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  • 1. Agvald-Öhman, C
    et al.
    Lund, B
    Edlund, Charlotta
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Multiresistant coagulase-negative staphylococci disseminate frequently between intubated patients in a multidisciplinary intensive care unit2004In: Critical Care, ISSN 1364-8535, E-ISSN 1466-609X, Vol. 8, no 1, R42-R47 p.Article in journal (Refereed)
    Abstract [en]

    Introduction The intensive care unit is burdened with a high frequency of nosocomial infections often caused by multiresistant nosocomial pathogens. Coagulase-negative staphylococci (CoNS) are reported to be the third causative agent of nosocomial infections and the most frequent cause of nosocomial bloodstream infections. CoNS are a part of the normal microflora of skin but can also colonize the nasal mucosa, the lower airways and invasive devices. The main aim of the present study was to investigate colonization and the rate of cross-transmissions of CoNS between intubated patients in a multidisciplinary intensive care unit. Materials and methods Twenty consecutive patients, ventilated for at least 3 days, were included. Samples were collected from the upper and lower airways. All samples were cultured quantitatively and CoNS were identified by morphology and biochemical tests. A total of 199 CoNS isolates from 17 patients were genetically fingerprinted by pulsed-field gel electrophoresis in order to identify clones and to monitor dissemination within and between patients. Results An unexpected high number of transmission events were detected. Five genotypes were each isolated from two or more patients, and 14/20 patients were involved in at least one and up to eight probable transmission events. Conclusions A frequent transmission of CoNS was found between patients in the intensive care unit. Although transmission of bacteria does not necessarily lead to infection, it is nevertheless an indication that infection control measures can be improved.

  • 2.
    Alkemar, Gunnar
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Stockholm University.
    Nygård, Odd
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Secondary structure of two regions in expansion segments ES3 and ES6 with the potential of forming a tertiary interaction in eukaryotic 40S ribosomal subunits2004In: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 10, no 3, 403-411 p.Article in journal (Refereed)
    Abstract [en]

    The 18S rRNA of the small eukaryotic ribosomal subunit contains several expansion segments. Electron microscopy data indicate that two of the largest expansion segments are juxtaposed in intact 40S subunits, and data from phylogenetic sequence comparisons indicate that these two expansion segments contain complementary sequences that could form a direct tertiary interaction on the ribosome. We have investigated the secondary structure of the two expansion segments in the region around the putative tertiary interaction. Ribosomes from yeast, wheat, and mouse-three organisms representing separate eukaryotic kingdoms-were isolated, and the structure of ES3 and part of the ES6 region were analyzed using the single-strand-specific chemical reagents CMCT and DMS and the double-strand-specific ribonuclease V1. The modification patterns were analyzed by primer extension and gel electrophoresis on an ABI 377 automated DNA sequencer. The investigated sequences were relatively exposed to chemical and enzymatic modification. This is in line with their indicated location on the surface at the solvent side of the subunit. The complementary ES3 and ES6 sequences were clearly inaccessible to single-strand modification, but available for cleavage by double-strand-specific RNase V1. The results are compatible with a direct helical interaction between bases in ES3 and ES6. Almost identical results were obtained with ribosomes from the three organisms investigated.

  • 3.
    Andrén, Elinor
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Naturliga halter – vad är det?: Historiska arkiv ger referensvärden.2005In: Miljötillståndet i egentliga Östersjön: Rapport 2005, Stockholm: Stockholms marina forskningscentrum , 2005, 50-62 p.Chapter in book (Other (popular science, discussion, etc.))
  • 4. Articus, Kristina
    et al.
    Mattsson, Jan-Eric
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Wedin, Mats
    Tibell, Leif
    Morphology and sequence data - conflict and concordance in a phylogeny of some European Usnea species2004Manuscript (preprint) (Other academic)
  • 5.
    Backman, Agneta
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Jansson, Janet K
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. SLU.
    Degradation of 4-chlorophenol at low temperature and during extreme temperature fluctuations by Arthrobacter chlorophenolicus A62004In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 48, no 2, 246-253 p.Article in journal (Refereed)
    Abstract [en]

    Low average temperatures and temperature fluctuations in temperate soils challenge the efficacy of microbial strains used for clean up of pollutants. In this study, we investigated the cold tolerance of Arthrobacter chlorophenolicus A6, a microorganism previously shown to degrade high concentrations of 4-chlorophenol at 28degreesC. Luciferase activity from a luc-tagged derivative of the strain (A6L) was used to monitor the metabolic status of the population during 4-chlorophenol degradation. The A6L strain could degrade 200-300 mug mL(-1) 4-chlorophenol in pure cultures incubated at 5degreesC, although rates of degradation, growth and the metabolic status of the cells were lower at 5degreesC compared to 28degreesC. When subjected to temperature fluctuations between 5 and 28degreesC, A6L continued to degrade 4-chlorophenol and remained active. In soil microcosm experiments, the degradation rates were significantly faster the first week at 28degreesC, compared to 5degreesC. However, this difference was no longer seen after 7 days, and equally low 4-chlorophenol concentrations were reached after 17 days at both temperatures. During 4-chlorophenol degradation in soil, CFU and luciferase activity values remained constant at both 5 and 28degreesC. However, once most of the 4-chlorophenol was degraded, both values decreased by 1-1.5 logarithmic values at 28degreesC, whereas they remained constant at 5degreesC, indicating a high survival of the cells at low temperatures. Because of the ability of A. chlorophenolicus A6 to degrade high concentrations of 4-chlorophenol at 5degreesC, together with its tolerance to temperature fluctuations and stress conditions found in soil, this strain is a promising candidate for bioaugmentation of chlorophenol-contaminated soil in temperate climates.

  • 6.
    Backman, Agneta
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Maraha, Ninwe
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Jansson, Janet K
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. SLU.
    Impact of temperature on the physiological status of a potential bioremediation inoculant, Arthrobacter chlorophenolicus A62004In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 70, no 5, 2952-2958 p.Article in journal (Refereed)
    Abstract [en]

    Arthrobacter chlorophenolicus A6 (A6) can degrade large amounts of 4-chlorophenol in soil at 5 and 28degreesC. In this study, we investigated the effects of temperature on the physiological status of this bacterium in pure culture and in soil. A derivative of A6 tagged with the gfp gene (encoding green fluorescent protein [GFP]) was used to specifically quantify A6 cells in soil. In addition, cyano-ditolyl-tetrazoliumchloride was used to stain GFP-fluorescent cells with an active electron transfer system ("viable cellis") whereas propidium iodide (PI) was used to stain cells with damaged membranes ("dead cells"). Another derivative of the strain (tagged with the firefly luciferase gene [luc]) was used to monitor the metabolic activity of the cell population, since the bioluminescence phenotype is dependent on cellular energy reserves. When the cells were incubated in soil at 28degreesC, the majority were stained with PI, indicating that they had lost their cell integrity. In addition, there was a corresponding decline in metabolic activity and in the ability to be grown in cultures on agar plates after incubation in soil at 28degreesC, indicating that the cells were dying under those conditions. When the cells were incubated in soil at 5degreesC, by contrast, the majority of the cells remained intact and a large fraction of the population remained metabolically active. A similar trend towards better cell survival at lower temperatures was found in pure-culture experiments. These results make A. chlorophenolicus A6 a good candidate for the treatment of chlorophenol-contaminated soil in cold climates.

  • 7. Beckman, M
    et al.
    Kihlmark, Madeleine
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Iverfeldt, K
    Hallberg, Einar
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Degradation of GFP-labelled POM121, a non-invasive sensor of nuclear apoptosis, precedes clustering of nuclear pores and externalisation of phosphatidylserine2004In: Apoptosis (London), ISSN 1360-8185, E-ISSN 1573-675X, Vol. 9, no 3, 363-368 p.Article in journal (Refereed)
    Abstract [en]

    The nuclear pore membrane protein POM121 is specifically degraded during apoptosis by a caspase-3-dependent process enabling early detection of apoptosis in living cells expressing POM121-GFP. Here we further investigated temporal aspects of apoptotic degradation of POM121-GFP. We demonstrate that decreased POM121-GFP fluorescence precedes annexin V-labelling of apoptotic cells. This indicates that degradation of the nuclear pore complex starts prior to redistribution of plasma membrane phosphatidylserine, which serves as a signal for phagocytotic elimination of apoptotic cells. Furthermore, a caspase-resistant GFP-labelled mutant of POM121 resisted degradation even in late apoptosis and was detected in clustered nuclear pores. Thus, it can be concluded that loss of POM121-GFP is a specific sensor of the activation of caspase-3-dependent proteolysis at the nuclear pores.

  • 8.
    Bjerling, Pernilla
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Uppsala University / University of Copenhagen, Denmark .
    Ekwall, Karl
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Egel, R
    Thon, G
    A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe2004In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 32, no 15, 4421-4428 p.Article in journal (Refereed)
    Abstract [en]

    The mating-type region of the fission yeast Schizosaccharomyces pombe comprises three loci: mat1, mat2-P and mat3-M. mat1 is expressed and determines the mating type of the cell. mat2-P and mat3-M are two storage cassettes located in a 17 kb heterochromatic region with features identical to those of mammalian heterochromatin. Mutations in the swi6(+), clr1(+), clr2(+), clr3(+), clr4(+) and clr6(+) genes were obtained in screens for factors necessary for silencing the mat2-P-mat3-M region. swi6(+) encodes a chromodomain protein, clr3(+) and clr6(+) histone deacetylases, and clr4(+) a histone methyltransferase. Here, we describe the cloning and characterization of clr2(+). The clr2(+) gene encodes a 62 kDa protein with no obvious sequence homologs. Deletion of clr2(+) not only affects transcriptional repression in the mating-type region, but also centromeric silencing and silencing of a PolII-transcribed gene inserted in the rDNA repeats. Using chromatin immunoprecipitation, we show that Clr2 is necessary for histone hypoacetylation in the mating-type region, suggesting that Clr2 acts upstream of histone deacetylases to promote transcriptional silencing.

  • 9.
    Björk, Mikael
    et al.
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Gilek, Michael
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Overview of Ecological RiskCharacterisation Methodologies: ERICA deliverable 4b2005Report (Other academic)
  • 10. Carlsson, J
    et al.
    Carlsson, J E L
    Olsén, K Håkan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Hansen, M M
    Eriksson, T
    Nilsson, J
    Kin-biased distribution in brown trout: an effect of redd location or kin recognition?2004In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 92, no 2, 53-60 p.Article in journal (Refereed)
    Abstract [en]

    A wide range of animals have been reported to show kin-biased behaviours, such as reduced aggressiveness and increased food sharing among relatives. However, less is known about whether wild animals also associate with relatives under natural conditions, which is a prerequisite to facilitate kin-biased behaviours and hence kin selection. We tested, by means of microsatellite polymorphism, correlations between pair-wise relatedness and pair-wise metric distance in wild brown trout ( Salmo trutta L.) under natural conditions in two streams. Our data show that young-of-the-year as well as older trout found close together also had a higher genetic relatedness in one of the two streams, whereas no relationship was found in the other stream. Very few half and full siblings were found in the second stream and under these conditions it is unlikely that kin-biased behaviours will receive positive selection. We discuss the underlying mechanisms for the observed structure and we specifically address the issue of whether the grouping of related individuals could reflect dispersal from the same spawning redds, or if it reflects active association with relatives, possibly conferring kin-selected advantages.

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

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

  • 12. Coppelstone, David
    et al.
    Björk, Mikael
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Gilek, Michael
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Ecological Risk Characterisation: An Interim Method for the ERICA Integrated Approach: ERICA deliverable D4a2005Report (Other academic)
  • 13. Ehrlén, Johan
    et al.
    Syrjänen, Kimmo
    Leimu, Roosa
    Garcia, Maria Begona
    Lehtilä, Kari
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Land use and population growth of Primula veris: an experimental demographic approach2005In: Journal of Applied Ecology, ISSN 0021-8901, E-ISSN 1365-2664, Vol. 42, no 2, 317-326 p.Article in journal (Refereed)
    Abstract [en]

    1. Changes in land use are the primary cause of decline for many plant species. Efficient management actions for such species must be based on knowledge of the key phases of the plant life cycles that respond most to changes in environmental factors. 2. To assess how grazing influences population viability of the perennial rosette herb Primula veris, we applied four experimental treatments to abandoned grasslands and recorded the demographic response in permanent plots and seed sowing experiments over 3 years. 3. Treatments had strong effects on population viability. Transition matrix models showed that cutting the surrounding vegetation had no effect on population growth rate (lambda). However, when this was combined with litter removal lambda increased to 1.46, compared with 1.11 in controls. With disturbance and complete removal of the surrounding vegetation the effect was even stronger, and lambda increased to 1.60. 4. Increases in lambda were primarily a result of increased growth of the smallest rosettes, and increased seedling production. In contrast, the performance of larger P. veris individuals was not affected by experimental treatments. 5. The higher the elasticity of a particular life cycle transition, the less the change in the transition rate caused by treatments. This suggests that plants are able partly to buffer the effects of environmental variation by minimizing changes in the life cycle transitions that are most important to population growth rate. 6. Synthesis and applications. Experimental demographic approaches provide an important tool for assessing how grazing and other types of management influence species viability, and help to unravel the mechanisms underlying such relationships. With such information it is possible to predict the effects of novel types of management and land-use scenarios on population viability. For P. veris, we identified seedling establishment as a key phase in the life cycle, and litter accumulation as a key environmental factor, suggesting that these should be prime targets for management. One practice that is likely to favour as well as seedling establishment preventing litter accumulation is late summer grazing.

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

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

  • 15.
    Ekwall, Karl
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    The RITS complex - A direct link between small RNA and heterochromatin2004In: Molecular Cell, ISSN 1097-2765, E-ISSN 1097-4164, Vol. 13, no 3, 304-305 p.Article in journal (Refereed)
  • 16.
    Ekwall, Karl
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    The roles of histone modifications and small RNA in centromere function2004In: Chromosome Research, ISSN 0967-3849, E-ISSN 1573-6849, Vol. 12, no 6, 535-542 p.Article in journal (Refereed)
    Abstract [en]

    Here, epigenetic regulation of centromeric chromatin in fission yeast (Schizosaccharomyces pombe) is reviewed, focussing on the role of histone modifications and the link to RNA interference (RNAi). Fission yeast centromeres are organized into two structurally and functionally distinct domains, both of which are required for centromere function. The central core domain anchors the kinetochore structure while the flanking heterochromatin domain is important for sister centromere cohesion. The chromatin structure of both domains is regulated epigenetically. In the central core domain, the histone H3 variant Cnp1(CENP-A) plays a key role. In the flanking heterochromatin domain, histones are kept underacetylated by the histone deacetylases (HDACs) Clr3, Clr6 and Sir2, and methylated by Clr4 methyltransferase (HMTase) to create a specific binding site for the Swi6 protein. Swi6 then directly mediates cohesin binding to the centromeric heterochromatin. Recently, a surprising link was made between heterochromatin formation and RNAi. Centromeric flanking repeats are transcribed and the transcripts processed by the RNAse III-like enzyme, Dicer (Dcr1), to produce small interfering RNAs ( siRNA), which direct formation of heterochromatin via the RNA-induced Initiation of Transcriptional Silencing (RITS) protein complex. Consequently Dicer, Argonaute (Ago1), an RNA-dependent RNA polymerase (Rdp1) and several hitherto uncharacterized Csp ( centromere suppressor of position effect) gene products implicated in the RNAi pathway at centromeres are required for sister chromatid cohesion.

  • 17.
    Engqvist, Robert
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Syntheses of some tri- and tetracyclic heterocycles containing an indole moiety2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis deals with the development of new synthetic methods leading to fused tri- and tetracyclic heterocycles, many of which have interesting biological activity such as antiviral and DNA intercalating properties. The reactions between isatins and 2-aminobenzylamine in acetic acid can give, depending on the conditions, either complex spirooxindoles or indolo[3,2-c]quinolin-6-ones. Proposed mechanisms are presented (involving a simpler form of spirooxindoles). These spirooxindoles can easily be obtained from isatins and 2-aminobenzylamine in methanol (Paper I). The previously unknown, but incorrectly claimed, linear isomer of indolo[3,2-c]quinolin-6one, i.e. indolo[2,3-b]quinolin-11-one, has been prepared for the first time by thermal (260 degrees C) cyclization of methyl 2 -phenylamino-indole-3 -carboxylate, which was in turn prepared in two steps from methyl indole-3 -carboxylate. The benzothiopyrano[2,3-b]indol-11-one and benzopyrano[2,3-b]indol-11-one could be prepared similarly (Papers I and II). Suitable 2-chloro-3-formylindoles have been used for the preparation of the alkaloids neocryptolepine, thienodolin and derivatives thereof (Papers III and IV). Finally, synthetic work towards potential metabolites of the lead compound B-220 is presented. We have described a method for reduction of the biologically interesting indolo[2,3b)quinoxalines with zinc, which are subsequently trapped with an appropriate anhydride to provide the corresponding mono or diacylated 5,1 1-dihydroindolo[2,3b]quinoxalines in good yields (paper V). Synthesis of hydroxy derivatives of B-220 can be effected from the appropriate methoxyisatins. Futher derivatives like the vinyl-, Nmethylaminoethyl- and Noxido derivatives of B-220 have also been synthesised.

  • 18.
    Engqvist, Robert
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    An improved synthesis of neocryptolepine2004In: Organic preparations and procedures international, ISSN 0030-4948, E-ISSN 1945-5453, Vol. 36, no 4, 386-390 p.Article in journal (Refereed)
  • 19.
    Engqvist, Robert
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Javaid, Atif
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Synthesis of thienodolin2004In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 12, 2589-2592 p.Article in journal (Refereed)
    Abstract [en]

    We report a total synthesis of the alkaloid thienodolin (1a), as well as its 5-chloro isomer 1b and its unsubstituted analogue 1c, in three steps from the corresponding oxindoles Ba-c. The preparation was achieved through an initial Vilsmeier-Haack-Arnold reaction (chloro-formylation) followed by protection at the indole nitrogen, creation of the fused thiophene ring by nucleophilic substitution at the 2-position and an intramolecular cyclization using mercaptoacetamide. This gave 1a, 1b and 1c in total yields of 42%, 35% and 37%, respectively.

  • 20.
    Engqvist, Robert
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Stensland, Birgitta
    AstraZeneca.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Reduction of indolo[2,3-b]quinoxalines2005In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 61, no 18, 4495-4500 p.Article in journal (Refereed)
    Abstract [en]

    Reduction of indolo[2,3-b]quinoxalines with zinc in the presence of an anhydride gave N,N-diacyl trapped 6,11-dihydroindolo[2,3-b]quinoxalines in 43-92% yields. When the reduction with zinc was performed in TFA/TFAA, an unexpected ring opened product was isolated in 49% yield. The structure of this product could be identified as 1,2-dihydro-1-trifluoroacetyl-3-[(2-trifluoroacetylamino)phenyl]quinoxal ine.

  • 21.
    Eriksson, Charlotta
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Rustum, Cecilia
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Stockholm University.
    Hallberg, Einar
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Dynamic properties of nuclear pore complex proteins in gp210 deficient cells2004In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 572, no 1-3, 261-265 p.Article in journal (Refereed)
    Abstract [en]

    Gp210, an integral membrane protein of the nuclear pore complex (NPC), is believed to be involved in NPC biogenesis. To test this hypothesis, we have investigated dynamic properties of the NPC and distribution of NPC proteins in NIH/ 3T3 cells lacking gp210. POM121 (the other integral NPC protein) and NUP107 (of the NUP107/160 complex) were correctly distributed at the nuclear pores in the absence of gp210. Furthermore, fluorescence recovery after photobleaching experiments showed that POM121 and NUP107 remained stably associated at the NPCs. We conclude that gp210 cannot be required for incorporation of POM121 or NUP107 or be required for maintaining NPC stability.

  • 22.
    Gallio, Marco
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    The Rhomboid family of intramembrane proteases, conserved regulators of cell communication2004Doctoral thesis, comprehensive summary (Other academic)
    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.

  • 23.
    Gallio, Marco
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Stockholm University / Karolinska Institute.
    Englund, C
    Stockholm University / Umeå University.
    Kylsten, Per
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Samakovlis, C
    Stockholm University.
    Rhomboid 3 orchestrates Slit-independent repulsion of tracheal branches at the CNS midline2004In: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 131, no 15, 3605-3614 p.Article in journal (Refereed)
    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.

  • 24.
    Gallio, Marco
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Kylsten, Per
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    The roughoid locus identifies a novel function involved in epidermal growth factor receptor signalling in DrosophilaManuscript (preprint) (Other academic)
  • 25. Gao, L L
    et al.
    Knogge, W
    Delp, Gabriele
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    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 tomato2004In: Molecular Plant-Microbe Interactions, ISSN 0894-0282, Vol. 17, no 10, 1103-1113 p.Article in journal (Refereed)
    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.

  • 26.
    Grahn, Mats
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Ny mat och gamla gener2004In: Forskare klargör myter om maten / [ed] Birgitta Johansson, Stockholm: Formas , 2004Chapter in book (Other (popular science, discussion, etc.))
  • 27.
    Hammer, Monica
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Towards implementation of the CBD ecosystem approach: Examples from Sweden2004In: Ways to promote the ideas behind the CBD's Ecosystem Approach in Central and Eastern Europe: report of the workshop convened by the German Federal Agency for Nature Conservation at the International Academy for Nature Conservation, Isle of Vilm, May 5 - 9, 2004 / [ed] Horst Korn, Bonn: BfN , 2004, 11-16 p.Conference paper (Other academic)
  • 28. Holmlund, Cecilia M
    et al.
    Hammer, Monica
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Effects of fish stocking on ecosystem services: An overview and case study using the Stockholm archipelago2004In: Environmental Management, ISSN 0364-152X, E-ISSN 1432-1009, Vol. 33, no 6, 799-820 p.Article in journal (Refereed)
    Abstract [en]

    In this article, we focus on documented and possible effects of fish stocking in terms of ecosystem services. The increasing use of fish stocking between 1970 and 2000 in the semiurban setting of Stockholm archipelago, Sweden, is used as case study. The objective is to analyze this management practice from an ecosystem perspective, accounting for both the ecological and social context of releasing fish. The results show that enhancements of four native species (Salmo S. trutta, Salmo salar, Stizostedion lucioperca, and Anguilla anguilla) have dominated over new introductions of one nonnative species. (Oncorhynchus mykiss). The major objective has been to increase fish catches for local resource users. Involved stakeholders include three management agencies, one hydropower company, and several local sport fishing associations. Documented effects focus on recapture and production rates. However, our analysis suggests that additional positive or negative effects on biodiversity, food web dynamics, mobile links, or ecological information may also result, with possible consequences for the long-term provision of food, game, and aesthetic values. We conclude that a more adaptive and cooperative management approach could benefit from a deeper analysis of where, when, and what species is released, by whom, which stakeholders that use the fish and those ecosystem services the fish generate, and of the role of formal and informal institutions for monitoring and evaluating the success of releasing fish.

  • 29. Hood, D W
    et al.
    Randle, G
    Cox, A D
    Makepeace, K
    Li, J J
    Schweda, Elke K H
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Richards, J C
    Moxon, E R
    Biosynthesis of cryptic lipopolysaccharide glycoforms in Haemophilus influenzae involves a mechanism similar to that required for O-antigen synthesis2004In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 186, no 21, 7429-7439 p.Article in journal (Refereed)
    Abstract [en]

    It is generally thought that mucosal bacterial pathogens of the genera Haemophilus, Neisseria, and Moraxella elaborate lipopolysaccharide (LPS) that is fundamentally different from that of enteric organisms that express O-specific polysaccharide side chains. Haemophilus influenzae elaborates short-chain LPS that has a role in the pathogenesis of H. influenzae infections. We show that the synthesis of LPS in this organism can no longer be as clearly distinguished from that in other gram-negative bacteria that express an O antigen. We provide evidence that a region of the H. influenzae genome, the hmg locus, is involved in the synthesis of glycoforms in which tetrasaccharide units are added en bloc, not stepwise, to the normal core glycoforms, similar to the biosynthesis of an O-antigen.

  • 30.
    Härlin, Mikael
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Classification nomenclature2004In: McGraw-Hill yearbook of science and technology, ISSN 0076-2016, 52-54 p.Article in journal (Other academic)
  • 31.
    Härlin, Mikael
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Vetenskapliga namn från ett mångvetenskapligt perspektiv2004In: Teknik & vetenskap, ISSN 1402-5701, Vol. 20, no 1, 48-48 p.Article in journal (Other (popular science, discussion, etc.))
  • 32.
    Härlin, Mikael
    et al.
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Thollesson, M
    Fundamentals of phylogenetic (and other) nomenclatures: an exchange of views2005In: Species plantarum 250 years: proceedings of the Species plantarum symposium held in Uppsala August 22-24, 2003 / [ed] Inga Hedberg, Uppsala: Acta Universitatis Upsaliensis , 2005, 141-151 p.Conference paper (Other academic)
  • 33.
    Jernberg, Cecilia
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Sullivan, A
    Karolinska Institute.
    Edlund, Charlotta
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Jansson, J K
    Swedish University of Agricultural Sciences.
    Monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism2005In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 71, no 1, 501-506 p.Article in journal (Refereed)
    Abstract [en]

    Terminal restriction fragment length polymorphism (T-RFLP) was investigated as a tool for monitoring the human intestinal microflora during antibiotic treatment and during ingestion of a probiotic product. Fecal samples from eight healthy volunteers were taken before, during, and after administration of clindamycin. During treatment, four subjects were given a probiotic, and four subjects were given a placebo. Changes in the microbial intestinal community composition and relative abundance of specific microbial populations in each subject were monitored by using viable counts and T-RFLP fingerprints. T-RFLP was also used to monitor specific bacterial populations that were either positively or negatively affected by clindamycin. Some dominant bacterial groups, such as Eubacterium spp., were easily monitored by T-RFLP, while they were hard to recover by cultivation. Furthermore, the two probiotic Lactobacillus strains were easily tracked by T-RFLP and were shown to be the dominant Lactobacillus community members in the intestinal microflora of subjects who received the probiotic.

  • 34.
    Johnson, Ann-Louise
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Sjögren, M
    Bohlin, L
    Synthesis of barettin2004In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 60, no 4, 961-965 p.Article in journal (Refereed)
    Abstract [en]

    The indole alkaloid barettin (with bromine in 6-position), isolated from the marine sponge Geodia Barretti, has been synthesised via a Horner-Wadsworth-Emmons type reaction from 6-bromoindole-3-carboxaldehyde to introduce the dehydro-functionality. Subsequent deprotection and cyclisation afforded the natural product in Z-conformation.

  • 35. Karlsson, C.
    et al.
    Korayem, A. M.
    Scherfer, C.
    Loseva, O.
    Dushay, Mitchell S.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Theopold, U.
    Proteomic analysis of the Drosophila larval hemolymph clot2004In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 279, no 50, 52033-52041 p.Article in journal (Refereed)
    Abstract [en]

    Components of the insect clot, an extremely rapid forming and critical part of insect immunity, are just beginning to be identified (1). Here we present a proteomic comparison of larval hemolymph before and after clotting to learn more about this process. This approach was supplemented by the identification of substrates for the enzyme transglutaminase, which plays a role in both vertebrate blood clotting (as factor XIIIa) and hemolymph coagulation in arthropods. Hemolymph proteins present in lower amounts after clotting include CG8502 (a protein with a mucin-type domain and a domain with similarity to cuticular components), CG11313 (a protein with similarity to prophenoloxidase-activating proteases), and two phenoloxidases, lipophorin, a secreted gelsolin, and CG15825, which had previously been isolated from clots (2). Proteins whose levels increase after clotting include a ferritin-subunit and two members of the immunoglobulin family with a high similarity to the small immunoglobulin-like molecules involved in mammalian innate immunity. Our results correlate with findings from another study of coagulation (2) that involved a different experimental approach. Proteomics allows the isolation of novel candidate clotting factors, leading to a more complete picture of clotting. In addition, our two-dimensional protein map of cell-free Drosophila hemolymph includes many additional proteins that were not found in studies performed on whole hemolymph.

  • 36.
    Kihlmark, Madeleine
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Stockholm University.
    Rustum, Cecilia
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Stockholm University.
    Eriksson, Charlotta
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Beckman, M
    Stockholm University.
    Iverfeldt, K
    Stockholm University.
    Hallberg, Einar
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Correlation between nucleocytoplasmic transport and caspase-3-dependent dismantling of nuclear pores during apoptosis2004In: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 293, no 2, 346-356 p.Article in journal (Refereed)
    Abstract [en]

    During apoptosis (also called programmed cell death), the chromatin condenses and the DNA is cleaved into oligonucleosomal fragments. Caspases are believed to play a major role in nuclear apoptosis. However, the relation between dismantling of nuclear pores, disruption of the nucleocytoplasmic barrier, and nuclear entry of caspases is unclear. We have analyzed nuclear import of the green fluorescent protein fused to a nuclear localization signal (GFP-NLS) in tissue culture cells undergoing apoptosis. Decreased nuclear accumulation of GFP-NLS could be detected at the onset of nuclear apoptosis manifested as dramatic condensation and redistribution of chromatin toward the nuclear periphery. At this step, dismantling of nuclear pores was already evident as indicated by proteolysis of the nuclear pore membrane protein POM121. Thus, disruption of nuclear compartmentalization correlated with early signs of nuclear pore damage. Both these events clearly preceded massive DNA fragmentation, detected by TUNEL assay. Furthermore, we show that in apoptotic cells, POM121 is specifically cleaved at aspartate-531 in its large C-terminal portion by a caspase-3-dependent mechanism. Cleavage of the C-terminal portion of POM121, which is adjoining the nuclear pore complex, is likely to disrupt interactions with other nuclear pore proteins affecting the stability of the pore complex. A temporal correlation of apoptotic events supports a model where caspase-dependent disassembly of nuclear pores and disruption of the nucleocytoplasmic barrier paves the way for nuclear entry of caspases and subsequent activation of CAD-mediated DNA fragmentation.

  • 37.
    Koeck, Philip J. B.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Missing data in image and signal processing: The case of binary objects2004In: Optik (Stuttgart), ISSN 0030-4026, Vol. 115, no 10, 459-472 p.Article in journal (Refereed)
    Abstract [en]

    I investigated which portions of the Fourier transform of binary signals, images and three-dimensional objects are necessary to correctly identify an object in the presence of noise. This is practically possible for very small binary data sets since the total number of possible objects is then very limited. There are for example 512 different binary images with 9 pixels. It is easy to see that this number soon becomes impractically large for bigger images or if one allows more than two possible pixel values. It turns out that even in the presence of large amounts of noise a relatively small portion of the Fourier transform is essential for deciding which of all possible binary objects the Fourier transform belongs to. These 'decision experiments' can be used as a standard for how well algorithms for retrieval of missing Fourier components perform. In another set of computer experiments I investigate the possibility of retrieving various missing Fourier components algorithmically. The main finding of this second set of computer experiments is that the simple retrieval algorithm (a limited form of 'projection onto convex sets') used falls very much short of what one might expect from the 'decision experiments'. I conclude with a discussion what this discrepancy might be due to and some suggestions how to improve the performance of retrieval algorithms for binary objects.

  • 38.
    Korayem, A M
    et al.
    Stockholms universitet / Assiut University, Assiut, Egypt.
    Fabbri, M
    University of Adelaide, Glen Osmond, South Australia.
    Takahashi, K
    National Institute of Genetics, Shizuoka, Japan.
    Scherfer, C
    Stockholms universitet.
    Lindgren, Malin
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Schmidt, O
    University of Adelaide, Glen Osmond, South Australia.
    Ueda, R
    National Institute of Genetics, Shizuoka, Japan.
    Dushay, Mitchell S
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Theopold, U
    Stockholms universitet / University of Adelaide, Glen Osmond, South Australia.
    A Drosophila salivary gland mucin is also expressed in immune tissues: evidence for a function in coagulation and the entrapment of bacteria2004In: Insect Biochemistry and Molecular Biology, ISSN 0965-1748, E-ISSN 1879-0240, Vol. 34, no 12, 1297-1304 p.Article in journal (Refereed)
    Abstract [en]

    Our studies on the developmental regulation of glycosylation in Drosophila melanogaster led us to identify and characterize gp 150, an ecdysone-regulated mucin that is found in hemocytes, the gut (peritrophic membrane) and in the salivary glands. We are particularly interested in mucin immune functions and found that gp 150 is released from larval hemocytes, becomes part of the clot and participates in the entrapment of bacteria. By RT-PCR and RNAi experiments, we identified gp 150 as the previously described 171-7, an ecdysone-induced salivary glue protein. We discuss the evolutionary and biochemical implications of the dual use of salivary proteins for immune functions in insects. Further molecular characterization of such shared proteins may enable a better understanding of the properties of proteins involved in containment and elimination of microbes, as well as hemostasis and wound repair.

  • 39. Kumblad, Linda
    et al.
    Bradshaw, Clare
    Gilek, Michael
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Bioaccurnulation of Cr-51, Ni-63 and C-14 in Baltic Sea benthos2005In: Environmental Pollution, ISSN 0269-7491, E-ISSN 1873-6424, Vol. 134, no 1, 45-56 p.Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea is a species-poor, semi-enclosed, brackish sea, whose sediments contain a wide range of contaminants, including sediment-associated metals and radionuclides. In this study, we have examined and compared bioaccumulation kinetics and assimilation efficiencies of sediment-associated Cr-51 Ni-63 and C-14 in three key benthic invertebrates (the deposit-feeding Monoporeia affinis, the facultative deposit-feeding Macoma baltica, and the omnivorous Halicryptus spinulosus). Our results demonstrate that (i) all radionuclides were accumulated, (ii) the different radionuclides were accumulated to various extents, (iii) small changes in organic carbon concentration can influence the accumulation, and (iv) the degree of accumulation differed only slightly between species. These processes, together with sediment resuspension and bioturbation, may remobilise trace metals from the sediment to the water and to higher trophic levels, and therefore should be taken into account in exposure models and ERAs.

  • 40.
    Landerholm, Malin K
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Li, J J
    Richards, J C
    Hood, D W
    Moxon, E R
    Schweda, Elke K H
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Characterization of novel structural features in the lipopolysaccharide of nondisease associated nontypeable Haemophilus influenzae2004In: European Journal of Biochemistry, ISSN 0014-2956, E-ISSN 1432-1033, Vol. 271, no 5, 941-953 p.Article in journal (Refereed)
    Abstract [en]

    Nontypeable Haemophilus influenzae (NTHi) is a common commensal of the human upper respiratory tract and is associated with otitis media in children. The structures of the oligosaccharide portions of NTHi lipopolysaccharide (LPS) from several otitis media isolates are now well characterized but it is not known whether there are structural differences in LPS from colonizing, nondisease associated strains. Structural analysis of LPS from nondisease associated NTHi strains 11 and 16 has been achieved by the application of high-field NMR techniques, ESI-MS, ESI-MSn, capillary electrophoresis coupled to ESI-MS, composition and linkage analyses on O-deacylated LPS and core oligosaccharide material. This is the first study to report structural details on LPS from strains taken from the nasopharynx from healthy individuals. Both strains express identical structures and contain the common element of H. influenzae LPS, L-alpha-D-Hepp-(1-->2)-[PEtn-->6]-L-alpha-D-Hepp-(1-->3)-[beta-D-Glcp-(1 -->4)]-L-alpha-D-Hepp-(1-->5)-[PPEtn-->4]-alpha-Kdop-(2-->6)-lipid A, in which each heptose is elongated by a single hexose residue with no further oligosaccharide extensions. In the major Hex3 glycoform, the terminal Hepp residue (HepIII) is substituted at the O-2 position by a beta-D-Galp residue and the central Hepp residue (HepII) is substituted at O-3 by a alpha-D-Glcp residue. Notably, the strains express two phosphocholine (PCho) substituents, one at the O-6 position of alpha-D-Glcp and the other at the O-6 position of beta-D-Galp. Major acetylation sites were identified at O-4 of Gal and O-3 of HepIII. Additionally, both strains express glycine, and strain 11 also expresses detectable amounts of N-acetylneuraminic acid.

  • 41. Larsson, Carl-Magnus
    et al.
    Jones, Celia
    Gomez-Ros, José Maria
    Zinger, Irène
    Sundell-Bergman, S.
    Avila, R.
    Brewitz, E.
    Howard, Brenda J.
    Beresford, Nick
    Barnett, C.L.
    Sanchez, A.L.
    Wright, S.M
    Strand, Per
    Brown, Justin
    Stenrud, H.
    Oughton, Deborah
    Thørring, H.
    Hosseini, A.
    Iosjep, M.
    Børretzen, P.
    Pröhl, Gerhard
    Taranenko, V.
    Cancio, David
    Real, A.
    Agüero, A.
    Robles, B.
    Suañez, A.
    Williams, Clive
    Saxén, Ritva
    Ilus, E.
    Kautsky, Ulrik
    Woodhead, D.
    Pentreath, J.
    Gilek, Michael
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Kumblad, L.
    Näslund, B.
    Skarphedinsdotti, H.
    Broed, R.
    Stark, K.
    Jones, Steve R.
    Patton, D.
    Vives i Batlle, J.
    Daniel, D.P.
    Vives Lynch, S.
    Garnier-Laplace, Jacqueline
    Fortin, C.
    Calmon, P.
    Bruchertseifer, F.
    Framework for assessment ofenvironmental impact of ionising radiationin major European ecosystems: FASSET deliverable 62004Report (Other academic)
  • 42.
    Loiske, Vesa-Matti
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Institutionalized Exchange as a Driving Force in Intensive Agriculture: An Iraqw Case Study2004In: Islands of intensive agriculture in Eastern Africa: past & present / [ed] Mats Widgren & John E.G. Sutton, London: Currey , 2004, 105-114 p.Chapter in book (Other academic)
  • 43.
    Lu, Zexun
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Tombolini, R
    Woo, S
    Zeilinger, S
    Lorito, M
    Jansson, Janet K
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. SLU.
    In vivo study of Trichoderma-pathogen-plant interactions, using constitutive and inducible green fluorescent protein reporter systems2004In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 70, no 5, 3073-3081 p.Article in journal (Refereed)
    Abstract [en]

    Plant tissue colonization by Trichoderma atroviride plays a critical role in the reduction of diseases caused by phytopathogenic fungi, but this process has not been thoroughly studied in situ. We monitored in Situ interactions between gfp-tagged biocontrol strains of T. atroviride and soilborne plant pathogens that were grown in cocultures and on cucumber seeds by confocal scanning laser microscopy and fluorescence stereomicroscopy. Spores of T. atroviride adhered to Pythium ultimum mycelia in coculture experiments. In mycoparasitic interactions of T. atroviride with P. ultimum or Rhizoctonia solani, the mycoparasitic hyphae grew alongside the pathogen mycelia, and this was followed by coiling and formation of specialized structures similar to hooks, appressoria, and papillae. The morphological changes observed depended on the pathogen tested. Branching of T. atroviride mycelium appeared to be an active response to the presence of the pathogenic host. Mycoparasitism of P. ultimum by T. atroviride occurred on cucumber seed surfaces while the seeds were germinating. The interaction of these fungi on the cucumber seeds was similar to the interaction observed in coculture experiments. Green fluorescent protein expression under the control of host-inducible promoters was also studied. The induction of specific Trichoderma genes was monitored visually in cocultures, on plant surfaces, and in soil in the presence of colloidal chitin or Rhizoctonia by confocal microscopy and fluorescence stereomicroscopy. These tools allowed initiation of the mycoparasitic gene expression cascade to be monitored in vivo.

  • 44. Lundström, A
    et al.
    Gallio, Marco
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Englund, C
    Steneberg, P
    Hemphälä, J
    Aspenström, P
    Keleman, K
    Falileeva, L
    Dickson, B J
    Samakovlis, C
    Vilse, a conserved Rac/Cdc42 GAP mediating Robo repulsion in tracheal cells and axons2004In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 18, no 17, 2161-2171 p.Article in journal (Refereed)
    Abstract [en]

    Slit proteins steer the migration of many cell types through their binding to Robo receptors, but how Robo controls cell motility is not clear. We describe the functional analysis of vilse, a Drosophila gene required for Robo repulsion in epithelial cells and axons. Vilse defines a conserved family of RhoGAPs (Rho GTPase-activating proteins), with representatives in flies and vertebrates. The phenotypes of vilse mutants resemble the tracheal and axonal phenotypes of Slit and Robo mutants at the CNS midline. Dosage-sensitive genetic interactions between vilse, slit, and robo mutants suggest that vilse is a component of robo signaling. Moreover, overexpression of Vilse in the trachea of robo mutants ameliorates the phenotypes of robo, indicating that Vilse acts downstream of Robo to mediate midline repulsion. Vilse and its human homolog bind directly to the intracellular domains of the corresponding Robo receptors and promote the hydrolysis of RacGTP and, less efficiently, of Cdc42GTP. These results together with genetic interaction experiments with robo, vilse, and rac mutants suggest a mechanism whereby Robo repulsion is mediated by the localized inactivation of Rac through Vilse.

  • 45.
    Lättman, Håkan
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Mattsson, Jan-Eric
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science, Biology.
    Milberg, Per
    IFM Biology, Conservation Ecology Group, Linköping University.
    Rapid changes in the epiphytic macrolichen flora in southern Sweden2004Conference paper (Other academic)
  • 46.
    Löfmark, Sonja
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Fang, Hong
    Karolinska Institutet.
    Hedberg, Maria
    Karolinska Institutet.
    Edlund, Charlotta
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Inducible metronidazole resistance and nim genes in clinical Bacteroides fragilis group isolates2005In: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 49, no 3, 1253-1256 p.Article in journal (Refereed)
    Abstract [en]

    Nitroimidazole resistance (nim) genes were detected in 2% of 1,502 clinical Bacteroides fragilis group strains isolated from 19 European countries, and a novel nim gene was identified. High metronidazole resistance could be induced in nim-positive strains, which emphasizes the importance of acknowledging metronidazole resistance in the clinical setting.

  • 47.
    Maraha, Ninwe
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Backman, Agneta
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Jansson, Janet K
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. SLU.
    Monitoring physiological status of GFP-tagged Pseudomonas fluorescens SBW25 under different nutrient conditions and in soil by flow cytometry2004In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 51, no 1, 123-132 p.Article in journal (Refereed)
    Abstract [en]

    Pseudomonas fluorescens SBW25, a plant growth promoting bacterium. has been widely studied due to its potential as an inoculum for improving crop yields. Environmental inoculants are usually applied oil seeds or directly to soil and to effectively promote plant growth they need to be viable and active. However, it is difficult to study the physiological status of specific microorganisms in complex environments, such as soil. In this study, our aim was to use molecular tools to specifically monitor the physiological status of P. fluorescens SBW25 in soil and ill pure cultures incubated under different nutritional conditions. The cells were previously tagged with marker genes (encoding green fluorescent protein and bacterial luciferase) to specifically track the cells in environmental samples. The physiological status of the cells was determined using the viability stains 5-cyano-2,3-ditolyl-tetrazolium chloride (CTC) and propidium iodide (PI), which stain active and dead cells, respectively. Luciferase activity was used to monitor the metabolic activity of the population. Most of the cells died after incubation for nine days in nutrient rich medium. By contrast when incubated under starvation conditions, most of the population was not stained with CTC or PI (i.e. intact but inactive cells), indicating that most of the cells were presumably dormant. In soil, a large fraction of the SBW25 cell population became inactive and died, as determined by a decline in luciferase activity and CTC-stained cells, an increase in PI-stained cells, and an inability of the cells to be cultured oil agar medium. However, approximately 60% of the population was unstained, presumably indicating that the cells entered a state of dormancy in soil similar to that observed under starvation conditions in pure cultures. These results demonstrate the applicability of this approach for monitoring the physiological status of specific cells under stress conditions, such as those experienced by environmental inoculants in soil.

  • 48.
    Mattsson, Jan-Eric
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Articus, Kristina
    The monophyletic groups of cetrarioid lichens2004In: Contributions to lichen taxonomy and biogeography: dedicated to Leif Tibell / [ed] Göran Thor, Anders Nordin, Inga Hedberg, Uppsala: Acta Upsaliensis Universitatis , 2004, 237-244 p.Chapter in book (Other academic)
  • 49.
    Mattsson, Jan-Eric
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Articus, Kristina
    Wiklund, Elisabeth
    Wedin, Mats
    Naturhistoriska riksmuseet.
    The monophyletic groups in the Parmeliaceae2004Manuscript (preprint) (Other academic)
  • 50.
    Mattsson, Jan-Eric
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Lättman, Håkan
    Chaos and order in teaching and research2004In: Contributions to lichen taxonomy and biogeography: dedicated to Leif Tibell / [ed] Göran Thor, Anders Nordin, Inga Hedberg, Uppsala: Acta Upsaliensis Universitatis , 2004, 245-255 p.Chapter in book (Other academic)
12 1 - 50 of 83
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