-specific lethal (MSL) complex and CREB-binding protein (CBP) are specifically studied. The MSL complex is a protein complex that mediates dosage compensation in flies. CBP protein is known as a transcriptional co-regulator in metazoans and it has histone acetyl transferase activity and CBP has been used to predict novel enhancers. Results: My studies of the binding sites of MSL complex shows that promoters and coding sequences of MSL-bound genes on the X-chromosome of Drosophila melanogaster can influence the spreading of the complex along the X-chromosome. Analysis of MSL binding sites when two non-coding roX RNAs are mutated shows that MSL-complex recruitment to high-affinity sites on the Xchromosome is independent of roX, and the role of roX RNAs is to prevent binding to repeats in autosomal sites. Functional analysis of MSL-bound genes using their dosage compensation status shows that the function of the MSL complex is to enhance the expression of short housekeeping genes, but MSL-independent mechanisms exist to achieve complete dosage compensation. Studies of the binding sites of the CBP protein show that, in early embryos, Dorsal in cooperation with GAGA factor (GAF) and factors like Medea and Dichaete target CBP to its binding sites. In the S2 cell line, GAF is identified as the targeting factor of CBP at promoters and enhancers, and GAF and CBP together are found to induce high levels of polymerase II pausing at promoters. In another study using integrated data analysis, CBP binding sites could be classified into polycomb protein binding sites, repressed enhancers, insulator protein-bound regions, active promoters, and active enhancers, and this suggested different potential roles for CBP. A new approach was also developed to eliminate technical bias in skewed experiments. Our study shows that in the case of skewed datasets it is always better to identify non-altered variables and to normalize the data using only such variables.

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  • 153.
    Philip, Philge
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Computational Life Science Cluster (CLiC), Umeå University, Sweden.
    Boija, Ann
    Dept. of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden.
    Mannervik, Mattias
    Dept. of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden.
    Stenberg, Per
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Computational Life Science Cluster (CLiC), Umeå University, Sweden.
    CBP functions outside of promoters and enhancers in Drosophila melanogasterManuscript (preprint) (Other academic)
  • 154.
    Philip, Philge
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Pettersson, Fredrik
    Umbio, 907 19 Umeå, Sweden.
    Stenberg, Per
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Sequence signatures involved in targeting the male-specific lethal complex to X-chromosomal genes in Drosophila melanogaster2012In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 13, p. 97-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: In Drosophila melanogaster, the dosage-compensation system that equalizes X-linked gene expression between males and females, thereby assuring that an appropriate balance is maintained between the expression of genes on the X chromosome(s) and the autosomes, is at least partially mediated by the Male-Specific Lethal (MSL) complex. This complex binds to genes with a preference for exons on the male X chromosome with a 3' bias, and it targets most expressed genes on the X chromosome. However, a number of genes are expressed but not targeted by the complex. High affinity sites seem to be responsible for initial recruitment of the complex to the X chromosome, but the targeting to and within individual genes is poorly understood.

    RESULTS: We have extensively examined X chromosome sequence variation within five types of gene features (promoters, 5' UTRs, coding sequences, introns, 3' UTRs) and intergenic sequences, and assessed its potential involvement in dosage compensation. Presented results show that: the X chromosome has a distinct sequence composition within its gene features; some of the detected variation correlates with genes targeted by the MSL-complex; the insulator protein BEAF-32 preferentially binds upstream of MSL-bound genes; BEAF-32 and MOF co-localizes in promoters; and that bound genes have a distinct sequence composition that shows a 3' bias within coding sequence.

    CONCLUSIONS: Although, many strongly bound genes are close to a high affinity site neither our promoter motif nor our coding sequence signatures show any correlation to HAS. Based on the results presented here, we believe that there are sequences in the promoters and coding sequences of targeted genes that have the potential to direct the secondary spreading of the MSL-complex to nearby genes.

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  • 155.
    Philip, Philge
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Stenberg, Per
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Male X-linked genes in Drosophila melanogaster are compensated independently of the Male-Specific Lethal complex2013In: Epigenetics & Chromatin, ISSN 1756-8935, E-ISSN 1756-8935, Vol. 6, no Article number: 35Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: In organisms where the two sexes have unequal numbers of X-chromosomes, the expression of X-linked genes needs to be balanced not only between the two sexes, but also between X and the autosomes. In Drosophila melanogaster, the Male-Specific Lethal (MSL) complex is believed to produce a 2-fold increase in expression of genes on the male X, thus restoring this balance.

    RESULTS: Here we show that almost all the genes on the male X are effectively compensated. However, many genes are compensated without any significant recruitment of the MSL-complex. These genes are very weakly, if at all, affected by mutations or RNAi against MSL-complex components. In addition, even the genes that are strongly bound by MSL rely on mechanisms other than the MSL-complex for proper compensation. We find that long, non-ubiquitously expressed genes tend to rely less on the MSL-complex for their compensation and genes that in addition are far from High Affinity Sites tend to not bind the complex at all or very weakly.

    CONCLUSIONS: We conclude that most of the compensation of X-linked genes is produced by an MSL-independent mechanism. Similar to the case of the MSL-mediated compensation we do not yet know the mechanism behind the MSL-independent compensation that appears to act preferentially on long genes. Even if we observe similarities, it remains to be seen if the mechanism is related to the buffering that is observed in autosomal aneuploidies.

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  • 156. Pontarp, Mikael
    et al.
    Bunnefeld, Lynsey
    Cabral, Juliano Sarmento
    Etienne, Rampal S.
    Fritz, Susanne A.
    Gillespie, Rosemary
    Graham, Catherine H.
    Hagen, Oskar
    Hartig, Florian
    Huang, Shan
    Jansson, Roland
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Maliet, Odile
    Münkemüller, Tamara
    Pellissier, Loïc
    Rangel, Thiago F.
    Storch, David
    Wiegand, Thorsten
    Hurlbert, Allen H.
    The Latitudinal Diversity Gradient: Novel Understanding through Mechanistic Eco-evolutionary2019In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 34, no 3, p. 211-223Article, review/survey (Refereed)
    Abstract [en]

    The latitudinal diversity gradient (LDG) is one of the most widely studied patterns in ecology, yet no consensus has been reached about its underlying causes. We argue that the reasons for this are the verbal nature of existing hypotheses, the failure to mechanistically link interacting ecological and evolutionary processes to the LDG, and the fact that empirical patterns are often consistent with multiple explanations. To address this issue, we synthesize current LDG hypotheses, uncovering their eco-evolutionary mechanisms, hidden assumptions, and commonalities. Furthermore, we propose mechanistic eco-evolutionary modeling and an inferential approach that makes use of geographic, phylogenetic, and trait-based patterns to assess the relative importance of different processes for generating the LDG.

  • 157. Rainey, Paul B.
    et al.
    Remigi, Philippe
    Farr, Andrew D.
    Lind, Peter A.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Darwin was right: where now for experimental evolution?2017In: Current Opinion in Genetics and Development, ISSN 0959-437X, E-ISSN 1879-0380, Vol. 47, p. 102-109Article in journal (Refereed)
    Abstract [en]

    Over the last two decades interest in direct realisation of evolutionary process and the possibilities presented by real time evolution experiments with microbes have escalated. Long-term selection experiments with bacteria have made increasingly transparent the process of evolution by natural selection. In this short article we consider what next for the field and do so by highlighting two areas of interest: the genotype-to-phenotype map and the constraints it imposes on evolution, and studies on major evolutionary transitions and in particular the importance of selection working over more than one timescale. The latter we discuss in light of new technologies that allow imposition of Darwinian properties on populations and communities and how this allows exploration of new avenues of research. We conclude by commenting on microbial communities and the operation of evolutionary processes that are likely intrinsic — and specific — to communities.

  • 158. Randall, Ricardo S.
    et al.
    Miyashima, Shunsuke
    Blomster, Tiina
    Zhang, Jing
    Elo, Annakaisa
    Karlberg, Anna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Immanen, Juha
    Nieminen, Kaisa
    Lee, Ji-Young
    Kakimoto, Tatsuo
    Blajecka, Karolina
    Melnyk, Charles W.
    Alcasabas, Annette
    Forzani, Celine
    Matsumoto-Kitano, Miho
    Maehoenen, Ari Pekka
    Bhalerao, Rishikesh
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Dewitte, Walter
    Helariutta, Ykae
    Murray, James A. H.
    AINTEGUMENTA and the D-type cyclin CYCD3;1 regulate root secondary growth and respond to cytokinins2015In: Biology Open, ISSN 2046-6390, Vol. 4, no 10, p. 1229-1236Article in journal (Refereed)
    Abstract [en]

    Higher plant vasculature is characterized by two distinct developmental phases. Initially, a well-defined radial primary pattern is established. In eudicots, this is followed by secondary growth, which involves development of the cambium and is required for efficient water and nutrient transport and wood formation. Regulation of secondary growth involves several phytohormones, and cytokinins have been implicated as key players, particularly in the activation of cell proliferation, but the molecular mechanisms mediating this hormonal control remain unknown. Here we show that the genes encoding the transcription factor AINTEGUMENTA (ANT) and the D-type cyclin CYCD3;1 are expressed in the vascular cambium of Arabidopsis roots, respond to cytokinins and are both required for proper root secondary thickening. Cytokinin regulation of ANT and CYCD3 also occurs during secondary thickening of poplar stems, suggesting this represents a conserved regulatory mechanism.

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  • 159.
    Rasmuson, Marianne
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Trends in genetics - before the molecular era2010In: Hereditas, ISSN 0018-0661, E-ISSN 1601-5223, Vol. 147, no 5, p. 243-249Article in journal (Refereed)
    Abstract [en]

    Genetics grew into a scientific discipline during the first decade of the twentieth century, it prospered and became acknowledged in its first half, it widened into the molecular field during its second half. This expansion attracted scientists from nearby branches such as biochemistry, biophysics, cell biology, statistics and computer science, which started to call themselves geneticists without deeper insights into the classical genetics. They may be unaware of how far the science had advanced already before the molecular window was opened. Then, what is the essence of genetics? It is involved in all aspects of biology, and has branched into different disciplines, rather far apart. Still it is held together by its core, the evolutionary coalescence of all living organisms on earth and their surprisingly great conformity in physiological and hereditary mechanisms. In the early definitions before the year 1900 the word variation is often included, most bluntly as the science of variation. Similarities and differences between parent and offspring are also emphasised. Inheritance causes similarities but not complete likeness. The name of the subject, genetics, was introduced by W. Bateson in 1906 and defined as the scientific study of the heredity of individuals. Later definitions have become more extensive and include not only the transmission of the hereditary factors but also their nature and the way in which they influence the living organism at different stages and at different levels, from molecules to populations and ecosystems.

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  • 160. Raychaudhuri, Saumya
    et al.
    Jain, Vibhu
    Dongre, Mitesh
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Oncology.
    Identification of a constitutively active variant of LuxO that affects production of HA/protease and biofilm development in a non-O1, non-O139 Vibrio cholerae O110.2006In: Gene, ISSN 0378-1119, E-ISSN 1879-0038, Vol. 369, p. 126-33Article in journal (Refereed)
    Abstract [en]

    Pathogenesis of Vibrio cholerae depends on the concerted action of numerous virulence factors that includes a secreted hemagglutinin (HA) protease. Recent studies have evidenced that the expression of these virulence factors as well as the genes responsible for biofilm development is subject to control by quorum sensing in this organism. At low cell density, LuxO, the pivotal regulator of quorum-sensing circuit, has been shown to be phosphorylated at aspartate-47. Working in concert with sigma-54, LuxO-P activates the downstream repressor, which turned out to be four sRNAs [Lenz, D.H., Mok, K.C., Lilley, B.N., Kulkarni, R.V., Wingreen, N.S., Bassler, B.L., 2004. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118, 69-82]. Subsequently, these sRNAs form complex with sRNA chaperone, Hfq. The Hfq-sRNA complex causes the destabilization of hapR mRNA transcript. HapR is a positive regulator of hapA that encodes HA/protease. At high cell density, dephosphorylation of LuxO impairs its function to activate the expression of sRNA, which in turn promotes HapR expression and causes protease production. It has been demonstrated that conversion of aspartate to glutamate (D47E) renders the LuxO molecule active without being phosphorylated. This variant of LuxO is referred as constitutively active LuxO or con-LuxO [Freeman, J.A., Bassler, B.L., 1999. A genetic analysis of the function of LuxO, a two-component response regulator involved in quorum sensing in Vibrio harveyi. Mol Microbiol 31, 665-677]. Other than D47E, mutation at L104Q also develops con-LuxO [Vance, R.E., Zhu, J., Mekalanos, J.J., 2003. A constitutively active variant of the quorum-sensing regulator LuxO affects protease production and biofilm formation in Vibrio cholerae. Infect. Immun. 71, 2571-2576]. The purpose of this study was to investigate the cause of protease negative phenotype of a non-O1, non-O139 strain of V. cholerae O110. In the process of exploring the nature of the phenotype, a constitutively active variant of LuxO molecule was characterized which represses protease production and enhances biofilm formation by this strain. Unlike luxU, disruption of luxO restored the protease production, which showed the constitutively active nature of LuxO protein in this strain.

  • 161. Robertson, Fiona M.
    et al.
    Gundappa, Manu Kumar
    Grammes, Fabian
    Hvidsten, Torgeir R.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
    Redmond, Anthony K.
    Lien, Sigbjørn
    Martin, Samuel A. M.
    Holland, Peter W. H.
    Sandve, Simen R.
    Macqueen, Daniel J.
    Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification2017In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 18, article id 111Article in journal (Refereed)
    Abstract [en]

    Background: The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separated from WGD. Salmonid fish, whose ancestor underwent WGD by autotetraploidization similar to 95 million years ago, fit such a 'time-lag' model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model, 'lineage-specific ohnologue resolution' (LORe), to address the consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. Results: Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One-quarter of each salmonid genome, harbouring at least 4550 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions >50 million years post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that potentially facilitated salmonid species radiation. We show that LORe ohnologues are enriched for different functions than 'older' ohnologues that began diverging in the salmonid ancestor. Conclusions: LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear 'explosively', but can arise gradually over tens of millions of years, promoting lineage-specific diversification regimes under prevailing ecological pressures.

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  • 162. Roe, Amanda D.
    et al.
    MacQuarrie, Chris J. K.
    Gros-Louis, Marie-Claude
    Simpson, J. Dale
    Lamarche, Josyanne
    Beardmore, Tannis
    Thompson, Stacey L.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Tanguay, Philippe
    Isabel, Nathalie
    Fitness dynamics within a poplar hybrid zone: I. Prezygotic and postzygotic barriers impacting a native poplar hybrid stand2014In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 4, no 9, p. 1629-1647Article in journal (Refereed)
    Abstract [en]

    Hybridization and introgression are pervasive evolutionary phenomena that provide insight into the selective forces that maintain species boundaries, permit gene flow, and control the direction of evolutionary change. Poplar trees (Populus L.) are well known for their ability to form viable hybrids and maintain their distinct species boundaries despite this interspecific gene flow. We sought to quantify the hybridization dynamics and postzygotic fitness within a hybrid stand of balsam poplar (Populus balsamifera L.), eastern cottonwood (P.deltoides Marsh.), and their natural hybrids to gain insight into the barriers maintaining this stable hybrid zone. We observed asymmetrical hybrid formation with P.deltoides acting as the seed parent, but with subsequent introgression biased toward P.balsamifera. Native hybrids expressed fitness traits intermediate to the parental species and were not universally unfit. That said, native hybrid seedlings were absent from the seedling population, which may indicate additional selective pressures controlling their recruitment. It is imperative that we understand the selective forces maintaining this native hybrid zone in order to quantify the impact of exotic poplar hybrids on this native system.

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  • 163. Roe, Amanda D.
    et al.
    MacQuarrie, Chris J. K.
    Gros-Louis, Marie-Claude
    Simpson, J. Dale
    Lamarche, Josyanne
    Beardmore, Tannis
    Thompson, Stacey L.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Tanguay, Philippe
    Isabel, Nathalie
    Fitness dynamics within a poplar hybrid zone: II. Impact of exotic sex on native poplars in an urban jungle2014In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 4, no 10, p. 1876-1889Article in journal (Refereed)
    Abstract [en]

    Trees bearing novel or exotic gene components are poised to contribute to the bioeconomy for a variety of purposes such as bioenergy production, phytoremediation, and carbon sequestration within the forestry sector, but sustainable release of trees with novel traits in large-scale plantations requires the quantification of risks posed to native tree populations. Over the last century, exotic hybrid poplars produced through artificial crosses were planted throughout eastern Canada as ornamentals or windbreaks and these exotics provide a proxy by which to examine the fitness of exotic poplar traits within the natural environment to assess risk of exotic gene escape, establishment, and spread into native gene pools. We assessed postzygotic fitness traits of native and exotic poplars within a naturally regenerated stand in eastern Canada (Quebec City, QC). Pure natives (P.balsamifera and P.deltoides spp. deltoides), native hybrids (P.deltoidesxP.balsamifera), and exotic hybrids (trees bearing Populus nigra and P.maximowiczii genetic components) were screened for reproductive biomass, yield, seed germination, and fungal disease susceptibility. Exotic hybrids expressed fitness traits intermediate to pure species and were not significantly different from native hybrids. They formed fully viable seed and backcrossed predominantly with P.balsamifera. These data show that exotic hybrids were not unfit and were capable of establishing and competing within the native stand. Future research will seek to examine the impact of exotic gene regions on associated biotic communities to fully quantify the risk exotic poplars pose to native poplar forests.

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  • 164. Rogers, AS
    et al.
    Andersson Escher, Stefan
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Pasetto, C
    Rosato, E
    Costa, R
    Kyriacou, CP
    A mutation in Drosophila simulans that lengthens the circadian period of locomotor activity2004In: Genetica, ISSN 0016-6707, E-ISSN 1573-6857, Vol. 120, no 1-3, p. 223-232Article in journal (Refereed)
    Abstract [en]

    The length of the Thr-Gly repeat within the period gene of Drosophilids, coevolves with its immediate flanking region to maintain the temperature compensation of the fly circadian clock. In Drosophila simulans, balancing selection appears to maintain a polymorphism in this region, with three repeat lengths carrying 23, 24 or 25 Thr-Gly pairs, each in complete linkage disequilibrium with a distinctive flanking region amino acid moiety. We wondered whether separating a specific length repeat from its associated flanking haplotype might have functional implications for the circadian clock. We fortuitously discovered a population of flies collected in Kenya, in which a chimeric Thr-Gly haplotype was segregating that carried the (Thr-Gly)(24) repeat, but the flanking region of a (Thr-Gly) 23 allele. One of the five isofemale lines that carried this 'mutant' Thr-Gly sequence showed a dramatically long and temperature-sensitive free-running circadian period. This phenotype was mapped to the X chromosome, close to the D. simulans per gene, but there was also a significant effect of a modifying autosomal locus or loci. It seems remarkable that such a mutant phenotype should be discovered in a screen of chimeric Thr-Gly regions.

  • 165.
    Rudin, Dag
    Umeå University.
    The isozyme technique - a short-cut to the genes of our forest trees?: illustrations using Pinus sylvestris L1977Doctoral thesis, comprehensive summary (Other academic)
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    The isozyme technique - a short-cut to the genes of our forest trees?
  • 166.
    Sabouri, Nasim
    et al.
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.
    McDonald, Karin R
    Webb, Christopher J
    Cristea, Ileana M
    Zakian, Virginia A
    DNA replication through hard-to-replicate sites, including both highly transcribed RNA Pol II and Pol III genes, requires the S. pombe Pfh1 helicase2012In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 26, no 6, p. 581-593Article in journal (Refereed)
    Abstract [en]

    Replication forks encounter impediments as they move through the genome, including natural barriers due to stable protein complexes and highly transcribed genes. Unlike lesions generated by exogenous damage, natural barriers are encountered in every S phase. Like humans, Schizosaccharomyces pombe encodes a single Pif1 family DNA helicase, Pfh1. Here, we show that Pfh1 is required for efficient fork movement in the ribosomal DNA, the mating type locus, tRNA, 5S ribosomal RNA genes, and genes that are highly transcribed by RNA polymerase II. In addition, converged replication forks accumulated at all of these sites in the absence of Pfh1. The effects of Pfh1 on DNA replication are likely direct, as it had high binding to sites whose replication was impaired in its absence. Replication in the absence of Pfh1 resulted in DNA damage specifically at those sites that bound high levels of Pfh1 in wild-type cells and whose replication was slowed in its absence. Cells depleted of Pfh1 were inviable if they also lacked the human TIMELESS homolog Swi1, a replisome component that stabilizes stalled forks. Thus, Pfh1 promotes DNA replication and separation of converged replication forks and suppresses DNA damage at hard-to-replicate sites.

  • 167.
    Sahlman, Janne
    et al.
    Seinäjoki Central Hospital, Seinäjoki, Finland.
    Pitkänen, Marja
    University Hospital of Kuopio, Kuopio, Finland.
    Prockop, Darwin
    Center fo Gene Therapy, MCP Hahnemann University School of Medicine, Philadelphia, Pensylvania, USA.
    Arita, Machiko
    Center fo Gene Therapy, MCP Hahnemann University School of Medicine, Philadelphia, Pensylvania, USA.
    Li, Shi-Wu
    Center fo Gene Therapy, MCP Hahnemann University School of Medicine, Philadelphia, Pensylvania, USA.
    Helminen, Heikki
    Department of Anatomy, University of Kuopio, Kuopio, Finland.
    Långsjö, Teemu
    Department of Anatomy, University of Kuopio, Kuopio, Finland.
    Puustjärvi, Kaija
    Helsinki University Hospital, Helsinki, Finland.
    Lammi, Mikko
    Department of Anatomy, University of Kuopio, Kuopio, Finland.
    A human COL2A1 gene with an Arg519Cys mutation causes osteochondrodysplasia in transgenic mice.2004In: Arthritis and Rheumatism, ISSN 0004-3591, E-ISSN 1529-0131, Vol. 50, no 10, p. 3153-3160, article id 15476249Article in journal (Refereed)
    Abstract [en]

    OBJECTIVE: An arginine-to-cysteine substitution at position 519 of the COL2A1 gene causes early generalized osteoarthritis with mild chondrodysplasia in humans. In this study, a human COL2A1 gene with the same mutation was introduced into a murine genome having 1 or no alleles of the murine Col2a1 gene, and the skeletal phenotypes of the transgenic mice were compared with those of control mice.

    METHODS: Mice with 1 allele of the normal murine Col2a1 gene and 1 allele of the mutated human COL2A1 gene (n = 10), those with no murine Col2a1 gene and 2 alleles of the mutated human COL2A1 gene (n = 13), those with no murine Col2a1 gene and only 1 allele of the mutated COL2A1 gene (n = 9), and normal control mice (n = 11) were studied for skeletal abnormalities, using radiographic imaging and light microscopic analyses of histologic sections. The collagen network of cartilage was also investigated with transmission electron microscopy.

    RESULTS: At 2 months of age, all transgenic mice had dysplastic changes in their long bones, flattened vertebral bodies, and osteoarthritic changes in their joints. The intervertebral discs of the transgenic animals were degenerated, and their histologic structure was disturbed. The changes were more severe in mice with no murine Col2a1 allele.

    CONCLUSION: The human COL2A1 gene with the Arg519Cys mutation causes osteochondrodysplasia in mice, as it does in humans.

  • 168. Salojarvi, Jarkko
    et al.
    Smolander, Olli-Pekka
    Nieminen, Kaisa
    Rajaraman, Sitaram
    Safronov, Omid
    Safdari, Pezhman
    Lamminmaki, Airi
    Immanen, Juha
    Lan, Tianying
    Tanskanen, Jaakko
    Rastas, Pasi
    Amiryousefi, Ali
    Jayaprakash, Balamuralikrishna
    Kammonen, Juhana I.
    Hagqvist, Risto
    Eswaran, Gugan
    Ahonen, Viivi Helena
    Serra, Juan Alonso
    Asiegbu, Fred O.
    Barajas-Lopez, Juan de Dios
    Blande, Daniel
    Blokhina, Olga
    Blomster, Tiina
    Broholm, Suvi
    Brosche, Mikael
    Cui, Fuqiang
    Dardick, Chris
    Ehonen, Sanna E.
    Elomaa, Paula
    Escamez, Sacha
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Fagerstedt, Kurt V.
    Fujii, Hiroaki
    Gauthier, Adrien
    Gollan, Peter J.
    Halimaa, Pauliina
    Heino, Pekka I.
    Himanen, Kristiina
    Hollender, Courtney
    Kangasjarvi, Saijaliisa
    Kauppinen, Leila
    Kelleher, Colin T.
    Kontunen-Soppela, Sari
    Koskinen, J. Patrik
    Kovalchuk, Andriy
    Karenlampi, Sirpa O.
    Karkonen, Anna K.
    Lim, Kean-Jin
    Leppala, Johanna
    Macpherson, Lee
    Mikola, Juha
    Mouhu, Katriina
    Mahonen, Ari Pekka
    Niinemets, Ulo
    Oksanen, Elina
    Overmyer, Kirk
    Palva, E. Tapio
    Pazouki, Leila
    Pennanen, Ville
    Puhakainen, Tuula
    Poczai, Peter
    Possen, Boy J. H. M.
    Punkkinen, Matleena
    Rahikainen, Moona M.
    Rousi, Matti
    Ruonala, Raili
    van der Schoot, Christiaan
    Shapiguzov, Alexey
    Sierla, Maija
    Sipila, Timo P.
    Sutela, Suvi
    Teeri, Teemu H.
    Tervahauta, Arja I.
    Vaattovaara, Aleksia
    Vahala, Jorma
    Vetchinnikova, Lidia
    Welling, Annikki
    Wrzaczek, Michael
    Xu, Enjun
    Paulin, Lars G.
    Schulman, Alan H.
    Lascoux, Martin
    Albert, Victor A.
    Auvinen, Petri
    Helariutta, Yka
    Kangasjarvi, Jaakko
    Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch2017In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 49, no 6, p. 904-912Article in journal (Refereed)
    Abstract [en]

    Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.

  • 169. Sandve, Simen R.
    et al.
    Rohlfs, Rori V.
    Hvidsten, Torgeir R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
    Subfunctionalization versus neofunctionalization after whole-genome duplication2018In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 50, no 7, p. 908-909Article in journal (Refereed)
  • 170.
    Saura, Anssi
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    A tale of two papers2014In: Hereditas, ISSN 0018-0661, E-ISSN 1601-5223, Vol. 151, no 6, p. 119-122Article in journal (Refereed)
    Abstract [en]

    Two papers published in HEREDITAS between 1921 and 1939 show how the attitude towards race biology changed in the course of the interwar period in the Nordic countries. In the early 1920s race biology was seen to constitute a legitimate science. Ordinary human genetics prevailed, however, over race biology already in the very beginning on the pages of HEREDITAS. Population thinking was introduced into the study of human heredity around the year 1930. It effectively contradicted the concept of the race. Interestingly, HEREDITAS does not carry a single paper on eugenics and sterilization. In 1939 we see a final repudiation of the doctrines on race. Times had changed and the National Socialists had usurped the doctrines of race in Germany.

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  • 171.
    Schiffthaler, Bastian
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bernhardsson, Carolina
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Ingvarsson, Par K.
    Street, Nathaniel R.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    BatchMap: A parallel implementation of the OneMap R package for fast computation of F-1 linkage maps in outcrossing species2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 12, article id e0189256Article in journal (Refereed)
    Abstract [en]

    With the rapid advancement of high throughput sequencing, large numbers of genetic markers can be readily and cheaply acquired, but most current software packages for genetic map construction cannot handle such dense input. Modern computer architectures and server farms represent untapped resources that can be used to enable higher marker densities to be processed in tractable time. Here we present a pipeline using a modified version of OneMap that parallelizes over bottleneck functions and achieves substantial speedups for producing a high density linkage map (N = 20,000). Using simulated data we show that the outcome is as accurate as the traditional pipeline. We further demonstrate that there is a direct relationship between the number of markers used and the level of deviation between true and estimated order, which in turn impacts the final size of a genetic map.

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  • 172.
    Schwartz, Yuri B.
    et al.
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Cavalli, Giacomo
    Three-Dimensional Genome Organization and Function in Drosophila2017In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 205, no 1, p. 5-24Article, review/survey (Refereed)
    Abstract [en]

    Understanding how the metazoan genome is used during development and cell differentiation is one of the major challenges in the postgenomic era. Early studies in Drosophila suggested that three-dimensional (3D) chromosome organization plays important regulatory roles in this process and recent technological advances started to reveal connections at the molecular level. Here we will consider general features of the architectural organization of the Drosophila genome, providing historical perspective and insights from recent work. We will compare the linear and spatial segmentation of the fly genome and focus on the two key regulators of genome architecture: insulator components and Polycomb group proteins. With its unique set of genetic tools and a compact, well annotated genome, Drosophila is poised to remain a model system of choice for rapid progress in understanding principles of genome organization and to serve as a proving ground for development of 3D genome-engineering techniques.

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  • 173. Schwartz, Yuri B.
    et al.
    Kahn, Tatyana G.
    Stenberg, Per
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Ohno, Katsuhito
    Bourgon, Richard
    Pirrotta, Vincenzo
    Alternative Epigenetic Chromatin States of Polycomb Target Genes2010In: PLoS Genetics, ISSN 1553-7390, Vol. 6, no 1, p. e1000805-Article in journal (Refereed)
    Abstract [en]

    Polycomb (PcG) regulation has been thought to produce stable long-term gene silencing. Genomic analyses in Drosophila and mammals, however, have shown that it targets many genes, which can switch state during development. Genetic evidence indicates that critical for the active state of PcG target genes are the histone methyltransferases Trithorax (TRX) and ASH1. Here we analyze the repertoire of alternative states in which PcG target genes are found in different Drosophila cell lines and the role of PcG proteins TRX and ASH1 in controlling these states. Using extensive genome-wide chromatin immunoprecipitation analysis, RNAi knockdowns, and quantitative RT-PCR, we show that, in addition to the known repressed state, PcG targets can reside in a transcriptionally active state characterized by formation of an extended domain enriched in ASH1, the N-terminal, but not C-terminal moiety of TRX and H3K27ac. ASH1/TRX N-ter domains and transcription are not incompatible with repressive marks, sometimes resulting in a "balanced" state modulated by both repressors and activators. Often however, loss of PcG repression results instead in a "void" state, lacking transcription, H3K27ac, or binding of TRX or ASH1. We conclude that PcG repression is dynamic, not static, and that the propensity of a target gene to switch states depends on relative levels of PcG, TRX, and activators. N-ter TRX plays a remarkable role that antagonizes PcG repression and preempts H3K27 methylation by acetylation. This role is distinct from that usually attributed to TRX/MLL proteins at the promoter. These results have important implications for Polycomb gene regulation, the "bivalent" chromatin state of embryonic stem cells, and gene expression in development.

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  • 174. Scott, Alison Dawn
    et al.
    Stenz, Noah W. M.
    Ingvarsson, Pär K.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Baum, David A.
    Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers2016In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 211, no 1, p. 186-193Article in journal (Refereed)
    Abstract [en]

    Polyploidy is common and an important evolutionary factor in most land plant lineages, but it is rare in gymnosperms. Coast redwood (Sequoia sempervirens) is one of just two polyploid conifer species and the only hexaploid. Evidence from fossil guard cell size suggests that polyploidy in Sequoia dates to the Eocene. Numerous hypotheses about the mechanism of polyploidy and parental genome donors have been proposed, based primarily on morphological and cytological data, but it remains unclear how Sequoia became polyploid and why this lineage overcame an apparent gymnosperm barrier to whole-genome duplication (WGD). We sequenced transcriptomes and used phylogenetic inference, Bayesian concordance analysis and paralog age distributions to resolve relationships among gene copies in hexaploid coast redwood and close relatives. Our data show that hexaploidy in coast redwood is best explained by autopolyploidy or, if there was allopolyploidy, it happened within the Californian redwood clade. We found that duplicate genes have more similar sequences than expected, given the age of the inferred polyploidization. Conflict between molecular and fossil estimates of WGD can be explained if diploidization occurred very slowly following polyploidization. We extrapolate from this to suggest that the rarity of polyploidy in gymnosperms may be due to slow diploidization in this clade.

  • 175. Seehausen, Ole
    et al.
    Butlin, Roger K.
    Keller, Irene
    Wagner, Catherine E.
    Boughman, Janette W.
    Hohenlohe, Paul A.
    Peichel, Catherine L.
    Saetre, Glenn-Peter
    Bank, Claudia
    Brannström, Åke
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Brelsford, Alan
    Clarkson, Chris S.
    Eroukhmanoff, Fabrice
    Feder, Jeffrey L.
    Fischer, Martin C.
    Foote, Andrew D.
    Franchini, Paolo
    Jiggins, Chris D.
    Jones, Felicity C.
    Lindholm, Anna K.
    Lucek, Kay
    Maan, Martine E.
    Marques, David A.
    Martin, Simon H.
    Matthews, Blake
    Meier, Joana I.
    Most, Markus
    Nachman, Michael W.
    Nonaka, Etsuko
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Rennison, Diana J.
    Schwarzer, Julia
    Watson, Eric T.
    Westram, Anja M.
    Widmer, Alex
    Genomics and the origin of species2014In: Nature reviews genetics, ISSN 1471-0056, E-ISSN 1471-0064, Vol. 15, no 3, p. 176-192Article, review/survey (Refereed)
    Abstract [en]

    Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.

  • 176.
    Seibt, Henrik
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Deciphering control of Mechano-Transcription Activators of σ54-RNA polymerase2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    To survive and proliferate, bacteria have to respond to a plethora of fluctuating signals within their habitats. Transcriptional control is one crucial entry point for such signal-responsive adaption responses. In this thesis I present new insights into the signal-responsive control of two specific transcriptional regulators that belong to a specialized class of mechano-transcriptional regulators. These regulators employ ATP-hydrolysis to engage and remodel σ54-RNA polymerase, which allows transcriptional initiation from the promoters they control. In the first part of my thesis I present findings on DmpR – the obligate activator of genes involved in (methyl)phenol catabolism by Pseudomonas putida. DmpR is a sensory-regulator that can only transition to its active multimeric form upon binding a phenolic compound and ATP. Previous work has established that binding of phenolic effectors by the N-terminal domain of DmpR relieves inter-domain repression of its central ATPase domain and further that a structured inter-domain linker between the phenolic- and ATP-binding domains is involved in coupling these processes. However, the mechanism underlying this coupling remained enigmatic. Here I present evidence that a tyrosine residue of the inter-domain linker (Y233) serves as a gatekeeper to constrain ATP-hydrolysis and phenolic-responsive transcriptional activation by DmpR. A model is presented in which binding of phenolics relocates Y233 from the ATP-binding site to synchronise signal-reception with multimerisation to provide appropriate sensitivity of the transcriptional response. Given that Y233 counterparts are present in many ligand-responsive mechano-transcriptional regulators, the model is likely to be pertinent for numerous members of this family. The finding that an alanine substitution of Y233 enhances transcriptional responses adds a new approach to manipulating the sensitivity of this class of proteins and thereby generate hyper-sensitive detectors of aromatic pollutants for use in safe guarding the environment.

    The second part of my thesis concerns VCA0117 – a master regulator of the type VI contractile nanomachinery of Vibrio cholerae, which it utilizes to introduce toxic proteins into both bacterial and eukaryotic cells. These type VI-mediated properties enable V. cholerae to establish infections and to thrive in niches co-occupied by predators and competing bacteria. VCA0117 is strictly required for functionality of the type VI system through its role in controlling production of a key type VI structural protein called Hcp, which is encoded within two small s54-dependent operons. This regulatory role is conserved in both pandemic and non-pandemic V. cholerae strains. However, while some strains come pre-equipped with a functional system, others do not, and require specific growth conditions of low temperature and high osmolarity for type VI expression. Within this work, integration of these regulatory growth signals was traced to the activity of the promoter controlling a large operon in which many components of the machinery and VCA0117 is itself encoded. This in turn elevates the levels of VCA0117, which is all that is required to overcome the need for the specialized growth conditions of low temperature and/or high osmolarity. A model is presented in which signal integration via the activity of the large operon promoter to elevate levels of VCA0117 ultimately dictates a sufficient supply of the missing Hcp component required for completion of a functional type VI machine. Repercussions of the proposed quantity-based regulatory circuit of VCA0117 for generating bacterial sub-populations that are differentially “fit” for different environmental eventualities are discussed.

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  • 177.
    Seibt, Henrik
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Aung, Kyaw Min
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Ishikawa, Takahiko
    Sjöström, Annika
    Atkinson, Gemma C.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Wai, Sun Nyunt
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Shingler, Victoria
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Elevated levels of VCA0117 in response to external signals activates type VI secretion in Vibrio cholerae A1552Manuscript (preprint) (Other academic)
  • 178.
    Seibt, Henrik
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Sauer, Uwe H.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Shingler, Victoria
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    The Y233 gatekeeper of DmpR modulates effector-responsive transcriptional control of δ54-RNA polymerase2019In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, no 4, p. 1321-1330Article in journal (Refereed)
    Abstract [en]

    DmpR is the obligate transcriptional activator of genes involved in (methyl)phenol catabolism by Pseudomonas putida. DmpR belongs to the AAA+ class of mechano‐transcriptional regulators that employ ATP‐hydrolysis to engage and remodel σ54‐RNA polymerase to allow transcriptional initiation. Previous work has established that binding of phenolic effectors by DmpR is a prerequisite to relieve interdomain repression and allow ATP‐binding to trigger transition to its active multimeric conformation, and further that a structured interdomain linker between the effector‐ and ATP‐binding domains is involved in coupling these processes. Here, we present evidence from ATPase and in vivo and in vitro transcription assays that a tyrosine residue of the interdomain linker (Y233) serves as a gatekeeper to constrain ATP‐hydrolysis and aromatic effector‐responsive transcriptional activation by DmpR. An alanine substitution of Y233A results in both increased ATPase activity and enhanced sensitivity to aromatic effectors. We propose a model in which effector‐binding relocates Y233 to synchronize signal‐reception with multimerisation to provide physiologically appropriate sensitivity of the transcriptional response. Given that Y233 counterparts are present in many ligand‐responsive mechano‐transcriptional regulators, the model is likely to be pertinent for numerous members of this family and has implications for development of enhanced sensitivity of biosensor used to detect pollutants.

  • 179. Sečenji, M
    et al.
    Lendvai, Á
    Miskolczi, Pal
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Institute of Plant Biology, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary.
    Kocsy, G
    Gallé, Á
    Szűcs, A
    Hoffmann, B
    Sárvári, É
    Schweizer, P
    Stein, N
    Dudits, D
    Györgyey, J
    Differences in root functions during long-term drought adaptation: comparison of active gene sets of two wheat genotypes2010In: Plant Biology, ISSN 1435-8603, E-ISSN 1438-8677, Vol. 12, no 6, p. 871-882Article in journal (Refereed)
    Abstract [en]

    In an attempt to shed light on the role of root systems in differential responses of wheat genotypes to long-term water limitation, transcriptional differences between two wheat genotypes (Triticum aestivum L., cv. Plainsman V and landrace Kobomugi) were identified during adaptation to moderate water stress at the tillering stage. Differences in organ sizes, water-use efficiency and seed production were detected in plants grown in soil, and root functions were characterised by expression profiling. The molecular genetic background of the behaviour of the two genotypes during this stress was revealed using a cDNA macroarray for transcript profiling of the roots. During a 4-week period of moderate water deficit, a set of up-regulated genes displaying transiently increased expression was identified in young plantlets, mostly in the second week in the roots of Kobomugi, while transcript levels remained constantly high in roots of Plainsman V. These genes encode proteins with various functions, such as transport, protein metabolism, osmoprotectant biosynthesis, cell wall biogenesis and detoxification, and also regulatory proteins. Oxidoreductases, peroxidases and cell wall-related genes were induced significantly only in Plainsman V, while induction of stress- and defence-related genes was more pronounced in Kobomugi. Real-time qPCR analysis of selected members of the glutathione S-transferase gene family revealed differences in regulation of family members in the two genotypes and confirmed the macroarray results. The TaGSTZ gene was stress-activated only in the roots of Kobomugi.

  • 180.
    Shungin, Dmitry
    et al.
    Umeå University, Faculty of Medicine, Department of Odontology. Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Medicine. Department of Clinical Sciences, Genetic & Molecular Epidemiology Unit, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden; Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States of America.
    Deng, Wei Q.
    Varga, Tibor V.
    Luan, Jian'an
    Mihailov, Evelin
    Metspalu, Andres
    Morris, Andrew P.
    Forouhi, Nita G.
    Lindgren, Cecilia
    Magnusson, Patrik K. E.
    Pedersen, Nancy L.
    Hallmans, Göran
    Umeå University, Faculty of Medicine, Department of Biobank Research.
    Chu, Audrey Y.
    Justice, Anne E.
    Graff, Mariaelisa
    Winkler, Thomas W.
    Rose, Lynda M.
    Langenberg, Claudia
    Cupples, L. Adrienne
    Ridker, Paul M.
    Wareham, Nicholas J.
    Ong, Ken K.
    Loos, Ruth J. F.
    Chasman, Daniel I.
    Ingelsson, Erik
    Kilpeläinen, Tuomas O.
    Scott, Robert A.
    Mägi, Reedik
    Paré, Guillaume
    Franks, Paul W.
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Medicine. Department of Clinical Sciences, Genetic & Molecular Epidemiology Unit, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden.
    Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions2017In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, no 6, article id e1006812Article in journal (Refereed)
    Abstract [en]

    Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (GxE) or gene-gene interactions. We modeled variance heterogeneity for blood lipids and BMI in up to 44,211 participants and investigated relationships between variance effects (P-v), GxE interaction effects (with smoking and physical activity), and marginal genetic effects (P-m). Correlations between P-v and P-m were stronger for SNPs with established marginal effects (Spearman's rho = 0.401 for triglycerides, and rho = 0.236 for BMI) compared to all SNPs. When P-v and P-m were compared for all pruned SNPs, only BMI was statistically significant (Spearman's rho = 0.010). Overall, SNPs with established marginal effects were overrepresented in the nominally significant part of the P-v distribution (P-binomial < 0.05). SNPs from the top 1% of the P-m distribution for BMI had more significant P-v values (Pmann-Whitney = 1.46x10(-5)), and the odds ratio of SNPs with nominally significant (< 0.05) P-m and P-v was 1.33 (95% CI: 1.12, 1.57) for BMI. Moreover, BMI SNPs with nominally significant GxE interaction P-values (Pint < 0.05) were enriched with nominally significant P-v values (P-binomial = 8.63x10(-9) and 8.52x10(-7) for SNP x smoking and SNP x physical activity, respectively). We conclude that some loci with strong marginal effects may be good candidates for GxE, and variance-based prioritization can be used to identify them.

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  • 181. Sidorenko, D. S.
    et al.
    Zykova, T. Yu
    Khoroshko, V. A.
    Pokholkova, G. , V
    Demakov, S. A.
    Larsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Belyaeva, E. S.
    Zhimulev, I. F.
    Polytene chromosomes reflect functional organization of the Drosophila genome2019In: Vavilovski Zhurnal Genetiki i Selektsii, ISSN 2500-0462, Vol. 23, no 2, p. 148-153Article, review/survey (Refereed)
    Abstract [en]

    Polytene chromosomes of Drosophila melanogaster are a convenient model for studying interphase chromosomes of eukaryotes. They are giant in size in comparison with diploid cell chromosomes and have a pattern of cross stripes resulting from the ordered chromatid arrangement. Each region of polytene chromosomes has a unique banding pattern. Using the model of four chromatin types that reveals domains of varying compaction degrees, we were able to correlate the physical and cytological maps of some polytene chromosome regions and to show the main properties of genetic and molecular organization of bands and interbands, that we describe in this review. On the molecular map of the genome, the interbands correspond to decompacted aquamarine chromatin and 5' ends of ubiquitously active genes. Gray bands contain lazurite and malachite chromatin, intermediate in the level of compaction, and, mainly, coding parts of genes. Dense black transcriptionally inactive bands are enriched in ruby chromatin. Localization of several dozens of interbands on the genome molecular map allowed us to study in detail their architecture according to the data of whole genome projects. The distribution of proteins and regulatory elements of the genome in the promoter regions of genes localized in the interbands shows that these parts of interbands are probably responsible for the formation of open chromatin that is visualized in polytene chromosomes as interbands.Thus, the permanent genetic activity of interbands and gray bands and the inactivity of genes in black bands are the basis of the universal banding pattern in the chromosomes of all Drosophila tissues. The smallest fourth chromosome of Drosophila with an atypical protein composition of chromatin is a special case. Using the model of four chromatin states and fluorescent in situ hybridization, its cytological map was refined and the genomic coordinates of all bands and interbands were determined. It was shown that, in spite of the peculiarities of this chromosome, its band organization in general corresponds to the rest of the genome. Extremely long genes of different Drosophila chromosomes do not fit the common scheme, since they can occupy a series of alternating bands and interbands (up to nine chromosomal structures) formed by parts of these genes.

  • 182.
    Sjödin, Andreas
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden.
    Öhrman, Caroline
    Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden.
    Bäckman, Stina
    Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden.
    Lärkeryd, Adrian
    Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden.
    Granberg, Malin
    Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden.
    Lundmark, Eva
    Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden.
    Karlsson, Edvin
    Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden.
    Nilsson, Elin
    Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden.
    Vallesi, Adriana
    cLaboratory of Eukaryotic Microbiology and Animal Biology, University of Camerino, Camerino, Macerata, Italy.
    Tellgren-Roth, Christian
    Uppsala Genome Center, National Genomics Infrastructure-Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Uppsala, Sweden.
    Stenberg, Per
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Thelaus, Johanna
    Division of CBRN Defence and Security, Swedish Defence Research Agency, FOI, Umeå, Sweden.
    Complete Genome Sequence of Francisella endociliophora Strain FSC1006, Isolated from a Laboratory Culture of the Marine Ciliate Euplotes raikovi2014In: Genome Announcements, ISSN 2169-8287, E-ISSN 2169-8287, Vol. 2, no 6, p. 6 e01227-14-Article in journal (Refereed)
    Abstract [en]

    A strain of Francisella endociliophora was isolated from a laboratory culture of the marine ciliate Euplotes raikovi. Here, we report the complete genome sequence of the bacterial strain FSC1006 (Francisella Strain Collection, Swedish Defence Research Agency, Umeå, Sweden).

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  • 183.
    Skottheim Honn, John
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Johansson, Linn
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Rasmuson Lestander, Asa
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Regulation of twin of eyeless during Drosophila development2016In: Gene Expression Patterns, ISSN 1567-133X, E-ISSN 1872-7298, Vol. 20, no 2, p. 120-129Article in journal (Refereed)
    Abstract [en]

    The Pax-6 protein is vital for eye development in all seeing animals, from sea urchins to humans. Either of the Pax6 genes in Drosophila (twin of eyeless and eyeless) can induce a gene cascade leading to formation of entire eyes when expressed ectopically. The twin of eyeless (toy) gene in Drosophila is expressed in the anterior region of the early fly embryo. At later stages it is expressed in the brain, ventral nerve cord and (eventually) the visual primordium that gives rise to the eye-antennal imaginal discs of the larvae. These discs subsequently form the major part of the adult head, including compound eyes. We have searched for genes that are required for normal toy expression in the early embryo to elucidate initiating events of eye organogenesis. Candidate genes identified by mutation analyses were subjected to further knock-out and miss-expression tests to investigate their interactions with toy. Our results indicate that the head-specific gap gene empty spiracles can act as a repressor of Toy, while ocelliless (oc) and spalt major (salm) appear to act as positive regulators of toy gene expression. (C) 2016 Elsevier B.V. All rights reserved.

  • 184. Slane, Daniel
    et al.
    Kong, Jixiang
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany.
    Jürgens, Gerd
    Bayer, Martin
    Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana2015In: Genomics Data, ISSN 1025-6059, E-ISSN 2213-5960, Vol. 4, p. 96-98Article in journal (Refereed)
    Abstract [en]

    In Arabidopsis, various cell type-specific whole-genome expression analyses have been conducted. However, the vast majority of these were performed with cellular RNA from root tissues or other easily accessible cell types [1]. Nuclear RNA was neglected for a long time as not being representative for transcriptomic studies. In recent years, however, there have been reports describing the validity of nuclear RNA for these types of studies [2] and [3]. Here we describe the generation, quality assessment and analysis of nuclear transcriptomic data from Arabidopsis embryos published by Slane et al. (2014) [4]. Comparison of nuclear with cellular gene expression demonstrated the usefulness of nuclear transcriptomics.

  • 185. Smouse, Peter E
    et al.
    Sork, Victoria L
    Scofield, Douglas G
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Grivet, Delphine
    Using seedling and pericarp tissues to determine maternal parentage of dispersed valley oak recruits2012In: Journal of Heredity, ISSN 0022-1503, E-ISSN 1465-7333, Vol. 103, no 2, p. 250-259Article in journal (Refereed)
    Abstract [en]

    The spatial pattern of established seedlings yields valuable information about variation in fecundity, dispersal, and spatial structure of distributed recruits, but separating maternal and paternal contributions in monoecious species has been hampered by the "2 parent'' problem. It is now possible to determine the maternal parentage of established recruits with genetic assay of maternally derived tissues of the seed or fruit, but the DNA of weathered maternal tissues often yields unreliable genotypes, reducing the practical range of such assay. We develop a mixed assay of seedling and seed (pericarp) tissues and illustrate it with distributed recruits of California valley oak (Quercus lobata Nee). Detailed analysis indicates correct maternal assignment rates of canopy patch recruits of 56% (seedling assay only) versus 94% (mixed assay). For open patch recruits, maternal assignment rates were less than 50% (seedling assay only) versus 91% (mixed assay). The strategy of choice is to use seedling genotypes to identify a small set of credible parental candidates and then deploy 3-4 well-chosen pericarp/endocarp loci to reduce that list to a single obvious maternal candidate. The increase in the number of recruits available for subsequent analysis is pronounced, increasing precision and statistical power for subsequent inference.

  • 186. Sniegula, Szymon
    et al.
    Johansson, Frank
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Nilsson-Örtman, Viktor
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Differentiation in developmental rate across geographic regions: a photoperiod driven latitude compensating mechanism?2012In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 121, no 7, p. 1073-1082Article in journal (Refereed)
    Abstract [en]

    Genetic differentiation and phenotypic plasticity in growth rates along latitudinal gradients may benefit our understanding of latitudinal compensating mechanisms in life history patterns. Here we explore latitudinal compensatory growth mechanisms with respect to photoperiod in northern and southern populations of two damselfly species, Coenagrion puella and C. pulchellum. In addition we compared size of field-collected adults from southern and northern populations. Eggs from females in copulating tandems were collected at two or three localities for each species in each geographic region. Eggs were transported to the laboratory and the experiment started when the eggs hatched. The role of photoperiod on the expression of larval growth rate was evaluated under controlled laboratory conditions. Both species had lower growth rate when reared in the northern photoperiod, which is counter to expectations if species use photoperiodic cues to trigger compensatory growth. Instead, both species displayed countergradient variation in growth rates, which probably enable northern populations to compensate for the shorter growth season in the north. The smaller size of field-collected adults from northern populations also supports the view that these species compensate for the shorter growth season by investing in growth and development but accomplish this at the expense of decreased final size.

  • 187. Soler, Marçal
    et al.
    Plasencia, Anna
    Lepikson-Neto, Jorge
    Camargo, Eduardo L. O.
    Dupas, Annabelle
    Ladouce, Nathalie
    Pesquet, Edouard
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Mounet, Fabien
    Larbat, Romain
    Grima-Pettenati, Jacqueline
    The Woody-Preferential Gene EgMYB88 Regulates the Biosynthesis of Phenylpropanoid-Derived Compounds in Wood2016In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, article id 1422Article in journal (Refereed)
    Abstract [en]

    Comparative phylogenetic analyses of the R2R3-MYB transcription factor family revealed that five subgroups were preferentially found in woody species and were totally absent from Brassicaceae and monocots (Soler et al., 2015). Here, we analyzed one of these subgroups (WPS-I) for which no gene had been yet characterized. Most Eucalyptus members of WPS-I are preferentially expressed in the vascular cambium, the secondary meristem responsible for tree radial growth. We focused on EgMYB88, which is the most specifically and highly expressed in vascular tissues, and showed that it behaves as a transcriptional activator in yeast. Then, we functionally characterized EgMYB88 in both transgenic Arabidopsis and poplar plants overexpressing either the native or the dominant repression form (fused to the Ethylene-responsive element binding factor-associated Amphiphilic Repression motif, EAR). The transgenic Arabidopsis lines had no phenotype whereas the poplar lines overexpressing EgMYB88 exhibited a substantial increase in the levels of the flavonoid catechin and of some salicinoid phenolic glycosides (salicortin, salireposide, and tremulacin), in agreement with the increase of the transcript levels of landmark biosynthetic genes. A change in the lignin structure (increase in the syringyl vs. guaiacyl, S/G ratio) was also observed. Poplar lines overexpressing the EgMYB88 dominant repression form did not show a strict opposite phenotype. The level of catechin was reduced, but the levels of the salicinoid phenolic glycosides and the S/G ratio remained unchanged. In addition, they showed a reduction in soluble oligolignols containing sinapyl p-hydroxybenzoate accompanied by a mild reduction of the insoluble lignin content. Altogether, these results suggest that EgMYB88, and more largely members of the WPS-I group, could control in cambium and in the first layers of differentiating xylem the biosynthesis of some phenylpropanoid-derived secondary metabolites including lignin.

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  • 188. Srivastava, Vaibhav
    et al.
    Obudulu, Ogonna
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Computational life science cluster (CLiC), Umeå University and Swedish University of Agricultural Sciences.
    Bygdell, Joakim
    Löfstedt, Tommy
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Computational life science cluster (CLiC), Umeå University.
    Rydén, Patrik
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. Umeå University, Faculty of Science and Technology, Department of Chemistry. Computational life science cluster (CLiC), Umeå University.
    Nilsson, Robert
    Ahnlund, Maria
    Johansson, Annika
    Jonsson, Pär
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Computational life science cluster (CLiC), Umeå University.
    Freyhult, Eva
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Clinical Bacteriology. Computational life science cluster (CLiC), Umeå University.
    Qvarnström, Johanna
    Karlsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Melzer, Michael
    Moritz, Thomas
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Computational life science cluster (CLiC), Umeå University.
    Hvidsten, Torgeir R
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Chemistry. Computational life science cluster (CLiC), Umeå University and Department of Chemistry, Biotechnology; Food Science, Norwegian, University of Life Sciences, Ås Norwegian, Norway.
    Wingsle, Gunnar
    OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants2013In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 14, article id 893Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams.

    RESULTS: The main categories that appear to be significantly influenced in the transgenic plants were pathways related to redox regulation, carbon metabolism and protein degradation, e.g. the glycolysis and pentose phosphate pathways (PPP). The results provide system-level information on ROS metabolism and responses to oxidative stress, and indicate that some initial responses to oxidative stress may share common pathways.

    CONCLUSION: The proposed data evaluation strategy shows an efficient way of compiling complex, multi-platform datasets to obtain significant biological information.

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  • 189.
    Stenberg, Per
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Lundberg, Lina E.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Johansson, Anna-Mia
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Rydén, Patrik
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. Umeå University, Faculty of Social Sciences, Department of Statistics.
    Svensson, Malin J.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Larsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Buffering of segmental and chromosomal aneuploidies in Drosophila melanogaster2009In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 5, no 5Article in journal (Refereed)
    Abstract [en]

    Chromosomal instability, which involves the deletion and duplication of chromosomes or chromosome parts, is a common feature of cancers, and deficiency screens are commonly used to detect genes involved in various biological pathways. However, despite their importance, the effects of deficiencies, duplications, and chromosome losses on the regulation of whole chromosomes and large chromosome domains are largely unknown. Therefore, to explore these effects, we examined expression patterns of genes in several Drosophila deficiency hemizygotes and a duplication hemizygote using microarrays. The results indicate that genes expressed in deficiency hemizygotes are significantly buffered, and that the buffering effect is general rather than being mainly mediated by feedback regulation of individual genes. In addition, differentially expressed genes in haploid condition appear to be generally more strongly buffered than ubiquitously expressed genes in haploid condition, but, among genes present in triploid condition, ubiquitously expressed genes are generally more strongly buffered than differentially expressed genes. Furthermore, we show that the 4th chromosome is compensated in response to dose differences. Our results suggest general mechanisms have evolved that stimulate or repress gene expression of aneuploid regions as appropriate, and on the 4th chromosome of Drosophila this compensation is mediated by Painting of Fourth (POF).

  • 190.
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Genomics of forest trees2019In: Molecular physiology and biotechnology of trees / [ed] Canovas, F M, Elsevier, 2019, p. 1-37Chapter in book (Refereed)
    Abstract [en]

    Over the past decade increasing availability and decreasing costs of "next" generation sequencing has revolutionised our ability to assay numerous aspects of genome function. Initially, massively parallel high throughput sequencing technologies resulted in a rapid increase in the number of published tree genomes and, to an even greater extent, transcriptome studies. Whereas previous genomics efforts were concentrated on a small number of model species, these new sequencing technologies have liberated the choice of species, particularly so assaying gene expression using RNA Sequencing and, more recently, for assays of epigenomics including genome structure and accessibility. These advances in sequencing throughput and cost enabled the first draft assemblies of the large (similar to 20 Gbp) genomes of a number of conifer species in addition to an ever-increasing number of angiosperm tree species, with more than 40 genomes now publicly available. The falling cost of sequencing has also enabled genome resequencing, genome wide association studies and population gene expression studies, the results of which are providing new insight into the developmental programs associated with wood formation, stress and disease tolerance, adaptive potential, population genetics and evolutionary history of tree species.

  • 191. Szal, Bożena
    et al.
    Jastrzębska, Agata
    Kulka, Marek
    Leśniak, Karolina
    Podgórska, Anna
    Pärnik, Tiit
    Ivanova, Hiie
    Keerberg, Olav
    Gardeström, Per
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Rychter, Anna M
    Influence of mitochondrial genome rearrangement on cucumber leaf carbon and nitrogen metabolism2010In: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 232, no 6, p. 1371-1382Article in journal (Refereed)
    Abstract [en]

    The MSC16 cucumber (Cucumis sativus L.) mitochondrial mutant was used to study the effect of mitochondrial dysfunction and disturbed subcellular redox state on leaf day/night carbon and nitrogen metabolism. We have shown that the mitochondrial dysfunction in MSC16 plants had no effect on photosynthetic CO(2) assimilation, but the concentration of soluble carbohydrates and starch was higher in leaves of MSC16 plants. Impaired mitochondrial respiratory chain activity was associated with the perturbation of mitochondrial TCA cycle manifested, e.g., by lowered decarboxylation rate. Mitochondrial dysfunction in MSC16 plants had different influence on leaf cell metabolism under dark or light conditions. In the dark, when the main mitochondrial function is the energy production, the altered activity of TCA cycle in mutated plants was connected with the accumulation of pyruvate and TCA cycle intermediates (citrate and 2-OG). In the light, when TCA activity is needed for synthesis of carbon skeletons required as the acceptors for NH(4) (+) assimilation, the concentration of pyruvate and TCA intermediates was tightly coupled with nitrate metabolism. Enhanced incorporation of ammonium group into amino acids structures in mutated plants has resulted in decreased concentration of organic acids and accumulation of Glu.

  • 192.
    Södergren, Agneta
    Umeå University, Faculty of Science and Technology.
    Frequency changes and equilibria in experimental populations of Drosophila melanogaster with three lethal carrying fourth chromosomes1979Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Populations where three different lethals are segregating as alleles have been analysed for the conditions of equilibrium and for the trends during elimination of one allele. Early and late selection as well as sexdependent and sexindependent selection has been taken into consideration.Cage populations of Drosophila melanogaster with different fourth chromosome lethals have been followed and compared to the theoretical model. When two marker chromosomes (ciDpol and spaCat) and one out of four recessive lethal chromosomes l(4)5, 1(4)8, 1(4)10 or l(4)14 were used, the same marker chromosome (ciDpol) became extinct in all populations. Early and late selective values which were obtained directly from the populations were compared to estimates of fitness components obtained in specially designed experiments of viability, developmental rate, mating ability and fecundity. When two out of the four recessive lethals and the marker chromosome, spaCat , were combined in new populations, all populations attained equilibrium withôut extinction. A correlation was found between the time of death of the lethal homozygotes and the equilibrium genotype frequencies. Overall selective values at equilibrium were estimated.

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    Frequency changes and equilibria in experimental populations of Drosophila melanogaster with three lethal carrying fourth chromosomes
  • 193.
    Tan, Biyue
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Stora Enso AB.
    Genomic selection and genome-wide association studies to dissect quantitative traits in forest trees2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The convergence of quantitative genetics of complex traits with genomic technologies is quickly becoming an innovative approach to explore fundamental genetic questions and also have practical consequences for implementations in tree breeding. In this thesis, I used genomic selection and genome-wide association studies (GWAS) to dissect the genetic basis of quantitative traits, i.e. growth, phenology and wood property traits. I also assessed the importance of dominance and epistatic effects in hybrid Eucalyptus. Both dominance and epistasis are important in hybrids, as they are the likely contributing to the genetic basis of heterosis. To successfully implement genomic selection models, several important factors have to be considered. I found that for a good model establishment, both the size and composition of the training population, as well as the number of SNPs to be important considered. Based on the optimal models, additive, dominance and epistasis genetic effects of growth and wood traits have been estimated to evaluate genetic parameters and how these influence the prediction accuracy, which can be used in selecting elite breeding individuals or clones. I also addressed the advantage of genotyping-based analyses by showing that we could accurately correct pedigree information errors. More importantly, genotyping-based analyses capture both Mendelian segregation variation within full-sib families and cryptic genetic links through unknown common ancestors, which are not available from traditional pedigree data. GWAS were used to analyse growth and phenology related traits. Using a single-trait GWAS method, we identified a region strongly associated with the timing of bud set in Populus tremula, a trait with high heritability. For the growth related traits, we found that a multi-traits GWAS approach was more powerful than single-trait analyses as it identified more associated SNPs in hybrid Eucalyptus. Moreover, many more novel associated SNPs were identified from considering over-dominance effects in the GWAS analyses. After annotating the associated SNPs I show that these functional candidate genes were related to growth and responding to abiotic and biotic stress. In summary, the results of genomic selection and GWAS provided a deeper understanding of the genetic backgrounds of quantitative traits in forest trees.

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  • 194.
    Tan, Biyue
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Biomaterials Division, Stora Enso AB, Nacka SE-13104, Sweden.
    Grattapaglia, Dario
    Martins, Gustavo Salgado
    Ferreira, Karina Zamprogno
    Sundberg, Björn
    Ingvarsson, Pär K.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Evaluating the accuracy of genomic prediction of growth and wood traits in two Eucalyptus species and their F-1 hybrids2017In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 17, article id 110Article in journal (Refereed)
    Abstract [en]

    Background: Genomic prediction is a genomics assisted breeding methodology that can increase genetic gains by accelerating the breeding cycle and potentially improving the accuracy of breeding values. In this study, we use 41,304 informative SNPs genotyped in a Eucalyptus breeding population involving 90 E. grandis and 78 E. urophylla parents and their 949 F-1 hybrids to develop genomic prediction models for eight phenotypic traits-basic density and pulp yield, circumference at breast height and height and tree volume scored at age three and six years. We assessed the impact of different genomic prediction methods, the composition and size of the training and validation set and the number and genomic location of SNPs on the predictive ability (PA). Results: Heritabilities estimated using the realized genomic relationship matrix (GRM) were considerably higher than estimates based on the expected pedigree, mainly due to inconsistencies in the expected pedigree that were readily corrected by the GRM. Moreover, the GRM more precisely capture Mendelian sampling among related individuals, such that the genetic covariance was based on the true proportion of the genome shared between individuals. PA improved considerably when increasing the size of the training set and by enhancing relatedness to the validation set. Prediction models trained on pure species parents could not predict well in F-1 hybrids, indicating that model training has to be carried out in hybrid populations if one is to predict in hybrid selection candidates. The different genomic prediction methods provided similar results for all traits, therefore either GBLUP or rrBLUP represents better compromises between computational time and prediction efficiency. Only slight improvement was observed in PA when more than 5000 SNPs were used for all traits. Using SNPs in intergenic regions provided slightly better PA than using SNPs sampled exclusively in genic regions. Conclusions: The size and composition of the training set and number of SNPs used are the two most important factors for model prediction, compared to the statistical methods and the genomic location of SNPs. Furthermore, training the prediction model based on pure parental species only provide limited ability to predict traits in interspecific hybrids. Our results provide additional promising perspectives for the implementation of genomic prediction in Eucalyptus breeding programs by the selection of interspecific hybrids.

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  • 195.
    Tan, Biyue
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Biomaterials Division, Stora Enso AB, SE-131 04, Nacka, Sweden.
    Grattapaglia, Dario
    Wu, Harry X.
    Ingvarsson, Pär K.
    Genomic relationships reveal significant dominance effects for growth in hybrid Eucalyptus2018In: Plant Science, ISSN 0168-9452, E-ISSN 1873-2259, Vol. 267, p. 84-93Article in journal (Refereed)
    Abstract [en]

    Non-additive genetic effects can be effectively exploited in control-pollinated families with the availability of genome-wide markers. We used 41,304 SNP markers and compared pedigree vs. marker-based genetic models by analysing height, diameter, basic density and pulp yield for Eucalyptus urophylla x E.grandis control-pollinated families represented by 949 informative individuals. We evaluated models accounting for additive, dominance, and first-order epistatic interactions (additive by additive, dominance by dominance, and additive by dominance). We showed that the models can capture a large proportion of the genetic variance from dominance and epistasis for growth traits as those components are typically not independent. We also showed that we could partition genetic variances more precisely when using relationship matrices derived from markers compared to using only pedigree information. In addition, phenotypic prediction accuracies were only slightly increased by including dominance effects for growth traits since estimates of non-additive variances yielded rather high standard errors. This novel result improves our current understanding of the architecture of quantitative traits and recommends accounting for dominance variance when developing genomic selection strategies in hybrid Eucalyptus.

  • 196.
    Tan, Biyue
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Stora Enso AB.
    Ingvarsson, Pär K.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Plant Biology, Swedish University of Agricultural Sciences.
    Multivariate genome-wide association identify loci for complex growth traits by considering additive and over-dominance effects in hybrid EucalyptusManuscript (preprint) (Other academic)
    Abstract [en]

    Genome-wide association studies are a powerful and widely used approach to decipher the genetic control of quantitative traits. One of the major challenges for traits in hybrid forest trees, such as hybrid Eucalyptus, is dissecting also non-additive effects for complex traits using a traditional linear mixed model. These non-additive effects, especially over-dominance effects, are one of most important hypotheses for the genetic basis of heterosis. In this study, we used a population including 949 F1 hybrids and their 174 parents, that were phenotyped for circumference at breast height and height at age of three years and six years, and also genotyped at 37,832 informative SNPs. Here we use and compare single-trait and multi-trait association models by accounting for additive and over-dominance effects, to evaluate genomic regions associated with the growth traits. For additive effect-based association model, nine significant SNPs were observed in multi-trait analyses, whereas only two unique SNPs were detected in single-trait analyses. These two SNPs were also identified in the multi-trait model. When evaluating over-dominance effects, 17 and 13 SNPs were identified from multi-trait and single-trait models, respectively. Moreover, more phenotypic variation can be explained by SNPs identified from multi-trait GWAS when including over-dominance effects. Overall, this study shows the added values of including over-dominance and considering multiple traits for identifying genomic regions that control traits of interest and that could contribute to heterosis in hybrids.

  • 197.
    Terebieniec, Barbara
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Using systems genetics to explore the complexity of leaf shape variation in Populus tremula2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Leaves are essential for sustaining humanity as they function as the energy and oxygen-producing organ of plants. Intensive research on physiological processes has contributed immensely to our understanding of the function of leaves. However, comparatively little is known about how leaf size and shape is determined. The aim of my PhD was to assay leaf shape variation among individuals of Populus tremula (European aspen) sampled across the distribution range of Sweden to characterize the genetic architecture underlying variation, including elucidating contributing molecular mechanisms.

    In this PhD I employed an integrated systems genetics and systems biology approach to identify genetic components of variation and to assign biological function to these. We integrated population-wide data on leaf shape, gene expression and genome variation from a collection of P. tremula genotypes and used this to perform genome-wide association studies. We then integrated these results with a systems biology transcriptomics study of leaf development to provide developmental and biological context. We demonstrate that our developmental gene expression series captured known homologs of functionally characterized Arabidopsis thaliana genes and biological processes of importance during leaf development. In addition to these known genes of high importance, we also identified many novel candidate genes. Our systems genetics approach identified numerous genes with a potential role in leaf development that was supported by the developmental time series. From our association studies and population analyses we have shown that there are no large-effect loci contributing to variation in leaf shape and that highly ranked loci associated with leaf shape are primarily located in the regulatory regions of genes. Furthermore, we identified loci controlling variation in gene expression and sets of genes with significant differential expression between groups of genotypes with highly contrasting leaf shapes. We show that genes with significant associations influencing expression among genotypes are enriched in the periphery of the corresponding gene co-expression network and that they experience relaxed selective constraint. Taken together, these results suggest that leaf shape is a highly complex trait controlled by a large number of loci, each contributing only a small effect, that those loci likely act via modulation of gene expression and that they do not show signals of adaptive selection. In addition, we adapted and optimized the method of spatial transcriptomics for use in plant species. This method provides a transcriptome-wide in situ, spatially-resolved assay of transcript expression at high spatial resolution.

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  • 198. Tiukova, Ievgeniia A.
    et al.
    Pita, Will de Barros
    Sundell, David
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Momeni, Majid Haddad
    Horn, Svein Jarle
    Stahlberg, Jerry
    de Morais, Marcos Antonio, Jr.
    Passoth, Volkmar
    Adaptation of Dekkera bruxellensis to lignocellulose-based substrate2014In: Biotechnology and applied biochemistry, ISSN 0885-4513, E-ISSN 1470-8744, Vol. 61, no 1, p. 51-57Article in journal (Refereed)
    Abstract [en]

    Adaptation of Dekkera bruxellensis to lignocellulose hydrolysate was investigated. Cells of D. bruxellensis were grown for 72 and 192H in batch and continuous culture, respectively (adapted cells). Cultivations in semisynthetic medium were run as controls (nonadapted cells). To test the adaptation, cells from these cultures were reinoculated in the lignocellulose medium, and growth and ethanol production characteristics were monitored. Cells adapted to lignocellulose hydrolysate had a shorter lag phase, grew faster, and produced a higher ethanol concentration as compared with nonadapted cells. A stability test showed that after cultivation in rich medium, cells partially lost the adapted phenotype but still showed faster growth and higher ethanol production as compared with nonadapted cells. Because alcohol dehydrogenase genes have been described to be involved in the adaptation to furfural in Saccharomyces cerevisiae, an analogous mechanism of adaptation to lignocelluloses hydrolysate of D. bruxellensis was hypothesized. However, gene expression analysis showed that genes homologous to S. cerevisiae ADH1 were not involved in the adaptation to lignocelluloses hydrolysate in D. bruxellensis.

  • 199. Tuskan, Gerald A.
    et al.
    DiFazio, Steve
    Faivre-Rampant, Patricia
    Gaudet, Muriel
    Harfouche, Antoine
    Jorge, Veronique
    Labbe, Jessy L.
    Ranjan, Priya
    Sabatti, Maurizio
    Slavov, Gancho
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Tschaplinski, Timothy J.
    Yin, Tongming
    The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis2012In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 8, no 3, p. 559-571Article, review/survey (Refereed)
    Abstract [en]

    Genetic determination of gender is a fundamental developmental and evolutionary process in plants. Although it appears that dioecy in Populus is genetically controlled, the precise gender-determining systems remain unclear. The recently released second draft assembly and annotated gene set of the Populus genome provided an opportunity to revisit this topic. We hypothesized that over evolutionary time, selective pressure has reformed the genome structure and gene composition in the peritelomeric region of the chromosome XIX, which has resulted in a distinctive genome structure and cluster of genes contributing to gender determination in Populus trichocarpa. Multiple lines of evidence support this working hypothesis. First, the peritelomeric region of the chromosome XIX contains significantly fewer single nucleotide polymorphisms than the rest of Populus genome and has a distinct evolutionary history. Second, the peritelomeric end of chromosome XIX contains the largest cluster of the nucleotide-binding site-leucine-rich repeat (NBS-LRR) class of disease resistance genes in the entire Populus genome. Third, there is a high occurrence of small microRNAs on chromosome XIX, which is coincident to the region containing the putative gender-determining locus and the major cluster of NBS-LRR genes. Further, by analyzing the metabolomic profiles of floral bud in male and female Populus trees using a gas chromatography-mass spectrometry, we found that there are gender-specific accumulations of phenolic glycosides. Taken together, these findings led to the hypothesis that resistance to and regulation of a floral pathogen and gender determination coevolved, and that these events triggered the emergence of a nascent sex chromosome. Further studies of chromosome XIX will provide new insights into the genetic control of gender determination in Populus.

  • 200. Tylewicz, S.
    et al.
    Petterle, A.
    Marttila, S.
    Miskolczi, P.
    Azeez, A.
    Singh, R. K.
    Immanen, J.
    Mähler, Niklas
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Hvidsten, Torgerir R.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
    Eklund, D. M.
    Bowman, J. L.
    Helariutta, Y.
    Bhalerao, R. P.
    Photoperiodic control of seasonal growth is mediated by ABA acting on cell-cell communication2018In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 360, no 6385, p. 212-214Article in journal (Refereed)
    Abstract [en]

    In temperate and boreal ecosystems, seasonal cycles of growth and dormancy allow perennial plants to adapt to winter conditions. We show, in hybrid aspen trees, that photoperiodic regulation of dormancy is mechanistically distinct from autumnal growth cessation. Dormancy sets in when symplastic intercellular communication through plasmodesmata is blocked by a process dependent on the phytohormone abscisic acid. The communication blockage prevents growth-promoting signals from accessing the meristem. Thus, precocious growth is disallowed during dormancy. The dormant period, which supports robust survival of the aspen tree in winter, is due to loss of access to growth-promoting signals.

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