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  • 51. Ekblom, Robert
    et al.
    Grahn, Mats
    Södertörn University, Avdelning Naturvetenskap.
    Höglund, Jacob
    Patterns of polymorphism in the MHC class II of a non-passerine bird, the great snipe (Gallinago media)2003In: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 54, no 10, p. 734-741Article in journal (Refereed)
    Abstract [en]

    The genomic organisation of the major histocompatibility complex (MHC) seems to vary considerably between different bird species. In order to understand this variation it is important to gather information from different species. We have, for the first time, investigated MHC class 11 polymorphism in a wader species, the great snipe (Gallinago media). Eleven alleles were found in five sequenced individuals; these come from at least three different loci, but RFLP data suggest that a larger number of genes may be present. For MHC genes, amino acid substitutions followed the, for MHC genes, general pattern of high non-synonymous substitution rates in peptide-binding regions, suggesting that the sequenced alleles may be expressed. The number of genes, lengths of introns and exon sequences of the great snipe MHC seem to be intermediate between those of chicken and passerine birds.

  • 52. Elmroth, K
    et al.
    Erkell, L J
    Nygren, Jonas
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Hultborn, R
    Radiation and hypothermia: Changes in DNA supercoiling in human diploid fibroblasts1999In: Anticancer Research, ISSN 0250-7005, E-ISSN 1791-7530, Vol. 19, no 6B, p. 5307-5311Article in journal (Refereed)
    Abstract [en]

    The influence of hypothermia (2 degrees, 15 degrees and 28 degrees C) ripen the effect of X-irradiation on chromatin from human diploid fibroblast cells (AG1518) was studied using the fluorescent halo assay. Rewinding of supercoils was inhibited in a dose-dependent manner when cells were irradiated with 4, 8 or 16 Gy. This inhibition of rewinding was reduced when cells were irradiated at subnormal temperatures compared with cells irradiated at 37 degrees C. One hour's preincubation at low temperature did nor influence rewinding. When AG1518 cells were irradiated at 37 degrees C in the presence of the radical scavenger DMSO (0.5 M), the radiation-induced damage was reduced. No additional protection of DMSO in hypothermic cells (2 degrees C) was found, possibly indicating that OH-radical-mediated effects al-e more temperature dependent. These results are similar to those recently found for the malignant MCF-7 cell line.

  • 53. Elmroth, K.
    et al.
    Nygren, Jonas
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Mårtensson, S.
    Ismail, I. H.
    Hammarsten, O.
    Cleavage of cellular DNA by calicheamicin γ12003In: DNA Repair, ISSN 1568-7864, E-ISSN 1568-7856, Vol. 2, no 4, p. 363-374Article in journal (Refereed)
    Abstract [en]

    It is assumed that the efficient antitumor activity of calicheamicin γ1 is mediated by its ability to introduce DNA double-strand breaks in cellular DNA. To test this assumption we have compared calicheamicin γ1-mediated cleavage of cellular DNA and purified plasmid DNA. Cleavage of purified plasmid DNA was not inhibited by excess tRNA or protein indicating that calicheamicin γ1 specifically targets DNA. Cleavage of plasmid DNA was not affected by incubation temperature. In contrast, cleavage of cellular DNA was 45-fold less efficient at 0°C as compared to 37° due to poor cell permeability at low temperatures. The ratio of DNA double-strand breaks (DSB) to single-stranded breaks (SSB) in cellular DNA was 1:3, close to the 1:2 ratio observed when calicheamicin γ1 cleaved purified plasmid DNA. DNA strand breaks introduced by calicheamicin γ1 were evenly distributed in the cell population as measured by the comet assay. Calicheamicin γ1-induced DSBs were repaired slowly but completely and resulted in high levels of H2AX phosphorylation and efficient cell cycle arrest. In addition, the DSB-repair deficient cell line Mo59J was hyper sensitive to calicheamicin γ. The data indicate that DSBs is the crucial damage after calicheamicin γ1 and that calicheamicin γ1-induced DSBs are recognized normally. The high DSB:SSB ratio, specificity for DNA and the even damage distribution makes calicheamicin γ1 a superior drug for studies of the DSB-response and emphasizes its usefulness in treatment of malignant disease.

  • 54. Elmroth, K.
    et al.
    Nygren, Jonas
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Stenerlöw, B.
    Hultborn, R.
    Chromatin- and temperature-dependent modulation of radiation-induced double-strand breaks2003In: International Journal of Radiation Biology, ISSN 0955-3002, E-ISSN 1362-3095, Vol. 79, no 10, p. 809-816Article in journal (Refereed)
    Abstract [en]

    Purpose: To investigate the influence of chromatin organization and scavenging capacity in relation to irradiation temperature on the induction of double-strand breaks (DSB) in structures derived from human diploid fibroblasts. Materials and methods: Agarose plugs with different chromatin structures (intact cells±wortmannin, permeabilized cells with condensed chromatin, nucleoids and DNA) were prepared and irradiated with X-rays at 2 or 37°C and lysed using two different lysis protocols (new ice-cold lysis or standard lysis at 37°C). Induction of DSB was determined by constant-field gel electrophoresis. Results: The dose-modifying factor (DMFtemp) for irradiation at 37 compared with 2°C was 0.92 in intact cells (i.e. more DSB induced at 2°C), but gradually increased to 1.5 in permeabilized cells, 2.2 in nucleoids and 2.6 in naked DNA, suggesting a role of chromatin organization for temperature modulation of DNA damage. In addition, DMFtemp was influenced by the presence of 0.1 M DMSO or 30 mM glutathione, but not by post-irradiation temperature. Conclusion: The protective effect of low temperature was correlated to the indirect effects of ionizing radiation and was not dependent on post-irradiation temperature. Reasons for a dose modifying factor <1 in intact cells are discussed.

  • 55.
    Elväng, Annelie M.
    et al.
    Stockholms universitet.
    Westerberg, Karolina
    Stockholms universitet.
    Jernberg, Cecilia
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Jansson, Janet K
    Södertörn University, Avdelning Naturvetenskap.
    Use of green fluorescent protein and luciferase biomarkers to monitor survival and activity of Arthrobacter chlorophenolicus A6 cells during degradation of 4-chlorophenol in soil2001In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 3, no 1, p. 32-42Article in journal (Refereed)
    Abstract [en]

    The recently isolated novel species Arthrobacter chlorophenolicus A6 is capable of growth on and degradation of high concentrations of 4-chlorophenol (up to 350 mug ml(-1)) as the sole carbon and energy source, This strain shows promise for bioremediation of environmental sites contaminated with high levels of chlorophenols. In this study, green fluorescent protein (gfp) or luciferase (luc) genes were used as biomarkers for monitoring cell number and activity, respectively, during degradation of 4-chlorophenol by A. chlorophenolicus cells. The individual marked strains, Arthrobacter chlorophenolicus A6L (luc-tagged) and Arthrobacter chlorophenolicus A6G (gfp-tagged), were monitored during degradation of 250 mug ml(-1) 4-chlorophenol in pure culture and 175 mug g(-1) 4-chlorophenol in soil microcosms. Both gene-tagged strains were capable of cleaning up the contaminated soil during 9 d incubation. During the bioremediation experiments, the luc-tagged cells were monitored using luminometry and the gfp tagged cells using flow cytometry, in addition to selective plate counting for both strains. The cells remained at high population levels in the soil (evidenced by GFP-fluorescent cell counts) and the A. chlorophenolicus A6L population was metabolically active (evidenced by luciferase activity measurements). These results demonstrate that the Arthrobacter chlorophenolicus A6 inoculum is effective for cleaning-up soil containing high concentrations of 4-chlorophenol.

  • 56.
    Engqvist, Robert
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Bergman, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Synthesis of benzothiopyrano[2,3-b]indol-11-one and benzopyrano[2,3-b]indol-11-one2003In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 59, no 48, p. 9649-9653Article in journal (Refereed)
    Abstract [en]

    The fused heterocycles benzothiopyrano[2,3-b]indol-11-one and benzopyrano[2,3-b]indol-11-one, have been prepared from methyl 3-indole carboxylate in two steps.

  • 57. Eriksson, S
    et al.
    Nygren, Jonas
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Ahnström, G
    Matrix association of early- and late-replicating chromatin studied by single-cell electrophoresis2002In: Biochimica et Biophysica Acta. Molecular Cell Research, ISSN 0167-4889, E-ISSN 1879-2596, Vol. 1590, no 1-3, p. 103-108Article in journal (Refereed)
    Abstract [en]

    CHO-K1 cells were synchronized at the G(1)/S border by mitotic shake-off and aphidicolin incubation. Pulse-labeling with tritium was done at 30 min, 2 or 5 h into the S-phase, with chase incubations for different times in non-radioactive medium. The cells were subjected to neutral microelectrophoresis to extend the DNA into "comets," after which the label was visualized through autoradiography. At zero chase time, all label was positioned in the head. The displacement of label into the tails increased with time, reaching a maximum at about 5 h after the pulse. A lag phase of 2 - 3 It was observed for the early-labeled cells before the displacement started. Also, more label was released after overnight serum starvation, but this was reversed through a 3-h incubation at normal growth conditions. It was found that late-replicating chromatin is organized in larger domains than early-replicating chromatin, and DNA polymerase seems to be an important organizer. Early-replicating chromatin has other important attachments to the nuclear matrix, dependent on metabolic activity.

  • 58. Facanha, A L O
    et al.
    Appelgren, Henrik
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Tabish, Mohammad
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Okorokov, L
    Ekwall, Karl
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    The endoplasmic reticulum cation P-type ATPase Cta4p is required for control of cell shape and microtubule dynamics2002In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 157, no 6, p. 1029-1039Article in journal (Refereed)
    Abstract [en]

    Here we describe the phenotypic characterization of the cta(4+) gene, encoding a novel member of the P4 family of P-type ATPases of fission yeast. The cta4Delta mutant is temperature sensitive and cold sensitive lethal and displays several morphological defects in cell polarity and cytokinesis. Microtubules are generally destabilized in cells lacking Cta4p. The microtubule length is decreased, and the number of microtubules per cell is increased. This is concomitant with an increase in the number of microtubule catastrophe events in the midzone of the cell. These defects are likely due to a general imbalance in cation homeostasis. Immunofluorescence microscopy and membrane fractionation experiments revealed that green fluorescent protein-tagged Cta4 localizes to the ER. Fluorescence resonance energy transfer experiments in living cells using the yellow cameleon indicator for Ca2+ indicated that Cta4p regulates the cellular Ca2+ concentration. Thus, our results reveal a link between cation homeostasis and the control of cell shape, microtubule dynamics, and cytokinesis, and appoint Ca2+ as a key ion in controlling these processes.

  • 59.
    Fang, Hong
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Univesity Hospital, Huddinge.
    Edlund, Charlotta
    Södertörn University, Avdelning Naturvetenskap. Karolinska Univesity Hospital, Huddinge.
    Hultenby, K
    Karolinska Univesity Hospital, Huddinge.
    Hedberg, M
    Karolinska Univesity Hospital, Huddinge.
    Effects of cefoxitin on the growth and morphology of Bacteroides thetaiotaomicron strains with different cefoxitin susceptibility2002In: Anaerobe, ISSN 1075-9964, E-ISSN 1095-8274, Vol. 8, no 2, p. 55-61Article in journal (Refereed)
    Abstract [en]

    To examine the effects of cefoxitin on bacterial growth and cell morphology, two pairs of Bacteroides thetaiotaomicron strains (238, 238 m and 1186, 1186 m) with different susceptibilities to this antibiotic were investigated in the present study. B. thetaiotaomicron 238m and 1186m were resistant laboratory mutants originating from the susceptible wild-type strains B. thetaiotaomicron 238 and 1186, respectively. It has been shown, in a previous study, that the mutant strains had alterations in their penicillin-binding proteins (PBPs) as compared to the parent strains. In the present study, strains 238 and 238m presented almost identical genomic fingerprints by PCR, so did strains 1186 and 1186m, which indicates that the parent and mutant strains have similar genomic background. In comparison with the parent strains, the growth rate of mutant strains was slower in cultures without antibiotic. The growth patterns challenged with cefoxitin were also different between the parent and the mutant strains. In case of the morphological responses to cefoxitin, the mutant strains were more resistant to the effect of cefoxitin than the parent strains. In conclusion, the growth patterns and the morphological changes induced by cefoxitin, of the investigated strains, were associated with the properties of PBPs. The resistant mutants with deficiency in PBPs grew slower than the susceptible parent strains, and cefoxitin caused filamentation at sub-MIC in B. thetaiotaomicron.

  • 60. Fang, Hong
    et al.
    Edlund, Charlotta
    Södertörn University, Avdelning Naturvetenskap.
    Nord, C E
    Hedberg, M
    Selection of cefoxitin-resistant Bacteroides thetaiotaomicron mutants and mechanisms involved in beta-lactam resistance2002In: Clinical Infectious Diseases, ISSN 1058-4838, E-ISSN 1537-6591, Vol. 35, p. S47-S53Article in journal (Refereed)
    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.

  • 61.
    Fang, Hong
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Edlund, Charlotta
    Södertörn University, 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 samples1999In: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 5, no 12, p. 753-758Article in journal (Refereed)
    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.

  • 62.
    Fang, Hong
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Hedberg, M
    Karolinska Institutet.
    Edlund, Charlotta
    Södertörn University, Avdelning Naturvetenskap. Karolinska Instiutet.
    Nord, C E
    Karolinska Institutet.
    Identification of the metallo-beta-lactamase gene from clinical isolates of Bacteroides fragilis1999In: Anaerobe, ISSN 1075-9964, E-ISSN 1095-8274, Vol. 5, no 3-4, p. 431-434Article in journal (Refereed)
    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.

  • 63. Filling, C
    et al.
    Berndt, Kurt D
    Södertörn University, 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/reductases2002In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 277, no 28, p. 25677-25684Article in journal (Refereed)
    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.

  • 64. Filling, C
    et al.
    Nordling, E
    Benach, J
    Berndt, Kurt D
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Ladenstein, R
    Jörnvall, H
    Oppermann, U
    Structural role of conserved Asn179 in the short-chain dehydrogenase/reductase scaffold2001In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 289, no 3, p. 712-717Article in journal (Refereed)
    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.

  • 65. Fischer, H
    et al.
    Zhang, X U
    O'Brien, K P
    Kylsten, Per
    Södertörn University, 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 OXR12001In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 281, no 3, p. 795-803Article in journal (Refereed)
    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.

  • 66.
    Flinn, Elizabeth M
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Intstitutet.
    Wallberg, A E
    Hermann, Stefan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Grant, P A
    Workman, J L
    Wright, Anthony P H
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Recruitment of Gen5-containing complexes during c-Myc-dependent gene activation - Structure and function aspects2002In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 277, no 26, p. 23399-23406Article in journal (Refereed)
    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.

  • 67. Foloppe, N
    et al.
    Sagemark, Johan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Nordstrand, K
    Berndt, Kurt D
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Nilsson, L
    Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: Comparison with functionally related proteins2001In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 310, no 2, p. 449-470Article in journal (Refereed)
    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.

  • 68. Frängsmyr, L.
    et al.
    Israelsson, A.
    Teglund, Stephen
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Matsunaga, T.
    Hammarström, S.
    Evolution of the carcinoembryonic antigen family. Structures of CGM9, CGM11 and pregnancy-specific glycoprotein promoters2000In: Tumor Biology, ISSN 1010-4283, E-ISSN 1423-0380, Vol. 21, no 2, p. 63-81Article in journal (Refereed)
    Abstract [en]

    Earlier studies have demonstrated that the genes of the human carcinoembryonic antigen (CEA) family can be divided into three subgroups, the CEA subgroup (n = 12), the pregnancy-specific glycoprotein (PSG) subgroup (n = 11), and a third subgroup (n = 6). To further characterize the CEA gene family, we have determined the genomic structures of CGM9 and CGM11, analyzed the promoter regions of all eleven PSGs, studied the CGM15-PSG13 intergenic region and the evolutionary relationships between the CEA family genes. CGM9, a typical CEA subgroup member, was a pseudogene with the exon structure [5'UTR-L-L/N-TM-Cyt-3'UTR]. CGM11 contained a mixture of exons derived from CEA and PSG subgroup genes. The formula of the CGM11 pseudogene was [5'UTRL- L/N-C-3'UTR]. Thus both genes lacked the IgC2-like domains typically found in CEA subfamily members. The upstream promoter regions of all eleven PSGs were characterized. All PSG promoters lacked the classical TATA and CCAAT elements, but had putative PEA3 box(es), CACCC box(es), a RARE box, and poly (dG-dT) repeats of different lengths. Five PSGs also had an SP1 site. The complete 10-kb intergenic region between CGM15 and PSG13 was sequenced. Clusters of different types of repetitive sequences were seen. The time of divergence of the CEA and PSG subfamilies was estimated to be 107.7 ± 17.1 million years, or at about the time of human-rodent divergence. Models for the evolution of CEA and PSG and the third family subgroup genes are proposed.

  • 69. Funk, C
    et al.
    Wiklund, R
    Schröder, Wolfgang P
    Södertörn University, Avdelning Naturvetenskap.
    Jansson, C
    D1' centers are less efficient than normal photosystem II centers2001In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 505, no 1, p. 113-117Article in journal (Refereed)
    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.

  • 70.
    Gallio, Marco
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Kylsten, Per
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Providencia may help find a function for a novel, widespread protein family2000In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 10, no 19, p. R693-R694Article in journal (Refereed)
  • 71.
    Gallio, Marco
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Sturgill, G
    Case Western Reserve University School of Medicine, Cleveland, USA.
    Rather, P
    Case Western Reserve University School of Medicine, Cleveland, USA.
    Kylsten, Per
    Södertörn University, Avdelning Naturvetenskap.
    A conserved mechanism for extracellular signaling in eukaryotes and prokaryotes2002In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 99, no 19, p. 12208-12213Article in journal (Refereed)
    Abstract [en]

    Epidermal growth factor receptor (EGFr) is a key mediator of cell communication during animal development and homeostasis. In Drosophila, the signaling event is commonly regulated by the polytopic membrane protein Rhomboid (RHO), which mediates the proteolytic activation of EGFr ligands, allowing the secretion of the active signal. Until very recently, the biochemical function of RHO had remained elusive. It is now believed that Drosophila RHO is the founder member of a previously undescribed family of serine proteases, and that it could be directly responsible for the unusual, intramembranous cleavage of EGFr ligands. Here we show that the function of RHO is conserved in Gram-negative bacteria. AarA, a Providencia stuartii RHO-related protein, is active in Drosophila on the fly EGFr ligands. Vice versa, Drosophila RHO-1 can effectively rescue the bacterium's ability to produce or release the signal that activates density-dependent gene regulation (or quorum sensing). This study provides the first evidence that prokaryotic and eukaryotic RHOs could have a conserved role in cell communication and that their biochemical properties could be more similar than previously anticipated.

  • 72.
    Gilek, Michael
    Södertörn University College, Avdelning Naturvetenskap.
    Extrapolation issues2003In: Radiation Effects on Plants and Animals: FASSET deliverable 4 / [ed] Dennis Woodhead, Irene Zinger, European Commission , 2003, p. 163-178Chapter in book (Other academic)
  • 73. Glaser, Elzbieta
    et al.
    Sjöling, Sara
    Södertörn University, Avdelning Naturvetenskap.
    Tanudji, Marcel
    Södertörn University, Avdelning Naturvetenskap.
    Whelan, James
    Mitochondrial protein import in plants: Signals, Sorting, Targeting, Processing and Regulation1998In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 38, no 1-2, p. 311-338Article in journal (Refereed)
    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.

  • 74.
    Grahn, Mats
    Södertörn University College, Avdelning Naturvetenskap.
    MHC genotype and ornamentation2000In: Animal signals: signalling and signal design in animal communication / [ed] Yngve Espmark, Trond Amundsen, Gunilla Rosenqvist, Trondheim: Tapir , 2000, p. 421-436Chapter in book (Other academic)
  • 75.
    Grahn, Mats
    Södertörn University College, Avdelning Naturvetenskap.
    Varför evolutionär medicin: en förklaringsmodell för sjukdom2001In: Tidsrkiften Medikament, ISSN 1402-3881, Vol. 5, p. 28-32Article in journal (Other (popular science, discussion, etc.))
  • 76. Grandin, Ulf
    et al.
    Lönn, Mikael
    Södertörn University, Avdelning Naturvetenskap.
    Rydin, Håkan
    Allozyme variation at a PGI locus in differently aged populations of Moehringia trinervia (Caryophyllaceae) in a successional area2002In: Nordic Journal of Botany, ISSN 0107-055X, E-ISSN 1756-1051, Vol. 22, no 3, p. 303-311Article in journal (Refereed)
    Abstract [en]

    We studied genetic effects of the colonisation process during primary succession by analysing allozyme variation at a PGI locus in differently aged populations of Moehringia trinervia, which is a selfing annual with low dispersal ability. The populations studied come from islands and shores created in the 1880s by a drop in the water table of a Swedish lake and from old parts of a large island and of the mainland. The population age is known from five vegetation analyses over a century. We have also analysed the genetic composition of M. trinervia derived from seeds in the soil. Mainland populations had a higher genetic diversity than island populations that were little differentiated and differed genetically from the mainland populations. There was no temporal trend in the distribution of genetic variation on the new islands. The presence of alleles in the extant populations was associated with the proportion of that allele in the seed bank, indicating a main recruitment from the seed bank and not by repeated immigrations. We suggest that some of the new islands were colonised by a few early founders from the mainland. Later colonisation has occurred between adjacent islands, which preserves the founder effect and could explain the uniform, low genetic variation in the island populations

  • 77. Granström, A
    et al.
    Gellerstedt, G
    Eriksson, Tord
    Södertörn University, Avdelning Naturvetenskap.
    On the chemical processes occurring during thermal yellowing of a TCF-bleached birch kraft pulp2002In: Nordic Pulp & Paper Research Journal, ISSN 0283-2631, E-ISSN 2000-0669, Vol. 17, no 4, p. 427-433Article in journal (Refereed)
    Abstract [en]

    The aim of this investigation was to survey the reactions taking place during heat-induced yellowing of a TCF-bleached birch kraft pulp bleached according to the sequence O Q P Q (PO). This was done by determining the metal profiles in pulp and aqueous pulp extracts before and after accelerated ageing of pulp. It was concluded that low-molecular substances were formed during heat treatment of the pulp. It was further shown that hexenuronic acid (HexA) groups were hydrolysed during the ageing and that the destruction of HexA significantly lowered the chelating properties of the pulp, implying a liberation of metal ions. Two different procedures to isolate the coloured compounds in an aqueous extract of aged pulp are reported. Analysis of the separated strongly coloured material revealed that manganese and iron as well as some dicarboxylic acids were enriched. It was also concluded that if iron ions were removed without hydrolysing HexA, the brightness stability could be improved. Finally some observations and conclusions from previous work are discussed.

  • 78. Greenberg, L A
    et al.
    Hernnäs, B
    Brönmark, D
    Dahl, J
    Eklöv, A
    Olsén, K Håkan
    Södertörn University, Avdelning Naturvetenskap.
    Effects of kinship on growth and movements of brown trout in field enclosures2002In: Ecology of Freshwater Fish, ISSN 0906-6691, E-ISSN 1600-0633, Vol. 11, no 4, p. 251-259Article in journal (Refereed)
    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.

  • 79. Grimm, T
    et al.
    Teglund, Stephan
    Södertörn University, 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 32001In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 505, no 1, p. 13-17Article in journal (Refereed)
    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.

  • 80.
    Grivas, Spiros
    Södertörn University, Avdelning Naturvetenskap.
    2,1,3-benzoselenadiazoles as valuable synthetic intermediates2000In: Current organic chemistry, ISSN 1385-2728, E-ISSN 1875-5348, Vol. 4, no 7, p. 707-726Article in journal (Refereed)
    Abstract [en]

    N-alkyl-1,2-benzenediamines, 4-substituted-3-nitro-1,2-benzenediamines and 3,4-diamino-2-nitrophenols are readily obtained by deselenation of alkyl quaternary salts of 2,1,3-benzoselenadiazoles (bsd) and 5-substituted-4-nitro-bsd. The latter are easily obtained by nitration of 5-X-bsd (X = Me, Br, Cl, F, OMe, NHMe). Nitration of 5-fluoro-bsd yields the 4-nitro derivatives that are accompanied by substantial amounts of the corresponding 4-nitro-bsd-5-ols. ipso-Nitration of 5-fluoro-4-methyl-bsd is followed by instantaneous hydrolysis to (+/-)-4-methyl-4-nitro-bsd-5(4H)-one. Batcho-Leimgruber indole synthesis on 5-methyl-4-nitro-bsd followed by reductive deselenation of 1,2,5-selenadiazolo[3,4-g]indole affords 6,7-diaminoindole. Cyclocondensation of 3-nitro-1,2-benzenediamines with acetylacetone provides a convenient route for the preparation of 2-methyl-4-nitrobenzimidazoles. Less-accessible 6-halo-5-nitro- and 6-methoxy-5-nitroquinoxalines are efficiently synthesized by regioselective condensation of alpha-dicarbonyls with 4-halo- and 4-methoxy-3-nitro-1,2-benzenediamines. The reactive halogen atom or methoxyl group ortho to the nitro substituent renders these quinoxalines versatile intermediates to further heterocycles. The Se-77, C-13 and H-1 NMR chemical shifts of sixteen bsd derivatives, and the C-13 NMR chemical shifts of eight derivatives of 2-methylquinoxalines are presented.

  • 81.
    Grivas, Spiros
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute / SLU.
    Schuisky, P
    SLU.
    Synthesis of imidazonaphthyridines and -quinolines1998In: Heterocycles, ISSN 0385-5414, E-ISSN 1881-0942, Vol. 48, no 8, p. 1575-1580Article in journal (Refereed)
    Abstract [en]

    Four 2-amino-3-methylimidazo[4,5-b][1,x]naphthyridines, x = 5-8 (6-9) have been obtained from aromatic aldehydes (11-14) and 2-amino-1-methyl-2-imidazolin-5-one (15) in one step. The N-1 - and N-3 -methyl isomers of 2-aminoimidazo-[4,5-b]quinoline (5 and 10) were prepared from 2-nitrobenzaldehyde via the isolated E-isomers of imidazolin-5-one (17) and imidazolin-4-one (20).

  • 82.
    Gulin, Sofia
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Kussak, A
    Jansson, P E
    Widmalm, G
    Structural studies of S-7, another exocellular polysaccharide containing 2-deoxy-arabino-hexuronic acid2001In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 331, no 3, p. 285-290Article in journal (Refereed)
    Abstract [en]

    The exocellular polysaccharide S-7, a heteropolysaccharide from Azotobacter indicus var, myxogenes has been studied using methylation analysis, Smith degradation, partial acid hydrolysis, NMR spectroscopy and mass spectrometry as the principal methods. It is concluded that the repeating unit has the following structure: -->4)-beta -D-Glcp-(1 -->4)-alpha -L-Rhap-(1 -->3)-beta -D-2-deoxy-arabino-HexpA-(1 --> 6 up arrow 1 beta -D-Glcp-(1 -->6)-beta -D-Glcp The absolute configuration of the deoxyhexuronic acid was deduced from H-1 NMR chemical shifts and is most likely D. Approximately two O-acetyl groups per repeating unit are present, one of which is presumably on the Rha residue. The structure bears great resemblance to another polysaccharide, recently studied, produced by Sphingomonas paucimobilis I-886.

  • 83.
    Gulin, Sofia
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Pupo, E
    Schweda, Elke K H
    Södertörn University, Avdelning Naturvetenskap.
    Hardy, E
    Linking mass spectrometry and slab-polyacrylamide gel electrophoresis by passive elution of lipopolysaccharides from reverse-stained gels: Analysis of gel-purified lipopolysaccharides from Haemophilus influenzae strain Rd2003In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 75, no 18, p. 4918-4924Article in journal (Refereed)
    Abstract [en]

    Haemophilus influenzae is an important cause of human disease, and its lipopolysaccharide (LPS) is known to be a major virulence factor. H. influenzae produces short-chain LPS of which the heterogeneity is often visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) using silver staining for detection. Individual bands have not previously been recovered by this method in quantities sufficient for mass spectrometry. In an attempt toward the development of sensitive mass spectrometrical strategies to be used in structural studies of H. influenzae LPS and LPS from other bacteria, we have applied here our previously described slab-PAGE-based micropurification method to obtain unmodified LPS fractions of high purity (>95%) from a crude LPS preparation of H. influenzae strain Rd. Two LPS-fractions were obtained which, after a procedure including mild acid hydrolysis, dephosphorylation, and permethylation of the resulting oligosaccharides, were subjected to tandem electrospray ionization mass spectrometry (ESI-MS/MS). The quantities of micropurified LPS fractions-the recovery of LPS in terms of total mass was 30%-were found sufficient to allow the characterization of LPS glycoforms. The ESI-MS spectra of the individual bands showed reduced heterogeneity. Furthermore, the integrity of the micropurified LPS was confirmed. The spectra-displayed molecular ions showed improved intensity, increased respective signal-to-noise ratios demonstrating the sensitivity of analysis. Consequently, both the direct determination of the molecular masses of the gel-separated LPS glycoforms and sequence analyses using ESI-MS/MS were possible.

  • 84. Gustafsson, Susanne
    et al.
    Lönn, Mikael
    Södertörn University, Avdelning Naturvetenskap.
    Genetic differentiation and habitat preference of flowering-time variants within Gymnadenia conopsea2003In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 91, p. 284-292Article in journal (Refereed)
    Abstract [en]

    Using fast-evolving microsatellites, more slowly evolving ITS markers and performing habitat analyses, we demonstrated a drastic genetic divergence and significant habitat differentiation between early- and late-flowering variants of plants morphologically belonging to Gymnadenia conopsea ssp conopsea. The two phenological variants can either be found in separate or in mixed populations. Information from microsatellite markers and ITS sequences indicated the occurrence of an early historical split between the two flowering-time variants, a split that has been maintained until the present time even within sympatric populations. Early-flowering variants were also far more genetically diverse, had more alleles per microsatellite locus and a wider habitat amplitude than late-flowering variants. As a comparison, we included G. odoratissima in the sequencing study. We found G. odoratissima to be most closely related to the early-flowering type. This indicates a more ancient divergence event between the two flowering-time variants within G. conopsea ssp conopsea than between the two different species G. odoratissima and the early-flowering variant of G. conopsea. Possible explanations to the results arrived at and possible mechanisms maintaining the genetic separation are discussed.

  • 85. Haas, S A
    et al.
    Hild, M
    Wright, Anthony P H
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Hain, T
    Talibi, D
    Vingron, M
    Genome-scale design of PCR primers and long oligomers for DNA microarrays2003In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 31, no 19, p. 5576-5581Article in journal (Refereed)
    Abstract [en]

    During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost importance for the successful production of such chips. We developed GenomePRIDE, a highly flexible and scalable software for designing primers/oligomers for large-scale projects. The program is able to generate either long oligomers (40-70 bases), or PCR primers for the amplification of gene-specific DNA fragments of user-defined length. Additionally, primers can be designed in-frame in order to facilitate large-scale cloning into expression vectors. Furthermore, GenomePRIDE can be adapted to specific applications such as the generation of genomic amplicon arrays or the design of fragments specific for alternative splice isoforms. We tested the performance of GenomePRIDE on the entire genomes of Listeria monocytogenes (1584 gene-specific PCRs, 48 long oligomers) as well as of eukaryotes such as Schizosaccharomyces pombe (5006 gene-specific PCRs), and Drosophila melanogaster (21306 gene-specific PCRs). With its computing speed of 1000 primer pairs per hour and a PCR amplification success of 99%, GenomePRIDE represents an extremely cost- and time-effective program.

  • 86.
    Hammer, Monica
    Södertörn University College, Avdelning Naturvetenskap.
    Ekosystemen tjänar oss2003In: Teknik & vetenskap, ISSN 1402-5701, no 3, p. -51Article in journal (Other (popular science, discussion, etc.))
  • 87.
    Hammer, Monica
    et al.
    Södertörn University, Avdelning Naturvetenskap. Stockholm University.
    Holmlund, Cecilia M
    Åqvist Almlöv, Maria
    Södertörn University, Avdelning Naturvetenskap. Stockholm University.
    Social-ecological feedback links for ecosystem management: a case study of fisheries in the Central Baltic Sea archipelago2003In: Ocean and Coastal Management, ISSN 0964-5691, E-ISSN 1873-524X, Vol. 46, no 6-7, p. 527-545Article in journal (Refereed)
    Abstract [en]

    In this paper, we address the implications of changing social-ecological feedback links for a sustainable management of coastal regions applying an ecosystem management perspective. This case study focuses on user patterns of fish resources in the Central Baltic Sea archipelago consisting of three sub-regions: Stockholm archipelago, Sweden, the Angstromland islands and the archipelago of SW Finland. The transition from a region, mainly relying on a mixture of local natural resources towards a region more dominated by the recreational demands of nearby large urban areas, has altered user patterns of fish resources. This transition has partly followed different pathways in the three sub-regions depending on how socio-economic driving forces have been manifested in management actions. Nevertheless, functioning ecosystems are still the basis for the delivery of ecosystem services and a living archipelago system. The significance of capturing and (re)building feedback links into management regarding knowledge on ecosystem services for a sustainable ecosystem management is discussed.

  • 88.
    Hassler, Björn
    Södertörn University College, Avdelning Naturvetenskap.
    Foreign Assistance as a Policy Instrument: Swedish Environmental Support to the Baltic States, 1991-962002In: Cooperation and Conflict, ISSN 0010-8367, E-ISSN 1460-3691, Vol. 37, no 1, p. 25-45Article in journal (Refereed)
    Abstract [en]

    Foreign assistance is often characterized by a mix of altruistic and self-interested considerations of the donor country. Swedish environmental support to the Baltic States during the 1991-96 period was designed primarily to promote Swedish interests. Based on a classification of the different supported issue-areas according to collective good content, it is clear that areas with large trans-boundary effects were favoured. The most important targets for Swedish assistance were wastewater treatment facilities, measures to decrease emissions from point sources and increased nuclear safety, while for example handling of solid waste and nature protection received scant attention. Since Sweden, like most other donors, required the recipient country to cover a significant proportion of the cost of every joint project with local funding, domestic financial resources were furthermore drawn to the areas preferred by the donors. Depending on the scarcity of investment funds as well as of administrative capacity in the Baltic States, other domestically prioritized environmental issue-areas were thus largely neglected.

  • 89.
    Hassler, Björn
    Södertörn University, Avdelning Naturvetenskap.
    Gains from bilateral cooperation: a tentative research agenda2003In: Sweden and Poland from a European Perspective: Some Aspects on the Integration Process / [ed] Yonhyok Choe, Björn Hassler, Stanislaw Zyborowicz, Huddinge: Södertörns högskola , 2003, p. 1-34Chapter in book (Other academic)
  • 90.
    Hassler, Björn
    Södertörn University College, Avdelning Naturvetenskap.
    ’Protecting the Baltic Sea: The Helsinki Convention and national interests’2003In: Yearbook of international co-operation on environment and development, 2003/2004, p. 33-43Article in journal (Other academic)
  • 91.
    Hassler, Björn
    Södertörn University College, Avdelning Naturvetenskap.
    Science and politics of foreign aid: Swedish environmental support to the Baltic States2003Book (Other academic)
  • 92.
    Hellblom, Frida
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Axelsson, Lennart
    External HCO3- dehydration maintained by acid zones in the plasma membrane is an important component of the photosynthetic carbon uptake in Ruppia cirrhosa2003In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 77, no 2-3, p. 173-181Article in journal (Refereed)
  • 93.
    Hermann, Stefan
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Berndt, Kurt D
    Södertörn University, Avdelning Naturvetenskap.
    Wright, Anthony P H
    Södertörn University, Avdelning Naturvetenskap.
    How transcriptional activators bind target proteins2001In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 276, no 43, p. 40127-40132Article in journal (Refereed)
    Abstract [en]

    The product of the proto-oncogene c-myc influences many cellular processes through the regulation of specific target genes. Through its transactivation domain (TAD), c-Myc protein interacts with several transcription factors, including TATA-binding protein (TBP). We present data that suggest that in contrast to some other transcriptional activators, an extended length of the c-Myc TAD is required for its binding to TBP. Our data also show that this interaction is a multistep process, in which a rapidly forming low affinity complex slowly converts to a more stable form. The initial complex formation results from ionic or polar interactions, whereas the slow conversion to a more stable form is hydrophobic in nature. Based on our results, we suggest two alternative models for activation domain/target protein interactions, which together provide a single universal paradigm for understanding activator-target factor interactions.

  • 94. Hjortswang, H I
    et al.
    Sundås Larsson, Annika
    Södertörn University, Avdelning Naturvetenskap.
    Bharathan, G
    Bozhkov, P V
    von Arnold, S
    Vahala, T
    KNOTTED1-like homeobox genes of a gymnosperm, Norway spruce, expressed during somatic embryogenesis2002In: Plant physiology and biochemistry (Paris), ISSN 0981-9428, E-ISSN 1873-2690, Vol. 40, no 10, p. 837-843Article in journal (Refereed)
    Abstract [en]

    Two Norway spruce (Picea abies (L.) Karst.) genes belonging to class I of the KNOTTED1-like homeobox (KNOX) genes, HBK2 and HBK3, were cloned with PCR-based methods. The expression of these and a previously characterised related gene, HBK1, in different organs and during somatic embryogenesis was studied with RTPCR. Transcripts of all three genes were detected in stems, roots and in cone buds, but not in needles. HBK1 and HBK3 are expressed throughout development in a normal cell line with embryogenic potential and in a cell line unable to form somatic embryos. HBK2 is expressed in the normal cell line, but not in the developmentally arrested cell line. This suggests that the HBK2 gene is involved in the somatic embryo development.

  • 95.
    Holmberg, Lovisa
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Nygård, Odd
    Södertörn University, Avdelning Naturvetenskap.
    Release of ribosome-bound 5S rRNA upon cleavage of the phosphodiester bond between nucleotides A54 and A55 in 5S rRNA2000In: Biological chemistry (Print), ISSN 1431-6730, E-ISSN 1437-4315, Vol. 381, no 11, p. 1041-1046Article in journal (Refereed)
    Abstract [en]

    Reticulocyte lysates contain ribosome-bound and free populations of 5S RNA. The free population is sensitive to nuclease cleavage in the internal loop B, at the phosphodiester bond connecting nucleotides A54 and A55. Similar cleavage sites were detected in 5S rRNA in 60S subunits and 80S ribosomes. However, 5S rRNA in reticulocyte polysomes is insensitive to cleavage unless ribosomes are salt-washed. This suggests that a translational factor protects the backbone surrounding A54 from cleavage in polysomes. Upon nuclease treatment of mouse 60S subunits or reticulocyte lysates a small population of ribosomes released its 5S rRNA together with ribosomal protein L5. Furthermore, rRNA sequences from 5.8S, 28S and 18S rRNA were released. In 18S rRNA the sequences mainly originate from the 630 loop and stem (helix 18) in the 5' domain, whereas in 28S rRNA a majority of fragments is derived from helices 47 and 81 in domains III and V, respectively. We speculate that this type of rRNA-fragmentation may mimic a ribosome degradation pathway.

  • 96. Hood, D W
    et al.
    Cox, A D
    Wakarchuk, W W
    Schur, M
    Schweda, Elke K H
    Södertörn University, Avdelning Naturvetenskap.
    Walsh, S L
    Deadman, M E
    Martin, A
    Moxon, E R
    Richards, J C
    Genetic basis for expression of the major globotetraose-containing lipopolysaccharide from H-influenzae strain Rd (RM118)2001In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 11, no 11, p. 957-967Article in journal (Refereed)
    Abstract [en]

    A genetic basis for the biosynthetic assembly of the globotetraose containing lipopolysaccharide (LPS) of Haemophilus influenzae strain RM118 (Rd) was determined by structural analysis of LPS derived from mutant strains. We have previously shown that the parent strain RM118 elaborates a population of LPS molecules made up of a series of related glycoforms differing in the degree of oligosaccharide chain extension from the distal heptose residue of a conserved phosphorylated inner-core element, L-alpha -D-Hepp-(1-->2)-L-alpha -D-Hepp-(1-->3)-[beta -D-Glcp-(1-->4)-]-L-alpha -D-Hepp-(1-->5)-alpha -Kdo. The fully extended LPS glycoform expresses the globotetraose structure, beta -D-GalpNAc-(1-->3)-alpha -D-Galp(1-->4)-beta -D-Galp-(1-->4)-beta -D-Glcp. A fingerprinting strategy was employed to establish the structure of LPS from strains mutated in putative glycosyltransferase genes compared to the parent strain. This involved glycose and linkage analysis on intact LPS samples and analysis of O-deacylated LPS samples by electrospray ionization mass spectrometry and 1D H-1-nuclear magnetic resonance spectroscopy. Four genes, lpsA, lic2A, lgtC, and lgtD, were required for sequential addition of the glycoses to the terminal inner-core heptose to give the globotetraose structure. lgtC and lgtD were shown to encode glycosyltransferases by enzymatic assays with synthetic acceptor molecules. This is the first genetic blueprint determined for H. influenzae LPS oligosaccharide biosynthesis, identifying genes Involved in the addition of each glycose residue.

  • 97. Härlin, Carina
    et al.
    Härlin, Mikael
    Södertörn University, Avdelning Naturvetenskap.
    Towards a historization of aposematism2003In: Evolutionary Ecology, ISSN 0269-7653, E-ISSN 1573-8477, Vol. 17, no 2, p. 197-212Article in journal (Refereed)
    Abstract [en]

    Aposematism is one of the oldest phenomena in evolutionary biology and still a major puzzle to biologists. Despite its evolutionary nature, most attempts to understand aposematism are devoid of phylogenetic components. In addition, most studies that do take phylogeny into account need to bring the analysis even further. We argue that in order to fully understand aposematism we must have a clear picture of the evolutionary history behind present behaviours. In this paper we frame aposematism in a phylogenetic context and argue that most studies still are wanting in terms of demonstrating aposematism. Aposematism is not an end product but rather evolutionary scenarios including character transformations as well as prey-predator interactions. Finally, we suggest that, regardless how we restrict the concept of aposematism, knowing the directions of events facilitate all kinds of comparisons with a promise of uniting functional and evolutionary aspects into a historization of aposematism.

  • 98.
    Härlin, Mikael
    Södertörn University, Avdelning Naturvetenskap.
    On the relationship between content, ancestor, and ancestry in phylogenetic nomenclature2003In: Cladistics, ISSN 0748-3007, E-ISSN 1096-0031, Vol. 19, no 2, p. 144-147Article in journal (Refereed)
    Abstract [en]

    In this paper I draw attention to the concepts of content and ancestry in phylogenetic nomenclature. I argue that these concepts are tightly linked and that they cannot be separated as suggested by Bryant and Cantino [Biol. Rev. 77 (2002) 39] in their recent response to a critique of phylogenetic nomenclature. In addition, I argue that the basic assumption in phylogenetic nomenclature that a taxon-name always refers to the same ancestor or ancestry is questionable.

  • 99.
    Härlin, Mikael
    Södertörn University, Avdelning Naturvetenskap.
    Taxon names as paradigms: the structure of nomenclatural revolutions2003In: Cladistics, ISSN 0748-3007, E-ISSN 1096-0031, Vol. 19, no 2, p. 138-143Article in journal (Refereed)
    Abstract [en]

    In the present paper I argue that the two systems of phylogenetic nomenclature hitherto proposed represent, in a generalized sense, two different philosophies for how science develops and progresses. The phylogenetic system of definition. initially proposed by de Queiroz and Gauthier [Syst. Zool. 39 (1990) 307], and later labeled PSD, is typically Popperian in the 'sense that science progresses toward truth by An accumulation of knowledge. Phylogenetic definitions of taxon names are assumed to adapt automatically to each new hypothesis of phylogeny, thereby reflecting better and better hypotheses. The phylogenetic system of reference proposed by Harlin [Zool. Scr. 27 (1998a) 381], on the other hand, is more Kuhnian, because it is built on the idea that successive hypotheses are incommensurable (and thus not cumulative) and that taxon names might be equalled with low-level paradigms.

  • 100. Högstrand, K.
    et al.
    Böhme, Jan
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    DNA damage caused by etoposide and γ-irradiation induces gene conversion of the MHC in a mouse non-germline testis cell line1999In: Mutation research, ISSN 0027-5107, E-ISSN 1873-135X, Vol. 423, no 1-2, p. 155-169Article in journal (Refereed)
    Abstract [en]

    We have explored the effects of γ-irradiation and etoposide on the gene conversion frequency between the endogenous major histocompatibility complex class II genes Abk and Ebd in a mouse testis cell line of non-germline origin with a polymerase chain reaction assay. Both γ-rays and etoposide were shown to increase the gene conversion frequency with up to 15-fold compared to untreated cells. Etoposide, which is an agent that stabilise a cleavable complex between DNA and DNA topoisomerase II, shows an increased induction of gene conversion events with increased dose of etoposide. Cells treated with γ-rays, which induce strand breaks, had an increased gene conversion frequency when they were subjected to low doses of irradiation, but increasing doses of irradiation did not lead to an increase of gene conversion events, which might reflect differences in the repair process depending on the extent and nature of the DNA damage. These results where DNA damage was shown to be able to induce gene conversion of endogenous genes in mouse testis cells suggests that the DNA repair system could be involved in the molecular genetic mechanism that results in gene conversion in higher eukaryotes like mammals.

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