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  • 101.
    Carlsson, Michaela
    Södertörn University College, School of Life Sciences.
    Vegetation succession in savanna determined by interaction of grazing, browsing and fire; a comparison between hypotheses.2005Independent thesis Basic level (degree of Bachelor), 10 points / 15 hpStudent thesis
    Abstract [en]

    Studies in tropical regions have shown that trees and grasses respond differently to fire, grazing and browsing. In African savannas, the responses to fire, grazing and browsing are different, determined by negative or positive correlations. Browsing may have other consequences than grazing because instead of increasing woody biomass it reduces it, causing increase in grass growth, leading to increase in fuel that results in more intense fires and decrease in woody biomass. Fire and herbivory are an important interactive disturbance factors affecting vegetation succession and the tree-grass dynamics in savanna environment. Several of the fire-herbivory interactions are landscape level effects, which is shown in 2 models. My hypothesis is that the tree-grass balances are determined by interactions of both grazing and fire. There have come new scientific data about fire and herbivory and the interaction effects on tree-grass dynamic and succession in the savanna. By analyzing my hypothesis through a comparison between hypotheses, Intermediate disturbance hypothesis, Janzen-Connell hypothesis and the Huston hypothesis, I propose several scenarios of the savanna tree-grass dynamics in East Africa, as a result of this comparison.

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  • 102. Carmichael, J B
    et al.
    Provost, P
    Ekwall, Karl
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Hobman, T C
    Ago1 and Dcr1, two core components of the RNA interference pathway, functionally diverge from Rdp1 in regulating cell cycle events in Schizosaccharomyces pombe2004In: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 15, no 3, p. 1425-1435Article in journal (Refereed)
    Abstract [en]

    In the fission yeast Schizosaccharomyces pombe, three genes that function in the RNA interference (RNAi) pathway, ago1(+), dcr1(+), and rdp1(+), have recently been shown to be important for timely formation of heterochromatin and accurate chromosome segregation. In the present study, we present evidence that null mutants for ago1(+) and dcr1(+) but not rdp1(+), exhibit abnormal cytokinesis, cell cycle arrest deficiencies, and mating defects. Subsequent analyses showed that ago1(+) and dcr1(+) are required for regulated hyperphosphorylation of Cdc2 when encountering genotoxic insults. Because rdp1(+) is dispensable for this process, the functions of ago1(+) and dcr1(+) in this pathway are presumably independent of their roles in RNAi-mediated heterochromatin formation and chromosome segregation. This was further supported by the finding that ago1(+) is a multicopy suppressor of the S-M checkpoint deficiency and cytokinesis defects associated with loss of Dcr1 function, but not for the chromosome segregation defects of this mutant. Accordingly, we conclude that Dcr1-dependent production of small interfering RNAs is not required for enactment and/or maintenance of certain cell cycle checkpoints and that Ago1 and Dcr1 functionally diverge from Rdp1 to control cell cycle events in fission yeast. Finally, exogenous expression of hGERp95/EIF2C2/hAgo2, a human Ago1 homolog implicated in posttranscriptional gene silencing, compensated for the loss of ago1(+) function in S. pombe. This suggests that PPD proteins may also be important for regulation of cell cycle events in higher eukaryotes.

  • 103.
    Caspillo, Nasim Reyhanian
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology. Örebro universitet.
    Hitting the mark: Studies of alterations in behaviour and fertility in ethinyl estradiol-exposed zebrafish and search related biomarkers2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, we have analysed the effects of EE2 on non-reproductive behaviours and fertility. We have showed that two doses of EE2 in male adult short-term exposures evokes opposite behaviours in the novel tank test. A lower dose induced increased bottom-dwelling, a sign of increased anxiety and a higher dose increased surface-dwelling, which would likely expose themselves to predation in a natural environment. Increased shoaling was observed in both exposures, possibly affecting feeding and reproduction opportunities. Fertility analysis of these fish demonstrated a complete inhibition of spawning in the highest dose group. To investigate mechanisms behind the spawning failure, we examined expression levels of genes involved in zebrafish sex differentiation and maintenance of gonadal function. We found downregulated transcription levels of male-predominant genes, suggesting a demasculinization of the testes contributing to functional sterility in these fish. We have demonstrated that non-reproductive behaviour in zebrafish is highly sensitive to EE2 exposure during development. After exposing male and female zebrafish to low doses of EE2 followed by remediation in clean water until adulthood, the fish displayed increased anxiety and shoaling behaviour, demonstrating persistent effects of EE2. Furthermore, behavioural effects were transferred to their progeny. Decreased fertilisation success of the developmentally exposed fish was observed in both sexes when mated to untreated animals of the opposite sex. These fertility effects persisted although the fish had a long remediation period, implying likely reduced fitness of fish populations in aquatic environments. Based on our findings on non-reproductive behaviours and fertility, we performed RNAsequencing analysis of the brain and testes in order to investigate possible biological mechanisms behind the persistent effects. There is a need for biomarkers allowing detection of both reversible and irreversible effects in animals exposed to estrogenic substances, hopefully contributing to better risk assessments for EDCs. Results from RNA-sequencing would serve as a basis for continued studies in pursuit of potential biomarkers.

  • 104. Ceron, Julian
    et al.
    Swoboda, Peter
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Caenorhabditis elegans comes of age2008In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 9, no 6, p. 312-Article in journal (Other academic)
  • 105. Chamakuri, Srinivas
    et al.
    Guduru, Shiva Krishna Reddy
    Pamu, Sreedhar
    Chandrasekar, Gayathri
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Kitambi, Satish Srinivas
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies. Karolinska institutet.
    Arya, Prabhat
    A Modular Approach to Build Macrocyclic Diversity in Aminoindoline Scaffolds Identifies Antiangiogenesis Agents from a Zebrafish Assay2013In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 19, p. 3959-3964Article in journal (Refereed)
    Abstract [en]

    A modular approach to explore the macrocyclic chemical space around an aminoindoline scaffold is developed. This is achieved by incorporating an amino acid moiety and subsequent stitching technology. Through screening of a zebrafish assay, several antiangiogenesis agents are identified.

  • 106.
    Chandrasekar, Gayathri
    et al.
    Södertörn University, School of Life Sciences.
    Lauter, Gilbert
    Södertörn University, School of Life Sciences.
    Hauptmann, Giselbert
    Södertörn University, School of Life Sciences.
    Distribution of corticotropin-releasing hormone in the developing zebrafish brain2007In: Journal of Comparative Neurology, ISSN 0021-9967, E-ISSN 1096-9861, Vol. 505, no 4, p. 337-351Article in journal (Refereed)
    Abstract [en]

    Corticotropin-releasing hormone (CRH) plays a central role in the physiological regulation of the hypothalamus-pituitary-adrenal/interrenal axis mediating endocrine, behavioral, autonomic, and immune responses to stress. Despite the wealth of knowledge about the physiological roles of CRH, the genetic mechanisms by which CRH neurons arise during development are poorly understood. As a first step toward analyzing the molecular and genetic pathways involved in CRH lineage specification, we describe the developmental distribution of CRH neurons in the embryonic zebrafish, a model organism for functional genomics and developmental biology. We searched available zebrafish expressed sequence tag (EST) databases for CRH-like sequences and identified one EST that contained the complete zebrafish CRH open reading frame (ORF). The CRH precursor sequence contained a signal peptide, the CRH peptide, and a cryptic peptide with a conserved sequence motif. RT-PCR analysis showed crh expression in a wide range of adult tissues as well as during embryonic and larval stages. By whole-mount in situ hybridization histochemistry, discrete crh-expressing cell clusters were found in different parts of the embryonic zebrafish brain, including telencephalon, preoptic region, hypothalamus, posterior tuberculum, thalamus, epiphysis, midbrain tegmentum, and rostral hindbrain and in the neural retina. The localization of crh mRNA within the preoptic region is consistent with the central role of CRH in the teleost stress response through activation of the hypothalamic-pituitary-interrenal axis. The widespread distribution of CRH-synthesizing cells outside the preoptic region suggests additional functions of CRH in the embryonic zebrafish brain.

  • 107. Chen, Nansheng
    et al.
    Mah, Allan
    Blacque, Oliver E.
    Chu, Jeffrey
    Phgora, Kiran
    Bakhoum, Mathieu W.
    Newbury, C. Rebecca Hunt
    Khattra, Jaswinder
    Chan, Susanna
    Go, Anne
    Efimenko, Evgeni
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Johnsen, Robert
    Phirke, Prasad
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Swoboda, Peter
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Marra, Marco
    Moerman, Donald G.
    Leroux, Michel R.
    Baillie, David L.
    Stein, Lincoln D.
    Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics2006In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 7, no 12, p. R126-Article in journal (Refereed)
    Abstract [en]

    Background: The recent availability of genome sequences of multiple related Caenorhabditis species has made it possible to identify, using comparative genomics, similarly transcribed genes in Caenorhabditis elegans and its sister species. Taking this approach, we have identified numerous novel ciliary genes in C. elegans, some of which may be orthologs of unidentified human ciliopathy genes. Results: By screening for genes possessing canonical X-box sequences in promoters of three Caenorhabditis species, namely C. elegans, C. briggsae and C. remanei, we identified 93 genes ( including known X-box regulated genes) that encode putative components of ciliated neurons in C. elegans and are subject to the same regulatory control. For many of these genes, restricted anatomical expression in ciliated cells was confirmed, and control of transcription by the ciliogenic DAF-19 RFX transcription factor was demonstrated by comparative transcriptional profiling of different tissue types and of daf-19(+) and daf-19(-) animals. Finally, we demonstrate that the dye-filling defect of dyf-5( mn400) animals, which is indicative of compromised exposure of cilia to the environment, is caused by a nonsense mutation in the serine/threonine protein kinase gene M04C9.5. Conclusion: Our comparative genomics-based predictions may be useful for identifying genes involved in human ciliopathies, including Bardet-Biedl Syndrome ( BBS), since the C. elegans orthologs of known human BBS genes contain X-box motifs and are required for normal dye filling in C. elegans ciliated neurons.

  • 108. Chin, T M
    et al.
    Berndt, Kurt D
    Universtity of Chicago, USA.
    Yang, N C C
    Self-Assembling Hexameric Helical Bundle Forming Peptides1992In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 114, no 6, p. 2279-2280Article in journal (Refereed)
  • 109.
    Cierlik, Izabela Anna
    Södertörn University College, School of Life Sciences.
    Regulation of callose synthases and beta-1,3-glucanases during aphid infestation on barley cv. Clipper2008Independent thesis Basic level (professional degree), 20 points / 30 hpStudent thesis
    Abstract [en]

    Plant resistance hypothesis says that under a period of time when a plant is exposed to powerful herbivore attack it will prioritise defence as a major metabolic function. In theory, induced plant defence (resistance) will provide opportunities for this organism to “invest” in other functions, in example growth when attackers are absent.

    One of the compounds taking part in plant defence is callose. This β-1,3-glucan is synthesised by callose synthase and broken down by β-1,3-glucanase. Deposition of callose occurs as a reaction to aphid attack an varies, depending on cultivars, and aphid species. In this experiment barley (Hordeum vulgare) cultivar Clipper is being infested with two types of aphids: Russian wheat aphid (RWA, Diuraphis noxia) and bird cherry-oat aphid (BCA, Rhopalosiphium padi) over a time period. Infestation by those two insects results in different callose formation and deposition level.

    Six sequences encoding for putative callose synthase genes and nine sequences encoding for β-1,3-glucanase were examined by RT-PCR and Real – Time PCR methods for different expression patterns.

    The results did not show any significant regulation of gene expression during RWA and BCA attack for any of these genes. Thus the pathway regulating aphid – induced callose deposition in barley reminds unresolved.

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    FULLTEXT01
  • 110.
    Cortobius Fredriksson, Moa
    Södertörn University College, School of Life Sciences.
    ProBenefit: Implementing the Convention on Biological Diversity in the Ecuadorian Amazon2009Independent thesis Basic level (degree of Bachelor), 15 credits / 22,5 HE creditsStudent thesis
    Abstract [en]

    Legislation on benefit sharing dates back to 1992 and the commandment of the UNConvention on Biological Diversity, hence implementation still has few cases to fall back on(CBD, 1992). The case study of the project ProBenefit presented by the thesis highlights howlack of deliberation can undermine a democratic process. The objective of the thesis is thatProBenefit’s attempt to implement the standards of the CBD on access and benefit sharingwill highlight not only problems met by this specific project, but difficulties that generallymeet democratic processes in contexts of high inequality. To define if the project ProBenefitsucceeded in carrying out a deliberative process the project will be analyzed by the criteria:access to information, representation, legitimacy and involvement.The population in the project area of ProBenefit had a long history of social marginalization,which made it hard for foreign projects to gain legitimacy. The lack of independentorganizations and the late establishment of the project, which resulted in time shortage, madeit impossible to prevent the distrust of the local population. The failure of the projectcoordinators to ensure active participation of all stakeholders resulted in a late and lowinvolvement of the local participants. The absence of independent organization also madedemocratic legitimacy of the process questionable. Even if ProBenefit had a vision ofdemocratic deliberation the project was unable to break down the prevailing unequal powerdistribution which resulted in an unsustainable process and failure. The conclusion of thethesis is that the attainment of deliberation foremost depends on how a project deals with theexisting distribution of power and how it succeeds in involving all stakeholders.

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  • 111. Crespo, Ana
    et al.
    Kauff, Frank
    Divakar, Pradeep K.
    del Prado, Ruth
    Perez-Ortega, Sergio
    Amo de Paz, Guillermo
    Ferencova, Zuzana
    Blanco, Oscar
    Roca-Valiente, Beatriz
    Nunez-Zapata, Jano
    Cubas, Paloma
    Argueello, Arturo
    Elix, John A.
    Esslinger, Theodore L.
    Hawksworth, David L.
    Millanes, Ana
    Carmen Molina, M.
    Wedin, Mats
    Ahti, Teuvo
    Aptroot, Andre
    Barreno, Eva
    Bungartz, Frank
    Calvelo, Susana
    Candan, Mehmet
    Cole, Mariette
    Ertz, Damien
    Goffinet, Bernard
    Lindblom, Louise
    Luecking, Robert
    Lutzoni, Francois
    Mattsson, Jan-Eric
    Södertörn University, School of Life Sciences, Environmental science. Södertörn University, School of Life Sciences, Biology.
    Ines Messuti, Maria
    Miadlikowska, Jolanta
    Piercey-Normore, Michele
    Rico, Victor J.
    Sipman, Harrie J. M.
    Schmitt, Imke
    Spribille, Toby
    Thell, Arne
    Thor, Goran
    Upreti, Dalip K.
    Lumbsch, H. Thorsten
    Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence2010In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 59, no 6, p. 1735-1753Article in journal (Refereed)
    Abstract [en]

    Parmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were monophyletic, some were not, and others, previously believed to be unrelated, fell within single monophyletic groups, indicating the need for a revision of the generic delimitations. This study aims to give an overview of current knowledge of the major clades of all parmelioid lichens. For this, we assembled a dataset of 762 specimens, including 31 of 33 currently accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae). We performed maximum likelihood and Bayesian analyses of combined datasets including two, three and four loci. Based on these phylogenies and the correlation of morphological and chemical characters that characterize monophyletic groups, we accept 27 genera within nine main clades. We re-circumscribe several genera and reduce Parmelaria to synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic rank and 15 new combinations are proposed (in the genera Flavoparmelia, Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short discussion of the accepted genera is provided and remaining challenges and areas requiring additional taxon sampling are identified.

  • 112. Cunnea, P M
    et al.
    Miranda-Vizuete, A
    Bertoli, G
    Simmen, T
    Damdimopoulos, A E
    Hermann, Stefan
    Södertörn University, Avdelning Naturvetenskap.
    Leinonen, S
    Huikko, M P
    Gustafsson, J A
    Sitia, R
    Spyrou, G
    ERdJ5, an endoplasmic reticulum (ER)-resident protein containing DnaJ and thioredoxin domains, is expressed in secretory cells or following ER stress2003In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 278, no 2, p. 1059-1066Article in journal (Refereed)
  • 113. Czene, S
    et al.
    Testa, E
    Nygren, Jonas
    Södertörn University, Avdelning Naturvetenskap.
    Belyaev, I
    Harms-Ringdahl, M
    DNA fragmentation and morphological changes in apoptotic human lymphocytes2002In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 294, no 4, p. 872-878Article in journal (Refereed)
    Abstract [en]

    Cell suspensions enriched in cells at various stages of apoptosis were obtained by separation of irradiated human peripheral blood lymphocytes on density gradients at different post-irradiation times. The state of DNA fragmentation in the cells was determined by comet assay and pulsed field gel electrophoresis. The morphologically distinguishable features of apoptosis such as chromatin condensation and cell shrinkage correlated with discrete stages of DNA fragmentation. It was found that greater than or equal to50kbp fragmentation of DNA occurs already in cells of normal density whereas the subsequent DNA fragmentation onto fragments <50 kbp occurs in parallel with cell shrinkage and simultaneous increase in cell density. The observed stages of DNA fragmentation seem to be separated in time that could allow in case of abortive apoptosis formation of chromosomal aberrations.

  • 114.
    Dahlman, Lena
    et al.
    Umeå universitet.
    Mattsson, Jan-Eric
    Westberg, Martin
    Naturhistoriska riksmuseet.
    Palmkvist, Kristin
    Umeå universitet.
    Choice of photobiont is more important than geographical origin or morphology in determining resource levels and metabolic capacity of lichens.2000Conference paper (Other academic)
  • 115.
    Daigle, N
    et al.
    European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
    Beaudouin, J
    European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
    Hartnell, L
    NIH Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), National Institutes of Health (NIH) - USA.
    Imreh, Gabriela
    Södertörn University, Avdelning Naturvetenskap.
    Hallberg, Einar
    Södertörn University, Avdelning Naturvetenskap.
    Lippincott-Schwartz, J
    NIH Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD), National Institutes of Health (NIH) - USA.
    Ellenberg, J
    European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
    Nuclear pore complexes form immobile networks and have a very low turnover in live mammalian cells2001In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 154, no 1, p. 71-84Article in journal (Refereed)
    Abstract [en]

    The nuclear pore complex (NPC) and its relationship to the nuclear envelope (NE) was characterized in living cells using POM121-green fluorescent protein (GFP) and GFP-Nup153, and GFP-lamin B1. No independent movement of single pore complexes was found within the plane of the NE in interphase. Only large arrays of NPCs moved slowly and synchronously during global changes in nuclear shape, strongly suggesting mechanical connections which form an NPC network. The nuclear lamina exhibited identical movements. NPC turnover measured by fluorescence recovery after photobleaching of POM121 was less than once per cell cycle. Nup153 association with NPCs was dynamic and turnover of this nucleoporin was three orders of magnitude faster. Overexpression of both nucleoporins induced the formation of annulate lamellae (AL) in the endoplasmic reticulum (ER). Turnover of AL pore complexes was much higher than in the NE (once every 2.5 min). During mitosis, POM121 and Nup153 were completely dispersed and mobile in the ER (POM121) or cytosol (Nup153) in metaphase, and rapidly redistributed to an immobilized pool around chromatin in late anaphase. Assembly and immobilization of both nucleoporins occurred before detectable recruitment of lamin B1, which is thus unlikely to mediate initiation of NPC assembly at the end of mitosis.

  • 116.
    Dalusi, Lucy
    et al.
    Amana Regional Referral Hospital, Dar es Salaam, Tanzania / University of Dar es Salaam, Dar es Salaam, Tanzania.
    Lyimo, Thomas J
    University of Dar es Salaam, Dar es Salaam, Tanzania.
    Lugomela, Charles
    University of Dar es Salaam, Dar es Salaam, Tanzania.
    Hosea, Ken M M
    University of Dar es Salaam, Dar es Salaam, Tanzania.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Toxigenic Vibrio cholerae identified in estuaries of Tanzania using PCR techniques2015In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 362, no 5, article id fnv009Article in journal (Refereed)
    Abstract [en]

    The current study assessed the occurrence of the Vibrio cholerae serogroups O1 and O139 in environmental samples along salinity gradients in three selected estuaries of Tanzania both through culture independent methods and by cultured bacteria. Occurrence of V. cholerae was determined by PCR targeting the V. cholerae outer membrane protein gene ompW. Furthermore, the presence of toxigenic strains and serogroups O1 and O139 was determined using multiplex PCR with specific primers targeting the cholera toxin gene subunit A, ctxA, and serotype specific primers, O1-rfb and O139-rfb, respectively. Results showed that V. cholerae occurred in approximately 10% (n = 185) of both the environmental samples and isolated bacteria. Eight of the bacteria isolates (n = 43) were confirmed as serogroup O1 while one belonged to serogroup O139, the first reported identification of this epidemic strain in East African coastal waters. All samples identified as serogroup O1 or O139 and a number of non-O1/O139 strains were ctxA positive. This study provides in situ evidence of the presence of pathogenic V. cholerae O1 and O139 and a number of V. cholerae non-O1/O139 that carry the cholera toxin gene in estuaries along the coast of Tanzania.

  • 117. Deadman, Mary E.
    et al.
    Lundström, Susanna L.
    Schweda, Elke K. H.
    Södertörn University, School of Life Sciences.
    Moxon, E. Richard
    Hood, Derek W.
    Specific amino acids of the glycosyltransferase LpsA direct the addition of glucose or galactose to the terminal inner core heptose of Haemophilus influenzae lipopolysaccharide via alternative linkages2006In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 281, no 40, p. 29455-29467Article in journal (Refereed)
    Abstract [en]

    Lipopolysaccharide is the major glycolipid of the cell wall of the bacterium Haemophilus influenzae, a Gram-negative commensal and pathogen of humans. Lipopolysaccharide is both a virulence determinant and a target for host immune responses. Glycosyltransferases have high donor and acceptor substrate specificities that are generally limited to catalysis of one unique glycosidic linkage. The H. influenzae glycosyltransferase LpsA is responsible for the addition of a hexose to the distal heptose of the inner core of the lipopolysaccharide molecule and belongs to the glycosyltransferase family 25. The hexose added can be either glucose or galactose and linkage to the heptose can be either beta 1-2 or beta 1-3. Each H. influenzae strain uniquely produces only one of the four possible combinations of linked sugar in its lipopolysaccharide. We show that, in any given strain, a specific allelic variant of LpsA directs the anomeric linkage and the added hexose, glucose, or galactose. Site-directed mutagenesis of a single key amino acid at position 151 changed the hexose added in vivo from glucose to galactose or vice versa. By constructing chimeric lpsA gene sequences, it was shown that the 3' end of the gene directs the anomeric linkage (beta 1-2 or beta 1-3) of the added hexose. The lpsA gene is the first known example where interstrain variation in lipopolysaccharide core structure is directed by the specific sequence of a genetic locus encoding enzymes directing one of four alternative possible sugar additions from the inner core.

  • 118.
    Dealtry, Simone
    et al.
    Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany .
    Ding, Guo-Chun
    Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany .
    Weichelt, Viola
    Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.
    Dunon, Vincent
    ivision of Soil and Water Management, KU Leuven, Heverlee, Belgium .
    Schlüter, Andreas
    Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Bielefeld, Germany.
    Martini, María Carla
    BBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina .
    Papa, María Florencia Del
    IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina .
    Lagares, Antonio
    IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.
    Amos, Gregory Charles Auton
    School of Life Sciences, University of Warwick, Warwick, United Kingdom .
    Wellington, Elizabeth Margaret Helen
    chool of Life Sciences, University of Warwick, Warwick, United Kingdom .
    Gaze, William Hugo
    School of Life Sciences, University of Warwick, Warwick, United Kingdom .
    Sipkema, Detmer
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands .
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Springael, Dirk
    Division of Soil and Water Management, KU Leuven, Heverlee, Belgium.
    Heuer, Holger
    Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany .
    van Elsas, Jan Dirk
    University of Groningen, Groningen, The Netherlands .
    Thomas, Christopher
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham, Warwick, United Kingdom .
    Smalla, Kornelia
    Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany .
    Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats.2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 2, article id e89922Article in journal (Refereed)
    Abstract [en]

    IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC-DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are "hot spots" of plasmids potentially carrying catabolic genes.

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  • 119.
    Degerholm, Jenny
    et al.
    Stockholm University.
    Gundersen, Kjell
    Stockholm University.
    Bergman, Birgitta
    Stockholm University.
    Söderbäck, Erik
    Stockholm University.
    Phosphorus-limited growth dynamics in two Baltic Sea cyanobacteria, Nodularia sp and Aphanizomenon sp.2006In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 58, no 3, p. 323-332Article in journal (Refereed)
    Abstract [en]

    Rates of carbon (C) specific growth and nitrogen (N(2)) fixation were monitored in cultures of Baltic Sea Nodularia and Aphanizomenon exposed to gradual limitation by inorganic phosphorus (P). Both cyanobacteria responded by decreased cellular P content followed by lowered rates of growth and N(2) fixation. C-specific growth and cellular N content changed faster in Aphanizomenon both when inorganic P was lowered as well as during reintroduction of P. Aphanizomenon also showed a more rapid increase in N-specific N(2) fixation associated with increased C-specific growth. When ambient concentrations of inorganic P declined, both cyanobacteria displayed higher rates of alkaline phosphatase (APase) activity. Lower substrate half-saturation constants (K(M)) and higher V(max) : K(M) ratio of the APase enzyme associated with Nodularia suggest a higher affinity for dissolved organic P (DOP) substrate than Aphanizomenon. Aphanizomenon, which appears more sensitive to changes in ambient dissolved inorganic P, may be adapted to environments with elevated concentrations of P or repeated intrusions of nutrient-rich water. Nodularia on the other hand, with its higher tolerance to increased P starvation may have an ecological advantage in stratified surface waters of the Baltic Sea during periods of low P availability.

  • 120.
    Delp, Gabriele
    et al.
    Södertörn University, School of Life Sciences, Biology. Södertörn University, School of Life Sciences, Molecular biology.
    Gradin, Therese
    Södertörn University, School of Life Sciences, Biology. Södertörn University, School of Life Sciences, Molecular biology.
    Ahman, Inger
    Jonsson, Lisbeth M. V.
    Södertörn University, School of Life Sciences, Biology. Södertörn University, School of Life Sciences, Molecular biology.
    Microarray analysis of the interaction between the aphid Rhopalosiphum padi and host plants reveals both differences and similarities between susceptible and partially resistant barley lines2009In: Molecular Genetics and Genomics, ISSN 1617-4615, E-ISSN 1617-4623, Vol. 281, no 3, p. 233-248Article in journal (Refereed)
    Abstract [en]

    The bird cherry-oat aphid (Rhopalosiphum padi L.) is an important pest on cereals causing plant growth reduction without specific leaf symptoms. Breeding of barley (Hordeum vulgare L.) for R. padi resistance shows that there are several resistance genes, reducing aphid growth. To identify candidate sequences for resistance-related genes, we performed microarray analysis of gene expression after aphid infestation in two susceptible and two partially resistant barley genotypes. One of the four lines is a descendant of two of the other genotypes. There were large differences in gene induction between the four lines, indicating substantial variation in response even between closely related genotypes. Genes induced in aphid-infested tissue were mainly related to defence, primary metabolism and signalling. Only 24 genes were induced in all lines, none of them related to oxidative stress or secondary metabolism. Few genes were down-regulated, with none being common to all four lines. There were differences in aphid-induced gene regulation between resistant and susceptible lines. Results from control plants without aphids also revealed differences in constitutive gene expression between the two types of lines. Candidate sequences for induced and constitutive resistance factors have been identified, among them a proteinase inhibitor, a serine/threonine kinase and several thionins.

  • 121.
    Dinnétz, Patrik
    Stockholm university.
    Male sterility, Protogyny and Pollen-Pistil interference in Plantago maritima (Plantaginaceae) a wind-pollinated, self-incompatible perennial1997In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 84, no 11, p. 1588-1594Article in journal (Refereed)
    Abstract [en]

    Evolution and maintenance of male sterility in seed plants can be explained by the maternal inheritance of mitochondria, which encode the trait, and by adaptive functions that enhance female fecundity in male-sterile compared to hermaphrodite individuals. Protogyny and male sterility can independently decrease the negative effect of pollen–pistil interference in selfincompatible species. In Plantago maritima, which possesses both traits, protogyny increases seed set in hermaphrodite individuals. This is shown both by a significantly positive association between seed set and retarded dehiscence of the anthers and by a more than 50% reduction in seed set following self-pollination. Male sterility does not seem to increase seed set further, as female and hermaphrodite plants do not differ significantly in mean seed set per capsule. Bagging experiments demonstrate strong self-incompatibility in the study populations. Hence, in P. maritima male sterility seems neither to prevent selfing nor to reduce the effect of pollen–pistil interference. Females had significantly larger stigmas than hermaphrodites, but seed set varied negatively with stigma length among females, indicating that the evolution of unisexuality in P. maritima is not due to prefertilization sex allocation. I therefore conclude that the genetical system of nucleocytoplasmic determination of gender is the main cause for maintenance of male sterility in P. maritima.

  • 122.
    Dinnétz, Patrik
    et al.
    Stockholm university.
    Jerling, Lenn
    Stockholm university.
    Gynodioecy in Plantago maritima L.; no compensation for loss of male function1997In: Acta Botanica Neerlandica, ISSN 0044-5983, E-ISSN 1365-2001, Vol. 46, no 2, p. 193-206Article in journal (Refereed)
    Abstract [en]

    Size, allocation of biomass, seed production of hermaphrodites and male steriles as well as germination, growth rate and survival among their progeny were compared between male fertile and male sterile cytoplasmic genotypes of Plantago maritima. The cytoplasmic genomes in angiosperms are predominantly maternally inherited. Thus we used the progeny originating from the male fertile and male sterile mothers in order to examine the relative success of the mothers. The progeny was grown together at three different densities in a greenhouse competition experiment. The results were analysed in a hierarchical model with siblings as replicates of mothers and mothers as replicates of sex-morphs. Differences between sex morphs were very small, but they were consistent in that the progeny from male steriles always performed less well than did the progeny from hermaphrodites. Male sterile progeny matched the hermaphrodite progeny best at the lowest density, where there was no effect of sex type on the level of individual performance. One explanation why hermaphrodites perform relatively better at higher densities could be that they are more plastic in their response to competition induced stress. This was indicated by density dependent allocation pattern of biomass to different parts of the plants, where the progeny of hermaphrodites appeared to be more plastic. The results from this experiment, and other studies, supports the idea that male sterility, if nucleo-cytoplasmically determined, can persist in a population even without any fitness advantages for females.

  • 123.
    Dinnétz, Patrik
    et al.
    Stockholm university.
    Jerling, Lenn
    Stockholm university.
    Spatial distribution of male sterility in Plantago maritima1998In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 81, p. 255-265Article in journal (Refereed)
    Abstract [en]

    Sexual polymorphism in angiosperms can be explained both by the functional responses of male and female function to autogamy and geitonogamy, and by the conflict between the nuclear and cytoplasmic genomes. In predominantly hermaphrodite species, cytoplasmically determined male sterility may persist in a population because of maternal inheritance, i.e, the loss of male function does not change the fitness of the cytoplasmic genome. However, in populations with cytoplasmic male sterility, male fertility is often restored by nuclear genes. Therefore, in populations with genetical substructure, the frequencies of the different sex-morphs will fluctuate depending on the presence of both the male sterile cytoplasms, and of their specific nuclear restorer genes. In Plantagomaritima, we showed that the frequencies of male sterility were highest in regions with the highest population turnover rates and that male sterile individuals were more frequently found in the lower, less dense parts of the meadows. This indicates that male sterile cytoplasms have their highest probabilities to escape their nuclear restorer genes during recolonisation in disturbed regions within populations. We also found that male sterile individuals dispersed their seeds a little bit further than did the hermaphrodites. This can be interpreted as an adaptive response to the local occurrence of nuclear restorer genes.

  • 124.
    Dionisi, Hebe
    et al.
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Matos, Marina
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Anselmino, Luciano
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Lozada, Mariana
    Patagonian Natl Res Ctr CENPAT CONICET, Buenos Aires, DF, Argentina.
    Mac Cormack, Walter
    Argentinean Antarctic Inst, Buenos Aires, DF, Argentina / Natl Univ Buenos Aires, Buenos Aires, DF, Argentina.
    Carroll, Jolynn
    Univ Tromsö, N-9001 Tromsö, Norway / Akvaplan Niva AS, FRAM High North Res Ctr Climate & Environm, Tromsö, Norway.
    Lundgren, Leif
    Stockholm University.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Chavarria, Krystle
    Lawrence Berkeley Natl Labs, Berkeley, CA USA.
    Henrissat, Bernard
    Ctr Natl Rech Sci, Marseille, France.
    Jansson, Janet
    Lawrence Berkeley Natl Labs, Berkeley, CA USA.
    Mining alginate lyases in sediment metagenomes from four geographically distant cold coastal environments2014In: New Biotechnology, ISSN 1871-6784, E-ISSN 1876-4347, Vol. 31, p. S69-S70Article in journal (Refereed)
  • 125.
    Divakar, Pradeep K.
    et al.
    Univ Complutense Madrid, Madrid, Spain.
    Crespo, Ana
    Univ Complutense Madrid, Madrid, Spain.
    Wedin, Mats
    Swedish Museum Nat Hist..
    Leavitt, Steven D.
    Field Museum, Chicago, USA..
    Hawksworth, David L.
    Univ Complutense Madrid, Madrid, Spain..
    Myllys, Leena
    Univ Helsinki, Bot Museum, Finnish Museum Nat Hist, Helsinki, Finland..
    McCune, Bruce
    Oregon State Univ, Corvallis, USA..
    Randlane, Tiina
    Univ Tartu, Tartu, Estonia..
    Bjerke, Jarle W.
    High North Res Ctr Climate & Environm, Norwegian Inst Nat Res NINA, FRAM, Tromso, Norway..
    Ohmura, Yoshihito
    Natl Museum Nat & Sci, Tsukuba, Japan..
    Schmitt, Imke
    Biodivers & Climate Res Ctr BiK F, Frankfurt, Germany.;Goethe Univ Frankfurt, Dept Biol Sci, Inst Ecol Evolut & Div, D-60438 Frankfurt, Germany..
    Boluda, Carlos G.
    Univ Complutense Madrid, Madrid, Spain..
    Alors, David
    Univ Complutense Madrid, Madrid, Spain..
    Roca-Valiente, Beatriz
    Univ Complutense Madrid, Madrid, Spain..
    Del-Prado, Ruth
    Univ Complutense Madrid, Madrid, Spain..
    Ruibal, Constantino
    Univ Complutense Madrid, Madrid, Spain..
    Buaruang, Kawinnat
    Univ Complutense Madrid, Madrid, Spain.;Ramkhamhang Univ, Bangkok, Thailand..
    Nunez-Zapata, Jano
    Univ Complutense Madrid, Madrid, Spain..
    Amo de Paz, Guillermo
    Univ Complutense Madrid, Madrid, Spain..
    Rico, Victor J.
    Univ Complutense Madrid, Madrid, Spain..
    Carmen Molina, M.
    Univ Rey Juan Carlos, Madrid, Spain..
    Elix, John A.
    Australian Natl Univ, Canberra, Australia..
    Esslinger, Theodore L.
    N Dakota State Univ, Fargo, USA..
    Tronstad, Inger Kristin K.
    Univ Tromso, Arctic Univ Norway, Tromso Univ Museum, Tromso, Norway..
    Lindgren, Hanna
    Univ Helsinki, Bot Museum, Finnish Museum Nat Hist, Helsinki, Finland..
    Ertz, Damien
    Natl Bot Garden Belgium, Meise, Belgium..
    Gueidan, Cecile
    Nat Hist Museum, London, England..
    Saag, Lauri
    Univ Tartu, Tartu, Estonia..
    Mark, Kristiina
    Univ Tartu, Tartu, Estonia..
    Singh, Garima
    Biodivers & Climate Res Ctr BiK F, Frankfurt, Germany..
    Dal Grande, Francesco
    Biodivers & Climate Res Ctr BiK F, Frankfurt, Germany..
    Parnmen, Sittiporn
    Field Museum, Chicago, IL 60605 USA.;Minist Publ Hlth, Nonthaburi, Thailand..
    Beck, Andreas
    Botan Staatssammlung, Munich, Germany..
    Benatti, Michel Navarro
    Inst Bot, Nucleo Pesquisa Micol, Sao Paulo, SP, Brazil..
    Blanchon, Dan
    Unitec Inst Technol, Auckland, New Zealand..
    Candan, Mehmet
    Anadolu Univ, Eskisehir, Turkey..
    Clerc, Philippe
    Conservatoire & Jardin Bot Ville Geneve, Chambesy, Switzerland..
    Goward, Trevor
    Univ British Columbia, UBC Herbarium, Beaty Museum, Vancouver, Canada..
    Grube, Martin
    Karl Franzens Univ Graz, Graz, Austria..
    Hodkinson, Brendan P.
    Univ Penn, , Philadelphia, USA..
    Hur, Jae-Seoun
    Sunchon Natl Univ, Korean Lichen Res Inst, Sunchon, South Korea..
    Kantvilas, Gintaras
    Tasmanian Herbarium, Hobart, Australia..
    Kirika, Paul M.
    Natl Museums Kenya, Nairobi, Kenya..
    Lendemer, James
    New York Bot Garden, Bronx, USA..
    Mattsson, Jan-Eric
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Ines Messuti, Maria
    Univ Comahue, CONICET, San Carlos De Bariloche, Rio Negro, Argentina..
    Miadlikowska, Jolanta
    Duke Univ, Dept Biol, Durham, USA..
    Nelsen, Matthew
    Field Museum, Chicago, USA..
    Ohlson, Jan I.
    Swedish Museum Nat Hist..
    Perez-Ortega, Sergio
    CSIC, Museo Nacl Ciencias Nat, Madrid, Spain..
    Saag, Andres
    Univ Tartu, Tartu, Estonia..
    Sipman, Harrie J. M.
    Free Univ Berlin, Berlin, Germany..
    Sohrabi, Mohammad
    Iranian Res Org Sci & Technol, Tehran, Iran..
    Thell, Arne
    Lund Univ..
    Thor, Goran
    Swedish Univ Agr Sci, Dept Ecol, SE-75007 Uppsala, Sweden..
    Truong, Camille
    Conservatoire & Jardin Bot Ville Geneve, CH-1292 Chambesy, Switzerland..
    Yahr, Rebecca
    Royal Bot Gardens, Edinburgh EH3 5LR, Midlothian, Scotland..
    Upreti, Dalip K.
    CSIR, Natl Bot Res Inst, Lucknow 226001, Uttar Pradesh, India..
    Cubas, Paloma
    Univ Complutense Madrid, Madrid, Spain..
    Lumbsch, H. Thorsten
    Field Museum, Chicago, USA..
    Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi2015In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 208, no 4, p. 1217-1226Article in journal (Refereed)
    Abstract [en]

    We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.

  • 126.
    Djupedal, Ingela
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Characterization of RNA polymerase II subunit Rpb7 in silencing and transcription2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The DNA in eukaryotes is arranged in fibres of chromatin. The chromatin may be more or less compacted and the degree of condensation of the chromatin affects the accessibility of the DNA. The accessibility of the DNA, in turn, affects transcription and gene regulation. Genes within inaccessible DNA are commonly repressed whereasgenes within accessible DNA are active and expressed. This thesis concerns the interplay between chromatin and transcription with focus on the function of the RNA polymerase II (pol II) subunit Rpb7. We have demonstrated that processing of centromeric transcripts by the ribonuclease III family protein Dcr1 is required for heterochromatin formation at the centromeres of Schizosaccharomyces pombe. A point mutation in the pol II subunit Rpb7 caused a specific defect in centromeric heterochromatin formation. We have shown i) that the centromeric transcripts that accumulate in dcr1delta cells are products of pol II, ii) the rpbG150D mutation is deficient in recognition and/or initiation of transcription from the centromeric promoter. Transcription by pol II within the centromeres was surprising since insertion of marker genes within these loci normally results in repression of pol II transcription. Here, paradoxically, pol II transcription was required for the construction of the inaccessible heterochromatin structure. Our analysis of sRNA in S. pombe revealed that most centromeric siRNA are originating from two clusters, which are repeated several times within the centromeres. This lead us to propose a model in which centromeric transcripts fold into double stranded structures that are processed by Dcr1. The resulting siRNAs may contribute with the starting signal for the RNAi feedback loop required for heterochromatin formation at the centromeres. Finally, we demonstrate that the genome-wide association of Rpb7 is nearly identical to that of the core pol II subunit Rpb2, indicating a general role for Rpb7 in transcription. We further show that the occupancy pattern of Rpb4, a pol II subunit that forms a subcomplex together with Rpb7, differs from those of Rpb2 and Rpb7. Rpb4 may therefore have a less general function in transcription than Rpb7. Hence, transcription by pol II is required not only for gene expression but also for repression via formation of inaccessible heterochromatin.

  • 127.
    Djupedal, Ingela
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Durand-Dubief, M.
    Babraham Institute, Cambridge, IK.
    Sinha, Indranil
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Differential Genome-wide Occupancies of RNA Polymerase II Subunits Rpb4 and Rpb7 in Fission YeastManuscript (preprint) (Other academic)
  • 128.
    Djupedal, Ingela
    et al.
    Södertörn University, School of Life Sciences.
    Ekwall, Karl
    Södertörn University, School of Life Sciences, Molecular biology.
    Epigenetics: heterochromatin meets RNAi2009In: Cell Research, ISSN 1001-0602, E-ISSN 1748-7838, Vol. 19, no 3, p. 282-295Article in journal (Refereed)
    Abstract [en]

    The term epigenetics refers to heritable changes not encoded by DNA. The organization of DNA into chromatin fibers affects gene expression in a heritable manner and is therefore one mechanism of epigenetic inheritance. Large parts of eukaryotic genomes consist of constitutively highly condensed heterochromatin, important for maintaining genome integrity but also for silencing of genes within. Small RNA, together with factors typically associated with RNA interference (RNAi) targets homologous DNA sequences and recruits factors that modify the chromatin, commonly resulting in formation of heterochromatin and silencing of target genes. The scope of this review is to provide an overview of the roles of small RNA and the RNAi components, Dicer, Argonaute and RNA dependent polymerases in epigenetic inheritance via heterochromatin formation, exemplified with pathways from unicellular eukaryotes, plants and animals.

  • 129.
    Djupedal, Ingela
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Kos-Braun, Isabelle C.
    University of Edinburgh, Edinburgh, UK / Universität Heidelberg, Heidelberg, Germany.
    Mosher, Rebecca A.
    University of Cambridge, Cambridge, UK.
    Söderholm, Niklas
    Karolinska Institutet.
    Simmer, Femke
    University of Edinburgh, Edinburgh, UK.
    Hardcastle, Thomas J.
    University of Cambridge, Cambridge, UK.
    Fender, Aurelie
    Uppsala universitet.
    Heidrich, Nadja
    Uppsala universitet.
    Kagansky, Alexander
    University of Edinburgh, Edinburgh, UK.
    Bayne, Elizabeth
    University of Edinburgh, Edinburgh, UK.
    Wagner, E. Gerhart H.
    Uppala universitet.
    Baulcombe, David C.
    University of Cambridge, Cambridge, UK.
    Allshire, Robin C.
    University of Edinburgh, Edinburgh, UK.
    Ekwall, Karl
    Södertörn University, School of Life Sciences, Molecular biology. Karolinska Institutet.
    Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA2009In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 28, no 24, p. 3832-3844Article in journal (Refereed)
    Abstract [en]

    The formation of heterochromatin at the centromeres in fission yeast depends on transcription of the outer repeats. These transcripts are processed into siRNAs that target homologous loci for heterochromatin formation. Here, high throughput sequencing of small RNA provides a comprehensive analysis of centromere-derived small RNAs. We found that the centromeric small RNAs are Dcr1 dependent, carry 50-monophosphates and are associated with Ago1. The majority of centromeric small RNAs originate from two remarkably well-conserved sequences that are present in all centromeres. The high degree of similarity suggests that this non-coding sequence in itself may be of importance. Consistent with this, secondary structure-probing experiments indicate that this centromeric RNA is partially double-stranded and is processed by Dicer in vitro. We further demonstrate the existence of small centromeric RNA in rdp1D cells. Our data suggest a pathway for siRNA generation that is distinct from the well-documented model involving RITS/RDRC. We propose that primary transcripts fold into hairpin-like structures that may be processed by Dcr1 into siRNAs, and that these siRNAs may initiate heterochromatin formation independent of RDRC activity. The EMBO Journal (2009) 28, 3832-3844. doi: 10.1038/emboj.2009.351; Published online 26 November 2009

  • 130.
    Djupedal, Ingela
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Portoso, M
    University of Edinburgh, Edinburgh, UK.
    Spåhr, H
    Karolinska Institutet.
    Bonilla, Carolina
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Gustafsson, C M
    Karolinska Institutet.
    Allshire, R C
    University of Edinburgh, Edinburgh, UK.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing2005In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 19, no 19, p. 2301-2306Article in journal (Refereed)
    Abstract [en]

    Fission yeast centromeric repeats are transcribed into small interfering RNA (siRNA) precursors (pre-siRNAs), which are processed by Dicer to direct heterochromatin formation. Recently, Rpb1 and Rpb2 subunits of RNA polymerase II (RNA Pol II) were shown to mediate RNA interference (RNAi)-directed chromatin modification but did not affect pre-siRNA levels. Here we show that another Pol II subunit, Rpb7 has a specific role in presiRNA transcription. We define a centromeric presiRNA promoter from which initiation is exquisitely sensitive to the rpb7-G150D mutation. In contrast to other Pol II subunits, Rpb7 promotes pre-siRNA transcription required for RNAi-directed chromatin silencing.

  • 131. Dryselius, Rikard
    et al.
    Nikravesh, Abbas
    Kulyté, Agné
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Goh, Shan
    Good, Liam
    Variable coordination of cotranscribed genes in Escherichia coli following antisense repression2006In: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 6, p. 97-Article in journal (Refereed)
    Abstract [en]

    Background: A majority of bacterial genes belong to tight clusters and operons, which complicates gene functional studies using conventional knock-out methods. Antisense agents can down-regulate the expression of genes without disrupting the genome because they bind mRNA and block its expression. However, it is unclear how antisense inhibition affects expression from genes that are cotranscribed with the target. Results: To examine the effects of antisense inhibition on cotranscribed genes, we constructed a plasmid expressing the two reporter genes gfp and DsRed as one transcriptional unit. Incubation with antisense peptide nucleic acid (PNA) targeted to the mRNA start codon region of either the upstream gfp or the downstream DsRed gene resulted in a complete expression discoordination from this artificial construct. The same approach was applied to the three cotranscribed genes in the endogenously expressed lac-operon (lacZ, Y and A) and partial downstream expression coordination was seen when the lacZ start codon was targeted with antisense PNA. Targeting the lacY mRNA start codon region showed no effect on the upstream lacZ gene expression whereas expression from the downstream lacA gene was affected as strongly as the lacY gene. Determination of lacZ and lacY mRNA levels revealed a pattern of reduction that was similar to the Lac-proteins, indicating a relation between translation inhibition and mRNA degradation as a response to antisense PNA treatment. Conclusion: The results show that antisense mediated repression of genes within operons affect cotranscribed genes to a variable degree. Target transcript stability appears to be closely related to inhibition of translation and presumably depends on translating ribosomes protecting the mRNA from intrinsic decay mechanisms. Therefore, for genes within operons and clusters it is likely that the nature of the target transcript will determine the inhibitory effects on cotranscribed genes. Consequently, no simple and specific methods for expression control of a single gene within polycistronic operons are available, and a thorough understanding of mRNA regulation and stability is required to understand the results from both knock-down and knock-out methods used in bacteria.

  • 132. Dubruille, R
    et al.
    Laurencon, A
    Vandaele, C
    Shishido, E
    Coulon-Bublex, M
    Swoboda, Peter
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Couble, P
    Kernan, M
    Durand, B
    Drosophila regulatory factor X is necessary for ciliated sensory neuron differentiation2002In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 129, no 23, p. 5487-5498Article in journal (Refereed)
    Abstract [en]

    Ciliated neurons play an important role in sensory perception in many animals. Modified cilia at dendrite endings serve as sites of sensory signal capture and transduction. We describe Drosophila mutations that affect the transcription factor RFX and genetic rescue experiments that demonstrate its central role in sensory cilium differentiation. Rfx mutant flies show defects in chemosensory and mechanosensory behaviors but have normal phototaxis, consistent with Rfx expression in ciliated sensory neurons and neuronal precursors but not in photoreceptors. The mutant behavioral phenotypes are correlated with abnormal function and structure of neuronal cilia, as shown by the loss of sensory transduction and by defects in ciliary morphology and ultrastructure. These results identify Rfx as an essential regulator of ciliated sensory neuron differentiation in Drosophild.

  • 133.
    Dumanski, Jan P.
    et al.
    Uppsala University.
    Rasi, Chiara
    Uppsala University.
    Lönn, Mikael
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Davies, Hanna
    Uppsala University.
    Ingelsson, Martin
    Uppsala University.
    Giedraitis, Vilmantas
    Uppsala University.
    Lannfelt, Lars
    Uppsala University.
    Magnusson, Patrik K. E.
    Karolinska Institutet.
    Lindgren, Cecilia M.
    University of Oxford, Oxford, United Kingdom.
    Morris, Andrew P.
    University of Oxford, Oxford, United Kingdom.
    Cesarini, David
    New York University, New York, USA.
    Johannesson, Magnus
    Stockholm School of Economics.
    Janson, Eva Tiensuu
    Uppsala University.
    Lind, Lars
    Uppsala University.
    Pedersen, Nancy L.
    Karolinska Institutet.
    Ingelsson, Erik
    Uppsala Univiversity.
    Forsberg, Lars A.
    Uppsala Univiversity.
    Smoking is associated with mosaic loss of chromosome Y2015In: Cancer Research, ISSN 0008-5472, E-ISSN 1538-7445, Vol. 75, article id 4683Article in journal (Other academic)
  • 134.
    Dumanski, Jan P
    et al.
    Uppsala University.
    Rasi, Chiara
    Uppsala University.
    Lönn, Mikael
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Davies, Hanna
    Uppsala University.
    Ingelsson, Martin
    Uppsala University.
    Giedraitis, Vilmantas
    Uppsala University.
    Lannfelt, Lars
    Uppsala University.
    Magnusson, Patrik K E
    Karolinska Institutet.
    Lindgren, Cecilia M
    Morris, Andrew P
    University of Liverpool, Liverpool, UK..
    Cesarini, David
    New York University, New York, USA..
    Johannesson, Magnus
    Stockholm School of Economics.
    Tiensuu Janson, Eva
    Uppsala University.
    Lind, Lars
    Uppsala University.
    Pedersen, Nancy L
    Karolinska Institutet.
    Ingelsson, Erik
    Uppsala University.
    Forsberg, Lars A
    Uppsala University.
    Smoking is associated with mosaic loss of chromosome Y2015In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 347, no 6217, p. 81-83Article in journal (Refereed)
    Abstract [en]

    Tobacco smoking is a risk factor for numerous disorders, including cancers affecting organs outside the respiratory tract. Epidemiological data suggest that smoking is a greater risk factor for these cancers in males compared to females. This observation, together with the fact that males have a higher incidence of and mortality from most non-sex-specific cancers, remains unexplained. Loss of chromosome Y (LOY) in blood cells is associated with increased risk of nonhematological tumors. We demonstrate here that smoking is associated with LOY in blood cells in three independent cohorts [TwinGene: odds ratio (OR) = 4.3, 95% CI = 2.8-6.7; ULSAM: OR = 2.4, 95% CI = 1.6-3.6; and PIVUS: OR = 3.5, 95% CI = 1.4-8.4] encompassing a total of 6014 men. The data also suggest that smoking has a transient and dose-dependent mutagenic effect on LOY status. The finding that smoking induces LOY thus links a preventable risk factor with the most common acquired human mutation.

  • 135. Dunleavy, Elaine M.
    et al.
    Pidoux, Alison L.
    Monet, Marie
    Bonilla, Carolina
    Richardson, William
    Hamilton, Georgina L.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institute.
    McLaughlin, Paul J.
    Allshire, Robin C.
    A NASP (N1/N2)-related protein, Sim3, binds CENP-A and is required for its deposition at fission yeast Centromeres2007In: Molecular Cell, ISSN 1097-2765, E-ISSN 1097-4164, Vol. 28, no 6, p. 1029-1044Article in journal (Refereed)
    Abstract [en]

    A defining feature of centromeres is the presence of the histone H3 variant CENP-A(Cnp1). It is not known how CENP-A(Cnp1) is specifically delivered to, and assembled into, centromeric chromatin. Through a screen for factors involved in kinetochore integrity in fission yeast, we identified Sim3. Sim3 is homologous to known histone binding proteins NASP(Human) and N1/N2(Xenopus) and aligns with Hif1(S. cerevisiae), defining the SHNi-TPR family. Sim3 is distributed throughout the nucleoplasm, yet it associates with CENP-A(Cnp1) and also binds H3. Cells defective in Sim3 function have reduced levels of CENP-A(CnP1) at centromeres (and increased H3) and display chromosome segregation defects. Sim3 is required to allow newly synthesized CENP-A(Cnp1) to accumulate at centromeres in S and G2 phase-arrested cells in a replication-independent mechanism. We propose that one function of Sim3 is to act as an escort that hands off CENP-A(Cnp1) to chromatin assembly factors, allowing its incorporation into centromeric chromatin.

  • 136.
    Durand-Dubief, Mickael
    et al.
    Södertörn University, School of Life Sciences.
    Ekwall, Karl
    Södertörn University, School of Life Sciences.
    Heterochromatin tells CENP-A where to go2008In: Bioessays, ISSN 0265-9247, E-ISSN 1521-1878, Vol. 30, no 6, p. 526-529Article in journal (Refereed)
    Abstract [en]

    The centromere is the region of the chromosome where the kinetochore forms. Kinetochores are the attachment sites for spindle microtubules that separate duplicated chromosomes in mitosis and meiosis. Kinetochore formation depends on a special chromatin structure containing the histone H3 variant CENP-A. The epigenetic mechanisms that maintain CENP-A chromatin throughout the cell cycle have been studied extensively but little is known about the mechanism that targets CENP-A to naked centromeric DNA templates. In a recent report published in Science,((1)) such de novo centromere assembly of CENP-A is shown to be dependent on heterochromatin and the RNA interference pathway.

  • 137.
    Durand-Dubief, Mickael
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Sinha, Indranil
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Fagerström-Billai, Fredrik
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Bonilla, Carolina
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Wright, Anthony
    Södertörn University, School of Life Sciences. Karolinska Instiutet.
    Grunstein, Michael
    University of California, Los Angeles, CA, USA.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    Specific functions for the fission yeast Sirtuins Hst2 and Hst4 in gene regulation and retrotransposon silencing2007In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 26, no 10, p. 2477-2488Article in journal (Refereed)
    Abstract [en]

    Expression profiling, ChiP-CHIP and phenotypic analysis were used to investigate the functional relationships of class III NAD(+)-dependent HDACs (Sirtuins) in fission yeast. We detected significant histone acetylation increases in Sirtuin mutants at their specific genomic binding targets and were thus able to identify an in vivo substrate preference for each Sirtuin. At heterochromatic loci, we demonstrate that although Hst2 is mainly cytoplasmic, a nuclear pool of Hst2 colocalizes with the other Sirtuins at silent regions (cen, mat, tel, rDNA), and that like the other Sirtuins, Hst2 is required for rDNA and centromeric silencing. Interestingly we found specific functions for the fission yeast Sirtuins Hst2 and Hst4 in gene regulation. Hst2 directly represses genes involved in transport and membrane function, whereas Hst4 represses amino-acid biosynthesis genes and Tf2 retrotransposons. A specific role for Hst4 in Tf2 50 mRNA processing was revealed. Thus, Sirtuins share functions at many genomic targets, but Hst2 and Hst4 have also evolved unique functions in gene regulation.

  • 138. Dzieciatkowska, Monika
    et al.
    Liu, Xin
    Heikema, Astrid P.
    Houliston, R. Scott
    van Belkum, Alex
    Schweda, Elke K. H.
    Södertörn University, School of Life Sciences.
    Gilbert, Michel
    Richards, James C.
    Li, Jianjun
    Rapid method for sensitive screening of oligosaccharide epitopes in the lipooligosaccharide from Campylobacter jejuni strains isolated from Guillain-Barre syndrome and Miller Fisher syndrome patients2008In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 46, no 10, p. 3429-3436Article in journal (Refereed)
    Abstract [en]

    Campylobacter jejuni lipooligosaccharide (LOS) can trigger Guillain-Barre syndrome (GBS) due to its similarity to human gangliosides. Rapid and accurate structural elucidation of the LOS glycan of a strain isolated from a GBS patient could help physicians determine the spectrum of anti-ganglioside antibodies likely to be found and therefore provide valuable assistance in establishing an appropriate course of treatment. The ability of implemented mass spectrometry-based approaches in a clinical setting has been limited by the laborious and time-consuming nature of the protocols, typically 3 to 4 days, used to prepare LOS. In order to improve the analytical throughput, microwave-assisted enzymatic digestion was investigated. In this study, the bacterial cells were suspended in 50 mu l of 20 mM ammonium acetate buffer containing DNase and RNase and treated by direct microwave irradiation for 3 min. Then, proteinase K was added and the samples were again microwaved. The intact LOS samples were analyzed using electrophoresis-assisted open-tubular liquid chromatography-mass spectrometry. The reliability of the rapid, high-throughput technique was demonstrated through analysis of LOS glycans from 73 C. jejuni strains. The structure was elucidated using material from a single colony. The total time for sample preparation and MS analysis is less than 60 min.

  • 139. Dzieciatkowska, Monika
    et al.
    Schweda, Elke K. H.
    Södertörn University, School of Life Sciences.
    Moxon, E. Richard
    Richards, James C.
    Li, Jianjun
    Characterization of intact lipopolysaccharides from the Haemophilus influenzae strain RM 118 using electrophoresis-assisted open-tubular liquid chromatography-mass spectrometry2008In: Electrophoresis, ISSN 0173-0835, E-ISSN 1522-2683, Vol. 29, no 10, p. 2171-2181Article in journal (Refereed)
    Abstract [en]

    We have applied an electrophoresis-assisted open-tubular LC-MS method for analyzing intact lipopolysaccharides (LPSs) from Haemophilus influenzae strain RM 118 (Rd). We were able to obtain structural information on both core oligosaccharides (OSs) and the lipid A moiety including the sialylation, glycylation, and the distribution of fatty acid residues on the disaccharide backbone of lipid A. The fragmentation patterns of sodiated and protonated LPS molecules were investigated for determining the location of sialic acid. It was found that the tandem mass spectra of sodiated ions provided unambiguous evidence of both sialylated lactose and sialylated lacto-N-neotetraose. In contrast, the fragment ions of protonated ions only offered the evidence for the existence of sialylated lacto-N-neotetraose. The lipid A of Gram-negative bacteria, as the principal endotoxic component of LP S, plays a major role in the pathogenesis of bacterial infections. We have previously characterized lipid. A species after mild acid hydrolysis of LPS during which lipid A precipitates. In this study, intact LPS was directly introduced to a tandem mass spectrometer. In-source dissociation strategy was employed, followed by multiple-stage MS/MS on the ions originating from the lipid part to obtain structural information. This is the first time that the structure of lipid A of H. influenzae was characterized by MS/MS on intact LPS molecules without any prior chemical modifications. In the same way information on the OS can be obtained by MS/MS by focusing on ions originating from core OS.

  • 140.
    Edin, Michaela
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Grivas, Spiros
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    First synthesis of 6,7-diaminoindole and 1,2,5-selenadiazolo[3,4-g]indole2000In: ARKIVOC, ISSN 1424-6376, no 1, p. 1-5Article in journal (Refereed)
    Abstract [en]

    5-Methyl-4-nitro-2,1,3-benzoselenadiazole (1) was converted into 1,2,5-selenadiazolo[3,4-g]indole (3) by the Batcho-Leimgruber indole synthesis. Subsequent deselenation afforded 6,7-diaminoindole (4) which on treatment with biacetyl afforded 2,3-dimethylpyrrolo[2,3-f]quinoxaline (5) in 80% yield from 3.

  • 141.
    Edlund, Anna
    Södertörn University, School of Life Sciences. SLU.
    Microbial diversity in Baltic Sea sediments2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis focuses on microbial community structures and their functions in Baltic Sea sediments. First we investigated the distribution of archaea and bacteria in Baltic Sea sediments along a eutrophication gradient. Community profile analysis of 16S rRNA genes using terminal restriction length polymorphism (T-RFLP) indicated that archaeal and bacterial communities were spatially heterogeneous. By employing statistical ordination methods we observed that archaea and bacteria were structured and impacted differently by environmental parameters that were significantly linked to eutrophication. In a separate study, we analyzed bacterial communities at a different site in the Baltic Sea that was heavily contaminated with polyaromatic hydrocarbons (PAHs) and several other pollutants. Sediment samples were collected before and after remediation by dredging in two consecutive years. A polyphasic experimental approach was used to assess growing bacteria and degradation genes in the sediments. The bacterial communities were significantly different before and after dredging of the sediment. Several isolates collected from contaminated sediments showed an intrinsic capacity for degradation of phenanthrene (a PAH model compound). Quantititative real-time PCR was used to monitor the abundance of degradation genes in sediment microcosms spiked with phenanthrene. Although both xylE and phnAc genes increased in abundance in the microcosms, the isolates only carried phnAc genes. Isolates with closest 16S rRNA gene sequence matches to Exigobacterium oxidotolerans, a Pseudomonas sp. and a Gammaproteobacterium were identified by all approaches used as growing bacteria that are capable of phenanthrene degradation. These isolates were assigned species and strain designations as follows: Exiguobacterium oxidotolerans AE3, Pseudomonas fluorescens AE1 and Pseudomonas migulae AE2. We also identified and studied the distribution of actively growing bacteria along red-ox profiles in Baltic Sea sediments. Community structures were found to be significantly different at different red-ox depths. Also, according to multivariate statistical ordination analysis organic carbon, nitrogen, and red-ox potential were crucial parameters for structuring the bacterial communities on a vertical scale. Novel lineages of bacteria were obtained by sequencing 16S rRNA genes from different red-ox depths and sampling stations indicating that bacterial diversity in Baltic Sea sediments is largely unexplored.

  • 142.
    Edlund, Anna
    et al.
    Södertörn University, School of Life Sciences. SLU.
    Jansson, Janet K.
    SLU.
    Changes in active bacterial communities before and after dredging of highly polluted Baltic Sea sediments2006In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 72, no 10, p. 6800-6807Article in journal (Refereed)
    Abstract [en]

    Bacteria residing in sediments have key functions in the marine food web. However, it has been difficult to correlate the identity and activity of bacteria in sediments due to lack of appropriate methods beyond cultivation-based techniques. Our aim was to use a combination of molecular approaches, bromodeoxyuridine incorporation and immunocapture, terminal restriction fragment length polymorphism, and cloning and sequencing of 16S rRNA genes to assess the composition of growing bacteria in Baltic Sea sediments. The study site was a highly polluted area off the Swedish coast. The sediments were sampled in two consecutive years, before and after remediation, by dredging of the top sediments. Levels of polyaromatic hydrocarbons (PAHs), mercury, and polychlorinated biphenyls were dramatically reduced as a result of the cleanup project. The compositions of growing members of the communities were significantly different at the two sampling periods. In particular, members from the class Deltaproteobacteria and genus Spirochaeta were more dominant before dredging, but members of the classes Gammaproteobacteria and the Flavobacteria represented the most dominant growing populations after dredging. We also cultivated isolates from the polluted sediments that could transform the model PAH compound, phenanthrene. Some of these isolates were confirmed as dominant growing populations by the molecular methods as well. This suite of methods enabled us to link the identity and activity of the members of the sediment communities.

  • 143.
    Edlund, Anna
    et al.
    Södertörn University, School of Life Sciences. SLU.
    Jansson, Janet K.
    SLU.
    Identification of metabolically active phenanthrene transforming bacteria in polluted Baltic Sea sedimentsManuscript (preprint) (Other academic)
  • 144.
    Edlund, Anna
    et al.
    Södertörn University, School of Life Sciences.
    Jansson, Janet K.
    Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments2008In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 65, no 3, p. 513-525Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to enrich and identify psychrotolerant phenanthrene-degrading bacteria from polluted Baltic Sea sediments. Polyaromatic hydrocarbon (PAH)-contaminated sediments were spiked with phenanthrene and incubated for 2 months in the presence of bromodeoxyuridine that is incorporated into the DNA of replicating cells. The bromodeoxyuridine-incorporated DNA was extracted by immunocapture and analyzed by terminal-restriction fragment length polymorphism and 16S rRNA gene cloning and sequencing to identify bacterial populations that were growing. In addition, degradation genes were quantified in the bromodeoxyuridine-incorporated DNA by real-time PCR. Phenanthrene concentrations decreased after 2 months of incubation in the phenanthrene-enriched sediments and this reduction correlated to increases in copy numbers of xylE and phnAc dioxygenase genes. Representatives of Exiguobacterium, Schewanella, Methylomonas, Pseudomonas, Bacteroides and an uncultured Deltaproteobacterium and a Gammaproteobacterium dominated the growing community in the phenanthrene-spiked sediments. Isolates that were closely related to three of these bacteria (two pseudomonads and an Exiguobacterium sp.) could reduce phenanthrene concentrations in pure cultures and they all harbored phnAc dioxygenase genes. These results confirm that this combination of culture-based and molecular approaches was useful for identification of actively growing bacterial species with a high potential for phenanthrene degradation.

  • 145.
    Edlund, Charlotta
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Alvan, G
    Barkholt, L
    Vacheron, F
    Nord, C E
    Pharmacokinetics and comparative effects of telithromycin (HMR 3647) and clarithromycin on the oropharyngeal and intestinal microflora2000In: Journal of Antimicrobial Chemotherapy, ISSN 0305-7453, E-ISSN 1460-2091, Vol. 46, no 5, p. 741-749Article in journal (Refereed)
    Abstract [en]

    The pharmacokinetics in plasma and saliva of a new ketolide, telithromycin (HMR 3647), and the effect on the normal oropharyngeal and intestinal microflora were studied in healthy volunteers and compared with those of clarithromycin. Ten subjects received 800 mg telithromycin perorally once daily and 10 other subjects received 500 mg clarithromycin bid for 10 days. Blood, saliva and faecal specimens were collected at defined intervals before, during and after administration for pharmacokinetic and microbiological analyses. In subjects receiving telithromycin, the mean C(max), AUC and C(24) (24 h) in saliva exceeded the values obtained from plasma, while saliva and serum pharmacokinetic parameters were in the same range for the clarithromycin group. The quantitative ecological disturbances in the normal microflora during administration of telithromycin were moderate and comparable to those associated with clarithromycin administration. No overgrowth of yeasts or Clostridium difficile occurred. Emergence of resistant strains was seen in both treatment groups. Administration of both telithromycin and clarithromycin was associated with significant increases in MICs for intestinal Bacteroides isolates, which persisted 2 weeks after discontinuation of treatment. In addition, a significant emergence of highly clarithromycin-resistant a-haemolytic streptococci, intestinal enterococci and Enterobacteriaceae was detected at day 10 in the clarithromycin group. In conclusion, administration of telithromycin resulted in high drug levels in saliva, which indicates a good therapeutic profile for throat infections. Telithromycin seems to have a more favourable ecological profile compared with clarithromycin in terms of resistance development in the normal microflora.

  • 146.
    Edlund, Charlotta
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Nord, C E
    Effect on the human normal microflora of oral antibiotics for treatment of urinary tract infections2000In: Journal of Antimicrobial Chemotherapy, ISSN 0305-7453, E-ISSN 1460-2091, Vol. 46, p. 41-48Article in journal (Refereed)
    Abstract [en]

    Oral administration of antibiotics for treatment of urinary tract infections (UTIs) can cause ecological disturbances in the normal intestinal microflora. Poorly absorbed drugs can reach the colon in active form, suppress susceptible microorganisms and disturb the ecological balance. Suppression of the normal microflora may lead to reduced colonization resistance with subsequent overgrowth of pre-existing, naturally resistant microorganisms, such as yeasts and Clostridium difficile. New colonization by resistant potential pathogens may also occur and may spread within the body or to other patients and cause severe infections. It is therefore important to learn more about the ecological effects of antibacterial agents on the human microflora. The impact on intestinal microorganisms of oral antibiotics used for the treatment of UTIs is reviewed here. Ampicillin, amoxycillin and co-amoxiclav suppress both the aerobic and anaerobic intestinal microflora with overgrowth of ampicillin-resistant Enterobacteriaceae. Pivmecillinam also affects the intestinal microflora, suppressing Escherichia coli, but does not have a major effect on the anaerobic microflora. Several orally administered cephalosporins, such as cefixime, cefpodoxime, cefprozil and ceftibuten, reduce the number of Enterobacteriaceae and increase the number of enterococci. Colonization with C. difficile has also been observed. Fluoroquinolones eliminate or strongly suppress intestinal Enterobacteriaceae, but affect enterococci and anaerobic bacteria only slightly. When antimicrobial agents are prescribed for the treatment of UTIs, not only the antimicrobial spectrum of the agent but also the potential ecological disturbances, including the risk of emergence of resistant strains, should be considered.

  • 147.
    Edlund, Charlotta
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Nord, C E
    The evaluation and prediction of the ecologic impact of antibiotics in human phase I and II trials2001In: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 7, p. 37-41Article in journal (Refereed)
  • 148.
    Edvardsson, Anna
    et al.
    Linköpings universitet.
    Petersson, Ulrika A.
    Södertörn University, School of Life Sciences. Stockholms universitet.
    Shapiguzov, Alexey
    Linköpings universitet.
    Schröder, Wolfgang P
    Södertörn University, School of Life Sciences. Umeå universitet.
    Vener, Alexander V.
    Linköpings universitet.
    Knockout of the cyclophilin AtCYP20-2 is compensated by oxidative activation of PPIase activity in the thylakoid lumen of Arabidopsis thalianaManuscript (preprint) (Other academic)
  • 149. Edvardsson, Anna
    et al.
    Shapiguzov, Alexey
    Petersson, Ulrika A.
    Södertörn University, School of Life Sciences. Stockholm University.
    Schröder, Wolfgang P.
    Vener, Alexander V.
    Immunophilin AtFKBP13 sustains all peptidyl-prolyl isomerase activity in the thylakoid lumen from Arabidopsis thaliana deficient in AtCYP20-22007In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 46, no 33, p. 9432-9442Article in journal (Refereed)
    Abstract [en]

    The physiological roles of immunophilins are unclear, but many possess peptidyl-prolyl isomerase (PPIase) activity, and they have been found in all organisms examined to date, implying that they are involved in fundamental, protein-folding processes. The chloroplast thylakoid lumen of the higher plant Arabidopsis thaliana contains up to 16 immunophilins (five cyclophilins and 11 FKBPs), but only two of them, AtCYP20-2 and AtFKBP13, have been found to be active PPIases, indicating that the other immunophilins in this cellular compartment may have lost their putative PPIase activities. To assess this possibility, we characterized two independent Arabidopsis knockout lines lacking AtCYP20-2 in enzymological and quantitative proteomic analyses. The PPIase activity in thylakoid lumen preparations of both mutants was equal to that of corresponding wild-type preparations, and comparative two-dimensional difference gel electrophoresis analyses of the lumenal proteins of the mutants and wild type showed that none of the potential PPIases was more abundant in the AtCYP20-2 deficient plants. Enzymatic analyses established that all PPIase activity in the mutant thylakoid lumen was attributable to AtFKBP13, and oxidative activation of this enzyme compensated for the lack of AtCYP20-2. Accordingly, sequence analyses of the potential catalytic domains of lumenal cyclophilins and FKBPs demonstrated that only AtCYP20-2 and AtFKBP13 possess all of the amino acid residues found to be essential for PPIase activity in earlier studies of human cyclophilin A and FKBP12. Thus, none of the immunophilins in the chloroplast thylakoid lumen of Arabidopsis except AtCYP20-2 and AtFKBP13 appear to possess prolyl isomerase activity toward peptide substrates.

  • 150.
    Efimenko, Evgeni
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    The study of sensory cilia development in caenorhabditis elegans2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Cilia and flagella are widespread eukaryotic subcellular components that are conserved from green algae to mammals. In different organisms they function in cell motility, movement of extracellular fluids and sensory reception. While the function and structural description of cilia and flagella are well established, very little is known about the developmental mechanisms by which cilia are generated and shaped and how their components are assembled into functional machineries. To answer these questions, we used sensory cilia development in the nematode Caenorhabditis elegansas a model system.

    The work described here developed from the initial discovery of the ciliogenic properties of the gene daf-19, which encodes the sole C. elegans member of the RFX-type transcription factors. All members of the RFX transcription factor family are characterized by the presence of a conserved DNA binding domain, which recognizes special motifs (X-boxes) in promoters of its target genes. By using a genome search approach for X-box promoter motif-containing genes (xbx genes) we identified a list of about 750 xbx genes (candidates). This list comprises some already known ciliary genes as well as new genes, many of which we hypothesize to be important for cilia development and functioning.

    A computational search for X-box motifs in the C. briggsae genome has demonstrated strong conservation of this motif between closely related nematode species. To find out whether RFX-type transcription factors can also regulate ciliogenic pathways in other organisms, we applied a similar search strategy to distant species such as the fruit fly Drosophila. Using X-box consensus sequences with varying degrees of refinement and subsequent gene expression analysis, we were able to identify a set of Drosophila xbx genes. Intriguingly, the majority of fly xbx genes that have homologs in C. elegans were down regulated in dRfx fly mutants, suggesting an evolutionary conserved role for RFX-type transcription factors in the regulation of ciliary genes.

    Using X-box matches as a prediction tool we were able to identify novel ciliary genes, dyf-2 and dyf-11, in the C. elegans genome. We cloned these genes by transgenic rescue of mutant phenotypes and by sequencing of mutant alleles. Loss of DYF-2 and DYF-11 functions selectively affects the assembly and motility of different intraflagellar transport (IFT) components, resulting in compromised protein transport within cilia, and subsequently in defective cilia structures and sensory functions. Importantly, the mouse orthologs of DYF-2 and DYF-11 also localize to cilia, pointing to evolutionarily conserved roles for these proteins in cilia biogenesis.

    In conclusion, our studies of the regulation of sensory cilia formation demonstrated how contributions of multiple factors are integrated into a developmental module that leads to the formation of the primary sensory organs, cilia. In addition, data obtained during the course of this study provide a useful resource for researchers interested in further identification and study of new genes implicated in cilia biogenesis and will have a significant impact on the understanding and treatment of cilia-based pathologies in humans.

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