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  • 201. Fang, Hong
    et al.
    Edlund, Charlotta
    Södertörns högskola, Avdelning Naturvetenskap.
    Nord, C E
    Hedberg, M
    Selection of cefoxitin-resistant Bacteroides thetaiotaomicron mutants and mechanisms involved in beta-lactam resistance2002Inngår i: Clinical Infectious Diseases, ISSN 1058-4838, E-ISSN 1537-6591, Vol. 35, s. S47-S53Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The beta-lactam antibiotics are the most widely used of all the groups of antimicrobials, but beta-lactam resistance is increasingly common among members of the Bacteroides fragilis group. Three major mechanisms are involved in beta-lactam resistance, and they act together in certain instances. In the present study, 2 resistant mutants (238m and 1186m) of Bacteroides thetaiotaomicron, obtained from clinical isolates (238 and 1186) by selection with increasing concentrations of cefoxitin, showed decreased susceptibilities to cefoxitin and other beta-lactam antibiotics. Alterations in both penicillin-binding proteins (PBPs) and outer-membrane proteins (OMPs) were observed in the mutants in comparison with their parent strains. The similar alteration in OMPs was also observed in clinical isolates. In conclusion, the beta-lactam-resistant mutants of B. thetaiotaomicron with deficiency in both PBPs and OMPs can be selected for by exposure to cefoxitin, and several mechanisms are involved in the beta-lactam resistance in the strains investigated.

  • 202.
    Fang, Hong
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Edlund, Charlotta
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Zhang, G.
    Karolinska Institutet.
    Hedberg, M.
    Karolinska Institutet.
    Detection of imipenem-resistant and metronidazole-resistant Bacteroides fragilis group strains in fecal samples1999Inngår i: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 5, nr 12, s. 753-758Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Objective: To investigate the imipenem and metronidazole resistance profiles of Bacteroides fragilis group strains in fecal samples and to detect the resistance genes (ccrA and nim) coding for imipenem and metronidazole resistance in B. fragilis group strains. Methods: In total, 925 fecal samples, 729 from consecutive diarrhea patients and 196 from healthy controls, were collected at Huddinge University Hospital in 1997. A modified disk diffusion method was employed to screen for imipenem-resistant and metronidazole-resistant B. fragilis group strains. In strains considered resistant by the modified disk diffusion method, the minimum inhibitory concentrations (MICs) were further determined by the agar dilution method. PCR assays were used to detect the carbapenem-hydrolyzing metallo-P-lactamase gene (ccrA) and the 5-nitroimidazole resistance genes (nim) in pure cultures (purePCR), directly from fecal samples through direct broth enrichment (dirPCR) and by immunomagnetic separation (imsPCR). Results: Two imipenem-resistant B. fragilis strains, one of which was simultaneously resistant to metronidazole, and two B. fragilis group strains with MICs near the breakpoint for metronidazole resistance, were isolated from the fecal samples of diarrhea patients. The ccrA gene was identified in all the imipenem-resistant B. fragilis strains by purePCR, dirPCR and imsPCR. The nim genes were also detectable by these PCR assays. Conclusions: The incidences of imipenem-resistant and metronidazole-resistant B. fragilis group strains were low in the investigated diarrhea patients. Simultaneous resistance to imipenem and metronidazole is of great concern in clinical medicine, and the proposed PCR assays may be useful in epidemiologic studies of distribution of resistance genes in the fecal microflora.

  • 203.
    Fang, Hong
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Hedberg, M
    Karolinska Institutet.
    Edlund, Charlotta
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Instiutet.
    Nord, C E
    Karolinska Institutet.
    Identification of the metallo-beta-lactamase gene from clinical isolates of Bacteroides fragilis1999Inngår i: Anaerobe, ISSN 1075-9964, E-ISSN 1095-8274, Vol. 5, nr 3-4, s. 431-434Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bacteroides fragilis is one of the organisms known to produce carbapenem-hydrolysing metallo-beta-lactamase, which can confer resistance to a wide variety of beta-lactams. The purpose of this study was to identify carbapenem-hydrolysing metallo-beta-lactamase-producing B. fragilis strains by means of PCR assay, nucleotide sequencing and enzyme inhibition studies. Ten beta-lactam-resistant B. fragilis isolates were investigated. Four imipenem-resistant strains among the 10 isolates gave positive reactions in the PCR assay. The nucleotide sequences of the PCR products from two imipenem-resistant strains shared >98% similarity with the metallo-beta-lactamase gene from B. fragilis TAL 3636, which was used as a control. The amino acid sequence homology between the two imipenem-resistant strains and B. fragilis TAL 3636 was 99.2%. These strains produced high amounts of Zn2+-dependent beta-lactamases which were inactivated by EDTA.

  • 204.
    Fanous, Nicola
    et al.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik.
    Lohsar, Iqra
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik.
    Kartläggning av externa effekter vid etablering av storskaliga solcellsparker: En fallstudie av tre storskaliga solcellsparker2022Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Det här är en stuide om externa effekter som kan uppstå vid etablering av solcellsparker och om hur sådana effekter kan påverka samhällsbeslut. Förnybara energikällor spelar en nyckeroll för att skapa en hållbar framtid, där storskaliga soclellsparker kan ses som ett hållbart alternativ till energikällor. Det finns en risk att Solcellsparker kan medföra globala och lokala negativa externa effekter och är därför intressant att studera. Studien bygger på en kvalitativ metod, där intervjuer med fya sakägare som har goda kunskaper och insikter om solcellsparker genomförts. Empiriskt material från fysisk planering, miljöbedömningar och andra pålitliga källor har använts för att besvara studiens frågeställningar. Resultaten visar att anläggningen av en solcellspark kan leda till en så kallad green vs. green-konflikt, där det finns olika intressen och åsikter. Genom att jämföra tre befintliga solcellsparker har vi sett vilken roll externa effekter spelar i beslutsfattande när det gäller att anlägga en solcellspark och hur väsentliga samhällintressen, till exempel livsmedelsförsörjning, också kan påverka beslut om att anlägga solcellsparker. Resultaten visar också att lokaliseringsprinicipen spelar en stor roll, genom att påverka vilka externa effekter som kan uppstå lokalt på platsen. 

    Fulltekst (pdf)
    fulltext
  • 205.
    Ferreira, Monica E.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska institutet.
    Studies of transcription factor domains and their interactions with other transcription factors2009Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The studies in this thesis deal with different questions concerning interactions of functional domains of factors involved in transcriptional regulation. The first study of this thesis is focused on the target factor binding mechanism of transcriptional activators. Many activators in evolutionary distant species are classified as acidic based on a high content of acidic residues in the activation domain and intrinsically unstructured in solution. Our results indicate that such activation domains interact with target factors through coupled binding and folding of the activation domain after an initial ionic interaction, and demonstrate the generality of this binding mechanism. We propose that target interaction through coupled binding and folding of the recruiting domain is important for the role of activators as regulators of transcription. In the following study we show that deletion of two regions that mediate interaction with activators in vitro prevents promoter recruitment of the SWI/SNF chromatinremodeling complex in vivo, and causes strongly reduced transcriptional activity of the corresponding genes. This study validates direct interaction between the Swi1- and Snf5 activator binding domains of the S. cerevisiae SWI/SNF complex and activators previously demonstrated in vitro, and importantly indicates that the activator binding domains are essential for the ability of SWI/SNF to function as co-activator. In the last study we investigate which domains are involved in distinct in vivo function of the paralogous co-repressors Tup11 and Tup12 of the Ssn6/Tup complex in S. pombe. Tup11 and Tup12 have been shown to differ in importance in context of a common complex for subsets of Ssn6/Tup target genes, and it was proposed that this might depend on divergence in the histone-interaction domain. Here we show that distinct in vivo roles of Tup12 do not depend on differences in the highly diverged histoneinteraction domain, but mainly on differences in the overall highly conserved WD40 repeat domain, which putatively mediates interaction with repressors and target factors such as histone modifying complexes and components of the transcriptional machinery. We propose that clusters of amino acids, putatively located in blade 3 of the WD40 repeat domain, could be important for interaction with distinct target factors of Tup11 and Tup12. Furthermore, we show that the stoichiometry of the Ssn6/Tup complex is likely to change under CaCl2 stress, by a mechanism involving changes in the relative cellular levels of the complex components.

  • 206.
    Ferreira, Monica E.
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Berndt, Kurt D.
    Södertörns högskola, Institutionen för livsvetenskaper, Kemi.
    Nilsson, Johan
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Wright, Anthony P. H.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    WD40 Domain Divergence Is Important for Functional Differences between he Fission Yeast Tup11 and Tup12 Co-Repressor Proteins2010Inngår i: PLOS ONE, E-ISSN 1932-6203, Vol. 5, nr 6, artikkel-id e11009Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have previously demonstrated that subsets of Ssn6/Tup target genes ave distinct requirements for the Schizosaccharomyces pombe homologs of he Tup1/Groucho/TLE co-repressor proteins, Tup11 and Tup12. The very igh level of divergence in the histone interacting repression domains f the two proteins suggested that determinants distinguishing Tup11 and up12 might be located in this domain. Here we have combined hylogenetic and structural analysis as well as phenotypic haracterization, under stress conditions that specifically require up12, to identify and characterize the domains involved in up12-specific action. The results indicate that divergence in the epression domain is not generally relevant for Tup12-specific function. nstead, we show that the more highly conserved C-terminal WD40 repeat omain of Tup12 is important for Tup12-specific function. Surface amino cid residues specific for the WD40 repeat domain of Tup12 proteins in ifferent fission yeasts are clustered in blade 3 of the propeller-like tructure that is characteristic of WD40 repeat domains. The Tup11 and up12 proteins in fission yeasts thus provide an excellent model system or studying the functional divergence of WD40 repeat domains.

  • 207.
    Ferreira, Monica E
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Hermann, Stefan
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Prochasson, P
    Stowers Institute for Medical Research, Kansas City, USA.
    Workman, J L
    Stowers Institute for Medical Research, Kansas City, USA.
    Berndt, Kurt D
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Wright, Athony P H
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Mechanism of transcription factor recruitment by acidic activators2005Inngår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 280, nr 23, s. 21779-21784Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Many transcriptional activators are intrinsically unstructured yet display unique, defined conformations when bound to target proteins. Target-induced folding provides a mechanism by which activators could form specific interactions with an array of structurally unrelated target proteins. Evidence for such a binding mechanism has been reported previously in the context of the interaction between the cancer-related c-Myc protein and the TATA-binding protein, which can be modeled as a two-step process in which a rapidly forming, low affinity complex slowly converts to a more stable form, consistent with a coupled binding and folding reaction. To test the generality of the target-induced folding model, we investigated the binding of two widely studied acidic activators, Gal4 and VP16, to a set of target proteins, including TATA-binding protein and the Swi1 and Snf5 subunits of the Swi/Snf chromatin remodeling complex. Using surface plasmon resonance, we show that these activator-target combinations also display bi-phasic kinetics suggesting two distinct steps. A fast initial binding phase that is inhibited by high ionic strength is followed by a slow phase that is favored by increased temperature. In all cases, overall affinity increases with temperature and, in most cases, with increased ionic strength. These results are consistent with a general mechanism for recruitment of transcriptional components to promoters by naturally occurring acidic activators, by which the initial contact is mediated predominantly through electrostatic interactions, whereas subsequent target-induced folding of the activator results in a stable complex.

  • 208.
    Ferreira, Monica E.
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Nilsson, Johan
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Berndt, Kurt D.
    Södertörns högskola, Institutionen för livsvetenskaper, Kemi. Karolinska Institutet.
    Wright, Anthony P. H.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska Institutet.
    Protein domains underlying functional divergence between the Tup11 and Tup12 co-repressor proteins in fission yeastManuskript (preprint) (Annet vitenskapelig)
  • 209.
    Ferreira, Monica E.
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska instiutet.
    Prochasson, Philippe
     Stowers Institute for Medical Research, Kansas City, MO, USA.
    Berndt, Kurt D.
    Södertörns högskola, Institutionen för livsvetenskaper, Kemi. Karolinska institutet.
    Workman, Jerry L.
    Stowers Institute for Medical Research, Kansas City, MO, USA.
    Wright, Anthony P. H.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska institutet.
    Activator-binding domains of the SWI/SNF chromatin remodeling complex characterized in vitro are required for its recruitment to promoters in vivo2009Inngår i: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 276, nr 9, s. 2557-2565Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Interaction between acidic activation domains and the activator-binding domains of Swi1 and Snf5 of the yeast SWI/SNF chromatin remodeling complex has previously been characterized in vitro. Although deletion of both activator-binding domains leads to phenotypes that differ from the wild-type, their relative importance for SWI/SNF recruitment to target genes has not been investigated. In the present study, we used chromatin immunoprecipitation assays to investigate the individual and collective importance of the activator-binding domains for SWI/SNF recruitment to genes within the GAL regulon in vivo. We also investigated the consequences of defective SWI/SNF recruitment for target gene activation. We demonstrate that deletion of both activator-binding domains essentially abolishes galactose-induced SWI/SNF recruitment and causes a reduction in transcriptional activation similar in magnitude to that associated with a complete loss of SWI/SNF activity. The activator-binding domains in Swi1 and Snf5 make approximately equal contributions to the recruitment of SWI/SNF to each of the genes studied. The requirement for SWI/SNF recruitment correlates with GAL genes that are highly and rapidly induced by galactose.

  • 210.
    Figueroa, Ricardo
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karloinska institutet.
    Gudise, Santhosh
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi. Karolinska institutet.
    Larsson, Veronica
    Karloinska institutet.
    Hallberg, Einar
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    A transmembrane inner nuclear membrane protein in the mitotic spindle2010Inngår i: Nucleus, ISSN 1949-1042, Vol. 1, nr 3, s. 249-253Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have recently characterized a novel transmembrane protein of the inner nuclear membrane of mammalian cells. The protein has two very interesting features. First, despite being an integral membrane protein it is able to concentrate in the membranes colocalizing with the mitotic spindle in metaphase and anaphase. Hence, the protein was named Samp1, Spindle associated membrane protein 1. Secondly, it displays a functional connection to centrosomes. This article discusses various aspects of Samp1 in relation to possible cellular function(s).

  • 211. Filling, C
    et al.
    Berndt, Kurt D
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Intitute.
    Benach, J
    Knapp, S
    Prozorovski, T
    Nordling, E
    Ladenstein, R
    Jörnvall, H
    Oppermann, U
    Critical residues for structure and catalysis in short-chain dehydrogenases/reductases2002Inngår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 277, nr 28, s. 25677-25684Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Short-chain dehydrogenases/reductases form a large, evolutionarily old family of NAD(P)(H)-dependent enzymes with over 60 genes found in the human genome. Despite low levels of sequence identity (often 10-30%), the three-dimensional structures display a highly similar alpha/beta folding pattern. We have analyzed the role of several conserved residues regarding folding, stability, steady-state kinetics, and coenzyme binding using bacterial 3beta/17beta-hydroxysteroid dehydrogenase and selected mutants. Structure determination of the wildtype enzyme at 1.2-Angstrom resolution by x-ray crystallography and docking analysis was used to interpret the biochemical data. Enzyme kinetic data from mutagenetic replacements emphasize the critical role of residues Thr-12, Asp-60, Asn-86, Asn-87, and Ala-88 in coenzyme binding and catalysis. The data also demonstrate essential interactions of Asn-111 with active site residues. A general role of its side chain interactions for maintenance of the active site configuration to build up a proton relay system is proposed. This extends the previously recognized catalytic triad of Ser-Tyr-Lys residues to form a tetrad of Asn-Ser-Tyr-Lys in the majority of characterized short-chain dehydrogenases/reductase enzymes.

  • 212. Filling, C
    et al.
    Nordling, E
    Benach, J
    Berndt, Kurt D
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institute.
    Ladenstein, R
    Jörnvall, H
    Oppermann, U
    Structural role of conserved Asn179 in the short-chain dehydrogenase/reductase scaffold2001Inngår i: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 289, nr 3, s. 712-717Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Short-chain dehydrogenases/reductases (SDR) constitute a large family of enzymes found in all forms of life. Despite a low level of sequence identity, the three-dimensional structures determined display a nearly superimposable alpha/beta folding pattern. We identified a conserved asparagine residue located within strand betaF and analyzed its role in the short-chain dehydrogenase/reductase architecture. Mutagenetic replacement of Asn179 by Ala in bacterial 3 beta /17 beta -hydroxysteroid dehydrogenase yields a folded, but enzymatically inactive enzyme, which is significantly more resistant to denaturation by guanidinium hydrochloride. Crystallographic analysis of the wild-type enzyme at 1.2-Angstrom resolution reveals a hydrogen bonding network, including a buried and well-ordered water molecule connecting strands betaE to betaF, a common feature found in 16 of 21 known three-dimensional structures of the family. Based on these results, we hypothesize that in mammalian 11 beta -hydroxysteroid dehydrogenase the essential Asn-linked glycosylation site, which corresponds to the conserved segment, displays similar structural features and has a central role to maintain the SDR scaffold.

  • 213. Fischer, H
    et al.
    Zhang, X U
    O'Brien, K P
    Kylsten, Per
    Södertörns högskola, Avdelning Naturvetenskap.
    Engvall, E
    C7, a novel nucleolar protein, is the mouse homologue of the Drosophila late puff product L82 and an isoform of human OXR12001Inngår i: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 281, nr 3, s. 795-803Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The C7 gene was identified in a project aimed to characterize differential gene expression upon attachment of cells to extracellular matrix proteins in vitro. C7 is the homologue of Drosophila L82, a late puff gene (Stowers et al. (1999) Dev. Biol. 213, 116-130) and human OXR1, a gene, which protects cells against oxidation (Volkert et al. (2000) Proc. Natl. Acad. Sci. USA 97, 14530-14535). All are transcribed into multiple splice forms with a common 3' domain. Additional members of this novel gene family are found in a number of eukaryotic species. In the mouse, the C7 gene is highly and broadly expressed during development in at least 4 splice forms, 3 of which were sequenced. In the adult, the C7 gene is most highly expressed in brain and testis. Antibodies to recombinant C7 protein localized to nucleoli in a variety of cell types, suggesting that C7 may be involved in the formation or function of this important organelle.

  • 214. Fisher, Linda
    et al.
    Samuelsson, Malin
    Jiang, Yang
    Ramberg, Veronica
    Figueroa, Ricardo
    Södertörns högskola, Institutionen för livsvetenskaper.
    Hallberg, Einar
    Södertörns högskola, Institutionen för livsvetenskaper.
    Langel, Ulo
    Iverfeldt, Kerstin
    Targeting cytokine expression in glial cells by cellular delivery of an NF-kappa B decoy2007Inngår i: Journal of Molecular Neuroscience, ISSN 0895-8696, E-ISSN 1559-1166, Vol. 31, nr 3, s. 209-219Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Inhibition of nuclear factor (NF)-kappa B has emerged as an important strategy for design of anti-inflammatory therapies. In neurodegenerative disorders like Alzheimer's disease, inflammatory reactions mediated by glial cells are believed to promote disease progression. Here, we report that uptake of a double-stranded oligonucleotide NF-kappa B decoy in rat primary glial cells is clearly facilitated by noncovalent binding to a cell-penetrating peptide, transportan 10, via a complementary peptide nucleic acid (PNA) sequence. Fluorescently labeled oligonucleotide decoy was detected in the cells within 1 h only when cells were incubated with the decoy in the presence of cell-penetrating peptide. Cellular delivery of the decoy also inhibited effects induced by a neurotoxic fragment of the Alzheimer beta-amyloid peptide in the presence of the inflammatory cytokine interleukin (IL)-1 beta. Pretreatment of the cells with the complex formed by the decoy and the cell-penetrating peptide-PNA resulted in 80% and 50% inhibition of the NF-kappa B binding activity and IL-6 mRNA expression, respectively.

  • 215.
    Flinn, Elizabeth M
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Intstitutet.
    Wallberg, A E
    Hermann, Stefan
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Grant, P A
    Workman, J L
    Wright, Anthony P H
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Recruitment of Gen5-containing complexes during c-Myc-dependent gene activation - Structure and function aspects2002Inngår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 277, nr 26, s. 23399-23406Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The N-terminal domain of c-Myc plays a key role in cellular transformation and is involved in both activation and repression of target genes as well as in modulated proteolysis of c-Myc via the proteasome. Given this functional complexity, it has been difficult to clarify the structures within the N terminus that contribute to these different processes as well as the mechanisms by which they function. We have used a simplified yeast model system to identify the primary determinants within the N terminus for W chromatin remodeling of a promoter, (ii) gene activation from a chromatin template in vivo, and (iii) interaction with highly purified Gcn5 complexes as well as other chromatin-remodeling complexes in vitro. The results identify two regions that contain autonomous chromatin opening and gene activation activity, but both regions are required for efficient interaction with chromatin-remodeling complexes in vitro. The conserved Myc boxes do not play a direct role in gene activation, and Myc box II is not generally required for in vitro interactions with remodeling complexes. The yeast SAGA complex, which is orthologous to the human GCN5-TRRAP complex that interacts with Myc in human cells, plays a role in Myc-mediated chromatin opening at the promoter but may also be involved in later steps of gene activation.

  • 216. Foloppe, N
    et al.
    Sagemark, Johan
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Nordstrand, K
    Berndt, Kurt D
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Nilsson, L
    Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: Comparison with functionally related proteins2001Inngår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 310, nr 2, s. 449-470Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The chemistry of active-site cysteine residues is central to the activity of thiol-disulfide oxidoreductases of the thioredoxin superfamily. In these reactions, a nucleophilic thiolate is required, but the associated pK(a), values differ vastly in the superfamily, from less than 4 in DsbA to greater than 7 in Trx. The factors that stabilize this thiolate are, however, not clearly established. The glutaredoxins (Grxs), which are members of this superfamily, contain a Cys-Pro-Tyr-Cys motif in their active site. In reduced Grxs, the pK(a) of the N-terminal active-site nucleophilic cysteine residue is lowered significantly, and the stabilization of the corresponding thiolate is expected to influence the redox potential of these enzymes. Here, we use a combination of long molecular dynamics (MD) simulations, pK(a) calculations, and experimental investigations to derive the structure and dynamics of the reduced active site from Escherichia coli Grx3, and investigate the factors that stabilize the thiolate. Several different MD simulations converged toward a consensus conformation for the active-site cysteine residues (Cys11 and Cys14), after a number of local conformational changes. Key features of the model were tested experimentally by measurement of NMR scalar coupling constants, and determination of pK(a) values of selected residues. The pK(a) values of the Grx3 active-site residues were calculated during the MD simulations, and support the underlying structural model. The structure of Grx3, in combination with the pK(a) calculations, indicate that the pK(a) of the N-terminal active-site cysteine residue in Grx3 is intermediate between that of its counterpart in DsbA and Trx. The pK(a) values in best agreement with experiment are obtained with a low (<4) protein dielectric constant. The calculated pK(a) values fluctuate significantly in response to protein dynamics, which underscores the importance of the details of the underlying structures when calculating pK(a) values. The thiolate of Cys11 is stabilized primarily by direct hydrogen bonding with the amide protons of Tyr13 and Cys14 and the thiol proton of Cys14, rather than by long range interactions from charged groups or from a helix macrodipole. From the comparison of reduced Grx3 with other members of the thioredoxin superfamily, a unifying theme for the structural basis of thiol pK(a) differences in this superfamily begins to emerge.

  • 217.
    Forsberg, Lars
    Södertörns högskola, Institutionen för livsvetenskaper.
    Genetic Aspects of Sexual Selection and Mate Choice in Salmonids2008Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The long-term genetic consequences of supportive breeding programs are not well understood. Nevertheless, stocking populations with hatchery-produced fish to compensate for losses of natural production are common practice, for example after constructions of hydroelectric power dams. Hatcheries typically fertilize eggs using ‘mixed-milt fertilizations’, without consideration to natural reproductive behaviours, and hence, natural selective regimes would be altered.

    Here, a series of experiments with focus on Mhc and mate choice in a population of brown trout (Salmo trutta L.) with a history of long-term stocking are presented. The major histocompatibility complex (Mhc) constitutes of genes coding for antigen presentation in the vertebrate immune system. In addition to the immunological function, Mhc genes might also influence reproductive behaviours such as mate choice. For example, in some species individuals are able to recognize Mhc genotypes of potential mates and to some extent base their mate choice on this information. Here, I address these questions on brown trout. Can the phenomena be observed in brown trout? Could such mechanisms help individuals to avoid inbreeding, or are other mechanisms important? How does the artificial rearing of fish for enhancement of natural populations relate to these issues?

    The results presented here, in combination with previous work, shows that several factors are important in the process of pair formation in salmonid species. For example, females of the studied population used more than a single criterion when choosing among the available mates Mhc genes and males with certain Mhc genotypes achieved more matings, possibly an effect from increased fighting ability. Further, the population appears to contain an unnatural high level of Mhc variation, and some results indicate that the population might suffer from outbreeding depression at the Mhc. These negative effects are most likely derived from compression of sub-populations after dam-construction, in combination with supportive breeding with no consideration to natural spawning behaviour.

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  • 218.
    Forsberg, Lars A.
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Uppsala University.
    Dannewitz, J.
    Petersson, E.
    Grahn, Mats
    Södertörns högskola, Institutionen för livsvetenskaper.
    Influence of genetic dissimilarity in the reproductive success and mate choice of brown trout - females fishing for optimal MHC dissimilarity2007Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 20, nr 5, s. 1859-1869Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We examined the reproductive success of 48 adult brown trout (Salmo trutta L.) which were allowed to reproduce in a stream that was controlled for the absence of other trout. Parentage analyses based on 11 microsatellites permitted us to infer reproductive success and mate choice preferences in situ. We found that pairs with intermediate major histocompatibility complex (MHC) dissimilarity mated more often than expected by chance. It appears that female choice was the driving force behind this observation because, compared with other individuals, males with intermediate MHC dissimilarity produced a larger proportion of offspring, whereas female reproductive output did not show this pattern. Hence, rather than seeking mates with maximal MHC dissimilarity, as found in several species, brown trout seemed to prefer mates of intermediate MHC difference, thus supporting an optimality-based model for MHC-dependent mate choice.

  • 219. Fox, K L
    et al.
    Yildirim, Håkan H
    Södertörns högskola, Institutionen för livsvetenskaper.
    Deadman, M E
    Schweda, Elke K H
    Södertörns högskola, Institutionen för livsvetenskaper.
    Moxon, E R
    Hood, D W
    Novel lipopolysaccharide biosynthetic genes containing tetranucleotide repeats in Haemophilus influenzae, identification of a gene for adding O-acetyl groups2005Inngår i: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 58, nr 1, s. 207-216Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Many of the genes for lipopolysaccharide (LPS) biosynthesis in Haemophilus influenzae are phase variable. The mechanism of this variable expression involves slippage of tetranucleotide repeats located within the reading frame of these genes. Based on this, we hypothesized that tetranucleotide repeat sequences might be used to identify as yet unrecognized LPS biosynthetic genes. Synthetic oligonucleotides (20 bases), representing all previously reported LPS-related tetranucleotide repeat sequences in H. influenzae, were used to probe a collection of 25 genetically and epidemiologically diverse strains of non-typeable H. influenzae. A novel gene identified through this strategy was a homologue of oafA, a putative O-antigen LPS acetylase of Salmonella typhimurium, that was present in all 25 non-typeable H. influenzae, 19 of which contained multiple copies of the tetranucleotide 5'-GCAA. Using lacZ fusions, we showed that these tetranucleotide repeats could mediate phase variation of this gene. Structural analysis of LPS showed that a major site of acetylation was the distal heptose (HepIII) of the LPS inner-core. An oafA deletion mutant showed absence of O-acetylation of HepIII. When compared with wild type, oafA mutants displayed increased susceptibility to complement-mediated killing by human serum, evidence that O-acetylation of LPS facilitates resistance to host immune clearance mechanisms. These results provide genetic and structural evidence that H. influenzae oafA is required for phase variable O-acetylation of LPS and functional evidence to support the role of O-acetylation of LPS in pathogenesis.

  • 220. Fox, Kate L.
    et al.
    Li, Jianjun
    Schweda, Elke K. H.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Vitiazeva, Arvara
    Makepeace, Katherine
    Jennings, Michael P.
    Moxon, E. Richard
    Hood, Derek W.
    Duplicate copies of lic1 direct the addition of multiple phosphocholine residues in the lipopolysaccharide of Haemophilus influenzae2008Inngår i: Infection and Immunity, ISSN 0019-9567, E-ISSN 1098-5522, Vol. 76, nr 2, s. 588-600Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The genes of the lic1 operon (lic1A to lic1D) are responsible for incorporation of phosphocholine (PCho) into the lipopolysaccharide (LPS) of Haemophilus influenzae. PCho plays a multifaceted role in the commensal and pathogenic lifestyles of a range of mucosal pathogens, including H. influenzae. Structural studies of the LPS of nontypeable H. influenzae (NTHI) have revealed that PCho can be linked to a hexose on any one of the oligosaccharide chain extensions from the conserved inner core triheptosyl backbone. In a collection of NTHI strains we found several strains in which there were two distinct but variant lic1D DNA sequences, genes predicted to encode the transferase responsible for directing the addition of PCho to LPS. The same isolates were also found to express concomitantly two PCho residues at distinct positions in their LPS. In one such NTHI isolate, isolate 1158, structural analysis of LPS from lic1 mutants confirmed that each of the two copies of lic1D directs the addition of PCho to a distinct location on the LPS. One position for PCho addition is a novel heptose, which is part of the oligosaccharide extension from the proximal heptose of the LPS inner core. Modification of the LPS by addition of two PCho residues resulted in increased binding of C-reactive protein and had consequential effects on the resistance of the organism to the killing effects of normal human serum compared to the effects of glycoforms containing one or no PCho. When bound, C-reactive protein leads to complement-mediated killing, indicating the potential biological significance of multiple PCho residues.

  • 221.
    Friberg, Olivia
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik.
    Ensjön under 200 år: En stratigrafisk studie om vad bevarade kiselalger i sediment kan berätta om klimat och markanvändning2021Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    Since 1750, human emissions of greenhouse gases have created a temperature increase, affecting the whole world. Diatoms, single-celled microscopic algae that lives in waters all over the world, have different environmental preferences such as the water depth at which the thrive, salinity, nutrients, pH-values and more. Diatoms also responds quickly to changing circumstances, which makes the suitable as environmental indicators. The purpose of the study is to investigate how the abundance and composition of diatoms has changed during the last 200 years in lake Ensjön, located just south of Norrköping, and to relate those changes both to climate change and known events and environmental factors in the area. 

    The survey is conducted by subsampling sediment cores from which each diatom sample was prepared in accordance with the scheme of Battarbee (1984). The diatoms in the samples were counted under a microscope and the results were analyzed and related to the Cyclotella-Aulacoseira-Fragilaria-theory (CAF) and documented historical events in the local environment. The result of the analysis shows that the composition and abundance of diatoms has changed during the last 200 years, and that this change is due to both climate change (temperature and precipitation increase) and the land-use history of Ensjön. The cahnges in composition of Aulacoseira spp. and Cyclotella spp., where Aulacoseira spp. is expected to decrease, and Cyclotella spp. is expected to increase with a rising temperature, match the CAF-theory for the most part. The change in composition also coincides with several documented environmental factors in the area, especially the change in use of fertilizers and herbicides in agriculture. 

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  • 222. Funk, C
    et al.
    Wiklund, R
    Schröder, Wolfgang P
    Södertörns högskola, Avdelning Naturvetenskap.
    Jansson, C
    D1' centers are less efficient than normal photosystem II centers2001Inngår i: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 505, nr 1, s. 113-117Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    One prominent difference between the photosystem II (PSII) reaction center protein D1 ' in Synechocystis 6803 and normal D1 is the replacement of Phe-186 in D1 with leucine in D1 '. Mutants of Synechocystis 6803 producing only D1 ', or containing engineered D1 proteins with Phe-186 substitutions, were analyzed by 77 K fluorescence emission spectra, chlorophyll a fluorescence induction yield and decay kinetics, and flash-induced oxygen evolution. Compared to D1-containing PSII centers, D1 ' centers exhibited a 50% reduction in variable chlorophyll a fluorescence yield, while the flash-induced O-2 evolution pattern was unaffected. In the F186 mutants, both the P680(+)/Q(A)(-) recombination and O-2 oscillation pattern were noticeably perturbed.

  • 223.
    Fürtenbach, Karin
    Södertörns högskola, Institutionen för livsvetenskaper.
    Characterization of two Protein Disulfide Oxidoreductases from Thermophilic Organisms Pyrococcus furiosus and Aquifex aeolicus: Characterization of two Protein Disulfide Oxidoreductases2008Independent thesis Basic level (professional degree), 20 poäng / 30 hpOppgave
    Abstract [en]

    Members of the thioredoxin superfamily of proteins catalyze disulfide bond reduction and oxidation using the active site C-X-X-C sequence. In hyperthermophilic organisms, cysteine side chains were expected in low abundance since they were not believed to endure the high temperatures under which they grow. Recently it has been found that disulfide bonds in hyperthermophiles are more frequent, the higher the growth temperature of the organism. This is perhaps used as an adaptation to high temperature in order to stabilize proteins under harsh conditions. A protein with sequence and structural similarities to mesophilic members of the thioredoxin superfamily, called protein disulfide oxidoreductases (PDO), has been found in the genomes of recently sequenced hyperthermophilic genomes. In this study PDOs from the hyperthermophiles Aquifex aeolicus (AaPDO) and Pyrococcus furiosus (PfPDO) have been investigated. The molecular weight is about 26 kDa and their structures are comprised of two homologous thioredoxin folds, referred to as the N-unit and the C-unit, each containing a C-X-X-C motif. The sequence identity between the two units and the two proteins is low, but they are still structurally very similar. The function of these proteins in vivo is unknown. As a first step in characterizing the activity of these proteins, the redox characteristics of these domains will be investigated. During this project, the genes for AaPDO and PfPDO have been cloned into overexpression vectors, expressed in E. coli and purified to homogeneity. To allow for individual study of the activities of two units, mutated proteins were prepared in which the cysteine residues of the N-unit (AaPDOnm and PfPDOnm) and of the C-unit (AaPDOcm and PfPDOcm) and purified. Circular dichroism spectra recorded of the wild type and mutants indicate that all purified proteins are folded and that the N- and C-unit active site mutants are structurally similar to the corresponding wild type proteins.

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  • 224.
    Gallio, Marco
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap. Karolinska Institutet.
    The Rhomboid family of intramembrane proteases, conserved regulators of cell communication2004Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The development of multicellular organisms relies heavily on cell communication. Cells send and receive complex sets of signals, harmonising their growth and differentiation with that of other, often distant, cell populations. In animals, the Epidermal Growth Factor Receptor (EGFR) is an important mediator of cell communication. EGFR activation regulates various developmental events in nematodes, insects and vertebrates. In addition, mutations in human EGFRs have been associated with a number of cancers. In Drosophila, a key event triggering EGFR signalling is the regulated release of the extracellular portion of EGFR ligands. Rhomboid (Rho), an unusual polytopic protease, cleaves the transmembrane, inactive ligand precursor into an active, soluble form. Both the target sequence and Rho s catalytic site are embedded within the membrane bilayer and for this reason the reaction has been described as regulated intramembrane proteolysis. The work presented in this thesis begins with the characterisation of a classical fly mutation, roughoid (ru). Our results indicate that ru acts as a novel, positive regulator of EGFR signalling during eye development in Drosophila. ru was subsequently identified as rhomboid-3, one of seven rhomboid related genes encoded in the fly genome. Unexpectedly, we found that sequences related to Rhomboid are also common in unicellular organisms. A single microbial Rho has been previously studied, the aarA gene from the human pathogen Providencia stuartii. Strikingly, AarA appears to have a corresponding function to that of the Drosophila Rho: it is necessary for the release of a peptide-signal, which mediates cell communication in P. stuartii. AarA was indeed capable of substituting for the fly Rho in vivo. Vice versa, the fly Rho-1 restored the ability of aarA mutant bacteria to produce the extracellular signal mediating cell communication. These results suggest that Rho-mediated proteolysis might represent a very ancient mechanism for cell communication. The Drosophila genome contains seven Rhomboids. We began to investigate the possibility of additional substrates by analyzing the respiratory system phenotype observed in ru/rho-3 mutant embryos. During embryogenesis, specialised tracheal branches target and invade the ventral nerve cord, part of the central nervous system (CNS). In ru/rho-3 mutants, these branches are misrouted, and inappropriately cross the CNS midline. Also in this context Rho-3 functions to activate an EGFR ligand. Yet, the results reveal an unusual role for the pathway in the repulsion of migrating epithelial cells. EGFR ligands act as chemoattractants for a variety of cells in vivo and in vitro, including tumors. Our results provide a proof of principle that the EGFR can also mediate repulsion from the signal source.

  • 225.
    Gallio, Marco
    et al.
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap. Stockholm University / Karolinska Institute.
    Englund, C
    Stockholm University / Umeå University.
    Kylsten, Per
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap.
    Samakovlis, C
    Stockholm University.
    Rhomboid 3 orchestrates Slit-independent repulsion of tracheal branches at the CNS midline2004Inngår i: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 131, nr 15, s. 3605-3614Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    EGF-receptor ligands act as chemoattractants for migrating epithelial cells during organogenesis and wound healing. We present evidence that Rhomboid 3/EGF signalling, which originates from the midline of the Drosophila ventral nerve cord, repels tracheal ganglionic branches and prevents them from crossing it. rho3 acts independently from the main midline repellent Slit, and originates from a different sub-population of midline cells: the VUM neurons. Expression of dominant-negative Egfr or Ras induces midline crosses, whereas activation of the Egfr or Ras in the leading cell of the ganglionic branch can induce premature turns away from the midline. This suggests that the level of Egfr intracellular signalling, rather than the asymmetric activation of the receptor on the cell surface, is an important determinant in ganglionic branch repulsion. We propose that Egfr activation provides a necessary switch for the interpretation of a yet unknown repellent function of the midline.

  • 226.
    Gallio, Marco
    et al.
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Kylsten, Per
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Providencia may help find a function for a novel, widespread protein family2000Inngår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 10, nr 19, s. R693-R694Artikkel i tidsskrift (Fagfellevurdert)
  • 227.
    Gallio, Marco
    et al.
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap. Karolinska Institutet.
    Kylsten, Per
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap.
    The roughoid locus identifies a novel function involved in epidermal growth factor receptor signalling in DrosophilaManuskript (preprint) (Annet vitenskapelig)
  • 228. Gao, L L
    et al.
    Knogge, W
    Delp, Gabriele
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap.
    Smith, F A
    Smith, S E
    Expression patterns of defense-related genes in different types of arbuscular mycorrhizal development in wild-type and mycorrhiza-defective mutant tomato2004Inngår i: Molecular Plant-Microbe Interactions, ISSN 0894-0282, E-ISSN 1943-7706, Vol. 17, nr 10, s. 1103-1113Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The expression of defense-related genes was analyzed in the interactions of six arbuscular mycorrhizal (AM) fungi with the roots of wild-type tomato (Lycopersicon esculentum Mill.) cv. 76R and of the near-isogenic mycorrhiza-defective mutant rmc. Depending on the fungal species, wild-type tomato forms both major morphological AM types, Arum and Paris. The mutant rmc blocks the penetration of the root surface or invasion of the root cortex by most species of AM fungi, but one fungus has been shown to develop normal mycorrhizas. In the wild-type tomato, accumulation of mRNA representing a number of defense-related genes was low in Arum-type interactions, consistent with findings for this AM morphotype in other plant species. In contrast, Paris-type colonization, particularly by members of the family Gigasporaceae, was accompanied by a substantial transient increase in expression of some defense-related genes. However, the extent of root colonization did not differ significantly in the two wild-type AM morphotypes, suggesting that accumulation of defense gene products per se does not limit mycorrhiza development. In the mutant, interactions in which the fungus failed to penetrate the root lacked significant accumulation of defense gene mRNAs. However, phenotypes in which the fungus penetrated epidermal or hypodermal cells were associated with an enhanced and more prolonged gene expression. These results are discussed in relation to the mechanisms that may underlie the specificity of the interactions between AM fungi and the rmc mutant.

  • 229. Gardeström, Johanna
    et al.
    Dahl, Ulrika
    Kotsalainen, Ola
    Maxson, Anders
    Elfwing, Tina
    Grahn, Mats
    Södertörns högskola, Institutionen för livsvetenskaper.
    Bengtsson, Bengt-Erik
    Breitholtz, Magnus
    Evidence of population genetic effects of long-term exposure to contaminated sediments - A multi-endpoint study with copepods2008Inngår i: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 86, nr 3, s. 426-436Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In the environment, pollution generally acts over long time scales and exerts exposure of multiple toxicants on the organisms living there. Recent findings show that pollution can alter the genetics of populations. However, few of these studies have focused on long-term exposure of mixtures of substances. The relatively short generation time (ca. 4-5 weeks in sediments) of the harpacticoid copepod Attheyella crassa makes it suitable for multi generational exposure studies. Here, A. crassa copepods were exposed for 60 and 120 days to naturally contaminated sediments (i.e., Svindersviken and Trosa; each in a concentration series including 50% contaminated sediment mixed with 50% control sediment and 100% contaminated sediment), and for 120 days to control sediment spiked with copper. We assayed changes in FST (fixation index), which indicates if there is any population subdivision (i.e., structure) between the samples, expected heterozygosity, percent polymorphic loci, as well as abundance. There was a significant decrease in total abundance after 60 days in both of the 100% naturally contaminated sediments. This abundance bottleneck recovered in the Trosa treatment after 120 days but not in the Svindersviken treatment. After 120 days, there were fewer males in the 100% naturally contaminated sediments compared to the control, possibly caused by smaller size of males resulting in higher surface: body volume ratio in contact with toxic chemicals. In the copper treatment there was a significant decrease in genetic diversity after 120 days, although abundance remained unchanged. Neither of the naturally contaminated sediments (50 and 100%) affected genetic diversity after 120 days but they all had high within treatment FST values, with highest FST in both 100% treatments. This indicates differentiation between the replicates and seems to be a consequence of multi-toxicant exposure, which likely caused selective mortality against highly sensitive genotypes. We further assayed two growth-related measures, i.e., RNA content and cephalothorax length, but none of these endpoints differed between any of the treatments and the control. In conclusion, the results of the present study support the hypothesis that toxicant exposure can reduce genetic diversity and cause population differentiation. Loss of genetic diversity is of great concern since it implies reduced adaptive potential of populations in the face of future environmental change.

  • 230. Gardeström, Johanna
    et al.
    Gorokhova, Elena
    Gilek, Michael
    Södertörns högskola, Institutionen för livsvetenskaper.
    Grahn, Mats
    Södertörns högskola, Institutionen för livsvetenskaper.
    Bengtsson, Bengt-Erik
    Breitholtz, Magnus
    A multilevel approach to predict toxicity in copepod populations: Assessment of growth, genetics, and population structure2006Inngår i: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 79, nr 1, s. 41-48Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    One of the goals of environmental risk assessment (ERA) is to understand effects of toxicant exposure on individual organisms and populations. We hypothesized that toxicant exposure can reduce genetic diversity and alter genotype composition, which may ultimately lead to a reduction in the average fitness of the exposed population. To test this hypothesis, we exposed a copepod, Nitocra psammophila, to a toxic reference compound and assayed resulting alterations in genetic structure, i.e. expected heterozygosity and percent polymorphic loci, as well as other population- and fitness-related measures, i.e. population abundance, demographic structure and juvenile growth. The copepods were exposed to 0.11-1.1 mu g of the pentabromo-substituted diphenyl ether (BDE-47) mg(-1) freeze-dried algae for 24 days (i.e. > 1 generation). There was no significant decline in total population abundance. However, there were significant alterations in population structure, manifested as diminished proportion of nauplii and increased proportion of copepodites. In addition, individual RNA content in copepodites decreased significantly in exposed individuals, indicating declined growth. Finally, in the exposed populations, heterozygosity was lower and genotype composition was altered compared to the controls. These results therefore confirm the hypothesized reduction in overall genetic variability resulting from toxicant exposure. Multilevel approaches, such as the one used in the present study, may help unravel subtle effects on the population level, thus increasing the predictive capacity of future ERA.

  • 231.
    Garrison, Julie A.
    et al.
    Stockholm University, Sweden.
    Motwani, Nisha H.
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap. Stockholm University, Sweden.
    Broman, Elias
    Stockholm University, Sweden.
    Nascimento, Francisco J. A.
    Stockholm University, Sweden.
    Molecular diet analysis enables detection of diatom and cyanobacteria DNA in the gut of Macoma balthica2022Inngår i: PLOS ONE, E-ISSN 1932-6203, Vol. 17, nr 11, artikkel-id e0278070Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Detritivores are essential to nutrient cycling, but are often neglected in trophic networks, due to difficulties with determining their diet. DNA analysis of gut contents shows promise of trophic link discrimination, but many unknown factors limit its usefulness. For example, DNA can be rapidly broken down, especially by digestion processes, and DNA provides only a snapshot of the gut contents at a specific time. Few studies have been performed on the length of time that prey DNA can be detected in consumer guts, and none so far using benthic detritivores. Eutrophication, along with climate change, is altering the phytoplankton communities in aquatic ecosystems, on which benthic detritivores in aphotic soft sediments depend. Nutrient-poor cyanobacteria blooms are increasing in frequency, duration, and magnitude in many water bodies, while nutrient-rich diatom spring blooms are shrinking in duration and magnitude, creating potential changes in diet of benthic detritivores. We performed an experiment to identify the taxonomy and quantify the abundance of phytoplankton DNA fragments on bivalve gut contents, and how long these fragments can be detected after consumption in the Baltic Sea clam Macoma balthica. Two common species of phytoplankton (the cyanobacteria Nodularia spumigena or the diatom Skeletonema marinoi) were fed to M. balthica from two regions (from the northern and southern Stockholm archipelago). After removing the food source, M. balthica gut contents were sampled every 24 hours for seven days to determine the number of 23S rRNA phytoplankton DNA copies and when the phytoplankton DNA could no longer be detected by quantitative PCR. We found no differences in diatom 18S rRNA gene fragments of the clams by region, but the southern clams showed significantly more cyanobacteria 16S rRNA gene fragments in their guts than the northern clams. Interestingly, the cyanobacteria and diatom DNA fragments were still detectable by qPCR in the guts of M. balthica one week after removal from its food source. However, DNA metabarcoding of the 23S rRNA phytoplankton gene found in the clam guts showed that added food (i.e. N. spumigena and S. marinoi) did not make up a majority of the detected diet. Our results suggest that these detritivorous clams therefore do not react as quickly as previously thought to fresh organic matter inputs, with other phytoplankton than large diatoms and cyanobacteria constituting the majority of their diet. This experiment demonstrates the viability of using molecular methods to determine feeding of detritivores, but further studies investigating how prey DNA signals can change over time in benthic detritivores will be needed before this method can be widely applicable to both models of ecological functions and conservation policy.

  • 232.
    Gatsinzi, Tom
    et al.
    Stockholm University.
    Ramberg, Veronica
    Stockholm University.
    Figueroa, Ricardo
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Iverfeldt, Kerstin
    Stockholm University.
    Hallberg, Einar
    Södertörns högskola, Institutionen för livsvetenskaper, Molekylärbiologi.
    Localized caspase sensors for live cell imaging of amyloid-β induced apoptosis2010Inngår i: Alzheimer's & Dementia: Journal of the Alzheimer's Association, ISSN 1552-5260, E-ISSN 1552-5279, Vol. 6, nr 4, Supplement, s. S259-S260Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    Background: Apoptosis is an evolutionary conserved cellular process important for normal development, maintenance of tissue homeostasis and an effective immune system. Cysteine-aspartic proteases, or caspases, are the major mediators of apoptosis, triggering processes which lead to cellular disruption. Dysregulation of apoptotic signaling has been shown to be involved in several pathological conditions, like cancer and degenerative disorders. Alzheimer's disease (AD) is the most common form of dementia involving massive cell death of neurons. However, the cause of AD at the present time is still unknown, although, amyloid-β (Aβ) peptide has been suggested to be the triggering factor. 

    Methods:In order to detect localized caspase activation in live cells we designed sensors for caspase-3, -6 and -9 utilizing fluorescence resonance energy transfer (FRET). The FRET-ing sensor molecules, consisting of CFP and YFP separated by a linker containing a specific caspase cleavage motif, were designed to signal caspase cleavage by the loss of FRET. Differentiated SH-SY5Y cells were used as a model system for neurodegeneration. The cells were treated with oligomeric Aβ42 or staurosporine as a positive control of apoptosis. The cleavage of the sensors during induced apoptosis was verified by western blot analysis. Time-lapse FRET microscopy was used to monitor caspase activity in different parts of the cells. 

    Results: In our study, when the cells were exposed to staurosporine we were able to detect local activity of caspase-6 initially in the soma of the cells, whereas caspase-6 activity in the neurites was delayed. Furthermore, our study shows that oligomeric Aβ42 is able to activate caspase-3, -6 and -9. In contrast to staurosporine, in Aβ42 treated cells loss of FRET occurred globally indicating that caspase was activated simultaneously in soma and axons. 

    Conclusions: In conclusion, we show that our caspase-sensors are able to detect local caspase activity in vitro. We also show that exposure to oligomeric Aβ42 results in global activation of caspases in differentiated SH-SY5Y cells.

  • 233.
    Georgiev, Alexander
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper, Biologi. Stockholm University.
    Leipus, Arunas
    Umeå University.
    Olsson, Ida
    Södertörns högskola, Institutionen för livsvetenskaper, Biologi.
    Berrez, Jean-Marc
    Södertörns högskola, Institutionen för livsvetenskaper, Biologi.
    Mutvei, Ann
    Södertörns högskola, Institutionen för livsvetenskaper, Biologi.
    Characterization of MYR1, a dosage suppressor of YPT6 and RIC1 deficient mutants2008Inngår i: Current Genetics, ISSN 0172-8083, E-ISSN 1432-0983, Vol. 53, nr 4, s. 235-247Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Membrane traffic is tightly regulated and the Rab protein family of small GTPases plays a central role in this regulation. One member of this family is the Saccharomyces cerevisae protein Ypt6. To search for new genes interacting with Ypt6-related pathways, we performed a genetic screen for high copy suppressors of ypt6 Delta temperature sensitivity at 35 degrees C. Among the suppressors, MYR1 was also able to suppress the temperature sensitive mutant lacking Ric1, a subunit of the Ypt6 guanine exchanging factor complex Ric1/Rgp1. Myr1 is characterized by a coiled coil region and a GYF domain, a protein module binding proline-rich sequences. Myr1 is able to bind membranes but is also associated with larger structures insoluble in Triton X-100. By immunofluorescence, Myr1 shows a network-like pattern as well as small foci. Overexpression of Myr1 influences nuclear envelope morphology and high levels are lethal. This lethality is rescued when the N-terminal region, containing the GYF domain, is deleted. The transcription profile of a myr1 Delta strain shows effects on genes involved in nuclear migration, Ras signalling and transcription. Taken together, these results suggest that Myr1 is a novel factor linked to the secretory pathway and important cellular regulatory mechanisms.

  • 234. Gerremo, Inge
    et al.
    Wramner, Per
    Södertörns högskola, Institutionen för livsvetenskaper, Coastal Management Research Center (COMREC).
    Diskussion och vägen framåt2006Inngår i: Jordbruk, handel och utveckling: mot ökad samstämmighet, Stockholm: Kungl. Skogs- och lantbruksakademien , 2006, s. 167-183Kapittel i bok, del av antologi (Annet (populærvitenskap, debatt, mm))
  • 235.
    Gilek, Michael
    et al.
    Stockholms universitet.
    Tedengren, Michael
    Kautsky, Nils
    Physiological performance and general histology of the blue mussle, Mytilus Edulis L, from the Baltic and North seas1992Inngår i: Netherlands Journal of Sea Research, ISSN 0077-7579, Vol. 30, s. 11-21Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A physiological approach has been proposed for studying the ecological consequences of diseases and parasitism in bivalve molluscs. We investigated effects of some naturally occurring non-lethal parasites and histological changes in the blue mussel, Mytilus edulis L., on some commonly used bivalve condition indices, viz the oxygen:nitrogen ratio, the scope for growth and the body condition index. We found no correlation between these physiological condition indices, which implies that an individual can be classified as in 'good condition' according to e.g. the O:N ratio and the body condition index, while at the same time this mussel may have a low scope for growth indicating a stressed status. This is probably because the O:N ratio, the scope for growth and the body condition index integrate metabolic processes over different periods of time. No general deleterious effects on these condition indices could be detected either due to parasitic infestation or general histological changes. Hence, it was not possible to translate detrimental effects of histological conditions directly into energy equivalents.

  • 236. Glaser, Elzbieta
    et al.
    Eriksson, AnnaCarin
    Sjöling, Sara
    Bifunctional role of the bc1 complex in plants Mitochondrial bc1 complex catalyses both electron transport and protein processing1994Inngår i: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 346, nr 1, s. 83-87Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Abstract Nuclear  encoded  mitochondrial  precursor  proteins  are  cleaved  to  mature  size products  by the  general  mitochondrial  processing  peptidase  (MPP). In  contrast  to  non-plant  sources  where  MPP  is  a matrix  enzyme,  the  plant  mitochondrial  MPP  is localised  in  the  inner  membrane  and  constitutes an  integral  part  of  the  bc,  complex  of  the  respiratory  chain.  Core  proteins  of  the  complex  are  immunologically  related  and  show  high  sequence similarity  to the MPP  subunits  from  non-plant  sources.  The bc,  complex  in plants  is thus  bifunctional,  being  involved  both  in respiration  and  in protein processing

  • 237. Glaser, Elzbieta
    et al.
    Sjöling, Sara
    Szigyarto, Cristina
    Eriksson, AnnaCarin
    Plant mitochondrial protein import: precursor processing is catalysed by the integrated mitochondrial processing peptidase (MPP)/bc1 complex and degradation by the ATP-dependent proteinase1996Inngår i: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1275, nr 1-2, s. 33-37Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Several hundreds of mitochondrial proteins are nuclear encoded and are synthesised on cytosolic polyribosomes as precursor proteins. Most of these precursors contain an N-terminal extension called presequence which functions as targeting signal and which is cleaved off after import. Despite the fact that there are no sequence similarities and no consensus for the cleavage site in mitochondrial presequences, cleavage of almost all presequences is catalysed by a single, highly specific metalloendopeptidase, called general mitochondrial processing peptidase (MPP). MPP in plants is integrated into the bc1, complex of the respiratory chain and both subunits, α-MPP and β-MPP, are identical to the core proteins of the complex. Despite the fact that the bc1 complex in plants is bifunctional, catalysing bothelectron transport and protein processing, these two functions are distinct. MPP belongs to the Pitrilysin family of peptidases, characterised by a zinc binding motif, HXXEH74–76E, involved in catalysis. Both the membrane-bound integrated MPP/bc1 complex of plants and the soluble mammalian MPP recognise similar higher-order structural elements upstream from the cleavage site that are important for processing. The secondary structure with flexibility and stabilising elements, hydrofobicity, charge and length seem to influence the interaction with MPP. The newly imported non-assembled precursor inside mitochondria is degraded by a proteinase that is distinct from MPP or any other previously characterised proteinases, a novel ATP-dependent, membrane-associated serine-type proteinase.

  • 238. Glaser, Elzbieta
    et al.
    Sjöling, Sara
    Södertörns högskola, Avdelning Naturvetenskap.
    Tanudji, Marcel
    Södertörns högskola, Avdelning Naturvetenskap.
    Whelan, James
    Mitochondrial protein import in plants: Signals, Sorting, Targeting, Processing and Regulation1998Inngår i: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 38, nr 1-2, s. 311-338Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Mitochondrial biogenesis requires a coordinated expression of both the nuclear and the organellar genomes and specific intracellular protein trafficking, processing and assembly machinery. Mostmitochondrial proteins are synthesised as precursor proteins containing an N-terminal extension which functions as a targeting signal, which is proteolytically cleaved off after import into mitochondria. We review our present knowledge on components and mechanisms involved in the mitochondrial proteinimport process in plants. This encompasses properties of targeting peptides, sorting of precursor proteinsbetween mitochondria and chloroplasts, signal recognition, mechanism of translocation across the mitochondrial membranes and the role of cytosolic and organellar molecular chaperones in this process. The mitochondrial protein processing in plants is catalysed by the mitochondrial processing peptidase (MPP), which in contrast to other sources, is integrated into the bc1 complex of the respiratory chain. This is the most studied component of the plant import machinery characterised to date. What are the biochemical consequences of the integration of the MPP into an oligomeric protein complex and how are several hundred presequences of precursor proteins with no sequence similarities and no consensus for cleavage, specifically cleaved off by MPP? Finally we will address the emerging area of the control of protein import into mitochondria.

  • 239. Glinwood, R.
    et al.
    Gradin, Therese
    Karpinska, Barbara
    Södertörns högskola, Institutionen för livsvetenskaper.
    Ahmed, E.
    Jonsson, Lisbeth
    Södertörns högskola, Institutionen för livsvetenskaper.
    Ninkovic, V.
    Aphid acceptance of barley exposed to volatile phytochemicals differs between plants exposed in daylight and darkness2007Inngår i: Plant Signalling & Behavior, ISSN 1559-2316, E-ISSN 1559-2324, Vol. 2, nr 5, s. 321-326Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    It is well known that volatile cues from damaged plants may induce resistance in neighboring plants. Much less is known about the effects of volatile interaction between undamaged plants. In this study, barley plants, Hordeum vulgare cv. Kara, were exposed to volatiles from undamaged plants of barley cv. Alva or thistle Cirsium vulgare, and to the volatile phytochemicals, methyl salicylate or methyl jasmonate. Exposures were made either during natural daylight or darkness. Acceptance of exposed plants by the aphid Rhopalosiphum padi was assessed, as well as the expression of putative marker genes for the different treatments. Aphid acceptance of plants exposed to either barley or C. vulgare was significantly reduced, and an effect of the volatiles from undamaged plants was confirmed by the induction of pathogenesis-related protein, PR1a in exposed plants. However the effect on aphid acceptance was seen only when plants were exposed during darkness, whereas PR1a was induced only after treatment during daylight. Aphid acceptance of plants exposed to either methyl salicylate or methyl jasmonate was significantly reduced, but only when plants were exposed to the chemicals during daylight. AOS2 (allene oxide synthase) was induced by methyl jasmonate and BCI-4 (barley chemical inducible gene-4) by methyl salicylate in both daylight and darkness. It is concluded that (a) the effects on aphids of exposing barley to volatile phytochemicals was influenced by the presence or absence of light and (b) the response of barley to methyl salicylate/methyl jasmonate and to volatiles from undamaged plants differed at the gene and herbivore level.

  • 240.
    Goodkin, K.
    et al.
    University of Miami, Miami, FL, United States.
    Heckman, T.
    Ohio University, Athens, OH, United States.
    Siegel, K.
    Columbia University, New York, NY, United States.
    Linsk, M.
    University of Illinois, Chicago, IL, United States.
    Khamis, I.
    University of Miami, Miami, FL, United States.
    Lee, D.
    University of Miami, Miami, FL, United States.
    Lecusay, Robert
    University of Miami, Miami, FL, United States.
    Poindexter, C. C.
    University of Illinois, Chicago, IL, United States.
    Mason, S. J.
    University of Illinois, Chicago, IL, United States.
    Suarez, P.
    University of Miami, Miami, FL, United States.
    Eisdorfer, C.
    University of Miami, Miami, FL, United States.
    "Putting a face" on HIV infection/AIDS in older adults: A psychosocial context2003Inngår i: Journal of Acquired Immune Deficiency Syndromes, ISSN 1525-4135, E-ISSN 1944-7884, Vol. 33, s. S171-S184Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Older HIV-1-seropositive individuals largely have not been investigated with respect to their psychosocial characteristics. In this article, the authors review research reported to date regarding the psychosocial context of this growing subgroup of HIV-1-infected individuals. Specifically, the authors consider the characteristics of mood state, life stressor burden, social support network, and coping strategies that individuals older than 50 years are more likely to adopt in adjusting to HIV-1 infection. The authors also separately consider issues of caregiving burden. Data supporting a theoretically based stressor-support-coping model are presented and related to targeting psychotherapeutic interventions for this age group.

  • 241. Gorokhova, Elena
    et al.
    Edlund, Anna
    Södertörns högskola, Institutionen för livsvetenskaper.
    Hajdu, Susanna
    Zhivotova, Elena N.
    Nucleic acid levels in copepods: dynamic response to phytoplankton blooms in the northern Baltic proper2007Inngår i: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 349, s. 213-225Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We examined changes in nucleic acids and concomitant population development of the copepods Acartia bifilosa and Eurytemora affinis in relation to the progress of the phytoplankton spring bloom in the northern Baltic proper. Individual RNA and DNA concentrations and their ratios in female copepods as well as copepod abundance and population structure were analyzed in 2 coastal areas that differed in the degree of eutrophication and phytoplankton development. During the study period (February to June 2002), bloom conditions were evident, with chlorophyll (chl) a values being 42% higher in the eutrophic area than in the reference area. In both areas, diatoms dominated; in the reference area, they were replaced by dinoflagellates toward the end of the bloom. Copepod RNA-DNA concentrations increased rapidly at the onset of the bloom and gradually decreased thereafter. Moreover, in the eutrophic area, both copepods had higher RNA content and RNA:DNA ratios throughout the study period, suggesting higher productivity in this area. In both species, we found positive correlations between RNA-based indices and chl a. Thus, as suggested by RNA dynamics, growth rates of A. bifilosa and E. affinis appear to respond rapidly to both temporal variation in spring phytoplankton stock and spatial variation due to the magnitude of the bloom. In addition, we found that species-specific RNA dynamics and RNA-chl a relationships differed between species, indicating possible differences in feeding preferences and growth potential.

  • 242.
    Goulas, Estelle
    et al.
    Umeå universitet / Université des Sciences et Technologies de Lille 1, France.
    Schubert, Maria
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Kieselbach, Thomas
    Umeå universitet.
    Kleczkowski, Leszek A.
    Umeå universitet.
    Gardeström, Per
    Umeå universitet.
    Schröder, Wolfgang P
    Umeå universitet.
    Hurry, Vaughan
    Umeå universitet.
    The chloroplast lumen and stromal proteomes of Arabidopsis thaliana show differential sensitivity to short- and long-term exposure to low temperature2006Inngår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 47, nr 5, s. 720-734Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cold acclimation and over-wintering by herbaceous plants are energetically expensive and are dependent on functional plastid metabolism. To understand how the stroma and the lumen proteomes adapt to low temperatures, we have taken a proteomic approach (difference gel electrophoresis) to identify proteins that changed in abundance in Arabidopsis chloroplasts during cold shock (1 day), and short- (10 days) and long-term (40 days) acclimation to 5 degrees C. We show that cold shock (1 day) results in minimal change in the plastid proteomes, while short-term (10 days) acclimation results in major changes in the stromal but few changes in the lumen proteome. Long-term acclimation (40 days) results in modulation of the proteomes of both compartments, with new proteins appearing in the lumen and further modulations in protein abundance occurring in the stroma. We identify 43 differentially displayed proteins that participate in photosynthesis, other plastid metabolic functions, hormone biosynthesis and stress sensing and signal transduction. These findings not only provide new insights into the cold response and acclimation of Arabidopsis, but also demonstrate the importance of studying changes in protein abundance within the relevant cellular compartment.

  • 243.
    Grahn, Mats
    Södertörns högskola, Avdelning Naturvetenskap.
    MHC genotype and ornamentation2000Inngår i: Animal signals: signalling and signal design in animal communication / [ed] Yngve Espmark, Trond Amundsen, Gunilla Rosenqvist, Trondheim: Tapir , 2000, s. 421-436Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 244.
    Grahn, Mats
    Södertörns högskola, Institutionen för kemi, biologi, geografi och miljövetenskap.
    Ny mat och gamla gener2004Inngår i: Forskare klargör myter om maten / [ed] Birgitta Johansson, Stockholm: Formas , 2004Kapittel i bok, del av antologi (Annet (populærvitenskap, debatt, mm))
  • 245.
    Grahn, Mats
    Södertörns högskola, Avdelning Naturvetenskap.
    Varför evolutionär medicin: en förklaringsmodell för sjukdom2001Inngår i: Tidsrkiften Medikament, ISSN 1402-3881, Vol. 5, s. 28-32Artikkel i tidsskrift (Annet (populærvitenskap, debatt, mm))
  • 246. Grahn, Mats
    et al.
    Langefors, Åsa
    von Schantz, Torbjörn
    The importance of mate choice in improving viability in captive populations1998Inngår i: Behavioural Ecology and Conservation Biology / [ed] Timothy M. Caro, New York: Oxford University Press , 1998, s. 341-363Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 247. Granlund, Irene
    et al.
    Storm, Patrik
    Schubert, Maria
    Södertörns högskola, Institutionen för livsvetenskaper.
    Garcia-Cerdan, Jose G.
    Funk, Christiane
    Schröder, Wolfgang P.
    The TL29 Protein is Lumen Located, Associated with PSII and Not an Ascorbate Peroxidase2009Inngår i: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 50, nr 11, s. 1898-1910Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The TL29 protein is one of the more abundant proteins in the thylakoid lumen of plant chloroplasts. Based on its sequence homology to ascorbate peroxidases, but without any supporting biochemical evidence, TL29 was suggested to be involved in the plant defense system against reactive oxygen species and consequently renamed to APX4. Our in vivo and in vitro analyses failed to show any peroxidase activity associated with TL29; it bound neither heme nor ascorbate. Recombinant overexpressed TL29 had no ascorbate-dependent peroxidase activity, and various mutational analyses aiming to convert TL29 into an ascorbate peroxidase failed. Furthermore, in the thylakoid lumen no such activity could be associated with TL29 and, additionally, TL29 knock-out mutants did not show any decreased peroxidase activity or increased content of radical oxygen species when grown under light stress. Instead we could show that TL29 is a lumen-located component associated with PSII.

  • 248.
    Granquist, Anna
    et al.
    Södertörns högskola, Lärarutbildningen.
    Mårdfjäll, Eva
    Södertörns högskola, Lärarutbildningen.
    Jag trivs bäst när havet svallar, och måsarna ger skri: En textanalytisk studie av biologisk mångfald i läroböcker2007Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    Biological diversity is one out of four dimensions, characterizing the subject of Biology ac-cording to the school curriculum. As a concept, biological diversity had its break through at the UN environmental conference in Rio de Janeiro in 1992, where the convention about bio-logical diversity, named CBD, was signed. According to the convention, almost all the na-tions of the world have engaged themselves to preserve the national diversity of species, in-cluding the diversity of genetics and ecological systems.

    This thesis focuses the biological diversity from the perspective of school books. The aim is to find out how the biological diversity is presented in biology books for students aged 12-15 years.

    In 1994, the current Swedish secondary and high school curriculum called LPO-94 was pre-sented. The biology books used in this study were published between 1994 and 2007, all of them exist in many editions and are published by three different publishers.

    The conclusion of the study is that all the biology books that were examined have reached different levels of the development in the field of biological diversity.

    Fulltekst (pdf)
    FULLTEXT01
  • 249. Greenberg, L A
    et al.
    Hernnäs, B
    Brönmark, D
    Dahl, J
    Eklöv, A
    Olsén, K Håkan
    Södertörns högskola, Avdelning Naturvetenskap.
    Effects of kinship on growth and movements of brown trout in field enclosures2002Inngår i: Ecology of Freshwater Fish, ISSN 0906-6691, E-ISSN 1600-0633, Vol. 11, nr 4, s. 251-259Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The effect of kinship on growth and use of space by individually PIT-tagged 1+ brown trout was studied for 11 weeks in eight stream enclosures. Each enclosure consisted of two sections, separated by a region containing PIT-detecting antennae, which enabled us to measure use of sections by all individuals. Two types of sibling groups were tested, a single sibling group, F1, consisting of four individuals that were reared together in hatchery tank 'a' (F1(a)) plus four additional siblings of the same family but raised in hatchery tank 'b' (F1(b)), and a mixed sibling group, consisting of four F1(a) individuals plus four siblings from a second family, F2. Based on kin theory and earlier laboratory studies, we expected that growth of the F1(a) individuals in the single sibling group to be greater than that of F1(a) individuals in the mixed family sibling group, but instead we found just the opposite. The variance of growth did not differ between treatments. Nor was there a difference in time F1(a) individuals spent together when they were in mixed versus single sibling groups. We did find that F1(a) individuals changed habitat more frequently than F2 individuals in the mixed sibling group but less frequently than F1(b) in the single sibling groups. Thus, our predictions based on kin theory for growth and behavior of brown trout were not supported by our data, and we suggest that the role of kin recognition for the ecology of salmonids deserves further attention.

  • 250. Grimm, T
    et al.
    Teglund, Stephan
    Södertörns högskola, Avdelning Naturvetenskap. Karolinska Institutet.
    Tackels, D
    Sangiorgi, E
    Gurrieri, F
    Schwartz, C
    Toftgard, R
    Genomic organization and embryonic expression of Suppressor of Fused, a candidate gene for the split-hand/split-foot malformation type 32001Inngår i: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 505, nr 1, s. 13-17Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The genes for human and mouse Suppressor of Fused (SU(FU)/Su(Fu)) in the Hedgehog signaling pathway were characterized and found to contain 12 exons. Human SU(FU) localized on chromosome 10q24-25 between the markers D10S192 and AFM183XB12. We detected three additional SU(FU) isoforms, two of which have lost their ability to interact with the transcription factor GLI1. Expression analysis using whole mount in situ hybridization revealed strong expression of Su(Fu) in various mouse embryonic tissues. SU(FU) was considered a candidate gene for the split-hand/split-foot malformation type 3 (SHFM3). However, no alterations in the SU(FU) gene were found in SHFM3 patients.

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